From 84170227c1bb6ea61568e7776ee5e10058168154 Mon Sep 17 00:00:00 2001
From: Luke R <luke.rasmussen@gmail.com>
Date: Tue, 28 May 2024 08:45:11 -0500
Subject: [PATCH 01/43] Added documentation around reproducibility checklist
 features

---
 docs/ReproducibilityChecklists-Planning.md | 37 ++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 docs/ReproducibilityChecklists-Planning.md

diff --git a/docs/ReproducibilityChecklists-Planning.md b/docs/ReproducibilityChecklists-Planning.md
new file mode 100644
index 0000000..92e7f53
--- /dev/null
+++ b/docs/ReproducibilityChecklists-Planning.md
@@ -0,0 +1,37 @@
+# Reproducible Research Checklists
+
+This document provides design guidance and general requirements for the reproducible research checklist feature in StatWrap.
+
+## Modes of Operation
+
+There are two modes of operation for the checklist:
+
+### 1. Automated information gathering / decision making (StatWrap)
+
+StatWrap will use information from project assets and user-entered metadata in order to provide information about reproducible research practices.  This will be used to **inform** users, but will not make a binary indicator (yes/no) about if a practice is "reproducible" or not.
+
+StatWrap should be configured to provide information about the following categories of data.  The way the data could be displayed is noted, but is not intended to limit the final implementation.  For each of these, there should be a service method that is able to perform the processed logic.  Unlike the actual checklist UI, these items are not configurable by the end user, they are built within StatWrap.
+
+1. **Summarize the software used** - this should include programming language(s) and dependencies.  Programming languages can be inferred from file extensions.  Dependencies can be inferred from specific references in code files (already processed by StatWrap), as well as dependency files used for specific languages (e.g., `requirements.txt` for Python).  StatWrap does not need to determine the specific version used in any environment if it is not specified elsewhere.
+2. **Multiple versions of a file** - use a heuristic from file names to determine if the user has versioned files using a naming convention, as opposed to using source control. For example, `main_analysis.R` and `main_analysis_v2.R` or `main_analysis-jd.R`.  StatWrap could use metrics other than the file name, such as similarity of file content, to further infer if the files are likely versioned.  For a grouping of files that StatWrap thinks are versioned, it should check attributes to:
+  1. See if any of the files are marked as 'archived'.
+  2. If more than one file is marked as an 'entry point'.
+3. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`.  If so, display these file(s)/folder(s) as the projecct documentation.
+4. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project.  This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`).  StatWrap should report which file(s) are using absolute paths.
+5. **Binary / proprietary file formats for data** - flag data files that are not purely text-based.  This can be done from a configureable list of file extensions.
+6. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
+	1. Input data - data flagged with an attribute of "Input / Raw Data", or data contained in folders using a configurable list of folder names (e.g., `raw`, `input`)
+	2. Derived data - data flagged with an attribute of "Derived", or data contained in folders using a configurable list of folder names (e.g., `output`, `derived`)
+	3. Data (general) - data files that we cannot otherwise categorize
+7. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps.  Note that a single code file may have multiple annotations:
+   1. Data acquisition - used to import / pull data. This would be flagged with an attribute of "Data acquisition".
+   2. Data processing - this would be flagged with an attribute of "Data processing"
+   3. Analysis - this would be flagged with an attribute of "Analysis"
+8. **Entry points** - StatWrap should list all code files flagged as entry points by the user.  If none, and code files exist, this should also be noted ("No entry point has been specified").  This could be combined with the previous item.
+9. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data.  Summarize these for the user as external assets that are being referenced.
+
+### 2. Human-entered information / decision making (user)
+
+This is more of the traditional "checklist", where the user is presented with a list of questions that they may attest to.  Some of the answers may be pre-filled using data collected by StatWrap as defined in the automated information gathering (previous section).
+
+(See proposal by Adi)
\ No newline at end of file

From db868760e2a32dc67d84263db55270852a01dc0d Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Wed, 26 Jun 2024 13:19:50 +0530
Subject: [PATCH 02/43] basic UI skeleton

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             |  12 ++
 .../ReproChecklists/ChecklistItem.css         |  87 ++++++++++
 .../ReproChecklists/ChecklistItem.js          | 163 ++++++++++++++++++
 .../ReproChecklists/ReproChecklists.css       |   8 +
 .../ReproChecklists/ReproChecklists.js        | 114 ++++++++++++
 docs/ReproducibilityChecklists-DataModels.md  |  80 +++++++++
 6 files changed, 464 insertions(+)
 create mode 100644 app/components/ReproChecklists/ChecklistItem.css
 create mode 100644 app/components/ReproChecklists/ChecklistItem.js
 create mode 100644 app/components/ReproChecklists/ReproChecklists.css
 create mode 100644 app/components/ReproChecklists/ReproChecklists.js
 create mode 100644 docs/ReproducibilityChecklists-DataModels.md

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index bfe6d42..56c790e 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -13,6 +13,7 @@ import Assets from './Assets/Assets';
 import Workflow from '../Workflow/Workflow';
 import People from '../People/People';
 import ProjectLog from '../ProjectLog/ProjectLog';
+import ReproChecklists from '../ReproChecklists/ReproChecklists';
 import ProjectNotes from '../ProjectNotes/ProjectNotes';
 import { ActionType, EntityType, DescriptionContentType } from '../../constants/constants';
 import AssetUtil from '../../utils/asset';
@@ -681,6 +682,13 @@ class Project extends Component<Props> {
           />
         ) : null;
 
+      const reproChecklists = <ReproChecklists
+        project={this.props.project}
+        onAddedNote={this.projectUpsertNoteHandler}
+        onUpdatedNote={this.projectUpsertNoteHandler}
+        onDeletedNote={this.projectDeleteNoteHandler}
+      />
+
       content = (
         <TabContext value={this.state.selectedTab}>
           <div className={styles.header}>
@@ -709,6 +717,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
+              <Tab label="Reproducibility Checklists" value="reproChecklists" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -729,6 +738,9 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
+          <TabPanel value="reproChecklists" classes={tabPanelStyle}>
+            {reproChecklists}
+          </TabPanel>
         </TabContext>
       );
     }
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
new file mode 100644
index 0000000..dc06332
--- /dev/null
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -0,0 +1,87 @@
+.item {
+  padding: 10px;
+  border-bottom: 1px solid #e5e5e5;
+}
+
+.header {
+  display: flex;
+  align-items: center;
+}
+
+.buttoncontainer {
+  margin-left: auto;
+  margin-right: 0;
+}
+
+.details {
+  padding-left: 20px;
+  margin-top: 10px;
+}
+
+.notes,
+.images,
+.urls,
+.subChecklists {
+  margin-top: 10px;
+}
+
+.notes ul,
+.images ul,
+.urls ul {
+  list-style-type: none;
+  padding-left: 0;
+}
+
+.notes li,
+.images li,
+.urls li {
+  margin-bottom: 5px;
+}
+
+.notes li strong {
+  display: block;
+}
+
+.timestamp {
+  display: block;
+  font-size: 12px;
+  color: #888;
+}
+
+.images img {
+  max-width: 100%;
+  height: auto;
+}
+
+.item button {
+  min-width: 50px;
+  height: 32px;
+  border: none;
+  border-radius: 4px;
+  cursor: pointer;
+  transition: background-color 0.3s ease;
+}
+
+.item button.yes {
+  background-color:#aa94d1;
+  color: white;
+}
+
+.item button.yesset {
+  background-color:rebeccapurple;
+  color: white;
+}
+
+.item button.no {
+  background-color: silver;
+  color: white;
+}
+
+.item button.noset {
+  background-color: grey;
+  color: white;
+}
+
+.item button:hover {
+  opacity: 0.9;
+}
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
new file mode 100644
index 0000000..3295803
--- /dev/null
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -0,0 +1,163 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import styles from './ChecklistItem.css';
+import NoteEditor from '../NoteEditor/NoteEditor';
+
+function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNote }) {
+  const [answer, setAnswer] = useState(item.answer);
+  const [notes, setNotes] = useState(item.userNotes || []);
+
+  const handleNoteUpdate = (note, text) => {
+    if (note) {
+      if (onUpdatedNote) {
+        onUpdatedNote(project, text, note);
+      }
+    } else {
+      if (onAddedNote) {
+        onAddedNote(project, text);
+      }
+    }
+  };
+
+  const handleNoteDelete = (note) => {
+    if (onDeletedNote) {
+      onDeletedNote(project, note);
+    }
+  };
+
+  useEffect(() => {
+    setNotes(item.userNotes || []);
+  }, [item.userNotes]);
+
+  return (
+    <div className={styles.item}>
+      <div className={styles.header}>
+        <span>{item.statement}</span>
+        <div className={styles.buttoncontainer}>
+          <button
+            className={answer === 'yes' ? styles.yesset : styles.yes}
+            onClick={() => setAnswer('yes')}
+          >
+            {'Yes'}
+          </button>
+          <button
+            className={answer === 'no' ? styles.noset : styles.no}
+            onClick={() => setAnswer('no')}
+          >
+            {'No'}
+          </button>
+        </div>
+      </div>
+      <div className={styles.details}>
+        {notes.length > 0 && (
+          <div className={styles.notes}>
+            <h4>Notes:</h4>
+            <ul>
+              {notes.map((note) => (
+                <li key={note.id}>
+                  <strong>{note.author}:</strong> {note.content}
+                  <span className={styles.timestamp}>{note.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        <NoteEditor
+          notes={notes}
+          onEditingComplete={handleNoteUpdate}
+          onDelete={handleNoteDelete}
+        />
+        {item.attachedImages.length > 0 && (
+          <div className={styles.images}>
+            <h4>Attached Images:</h4>
+            <ul>
+              {item.attachedImages.map((image) => (
+                <li key={image.id}>
+                  <img src={URL.createObjectURL(image.data)} alt="attached" />
+                  <span className={styles.timestamp}>{image.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        {item.attachedURLs.length > 0 && (
+          <div className={styles.urls}>
+            <h4>Attached URLs:</h4>
+            <ul>
+              {item.attachedURLs.map((url) => (
+                <li key={url.id}>
+                  <a href={url.hyperlink} target="">
+                    {url.hyperlink}
+                  </a>
+                  <span className={styles.timestamp}>{url.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        {item.subChecklists.length > 0 && (
+          <div className={styles.subChecklists}>
+            <h4>Sub-Checklists:</h4>
+            {item.subChecklists.map((subItem) => (
+              <ChecklistItem
+                key={subItem.id}
+                item={subItem}
+                project={project}
+                onUpdatedNote={onUpdatedNote}
+                onDeletedNote={onDeletedNote}
+                onAddedNote={onAddedNote}
+              />
+            ))}
+          </div>
+        )}
+      </div>
+    </div>
+  );
+}
+
+ChecklistItem.propTypes = {
+  item: PropTypes.shape({
+    id: PropTypes.string.isRequired,
+    statement: PropTypes.string.isRequired,
+    type: PropTypes.string.isRequired,
+    answer: PropTypes.string.isRequired,
+    userNotes: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        author: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+        content: PropTypes.string.isRequired,
+      })
+    ),
+    attachedImages: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        data: PropTypes.instanceOf(Blob).isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    attachedURLs: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        hyperlink: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    subChecklists: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        statement: PropTypes.string.isRequired,
+        type: PropTypes.string.isRequired,
+        answer: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    updated: PropTypes.string.isRequired,
+  }).isRequired,
+  project: PropTypes.object.isRequired,
+  onUpdatedNote: PropTypes.func.isRequired,
+  onDeletedNote: PropTypes.func.isRequired,
+  onAddedNote: PropTypes.func.isRequired,
+};
+
+export default ChecklistItem;
diff --git a/app/components/ReproChecklists/ReproChecklists.css b/app/components/ReproChecklists/ReproChecklists.css
new file mode 100644
index 0000000..aa2d05b
--- /dev/null
+++ b/app/components/ReproChecklists/ReproChecklists.css
@@ -0,0 +1,8 @@
+.container {
+  padding: 20px;
+}
+
+h2 {
+  margin-bottom: 20px;
+  font-size: 24px;
+}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
new file mode 100644
index 0000000..e1b87ea
--- /dev/null
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -0,0 +1,114 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import ChecklistItem from './ChecklistItem';
+
+const dummyChecklistItems = [
+  {
+    id: '1',
+    statement: 'First checklist item statement',
+    type: 'Type1',
+    answer: 'yes',
+    userNotes: [
+      {
+        id: 'note1',
+        author: 'Author1',
+        updated: '2024-06-01',
+        content: 'First note content',
+      },
+    ],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists: [],
+    updated: '2024-06-01',
+  },
+  {
+    id: '2',
+    statement: 'Second checklist item statement',
+    type: 'Type2',
+    answer: 'no',
+    userNotes: [
+      {
+        id: 'note2',
+        author: 'Author2',
+        updated: '2024-06-02',
+        content: 'Second note content',
+      },
+    ],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists: [],
+    updated: '2024-06-02',
+  },
+];
+
+function ReproChecklists(props) {
+  const { project, checklistItems, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+
+  return (
+    <div>
+      {checklistItems.map(item => (
+        <ChecklistItem
+          key={item.id}
+          item={item}
+          project={project}
+          onUpdatedNote={onUpdatedNote}
+          onDeletedNote={onDeletedNote}
+          onAddedNote={onAddedNote}
+        />
+      ))}
+    </div>
+  );
+}
+
+ReproChecklists.propTypes = {
+  project: PropTypes.object.isRequired,
+  checklistItems: PropTypes.arrayOf(
+    PropTypes.shape({
+      id: PropTypes.string.isRequired,
+      statement: PropTypes.string.isRequired,
+      type: PropTypes.string.isRequired,
+      answer: PropTypes.string.isRequired,
+      userNotes: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          author: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+          content: PropTypes.string.isRequired,
+        })
+      ),
+      attachedImages: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          data: PropTypes.instanceOf(Blob).isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      attachedURLs: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          hyperlink: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      subChecklists: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          statement: PropTypes.string.isRequired,
+          type: PropTypes.string.isRequired,
+          answer: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      updated: PropTypes.string.isRequired,
+    })
+  ).isRequired,
+  onUpdatedNote: PropTypes.func.isRequired,
+  onDeletedNote: PropTypes.func.isRequired,
+  onAddedNote: PropTypes.func.isRequired,
+};
+
+ReproChecklists.defaultProps = {
+  checklistItems: dummyChecklistItems,
+};
+
+export default ReproChecklists;
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
new file mode 100644
index 0000000..0d77350
--- /dev/null
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -0,0 +1,80 @@
+## Checklist Object
+
+### About
+
+The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklists.
+
+### Attributes
+
+| Attribute          | Type       | Description                                                                                                                                               |
+| ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                                |
+| `statement`        | String     | The statement or question associated with the checklist item.                                                                                              |
+| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                      |
+| `answer`           | String     | Stores the user's response to the checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                                         |
+| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                                  |
+| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                                  |
+| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                     |
+| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                                    |
+| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                         |
+
+### Sub-Checklist Object
+
+#### About
+
+The **Sub-Checklist Object** represents a sub-item within a checklist item. It shares similar attributes with the Checklist Object, except for attachments, but is nested within the parent checklist item.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                           |
+| `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
+| `type`          | String   | Indicates the type of sub-checklist item, such as boolean or descriptive.                                                                                  |
+| `answer`        | String   | Stores the user's response to the sub-checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                         |
+| `updated`       | String   | The timestamp indicating when the sub-checklist item was last updated.                                                                                     |
+
+### Note Object
+
+#### About
+
+The **Note Object** stores user-added note associated with checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the note.                                                                                                                         |
+| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                                                |
+| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                   |
+| `content`       | String   | The text content of the note.                                                                                                                             |
+
+### Image Object
+
+#### About
+
+The **Image Object** stores image data of the image attached to checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the image.                                                                                                                        |
+| `data`          | Blob     | The image data of the attached image.                                                                                                                     |
+| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                  |
+
+### URL Object
+
+#### About
+
+The **URL Object** stores hyperlink of the URL attached to checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                          |
+| `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
+| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                    |
+
+This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.

From 582e3b22131fab229149bcded3dae536fb1be170 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Wed, 26 Jun 2024 19:58:37 +0530
Subject: [PATCH 03/43] minor corrections

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js                 |  8 ++++----
 app/components/ReproChecklists/ChecklistItem.css  |  2 +-
 app/components/ReproChecklists/ChecklistItem.js   | 15 +--------------
 app/components/ReproChecklists/ReproChecklists.js |  3 +++
 docs/ReproducibilityChecklists-DataModels.md      |  1 +
 5 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 56c790e..7a11409 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -682,7 +682,7 @@ class Project extends Component<Props> {
           />
         ) : null;
 
-      const reproChecklists = <ReproChecklists
+      const Checklists = <ReproChecklists
         project={this.props.project}
         onAddedNote={this.projectUpsertNoteHandler}
         onUpdatedNote={this.projectUpsertNoteHandler}
@@ -717,7 +717,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
-              <Tab label="Reproducibility Checklists" value="reproChecklists" classes={tabStyle} />
+              <Tab label="Checklists" value="Checklists" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -738,8 +738,8 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
-          <TabPanel value="reproChecklists" classes={tabPanelStyle}>
-            {reproChecklists}
+          <TabPanel value="Checklists" classes={tabPanelStyle}>
+            {Checklists}
           </TabPanel>
         </TabContext>
       );
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index dc06332..fe4647a 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -8,7 +8,7 @@
   align-items: center;
 }
 
-.buttoncontainer {
+.buttonContainer {
   margin-left: auto;
   margin-right: 0;
 }
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 3295803..382719d 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -33,7 +33,7 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
     <div className={styles.item}>
       <div className={styles.header}>
         <span>{item.statement}</span>
-        <div className={styles.buttoncontainer}>
+        <div className={styles.buttonContainer}>
           <button
             className={answer === 'yes' ? styles.yesset : styles.yes}
             onClick={() => setAnswer('yes')}
@@ -49,19 +49,6 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         </div>
       </div>
       <div className={styles.details}>
-        {notes.length > 0 && (
-          <div className={styles.notes}>
-            <h4>Notes:</h4>
-            <ul>
-              {notes.map((note) => (
-                <li key={note.id}>
-                  <strong>{note.author}:</strong> {note.content}
-                  <span className={styles.timestamp}>{note.updated}</span>
-                </li>
-              ))}
-            </ul>
-          </div>
-        )}
         <NoteEditor
           notes={notes}
           onEditingComplete={handleNoteUpdate}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index e1b87ea..c5732af 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -1,6 +1,7 @@
 import React from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
+import { Typography } from '@mui/material';
 
 const dummyChecklistItems = [
   {
@@ -46,6 +47,8 @@ function ReproChecklists(props) {
 
   return (
     <div>
+      <Typography variant='h5' align='center'>Reproducibility Checklists</Typography>
+      <br />
       {checklistItems.map(item => (
         <ChecklistItem
           key={item.id}
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index 0d77350..62b4286 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -39,6 +39,7 @@ The **Sub-Checklist Object** represents a sub-item within a checklist item. It s
 #### About
 
 The **Note Object** stores user-added note associated with checklist items.
+This follows the same structure as the existing [notes data type](https://github.com/StatTag/StatWrap/blob/master/docs/Notes.md)
 
 #### Attributes
 

From cfbfb443ca22fe68b02d87d92abf31774db06606 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 6 Aug 2024 17:18:54 +0530
Subject: [PATCH 04/43] adds image and url component UI

---
 .../ReproChecklists/ChecklistItem.css         | 120 ++++++++++++++++--
 .../ReproChecklists/ChecklistItem.js          |  66 +++++++---
 .../ReproChecklists/ReproChecklists.js        |  97 ++++++++++++--
 docs/ReproducibilityChecklists-DataModels.md  |  41 +++---
 4 files changed, 263 insertions(+), 61 deletions(-)

diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index fe4647a..a1ce89b 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -3,8 +3,12 @@
   border-bottom: 1px solid #e5e5e5;
 }
 
+.header span {
+  max-width: 83%;
+}
+
 .header {
-  display: flex;
+  display:flex;
   align-items: center;
 }
 
@@ -18,28 +22,47 @@
   margin-top: 10px;
 }
 
-.notes,
 .images,
 .urls,
 .subChecklists {
   margin-top: 10px;
 }
 
-.notes ul,
-.images ul,
+.images ul{
+  list-style-type: none;
+  padding-left: 0;
+  display: flex;
+  overflow-x: auto;
+  white-space: nowrap;
+}
+
 .urls ul {
   list-style-type: none;
   padding-left: 0;
+  max-height: 200px;
+  overflow-y: auto;
+  white-space: nowrap;
 }
 
-.notes li,
-.images li,
-.urls li {
+.images li{
+  margin-right: 10px;
   margin-bottom: 5px;
+  padding-right: 5px;
+  position: relative;
 }
 
-.notes li strong {
-  display: block;
+.urls li{
+  margin-right: 10px;
+  margin-bottom: 5px;
+  padding-bottom: 5px;
+  position: relative;
+}
+
+.images li:not(:last-child) {
+  border-right: 1px solid #ccc;
+}
+.urls li:not(:last-child) {
+  border-bottom: 1px solid #ccc;
 }
 
 .timestamp {
@@ -49,8 +72,40 @@
 }
 
 .images img {
-  max-width: 100%;
   height: auto;
+  max-height: 150px;
+  transition: max-height 0.3s ease;
+  display: block;
+  margin-top: 5px;
+}
+
+.imageContent,
+.urlContent {
+  max-height: 0;
+  overflow: hidden;
+  transition: max-height 0.3s ease;
+}
+
+.imageContent.show,
+.urlContent.show {
+  max-height: 500px;
+}
+
+.urls a {
+  text-decoration: none;
+  color: #007bff;
+  display: block;
+  margin-top: 5px;
+}
+
+.urls a:hover {
+  color: darkblue;
+}
+
+.images p,
+.urls p {
+  margin-top: 8px;
+  font-size: 15px;
 }
 
 .item button {
@@ -63,12 +118,12 @@
 }
 
 .item button.yes {
-  background-color:#aa94d1;
+  background-color: #aa94d1;
   color: white;
 }
 
 .item button.yesset {
-  background-color:rebeccapurple;
+  background-color: rebeccapurple;
   color: white;
 }
 
@@ -85,3 +140,44 @@
 .item button:hover {
   opacity: 0.9;
 }
+
+.headerWithButton {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+}
+
+.dropdownButton {
+  background-color: #f8f9fa;
+  color: #333;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 14px;
+  transition: background-color 0.3s ease;
+}
+
+.dropdownButton:hover {
+  background-color: #e9ecef;
+}
+
+.dropdownContent {
+  display: none;
+  padding: 10px;
+  background-color: #f8f9fa;
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  margin-top: 5px;
+  transition: max-height 0.3s ease;
+}
+
+.dropdownContent.show {
+  display: block;
+  max-height: 500px;
+}
+
+.imageTitle,
+.urlTitle {
+  font-size: 16px;
+}
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 382719d..f19e1b8 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -6,6 +6,8 @@ import NoteEditor from '../NoteEditor/NoteEditor';
 function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNote }) {
   const [answer, setAnswer] = useState(item.answer);
   const [notes, setNotes] = useState(item.userNotes || []);
+  const [showImages, setShowImages] = useState(false);
+  const [showURLs, setShowURLs] = useState(false);
 
   const handleNoteUpdate = (note, text) => {
     if (note) {
@@ -56,30 +58,48 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         />
         {item.attachedImages.length > 0 && (
           <div className={styles.images}>
-            <h4>Attached Images:</h4>
-            <ul>
-              {item.attachedImages.map((image) => (
-                <li key={image.id}>
-                  <img src={URL.createObjectURL(image.data)} alt="attached" />
-                  <span className={styles.timestamp}>{image.updated}</span>
-                </li>
-              ))}
-            </ul>
+            <div className={styles.headerWithButton}>
+              <h4>Attached Images:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
+                {showImages ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
+              <ul>
+                {item.attachedImages.map((image) => (
+                  <li key={image.id}>
+                    <span className={styles.imageTitle}>{image.title}</span>
+                    <img src={image.uri} alt="attached" />
+                    <p>{image.description}</p>
+                    <span className={styles.timestamp}>{image.updated}</span>
+                  </li>
+                ))}
+              </ul>
+            </div>
           </div>
         )}
         {item.attachedURLs.length > 0 && (
           <div className={styles.urls}>
-            <h4>Attached URLs:</h4>
-            <ul>
-              {item.attachedURLs.map((url) => (
-                <li key={url.id}>
-                  <a href={url.hyperlink} target="">
-                    {url.hyperlink}
-                  </a>
-                  <span className={styles.timestamp}>{url.updated}</span>
-                </li>
-              ))}
-            </ul>
+            <div className={styles.headerWithButton}>
+              <h4>Attached URLs:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
+                {showURLs ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
+              <ul>
+                {item.attachedURLs.map((url) => (
+                  <li key={url.id}>
+                    <span className={styles.urlTitle}>{url.title}</span>
+                    <a href={url.hyperlink} target="">
+                      {url.hyperlink}
+                    </a>
+                    <p>{url.description}</p>
+                    <span className={styles.timestamp}>{url.updated}</span>
+                  </li>
+                ))}
+              </ul>
+            </div>
           </div>
         )}
         {item.subChecklists.length > 0 && (
@@ -119,7 +139,9 @@ ChecklistItem.propTypes = {
     attachedImages: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
-        data: PropTypes.instanceOf(Blob).isRequired,
+        uri: PropTypes.string.isRequired,
+        title: PropTypes.string.isRequired,
+        description: PropTypes.string.isRequired,
         updated: PropTypes.string.isRequired,
       })
     ),
@@ -127,6 +149,8 @@ ChecklistItem.propTypes = {
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         hyperlink: PropTypes.string.isRequired,
+        title: PropTypes.string.isRequired,
+        description: PropTypes.string.isRequired,
         updated: PropTypes.string.isRequired,
       })
     ),
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index c5732af..a8a0de8 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -1,12 +1,12 @@
-import React from 'react';
+import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
-
+// /home/adi/Pictures/Screenshots/maskedvt.png
 const dummyChecklistItems = [
   {
     id: '1',
-    statement: 'First checklist item statement',
+    statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
     answer: 'yes',
     userNotes: [
@@ -17,8 +17,52 @@ const dummyChecklistItems = [
         content: 'First note content',
       },
     ],
-    attachedImages: [],
-    attachedURLs: [],
+    attachedImages: [
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+    ],
+    attachedURLs: [
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+    ],
     subChecklists: [],
     updated: '2024-06-01',
   },
@@ -43,7 +87,38 @@ const dummyChecklistItems = [
 ];
 
 function ReproChecklists(props) {
-  const { project, checklistItems, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const [checklistItems, setChecklistItems] = useState(dummyChecklistItems);
+
+  useEffect(() => {
+    if (project && Array.isArray(project.assets)) {
+      const imageAssets = [];
+
+      const findImageAssets = (asset) => {
+        if (asset.type === 'image') {
+          imageAssets.push(asset);
+        }
+        if (asset.children) {
+          asset.children.forEach(findImageAssets);
+        }
+      };
+
+      project.assets.forEach(findImageAssets);
+
+      const updatedItems = dummyChecklistItems.map(item => ({
+        ...item,
+        attachedImages: imageAssets.map(asset => ({
+          id: asset.id,
+          uri: asset.uri,
+          title: asset.title || 'Image',
+          description: asset.description || 'About Image',
+          updated: asset.updated || 'NA',
+        })),
+      }));
+
+      setChecklistItems(updatedItems);
+    }
+  }, [project]);
 
   return (
     <div>
@@ -65,7 +140,7 @@ function ReproChecklists(props) {
 
 ReproChecklists.propTypes = {
   project: PropTypes.object.isRequired,
-  checklistItems: PropTypes.arrayOf(
+  reproChecklist: PropTypes.arrayOf(
     PropTypes.shape({
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
@@ -82,7 +157,9 @@ ReproChecklists.propTypes = {
       attachedImages: PropTypes.arrayOf(
         PropTypes.shape({
           id: PropTypes.string.isRequired,
-          data: PropTypes.instanceOf(Blob).isRequired,
+          uri: PropTypes.string.isRequired,
+          title: PropTypes.string.isRequired,
+          description: PropTypes.string.isRequired,
           updated: PropTypes.string.isRequired,
         })
       ),
@@ -90,6 +167,8 @@ ReproChecklists.propTypes = {
         PropTypes.shape({
           id: PropTypes.string.isRequired,
           hyperlink: PropTypes.string.isRequired,
+          title: PropTypes.string.isRequired,
+          description: PropTypes.string.isRequired,
           updated: PropTypes.string.isRequired,
         })
       ),
@@ -111,7 +190,7 @@ ReproChecklists.propTypes = {
 };
 
 ReproChecklists.defaultProps = {
-  checklistItems: dummyChecklistItems,
+  reproChecklist: dummyChecklistItems,
 };
 
 export default ReproChecklists;
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index 62b4286..a60cd4f 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -8,15 +8,15 @@ The **Checklist Object** represents a single checklist item within the reproduci
 
 | Attribute          | Type       | Description                                                                                                                                               |
 | ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                                |
-| `statement`        | String     | The statement or question associated with the checklist item.                                                                                              |
-| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                      |
+| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                     |
+| `statement`        | String     | The statement or question associated with the checklist item.                                                                                             |
+| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                     |
 | `answer`           | String     | Stores the user's response to the checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                                         |
-| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                                  |
-| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                                  |
-| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                     |
-| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                                    |
-| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                         |
+| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                               |
+| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                              |
+| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
+| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                        |
+| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                        |
 
 ### Sub-Checklist Object
 
@@ -26,9 +26,9 @@ The **Sub-Checklist Object** represents a sub-item within a checklist item. It s
 
 #### Attributes
 
-| Attribute       | Type     | Description                                                                                                                                               |
-| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                           |
+| Attribute       | Type     | Description                                                                                                                                                |
+| --------------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                  |
 | `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
 | `type`          | String   | Indicates the type of sub-checklist item, such as boolean or descriptive.                                                                                  |
 | `answer`        | String   | Stores the user's response to the sub-checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                         |
@@ -45,9 +45,9 @@ This follows the same structure as the existing [notes data type](https://github
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the note.                                                                                                                         |
-| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                                                |
-| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                   |
+| `id`            | UUID     | A generated unique identifier for the note.                                                                                                               |
+| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                      |
+| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                  |
 | `content`       | String   | The text content of the note.                                                                                                                             |
 
 ### Image Object
@@ -60,9 +60,10 @@ The **Image Object** stores image data of the image attached to checklist items.
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the image.                                                                                                                        |
-| `data`          | Blob     | The image data of the attached image.                                                                                                                     |
-| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                  |
+| `id`            | UUID     | A generated unique identifier for the image.                                                                                                              |
+| `title`         | String   | The title of the image.                                                                                                                                   |
+| `description`   | String   | A brief description of the image.                                                                                                                         |
+| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                 |
 
 ### URL Object
 
@@ -74,8 +75,10 @@ The **URL Object** stores hyperlink of the URL attached to checklist items.
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                          |
+| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                |
 | `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
-| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                    |
+| `title`         | String   | The title of the URL.                                                                                                                                     |
+| `description`   | String   | A brief description of the URL.                                                                                                                           |
+| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                   |
 
 This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.

From 01e546e92ffd25988efab4d5289e16658693d834 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 30 Aug 2024 19:37:24 +0530
Subject: [PATCH 05/43] data structure modification and method to list project
 languages

---
 app/components/ProjectNotes/ProjectNotes.js   |   2 +-
 .../ReproChecklists/ChecklistItem.js          |  57 ++++++++--
 .../ReproChecklists/ReproChecklists.js        | 105 ++++++++++--------
 app/utils/asset.js                            |   2 +-
 4 files changed, 109 insertions(+), 57 deletions(-)

diff --git a/app/components/ProjectNotes/ProjectNotes.js b/app/components/ProjectNotes/ProjectNotes.js
index 6df8f1f..7286e4f 100644
--- a/app/components/ProjectNotes/ProjectNotes.js
+++ b/app/components/ProjectNotes/ProjectNotes.js
@@ -157,7 +157,7 @@ function projectNotes(props) {
         });
       }
 
-      const mappedPersonNotes = [];
+      let mappedPersonNotes = [];
       if (props.project.people) {
         props.project.people.forEach((p) => {
           if (p && p.notes) {
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index f19e1b8..1df4748 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -8,6 +8,7 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
   const [notes, setNotes] = useState(item.userNotes || []);
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
+  const [allImages, setAllImages] = useState([]);
 
   const handleNoteUpdate = (note, text) => {
     if (note) {
@@ -27,6 +28,24 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
     }
   };
 
+  useEffect(() => {
+    if (project && Array.isArray(project.assets)) {
+      const imageAssets = [];
+      const findImageAssets = (asset) => {
+        if (asset.type === 'image') {
+          imageAssets.push(asset.uri);
+        }
+        if (asset.children) {
+          asset.children.forEach(findImageAssets);
+        }
+      };
+
+      setAllImages(imageAssets);
+
+      project.assets.forEach(findImageAssets);
+    }
+  }, [project]);
+
   useEffect(() => {
     setNotes(item.userNotes || []);
   }, [item.userNotes]);
@@ -37,19 +56,37 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         <span>{item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
-            className={answer === 'yes' ? styles.yesset : styles.yes}
-            onClick={() => setAnswer('yes')}
+            className={answer ? styles.yesset : styles.yes}
+            onClick={() => setAnswer(true)}
           >
             {'Yes'}
           </button>
           <button
-            className={answer === 'no' ? styles.noset : styles.no}
-            onClick={() => setAnswer('no')}
+            className={answer  ? styles.noset : styles.no}
+            onClick={() => setAnswer(false)}
           >
             {'No'}
           </button>
         </div>
       </div>
+      <div className={styles.scanResult}>
+        {item.scanResult &&
+          Object.keys(item.scanResult).map((key) => {
+            return (
+            <div key={key}>
+              <span>{key}</span>
+              <ul>
+                {item.scanResult[key].length ? (
+                  item.scanResult[key].map((answer) => (
+                    <li key={answer}>{answer}</li>
+                  ))
+                ) : (
+                  <li>No answers available</li>
+                )}
+              </ul>
+            </div>
+          )})}
+      </div>
       <div className={styles.details}>
         <NoteEditor
           notes={notes}
@@ -127,7 +164,10 @@ ChecklistItem.propTypes = {
     id: PropTypes.string.isRequired,
     statement: PropTypes.string.isRequired,
     type: PropTypes.string.isRequired,
-    answer: PropTypes.string.isRequired,
+    answer: PropTypes.bool.isRequired,
+    scanResult: PropTypes.objectOf(
+      PropTypes.arrayOf(PropTypes.string)
+    ),
     userNotes: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
@@ -159,11 +199,12 @@ ChecklistItem.propTypes = {
         id: PropTypes.string.isRequired,
         statement: PropTypes.string.isRequired,
         type: PropTypes.string.isRequired,
-        answer: PropTypes.string.isRequired,
-        updated: PropTypes.string.isRequired,
+        answer: PropTypes.bool.isRequired,
+        scanResult: PropTypes.objectOf(
+          PropTypes.arrayOf(PropTypes.string)
+        ),
       })
     ),
-    updated: PropTypes.string.isRequired,
   }).isRequired,
   project: PropTypes.object.isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index a8a0de8..babdb0a 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -2,13 +2,16 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
-// /home/adi/Pictures/Screenshots/maskedvt.png
-const dummyChecklistItems = [
+const path = require('path');
+const AssetsConfig = require('../../constants/assets-config');
+
+const reproducibilityChecklist = [
   {
     id: '1',
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
-    answer: 'yes',
+    bool: true,
+    answerList: {},
     userNotes: [
       {
         id: 'note1',
@@ -23,21 +26,18 @@ const dummyChecklistItems = [
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
       {
-        id: 'image1',
+        id: 'image2',
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
       {
-        id: 'image1',
+        id: 'image3',
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
     ],
     attachedURLs: [
@@ -46,31 +46,28 @@ const dummyChecklistItems = [
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
       {
-        id: 'url1',
+        id: 'url2',
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
       {
-        id: 'url1',
+        id: 'url3',
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
     ],
     subChecklists: [],
-    updated: '2024-06-01',
   },
   {
     id: '2',
     statement: 'Second checklist item statement',
     type: 'Type2',
-    answer: 'no',
+    bool: false,
+    answerList: {},
     userNotes: [
       {
         id: 'note2',
@@ -82,41 +79,51 @@ const dummyChecklistItems = [
     attachedImages: [],
     attachedURLs: [],
     subChecklists: [],
-    updated: '2024-06-02',
   },
+  {
+    id: '3',
+    statement: 'List of all the languages used and the dependencies of the project',
+    type: 'List',
+    bool: true,
+    answerList: {},
+    userNotes: [],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists:[],
+  }
 ];
 
-function ReproChecklists(props) {
-  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
-  const [checklistItems, setChecklistItems] = useState(dummyChecklistItems);
+const languages = new Set();
+const dependencies = new Set();
 
-  useEffect(() => {
-    if (project && Array.isArray(project.assets)) {
-      const imageAssets = [];
-
-      const findImageAssets = (asset) => {
-        if (asset.type === 'image') {
-          imageAssets.push(asset);
-        }
-        if (asset.children) {
-          asset.children.forEach(findImageAssets);
+function findAssetLanguagesAndDependencies(asset) {
+  if (asset.contentTypes.includes('code') && asset.type === 'file') {
+    const lastSep = asset.uri.lastIndexOf(path.sep);
+    const fileName = asset.uri.substring(lastSep + 1);
+    const ext = fileName.split('.').pop();
+    if(ext){
+      AssetsConfig.contentTypes.forEach((contentType) => {
+        if(contentType.extensions.includes(ext)) {
+          languages.add(contentType.name);
         }
-      };
+      });
+    }
+  }
 
-      project.assets.forEach(findImageAssets);
+  if(asset.children){
+    asset.children.forEach(findAssetLanguagesAndDependencies);
+  }
+
+  reproducibilityChecklist[2].answerList = {languages: Array.from(languages),dependencies: Array.from(dependencies) };
+}
 
-      const updatedItems = dummyChecklistItems.map(item => ({
-        ...item,
-        attachedImages: imageAssets.map(asset => ({
-          id: asset.id,
-          uri: asset.uri,
-          title: asset.title || 'Image',
-          description: asset.description || 'About Image',
-          updated: asset.updated || 'NA',
-        })),
-      }));
+function ReproChecklists(props) {
+  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
 
-      setChecklistItems(updatedItems);
+  useEffect(() => {
+    if (project && project.assets) {
+      findAssetLanguagesAndDependencies(project.assets);
     }
   }, [project]);
 
@@ -145,7 +152,10 @@ ReproChecklists.propTypes = {
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
       type: PropTypes.string.isRequired,
-      answer: PropTypes.string.isRequired,
+      bool: PropTypes.bool.isRequired,
+      answerList: PropTypes.objectOf(
+        PropTypes.arrayOf(PropTypes.string)
+      ),
       userNotes: PropTypes.arrayOf(
         PropTypes.shape({
           id: PropTypes.string.isRequired,
@@ -177,11 +187,12 @@ ReproChecklists.propTypes = {
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
           type: PropTypes.string.isRequired,
-          answer: PropTypes.string.isRequired,
-          updated: PropTypes.string.isRequired,
+          bool: PropTypes.bool.isRequired,
+          answerList: PropTypes.objectOf(
+            PropTypes.arrayOf(PropTypes.string)
+          ),
         })
       ),
-      updated: PropTypes.string.isRequired,
     })
   ).isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
@@ -190,7 +201,7 @@ ReproChecklists.propTypes = {
 };
 
 ReproChecklists.defaultProps = {
-  reproChecklist: dummyChecklistItems,
+  reproChecklist: reproducibilityChecklist,
 };
 
 export default ReproChecklists;
diff --git a/app/utils/asset.js b/app/utils/asset.js
index afa3256..7a8bd49 100644
--- a/app/utils/asset.js
+++ b/app/utils/asset.js
@@ -1,5 +1,5 @@
 /* eslint-disable no-underscore-dangle */
-import path from 'path';
+const path = require('path');
 import last from 'lodash/last';
 import constants from '../constants/constants';
 

From e20caf62c1fc7727bfd70390258b65f04faa26de Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 30 Aug 2024 20:05:00 +0530
Subject: [PATCH 06/43] smol fix

---
 .../ReproChecklists/ReproChecklists.js        | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index babdb0a..ff62dba 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -10,8 +10,8 @@ const reproducibilityChecklist = [
     id: '1',
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
-    bool: true,
-    answerList: {},
+    answer: true,
+    scanResult: {},
     userNotes: [
       {
         id: 'note1',
@@ -66,8 +66,8 @@ const reproducibilityChecklist = [
     id: '2',
     statement: 'Second checklist item statement',
     type: 'Type2',
-    bool: false,
-    answerList: {},
+    answer: false,
+    scanResult: {},
     userNotes: [
       {
         id: 'note2',
@@ -84,8 +84,8 @@ const reproducibilityChecklist = [
     id: '3',
     statement: 'List of all the languages used and the dependencies of the project',
     type: 'List',
-    bool: true,
-    answerList: {},
+    answer: true,
+    scanResult: {},
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
@@ -152,8 +152,8 @@ ReproChecklists.propTypes = {
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
       type: PropTypes.string.isRequired,
-      bool: PropTypes.bool.isRequired,
-      answerList: PropTypes.objectOf(
+      answer: PropTypes.bool.isRequired,
+      scanResult: PropTypes.objectOf(
         PropTypes.arrayOf(PropTypes.string)
       ),
       userNotes: PropTypes.arrayOf(
@@ -187,8 +187,8 @@ ReproChecklists.propTypes = {
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
           type: PropTypes.string.isRequired,
-          bool: PropTypes.bool.isRequired,
-          answerList: PropTypes.objectOf(
+          answer: PropTypes.bool.isRequired,
+          scanResult: PropTypes.objectOf(
             PropTypes.arrayOf(PropTypes.string)
           ),
         })

From d1f0c2952630fa1d98cd4e9831ef5ded19766a8c Mon Sep 17 00:00:00 2001
From: "Luke R." <lrasmus@users.noreply.github.com>
Date: Tue, 3 Sep 2024 06:37:27 -0500
Subject: [PATCH 07/43] Update ReproducibilityChecklists-Planning.md

Fixed formatting
---
 docs/ReproducibilityChecklists-Planning.md | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/docs/ReproducibilityChecklists-Planning.md b/docs/ReproducibilityChecklists-Planning.md
index 92e7f53..d4b4801 100644
--- a/docs/ReproducibilityChecklists-Planning.md
+++ b/docs/ReproducibilityChecklists-Planning.md
@@ -14,24 +14,26 @@ StatWrap should be configured to provide information about the following categor
 
 1. **Summarize the software used** - this should include programming language(s) and dependencies.  Programming languages can be inferred from file extensions.  Dependencies can be inferred from specific references in code files (already processed by StatWrap), as well as dependency files used for specific languages (e.g., `requirements.txt` for Python).  StatWrap does not need to determine the specific version used in any environment if it is not specified elsewhere.
 2. **Multiple versions of a file** - use a heuristic from file names to determine if the user has versioned files using a naming convention, as opposed to using source control. For example, `main_analysis.R` and `main_analysis_v2.R` or `main_analysis-jd.R`.  StatWrap could use metrics other than the file name, such as similarity of file content, to further infer if the files are likely versioned.  For a grouping of files that StatWrap thinks are versioned, it should check attributes to:
-  1. See if any of the files are marked as 'archived'.
-  2. If more than one file is marked as an 'entry point'.
-3. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`.  If so, display these file(s)/folder(s) as the projecct documentation.
-4. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project.  This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`).  StatWrap should report which file(s) are using absolute paths.
-5. **Binary / proprietary file formats for data** - flag data files that are not purely text-based.  This can be done from a configureable list of file extensions.
-6. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
+
+    1. See if any of the files are marked as 'archived'.
+    2. If more than one file is marked as an 'entry point'.
+
+4. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`.  If so, display these file(s)/folder(s) as the projecct documentation.
+5. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project.  This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`).  StatWrap should report which file(s) are using absolute paths.
+6. **Binary / proprietary file formats for data** - flag data files that are not purely text-based.  This can be done from a configureable list of file extensions.
+7. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
 	1. Input data - data flagged with an attribute of "Input / Raw Data", or data contained in folders using a configurable list of folder names (e.g., `raw`, `input`)
 	2. Derived data - data flagged with an attribute of "Derived", or data contained in folders using a configurable list of folder names (e.g., `output`, `derived`)
 	3. Data (general) - data files that we cannot otherwise categorize
-7. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps.  Note that a single code file may have multiple annotations:
+8. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps.  Note that a single code file may have multiple annotations:
    1. Data acquisition - used to import / pull data. This would be flagged with an attribute of "Data acquisition".
    2. Data processing - this would be flagged with an attribute of "Data processing"
    3. Analysis - this would be flagged with an attribute of "Analysis"
-8. **Entry points** - StatWrap should list all code files flagged as entry points by the user.  If none, and code files exist, this should also be noted ("No entry point has been specified").  This could be combined with the previous item.
-9. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data.  Summarize these for the user as external assets that are being referenced.
+9. **Entry points** - StatWrap should list all code files flagged as entry points by the user.  If none, and code files exist, this should also be noted ("No entry point has been specified").  This could be combined with the previous item.
+10. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data.  Summarize these for the user as external assets that are being referenced.
 
 ### 2. Human-entered information / decision making (user)
 
 This is more of the traditional "checklist", where the user is presented with a list of questions that they may attest to.  Some of the answers may be pre-filled using data collected by StatWrap as defined in the automated information gathering (previous section).
 
-(See proposal by Adi)
\ No newline at end of file
+(See proposal by Adi)

From 84d88878f9b5b830bb9c0d752e8d1b6220c39a06 Mon Sep 17 00:00:00 2001
From: Luke R <luke.rasmussen@gmail.com>
Date: Tue, 28 May 2024 08:45:11 -0500
Subject: [PATCH 08/43] Added documentation around reproducibility checklist
 features

---
 docs/ReproducibilityChecklists-Planning.md | 37 ++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 docs/ReproducibilityChecklists-Planning.md

diff --git a/docs/ReproducibilityChecklists-Planning.md b/docs/ReproducibilityChecklists-Planning.md
new file mode 100644
index 0000000..92e7f53
--- /dev/null
+++ b/docs/ReproducibilityChecklists-Planning.md
@@ -0,0 +1,37 @@
+# Reproducible Research Checklists
+
+This document provides design guidance and general requirements for the reproducible research checklist feature in StatWrap.
+
+## Modes of Operation
+
+There are two modes of operation for the checklist:
+
+### 1. Automated information gathering / decision making (StatWrap)
+
+StatWrap will use information from project assets and user-entered metadata in order to provide information about reproducible research practices.  This will be used to **inform** users, but will not make a binary indicator (yes/no) about if a practice is "reproducible" or not.
+
+StatWrap should be configured to provide information about the following categories of data.  The way the data could be displayed is noted, but is not intended to limit the final implementation.  For each of these, there should be a service method that is able to perform the processed logic.  Unlike the actual checklist UI, these items are not configurable by the end user, they are built within StatWrap.
+
+1. **Summarize the software used** - this should include programming language(s) and dependencies.  Programming languages can be inferred from file extensions.  Dependencies can be inferred from specific references in code files (already processed by StatWrap), as well as dependency files used for specific languages (e.g., `requirements.txt` for Python).  StatWrap does not need to determine the specific version used in any environment if it is not specified elsewhere.
+2. **Multiple versions of a file** - use a heuristic from file names to determine if the user has versioned files using a naming convention, as opposed to using source control. For example, `main_analysis.R` and `main_analysis_v2.R` or `main_analysis-jd.R`.  StatWrap could use metrics other than the file name, such as similarity of file content, to further infer if the files are likely versioned.  For a grouping of files that StatWrap thinks are versioned, it should check attributes to:
+  1. See if any of the files are marked as 'archived'.
+  2. If more than one file is marked as an 'entry point'.
+3. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`.  If so, display these file(s)/folder(s) as the projecct documentation.
+4. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project.  This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`).  StatWrap should report which file(s) are using absolute paths.
+5. **Binary / proprietary file formats for data** - flag data files that are not purely text-based.  This can be done from a configureable list of file extensions.
+6. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
+	1. Input data - data flagged with an attribute of "Input / Raw Data", or data contained in folders using a configurable list of folder names (e.g., `raw`, `input`)
+	2. Derived data - data flagged with an attribute of "Derived", or data contained in folders using a configurable list of folder names (e.g., `output`, `derived`)
+	3. Data (general) - data files that we cannot otherwise categorize
+7. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps.  Note that a single code file may have multiple annotations:
+   1. Data acquisition - used to import / pull data. This would be flagged with an attribute of "Data acquisition".
+   2. Data processing - this would be flagged with an attribute of "Data processing"
+   3. Analysis - this would be flagged with an attribute of "Analysis"
+8. **Entry points** - StatWrap should list all code files flagged as entry points by the user.  If none, and code files exist, this should also be noted ("No entry point has been specified").  This could be combined with the previous item.
+9. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data.  Summarize these for the user as external assets that are being referenced.
+
+### 2. Human-entered information / decision making (user)
+
+This is more of the traditional "checklist", where the user is presented with a list of questions that they may attest to.  Some of the answers may be pre-filled using data collected by StatWrap as defined in the automated information gathering (previous section).
+
+(See proposal by Adi)
\ No newline at end of file

From 19eb76833790e8cc8ee0056ef037c0aee77bd7f0 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Wed, 26 Jun 2024 13:19:50 +0530
Subject: [PATCH 09/43] basic UI skeleton

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             |  12 ++
 .../ReproChecklists/ChecklistItem.css         |  87 ++++++++++
 .../ReproChecklists/ChecklistItem.js          | 163 ++++++++++++++++++
 .../ReproChecklists/ReproChecklists.css       |   8 +
 .../ReproChecklists/ReproChecklists.js        | 114 ++++++++++++
 docs/ReproducibilityChecklists-DataModels.md  |  80 +++++++++
 6 files changed, 464 insertions(+)
 create mode 100644 app/components/ReproChecklists/ChecklistItem.css
 create mode 100644 app/components/ReproChecklists/ChecklistItem.js
 create mode 100644 app/components/ReproChecklists/ReproChecklists.css
 create mode 100644 app/components/ReproChecklists/ReproChecklists.js
 create mode 100644 docs/ReproducibilityChecklists-DataModels.md

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index bfe6d42..56c790e 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -13,6 +13,7 @@ import Assets from './Assets/Assets';
 import Workflow from '../Workflow/Workflow';
 import People from '../People/People';
 import ProjectLog from '../ProjectLog/ProjectLog';
+import ReproChecklists from '../ReproChecklists/ReproChecklists';
 import ProjectNotes from '../ProjectNotes/ProjectNotes';
 import { ActionType, EntityType, DescriptionContentType } from '../../constants/constants';
 import AssetUtil from '../../utils/asset';
@@ -681,6 +682,13 @@ class Project extends Component<Props> {
           />
         ) : null;
 
+      const reproChecklists = <ReproChecklists
+        project={this.props.project}
+        onAddedNote={this.projectUpsertNoteHandler}
+        onUpdatedNote={this.projectUpsertNoteHandler}
+        onDeletedNote={this.projectDeleteNoteHandler}
+      />
+
       content = (
         <TabContext value={this.state.selectedTab}>
           <div className={styles.header}>
@@ -709,6 +717,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
+              <Tab label="Reproducibility Checklists" value="reproChecklists" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -729,6 +738,9 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
+          <TabPanel value="reproChecklists" classes={tabPanelStyle}>
+            {reproChecklists}
+          </TabPanel>
         </TabContext>
       );
     }
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
new file mode 100644
index 0000000..dc06332
--- /dev/null
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -0,0 +1,87 @@
+.item {
+  padding: 10px;
+  border-bottom: 1px solid #e5e5e5;
+}
+
+.header {
+  display: flex;
+  align-items: center;
+}
+
+.buttoncontainer {
+  margin-left: auto;
+  margin-right: 0;
+}
+
+.details {
+  padding-left: 20px;
+  margin-top: 10px;
+}
+
+.notes,
+.images,
+.urls,
+.subChecklists {
+  margin-top: 10px;
+}
+
+.notes ul,
+.images ul,
+.urls ul {
+  list-style-type: none;
+  padding-left: 0;
+}
+
+.notes li,
+.images li,
+.urls li {
+  margin-bottom: 5px;
+}
+
+.notes li strong {
+  display: block;
+}
+
+.timestamp {
+  display: block;
+  font-size: 12px;
+  color: #888;
+}
+
+.images img {
+  max-width: 100%;
+  height: auto;
+}
+
+.item button {
+  min-width: 50px;
+  height: 32px;
+  border: none;
+  border-radius: 4px;
+  cursor: pointer;
+  transition: background-color 0.3s ease;
+}
+
+.item button.yes {
+  background-color:#aa94d1;
+  color: white;
+}
+
+.item button.yesset {
+  background-color:rebeccapurple;
+  color: white;
+}
+
+.item button.no {
+  background-color: silver;
+  color: white;
+}
+
+.item button.noset {
+  background-color: grey;
+  color: white;
+}
+
+.item button:hover {
+  opacity: 0.9;
+}
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
new file mode 100644
index 0000000..3295803
--- /dev/null
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -0,0 +1,163 @@
+import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
+import styles from './ChecklistItem.css';
+import NoteEditor from '../NoteEditor/NoteEditor';
+
+function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNote }) {
+  const [answer, setAnswer] = useState(item.answer);
+  const [notes, setNotes] = useState(item.userNotes || []);
+
+  const handleNoteUpdate = (note, text) => {
+    if (note) {
+      if (onUpdatedNote) {
+        onUpdatedNote(project, text, note);
+      }
+    } else {
+      if (onAddedNote) {
+        onAddedNote(project, text);
+      }
+    }
+  };
+
+  const handleNoteDelete = (note) => {
+    if (onDeletedNote) {
+      onDeletedNote(project, note);
+    }
+  };
+
+  useEffect(() => {
+    setNotes(item.userNotes || []);
+  }, [item.userNotes]);
+
+  return (
+    <div className={styles.item}>
+      <div className={styles.header}>
+        <span>{item.statement}</span>
+        <div className={styles.buttoncontainer}>
+          <button
+            className={answer === 'yes' ? styles.yesset : styles.yes}
+            onClick={() => setAnswer('yes')}
+          >
+            {'Yes'}
+          </button>
+          <button
+            className={answer === 'no' ? styles.noset : styles.no}
+            onClick={() => setAnswer('no')}
+          >
+            {'No'}
+          </button>
+        </div>
+      </div>
+      <div className={styles.details}>
+        {notes.length > 0 && (
+          <div className={styles.notes}>
+            <h4>Notes:</h4>
+            <ul>
+              {notes.map((note) => (
+                <li key={note.id}>
+                  <strong>{note.author}:</strong> {note.content}
+                  <span className={styles.timestamp}>{note.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        <NoteEditor
+          notes={notes}
+          onEditingComplete={handleNoteUpdate}
+          onDelete={handleNoteDelete}
+        />
+        {item.attachedImages.length > 0 && (
+          <div className={styles.images}>
+            <h4>Attached Images:</h4>
+            <ul>
+              {item.attachedImages.map((image) => (
+                <li key={image.id}>
+                  <img src={URL.createObjectURL(image.data)} alt="attached" />
+                  <span className={styles.timestamp}>{image.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        {item.attachedURLs.length > 0 && (
+          <div className={styles.urls}>
+            <h4>Attached URLs:</h4>
+            <ul>
+              {item.attachedURLs.map((url) => (
+                <li key={url.id}>
+                  <a href={url.hyperlink} target="">
+                    {url.hyperlink}
+                  </a>
+                  <span className={styles.timestamp}>{url.updated}</span>
+                </li>
+              ))}
+            </ul>
+          </div>
+        )}
+        {item.subChecklists.length > 0 && (
+          <div className={styles.subChecklists}>
+            <h4>Sub-Checklists:</h4>
+            {item.subChecklists.map((subItem) => (
+              <ChecklistItem
+                key={subItem.id}
+                item={subItem}
+                project={project}
+                onUpdatedNote={onUpdatedNote}
+                onDeletedNote={onDeletedNote}
+                onAddedNote={onAddedNote}
+              />
+            ))}
+          </div>
+        )}
+      </div>
+    </div>
+  );
+}
+
+ChecklistItem.propTypes = {
+  item: PropTypes.shape({
+    id: PropTypes.string.isRequired,
+    statement: PropTypes.string.isRequired,
+    type: PropTypes.string.isRequired,
+    answer: PropTypes.string.isRequired,
+    userNotes: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        author: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+        content: PropTypes.string.isRequired,
+      })
+    ),
+    attachedImages: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        data: PropTypes.instanceOf(Blob).isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    attachedURLs: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        hyperlink: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    subChecklists: PropTypes.arrayOf(
+      PropTypes.shape({
+        id: PropTypes.string.isRequired,
+        statement: PropTypes.string.isRequired,
+        type: PropTypes.string.isRequired,
+        answer: PropTypes.string.isRequired,
+        updated: PropTypes.string.isRequired,
+      })
+    ),
+    updated: PropTypes.string.isRequired,
+  }).isRequired,
+  project: PropTypes.object.isRequired,
+  onUpdatedNote: PropTypes.func.isRequired,
+  onDeletedNote: PropTypes.func.isRequired,
+  onAddedNote: PropTypes.func.isRequired,
+};
+
+export default ChecklistItem;
diff --git a/app/components/ReproChecklists/ReproChecklists.css b/app/components/ReproChecklists/ReproChecklists.css
new file mode 100644
index 0000000..aa2d05b
--- /dev/null
+++ b/app/components/ReproChecklists/ReproChecklists.css
@@ -0,0 +1,8 @@
+.container {
+  padding: 20px;
+}
+
+h2 {
+  margin-bottom: 20px;
+  font-size: 24px;
+}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
new file mode 100644
index 0000000..e1b87ea
--- /dev/null
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -0,0 +1,114 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import ChecklistItem from './ChecklistItem';
+
+const dummyChecklistItems = [
+  {
+    id: '1',
+    statement: 'First checklist item statement',
+    type: 'Type1',
+    answer: 'yes',
+    userNotes: [
+      {
+        id: 'note1',
+        author: 'Author1',
+        updated: '2024-06-01',
+        content: 'First note content',
+      },
+    ],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists: [],
+    updated: '2024-06-01',
+  },
+  {
+    id: '2',
+    statement: 'Second checklist item statement',
+    type: 'Type2',
+    answer: 'no',
+    userNotes: [
+      {
+        id: 'note2',
+        author: 'Author2',
+        updated: '2024-06-02',
+        content: 'Second note content',
+      },
+    ],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists: [],
+    updated: '2024-06-02',
+  },
+];
+
+function ReproChecklists(props) {
+  const { project, checklistItems, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+
+  return (
+    <div>
+      {checklistItems.map(item => (
+        <ChecklistItem
+          key={item.id}
+          item={item}
+          project={project}
+          onUpdatedNote={onUpdatedNote}
+          onDeletedNote={onDeletedNote}
+          onAddedNote={onAddedNote}
+        />
+      ))}
+    </div>
+  );
+}
+
+ReproChecklists.propTypes = {
+  project: PropTypes.object.isRequired,
+  checklistItems: PropTypes.arrayOf(
+    PropTypes.shape({
+      id: PropTypes.string.isRequired,
+      statement: PropTypes.string.isRequired,
+      type: PropTypes.string.isRequired,
+      answer: PropTypes.string.isRequired,
+      userNotes: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          author: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+          content: PropTypes.string.isRequired,
+        })
+      ),
+      attachedImages: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          data: PropTypes.instanceOf(Blob).isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      attachedURLs: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          hyperlink: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      subChecklists: PropTypes.arrayOf(
+        PropTypes.shape({
+          id: PropTypes.string.isRequired,
+          statement: PropTypes.string.isRequired,
+          type: PropTypes.string.isRequired,
+          answer: PropTypes.string.isRequired,
+          updated: PropTypes.string.isRequired,
+        })
+      ),
+      updated: PropTypes.string.isRequired,
+    })
+  ).isRequired,
+  onUpdatedNote: PropTypes.func.isRequired,
+  onDeletedNote: PropTypes.func.isRequired,
+  onAddedNote: PropTypes.func.isRequired,
+};
+
+ReproChecklists.defaultProps = {
+  checklistItems: dummyChecklistItems,
+};
+
+export default ReproChecklists;
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
new file mode 100644
index 0000000..0d77350
--- /dev/null
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -0,0 +1,80 @@
+## Checklist Object
+
+### About
+
+The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklists.
+
+### Attributes
+
+| Attribute          | Type       | Description                                                                                                                                               |
+| ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                                |
+| `statement`        | String     | The statement or question associated with the checklist item.                                                                                              |
+| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                      |
+| `answer`           | String     | Stores the user's response to the checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                                         |
+| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                                  |
+| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                                  |
+| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                     |
+| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                                    |
+| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                         |
+
+### Sub-Checklist Object
+
+#### About
+
+The **Sub-Checklist Object** represents a sub-item within a checklist item. It shares similar attributes with the Checklist Object, except for attachments, but is nested within the parent checklist item.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                           |
+| `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
+| `type`          | String   | Indicates the type of sub-checklist item, such as boolean or descriptive.                                                                                  |
+| `answer`        | String   | Stores the user's response to the sub-checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                         |
+| `updated`       | String   | The timestamp indicating when the sub-checklist item was last updated.                                                                                     |
+
+### Note Object
+
+#### About
+
+The **Note Object** stores user-added note associated with checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the note.                                                                                                                         |
+| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                                                |
+| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                   |
+| `content`       | String   | The text content of the note.                                                                                                                             |
+
+### Image Object
+
+#### About
+
+The **Image Object** stores image data of the image attached to checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the image.                                                                                                                        |
+| `data`          | Blob     | The image data of the attached image.                                                                                                                     |
+| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                  |
+
+### URL Object
+
+#### About
+
+The **URL Object** stores hyperlink of the URL attached to checklist items.
+
+#### Attributes
+
+| Attribute       | Type     | Description                                                                                                                                               |
+| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                          |
+| `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
+| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                    |
+
+This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.

From a3599a738e2652086f4c50c8fc986bfa1b1eb137 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Wed, 26 Jun 2024 19:58:37 +0530
Subject: [PATCH 10/43] minor corrections

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js                 |  8 ++++----
 app/components/ReproChecklists/ChecklistItem.css  |  2 +-
 app/components/ReproChecklists/ChecklistItem.js   | 15 +--------------
 app/components/ReproChecklists/ReproChecklists.js |  3 +++
 docs/ReproducibilityChecklists-DataModels.md      |  1 +
 5 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 56c790e..7a11409 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -682,7 +682,7 @@ class Project extends Component<Props> {
           />
         ) : null;
 
-      const reproChecklists = <ReproChecklists
+      const Checklists = <ReproChecklists
         project={this.props.project}
         onAddedNote={this.projectUpsertNoteHandler}
         onUpdatedNote={this.projectUpsertNoteHandler}
@@ -717,7 +717,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
-              <Tab label="Reproducibility Checklists" value="reproChecklists" classes={tabStyle} />
+              <Tab label="Checklists" value="Checklists" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -738,8 +738,8 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
-          <TabPanel value="reproChecklists" classes={tabPanelStyle}>
-            {reproChecklists}
+          <TabPanel value="Checklists" classes={tabPanelStyle}>
+            {Checklists}
           </TabPanel>
         </TabContext>
       );
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index dc06332..fe4647a 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -8,7 +8,7 @@
   align-items: center;
 }
 
-.buttoncontainer {
+.buttonContainer {
   margin-left: auto;
   margin-right: 0;
 }
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 3295803..382719d 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -33,7 +33,7 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
     <div className={styles.item}>
       <div className={styles.header}>
         <span>{item.statement}</span>
-        <div className={styles.buttoncontainer}>
+        <div className={styles.buttonContainer}>
           <button
             className={answer === 'yes' ? styles.yesset : styles.yes}
             onClick={() => setAnswer('yes')}
@@ -49,19 +49,6 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         </div>
       </div>
       <div className={styles.details}>
-        {notes.length > 0 && (
-          <div className={styles.notes}>
-            <h4>Notes:</h4>
-            <ul>
-              {notes.map((note) => (
-                <li key={note.id}>
-                  <strong>{note.author}:</strong> {note.content}
-                  <span className={styles.timestamp}>{note.updated}</span>
-                </li>
-              ))}
-            </ul>
-          </div>
-        )}
         <NoteEditor
           notes={notes}
           onEditingComplete={handleNoteUpdate}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index e1b87ea..c5732af 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -1,6 +1,7 @@
 import React from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
+import { Typography } from '@mui/material';
 
 const dummyChecklistItems = [
   {
@@ -46,6 +47,8 @@ function ReproChecklists(props) {
 
   return (
     <div>
+      <Typography variant='h5' align='center'>Reproducibility Checklists</Typography>
+      <br />
       {checklistItems.map(item => (
         <ChecklistItem
           key={item.id}
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index 0d77350..62b4286 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -39,6 +39,7 @@ The **Sub-Checklist Object** represents a sub-item within a checklist item. It s
 #### About
 
 The **Note Object** stores user-added note associated with checklist items.
+This follows the same structure as the existing [notes data type](https://github.com/StatTag/StatWrap/blob/master/docs/Notes.md)
 
 #### Attributes
 

From f8ec2066df7122c2bdc5e3097f38741a2006beb5 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 6 Aug 2024 17:18:54 +0530
Subject: [PATCH 11/43] adds image and url component UI

---
 .../ReproChecklists/ChecklistItem.css         | 120 ++++++++++++++++--
 .../ReproChecklists/ChecklistItem.js          |  66 +++++++---
 .../ReproChecklists/ReproChecklists.js        |  97 ++++++++++++--
 docs/ReproducibilityChecklists-DataModels.md  |  41 +++---
 4 files changed, 263 insertions(+), 61 deletions(-)

diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index fe4647a..a1ce89b 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -3,8 +3,12 @@
   border-bottom: 1px solid #e5e5e5;
 }
 
+.header span {
+  max-width: 83%;
+}
+
 .header {
-  display: flex;
+  display:flex;
   align-items: center;
 }
 
@@ -18,28 +22,47 @@
   margin-top: 10px;
 }
 
-.notes,
 .images,
 .urls,
 .subChecklists {
   margin-top: 10px;
 }
 
-.notes ul,
-.images ul,
+.images ul{
+  list-style-type: none;
+  padding-left: 0;
+  display: flex;
+  overflow-x: auto;
+  white-space: nowrap;
+}
+
 .urls ul {
   list-style-type: none;
   padding-left: 0;
+  max-height: 200px;
+  overflow-y: auto;
+  white-space: nowrap;
 }
 
-.notes li,
-.images li,
-.urls li {
+.images li{
+  margin-right: 10px;
   margin-bottom: 5px;
+  padding-right: 5px;
+  position: relative;
 }
 
-.notes li strong {
-  display: block;
+.urls li{
+  margin-right: 10px;
+  margin-bottom: 5px;
+  padding-bottom: 5px;
+  position: relative;
+}
+
+.images li:not(:last-child) {
+  border-right: 1px solid #ccc;
+}
+.urls li:not(:last-child) {
+  border-bottom: 1px solid #ccc;
 }
 
 .timestamp {
@@ -49,8 +72,40 @@
 }
 
 .images img {
-  max-width: 100%;
   height: auto;
+  max-height: 150px;
+  transition: max-height 0.3s ease;
+  display: block;
+  margin-top: 5px;
+}
+
+.imageContent,
+.urlContent {
+  max-height: 0;
+  overflow: hidden;
+  transition: max-height 0.3s ease;
+}
+
+.imageContent.show,
+.urlContent.show {
+  max-height: 500px;
+}
+
+.urls a {
+  text-decoration: none;
+  color: #007bff;
+  display: block;
+  margin-top: 5px;
+}
+
+.urls a:hover {
+  color: darkblue;
+}
+
+.images p,
+.urls p {
+  margin-top: 8px;
+  font-size: 15px;
 }
 
 .item button {
@@ -63,12 +118,12 @@
 }
 
 .item button.yes {
-  background-color:#aa94d1;
+  background-color: #aa94d1;
   color: white;
 }
 
 .item button.yesset {
-  background-color:rebeccapurple;
+  background-color: rebeccapurple;
   color: white;
 }
 
@@ -85,3 +140,44 @@
 .item button:hover {
   opacity: 0.9;
 }
+
+.headerWithButton {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+}
+
+.dropdownButton {
+  background-color: #f8f9fa;
+  color: #333;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 14px;
+  transition: background-color 0.3s ease;
+}
+
+.dropdownButton:hover {
+  background-color: #e9ecef;
+}
+
+.dropdownContent {
+  display: none;
+  padding: 10px;
+  background-color: #f8f9fa;
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  margin-top: 5px;
+  transition: max-height 0.3s ease;
+}
+
+.dropdownContent.show {
+  display: block;
+  max-height: 500px;
+}
+
+.imageTitle,
+.urlTitle {
+  font-size: 16px;
+}
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 382719d..f19e1b8 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -6,6 +6,8 @@ import NoteEditor from '../NoteEditor/NoteEditor';
 function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNote }) {
   const [answer, setAnswer] = useState(item.answer);
   const [notes, setNotes] = useState(item.userNotes || []);
+  const [showImages, setShowImages] = useState(false);
+  const [showURLs, setShowURLs] = useState(false);
 
   const handleNoteUpdate = (note, text) => {
     if (note) {
@@ -56,30 +58,48 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         />
         {item.attachedImages.length > 0 && (
           <div className={styles.images}>
-            <h4>Attached Images:</h4>
-            <ul>
-              {item.attachedImages.map((image) => (
-                <li key={image.id}>
-                  <img src={URL.createObjectURL(image.data)} alt="attached" />
-                  <span className={styles.timestamp}>{image.updated}</span>
-                </li>
-              ))}
-            </ul>
+            <div className={styles.headerWithButton}>
+              <h4>Attached Images:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
+                {showImages ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
+              <ul>
+                {item.attachedImages.map((image) => (
+                  <li key={image.id}>
+                    <span className={styles.imageTitle}>{image.title}</span>
+                    <img src={image.uri} alt="attached" />
+                    <p>{image.description}</p>
+                    <span className={styles.timestamp}>{image.updated}</span>
+                  </li>
+                ))}
+              </ul>
+            </div>
           </div>
         )}
         {item.attachedURLs.length > 0 && (
           <div className={styles.urls}>
-            <h4>Attached URLs:</h4>
-            <ul>
-              {item.attachedURLs.map((url) => (
-                <li key={url.id}>
-                  <a href={url.hyperlink} target="">
-                    {url.hyperlink}
-                  </a>
-                  <span className={styles.timestamp}>{url.updated}</span>
-                </li>
-              ))}
-            </ul>
+            <div className={styles.headerWithButton}>
+              <h4>Attached URLs:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
+                {showURLs ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
+              <ul>
+                {item.attachedURLs.map((url) => (
+                  <li key={url.id}>
+                    <span className={styles.urlTitle}>{url.title}</span>
+                    <a href={url.hyperlink} target="">
+                      {url.hyperlink}
+                    </a>
+                    <p>{url.description}</p>
+                    <span className={styles.timestamp}>{url.updated}</span>
+                  </li>
+                ))}
+              </ul>
+            </div>
           </div>
         )}
         {item.subChecklists.length > 0 && (
@@ -119,7 +139,9 @@ ChecklistItem.propTypes = {
     attachedImages: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
-        data: PropTypes.instanceOf(Blob).isRequired,
+        uri: PropTypes.string.isRequired,
+        title: PropTypes.string.isRequired,
+        description: PropTypes.string.isRequired,
         updated: PropTypes.string.isRequired,
       })
     ),
@@ -127,6 +149,8 @@ ChecklistItem.propTypes = {
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         hyperlink: PropTypes.string.isRequired,
+        title: PropTypes.string.isRequired,
+        description: PropTypes.string.isRequired,
         updated: PropTypes.string.isRequired,
       })
     ),
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index c5732af..a8a0de8 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -1,12 +1,12 @@
-import React from 'react';
+import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
-
+// /home/adi/Pictures/Screenshots/maskedvt.png
 const dummyChecklistItems = [
   {
     id: '1',
-    statement: 'First checklist item statement',
+    statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
     answer: 'yes',
     userNotes: [
@@ -17,8 +17,52 @@ const dummyChecklistItems = [
         content: 'First note content',
       },
     ],
-    attachedImages: [],
-    attachedURLs: [],
+    attachedImages: [
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'image1',
+        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
+        title: 'Dummy Image',
+        description: 'This is a dummy image description',
+        updated: '2024-06-09',
+      },
+    ],
+    attachedURLs: [
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+      {
+        id: 'url1',
+        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
+        title: 'StatWrap URL',
+        description: 'This is URL description',
+        updated: '2024-06-09',
+      },
+    ],
     subChecklists: [],
     updated: '2024-06-01',
   },
@@ -43,7 +87,38 @@ const dummyChecklistItems = [
 ];
 
 function ReproChecklists(props) {
-  const { project, checklistItems, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const [checklistItems, setChecklistItems] = useState(dummyChecklistItems);
+
+  useEffect(() => {
+    if (project && Array.isArray(project.assets)) {
+      const imageAssets = [];
+
+      const findImageAssets = (asset) => {
+        if (asset.type === 'image') {
+          imageAssets.push(asset);
+        }
+        if (asset.children) {
+          asset.children.forEach(findImageAssets);
+        }
+      };
+
+      project.assets.forEach(findImageAssets);
+
+      const updatedItems = dummyChecklistItems.map(item => ({
+        ...item,
+        attachedImages: imageAssets.map(asset => ({
+          id: asset.id,
+          uri: asset.uri,
+          title: asset.title || 'Image',
+          description: asset.description || 'About Image',
+          updated: asset.updated || 'NA',
+        })),
+      }));
+
+      setChecklistItems(updatedItems);
+    }
+  }, [project]);
 
   return (
     <div>
@@ -65,7 +140,7 @@ function ReproChecklists(props) {
 
 ReproChecklists.propTypes = {
   project: PropTypes.object.isRequired,
-  checklistItems: PropTypes.arrayOf(
+  reproChecklist: PropTypes.arrayOf(
     PropTypes.shape({
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
@@ -82,7 +157,9 @@ ReproChecklists.propTypes = {
       attachedImages: PropTypes.arrayOf(
         PropTypes.shape({
           id: PropTypes.string.isRequired,
-          data: PropTypes.instanceOf(Blob).isRequired,
+          uri: PropTypes.string.isRequired,
+          title: PropTypes.string.isRequired,
+          description: PropTypes.string.isRequired,
           updated: PropTypes.string.isRequired,
         })
       ),
@@ -90,6 +167,8 @@ ReproChecklists.propTypes = {
         PropTypes.shape({
           id: PropTypes.string.isRequired,
           hyperlink: PropTypes.string.isRequired,
+          title: PropTypes.string.isRequired,
+          description: PropTypes.string.isRequired,
           updated: PropTypes.string.isRequired,
         })
       ),
@@ -111,7 +190,7 @@ ReproChecklists.propTypes = {
 };
 
 ReproChecklists.defaultProps = {
-  checklistItems: dummyChecklistItems,
+  reproChecklist: dummyChecklistItems,
 };
 
 export default ReproChecklists;
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index 62b4286..a60cd4f 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -8,15 +8,15 @@ The **Checklist Object** represents a single checklist item within the reproduci
 
 | Attribute          | Type       | Description                                                                                                                                               |
 | ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                                |
-| `statement`        | String     | The statement or question associated with the checklist item.                                                                                              |
-| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                      |
+| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                     |
+| `statement`        | String     | The statement or question associated with the checklist item.                                                                                             |
+| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                     |
 | `answer`           | String     | Stores the user's response to the checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                                         |
-| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                                  |
-| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                                  |
-| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                     |
-| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                                    |
-| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                         |
+| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                               |
+| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                              |
+| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
+| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                        |
+| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                        |
 
 ### Sub-Checklist Object
 
@@ -26,9 +26,9 @@ The **Sub-Checklist Object** represents a sub-item within a checklist item. It s
 
 #### Attributes
 
-| Attribute       | Type     | Description                                                                                                                                               |
-| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                           |
+| Attribute       | Type     | Description                                                                                                                                                |
+| --------------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                  |
 | `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
 | `type`          | String   | Indicates the type of sub-checklist item, such as boolean or descriptive.                                                                                  |
 | `answer`        | String   | Stores the user's response to the sub-checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                         |
@@ -45,9 +45,9 @@ This follows the same structure as the existing [notes data type](https://github
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the note.                                                                                                                         |
-| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                                                |
-| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                   |
+| `id`            | UUID     | A generated unique identifier for the note.                                                                                                               |
+| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                      |
+| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                  |
 | `content`       | String   | The text content of the note.                                                                                                                             |
 
 ### Image Object
@@ -60,9 +60,10 @@ The **Image Object** stores image data of the image attached to checklist items.
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the image.                                                                                                                        |
-| `data`          | Blob     | The image data of the attached image.                                                                                                                     |
-| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                  |
+| `id`            | UUID     | A generated unique identifier for the image.                                                                                                              |
+| `title`         | String   | The title of the image.                                                                                                                                   |
+| `description`   | String   | A brief description of the image.                                                                                                                         |
+| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                 |
 
 ### URL Object
 
@@ -74,8 +75,10 @@ The **URL Object** stores hyperlink of the URL attached to checklist items.
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                          |
+| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                |
 | `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
-| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                    |
+| `title`         | String   | The title of the URL.                                                                                                                                     |
+| `description`   | String   | A brief description of the URL.                                                                                                                           |
+| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                   |
 
 This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.

From ebd9bab7210f2abffecaf5cad20426ab29b30310 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 30 Aug 2024 19:37:24 +0530
Subject: [PATCH 12/43] data structure modification and method to list project
 languages

---
 app/components/ProjectNotes/ProjectNotes.js   |   2 +-
 .../ReproChecklists/ChecklistItem.js          |  57 ++++++++--
 .../ReproChecklists/ReproChecklists.js        | 105 ++++++++++--------
 app/utils/asset.js                            |   2 +-
 4 files changed, 109 insertions(+), 57 deletions(-)

diff --git a/app/components/ProjectNotes/ProjectNotes.js b/app/components/ProjectNotes/ProjectNotes.js
index 6df8f1f..7286e4f 100644
--- a/app/components/ProjectNotes/ProjectNotes.js
+++ b/app/components/ProjectNotes/ProjectNotes.js
@@ -157,7 +157,7 @@ function projectNotes(props) {
         });
       }
 
-      const mappedPersonNotes = [];
+      let mappedPersonNotes = [];
       if (props.project.people) {
         props.project.people.forEach((p) => {
           if (p && p.notes) {
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index f19e1b8..1df4748 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -8,6 +8,7 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
   const [notes, setNotes] = useState(item.userNotes || []);
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
+  const [allImages, setAllImages] = useState([]);
 
   const handleNoteUpdate = (note, text) => {
     if (note) {
@@ -27,6 +28,24 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
     }
   };
 
+  useEffect(() => {
+    if (project && Array.isArray(project.assets)) {
+      const imageAssets = [];
+      const findImageAssets = (asset) => {
+        if (asset.type === 'image') {
+          imageAssets.push(asset.uri);
+        }
+        if (asset.children) {
+          asset.children.forEach(findImageAssets);
+        }
+      };
+
+      setAllImages(imageAssets);
+
+      project.assets.forEach(findImageAssets);
+    }
+  }, [project]);
+
   useEffect(() => {
     setNotes(item.userNotes || []);
   }, [item.userNotes]);
@@ -37,19 +56,37 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
         <span>{item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
-            className={answer === 'yes' ? styles.yesset : styles.yes}
-            onClick={() => setAnswer('yes')}
+            className={answer ? styles.yesset : styles.yes}
+            onClick={() => setAnswer(true)}
           >
             {'Yes'}
           </button>
           <button
-            className={answer === 'no' ? styles.noset : styles.no}
-            onClick={() => setAnswer('no')}
+            className={answer  ? styles.noset : styles.no}
+            onClick={() => setAnswer(false)}
           >
             {'No'}
           </button>
         </div>
       </div>
+      <div className={styles.scanResult}>
+        {item.scanResult &&
+          Object.keys(item.scanResult).map((key) => {
+            return (
+            <div key={key}>
+              <span>{key}</span>
+              <ul>
+                {item.scanResult[key].length ? (
+                  item.scanResult[key].map((answer) => (
+                    <li key={answer}>{answer}</li>
+                  ))
+                ) : (
+                  <li>No answers available</li>
+                )}
+              </ul>
+            </div>
+          )})}
+      </div>
       <div className={styles.details}>
         <NoteEditor
           notes={notes}
@@ -127,7 +164,10 @@ ChecklistItem.propTypes = {
     id: PropTypes.string.isRequired,
     statement: PropTypes.string.isRequired,
     type: PropTypes.string.isRequired,
-    answer: PropTypes.string.isRequired,
+    answer: PropTypes.bool.isRequired,
+    scanResult: PropTypes.objectOf(
+      PropTypes.arrayOf(PropTypes.string)
+    ),
     userNotes: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
@@ -159,11 +199,12 @@ ChecklistItem.propTypes = {
         id: PropTypes.string.isRequired,
         statement: PropTypes.string.isRequired,
         type: PropTypes.string.isRequired,
-        answer: PropTypes.string.isRequired,
-        updated: PropTypes.string.isRequired,
+        answer: PropTypes.bool.isRequired,
+        scanResult: PropTypes.objectOf(
+          PropTypes.arrayOf(PropTypes.string)
+        ),
       })
     ),
-    updated: PropTypes.string.isRequired,
   }).isRequired,
   project: PropTypes.object.isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index a8a0de8..babdb0a 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -2,13 +2,16 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
-// /home/adi/Pictures/Screenshots/maskedvt.png
-const dummyChecklistItems = [
+const path = require('path');
+const AssetsConfig = require('../../constants/assets-config');
+
+const reproducibilityChecklist = [
   {
     id: '1',
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
-    answer: 'yes',
+    bool: true,
+    answerList: {},
     userNotes: [
       {
         id: 'note1',
@@ -23,21 +26,18 @@ const dummyChecklistItems = [
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
       {
-        id: 'image1',
+        id: 'image2',
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
       {
-        id: 'image1',
+        id: 'image3',
         uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
         title: 'Dummy Image',
         description: 'This is a dummy image description',
-        updated: '2024-06-09',
       },
     ],
     attachedURLs: [
@@ -46,31 +46,28 @@ const dummyChecklistItems = [
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
       {
-        id: 'url1',
+        id: 'url2',
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
       {
-        id: 'url1',
+        id: 'url3',
         hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
         title: 'StatWrap URL',
         description: 'This is URL description',
-        updated: '2024-06-09',
       },
     ],
     subChecklists: [],
-    updated: '2024-06-01',
   },
   {
     id: '2',
     statement: 'Second checklist item statement',
     type: 'Type2',
-    answer: 'no',
+    bool: false,
+    answerList: {},
     userNotes: [
       {
         id: 'note2',
@@ -82,41 +79,51 @@ const dummyChecklistItems = [
     attachedImages: [],
     attachedURLs: [],
     subChecklists: [],
-    updated: '2024-06-02',
   },
+  {
+    id: '3',
+    statement: 'List of all the languages used and the dependencies of the project',
+    type: 'List',
+    bool: true,
+    answerList: {},
+    userNotes: [],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklists:[],
+  }
 ];
 
-function ReproChecklists(props) {
-  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
-  const [checklistItems, setChecklistItems] = useState(dummyChecklistItems);
+const languages = new Set();
+const dependencies = new Set();
 
-  useEffect(() => {
-    if (project && Array.isArray(project.assets)) {
-      const imageAssets = [];
-
-      const findImageAssets = (asset) => {
-        if (asset.type === 'image') {
-          imageAssets.push(asset);
-        }
-        if (asset.children) {
-          asset.children.forEach(findImageAssets);
+function findAssetLanguagesAndDependencies(asset) {
+  if (asset.contentTypes.includes('code') && asset.type === 'file') {
+    const lastSep = asset.uri.lastIndexOf(path.sep);
+    const fileName = asset.uri.substring(lastSep + 1);
+    const ext = fileName.split('.').pop();
+    if(ext){
+      AssetsConfig.contentTypes.forEach((contentType) => {
+        if(contentType.extensions.includes(ext)) {
+          languages.add(contentType.name);
         }
-      };
+      });
+    }
+  }
 
-      project.assets.forEach(findImageAssets);
+  if(asset.children){
+    asset.children.forEach(findAssetLanguagesAndDependencies);
+  }
+
+  reproducibilityChecklist[2].answerList = {languages: Array.from(languages),dependencies: Array.from(dependencies) };
+}
 
-      const updatedItems = dummyChecklistItems.map(item => ({
-        ...item,
-        attachedImages: imageAssets.map(asset => ({
-          id: asset.id,
-          uri: asset.uri,
-          title: asset.title || 'Image',
-          description: asset.description || 'About Image',
-          updated: asset.updated || 'NA',
-        })),
-      }));
+function ReproChecklists(props) {
+  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
 
-      setChecklistItems(updatedItems);
+  useEffect(() => {
+    if (project && project.assets) {
+      findAssetLanguagesAndDependencies(project.assets);
     }
   }, [project]);
 
@@ -145,7 +152,10 @@ ReproChecklists.propTypes = {
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
       type: PropTypes.string.isRequired,
-      answer: PropTypes.string.isRequired,
+      bool: PropTypes.bool.isRequired,
+      answerList: PropTypes.objectOf(
+        PropTypes.arrayOf(PropTypes.string)
+      ),
       userNotes: PropTypes.arrayOf(
         PropTypes.shape({
           id: PropTypes.string.isRequired,
@@ -177,11 +187,12 @@ ReproChecklists.propTypes = {
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
           type: PropTypes.string.isRequired,
-          answer: PropTypes.string.isRequired,
-          updated: PropTypes.string.isRequired,
+          bool: PropTypes.bool.isRequired,
+          answerList: PropTypes.objectOf(
+            PropTypes.arrayOf(PropTypes.string)
+          ),
         })
       ),
-      updated: PropTypes.string.isRequired,
     })
   ).isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
@@ -190,7 +201,7 @@ ReproChecklists.propTypes = {
 };
 
 ReproChecklists.defaultProps = {
-  reproChecklist: dummyChecklistItems,
+  reproChecklist: reproducibilityChecklist,
 };
 
 export default ReproChecklists;
diff --git a/app/utils/asset.js b/app/utils/asset.js
index afa3256..7a8bd49 100644
--- a/app/utils/asset.js
+++ b/app/utils/asset.js
@@ -1,5 +1,5 @@
 /* eslint-disable no-underscore-dangle */
-import path from 'path';
+const path = require('path');
 import last from 'lodash/last';
 import constants from '../constants/constants';
 

From 78d3aef6fcb8c387c56caa5aaeeb03c515d48f2e Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 30 Aug 2024 20:05:00 +0530
Subject: [PATCH 13/43] smol fix

---
 .../ReproChecklists/ReproChecklists.js        | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index babdb0a..ff62dba 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -10,8 +10,8 @@ const reproducibilityChecklist = [
     id: '1',
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     type: 'Type1',
-    bool: true,
-    answerList: {},
+    answer: true,
+    scanResult: {},
     userNotes: [
       {
         id: 'note1',
@@ -66,8 +66,8 @@ const reproducibilityChecklist = [
     id: '2',
     statement: 'Second checklist item statement',
     type: 'Type2',
-    bool: false,
-    answerList: {},
+    answer: false,
+    scanResult: {},
     userNotes: [
       {
         id: 'note2',
@@ -84,8 +84,8 @@ const reproducibilityChecklist = [
     id: '3',
     statement: 'List of all the languages used and the dependencies of the project',
     type: 'List',
-    bool: true,
-    answerList: {},
+    answer: true,
+    scanResult: {},
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
@@ -152,8 +152,8 @@ ReproChecklists.propTypes = {
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
       type: PropTypes.string.isRequired,
-      bool: PropTypes.bool.isRequired,
-      answerList: PropTypes.objectOf(
+      answer: PropTypes.bool.isRequired,
+      scanResult: PropTypes.objectOf(
         PropTypes.arrayOf(PropTypes.string)
       ),
       userNotes: PropTypes.arrayOf(
@@ -187,8 +187,8 @@ ReproChecklists.propTypes = {
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
           type: PropTypes.string.isRequired,
-          bool: PropTypes.bool.isRequired,
-          answerList: PropTypes.objectOf(
+          answer: PropTypes.bool.isRequired,
+          scanResult: PropTypes.objectOf(
             PropTypes.arrayOf(PropTypes.string)
           ),
         })

From aecf359f7b0a2372c08af43eb8841d65d260431a Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sun, 22 Sep 2024 23:07:45 +0530
Subject: [PATCH 14/43] implements feature to add images and urls

---
 app/components/Project/Project.js             |   4 +-
 .../ReproChecklists/ChecklistItem.css         | 126 ++++++++-
 .../ReproChecklists/ChecklistItem.js          | 258 +++++++++++++-----
 .../ReproChecklists/Modal/Modal.css           |  52 ++++
 app/components/ReproChecklists/Modal/Modal.js |  45 +++
 .../ReproChecklists/ReproChecklists.js        | 106 ++++---
 app/constants/assets-config.js                |   7 +-
 app/constants/constants.js                    |   1 +
 8 files changed, 465 insertions(+), 134 deletions(-)
 create mode 100644 app/components/ReproChecklists/Modal/Modal.css
 create mode 100644 app/components/ReproChecklists/Modal/Modal.js

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 7a11409..6968312 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -682,7 +682,7 @@ class Project extends Component<Props> {
           />
         ) : null;
 
-      const Checklists = <ReproChecklists
+      const checklists = <ReproChecklists
         project={this.props.project}
         onAddedNote={this.projectUpsertNoteHandler}
         onUpdatedNote={this.projectUpsertNoteHandler}
@@ -739,7 +739,7 @@ class Project extends Component<Props> {
             {projectLog}
           </TabPanel>
           <TabPanel value="Checklists" classes={tabPanelStyle}>
-            {Checklists}
+            {checklists}
           </TabPanel>
         </TabContext>
       );
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index a1ce89b..0daa9f9 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -9,14 +9,33 @@
 
 .header {
   display:flex;
-  align-items: center;
+  justify-content: center;
 }
 
+.statement {
+  font-size: 18px;
+  font-weight: bold;
+  margin-right: 5px;
+  margin-bottom: 10px;
+}
 .buttonContainer {
+  display: flex;
   margin-left: auto;
   margin-right: 0;
 }
 
+.scanResult {
+  font-size: medium;
+  font-family:'Courier New', Courier, monospace;
+}
+
+.scanKey {
+}
+
+.scanList {
+  margin-top: 4px;
+}
+
 .details {
   padding-left: 20px;
   margin-top: 10px;
@@ -91,6 +110,80 @@
   max-height: 500px;
 }
 
+.subChecksContent {
+  overflow: hidden;
+  max-height: 0;
+  transition: max-height 0.3s ease;
+}
+
+.subChecksContent.show {
+  max-height: 1000px;
+}
+
+.image {
+  text-wrap: wrap;
+}
+.url {
+  background-color:#f2ebff;
+  border:1px solid rebeccapurple;
+  padding: 7px;
+  padding-right: 0px;
+  border-radius: 5px;
+  text-wrap: wrap;
+  word-wrap: break-word;
+}
+
+.selectedImage {
+  display: block;
+  width: 100%;
+  max-width: 300px;
+  margin-bottom: 10px;
+}
+
+.hyperlink {
+  display: flex;
+  justify-content: space-evenly;
+  margin-bottom: 10px;
+}
+
+.urlHeader {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+}
+
+.btn {
+  background: none;
+  padding-right: 0px;
+  margin-right: 0px;
+}
+
+.doneButton {
+  background-color: transparent;
+  color: #2bc621;
+  border-radius: 5px;
+  cursor: pointer;
+  margin-right: 0px;
+  transition: background-color 0.3s ease;
+}
+
+.doneButton:hover {
+  background-color: #dfd2f7;
+}
+
+.copyButton {
+  background-color: transparent;
+  color: rebeccapurple;
+  border-radius: 5px;
+  cursor: pointer;
+  margin-right: 0px;
+  transition: background-color 0.3s ease;
+}
+
+.copyButton:hover {
+  background-color: #dfd2f7;
+}
+
 .urls a {
   text-decoration: none;
   color: #007bff;
@@ -141,6 +234,33 @@
   opacity: 0.9;
 }
 
+.addImagesButton, .addUrlsButton {
+  background-color: #aa94d1;
+  color: #fff;
+  cursor: pointer;
+  padding: 5px 10px;
+  margin-top: 5px;
+  border-radius: 4px;
+  font-size: 16px;
+  transition: background-color 0.3s ease;
+}
+
+.addImagesButton:hover, .addUrlsButton:hover {
+  background-color: #8b6fb3;
+}
+
+.addIcon {
+  height: 28px;
+  width: 28px;
+  color: rebeccapurple;
+  cursor: pointer;
+  transition: color 0.5s ease;
+}
+
+.addIcon:hover {
+  opacity: 0.8;
+}
+
 .headerWithButton {
   display: flex;
   align-items: center;
@@ -177,7 +297,7 @@
   max-height: 500px;
 }
 
-.imageTitle,
-.urlTitle {
+.urlText, .imageText {
   font-size: 16px;
+  font-weight: 600;
 }
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 1df4748..71318de 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -2,13 +2,46 @@ import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../NoteEditor/NoteEditor';
+import { AddBox, ContentCopy , Done} from '@mui/icons-material';
+import Modal from './Modal/Modal';
 
-function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNote }) {
-  const [answer, setAnswer] = useState(item.answer);
-  const [notes, setNotes] = useState(item.userNotes || []);
+function ChecklistItem(props) {
+  const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate } = props;
+  const [checklistItem, setChecklistItem] = useState(item);
+  const [addImages, setAddImages] = useState(false);
+  const [addURL, setAddURL] = useState(false);
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
-  const [allImages, setAllImages] = useState([]);
+  const [showSubChecks, setShowSubChecks] = useState(false);
+  const [imageModal, setImageModal] = useState({isOpen: false, image: ''});
+  const [copiedUrlId, setCopiedUrlId] = useState(null);
+
+  const handleSubmitImage = (e) => {
+    e.preventDefault();
+    const img ={id: checklistItem.attachedImages.length + 1, uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
+    const updatedItem = { ...item, attachedImages: [...checklistItem.attachedImages, img] };
+    onItemUpdate(updatedItem);
+    setChecklistItem(updatedItem);
+    setImageModal({isOpen: false, image: ''});
+  }
+
+  const handleSubmitUrl = (e) => {
+    e.preventDefault();
+    const url = {id: checklistItem.attachedURLs.length + 1, hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
+    const updatedItem = { ...item, attachedURLs: [...checklistItem.attachedURLs, url] };
+    onItemUpdate(updatedItem);
+    setChecklistItem(updatedItem);
+    setAddURL(false);
+  }
+
+  const handleCopy = (urlId, hyperlink) => {
+    navigator.clipboard.writeText(hyperlink).then(() => {
+      setCopiedUrlId(urlId);
+      setTimeout(() => {
+        setCopiedUrlId(null);
+      }, 3000);
+    });
+  };
 
   const handleNoteUpdate = (note, text) => {
     if (note) {
@@ -28,56 +61,53 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
     }
   };
 
-  useEffect(() => {
-    if (project && Array.isArray(project.assets)) {
-      const imageAssets = [];
-      const findImageAssets = (asset) => {
-        if (asset.type === 'image') {
-          imageAssets.push(asset.uri);
-        }
-        if (asset.children) {
-          asset.children.forEach(findImageAssets);
-        }
-      };
+  let imageComponent = null;
+  let urlComponent = null;
 
-      setAllImages(imageAssets);
-
-      project.assets.forEach(findImageAssets);
-    }
-  }, [project]);
-
-  useEffect(() => {
-    setNotes(item.userNotes || []);
-  }, [item.userNotes]);
+  imageComponent = <img src={imageModal.image} alt="selected" className={styles.selectedImage}/>;
+  urlComponent = (
+    <div className={styles.hyperlink}>
+      <label htmlFor="hyperlink">URL:</label>
+      <input type="text" id="hyperlink" name="hyperlink"/>
+    </div>
+  )
 
   return (
     <div className={styles.item}>
       <div className={styles.header}>
-        <span>{item.statement}</span>
+        <span className={styles.statement}>{checklistItem.statement}</span>
         <div className={styles.buttonContainer}>
           <button
-            className={answer ? styles.yesset : styles.yes}
-            onClick={() => setAnswer(true)}
+            className={checklistItem.answer ? styles.yesset : styles.yes}
+            onClick={() => {
+              const updatedItem = { ...item, answer: true };
+              setChecklistItem(updatedItem);
+              onItemUpdate(updatedItem);
+            }}
           >
             {'Yes'}
           </button>
           <button
-            className={answer  ? styles.noset : styles.no}
-            onClick={() => setAnswer(false)}
+            className={checklistItem.answer  ? styles.no : styles.noset}
+            onClick={() => {
+              const updatedItem = { ...item, answer: false };
+              setChecklistItem(updatedItem);
+              onItemUpdate(updatedItem);
+            }}
           >
             {'No'}
           </button>
         </div>
       </div>
       <div className={styles.scanResult}>
-        {item.scanResult &&
-          Object.keys(item.scanResult).map((key) => {
+        {checklistItem.scanResult &&
+          Object.keys(checklistItem.scanResult).map((key) => {
             return (
             <div key={key}>
-              <span>{key}</span>
-              <ul>
-                {item.scanResult[key].length ? (
-                  item.scanResult[key].map((answer) => (
+              <span className={styles.scanKey}>{key}</span>
+              <ul className={styles.scanList}>
+                {checklistItem.scanResult[key].length ? (
+                  checklistItem.scanResult[key].map((answer) => (
                     <li key={answer}>{answer}</li>
                   ))
                 ) : (
@@ -89,11 +119,11 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
       </div>
       <div className={styles.details}>
         <NoteEditor
-          notes={notes}
+          notes={checklistItem.userNotes}
           onEditingComplete={handleNoteUpdate}
           onDelete={handleNoteDelete}
         />
-        {item.attachedImages.length > 0 && (
+        {checklistItem.attachedImages.length > 0 && (
           <div className={styles.images}>
             <div className={styles.headerWithButton}>
               <h4>Attached Images:</h4>
@@ -103,19 +133,42 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
             </div>
             <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
               <ul>
-                {item.attachedImages.map((image) => (
-                  <li key={image.id}>
-                    <span className={styles.imageTitle}>{image.title}</span>
-                    <img src={image.uri} alt="attached" />
+                {checklistItem.attachedImages.map((image) => (
+                  <li key={image} className={styles.image}>
+                    <span className={styles.imageText}>{image.title}</span>
+                    <img src={image.uri} alt="attached"/>
                     <p>{image.description}</p>
-                    <span className={styles.timestamp}>{image.updated}</span>
                   </li>
                 ))}
               </ul>
             </div>
           </div>
         )}
-        {item.attachedURLs.length > 0 && (
+        {imageAssets.length > 0 && (
+          <div className={styles.images}>
+            <button className={styles.addImagesButton} onClick={() => setAddImages(!addImages)}>
+              Add Images
+            </button>
+            <div className={`${styles.imageContent} ${addImages ? styles.show : ''}`}>
+              <ul>
+                {imageAssets.map((image) => (
+                  <li key={image} className={styles.header}>
+                    <AddBox className={styles.addIcon}  onClick={()=>setImageModal({isOpen: true, image: image})}/>
+                    <img src={image} alt="project image" />
+                  </li>
+                ))}
+              </ul>
+            </div>
+          </div>
+        )}
+        <Modal
+          isOpen={imageModal.isOpen}
+          onClose={()=>setImageModal({isOpen: false, image: ''})}
+          onSubmit={handleSubmitImage}
+          title="Image"
+          component={imageComponent}
+        />
+        {checklistItem.attachedURLs.length > 0 && (
           <div className={styles.urls}>
             <div className={styles.headerWithButton}>
               <h4>Attached URLs:</h4>
@@ -125,33 +178,102 @@ function ChecklistItem({ item, project, onUpdatedNote, onDeletedNote, onAddedNot
             </div>
             <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
               <ul>
-                {item.attachedURLs.map((url) => (
-                  <li key={url.id}>
-                    <span className={styles.urlTitle}>{url.title}</span>
-                    <a href={url.hyperlink} target="">
-                      {url.hyperlink}
-                    </a>
-                    <p>{url.description}</p>
-                    <span className={styles.timestamp}>{url.updated}</span>
-                  </li>
+                {checklistItem.attachedURLs.map((url) => (
+                  <div>
+                    <div>
+                      <li key={url.id} className={styles.url}>
+                        <div className={styles.urlHeader}>
+                          <span className={styles.urlText}>{url.title}</span>
+                          {copiedUrlId === url.id ? (
+                            <button className={styles.btn} title="Copied!">
+                              <Done className={styles.doneButton} />
+                            </button>
+                          ) : (
+                            <button className={styles.btn} title="Copy URL">
+                              <ContentCopy
+                                className={styles.copyButton}
+                                onClick={() => handleCopy(url.id, url.hyperlink)}
+                              />
+                            </button>
+                          )}
+                        </div>
+                        <a href={url.hyperlink} target="">
+                          {url.hyperlink}
+                        </a>
+                        <p>{url.description}</p>
+                      </li>
+                    </div>
+                    <hr/>
+                  </div>
                 ))}
               </ul>
             </div>
           </div>
         )}
-        {item.subChecklists.length > 0 && (
+        <div>
+          <button className={styles.addUrlsButton} onClick={() => setAddURL(true)}>
+            Add URLs
+          </button>
+        </div>
+        <Modal
+          isOpen={addURL}
+          onClose={()=>setAddURL(false)}
+          onSubmit={handleSubmitUrl}
+          title="URL"
+          component={urlComponent}
+        />
+        {checklistItem.subChecklists.length > 0 && (
           <div className={styles.subChecklists}>
-            <h4>Sub-Checklists:</h4>
-            {item.subChecklists.map((subItem) => (
-              <ChecklistItem
-                key={subItem.id}
-                item={subItem}
-                project={project}
-                onUpdatedNote={onUpdatedNote}
-                onDeletedNote={onDeletedNote}
-                onAddedNote={onAddedNote}
-              />
-            ))}
+            <div className={styles.headerWithButton}>
+              <h4>Sub-Checklists:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowSubChecks(!showSubChecks)}>
+                {showSubChecks ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.subChecksContent} ${showSubChecks ? styles.show : ''}`}>
+              <ul>
+                {checklistItem.subChecklists.map((subCheck) => (
+                  <li key={subCheck.id}>
+                  <div className={styles.header}>
+                    <span>{subCheck.statement}</span>
+                    <div className={styles.buttonContainer}>
+                      <button
+                        className={subCheck.answer ? styles.yesset : styles.yes}
+                        onClick={() => {
+                          // update the subchecklist item corresponding to the subchecklist id
+                          const updatedItem = { ...item, subChecklists: checklistItem.subChecklists.map((sub) => {
+                            if (sub.id === subCheck.id) {
+                              return { ...sub, answer: true };
+                            }
+                            return sub;
+                          })};
+                          onItemUpdate(updatedItem);
+                          setChecklistItem(updatedItem);
+                        }}
+                      >
+                        {'Yes'}
+                      </button>
+                      <button
+                        className={subCheck.answer ? styles.no : styles.noset}
+                        onClick={() => {
+                          const updatedItem = { ...item, subChecklists: checklistItem.subChecklists.map((sub) => {
+                            if (sub.id === subCheck.id) {
+                              return { ...sub, answer: false };
+                            }
+                            return sub;
+                          })};
+                          onItemUpdate(updatedItem);
+                          setChecklistItem(updatedItem);
+                        }}
+                      >
+                        {'No'}
+                      </button>
+                    </div>
+                  </div>
+                  </li>
+                ))}
+              </ul>
+            </div>
           </div>
         )}
       </div>
@@ -163,7 +285,6 @@ ChecklistItem.propTypes = {
   item: PropTypes.shape({
     id: PropTypes.string.isRequired,
     statement: PropTypes.string.isRequired,
-    type: PropTypes.string.isRequired,
     answer: PropTypes.bool.isRequired,
     scanResult: PropTypes.objectOf(
       PropTypes.arrayOf(PropTypes.string)
@@ -182,7 +303,6 @@ ChecklistItem.propTypes = {
         uri: PropTypes.string.isRequired,
         title: PropTypes.string.isRequired,
         description: PropTypes.string.isRequired,
-        updated: PropTypes.string.isRequired,
       })
     ),
     attachedURLs: PropTypes.arrayOf(
@@ -191,22 +311,18 @@ ChecklistItem.propTypes = {
         hyperlink: PropTypes.string.isRequired,
         title: PropTypes.string.isRequired,
         description: PropTypes.string.isRequired,
-        updated: PropTypes.string.isRequired,
       })
     ),
     subChecklists: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         statement: PropTypes.string.isRequired,
-        type: PropTypes.string.isRequired,
         answer: PropTypes.bool.isRequired,
-        scanResult: PropTypes.objectOf(
-          PropTypes.arrayOf(PropTypes.string)
-        ),
       })
     ),
   }).isRequired,
   project: PropTypes.object.isRequired,
+  imageAssets: PropTypes.arrayOf(PropTypes.string),
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
diff --git a/app/components/ReproChecklists/Modal/Modal.css b/app/components/ReproChecklists/Modal/Modal.css
new file mode 100644
index 0000000..9af4cfd
--- /dev/null
+++ b/app/components/ReproChecklists/Modal/Modal.css
@@ -0,0 +1,52 @@
+.modal {
+  display: flex;
+  justify-content: center;
+  align-items: center;
+}
+
+.form {
+  background-color: #fff;
+  padding: 20px;
+  padding-top: 0px;
+  border-radius: 8px;
+  max-width: 300px;
+  width: 100%;
+  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+}
+
+.header {
+  display:flex;
+  justify-content: center;
+}
+
+.title {
+  display: flex;
+  justify-content: space-evenly;
+}
+.description {
+  display: flex;
+  justify-content: space-evenly;
+  height: 50px;
+  margin-top: 10px;
+}
+
+.submit {
+  display: flex;
+  justify-content: end;
+  margin-top: 5px;
+}
+
+.submitButton {
+  background-color: #ccc;
+  color: #000;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 15px;
+  transition: background-color 0.3s ease;
+}
+
+.submitButton:hover {
+  background-color: #e5e5e5;
+}
diff --git a/app/components/ReproChecklists/Modal/Modal.js b/app/components/ReproChecklists/Modal/Modal.js
new file mode 100644
index 0000000..d6ee30a
--- /dev/null
+++ b/app/components/ReproChecklists/Modal/Modal.js
@@ -0,0 +1,45 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import styles from './Modal.css';
+import { Modal } from '@mui/material';
+
+function AttachModal(props) {
+  const { isOpen, onClose, onSubmit, title, component } = props;
+  return (
+    <Modal
+          open={isOpen}
+          onClose={onClose}
+          aria-labelledby="modal-title"
+          aria-describedby="modal-description"
+          className={styles.modal}
+    >
+      <form onSubmit={onSubmit} className={styles.form}>
+          <div className={styles.header}>
+            <h3>Attach {title}</h3>
+          </div>
+          {component}
+          <div className={styles.title}>
+            <label htmlFor="title">Title:</label>
+            <input type="text" id="title" name="title"/>
+          </div>
+          <div className={styles.description}>
+            <label htmlFor="description">Description:</label>
+            <textarea id="description" name="description" />
+          </div>
+          <div className={styles.submit}>
+            <button type="submit" className={styles.submitButton}>Submit</button>
+          </div>
+        </form>
+    </Modal>
+  );
+}
+
+AttachModal.propTypes = {
+  isOpen: PropTypes.bool.isRequired,
+  onClose: PropTypes.func.isRequired,
+  onSubmit: PropTypes.func.isRequired,
+  title: PropTypes.string.isRequired,
+  component: PropTypes.element.isRequired,
+};
+
+export default AttachModal;
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index ff62dba..4305f4a 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -2,6 +2,7 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
+
 const path = require('path');
 const AssetsConfig = require('../../constants/assets-config');
 
@@ -9,7 +10,6 @@ const reproducibilityChecklist = [
   {
     id: '1',
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
-    type: 'Type1',
     answer: true,
     scanResult: {},
     userNotes: [
@@ -20,52 +20,13 @@ const reproducibilityChecklist = [
         content: 'First note content',
       },
     ],
-    attachedImages: [
-      {
-        id: 'image1',
-        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
-        title: 'Dummy Image',
-        description: 'This is a dummy image description',
-      },
-      {
-        id: 'image2',
-        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
-        title: 'Dummy Image',
-        description: 'This is a dummy image description',
-      },
-      {
-        id: 'image3',
-        uri: '/home/adi/Pictures/Screenshots/maskedvt.png',
-        title: 'Dummy Image',
-        description: 'This is a dummy image description',
-      },
-    ],
-    attachedURLs: [
-      {
-        id: 'url1',
-        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
-        title: 'StatWrap URL',
-        description: 'This is URL description',
-      },
-      {
-        id: 'url2',
-        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
-        title: 'StatWrap URL',
-        description: 'This is URL description',
-      },
-      {
-        id: 'url3',
-        hyperlink: 'https://github.com/StatTag/StatWrap/blob/master/app/services/user.js',
-        title: 'StatWrap URL',
-        description: 'This is URL description',
-      },
-    ],
+    attachedImages: [],
+    attachedURLs: [],
     subChecklists: [],
   },
   {
     id: '2',
-    statement: 'Second checklist item statement',
-    type: 'Type2',
+    statement: 'Second checklist item statement.',
     answer: false,
     scanResult: {},
     userNotes: [
@@ -82,29 +43,40 @@ const reproducibilityChecklist = [
   },
   {
     id: '3',
-    statement: 'List of all the languages used and the dependencies of the project',
-    type: 'List',
+    statement: 'List of all the languages used and the dependencies of the project.',
     answer: true,
     scanResult: {},
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
-    subChecklists:[],
+    subChecklists:[
+      {
+        id: '3.1',
+        statement: 'Are all the languages used in the project listed?',
+        answer: true,
+      },
+      {
+        id: '3.2',
+        statement: 'Are all the dependencies of the project listed?',
+        answer: false,
+      },
+    ],
   }
 ];
 
-const languages = new Set();
-const dependencies = new Set();
+const languages = {};
+const dependencies = {};
+const imageAssets = {};
 
 function findAssetLanguagesAndDependencies(asset) {
-  if (asset.contentTypes.includes('code') && asset.type === 'file') {
+  if (asset.type === 'file' && asset.contentTypes.includes('code') ) {
     const lastSep = asset.uri.lastIndexOf(path.sep);
     const fileName = asset.uri.substring(lastSep + 1);
     const ext = fileName.split('.').pop();
     if(ext){
       AssetsConfig.contentTypes.forEach((contentType) => {
         if(contentType.extensions.includes(ext)) {
-          languages.add(contentType.name);
+          languages[contentType.name] = true;
         }
       });
     }
@@ -114,31 +86,55 @@ function findAssetLanguagesAndDependencies(asset) {
     asset.children.forEach(findAssetLanguagesAndDependencies);
   }
 
-  reproducibilityChecklist[2].answerList = {languages: Array.from(languages),dependencies: Array.from(dependencies) };
+  reproducibilityChecklist[2].scanResult = {
+    languages: Object.keys(languages),
+    dependencies: Object.keys(dependencies)
+  };
 }
 
+function findImageAssets(asset) {
+  if (asset.type === 'file' && asset.contentTypes.includes('image')) {
+    imageAssets[asset.uri] = true;
+  }
+  if (asset.children) {
+    asset.children.forEach(findImageAssets);
+  }
+};
+
 function ReproChecklists(props) {
   const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
   const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
+  const [allImages, setAllImages] = useState([]);
 
   useEffect(() => {
     if (project && project.assets) {
       findAssetLanguagesAndDependencies(project.assets);
+      findImageAssets(project.assets);
+      setAllImages(Object.keys(imageAssets));
     }
   }, [project]);
 
+  const handleItemUpdate = (updatedItem) => {
+    const updatedChecklistItems = checklistItems.map(item =>
+      item.id === updatedItem.id ? updatedItem : item
+    );
+    setChecklistItems(updatedChecklistItems);
+  };
+
   return (
     <div>
-      <Typography variant='h5' align='center'>Reproducibility Checklists</Typography>
+      <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklists</Typography>
       <br />
       {checklistItems.map(item => (
         <ChecklistItem
           key={item.id}
           item={item}
           project={project}
+          imageAssets={allImages}
           onUpdatedNote={onUpdatedNote}
           onDeletedNote={onDeletedNote}
           onAddedNote={onAddedNote}
+          onItemUpdate={handleItemUpdate}
         />
       ))}
     </div>
@@ -151,7 +147,6 @@ ReproChecklists.propTypes = {
     PropTypes.shape({
       id: PropTypes.string.isRequired,
       statement: PropTypes.string.isRequired,
-      type: PropTypes.string.isRequired,
       answer: PropTypes.bool.isRequired,
       scanResult: PropTypes.objectOf(
         PropTypes.arrayOf(PropTypes.string)
@@ -186,15 +181,12 @@ ReproChecklists.propTypes = {
         PropTypes.shape({
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
-          type: PropTypes.string.isRequired,
           answer: PropTypes.bool.isRequired,
-          scanResult: PropTypes.objectOf(
-            PropTypes.arrayOf(PropTypes.string)
-          ),
         })
       ),
     })
   ).isRequired,
+  imageAssets: PropTypes.arrayOf(PropTypes.string),
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
diff --git a/app/constants/assets-config.js b/app/constants/assets-config.js
index f5bdb7f..fd1d9a2 100644
--- a/app/constants/assets-config.js
+++ b/app/constants/assets-config.js
@@ -25,7 +25,7 @@ module.exports = {
       details: 'Does this asset contain sensitive information (PHI, PII, passwords, secrets)',
       type: 'bool',
       default: false,
-      appliesTo: ['code', 'data', 'documentation'],
+      appliesTo: ['code', 'data', 'documentation', 'image'],
     },
   ],
   contentTypes: [
@@ -104,6 +104,11 @@ module.exports = {
       extensions: ['txt'],
       categories: ['documentation'],
     },
+    {
+      name: 'Image',
+      extensions: ['jpg', 'jpeg', 'png', 'gif', 'svg', 'webp'],
+      categories: ['image'],
+    },
     // In the patterns, don't use /g. TIL (after hours of debugging), global state preserves
     // where it's checking between calls, so you can call .test() multiple times on the same
     // string and you will get different results (https://stackoverflow.com/a/2630538/5670646).
diff --git a/app/constants/constants.js b/app/constants/constants.js
index b5b68aa..63620f1 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -29,6 +29,7 @@ module.exports = {
     CODE: 'code',
     DATA: 'data',
     DOCUMENTATION: 'documentation',
+    IMAGE: 'image',
     OTHER: 'other',
   },
 

From 3f6e46503b5db43b00add22bc527a070dc37b2c1 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sun, 22 Sep 2024 23:58:36 +0530
Subject: [PATCH 15/43] feature to delete images and urls

---
 .../ReproChecklists/ChecklistItem.css         | 24 +++++----
 .../ReproChecklists/ChecklistItem.js          | 52 +++++++++++++------
 2 files changed, 51 insertions(+), 25 deletions(-)

diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index 0daa9f9..e509671 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -146,24 +146,17 @@
   margin-bottom: 10px;
 }
 
-.urlHeader {
+.urlHeader, .imageHeader {
   display: flex;
   justify-content: space-between;
   align-items: center;
 }
 
-.btn {
-  background: none;
-  padding-right: 0px;
-  margin-right: 0px;
-}
-
 .doneButton {
   background-color: transparent;
   color: #2bc621;
   border-radius: 5px;
   cursor: pointer;
-  margin-right: 0px;
   transition: background-color 0.3s ease;
 }
 
@@ -176,7 +169,6 @@
   color: rebeccapurple;
   border-radius: 5px;
   cursor: pointer;
-  margin-right: 0px;
   transition: background-color 0.3s ease;
 }
 
@@ -184,6 +176,20 @@
   background-color: #dfd2f7;
 }
 
+.delButton {
+  background-color: transparent;
+  color: rebeccapurple;
+  border-radius: 5px;
+  cursor: pointer;
+  margin-left: 5px;
+  margin-right: 5px;
+  transition: background-color 0.3s ease;
+}
+
+.delButton:hover {
+  background-color: #dfd2f7;
+}
+
 .urls a {
   text-decoration: none;
   color: #007bff;
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 71318de..29328cc 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -2,7 +2,7 @@ import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../NoteEditor/NoteEditor';
-import { AddBox, ContentCopy , Done} from '@mui/icons-material';
+import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
 import Modal from './Modal/Modal';
 
 function ChecklistItem(props) {
@@ -18,7 +18,7 @@ function ChecklistItem(props) {
 
   const handleSubmitImage = (e) => {
     e.preventDefault();
-    const img ={id: checklistItem.attachedImages.length + 1, uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
+    const img = {id: Math.random().toString(36).substr(2, 9), uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
     const updatedItem = { ...item, attachedImages: [...checklistItem.attachedImages, img] };
     onItemUpdate(updatedItem);
     setChecklistItem(updatedItem);
@@ -27,7 +27,7 @@ function ChecklistItem(props) {
 
   const handleSubmitUrl = (e) => {
     e.preventDefault();
-    const url = {id: checklistItem.attachedURLs.length + 1, hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
+    const url = {id: Math.random().toString(36).substr(2, 9), hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
     const updatedItem = { ...item, attachedURLs: [...checklistItem.attachedURLs, url] };
     onItemUpdate(updatedItem);
     setChecklistItem(updatedItem);
@@ -43,6 +43,18 @@ function ChecklistItem(props) {
     });
   };
 
+  const handleDeleteUrl = (urlId) => {
+    const updatedItem = { ...item, attachedURLs: checklistItem.attachedURLs.filter((url) => url.id !== urlId) };
+    onItemUpdate(updatedItem);
+    setChecklistItem(updatedItem);
+  };
+
+  const handleDeleteImage = (imageId) => {
+    const updatedItem = { ...item, attachedImages: checklistItem.attachedImages.filter((image) => image.id !== imageId) };
+    onItemUpdate(updatedItem);
+    setChecklistItem(updatedItem);
+  };
+
   const handleNoteUpdate = (note, text) => {
     if (note) {
       if (onUpdatedNote) {
@@ -135,7 +147,13 @@ function ChecklistItem(props) {
               <ul>
                 {checklistItem.attachedImages.map((image) => (
                   <li key={image} className={styles.image}>
-                    <span className={styles.imageText}>{image.title}</span>
+                    <div className={styles.imageHeader}>
+                      <span className={styles.imageText}>{image.title}</span>
+                      <Delete
+                        className={styles.delButton}
+                        onClick={() => handleDeleteImage(image.id)}
+                      />
+                    </div>
                     <img src={image.uri} alt="attached"/>
                     <p>{image.description}</p>
                   </li>
@@ -184,18 +202,20 @@ function ChecklistItem(props) {
                       <li key={url.id} className={styles.url}>
                         <div className={styles.urlHeader}>
                           <span className={styles.urlText}>{url.title}</span>
-                          {copiedUrlId === url.id ? (
-                            <button className={styles.btn} title="Copied!">
-                              <Done className={styles.doneButton} />
-                            </button>
-                          ) : (
-                            <button className={styles.btn} title="Copy URL">
-                              <ContentCopy
-                                className={styles.copyButton}
-                                onClick={() => handleCopy(url.id, url.hyperlink)}
-                              />
-                            </button>
-                          )}
+                          <div>
+                            {copiedUrlId === url.id ? (
+                                <Done className={styles.doneButton} />
+                            ) : (
+                                <ContentCopy
+                                  className={styles.copyButton}
+                                  onClick={() => handleCopy(url.id, url.hyperlink)}
+                                />
+                            )}
+                            <Delete
+                              className={styles.delButton}
+                              onClick={() => handleDeleteUrl(url.id)}
+                            />
+                          </div>
                         </div>
                         <a href={url.hyperlink} target="">
                           {url.hyperlink}

From c63b971b9f44bef8369262e535847e37241b9542 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Mon, 23 Sep 2024 00:00:21 +0530
Subject: [PATCH 16/43] generate reproducility report from checklists data and
 download in pdf format

---
 .../ReproChecklists/ReproChecklists.css       |  29 ++-
 .../ReproChecklists/ReproChecklists.js        | 194 ++++++++++++++++++
 app/images/no.png                             | Bin 0 -> 25878 bytes
 app/images/yes.png                            | Bin 0 -> 22146 bytes
 package.json                                  |   1 +
 yarn.lock                                     | 144 +++++++++++--
 6 files changed, 351 insertions(+), 17 deletions(-)
 create mode 100644 app/images/no.png
 create mode 100644 app/images/yes.png

diff --git a/app/components/ReproChecklists/ReproChecklists.css b/app/components/ReproChecklists/ReproChecklists.css
index aa2d05b..fc3d29f 100644
--- a/app/components/ReproChecklists/ReproChecklists.css
+++ b/app/components/ReproChecklists/ReproChecklists.css
@@ -1,8 +1,27 @@
-.container {
-  padding: 20px;
+.downloadContainer {
+  position: fixed;
+  bottom: 10px;
+  right: 20px;
 }
 
-h2 {
-  margin-bottom: 20px;
-  font-size: 24px;
+.downloadButton {
+  background-color: #639;
+  padding-right: 4px;
+  padding-left: 5px;
+  box-shadow: 0 4px 8px rgba(0,0,0,0.4);
+}
+
+.downloadButton:hover {
+  opacity: 0.9;
+}
+
+.buttonContent {
+  display: flex;
+  color: white;
+  font-size: 16px;
+}
+
+.buttonText {
+  margin-top: 3px;
+  margin-right: 2px;
 }
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index 4305f4a..bfccff9 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -1,9 +1,16 @@
 import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
+import styles from './ReproChecklists.css';
 import ChecklistItem from './ChecklistItem';
 import { Typography } from '@mui/material';
+import { SaveAlt } from '@mui/icons-material';
+import pdfMake from 'pdfmake/build/pdfmake';
+import pdfFonts from 'pdfmake/build/vfs_fonts';
+
+pdfMake.vfs = pdfFonts.pdfMake.vfs;
 
 const path = require('path');
+const fs = require('fs');
 const AssetsConfig = require('../../constants/assets-config');
 
 const reproducibilityChecklist = [
@@ -101,6 +108,40 @@ function findImageAssets(asset) {
   }
 };
 
+
+function convertImageToBase64(filePath) {
+  try {
+    const file = fs.readFileSync(filePath);
+    const ext = path.extname(filePath).toLowerCase();
+    let mimeType;
+    switch (ext) {
+      case '.jpg':
+      case '.jpeg':
+        mimeType = 'image/jpeg';
+        break;
+      case '.png':
+        mimeType = 'image/png';
+        break;
+      case '.gif':
+        mimeType = 'image/gif';
+        break;
+      case '.webp':
+        mimeType = 'image/webp';
+        break;
+      case '.svg':
+        mimeType = 'image/svg+xml';
+        break;
+      default:
+        mimeType = 'application/octet-stream';
+    }
+    return `data:${mimeType};base64,${file.toString('base64')}`;
+  } catch (error) {
+    console.error('Error converting image to Base64:', error);
+    return null;
+  }
+};
+
+
 function ReproChecklists(props) {
   const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
   const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
@@ -121,6 +162,147 @@ function ReproChecklists(props) {
     setChecklistItems(updatedChecklistItems);
   };
 
+  const handleReportGeneration = () => {
+    const checkedIcon = convertImageToBase64(path.join(__dirname, 'images/yes.png'));
+    const uncheckedIcon = convertImageToBase64(path.join(__dirname, 'images/no.png'));
+    const statWrapLogo = convertImageToBase64(path.join(__dirname, 'images/banner.png'));
+
+    const documentDefinition = {
+      content: [
+        {
+          image: statWrapLogo,
+          width: 150,
+          alignment: 'center',
+        },
+        {
+          text: 'Reproducibility Checklists Report',
+          style: 'mainHeader',
+          alignment: 'center',
+          margin: [0, 20],
+        },
+        {
+          text: 'Project Overview',
+          style: 'sectionHeader',
+          margin: [0, 10],
+        },
+        {
+          text: `Project Name: ${project.name}`,
+          margin: [0, 5],
+        },
+        {
+          text: `Date: ${new Date().toLocaleDateString()}`,
+          margin: [0, 5],
+        },
+        {
+          text: `Checklist Summary`,
+          style: 'sectionHeader',
+          margin: [0, 10],
+        },
+        ...checklistItems.map((item, index) => {
+          let subChecklists = [];
+          if (item.subChecklists && item.subChecklists.length > 0) {
+            subChecklists = item.subChecklists.map((subItem, subIndex) => ({
+              columns: [
+                {
+                  text: `${index + 1}.${subIndex + 1} ${subItem.statement}`,
+                  margin: [15, 5],
+                  width: '*',
+                  alignment: 'left',
+                },
+                {
+                  image: subItem.answer ? checkedIcon : uncheckedIcon,
+                  width: 15,
+                  height: 15,
+                  alignment: 'right',
+                  margin: [0, 6, 1, 0],
+                },
+              ],
+              columnGap: 0,
+            }));
+          }
+
+          let images = [];
+          if(item.attachedImages && item.attachedImages.length > 0){
+            images = item.attachedImages.map((image) => {
+              const base64Image = convertImageToBase64(image.uri);
+              if (base64Image) {
+                return [
+                  {
+                    image: base64Image,
+                    width: 150,
+                    margin: [0, 5],
+                    alignment: 'center',
+                  },
+                  {
+                    text: `${image.title}`,
+                    style: 'imageTitle',
+                    margin: [0, 2],
+                    alignment: 'center',
+                  },
+                ];
+              }
+              return { text: `Failed to load image: ${image.uri}`, color: 'red' };
+            });
+          }
+
+          return [
+            {
+              columns: [
+                {
+                  text: `${index + 1}. `,
+                  width: 10,
+                  margin: [0, 10],
+                  alignment: 'left',
+                },
+                {
+                  text: `${item.statement}`,
+                  margin: [0, 10],
+                  width: '*',
+                  alignment: 'left',
+                },
+                {
+                  image: item.answer ? checkedIcon : uncheckedIcon,
+                  width: 20,
+                  height: 20,
+                  alignment: 'right',
+                  margin: [0, 10],
+                },
+              ],
+              columnGap: 5,
+            },
+            ...subChecklists,
+            images.length > 0 ? { text: 'Related Images:', style: 'subheader', margin: [0, 10] } : '',
+            {
+              columns: images,
+              columnGap: 5,
+              width: '*',
+              wrap: true,
+              margin: [0, 5],
+            }
+          ];
+        }).flat(),
+      ],
+      styles: {
+        mainHeader: { fontSize: 22, bold: true, color: '#663399' },
+        sectionHeader: { fontSize: 18, bold: true, color: '#8b6fb3', margin: [0, 20] },
+        header: { fontSize: 16, bold: true },
+      },
+      defaultStyle: {
+        fontSize: 12,
+      },
+      pageMargins: [40, 25, 40, 60],
+      footer: function (currentPage, pageCount) {
+        return {
+          text: `Page ${currentPage} of ${pageCount}`,
+          alignment: 'center',
+          margin: [0, 30],
+        };
+      },
+    };
+
+    pdfMake.createPdf(documentDefinition).download('Reproducibility_Checklist_Report.pdf');
+  };
+
   return (
     <div>
       <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklists</Typography>
@@ -137,6 +319,18 @@ function ReproChecklists(props) {
           onItemUpdate={handleItemUpdate}
         />
       ))}
+      <br />
+      <div className={styles.downloadContainer}>
+        <button
+          onClick={handleReportGeneration}
+          className={styles.downloadButton}
+        >
+          <div className={styles.buttonContent}>
+            <span className={styles.buttonText}>Report</span>
+            <SaveAlt />
+          </div>
+        </button>
+      </div>
     </div>
   );
 }
diff --git a/app/images/no.png b/app/images/no.png
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zu$mZNwC3EMcWGecZP*$*&^yb*A?uSo$ZU#7Z3;Xd*p@t!_(dV<ckNkUi7e0!grahU
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He;WRO%e9S_

literal 0
HcmV?d00001

diff --git a/package.json b/package.json
index 567a431..5b80950 100644
--- a/package.json
+++ b/package.json
@@ -244,6 +244,7 @@
     "jest-extended": "4.0.2",
     "jest-os-detection": "^1.3.1",
     "lodash": "^4.17.21",
+    "pdfmake": "^0.2.12",
     "pluralize": "^8.0.0",
     "postcss": "^8.4.38",
     "postcss-less": "^6.0.0",
diff --git a/yarn.lock b/yarn.lock
index 55c5dac..9746bdf 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1877,6 +1877,43 @@
   resolved "https://registry.yarnpkg.com/@floating-ui/utils/-/utils-0.2.1.tgz#16308cea045f0fc777b6ff20a9f25474dd8293d2"
   integrity sha512-9TANp6GPoMtYzQdt54kfAyMmz1+osLlXdg2ENroU7zzrtflTLrrC/lgrIfaSe+Wu0b89GKccT7vxXA0MoAIO+Q==
 
+"@foliojs-fork/fontkit@^1.9.1":
+  version "1.9.2"
+  resolved "https://registry.yarnpkg.com/@foliojs-fork/fontkit/-/fontkit-1.9.2.tgz#94241c195bc6204157bc84c33f34bdc967eca9c3"
+  integrity sha512-IfB5EiIb+GZk+77TRB86AHroVaqfq8JRFlUbz0WEwsInyCG0epX2tCPOy+UfaWPju30DeVoUAXfzWXmhn753KA==
+  dependencies:
+    "@foliojs-fork/restructure" "^2.0.2"
+    brotli "^1.2.0"
+    clone "^1.0.4"
+    deep-equal "^1.0.0"
+    dfa "^1.2.0"
+    tiny-inflate "^1.0.2"
+    unicode-properties "^1.2.2"
+    unicode-trie "^2.0.0"
+
+"@foliojs-fork/linebreak@^1.1.1":
+  version "1.1.2"
+  resolved "https://registry.yarnpkg.com/@foliojs-fork/linebreak/-/linebreak-1.1.2.tgz#32fee03d5431fa73284373439e172e451ae1e2da"
+  integrity sha512-ZPohpxxbuKNE0l/5iBJnOAfUaMACwvUIKCvqtWGKIMv1lPYoNjYXRfhi9FeeV9McBkBLxsMFWTVVhHJA8cyzvg==
+  dependencies:
+    base64-js "1.3.1"
+    unicode-trie "^2.0.0"
+
+"@foliojs-fork/pdfkit@^0.14.0":
+  version "0.14.0"
+  resolved "https://registry.yarnpkg.com/@foliojs-fork/pdfkit/-/pdfkit-0.14.0.tgz#ed1868050edd2904284655f8dcddd56b49576c98"
+  integrity sha512-nMOiQAv6id89MT3tVTCgc7HxD5ZMANwio2o5yvs5sexQkC0KI3BLaLakpsrHmFfeGFAhqPmZATZGbJGXTUebpg==
+  dependencies:
+    "@foliojs-fork/fontkit" "^1.9.1"
+    "@foliojs-fork/linebreak" "^1.1.1"
+    crypto-js "^4.2.0"
+    png-js "^1.0.0"
+
+"@foliojs-fork/restructure@^2.0.2":
+  version "2.0.2"
+  resolved "https://registry.yarnpkg.com/@foliojs-fork/restructure/-/restructure-2.0.2.tgz#73759aba2aff1da87b7c4554e6839c70d43c92b4"
+  integrity sha512-59SgoZ3EXbkfSX7b63tsou/SDGzwUEK6MuB5sKqgVK1/XE0fxmpsOb9DQI8LXW3KfGnAjImCGhhEb7uPPAUVNA==
+
 "@fortawesome/fontawesome-common-types@6.5.2":
   version "6.5.2"
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-6.5.2.tgz#eaf2f5699f73cef198454ebc0c414e3688898179"
@@ -4252,7 +4289,12 @@ base64-arraybuffer@0.1.5:
   resolved "https://registry.yarnpkg.com/base64-arraybuffer/-/base64-arraybuffer-0.1.5.tgz#73926771923b5a19747ad666aa5cd4bf9c6e9ce8"
   integrity sha512-437oANT9tP582zZMwSvZGy2nmSeAb8DW2me3y+Uv1Wp2Rulr8Mqlyrv3E7MLxmsiaPSMMDmiDVzgE+e8zlMx9g==
 
-base64-js@^1.0.2, base64-js@^1.1.2, base64-js@^1.3.1, base64-js@^1.5.1:
+base64-js@1.3.1:
+  version "1.3.1"
+  resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.3.1.tgz#58ece8cb75dd07e71ed08c736abc5fac4dbf8df1"
+  integrity sha512-mLQ4i2QO1ytvGWFWmcngKO//JXAQueZvwEKtjgQFM4jIK0kU+ytMfplL8j+n5mspOfjHwoAg+9yhb7BwAHm36g==
+
+base64-js@^1.0.2, base64-js@^1.1.2, base64-js@^1.3.0, base64-js@^1.3.1, base64-js@^1.5.1:
   version "1.5.1"
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a"
   integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
@@ -4424,7 +4466,7 @@ brorand@^1.0.1, brorand@^1.1.0:
   resolved "https://registry.yarnpkg.com/brorand/-/brorand-1.1.0.tgz#12c25efe40a45e3c323eb8675a0a0ce57b22371f"
   integrity sha512-cKV8tMCEpQs4hK/ik71d6LrPOnpkpGBR0wzxqr68g2m/LB2GxVYQroAjMJZRVM1Y4BCjCKc3vAamxSzOY2RP+w==
 
-brotli@^1.3.1:
+brotli@^1.2.0, brotli@^1.3.1:
   version "1.3.3"
   resolved "https://registry.yarnpkg.com/brotli/-/brotli-1.3.3.tgz#7365d8cc00f12cf765d2b2c898716bcf4b604d48"
   integrity sha512-oTKjJdShmDuGW94SyyaoQvAjf30dZaHnjJ8uAF+u2/vGJkJbJPJAT1gDiOJP5v1Zb6f9KEyW/1HpuaWIXtGHPg==
@@ -5032,7 +5074,7 @@ clone-response@^1.0.2:
   dependencies:
     mimic-response "^1.0.0"
 
-clone@^1.0.2:
+clone@^1.0.2, clone@^1.0.4:
   version "1.0.4"
   resolved "https://registry.yarnpkg.com/clone/-/clone-1.0.4.tgz#da309cc263df15994c688ca902179ca3c7cd7c7e"
   integrity sha512-JQHZ2QMW6l3aH/j6xCqQThY/9OH4D/9ls34cgkUBiEeocRTU04tHfKPBsUK1PqZCUQM7GiA0IIXJSuXHI64Kbg==
@@ -5550,6 +5592,11 @@ crypto-browserify@^3.11.0:
     randombytes "^2.0.0"
     randomfill "^1.0.3"
 
+crypto-js@^4.2.0:
+  version "4.2.0"
+  resolved "https://registry.yarnpkg.com/crypto-js/-/crypto-js-4.2.0.tgz#4d931639ecdfd12ff80e8186dba6af2c2e856631"
+  integrity sha512-KALDyEYgpY+Rlob/iriUtjV6d5Eq+Y191A5g4UqLAi8CyGP9N1+FdVbkc1SxKc2r4YAYqG8JzO2KGL+AizD70Q==
+
 css-color-keywords@^1.0.0:
   version "1.0.0"
   resolved "https://registry.yarnpkg.com/css-color-keywords/-/css-color-keywords-1.0.0.tgz#fea2616dc676b2962686b3af8dbdbe180b244e05"
@@ -6284,6 +6331,11 @@ devtron@^1.4.0:
     highlight.js "^9.3.0"
     humanize-plus "^1.8.1"
 
+dfa@^1.2.0:
+  version "1.2.0"
+  resolved "https://registry.yarnpkg.com/dfa/-/dfa-1.2.0.tgz#96ac3204e2d29c49ea5b57af8d92c2ae12790657"
+  integrity sha512-ED3jP8saaweFTjeGX8HQPjeC1YYyZs98jGNZx6IiBvxW7JG5v492kamAQB3m2wop07CvU/RQmzcKr6bgcC5D/Q==
+
 diff-sequences@^29.6.3:
   version "29.6.3"
   resolved "https://registry.yarnpkg.com/diff-sequences/-/diff-sequences-29.6.3.tgz#4deaf894d11407c51efc8418012f9e70b84ea921"
@@ -8858,7 +8910,7 @@ iconv-lite@0.4.24:
   dependencies:
     safer-buffer ">= 2.1.2 < 3"
 
-iconv-lite@0.6, iconv-lite@^0.6.2:
+iconv-lite@0.6, iconv-lite@^0.6.2, iconv-lite@^0.6.3:
   version "0.6.3"
   resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.6.3.tgz#a52f80bf38da1952eb5c681790719871a1a72501"
   integrity sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==
@@ -11934,16 +11986,16 @@ p-try@^2.0.0:
   resolved "https://registry.yarnpkg.com/p-try/-/p-try-2.2.0.tgz#cb2868540e313d61de58fafbe35ce9004d5540e6"
   integrity sha512-R4nPAVTAU0B9D35/Gk3uJf/7XYbQcyohSKdvAxIRSNghFl4e71hVoGnBNQz9cWaXxO2I10KTC+3jMdvvoKw6dQ==
 
+pako@^0.2.5, pako@~0.2.5:
+  version "0.2.9"
+  resolved "https://registry.yarnpkg.com/pako/-/pako-0.2.9.tgz#f3f7522f4ef782348da8161bad9ecfd51bf83a75"
+  integrity sha512-NUcwaKxUxWrZLpDG+z/xZaCgQITkA/Dv4V/T6bw7VON6l1Xz/VnrBqrYjZQ12TamKHzITTfOEIYUj48y2KXImA==
+
 pako@^1.0.10, pako@~1.0.2, pako@~1.0.5:
   version "1.0.11"
   resolved "https://registry.yarnpkg.com/pako/-/pako-1.0.11.tgz#6c9599d340d54dfd3946380252a35705a6b992bf"
   integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==
 
-pako@~0.2.5:
-  version "0.2.9"
-  resolved "https://registry.yarnpkg.com/pako/-/pako-0.2.9.tgz#f3f7522f4ef782348da8161bad9ecfd51bf83a75"
-  integrity sha512-NUcwaKxUxWrZLpDG+z/xZaCgQITkA/Dv4V/T6bw7VON6l1Xz/VnrBqrYjZQ12TamKHzITTfOEIYUj48y2KXImA==
-
 parallel-transform@^1.1.0:
   version "1.2.0"
   resolved "https://registry.yarnpkg.com/parallel-transform/-/parallel-transform-1.2.0.tgz#9049ca37d6cb2182c3b1d2c720be94d14a5814fc"
@@ -12163,6 +12215,16 @@ pbkdf2@^3.0.3:
     safe-buffer "^5.0.1"
     sha.js "^2.4.8"
 
+pdfmake@^0.2.12:
+  version "0.2.12"
+  resolved "https://registry.yarnpkg.com/pdfmake/-/pdfmake-0.2.12.tgz#5156f91ff73797947942aa342423bedaa0c0bc93"
+  integrity sha512-TFsqaG6KVtk+TWermmJNNwom3wmB/xiz07prM74KBhdM+7pz3Uwq2b0uoqhhQRn6cYUTpL8lXZY6xF011o1YcQ==
+  dependencies:
+    "@foliojs-fork/linebreak" "^1.1.1"
+    "@foliojs-fork/pdfkit" "^0.14.0"
+    iconv-lite "^0.6.3"
+    xmldoc "^1.1.2"
+
 pend@~1.2.0:
   version "1.2.0"
   resolved "https://registry.yarnpkg.com/pend/-/pend-1.2.0.tgz#7a57eb550a6783f9115331fcf4663d5c8e007a50"
@@ -12270,6 +12332,11 @@ pluralize@^8.0.0:
   resolved "https://registry.yarnpkg.com/pluralize/-/pluralize-8.0.0.tgz#1a6fa16a38d12a1901e0320fa017051c539ce3b1"
   integrity sha512-Nc3IT5yHzflTfbjgqWcCPpo7DaKy4FnpB0l/zCAW0Tc7jxAiuqSxHasntB3D7887LSrA93kDJ9IXovxJYxyLCA==
 
+png-js@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/png-js/-/png-js-1.0.0.tgz#e5484f1e8156996e383aceebb3789fd75df1874d"
+  integrity sha512-k+YsbhpA9e+EFfKjTCH3VW6aoKlyNYI6NYdTfDL4CIvFnvsuO84ttonmZE7rc+v23SLTH8XX+5w/Ak9v0xGY4g==
+
 posix-character-classes@^0.1.0:
   version "0.1.1"
   resolved "https://registry.yarnpkg.com/posix-character-classes/-/posix-character-classes-0.1.1.tgz#01eac0fe3b5af71a2a6c02feabb8c1fef7e00eab"
@@ -14385,7 +14452,16 @@ string-natural-compare@^3.0.1:
   resolved "https://registry.yarnpkg.com/string-natural-compare/-/string-natural-compare-3.0.1.tgz#7a42d58474454963759e8e8b7ae63d71c1e7fdf4"
   integrity sha512-n3sPwynL1nwKi3WJ6AIsClwBMa0zTi54fn2oLU6ndfTSIO05xaznjSf15PcBZU6FNWbmN5Q6cxT4V5hGvB4taw==
 
-"string-width-cjs@npm:string-width@^4.2.0", "string-width@^1.0.2 || 2 || 3 || 4", string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3:
+"string-width-cjs@npm:string-width@^4.2.0":
+  version "4.2.3"
+  resolved "https://registry.yarnpkg.com/string-width/-/string-width-4.2.3.tgz#269c7117d27b05ad2e536830a8ec895ef9c6d010"
+  integrity sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==
+  dependencies:
+    emoji-regex "^8.0.0"
+    is-fullwidth-code-point "^3.0.0"
+    strip-ansi "^6.0.1"
+
+"string-width@^1.0.2 || 2 || 3 || 4", string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3:
   version "4.2.3"
   resolved "https://registry.yarnpkg.com/string-width/-/string-width-4.2.3.tgz#269c7117d27b05ad2e536830a8ec895ef9c6d010"
   integrity sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==
@@ -14530,7 +14606,14 @@ string_decoder@~1.1.1:
   dependencies:
     safe-buffer "~5.1.0"
 
-"strip-ansi-cjs@npm:strip-ansi@^6.0.1", strip-ansi@^6.0.0, strip-ansi@^6.0.1:
+"strip-ansi-cjs@npm:strip-ansi@^6.0.1":
+  version "6.0.1"
+  resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9"
+  integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==
+  dependencies:
+    ansi-regex "^5.0.1"
+
+strip-ansi@^6.0.0, strip-ansi@^6.0.1:
   version "6.0.1"
   resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9"
   integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==
@@ -14966,6 +15049,11 @@ timers-browserify@^2.0.4:
   dependencies:
     setimmediate "^1.0.4"
 
+tiny-inflate@^1.0.0, tiny-inflate@^1.0.2:
+  version "1.0.3"
+  resolved "https://registry.yarnpkg.com/tiny-inflate/-/tiny-inflate-1.0.3.tgz#122715494913a1805166aaf7c93467933eea26c4"
+  integrity sha512-pkY1fj1cKHb2seWDy0B16HeWyczlJA9/WW3u3c4z/NiWDsO3DOU5D7nhTLE9CF0yXv/QZFY7sEJmj24dK+Rrqw==
+
 tiny-invariant@^1.0.2:
   version "1.3.3"
   resolved "https://registry.yarnpkg.com/tiny-invariant/-/tiny-invariant-1.3.3.tgz#46680b7a873a0d5d10005995eb90a70d74d60127"
@@ -15305,11 +15393,27 @@ unicode-match-property-value-ecmascript@^2.1.0:
   resolved "https://registry.yarnpkg.com/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.1.0.tgz#cb5fffdcd16a05124f5a4b0bf7c3770208acbbe0"
   integrity sha512-qxkjQt6qjg/mYscYMC0XKRn3Rh0wFPlfxB0xkt9CfyTvpX1Ra0+rAmdX2QyAobptSEvuy4RtpPRui6XkV+8wjA==
 
+unicode-properties@^1.2.2:
+  version "1.4.1"
+  resolved "https://registry.yarnpkg.com/unicode-properties/-/unicode-properties-1.4.1.tgz#96a9cffb7e619a0dc7368c28da27e05fc8f9be5f"
+  integrity sha512-CLjCCLQ6UuMxWnbIylkisbRj31qxHPAurvena/0iwSVbQ2G1VY5/HjV0IRabOEbDHlzZlRdCrD4NhB0JtU40Pg==
+  dependencies:
+    base64-js "^1.3.0"
+    unicode-trie "^2.0.0"
+
 unicode-property-aliases-ecmascript@^2.0.0:
   version "2.1.0"
   resolved "https://registry.yarnpkg.com/unicode-property-aliases-ecmascript/-/unicode-property-aliases-ecmascript-2.1.0.tgz#43d41e3be698bd493ef911077c9b131f827e8ccd"
   integrity sha512-6t3foTQI9qne+OZoVQB/8x8rk2k1eVy1gRXhV3oFQ5T6R1dqQ1xtin3XqSlx3+ATBkliTaR/hHyJBm+LVPNM8w==
 
+unicode-trie@^2.0.0:
+  version "2.0.0"
+  resolved "https://registry.yarnpkg.com/unicode-trie/-/unicode-trie-2.0.0.tgz#8fd8845696e2e14a8b67d78fa9e0dd2cad62fec8"
+  integrity sha512-x7bc76x0bm4prf1VLg79uhAzKw8DVboClSN5VxJuQ+LKDOVEW9CdH+VY7SP+vX7xCYQqzzgQpFqz15zeLvAtZQ==
+  dependencies:
+    pako "^0.2.5"
+    tiny-inflate "^1.0.0"
+
 unified@^9.0.0:
   version "9.2.2"
   resolved "https://registry.yarnpkg.com/unified/-/unified-9.2.2.tgz#67649a1abfc3ab85d2969502902775eb03146975"
@@ -15997,7 +16101,16 @@ worker-farm@^1.7.0:
   dependencies:
     errno "~0.1.7"
 
-"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0:
+"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0":
+  version "7.0.0"
+  resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43"
+  integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==
+  dependencies:
+    ansi-styles "^4.0.0"
+    string-width "^4.1.0"
+    strip-ansi "^6.0.0"
+
+wrap-ansi@^7.0.0:
   version "7.0.0"
   resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43"
   integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==
@@ -16073,6 +16186,13 @@ xmlbuilder@>=11.0.1, xmlbuilder@^15.1.1:
   resolved "https://registry.yarnpkg.com/xmlbuilder/-/xmlbuilder-15.1.1.tgz#9dcdce49eea66d8d10b42cae94a79c3c8d0c2ec5"
   integrity sha512-yMqGBqtXyeN1e3TGYvgNgDVZ3j84W4cwkOXQswghol6APgZWaff9lnbvN7MHYJOiXsvGPXtjTYJEiC9J2wv9Eg==
 
+xmldoc@^1.1.2:
+  version "1.3.0"
+  resolved "https://registry.yarnpkg.com/xmldoc/-/xmldoc-1.3.0.tgz#7823225b096c74036347c9ec5924d06b6a3cebab"
+  integrity sha512-y7IRWW6PvEnYQZNZFMRLNJw+p3pezM4nKYPfr15g4OOW9i8VpeydycFuipE2297OvZnh3jSb2pxOt9QpkZUVng==
+  dependencies:
+    sax "^1.2.4"
+
 xmlhttprequest-ssl@1.5.3:
   version "1.5.3"
   resolved "https://registry.yarnpkg.com/xmlhttprequest-ssl/-/xmlhttprequest-ssl-1.5.3.tgz#185a888c04eca46c3e4070d99f7b49de3528992d"

From 5ab60cc2dee4fc88c3ec5db5b83a751597844fa4 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Mon, 23 Sep 2024 11:19:03 +0530
Subject: [PATCH 17/43] integrated userNotes with underlying project notes

---
 .../ReproChecklists/ChecklistItem.js          | 55 ++++++++-----------
 .../ReproChecklists/ReproChecklists.js        | 49 +++++++++++------
 2 files changed, 57 insertions(+), 47 deletions(-)

diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 29328cc..038a7c0 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -7,7 +7,6 @@ import Modal from './Modal/Modal';
 
 function ChecklistItem(props) {
   const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate } = props;
-  const [checklistItem, setChecklistItem] = useState(item);
   const [addImages, setAddImages] = useState(false);
   const [addURL, setAddURL] = useState(false);
   const [showImages, setShowImages] = useState(false);
@@ -16,21 +15,21 @@ function ChecklistItem(props) {
   const [imageModal, setImageModal] = useState({isOpen: false, image: ''});
   const [copiedUrlId, setCopiedUrlId] = useState(null);
 
+  console.log('ChecklistItem Note', item.userNotes);
+
   const handleSubmitImage = (e) => {
     e.preventDefault();
     const img = {id: Math.random().toString(36).substr(2, 9), uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
-    const updatedItem = { ...item, attachedImages: [...checklistItem.attachedImages, img] };
+    const updatedItem = { ...item, attachedImages: [...item.attachedImages, img] };
     onItemUpdate(updatedItem);
-    setChecklistItem(updatedItem);
     setImageModal({isOpen: false, image: ''});
   }
 
   const handleSubmitUrl = (e) => {
     e.preventDefault();
     const url = {id: Math.random().toString(36).substr(2, 9), hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
-    const updatedItem = { ...item, attachedURLs: [...checklistItem.attachedURLs, url] };
+    const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, url] };
     onItemUpdate(updatedItem);
-    setChecklistItem(updatedItem);
     setAddURL(false);
   }
 
@@ -44,18 +43,17 @@ function ChecklistItem(props) {
   };
 
   const handleDeleteUrl = (urlId) => {
-    const updatedItem = { ...item, attachedURLs: checklistItem.attachedURLs.filter((url) => url.id !== urlId) };
+    const updatedItem = { ...item, attachedURLs: item.attachedURLs.filter((url) => url.id !== urlId) };
     onItemUpdate(updatedItem);
-    setChecklistItem(updatedItem);
   };
 
   const handleDeleteImage = (imageId) => {
-    const updatedItem = { ...item, attachedImages: checklistItem.attachedImages.filter((image) => image.id !== imageId) };
+    const updatedItem = { ...item, attachedImages: item.attachedImages.filter((image) => image.id !== imageId) };
     onItemUpdate(updatedItem);
-    setChecklistItem(updatedItem);
   };
 
   const handleNoteUpdate = (note, text) => {
+    text = `Checklist ${item.id}: ` + text;
     if (note) {
       if (onUpdatedNote) {
         onUpdatedNote(project, text, note);
@@ -87,23 +85,21 @@ function ChecklistItem(props) {
   return (
     <div className={styles.item}>
       <div className={styles.header}>
-        <span className={styles.statement}>{checklistItem.statement}</span>
+        <span className={styles.statement}>{item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
-            className={checklistItem.answer ? styles.yesset : styles.yes}
+            className={item.answer ? styles.yesset : styles.yes}
             onClick={() => {
               const updatedItem = { ...item, answer: true };
-              setChecklistItem(updatedItem);
               onItemUpdate(updatedItem);
             }}
           >
             {'Yes'}
           </button>
           <button
-            className={checklistItem.answer  ? styles.no : styles.noset}
+            className={item.answer  ? styles.no : styles.noset}
             onClick={() => {
               const updatedItem = { ...item, answer: false };
-              setChecklistItem(updatedItem);
               onItemUpdate(updatedItem);
             }}
           >
@@ -112,14 +108,14 @@ function ChecklistItem(props) {
         </div>
       </div>
       <div className={styles.scanResult}>
-        {checklistItem.scanResult &&
-          Object.keys(checklistItem.scanResult).map((key) => {
+        {item.scanResult &&
+          Object.keys(item.scanResult).map((key) => {
             return (
             <div key={key}>
               <span className={styles.scanKey}>{key}</span>
               <ul className={styles.scanList}>
-                {checklistItem.scanResult[key].length ? (
-                  checklistItem.scanResult[key].map((answer) => (
+                {item.scanResult[key].length ? (
+                  item.scanResult[key].map((answer) => (
                     <li key={answer}>{answer}</li>
                   ))
                 ) : (
@@ -131,11 +127,11 @@ function ChecklistItem(props) {
       </div>
       <div className={styles.details}>
         <NoteEditor
-          notes={checklistItem.userNotes}
+          notes={item.userNotes}
           onEditingComplete={handleNoteUpdate}
           onDelete={handleNoteDelete}
         />
-        {checklistItem.attachedImages.length > 0 && (
+        {item.attachedImages.length > 0 && (
           <div className={styles.images}>
             <div className={styles.headerWithButton}>
               <h4>Attached Images:</h4>
@@ -145,7 +141,7 @@ function ChecklistItem(props) {
             </div>
             <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
               <ul>
-                {checklistItem.attachedImages.map((image) => (
+                {item.attachedImages.map((image) => (
                   <li key={image} className={styles.image}>
                     <div className={styles.imageHeader}>
                       <span className={styles.imageText}>{image.title}</span>
@@ -171,7 +167,7 @@ function ChecklistItem(props) {
               <ul>
                 {imageAssets.map((image) => (
                   <li key={image} className={styles.header}>
-                    <AddBox className={styles.addIcon}  onClick={()=>setImageModal({isOpen: true, image: image})}/>
+                    <AddBox className={styles.addIcon}  onClick={()=> setImageModal({isOpen: true, image: image})}/>
                     <img src={image} alt="project image" />
                   </li>
                 ))}
@@ -186,7 +182,7 @@ function ChecklistItem(props) {
           title="Image"
           component={imageComponent}
         />
-        {checklistItem.attachedURLs.length > 0 && (
+        {item.attachedURLs.length > 0 && (
           <div className={styles.urls}>
             <div className={styles.headerWithButton}>
               <h4>Attached URLs:</h4>
@@ -196,7 +192,7 @@ function ChecklistItem(props) {
             </div>
             <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
               <ul>
-                {checklistItem.attachedURLs.map((url) => (
+                {item.attachedURLs.map((url) => (
                   <div>
                     <div>
                       <li key={url.id} className={styles.url}>
@@ -242,7 +238,7 @@ function ChecklistItem(props) {
           title="URL"
           component={urlComponent}
         />
-        {checklistItem.subChecklists.length > 0 && (
+        {item.subChecklists.length > 0 && (
           <div className={styles.subChecklists}>
             <div className={styles.headerWithButton}>
               <h4>Sub-Checklists:</h4>
@@ -252,7 +248,7 @@ function ChecklistItem(props) {
             </div>
             <div className={`${styles.subChecksContent} ${showSubChecks ? styles.show : ''}`}>
               <ul>
-                {checklistItem.subChecklists.map((subCheck) => (
+                {item.subChecklists.map((subCheck) => (
                   <li key={subCheck.id}>
                   <div className={styles.header}>
                     <span>{subCheck.statement}</span>
@@ -260,15 +256,13 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.yesset : styles.yes}
                         onClick={() => {
-                          // update the subchecklist item corresponding to the subchecklist id
-                          const updatedItem = { ...item, subChecklists: checklistItem.subChecklists.map((sub) => {
+                          const updatedItem = { ...item, subChecklists: item.subChecklists.map((sub) => {
                             if (sub.id === subCheck.id) {
                               return { ...sub, answer: true };
                             }
                             return sub;
                           })};
                           onItemUpdate(updatedItem);
-                          setChecklistItem(updatedItem);
                         }}
                       >
                         {'Yes'}
@@ -276,14 +270,13 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.no : styles.noset}
                         onClick={() => {
-                          const updatedItem = { ...item, subChecklists: checklistItem.subChecklists.map((sub) => {
+                          const updatedItem = { ...item, subChecklists: item.subChecklists.map((sub) => {
                             if (sub.id === subCheck.id) {
                               return { ...sub, answer: false };
                             }
                             return sub;
                           })};
                           onItemUpdate(updatedItem);
-                          setChecklistItem(updatedItem);
                         }}
                       >
                         {'No'}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index bfccff9..9d5ef3c 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -19,14 +19,7 @@ const reproducibilityChecklist = [
     statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
     answer: true,
     scanResult: {},
-    userNotes: [
-      {
-        id: 'note1',
-        author: 'Author1',
-        updated: '2024-06-01',
-        content: 'First note content',
-      },
-    ],
+    userNotes: [],
     attachedImages: [],
     attachedURLs: [],
     subChecklists: [],
@@ -36,14 +29,7 @@ const reproducibilityChecklist = [
     statement: 'Second checklist item statement.',
     answer: false,
     scanResult: {},
-    userNotes: [
-      {
-        id: 'note2',
-        author: 'Author2',
-        updated: '2024-06-02',
-        content: 'Second note content',
-      },
-    ],
+    userNotes: [],
     attachedImages: [],
     attachedURLs: [],
     subChecklists: [],
@@ -108,6 +94,26 @@ function findImageAssets(asset) {
   }
 };
 
+function findChecklistNotesFromProject(project) {
+  const checklistNotes = {};
+  project.notes.forEach((note) => {
+    if (note.content.startsWith('Checklist') && note.content.includes(':')) {
+      const id = note.content.split(':')[0].split(' ')[1];
+      if (!checklistNotes[id]) {
+        checklistNotes[id] = [];
+      }
+      const checklistNote = {
+        id: note.id,
+        author: note.author,
+        updated: note.updated,
+        content: note.content.split(':')[1].trim(),
+      };
+      checklistNotes[id].push(checklistNote);
+    }
+  });
+  return checklistNotes;
+}
+
 
 function convertImageToBase64(filePath) {
   try {
@@ -151,6 +157,17 @@ function ReproChecklists(props) {
     if (project && project.assets) {
       findAssetLanguagesAndDependencies(project.assets);
       findImageAssets(project.assets);
+      const checklistNotes = findChecklistNotesFromProject(project);
+      const updatedChecklistItems = checklistItems.map((item) => {
+        if (checklistNotes[item.id]) {
+          return {
+            ...item,
+            userNotes: checklistNotes[item.id],
+          };
+        }
+        return item;
+      });
+      setChecklistItems(updatedChecklistItems);
       setAllImages(Object.keys(imageAssets));
     }
   }, [project]);

From 256692b2d73f2a3c15c9960867a4fe65fd66f8e8 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 24 Sep 2024 23:39:34 +0530
Subject: [PATCH 18/43] adding related urls in repro. report

---
 .../ReproChecklists/ChecklistItem.js          | 15 ++---
 .../ReproChecklists/ReproChecklists.js        | 57 ++++++++++++++-----
 yarn.lock                                     | 12 ++++
 3 files changed, 63 insertions(+), 21 deletions(-)

diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 038a7c0..0971270 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -5,6 +5,8 @@ import NoteEditor from '../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
 import Modal from './Modal/Modal';
 
+const { v4: uuidv4 } = require('uuid');
+
 function ChecklistItem(props) {
   const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate } = props;
   const [addImages, setAddImages] = useState(false);
@@ -15,11 +17,9 @@ function ChecklistItem(props) {
   const [imageModal, setImageModal] = useState({isOpen: false, image: ''});
   const [copiedUrlId, setCopiedUrlId] = useState(null);
 
-  console.log('ChecklistItem Note', item.userNotes);
-
   const handleSubmitImage = (e) => {
     e.preventDefault();
-    const img = {id: Math.random().toString(36).substr(2, 9), uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
+    const img = {id: uuidv4(), uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
     const updatedItem = { ...item, attachedImages: [...item.attachedImages, img] };
     onItemUpdate(updatedItem);
     setImageModal({isOpen: false, image: ''});
@@ -27,7 +27,7 @@ function ChecklistItem(props) {
 
   const handleSubmitUrl = (e) => {
     e.preventDefault();
-    const url = {id: Math.random().toString(36).substr(2, 9), hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
+    const url = {id: uuidv4(), hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
     const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, url] };
     onItemUpdate(updatedItem);
     setAddURL(false);
@@ -53,14 +53,13 @@ function ChecklistItem(props) {
   };
 
   const handleNoteUpdate = (note, text) => {
-    text = `Checklist ${item.id}: ` + text;
     if (note) {
       if (onUpdatedNote) {
-        onUpdatedNote(project, text, note);
+        onUpdatedNote(project, `Checklist ${item.id}: ` + text, note);
       }
     } else {
       if (onAddedNote) {
-        onAddedNote(project, text);
+        onAddedNote(project, `Checklist ${item.id}: ` + text);
       }
     }
   };
@@ -69,6 +68,8 @@ function ChecklistItem(props) {
     if (onDeletedNote) {
       onDeletedNote(project, note);
     }
+    const updatedItem = { ...item, userNotes: item.userNotes.filter((n) => n.id !== note.id) };
+    onItemUpdate(updatedItem);
   };
 
   let imageComponent = null;
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index 9d5ef3c..b4914d8 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -243,22 +243,48 @@ function ReproChecklists(props) {
             images = item.attachedImages.map((image) => {
               const base64Image = convertImageToBase64(image.uri);
               if (base64Image) {
-                return [
+                return {
+                  unbreakable: true,
+                  stack: [
+                    {
+                      image: base64Image,
+                      width: 150,
+                      margin: [0, 5],
+                      alignment: 'center',
+                    },
+                    {
+                      text: image.title,
+                      margin: [0, 2],
+                      alignment: 'center',
+                    },
+                  ],
+                };
+              }
+              return { text: `Failed to load image: ${image.uri}`, color: 'red' };
+            });
+          }
+
+          let urls = [];
+          if(item.attachedURLs && item.attachedURLs.length > 0){
+            console.log(item.attachedURLs);
+            urls = item.attachedURLs.map((url) => {
+              return {
+                unbreakable: true,
+                stack: [
                   {
-                    image: base64Image,
-                    width: 150,
-                    margin: [0, 5],
-                    alignment: 'center',
+                    text: url.hyperlink,
+                    margin: [15, 1],
+                    alignment: 'left',
+                    style: 'hyperlink',
+                    link: url.hyperlink,
                   },
                   {
-                    text: `${image.title}`,
-                    style: 'imageTitle',
-                    margin: [0, 2],
-                    alignment: 'center',
+                    text: `${url.title}`,
+                    margin: [15, 5],
+                    alignment: 'left',
                   },
-                ];
-              }
-              return { text: `Failed to load image: ${image.uri}`, color: 'red' };
+                ],
+              };
             });
           }
 
@@ -288,14 +314,16 @@ function ReproChecklists(props) {
               columnGap: 5,
             },
             ...subChecklists,
-            images.length > 0 ? { text: 'Related Images:', style: 'subheader', margin: [0, 10] } : '',
+            images.length > 0 ? { text: 'Related Images:', margin: [0, 10] } : '',
             {
               columns: images,
               columnGap: 5,
               width: '*',
               wrap: true,
               margin: [0, 5],
-            }
+            },
+            urls.length > 0 ? { text: 'Related URLs:', margin: [0, 10] } : '',
+            ...urls,
           ];
         }).flat(),
       ],
@@ -303,6 +331,7 @@ function ReproChecklists(props) {
         mainHeader: { fontSize: 22, bold: true, color: '#663399' },
         sectionHeader: { fontSize: 18, bold: true, color: '#8b6fb3', margin: [0, 20] },
         header: { fontSize: 16, bold: true },
+        hyperlink: { color: '#0000EE' },
       },
       defaultStyle: {
         fontSize: 12,
diff --git a/yarn.lock b/yarn.lock
index 9746bdf..fbea7ad 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -6138,6 +6138,18 @@ dedent@^1.0.0:
   resolved "https://registry.yarnpkg.com/dedent/-/dedent-1.5.1.tgz#4f3fc94c8b711e9bb2800d185cd6ad20f2a90aff"
   integrity sha512-+LxW+KLWxu3HW3M2w2ympwtqPrqYRzU8fqi6Fhd18fBALe15blJPI/I4+UHveMVG6lJqB4JNd4UG0S5cnVHwIg==
 
+deep-equal@^1.0.0:
+  version "1.1.2"
+  resolved "https://registry.yarnpkg.com/deep-equal/-/deep-equal-1.1.2.tgz#78a561b7830eef3134c7f6f3a3d6af272a678761"
+  integrity sha512-5tdhKF6DbU7iIzrIOa1AOUt39ZRm13cmL1cGEh//aqR8x9+tNfbywRf0n5FD/18OKMdo7DNEtrX2t22ZAkI+eg==
+  dependencies:
+    is-arguments "^1.1.1"
+    is-date-object "^1.0.5"
+    is-regex "^1.1.4"
+    object-is "^1.1.5"
+    object-keys "^1.1.1"
+    regexp.prototype.flags "^1.5.1"
+
 deep-equal@^2.0.5:
   version "2.2.3"
   resolved "https://registry.yarnpkg.com/deep-equal/-/deep-equal-2.2.3.tgz#af89dafb23a396c7da3e862abc0be27cf51d56e1"

From 15adfb21bb5eec7bf438e0684b33795fdb83b98f Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Wed, 25 Sep 2024 00:17:04 +0530
Subject: [PATCH 19/43] fixes

---
 .../ReproChecklists/ReproChecklists.js         | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index b4914d8..bf0187d 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -60,6 +60,7 @@ const reproducibilityChecklist = [
 const languages = {};
 const dependencies = {};
 const imageAssets = {};
+const checklistNotes = {};
 
 function findAssetLanguagesAndDependencies(asset) {
   if (asset.type === 'file' && asset.contentTypes.includes('code') ) {
@@ -94,9 +95,8 @@ function findImageAssets(asset) {
   }
 };
 
-function findChecklistNotesFromProject(project) {
-  const checklistNotes = {};
-  project.notes.forEach((note) => {
+function findChecklistNotes(notes) {
+  notes.forEach((note) => {
     if (note.content.startsWith('Checklist') && note.content.includes(':')) {
       const id = note.content.split(':')[0].split(' ')[1];
       if (!checklistNotes[id]) {
@@ -154,10 +154,14 @@ function ReproChecklists(props) {
   const [allImages, setAllImages] = useState([]);
 
   useEffect(() => {
-    if (project && project.assets) {
-      findAssetLanguagesAndDependencies(project.assets);
-      findImageAssets(project.assets);
-      const checklistNotes = findChecklistNotesFromProject(project);
+    if (project) {
+      if(project.assets) {
+        findAssetLanguagesAndDependencies(project.assets);
+        findImageAssets(project.assets);
+      }
+      if(project.notes){
+        findChecklistNotes(project.notes);
+      }
       const updatedChecklistItems = checklistItems.map((item) => {
         if (checklistNotes[item.id]) {
           return {

From 1908d1fc299f3a8777f484612d1a8de2d5baf2c9 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 26 Sep 2024 01:33:11 +0530
Subject: [PATCH 20/43] feature to add asset filepaths as URI and minor other
 changes in form fields requirements

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             |   5 +-
 .../ReproChecklists/ChecklistItem.css         |  20 +-
 .../ReproChecklists/ChecklistItem.js          | 182 +++++++++++++-----
 .../ReproChecklists/Modal/Modal.css           |  19 +-
 app/components/ReproChecklists/Modal/Modal.js |   7 +-
 .../ReproChecklists/ReproChecklists.js        |  59 +++---
 6 files changed, 217 insertions(+), 75 deletions(-)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 6968312..74a174a 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -687,6 +687,7 @@ class Project extends Component<Props> {
         onAddedNote={this.projectUpsertNoteHandler}
         onUpdatedNote={this.projectUpsertNoteHandler}
         onDeletedNote={this.projectDeleteNoteHandler}
+        onSelectedAsset={this.assetSelectedHandler}
       />
 
       content = (
@@ -717,7 +718,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
-              <Tab label="Checklists" value="Checklists" classes={tabStyle} />
+              <Tab label="Checklists" value="checklists" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -738,7 +739,7 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
-          <TabPanel value="Checklists" classes={tabPanelStyle}>
+          <TabPanel value="checklists" classes={tabPanelStyle}>
             {checklists}
           </TabPanel>
         </TabContext>
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklists/ChecklistItem.css
index e509671..4992da7 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklists/ChecklistItem.css
@@ -42,11 +42,13 @@
 }
 
 .images,
-.urls,
 .subChecklists {
   margin-top: 10px;
 }
 
+.urls {
+}
+
 .images ul{
   list-style-type: none;
   padding-left: 0;
@@ -307,3 +309,19 @@
   font-size: 16px;
   font-weight: 600;
 }
+
+.tree {
+  width: 50%;
+  display: inline-block;
+  vertical-align: top;
+}
+
+.toolbar {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+}
+
+.toolbarButton {
+  font-size: 0.8rem !important;
+}
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index 2c0ee45..b2e7cf4 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -3,19 +3,48 @@ import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
+import { Box, IconButton, Tabs, Tab } from '@mui/material';
+import { TabContext, TabPanel } from '@mui/lab';
+import { FaFolderOpen, FaFolderMinus, FaPlusSquare } from 'react-icons/fa';
 import Modal from './Modal/Modal';
+import AssetTree from '../AssetTree/AssetTree';
+import AssetUtil from '../../utils/asset';
 
 const { v4: uuidv4 } = require('uuid');
 
 function ChecklistItem(props) {
-  const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate } = props;
+  const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate, onSelectedAsset } = props;
+
+  const treeRef = React.useRef(null);
+
   const [addImages, setAddImages] = useState(false);
   const [addURL, setAddURL] = useState(false);
+  const [addFile, setAddFile] = useState(false);
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
   const [showSubChecks, setShowSubChecks] = useState(false);
   const [imageModal, setImageModal] = useState({isOpen: false, image: ''});
   const [copiedUrlId, setCopiedUrlId] = useState(null);
+  const [selectedTab, setSelectedTab] = useState('urls');
+  const [selectedAsset, setSelectedAsset] = useState();
+
+  const handleTabChange = (event, newValue) => {
+    setSelectedTab(newValue);
+  };
+
+  const handleSelectAsset = (selAsset) => {
+    let asset = selAsset;
+    if (asset && (asset.contentTypes === null || asset.contentTypes === undefined)) {
+      if (project && project.assets) {
+        asset = AssetUtil.findDescendantAssetByUri(project.assets, asset.uri);
+      }
+    }
+
+    setSelectedAsset(asset);
+    if (onSelectedAsset) {
+      onSelectedAsset(asset);
+    }
+  };
 
   const handleSubmitImage = (e) => {
     e.preventDefault();
@@ -23,6 +52,7 @@ function ChecklistItem(props) {
     const updatedItem = { ...item, attachedImages: [...item.attachedImages, img] };
     onItemUpdate(updatedItem);
     setImageModal({isOpen: false, image: ''});
+    setShowImages(true);
   }
 
   const handleSubmitUrl = (e) => {
@@ -31,6 +61,8 @@ function ChecklistItem(props) {
     const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, url] };
     onItemUpdate(updatedItem);
     setAddURL(false);
+    setAddFile(false);
+    setShowURLs(true);
   }
 
   const handleCopy = (urlId, hyperlink) => {
@@ -53,6 +85,10 @@ function ChecklistItem(props) {
   };
 
   const handleNoteUpdate = (note, text) => {
+    if (!text) {
+      console.log("Detected an empty new note - this will not be created");
+      return;
+    }
     if (note) {
       if (onUpdatedNote) {
         onUpdatedNote(project, `Checklist ${item.id}: ` + text, note);
@@ -75,12 +111,19 @@ function ChecklistItem(props) {
 
   let imageComponent = null;
   let urlComponent = null;
+  let fileComponent = null;
 
   imageComponent = <img src={imageModal.image} alt="selected" className={styles.selectedImage}/>;
   urlComponent = (
     <div className={styles.hyperlink}>
       <label htmlFor="hyperlink">URL:</label>
-      <input type="text" id="hyperlink" name="hyperlink"/>
+      <input type="url" id="hyperlink" name="hyperlink" required/>
+    </div>
+  )
+  fileComponent = (
+    <div className={styles.hyperlink}>
+      <label htmlFor="hyperlink">File Path:</label>
+      <input type="text" id="hyperlink" name="hyperlink" value={selectedAsset&&selectedAsset.uri} required/>
     </div>
   )
 
@@ -184,50 +227,103 @@ function ChecklistItem(props) {
           title="Image"
           component={imageComponent}
         />
-        {item.attachedURLs.length > 0 && (
-          <div className={styles.urls}>
-            <div className={styles.headerWithButton}>
-              <h4>Attached URLs:</h4>
-              <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
-                {showURLs ? 'Hide' : 'Show'}
-              </button>
+        <TabContext value={selectedTab}>
+          <Tabs value={selectedTab} onChange={handleTabChange} aria-label="tabs">
+            <Tab label="Assets" value="assets" />
+            <Tab label="URLs" value="urls" />
+          </Tabs>
+          <TabPanel value="assets" style={{paddingTop : '5px', paddingLeft : '5px', paddingBottom : '5px'}}>
+            <div className={styles.tree}>
+              <div className={styles.toolbar}>
+                <IconButton
+                  onClick={() => treeRef.current.setExpandAll(true)}
+                  className={styles.toolbarButton}
+                  aria-label="expand all tree items"
+                  fontSize="small"
+                >
+                  <FaFolderOpen fontSize="small" /> &nbsp;Expand
+                </IconButton>
+                <IconButton
+                  onClick={() => treeRef.current.setExpandAll(false)}
+                  className={styles.toolbarButton}
+                  aria-label="collapse all tree items"
+                  fontSize="small"
+                >
+                  <FaFolderMinus fontSize="small" /> &nbsp;Collapse
+                </IconButton>
+                <IconButton
+                  onClick={() => setAddFile(true)}
+                  className={styles.toolbarButton}
+                  aria-label="add selected asset"
+                  fontSize="small"
+                >
+                  <FaPlusSquare fontSize="small" /> &nbsp;Add Selected Asset
+                </IconButton>
+              </div>
+              <AssetTree
+                assets={project.assets}
+                ref={treeRef}
+                onSelectAsset={handleSelectAsset}
+                selectedAsset={selectedAsset}
+              />
             </div>
-            <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
-              <ul>
-                {item.attachedURLs.map((url) => (
-                  <div>
-                    <div>
-                      <li key={url.id} className={styles.url}>
-                        <div className={styles.urlHeader}>
-                          <span className={styles.urlText}>{url.title}</span>
-                          <div>
-                            {copiedUrlId === url.id ? (
-                                <Done className={styles.doneButton} />
-                            ) : (
-                                <ContentCopy
-                                  className={styles.copyButton}
-                                  onClick={() => handleCopy(url.id, url.hyperlink)}
+          </TabPanel>
+          <TabPanel value="urls" style={{paddingTop : '5px', paddingLeft : '15px', paddingBottom : '5px'}}>
+            {item.attachedURLs.length > 0 ? (
+              <div className={styles.urls}>
+                <div className={styles.headerWithButton}>
+                  <h4>Attached URLs:</h4>
+                  <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
+                    {showURLs ? 'Hide' : 'Show'}
+                  </button>
+                </div>
+                <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
+                  <ul>
+                    {item.attachedURLs.map((url) => (
+                      <div key={url.id}>
+                        <div>
+                          <li className={styles.url}>
+                            <div className={styles.urlHeader}>
+                              <span className={styles.urlText}>{url.title}</span>
+                              <div>
+                                {copiedUrlId === url.id ? (
+                                  <Done className={styles.doneButton} />
+                                ) : (
+                                  <ContentCopy
+                                    className={styles.copyButton}
+                                    onClick={() => handleCopy(url.id, url.hyperlink)}
+                                  />
+                                )}
+                                <Delete
+                                  className={styles.delButton}
+                                  onClick={() => handleDeleteUrl(url.id)}
                                 />
-                            )}
-                            <Delete
-                              className={styles.delButton}
-                              onClick={() => handleDeleteUrl(url.id)}
-                            />
-                          </div>
+                              </div>
+                            </div>
+                            <a href={url.hyperlink} target="">
+                              {url.hyperlink}
+                            </a>
+                            <p>{url.description}</p>
+                          </li>
                         </div>
-                        <a href={url.hyperlink} target="">
-                          {url.hyperlink}
-                        </a>
-                        <p>{url.description}</p>
-                      </li>
-                    </div>
-                    <hr/>
-                  </div>
-                ))}
-              </ul>
-            </div>
-          </div>
-        )}
+                        <hr />
+                      </div>
+                    ))}
+                  </ul>
+                </div>
+              </div>
+            ) : (
+              <p>No URLs attached.</p>
+            )}
+          </TabPanel>
+        </TabContext>
+        <Modal
+          isOpen={addFile}
+          onClose={()=>setAddFile(false)}
+          onSubmit={handleSubmitUrl}
+          title="URL"
+          component={fileComponent}
+        />
         <div>
           <button className={styles.addUrlsButton} onClick={() => setAddURL(true)}>
             Add URLs
diff --git a/app/components/ReproChecklists/Modal/Modal.css b/app/components/ReproChecklists/Modal/Modal.css
index 9af4cfd..5368cb4 100644
--- a/app/components/ReproChecklists/Modal/Modal.css
+++ b/app/components/ReproChecklists/Modal/Modal.css
@@ -37,7 +37,7 @@
 }
 
 .submitButton {
-  background-color: #ccc;
+  background-color: #aa94d1;
   color: #000;
   border: none;
   cursor: pointer;
@@ -48,5 +48,20 @@
 }
 
 .submitButton:hover {
-  background-color: #e5e5e5;
+  opacity: 0.9;
+}
+
+.cancelButton {
+  background-color: #ccc;
+  color: #000;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 15px;
+  transition: background-color 0.3s ease;
+}
+
+.cancelButton:hover {
+  opacity: 0.9;
 }
diff --git a/app/components/ReproChecklists/Modal/Modal.js b/app/components/ReproChecklists/Modal/Modal.js
index d6ee30a..343f248 100644
--- a/app/components/ReproChecklists/Modal/Modal.js
+++ b/app/components/ReproChecklists/Modal/Modal.js
@@ -13,21 +13,22 @@ function AttachModal(props) {
           aria-describedby="modal-description"
           className={styles.modal}
     >
-      <form onSubmit={onSubmit} className={styles.form}>
+      <form onSubmit = {onSubmit} className={styles.form}>
           <div className={styles.header}>
             <h3>Attach {title}</h3>
           </div>
           {component}
           <div className={styles.title}>
             <label htmlFor="title">Title:</label>
-            <input type="text" id="title" name="title"/>
+            <input type="text" id="title" name="title" required/>
           </div>
           <div className={styles.description}>
             <label htmlFor="description">Description:</label>
-            <textarea id="description" name="description" />
+            <textarea id="description" name="description" required/>
           </div>
           <div className={styles.submit}>
             <button type="submit" className={styles.submitButton}>Submit</button>
+            <button type="button" className={styles.cancelButton} onClick = {onClose}>Cancel</button>
           </div>
         </form>
     </Modal>
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index bf0187d..ba3f25f 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -60,7 +60,6 @@ const reproducibilityChecklist = [
 const languages = {};
 const dependencies = {};
 const imageAssets = {};
-const checklistNotes = {};
 
 function findAssetLanguagesAndDependencies(asset) {
   if (asset.type === 'file' && asset.contentTypes.includes('code') ) {
@@ -96,6 +95,7 @@ function findImageAssets(asset) {
 };
 
 function findChecklistNotes(notes) {
+  const checklistNotes = {};
   notes.forEach((note) => {
     if (note.content.startsWith('Checklist') && note.content.includes(':')) {
       const id = note.content.split(':')[0].split(' ')[1];
@@ -149,7 +149,7 @@ function convertImageToBase64(filePath) {
 
 
 function ReproChecklists(props) {
-  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote } = props;
+  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
   const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
   const [allImages, setAllImages] = useState([]);
 
@@ -158,21 +158,21 @@ function ReproChecklists(props) {
       if(project.assets) {
         findAssetLanguagesAndDependencies(project.assets);
         findImageAssets(project.assets);
+        setAllImages(Object.keys(imageAssets));
       }
       if(project.notes){
-        findChecklistNotes(project.notes);
+        const checklistNotes = findChecklistNotes(project.notes);
+        const updatedChecklistItems = checklistItems.map((item) => {
+          if (checklistNotes[item.id]) {
+            return {
+              ...item,
+              userNotes: checklistNotes[item.id],
+            };
+          }
+          return item;
+        });
+        setChecklistItems(updatedChecklistItems);
       }
-      const updatedChecklistItems = checklistItems.map((item) => {
-        if (checklistNotes[item.id]) {
-          return {
-            ...item,
-            userNotes: checklistNotes[item.id],
-          };
-        }
-        return item;
-      });
-      setChecklistItems(updatedChecklistItems);
-      setAllImages(Object.keys(imageAssets));
     }
   }, [project]);
 
@@ -270,22 +270,32 @@ function ReproChecklists(props) {
 
           let urls = [];
           if(item.attachedURLs && item.attachedURLs.length > 0){
-            console.log(item.attachedURLs);
-            urls = item.attachedURLs.map((url) => {
+            urls = item.attachedURLs.map((url, urlIndex) => {
               return {
                 unbreakable: true,
-                stack: [
+                columns: [
                   {
-                    text: url.hyperlink,
-                    margin: [15, 1],
+                    text: `${urlIndex + 1}. `,
+                    width: 25,
+                    margin: [15, 1 , 0, 0],
                     alignment: 'left',
-                    style: 'hyperlink',
-                    link: url.hyperlink,
                   },
                   {
-                    text: `${url.title}`,
-                    margin: [15, 5],
-                    alignment: 'left',
+                    stack: [
+                      {
+                        text: url.title,
+                        margin: [5, 1],
+                        alignment: 'left',
+                        style: 'hyperlink',
+                        link: url.hyperlink,
+                      },
+                      {
+                        text: url.description,
+                        margin: [5, 5],
+                        alignment: 'left',
+                      },
+                    ],
+                    width: '470',
                   },
                 ],
               };
@@ -367,6 +377,7 @@ function ReproChecklists(props) {
           onDeletedNote={onDeletedNote}
           onAddedNote={onAddedNote}
           onItemUpdate={handleItemUpdate}
+          onSelectedAsset={onSelectedAsset}
         />
       ))}
       <br />

From 96013ef17afde77c40aa4c79d9411236670bf2b8 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 10 Oct 2024 22:20:46 +0530
Subject: [PATCH 21/43] minor checklist and report fixes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ReproChecklists/ChecklistItem.js          |   2 +-
 .../ReproChecklists/ReproChecklists.css       |   8 +
 .../ReproChecklists/ReproChecklists.js        | 154 ++++++++++++------
 app/images/no.png                             | Bin 25878 -> 0 bytes
 app/images/yes.png                            | Bin 22146 -> 7827 bytes
 5 files changed, 117 insertions(+), 47 deletions(-)
 delete mode 100644 app/images/no.png

diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklists/ChecklistItem.js
index b2e7cf4..7ff2ea9 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklists/ChecklistItem.js
@@ -130,7 +130,7 @@ function ChecklistItem(props) {
   return (
     <div className={styles.item}>
       <div className={styles.header}>
-        <span className={styles.statement}>{item.statement}</span>
+        <span className={styles.statement}>{item.id}. {item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
             className={item.answer ? styles.yesset : styles.yes}
diff --git a/app/components/ReproChecklists/ReproChecklists.css b/app/components/ReproChecklists/ReproChecklists.css
index fc3d29f..6c30d4b 100644
--- a/app/components/ReproChecklists/ReproChecklists.css
+++ b/app/components/ReproChecklists/ReproChecklists.css
@@ -25,3 +25,11 @@
   margin-top: 3px;
   margin-right: 2px;
 }
+
+.dialogTitle {
+  color: white;
+}
+
+.dialogContent {
+  padding-bottom: 5px;
+}
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklists/ReproChecklists.js
index ba3f25f..67676c8 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklists/ReproChecklists.js
@@ -2,7 +2,7 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ReproChecklists.css';
 import ChecklistItem from './ChecklistItem';
-import { Typography } from '@mui/material';
+import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { SaveAlt } from '@mui/icons-material';
 import pdfMake from 'pdfmake/build/pdfmake';
 import pdfFonts from 'pdfmake/build/vfs_fonts';
@@ -152,6 +152,7 @@ function ReproChecklists(props) {
   const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
   const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
   const [allImages, setAllImages] = useState([]);
+  const [openExportDialog, setOpenExportDialog] = useState(false);
 
   useEffect(() => {
     if (project) {
@@ -183,9 +184,8 @@ function ReproChecklists(props) {
     setChecklistItems(updatedChecklistItems);
   };
 
-  const handleReportGeneration = () => {
+  const handleReportGeneration = (exportNotes) => {
     const checkedIcon = convertImageToBase64(path.join(__dirname, 'images/yes.png'));
-    const uncheckedIcon = convertImageToBase64(path.join(__dirname, 'images/no.png'));
     const statWrapLogo = convertImageToBase64(path.join(__dirname, 'images/banner.png'));
 
     const documentDefinition = {
@@ -215,11 +215,34 @@ function ReproChecklists(props) {
           margin: [0, 5],
         },
         {
-          text: `Checklist Summary`,
-          style: 'sectionHeader',
-          margin: [0, 10],
+          columns: [
+            {
+              text: `Checklist Summary`,
+              style: 'sectionHeader',
+              margin: [0, 10],
+            },
+            {
+              text: 'Yes',
+              margin: [0, 12, 5, 0],
+              width: 30,
+              alignment: 'right',
+              fontSize: 16,
+              bold: true,
+              noWrap: true,
+            },
+            {
+              text: 'No',
+              margin: [0, 12],
+              width: 40,
+              alignment: 'right',
+              fontSize: 16,
+              bold: true,
+              noWrap: true,
+            },
+          ],
         },
         ...checklistItems.map((item, index) => {
+          const maxWidth = 450;
           let subChecklists = [];
           if (item.subChecklists && item.subChecklists.length > 0) {
             subChecklists = item.subChecklists.map((subItem, subIndex) => ({
@@ -230,44 +253,62 @@ function ReproChecklists(props) {
                   width: '*',
                   alignment: 'left',
                 },
-                {
-                  image: subItem.answer ? checkedIcon : uncheckedIcon,
+                subItem.answer ? {
+                  image: checkedIcon,
+                  width: 15,
+                  alignment: 'right',
+                  margin: [0, 5, 25, 0],
+                } : {
+                  image: checkedIcon,
                   width: 15,
-                  height: 15,
                   alignment: 'right',
-                  margin: [0, 6, 1, 0],
+                  margin: [0, 5, 1, 0],
                 },
               ],
               columnGap: 0,
             }));
           }
 
+          let notes = [];
+          if (exportNotes && item.userNotes && item.userNotes.length > 0) {
+            notes = item.userNotes.map((note, noteIndex) => ({
+              text: `${noteIndex + 1}. ${note.content}`,
+              margin: [20, 2],
+              width: maxWidth,
+            }));
+          }
+
           let images = [];
+          const imageWidth = 135;
           if(item.attachedImages && item.attachedImages.length > 0){
             images = item.attachedImages.map((image) => {
               const base64Image = convertImageToBase64(image.uri);
               if (base64Image) {
                 return {
-                  unbreakable: true,
-                  stack: [
-                    {
-                      image: base64Image,
-                      width: 150,
-                      margin: [0, 5],
-                      alignment: 'center',
-                    },
-                    {
-                      text: image.title,
-                      margin: [0, 2],
-                      alignment: 'center',
-                    },
-                  ],
+                  image: base64Image,
+                  width: imageWidth,
+                  margin: [0, 5],
+                  alignment: 'center',
                 };
               }
               return { text: `Failed to load image: ${image.uri}`, color: 'red' };
             });
           }
 
+          // imageWidth*n + calumnGap*(n-1) <= maxWidth - leftMargin - rightMargin
+          // 135*n + 10*(n-1) <= 450 - 20 - 0;
+          // n <= 440/145 --> n = 3
+          const imagesPerRow = Math.floor((maxWidth - 20 + 10) / (imageWidth + 10));
+
+          let imageRows = [];
+          for (let i = 0; i < images.length; i += imagesPerRow) {
+            imageRows.push({
+              columns: images.slice(i, i + imagesPerRow),
+              columnGap: 10,
+              margin: [20, 5],
+            });
+          }
+
           let urls = [];
           if(item.attachedURLs && item.attachedURLs.length > 0){
             urls = item.attachedURLs.map((url, urlIndex) => {
@@ -277,25 +318,26 @@ function ReproChecklists(props) {
                   {
                     text: `${urlIndex + 1}. `,
                     width: 25,
-                    margin: [15, 1 , 0, 0],
+                    margin: [20, 1 , 0, 0],
                     alignment: 'left',
+                    noWrap: true,
                   },
                   {
                     stack: [
                       {
                         text: url.title,
-                        margin: [5, 1],
+                        margin: [7, 1],
                         alignment: 'left',
                         style: 'hyperlink',
                         link: url.hyperlink,
                       },
                       {
                         text: url.description,
-                        margin: [5, 5],
+                        margin: [7, 3],
                         alignment: 'left',
                       },
                     ],
-                    width: '470',
+                    width: maxWidth,
                   },
                 ],
               };
@@ -313,30 +355,32 @@ function ReproChecklists(props) {
                 },
                 {
                   text: `${item.statement}`,
-                  margin: [0, 10],
-                  width: '*',
+                  margin: [0, 10, 25, 0],
+                  width: maxWidth,
                   alignment: 'left',
+                  bold: true,
                 },
-                {
-                  image: item.answer ? checkedIcon : uncheckedIcon,
-                  width: 20,
-                  height: 20,
+                item.answer ? {
+                  image: checkedIcon,
+                  width: 15,
                   alignment: 'right',
-                  margin: [0, 10],
+                  marginRight: 10,
+                  marginTop: 12,
+                } : {
+                  image: checkedIcon,
+                  width: 15,
+                  marginLeft: 28,
+                  marginTop: 12,
                 },
               ],
               columnGap: 5,
             },
             ...subChecklists,
-            images.length > 0 ? { text: 'Related Images:', margin: [0, 10] } : '',
-            {
-              columns: images,
-              columnGap: 5,
-              width: '*',
-              wrap: true,
-              margin: [0, 5],
-            },
-            urls.length > 0 ? { text: 'Related URLs:', margin: [0, 10] } : '',
+            notes.length > 0 ? { text: 'Notes:', margin: [15, 5] } : '',
+            ...notes,
+            images.length > 0 ? { text: 'Related Images:', margin: [15, 10] } : '',
+            ...imageRows,
+            urls.length > 0 ? { text: 'Related URLs:', margin: [15, 10] } : '',
             ...urls,
           ];
         }).flat(),
@@ -344,7 +388,6 @@ function ReproChecklists(props) {
       styles: {
         mainHeader: { fontSize: 22, bold: true, color: '#663399' },
         sectionHeader: { fontSize: 18, bold: true, color: '#8b6fb3', margin: [0, 20] },
-        header: { fontSize: 16, bold: true },
         hyperlink: { color: '#0000EE' },
       },
       defaultStyle: {
@@ -361,6 +404,7 @@ function ReproChecklists(props) {
     };
 
     pdfMake.createPdf(documentDefinition).download('Reproducibility_Checklist_Report.pdf');
+    setOpenExportDialog(false);
   };
 
   return (
@@ -383,7 +427,7 @@ function ReproChecklists(props) {
       <br />
       <div className={styles.downloadContainer}>
         <button
-          onClick={handleReportGeneration}
+          onClick={() => setOpenExportDialog(true)}
           className={styles.downloadButton}
         >
           <div className={styles.buttonContent}>
@@ -392,6 +436,24 @@ function ReproChecklists(props) {
           </div>
         </button>
       </div>
+
+      <Dialog open={openExportDialog} onClose={() => setOpenExportDialog(false)}>
+        <DialogTitle className={styles.dialogTitle}>Export Report</DialogTitle>
+        <DialogContent className={styles.dialogContent}>
+          <DialogContentText>
+            Do you want to include the checklist notes in the exported reproducibility checklist?
+          </DialogContentText>
+        </DialogContent>
+        <DialogActions>
+          <Button onClick={() => handleReportGeneration(true)} color="primary">
+            Yes
+          </Button>
+          <Button onClick={() => handleReportGeneration(false)} color="primary" autoFocus>
+            No
+          </Button>
+        </DialogActions>
+      </Dialog>
+
     </div>
   );
 }
diff --git a/app/images/no.png b/app/images/no.png
deleted file mode 100644
index a79e80aebd55bb7f95953710f8e51c1b0b67a12a..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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zaq|H^AsFl<1hjGdYfq{Cx%hz9<Q>#zPRTP>wJ@|+*k6+JuiiD{I{lP@TNY1O3#N%y
He;WRO%e9S_


From 2e85ab96eb6ff6dc0777f05af3a6a5066b1105e2 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 10 Oct 2024 22:53:50 +0530
Subject: [PATCH 22/43] changes checklists to checklist everywhere

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             | 10 +++---
 .../ChecklistItem.css                         |  2 +-
 .../ChecklistItem.js                          | 14 ++++----
 .../Modal/Modal.css                           |  0
 .../Modal/Modal.js                            |  0
 .../ReproChecklist.css}                       |  0
 .../ReproChecklist.js}                        | 32 +++++++++----------
 docs/ReproducibilityChecklists-DataModels.md  |  4 +--
 docs/ReproducibilityChecklists-Planning.md    |  2 +-
 9 files changed, 32 insertions(+), 32 deletions(-)
 rename app/components/{ReproChecklists => ReproChecklist}/ChecklistItem.css (99%)
 rename app/components/{ReproChecklists => ReproChecklist}/ChecklistItem.js (98%)
 rename app/components/{ReproChecklists => ReproChecklist}/Modal/Modal.css (100%)
 rename app/components/{ReproChecklists => ReproChecklist}/Modal/Modal.js (100%)
 rename app/components/{ReproChecklists/ReproChecklists.css => ReproChecklist/ReproChecklist.css} (100%)
 rename app/components/{ReproChecklists/ReproChecklists.js => ReproChecklist/ReproChecklist.js} (96%)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 74a174a..95507d3 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -13,7 +13,7 @@ import Assets from './Assets/Assets';
 import Workflow from '../Workflow/Workflow';
 import People from '../People/People';
 import ProjectLog from '../ProjectLog/ProjectLog';
-import ReproChecklists from '../ReproChecklists/ReproChecklists';
+import ReproChecklist from '../ReproChecklist/ReproChecklist';
 import ProjectNotes from '../ProjectNotes/ProjectNotes';
 import { ActionType, EntityType, DescriptionContentType } from '../../constants/constants';
 import AssetUtil from '../../utils/asset';
@@ -682,7 +682,7 @@ class Project extends Component<Props> {
           />
         ) : null;
 
-      const checklists = <ReproChecklists
+      const checklist = <ReproChecklist
         project={this.props.project}
         onAddedNote={this.projectUpsertNoteHandler}
         onUpdatedNote={this.projectUpsertNoteHandler}
@@ -718,7 +718,7 @@ class Project extends Component<Props> {
               <Tab label="People" value="people" classes={tabStyle} />
               <Tab label="Notes" value="projectNotes" classes={tabStyle} />
               <Tab label="Project Log" value="projectLog" classes={tabStyle} />
-              <Tab label="Checklists" value="checklists" classes={tabStyle} />
+              <Tab label="Checklist" value="checklist" classes={tabStyle} />
             </Tabs>
           </div>
           <TabPanel value="about" classes={tabPanelStyle}>
@@ -739,8 +739,8 @@ class Project extends Component<Props> {
           <TabPanel value="projectLog" classes={tabPanelStyle}>
             {projectLog}
           </TabPanel>
-          <TabPanel value="checklists" classes={tabPanelStyle}>
-            {checklists}
+          <TabPanel value="checklist" classes={tabPanelStyle}>
+            {checklist}
           </TabPanel>
         </TabContext>
       );
diff --git a/app/components/ReproChecklists/ChecklistItem.css b/app/components/ReproChecklist/ChecklistItem.css
similarity index 99%
rename from app/components/ReproChecklists/ChecklistItem.css
rename to app/components/ReproChecklist/ChecklistItem.css
index 4992da7..820737e 100644
--- a/app/components/ReproChecklists/ChecklistItem.css
+++ b/app/components/ReproChecklist/ChecklistItem.css
@@ -42,7 +42,7 @@
 }
 
 .images,
-.subChecklists {
+.subChecklist {
   margin-top: 10px;
 }
 
diff --git a/app/components/ReproChecklists/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem.js
similarity index 98%
rename from app/components/ReproChecklists/ChecklistItem.js
rename to app/components/ReproChecklist/ChecklistItem.js
index 7ff2ea9..f8af276 100644
--- a/app/components/ReproChecklists/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem.js
@@ -336,17 +336,17 @@ function ChecklistItem(props) {
           title="URL"
           component={urlComponent}
         />
-        {item.subChecklists.length > 0 && (
-          <div className={styles.subChecklists}>
+        {item.subChecklist.length > 0 && (
+          <div className={styles.subChecklist}>
             <div className={styles.headerWithButton}>
-              <h4>Sub-Checklists:</h4>
+              <h4>Sub-Checklist:</h4>
               <button className={styles.dropdownButton} onClick={() => setShowSubChecks(!showSubChecks)}>
                 {showSubChecks ? 'Hide' : 'Show'}
               </button>
             </div>
             <div className={`${styles.subChecksContent} ${showSubChecks ? styles.show : ''}`}>
               <ul>
-                {item.subChecklists.map((subCheck) => (
+                {item.subChecklist.map((subCheck) => (
                   <li key={subCheck.id}>
                   <div className={styles.header}>
                     <span>{subCheck.statement}</span>
@@ -354,7 +354,7 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.yesset : styles.yes}
                         onClick={() => {
-                          const updatedItem = { ...item, subChecklists: item.subChecklists.map((sub) => {
+                          const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
                             if (sub.id === subCheck.id) {
                               return { ...sub, answer: true };
                             }
@@ -368,7 +368,7 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.no : styles.noset}
                         onClick={() => {
-                          const updatedItem = { ...item, subChecklists: item.subChecklists.map((sub) => {
+                          const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
                             if (sub.id === subCheck.id) {
                               return { ...sub, answer: false };
                             }
@@ -424,7 +424,7 @@ ChecklistItem.propTypes = {
         description: PropTypes.string.isRequired,
       })
     ),
-    subChecklists: PropTypes.arrayOf(
+    subChecklist: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         statement: PropTypes.string.isRequired,
diff --git a/app/components/ReproChecklists/Modal/Modal.css b/app/components/ReproChecklist/Modal/Modal.css
similarity index 100%
rename from app/components/ReproChecklists/Modal/Modal.css
rename to app/components/ReproChecklist/Modal/Modal.css
diff --git a/app/components/ReproChecklists/Modal/Modal.js b/app/components/ReproChecklist/Modal/Modal.js
similarity index 100%
rename from app/components/ReproChecklists/Modal/Modal.js
rename to app/components/ReproChecklist/Modal/Modal.js
diff --git a/app/components/ReproChecklists/ReproChecklists.css b/app/components/ReproChecklist/ReproChecklist.css
similarity index 100%
rename from app/components/ReproChecklists/ReproChecklists.css
rename to app/components/ReproChecklist/ReproChecklist.css
diff --git a/app/components/ReproChecklists/ReproChecklists.js b/app/components/ReproChecklist/ReproChecklist.js
similarity index 96%
rename from app/components/ReproChecklists/ReproChecklists.js
rename to app/components/ReproChecklist/ReproChecklist.js
index 67676c8..a84f754 100644
--- a/app/components/ReproChecklists/ReproChecklists.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -1,6 +1,6 @@
 import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
-import styles from './ReproChecklists.css';
+import styles from './ReproChecklist.css';
 import ChecklistItem from './ChecklistItem';
 import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { SaveAlt } from '@mui/icons-material';
@@ -22,7 +22,7 @@ const reproducibilityChecklist = [
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
-    subChecklists: [],
+    subChecklist: [],
   },
   {
     id: '2',
@@ -32,7 +32,7 @@ const reproducibilityChecklist = [
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
-    subChecklists: [],
+    subChecklist: [],
   },
   {
     id: '3',
@@ -42,7 +42,7 @@ const reproducibilityChecklist = [
     userNotes: [],
     attachedImages: [],
     attachedURLs: [],
-    subChecklists:[
+    subChecklist:[
       {
         id: '3.1',
         statement: 'Are all the languages used in the project listed?',
@@ -148,7 +148,7 @@ function convertImageToBase64(filePath) {
 };
 
 
-function ReproChecklists(props) {
+function ReproChecklist(props) {
   const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
   const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
   const [allImages, setAllImages] = useState([]);
@@ -196,7 +196,7 @@ function ReproChecklists(props) {
           alignment: 'center',
         },
         {
-          text: 'Reproducibility Checklists Report',
+          text: 'Reproducibility Checklist',
           style: 'mainHeader',
           alignment: 'center',
           margin: [0, 20],
@@ -243,9 +243,9 @@ function ReproChecklists(props) {
         },
         ...checklistItems.map((item, index) => {
           const maxWidth = 450;
-          let subChecklists = [];
-          if (item.subChecklists && item.subChecklists.length > 0) {
-            subChecklists = item.subChecklists.map((subItem, subIndex) => ({
+          let subChecklist = [];
+          if (item.subChecklist && item.subChecklist.length > 0) {
+            subChecklist = item.subChecklist.map((subItem, subIndex) => ({
               columns: [
                 {
                   text: `${index + 1}.${subIndex + 1} ${subItem.statement}`,
@@ -375,7 +375,7 @@ function ReproChecklists(props) {
               ],
               columnGap: 5,
             },
-            ...subChecklists,
+            ...subChecklist,
             notes.length > 0 ? { text: 'Notes:', margin: [15, 5] } : '',
             ...notes,
             images.length > 0 ? { text: 'Related Images:', margin: [15, 10] } : '',
@@ -403,13 +403,13 @@ function ReproChecklists(props) {
       },
     };
 
-    pdfMake.createPdf(documentDefinition).download('Reproducibility_Checklist_Report.pdf');
+    pdfMake.createPdf(documentDefinition).download('Reproducibility_Checklist.pdf');
     setOpenExportDialog(false);
   };
 
   return (
     <div>
-      <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklists</Typography>
+      <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklist</Typography>
       <br />
       {checklistItems.map(item => (
         <ChecklistItem
@@ -458,7 +458,7 @@ function ReproChecklists(props) {
   );
 }
 
-ReproChecklists.propTypes = {
+ReproChecklist.propTypes = {
   project: PropTypes.object.isRequired,
   reproChecklist: PropTypes.arrayOf(
     PropTypes.shape({
@@ -494,7 +494,7 @@ ReproChecklists.propTypes = {
           updated: PropTypes.string.isRequired,
         })
       ),
-      subChecklists: PropTypes.arrayOf(
+      subChecklist: PropTypes.arrayOf(
         PropTypes.shape({
           id: PropTypes.string.isRequired,
           statement: PropTypes.string.isRequired,
@@ -509,8 +509,8 @@ ReproChecklists.propTypes = {
   onAddedNote: PropTypes.func.isRequired,
 };
 
-ReproChecklists.defaultProps = {
+ReproChecklist.defaultProps = {
   reproChecklist: reproducibilityChecklist,
 };
 
-export default ReproChecklists;
+export default ReproChecklist;
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index a60cd4f..38bb94e 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -2,7 +2,7 @@
 
 ### About
 
-The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklists.
+The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklist.
 
 ### Attributes
 
@@ -15,7 +15,7 @@ The **Checklist Object** represents a single checklist item within the reproduci
 | `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                               |
 | `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                              |
 | `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
-| `subChecklists`    | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                        |
+| `subChecklist`    | Array ([]Sub_checklist)| An array containing sub-checklist associated with the checklist item.                                                                        |
 | `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                        |
 
 ### Sub-Checklist Object
diff --git a/docs/ReproducibilityChecklists-Planning.md b/docs/ReproducibilityChecklists-Planning.md
index d4b4801..3220f2d 100644
--- a/docs/ReproducibilityChecklists-Planning.md
+++ b/docs/ReproducibilityChecklists-Planning.md
@@ -1,4 +1,4 @@
-# Reproducible Research Checklists
+# Reproducible Research Checklist
 
 This document provides design guidance and general requirements for the reproducible research checklist feature in StatWrap.
 

From afc6e77389c3dfba307261116938e5b5809662b0 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 11 Oct 2024 00:07:42 +0530
Subject: [PATCH 23/43] saving changes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ReproChecklist/ChecklistItem.css          |  48 +++++
 .../ReproChecklist/ChecklistItem.js           | 172 +++++-------------
 2 files changed, 91 insertions(+), 129 deletions(-)

diff --git a/app/components/ReproChecklist/ChecklistItem.css b/app/components/ReproChecklist/ChecklistItem.css
index 820737e..da1cc01 100644
--- a/app/components/ReproChecklist/ChecklistItem.css
+++ b/app/components/ReproChecklist/ChecklistItem.css
@@ -7,6 +7,15 @@
   max-width: 83%;
 }
 
+.statementHeader {
+  display:flex;
+  justify-content: center;
+  border: 1px solid #e5e5e5;
+  border-radius: 7px;
+  background-color: #f1f1f1;
+  padding: 10px 10px 0px 10px;
+}
+
 .header {
   display:flex;
   justify-content: center;
@@ -22,6 +31,7 @@
   display: flex;
   margin-left: auto;
   margin-right: 0;
+  margin-bottom: 10px;
 }
 
 .scanResult {
@@ -325,3 +335,41 @@
 .toolbarButton {
   font-size: 0.8rem !important;
 }
+
+.submitButton {
+  background-color: #aa94d1;
+  color: #000;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 15px;
+  transition: background-color 0.3s ease;
+}
+
+.submitButton:hover {
+  opacity: 0.9;
+}
+
+.cancelButton {
+  background-color: #ccc;
+  color: #000;
+  border: none;
+  cursor: pointer;
+  padding: 5px 10px;
+  border-radius: 4px;
+  font-size: 15px;
+  transition: background-color 0.3s ease;
+}
+
+.cancelButton:hover {
+  opacity: 0.9;
+}
+
+.dialogTitle {
+  color: white;
+}
+
+.dialogContent {
+  padding-bottom: 5px;
+}
diff --git a/app/components/ReproChecklist/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem.js
index f8af276..c23df92 100644
--- a/app/components/ReproChecklist/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem.js
@@ -3,7 +3,7 @@ import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
-import { Box, IconButton, Tabs, Tab } from '@mui/material';
+import { Box, IconButton, Tabs, Tab, Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { TabContext, TabPanel } from '@mui/lab';
 import { FaFolderOpen, FaFolderMinus, FaPlusSquare } from 'react-icons/fa';
 import Modal from './Modal/Modal';
@@ -129,7 +129,7 @@ function ChecklistItem(props) {
 
   return (
     <div className={styles.item}>
-      <div className={styles.header}>
+      <div className={styles.statementHeader}>
         <span className={styles.statement}>{item.id}. {item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
@@ -176,63 +176,9 @@ function ChecklistItem(props) {
           onEditingComplete={handleNoteUpdate}
           onDelete={handleNoteDelete}
         />
-        {item.attachedImages.length > 0 && (
-          <div className={styles.images}>
-            <div className={styles.headerWithButton}>
-              <h4>Attached Images:</h4>
-              <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
-                {showImages ? 'Hide' : 'Show'}
-              </button>
-            </div>
-            <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
-              <ul>
-                {item.attachedImages.map((image) => (
-                  <li key={image} className={styles.image}>
-                    <div className={styles.imageHeader}>
-                      <span className={styles.imageText}>{image.title}</span>
-                      <Delete
-                        className={styles.delButton}
-                        onClick={() => handleDeleteImage(image.id)}
-                      />
-                    </div>
-                    <img src={image.uri} alt="attached"/>
-                    <p>{image.description}</p>
-                  </li>
-                ))}
-              </ul>
-            </div>
-          </div>
-        )}
-        {imageAssets.length > 0 && (
-          <div className={styles.images}>
-            <button className={styles.addImagesButton} onClick={() => setAddImages(!addImages)}>
-              Add Images
-            </button>
-            <div className={`${styles.imageContent} ${addImages ? styles.show : ''}`}>
-              <ul>
-                {imageAssets.map((image) => (
-                  <li key={image} className={styles.header}>
-                    <AddBox className={styles.addIcon}  onClick={()=> setImageModal({isOpen: true, image: image})}/>
-                    <img src={image} alt="project image" />
-                  </li>
-                ))}
-              </ul>
-            </div>
-          </div>
-        )}
-        <Modal
-          isOpen={imageModal.isOpen}
-          onClose={()=>setImageModal({isOpen: false, image: ''})}
-          onSubmit={handleSubmitImage}
-          title="Image"
-          component={imageComponent}
-        />
-        <TabContext value={selectedTab}>
-          <Tabs value={selectedTab} onChange={handleTabChange} aria-label="tabs">
-            <Tab label="Assets" value="assets" />
-            <Tab label="URLs" value="urls" />
-          </Tabs>
-          <TabPanel value="assets" style={{paddingTop : '5px', paddingLeft : '5px', paddingBottom : '5px'}}>
+        <Dialog open={addFile} onClose={() => setAddFile(false)}>
+          <DialogTitle className={styles.dialogTitle}>Add Asset Reference</DialogTitle>
+          <DialogContent className={styles.dialogContent}>
             <div className={styles.tree}>
               <div className={styles.toolbar}>
                 <IconButton
@@ -244,10 +190,10 @@ function ChecklistItem(props) {
                   <FaFolderOpen fontSize="small" /> &nbsp;Expand
                 </IconButton>
                 <IconButton
-                  onClick={() => treeRef.current.setExpandAll(false)}
                   className={styles.toolbarButton}
                   aria-label="collapse all tree items"
                   fontSize="small"
+                  onClick={() => treeRef.current.setExpandAll(false)}
                 >
                   <FaFolderMinus fontSize="small" /> &nbsp;Collapse
                 </IconButton>
@@ -267,75 +213,43 @@ function ChecklistItem(props) {
                 selectedAsset={selectedAsset}
               />
             </div>
-          </TabPanel>
-          <TabPanel value="urls" style={{paddingTop : '5px', paddingLeft : '15px', paddingBottom : '5px'}}>
-            {item.attachedURLs.length > 0 ? (
-              <div className={styles.urls}>
-                <div className={styles.headerWithButton}>
-                  <h4>Attached URLs:</h4>
-                  <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
-                    {showURLs ? 'Hide' : 'Show'}
-                  </button>
-                </div>
-                <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
-                  <ul>
-                    {item.attachedURLs.map((url) => (
-                      <div key={url.id}>
-                        <div>
-                          <li className={styles.url}>
-                            <div className={styles.urlHeader}>
-                              <span className={styles.urlText}>{url.title}</span>
-                              <div>
-                                {copiedUrlId === url.id ? (
-                                  <Done className={styles.doneButton} />
-                                ) : (
-                                  <ContentCopy
-                                    className={styles.copyButton}
-                                    onClick={() => handleCopy(url.id, url.hyperlink)}
-                                  />
-                                )}
-                                <Delete
-                                  className={styles.delButton}
-                                  onClick={() => handleDeleteUrl(url.id)}
-                                />
-                              </div>
-                            </div>
-                            <a href={url.hyperlink} target="">
-                              {url.hyperlink}
-                            </a>
-                            <p>{url.description}</p>
-                          </li>
-                        </div>
-                        <hr />
-                      </div>
-                    ))}
-                  </ul>
-                </div>
-              </div>
-            ) : (
-              <p>No URLs attached.</p>
-            )}
-          </TabPanel>
-        </TabContext>
-        <Modal
-          isOpen={addFile}
-          onClose={()=>setAddFile(false)}
-          onSubmit={handleSubmitUrl}
-          title="URL"
-          component={fileComponent}
-        />
-        <div>
-          <button className={styles.addUrlsButton} onClick={() => setAddURL(true)}>
-            Add URLs
-          </button>
-        </div>
-        <Modal
-          isOpen={addURL}
-          onClose={()=>setAddURL(false)}
-          onSubmit={handleSubmitUrl}
-          title="URL"
-          component={urlComponent}
-        />
+          </DialogContent>
+          <DialogActions>
+            <Button onClick={() => handleSubmitUrl()} className={styles.submitButton}>
+              Add
+            </Button>
+            <Button className={styles.cancelButton} autoFocus>
+              Cancel
+            </Button>
+          </DialogActions>
+        </Dialog>
+        {item.attachedImages.length > 0 && (
+          <div className={styles.images}>
+            <div className={styles.headerWithButton}>
+              <h4>Attached Images:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
+                {showImages ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
+              <ul>
+                {item.attachedImages.map((image) => (
+                  <li key={image} className={styles.image}>
+                    <div className={styles.imageHeader}>
+                      <span className={styles.imageText}>{image.title}</span>
+                      <Delete
+                        className={styles.delButton}
+                        onClick={() => handleDeleteImage(image.id)}
+                      />
+                    </div>
+                    <img src={image.uri} alt="attached"/>
+                    <p>{image.description}</p>
+                  </li>
+                ))}
+              </ul>
+            </div>
+          </div>
+        )}
         {item.subChecklist.length > 0 && (
           <div className={styles.subChecklist}>
             <div className={styles.headerWithButton}>

From 2eff7e74b2ca6b47ed3f2480e5d1c9775ac5ef27 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 11 Oct 2024 02:30:30 +0530
Subject: [PATCH 24/43] 1 and 3 left

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ReproChecklist/ChecklistItem.css          |  44 +++-
 .../ReproChecklist/ChecklistItem.js           | 221 +++++++++++-------
 2 files changed, 181 insertions(+), 84 deletions(-)

diff --git a/app/components/ReproChecklist/ChecklistItem.css b/app/components/ReproChecklist/ChecklistItem.css
index da1cc01..f4c56c9 100644
--- a/app/components/ReproChecklist/ChecklistItem.css
+++ b/app/components/ReproChecklist/ChecklistItem.css
@@ -13,7 +13,20 @@
   border: 1px solid #e5e5e5;
   border-radius: 7px;
   background-color: #f1f1f1;
-  padding: 10px 10px 0px 10px;
+  padding: 10px 10px 0;
+}
+
+.expandButton {
+  background: none;
+  padding-left: 0px;
+  margin-right: 0px;
+  align-items: center;
+  display: flex;
+}
+
+.chevron {
+  padding: 10px;
+  font-size: 1.2rem;
 }
 
 .header {
@@ -27,6 +40,7 @@
   margin-right: 5px;
   margin-bottom: 10px;
 }
+
 .buttonContainer {
   display: flex;
   margin-left: auto;
@@ -92,6 +106,7 @@
 .images li:not(:last-child) {
   border-right: 1px solid #ccc;
 }
+
 .urls li:not(:last-child) {
   border-bottom: 1px solid #ccc;
 }
@@ -135,11 +150,12 @@
 .image {
   text-wrap: wrap;
 }
+
 .url {
   background-color:#f2ebff;
   border:1px solid rebeccapurple;
   padding: 7px;
-  padding-right: 0px;
+  padding-right: 0;
   border-radius: 5px;
   text-wrap: wrap;
   word-wrap: break-word;
@@ -328,8 +344,8 @@
 
 .toolbar {
   display: flex;
+  width: 100%;
   justify-content: space-between;
-  align-items: center;
 }
 
 .toolbarButton {
@@ -343,7 +359,7 @@
   cursor: pointer;
   padding: 5px 10px;
   border-radius: 4px;
-  font-size: 15px;
+  font-size: 20px;
   transition: background-color 0.3s ease;
 }
 
@@ -358,7 +374,7 @@
   cursor: pointer;
   padding: 5px 10px;
   border-radius: 4px;
-  font-size: 15px;
+  font-size: 20px;
   transition: background-color 0.3s ease;
 }
 
@@ -368,8 +384,26 @@
 
 .dialogTitle {
   color: white;
+  display: flex;
+  justify-content: center;
 }
 
 .dialogContent {
   padding-bottom: 5px;
+  display: flex;
+  justify-content: center;
+}
+
+.title {
+  display: flex;
+  justify-content: flex-end;
+}
+.description {
+  display: flex;
+  justify-content: flex-end;
+  margin-top: 10px;
+}
+
+.form {
+  margin-top: 20px;
 }
diff --git a/app/components/ReproChecklist/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem.js
index c23df92..433904c 100644
--- a/app/components/ReproChecklist/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem.js
@@ -3,9 +3,8 @@ import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
-import { Box, IconButton, Tabs, Tab, Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
-import { TabContext, TabPanel } from '@mui/lab';
-import { FaFolderOpen, FaFolderMinus, FaPlusSquare } from 'react-icons/fa';
+import { IconButton, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
+import { FaFolderOpen, FaFolderMinus, FaChevronUp, FaChevronDown } from 'react-icons/fa';
 import Modal from './Modal/Modal';
 import AssetTree from '../AssetTree/AssetTree';
 import AssetUtil from '../../utils/asset';
@@ -17,20 +16,15 @@ function ChecklistItem(props) {
 
   const treeRef = React.useRef(null);
 
-  const [addImages, setAddImages] = useState(false);
-  const [addURL, setAddURL] = useState(false);
-  const [addFile, setAddFile] = useState(false);
+  const [expanded, setExpanded] = useState(false);
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
   const [showSubChecks, setShowSubChecks] = useState(false);
-  const [imageModal, setImageModal] = useState({isOpen: false, image: ''});
   const [copiedUrlId, setCopiedUrlId] = useState(null);
-  const [selectedTab, setSelectedTab] = useState('urls');
   const [selectedAsset, setSelectedAsset] = useState();
-
-  const handleTabChange = (event, newValue) => {
-    setSelectedTab(newValue);
-  };
+  const [addAsset, setAddAsset] = useState(false);
+  const [assetTitle, setAssetTitle] = useState('');
+  const [assetDescription, setAssetDescription] = useState('');
 
   const handleSelectAsset = (selAsset) => {
     let asset = selAsset;
@@ -40,29 +34,50 @@ function ChecklistItem(props) {
       }
     }
 
+    if (asset && asset.uri) {
+      if (asset.type === 'file') {
+        const fileName = AssetUtil.getAssetNameFromUri(asset.uri);
+        setAssetTitle(fileName);
+      } else if (asset.type === 'url') {
+        setAssetTitle(asset.uri);
+      } else {
+        setAssetTitle('');
+      }
+    }
+
     setSelectedAsset(asset);
     if (onSelectedAsset) {
       onSelectedAsset(asset);
     }
   };
 
-  const handleSubmitImage = (e) => {
-    e.preventDefault();
-    const img = {id: uuidv4(), uri: imageModal.image, title: e.target.title.value, description: e.target.description.value};
-    const updatedItem = { ...item, attachedImages: [...item.attachedImages, img] };
-    onItemUpdate(updatedItem);
-    setImageModal({isOpen: false, image: ''});
-    setShowImages(true);
-  }
+  const handleAddAsset = () => {
+    if (!selectedAsset) {
+      console.log("No asset selected - cannot add asset reference");
+      return;
+    }
+    if (!assetTitle) {
+      console.log("No title provided - cannot add asset reference");
+      return;
+    }
 
-  const handleSubmitUrl = (e) => {
-    e.preventDefault();
-    const url = {id: uuidv4(), hyperlink: e.target.hyperlink.value, title: e.target.title.value, description: e.target.description.value};
-    const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, url] };
-    onItemUpdate(updatedItem);
-    setAddURL(false);
-    setAddFile(false);
-    setShowURLs(true);
+    if (selectedAsset.type === 'file') {
+      if(selectedAsset.contentTypes.includes('image')) {
+        const updatedItem = { ...item, attachedImages: [...item.attachedImages, {id: uuidv4(), uri: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
+        onItemUpdate(updatedItem);
+        setShowImages(true);
+      } else {
+        const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, {id: uuidv4(), hyperlink: AssetUtil.absoluteToRelativePath(project.path, selectedAsset), title: assetTitle, description: assetDescription}] };
+        onItemUpdate(updatedItem);
+        setShowURLs(true);
+      }
+    } else if (selectedAsset.type === 'url') {
+      const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, {id: uuidv4(), hyperlink: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
+      onItemUpdate(updatedItem);
+      setShowURLs(true);
+    }
+
+    setAddAsset(false);
   }
 
   const handleCopy = (urlId, hyperlink) => {
@@ -109,27 +124,12 @@ function ChecklistItem(props) {
     onItemUpdate(updatedItem);
   };
 
-  let imageComponent = null;
-  let urlComponent = null;
-  let fileComponent = null;
-
-  imageComponent = <img src={imageModal.image} alt="selected" className={styles.selectedImage}/>;
-  urlComponent = (
-    <div className={styles.hyperlink}>
-      <label htmlFor="hyperlink">URL:</label>
-      <input type="url" id="hyperlink" name="hyperlink" required/>
-    </div>
-  )
-  fileComponent = (
-    <div className={styles.hyperlink}>
-      <label htmlFor="hyperlink">File Path:</label>
-      <input type="text" id="hyperlink" name="hyperlink" value={selectedAsset&&selectedAsset.uri} required/>
-    </div>
-  )
-
   return (
     <div className={styles.item}>
       <div className={styles.statementHeader}>
+        <button className={styles.expandButton}>
+          {expanded ? <FaChevronUp className={styles.chevron} onClick={() => setExpanded(false)} /> : <FaChevronDown  className={styles.chevron} onClick={() => setExpanded(true)} />}
+        </button>
         <span className={styles.statement}>{item.id}. {item.statement}</span>
         <div className={styles.buttonContainer}>
           <button
@@ -152,31 +152,36 @@ function ChecklistItem(props) {
           </button>
         </div>
       </div>
-      <div className={styles.scanResult}>
-        {item.scanResult &&
-          Object.keys(item.scanResult).map((key) => {
-            return (
-            <div key={key}>
-              <span className={styles.scanKey}>{key}</span>
-              <ul className={styles.scanList}>
-                {item.scanResult[key].length ? (
-                  item.scanResult[key].map((answer) => (
-                    <li key={answer}>{answer}</li>
-                  ))
-                ) : (
-                  <li>No answers available</li>
-                )}
-              </ul>
-            </div>
-          )})}
-      </div>
-      <div className={styles.details}>
+      {expanded && <div className={styles.details}>
+        <div className={styles.scanResult}>
+          {item.scanResult &&
+            Object.keys(item.scanResult).map((key) => {
+              return (
+              <div key={key}>
+                <span className={styles.scanKey}>{key}</span>
+                <ul className={styles.scanList}>
+                  {item.scanResult[key].length ? (
+                    item.scanResult[key].map((answer) => (
+                      <li key={answer}>{answer}</li>
+                    ))
+                  ) : (
+                    <li>No answers available</li>
+                  )}
+                </ul>
+              </div>
+            )})}
+        </div>
         <NoteEditor
           notes={item.userNotes}
           onEditingComplete={handleNoteUpdate}
           onDelete={handleNoteDelete}
         />
-        <Dialog open={addFile} onClose={() => setAddFile(false)}>
+        <div>
+          <button className={styles.addUrlsButton} onClick={() => setAddAsset(true)}>
+            Add Asset Reference
+          </button>
+        </div>
+        <Dialog open={addAsset} onClose={() => setAddAsset(false)}>
           <DialogTitle className={styles.dialogTitle}>Add Asset Reference</DialogTitle>
           <DialogContent className={styles.dialogContent}>
             <div className={styles.tree}>
@@ -197,14 +202,6 @@ function ChecklistItem(props) {
                 >
                   <FaFolderMinus fontSize="small" /> &nbsp;Collapse
                 </IconButton>
-                <IconButton
-                  onClick={() => setAddFile(true)}
-                  className={styles.toolbarButton}
-                  aria-label="add selected asset"
-                  fontSize="small"
-                >
-                  <FaPlusSquare fontSize="small" /> &nbsp;Add Selected Asset
-                </IconButton>
               </div>
               <AssetTree
                 assets={project.assets}
@@ -213,16 +210,82 @@ function ChecklistItem(props) {
                 selectedAsset={selectedAsset}
               />
             </div>
+            <div className={styles.form}>
+              <div className={styles.title}>
+                <label htmlFor="title">Title:</label>
+                <input
+                  type="text"
+                  id="title"
+                  name="title"
+                  value={assetTitle}
+                  onChange={(e) => setAssetTitle(e.target.value)}
+                  required
+                />
+              </div>
+              <div className={styles.description}>
+                <label htmlFor="description">Description:</label>
+                <input
+                  id="description"
+                  name="description"
+                  value={assetDescription}
+                  onChange={(e) => setAssetDescription(e.target.value)}
+                />
+              </div>
+            </div>
           </DialogContent>
           <DialogActions>
-            <Button onClick={() => handleSubmitUrl()} className={styles.submitButton}>
+            <button onClick={() => handleAddAsset()} className={styles.submitButton}>
               Add
-            </Button>
-            <Button className={styles.cancelButton} autoFocus>
+            </button>
+            <button onClick={() => setAddAsset(false)} className={styles.cancelButton} autoFocus>
               Cancel
-            </Button>
+            </button>
           </DialogActions>
         </Dialog>
+        {item.attachedURLs.length > 0 && (
+          <div className={styles.urls}>
+            <div className={styles.headerWithButton}>
+              <h4>Attached URLs:</h4>
+              <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
+                {showURLs ? 'Hide' : 'Show'}
+              </button>
+            </div>
+            <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
+              <ul>
+                {item.attachedURLs.map((url) => (
+                  <div key={url.id}>
+                    <div>
+                      <li className={styles.url}>
+                        <div className={styles.urlHeader}>
+                          <span className={styles.urlText}>{url.title}</span>
+                          <div>
+                            {copiedUrlId === url.id ? (
+                              <Done className={styles.doneButton} />
+                            ) : (
+                              <ContentCopy
+                                className={styles.copyButton}
+                                onClick={() => handleCopy(url.id, url.hyperlink)}
+                              />
+                            )}
+                            <Delete
+                              className={styles.delButton}
+                              onClick={() => handleDeleteUrl(url.id)}
+                            />
+                          </div>
+                        </div>
+                        <a href={url.hyperlink} target="">
+                          {url.hyperlink}
+                        </a>
+                        <p>{url.description}</p>
+                      </li>
+                    </div>
+                    <hr />
+                  </div>
+                ))}
+              </ul>
+            </div>
+          </div>
+        )}
         {item.attachedImages.length > 0 && (
           <div className={styles.images}>
             <div className={styles.headerWithButton}>
@@ -301,7 +364,7 @@ function ChecklistItem(props) {
             </div>
           </div>
         )}
-      </div>
+      </div>}
     </div>
   );
 }

From 48f8f3836baa7ac59f3dc400e257f0010e650549 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 12 Oct 2024 01:52:11 +0530
Subject: [PATCH 25/43] save checklist entity progress

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             | 21 +++++---
 .../ReproChecklist/ReproChecklist.js          | 53 +++----------------
 app/constants/constants.js                    |  2 +
 app/constants/messages.js                     |  5 ++
 .../CreateProjectDialog.js                    | 49 +++++++++++++++++
 app/containers/ProjectPage/ProjectPage.js     | 23 ++++++++
 app/main.dev.js                               | 39 ++++++++++++++
 app/services/checklist.js                     | 46 ++++++++++++++++
 8 files changed, 184 insertions(+), 54 deletions(-)
 create mode 100644 app/services/checklist.js

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 95507d3..d21d267 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -682,13 +682,18 @@ class Project extends Component<Props> {
           />
         ) : null;
 
-      const checklist = <ReproChecklist
-        project={this.props.project}
-        onAddedNote={this.projectUpsertNoteHandler}
-        onUpdatedNote={this.projectUpsertNoteHandler}
-        onDeletedNote={this.projectDeleteNoteHandler}
-        onSelectedAsset={this.assetSelectedHandler}
-      />
+      const checklist =
+        this.props.project && this.props.checklist ? (
+          <ReproChecklist
+            project={this.props.project}
+            checklist={this.props.checklist.checklist}
+            error={this.props.checklist.errorMessage}
+            onAddedNote={this.projectUpsertNoteHandler}
+            onUpdatedNote={this.projectUpsertNoteHandler}
+            onDeletedNote={this.projectDeleteNoteHandler}
+            onSelectedAsset={this.assetSelectedHandler}
+          />
+        ) : null;
 
       content = (
         <TabContext value={this.state.selectedTab}>
@@ -770,6 +775,7 @@ Project.propTypes = {
   // This object has the following structure:
   // {
   // }
+  checklist: PropTypes.object,
   configuration: PropTypes.object,
   assetDynamicDetails: PropTypes.object
 };
@@ -780,6 +786,7 @@ Project.defaultProps = {
   onUpdated: null,
   onAssetSelected: null,
   logs: null,
+  checklist: null,
   configuration: null,
   assetDynamicDetails: null
 };
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index a84f754..b0659c4 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -149,8 +149,8 @@ function convertImageToBase64(filePath) {
 
 
 function ReproChecklist(props) {
-  const { project, reproChecklist, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
-  const [checklistItems, setChecklistItems] = useState(reproducibilityChecklist);
+  const { project, checklist, error, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
+  const [checklistItems, setChecklistItems] = useState(checklist);
   const [allImages, setAllImages] = useState([]);
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
@@ -460,57 +460,16 @@ function ReproChecklist(props) {
 
 ReproChecklist.propTypes = {
   project: PropTypes.object.isRequired,
-  reproChecklist: PropTypes.arrayOf(
-    PropTypes.shape({
-      id: PropTypes.string.isRequired,
-      statement: PropTypes.string.isRequired,
-      answer: PropTypes.bool.isRequired,
-      scanResult: PropTypes.objectOf(
-        PropTypes.arrayOf(PropTypes.string)
-      ),
-      userNotes: PropTypes.arrayOf(
-        PropTypes.shape({
-          id: PropTypes.string.isRequired,
-          author: PropTypes.string.isRequired,
-          updated: PropTypes.string.isRequired,
-          content: PropTypes.string.isRequired,
-        })
-      ),
-      attachedImages: PropTypes.arrayOf(
-        PropTypes.shape({
-          id: PropTypes.string.isRequired,
-          uri: PropTypes.string.isRequired,
-          title: PropTypes.string.isRequired,
-          description: PropTypes.string.isRequired,
-          updated: PropTypes.string.isRequired,
-        })
-      ),
-      attachedURLs: PropTypes.arrayOf(
-        PropTypes.shape({
-          id: PropTypes.string.isRequired,
-          hyperlink: PropTypes.string.isRequired,
-          title: PropTypes.string.isRequired,
-          description: PropTypes.string.isRequired,
-          updated: PropTypes.string.isRequired,
-        })
-      ),
-      subChecklist: PropTypes.arrayOf(
-        PropTypes.shape({
-          id: PropTypes.string.isRequired,
-          statement: PropTypes.string.isRequired,
-          answer: PropTypes.bool.isRequired,
-        })
-      ),
-    })
-  ).isRequired,
-  imageAssets: PropTypes.arrayOf(PropTypes.string),
+  checklist: PropTypes.arrayOf(PropTypes.object),
+  error: PropTypes.string,
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
+  onSelectedAsset: PropTypes.func.isRequired,
 };
 
 ReproChecklist.defaultProps = {
-  reproChecklist: reproducibilityChecklist,
+  checklist: reproducibilityChecklist,
 };
 
 export default ReproChecklist;
diff --git a/app/constants/constants.js b/app/constants/constants.js
index 63620f1..dd8c2ea 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -36,6 +36,7 @@ module.exports = {
   StatWrapFiles: {
     BASE_FOLDER: '.statwrap',
     LOG: '.statwrap.log',
+    CHECKLIST: '.statwrap.checklist',
   },
 
   ActionType: {
@@ -64,6 +65,7 @@ module.exports = {
     PROJECT: 'project',
     PERSON: 'person',
     ASSET: 'asset',
+    CHECKLIST: 'checklist',
   },
 
   DescriptionContentType: {
diff --git a/app/constants/messages.js b/app/constants/messages.js
index eb3b976..d1eb172 100644
--- a/app/constants/messages.js
+++ b/app/constants/messages.js
@@ -34,6 +34,11 @@ module.exports = {
   LOAD_PROJECT_LOG_REQUEST: 'statwrap-load-project-log-request',
   LOAD_PROJECT_LOG_RESPONSE: 'statwrap-load-project-log-response',
 
+  WRITE_PROJECT_CHECKLIST_REQUEST: 'statwrap-write-project-checklist-request',
+  WRITE_PROJECT_CHECKLIST_RESPONSE: 'statwrap-write-project-checklist-response',
+  LOAD_PROJECT_CHECKLIST_REQUEST: 'statwrap-load-project-checklist-request',
+  LOAD_PROJECT_CHECKLIST_RESPONSE: 'statwrap-load-project-checklist-response',
+
   // LOAD_PROJECT_CHANGES_REQUEST: 'statwrap-load-project-changes-request',
   // LOAD_PROJECT_CHANGES_RESPONSE: 'statwrap-load-project-changes-response',
 
diff --git a/app/containers/CreateProjectDialog/CreateProjectDialog.js b/app/containers/CreateProjectDialog/CreateProjectDialog.js
index 741ae72..30d90c9 100644
--- a/app/containers/CreateProjectDialog/CreateProjectDialog.js
+++ b/app/containers/CreateProjectDialog/CreateProjectDialog.js
@@ -27,6 +27,50 @@ function PaperComponent(props) {
   );
 }
 
+const reproducibilityChecklist = [
+  {
+    id: '1',
+    statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
+    answer: true,
+    scanResult: {},
+    userNotes: [],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklist: [],
+  },
+  {
+    id: '2',
+    statement: 'Second checklist item statement.',
+    answer: false,
+    scanResult: {},
+    userNotes: [],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklist: [],
+  },
+  {
+    id: '3',
+    statement: 'List of all the languages used and the dependencies of the project.',
+    answer: true,
+    scanResult: {},
+    userNotes: [],
+    attachedImages: [],
+    attachedURLs: [],
+    subChecklist:[
+      {
+        id: '3.1',
+        statement: 'Are all the languages used in the project listed?',
+        answer: true,
+      },
+      {
+        id: '3.2',
+        statement: 'Are all the dependencies of the project listed?',
+        answer: false,
+      },
+    ],
+  }
+];
+
 class CreateProjectDialog extends Component {
   static validateProjectDirectory(step, directory, name) {
     const hasDirectory = directory && directory !== '';
@@ -160,6 +204,11 @@ class CreateProjectDialog extends Component {
           'info',
           this.context,
         );
+        ipcRenderer.send(
+          Messages.WRITE_PROJECT_CHECKLIST_REQUEST,
+          response.project.path,
+          reproducibilityChecklist,
+        )
       }
       this.props.onClose(true);
     } else {
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index 3607bda..9dcf1e6 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -37,6 +37,8 @@ class ProjectPage extends Component {
       // The logs (aka Project Log) for the selected project
       selectedProjectLogs: null,
 
+      selectedProjectChecklist: null,
+
       // UI element to inform us what the popup project list menu is attached to
       projectListMenuAnchor: null,
 
@@ -66,6 +68,7 @@ class ProjectPage extends Component {
     this.handleUpdateProjectResponse = this.handleUpdateProjectResponse.bind(this);
     this.handleLoadProjectLogResponse = this.handleLoadProjectLogResponse.bind(this);
     this.handleRefreshProjectLog = this.handleRefreshProjectLog.bind(this);
+    this.handleLoadProjectChecklistResponse =this.handleLoadProjectChecklistResponse.bind(this);
     this.handleScanAssetDynamicDetailsResponse =
       this.handleScanAssetDynamicDetailsResponse.bind(this);
     this.handleAssetSelected = this.handleAssetSelected.bind(this);
@@ -88,6 +91,9 @@ class ProjectPage extends Component {
     ipcRenderer.on(Messages.LOAD_PROJECT_LOG_RESPONSE, this.handleLoadProjectLogResponse);
     ipcRenderer.on(Messages.WRITE_PROJECT_LOG_RESPONSE, this.handleRefreshProjectLog);
 
+    ipcRenderer.on(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, this.handleLoadProjectChecklistResponse);
+    ipcRenderer.on(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectLog);
+
     ipcRenderer.on(
       Messages.SCAN_ASSET_DYNAMIC_DETAILS_RESPONSE,
       this.handleScanAssetDynamicDetailsResponse,
@@ -123,6 +129,8 @@ class ProjectPage extends Component {
       this.handleLoadProjectLogResponse,
     );
     ipcRenderer.removeListener(Messages.WRITE_PROJECT_LOG_RESPONSE, this.handleRefreshProjectLog);
+    ipcRenderer.removeListener(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, this.handleLoadProjectChecklistResponse);
+    ipcRenderer.removeListener(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectLog);
     ipcRenderer.removeListener(
       Messages.SCAN_ASSET_DYNAMIC_DETAILS_RESPONSE,
       this.handleScanAssetDynamicDetailsResponse,
@@ -160,6 +168,7 @@ class ProjectPage extends Component {
 
   handleRefreshProjectLog() {
     ipcRenderer.send(Messages.LOAD_PROJECT_LOG_REQUEST, this.state.selectedProject);
+    ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, this.state.selectedProject);
   }
 
   /**
@@ -191,6 +200,17 @@ class ProjectPage extends Component {
     }
   }
 
+  handleLoadProjectChecklistResponse(sender, response) {
+    if (!response || !response.projectId) {
+      return;
+    }
+
+    if (this.state.selectedProject && response.projectId === this.state.selectedProject.id) {
+      console.log('ProjectPage.handleLoadProjectChecklistResponse: ', response);
+      this.setState({ selectedProjectChecklist: response });
+    }
+  }
+
   refreshProjectsHandler() {
     this.setState({ loaded: false });
     ipcRenderer.send(Messages.LOAD_PROJECT_LIST_REQUEST);
@@ -203,6 +223,7 @@ class ProjectPage extends Component {
       const foundProject = this.state.projects.find((project) => project.id === response.projectId);
       if (foundProject) {
         ipcRenderer.send(Messages.LOAD_PROJECT_LOG_REQUEST, foundProject);
+        ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, foundProject);
       }
     }
   }
@@ -278,6 +299,7 @@ class ProjectPage extends Component {
     this.setState({ selectedProject: project });
     ipcRenderer.send(Messages.SCAN_PROJECT_REQUEST, project);
     ipcRenderer.send(Messages.LOAD_PROJECT_LOG_REQUEST, project);
+    ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, project);
   }
 
   handleProjectUpdate(project, actionType, entityType, entityKey, title, description, details) {
@@ -350,6 +372,7 @@ class ProjectPage extends Component {
           <Project
             project={this.state.selectedProject}
             logs={this.state.selectedProjectLogs}
+            checklist={this.state.selectedProjectChecklist}
             onUpdated={this.handleProjectUpdate}
             onAssetSelected={this.handleAssetSelected}
             configuration={{ assetAttributes: this.state.assetAttributes }}
diff --git a/app/main.dev.js b/app/main.dev.js
index b403817..9202760 100644
--- a/app/main.dev.js
+++ b/app/main.dev.js
@@ -34,6 +34,7 @@ import AssetsConfig from './constants/assets-config';
 import AssetUtil from './utils/asset';
 import ProjectUtil from './utils/project';
 import LogService from './services/log';
+import ChecklistService from './services/checklist';
 
 // Initialize @electron/remote
 initialize();
@@ -53,6 +54,7 @@ const projectService = new ProjectService();
 const projectListService = new ProjectListService();
 const sourceControlService = new SourceControlService();
 const logService = new LogService();
+const checklistService = new ChecklistService();
 
 // The LogWatcherService requires a window from which we can send messages, so we can't
 // construct it until the BrowserWindow is created.
@@ -664,6 +666,43 @@ ipcMain.on(Messages.LOAD_PROJECT_LOG_REQUEST, async (event, project) => {
   });
 });
 
+ipcMain.on(
+  Messages.WRITE_PROJECT_CHECKLIST_REQUEST,
+  async (event, projectPath, checklist) => {
+    checklistService.writeChecklist(projectPath, checklist);
+    event.sender.send(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE);
+  },
+);
+
+ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
+  const response = {
+    projectId: project ? project.id : null,
+    checklist: null,
+    error: false,
+    errorMessage: '',
+  };
+  if (!project) {
+    response.error = true;
+    response.errorMessage = 'No project was selected';
+    event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
+    return;
+  }
+
+  checklistService.loadChecklists(project.path, (error, checklist) =>{
+    if (error || !checklist) {
+      response.error = true;
+      response.errorMessage = `There was an error reading the project checklist ${error}`;
+      event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
+      return;
+    }
+
+    (async () => {
+      response.checklist = checklist;
+      event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
+    })();
+  });
+});
+
 /**
  * Given a project, update its information and save that information to the project
  * configuration file.
diff --git a/app/services/checklist.js b/app/services/checklist.js
new file mode 100644
index 0000000..ab9c242
--- /dev/null
+++ b/app/services/checklist.js
@@ -0,0 +1,46 @@
+import Constants from '../constants/constants';
+
+const fs = require('fs');
+const path = require('path');
+
+export default class ChecklistService {
+  writeChecklist(projectPath, checklist) {
+    if (!projectPath || !checklist) {
+      throw new Error('Invalid project path or checklist data');
+    }
+
+    const checklistFilePath = path.join(
+      projectPath,
+      Constants.StatWrapFiles.BASE_FOLDER,
+      Constants.StatWrapFiles.CHECKLIST,
+    );
+
+    fs.writeFileSync(checklistFilePath, JSON.stringify(checklist, null, 2), 'utf-8');
+  }
+
+  loadChecklists(projectPath, callback) {
+    if (!projectPath) {
+      callback('The project path must be specified', null);
+      return;
+    }
+
+    const checklistFilePath = path.join(
+      projectPath,
+      Constants.StatWrapFiles.BASE_FOLDER,
+      Constants.StatWrapFiles.CHECKLIST,
+    );
+
+    if (!fs.existsSync(checklistFilePath)) {
+      callback('Checklist file not found', null);
+      return;
+    }
+
+    try {
+      const data = fs.readFileSync(checklistFilePath, 'utf-8');
+      const checklists = JSON.parse(data);
+      callback(null, checklists);
+    } catch (err) {
+      callback('Error reading or parsing checklist file', null);
+    }
+  }
+}

From 13c2ab180b725bb47acd939b5e4ae47c25d96f8b Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 12 Oct 2024 02:05:56 +0530
Subject: [PATCH 26/43] some cleanup and fixes for previous pr

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ReproChecklist/ChecklistItem.js           | 15 ++---
 app/components/ReproChecklist/Modal/Modal.css | 67 -------------------
 app/components/ReproChecklist/Modal/Modal.js  | 46 -------------
 .../ReproChecklist/ReproChecklist.js          | 16 +----
 app/constants/constants.js                    |  1 +
 5 files changed, 10 insertions(+), 135 deletions(-)
 delete mode 100644 app/components/ReproChecklist/Modal/Modal.css
 delete mode 100644 app/components/ReproChecklist/Modal/Modal.js

diff --git a/app/components/ReproChecklist/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem.js
index 433904c..50f23b4 100644
--- a/app/components/ReproChecklist/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem.js
@@ -5,14 +5,14 @@ import NoteEditor from '../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
 import { IconButton, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { FaFolderOpen, FaFolderMinus, FaChevronUp, FaChevronDown } from 'react-icons/fa';
-import Modal from './Modal/Modal';
 import AssetTree from '../AssetTree/AssetTree';
 import AssetUtil from '../../utils/asset';
+import Constants from '../../constants/constants';
 
 const { v4: uuidv4 } = require('uuid');
 
 function ChecklistItem(props) {
-  const { item, project, imageAssets, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate, onSelectedAsset } = props;
+  const { item, project, onUpdatedNote, onDeletedNote, onAddedNote, onItemUpdate, onSelectedAsset } = props;
 
   const treeRef = React.useRef(null);
 
@@ -35,10 +35,10 @@ function ChecklistItem(props) {
     }
 
     if (asset && asset.uri) {
-      if (asset.type === 'file') {
+      if (asset.type === Constants.AssetType.FILE) {
         const fileName = AssetUtil.getAssetNameFromUri(asset.uri);
         setAssetTitle(fileName);
-      } else if (asset.type === 'url') {
+      } else if (asset.type === Constants.AssetType.URL) {
         setAssetTitle(asset.uri);
       } else {
         setAssetTitle('');
@@ -61,8 +61,8 @@ function ChecklistItem(props) {
       return;
     }
 
-    if (selectedAsset.type === 'file') {
-      if(selectedAsset.contentTypes.includes('image')) {
+    if (selectedAsset.type === Constants.AssetType.FILE) {
+      if(selectedAsset.contentTypes.includes(Constants.AssetContentType.IMAGE)) {
         const updatedItem = { ...item, attachedImages: [...item.attachedImages, {id: uuidv4(), uri: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
         onItemUpdate(updatedItem);
         setShowImages(true);
@@ -71,7 +71,7 @@ function ChecklistItem(props) {
         onItemUpdate(updatedItem);
         setShowURLs(true);
       }
-    } else if (selectedAsset.type === 'url') {
+    } else if (selectedAsset.type === Constants.AssetType.URL) {
       const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, {id: uuidv4(), hyperlink: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
       onItemUpdate(updatedItem);
       setShowURLs(true);
@@ -410,7 +410,6 @@ ChecklistItem.propTypes = {
     ),
   }).isRequired,
   project: PropTypes.object.isRequired,
-  imageAssets: PropTypes.arrayOf(PropTypes.string),
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
diff --git a/app/components/ReproChecklist/Modal/Modal.css b/app/components/ReproChecklist/Modal/Modal.css
deleted file mode 100644
index 5368cb4..0000000
--- a/app/components/ReproChecklist/Modal/Modal.css
+++ /dev/null
@@ -1,67 +0,0 @@
-.modal {
-  display: flex;
-  justify-content: center;
-  align-items: center;
-}
-
-.form {
-  background-color: #fff;
-  padding: 20px;
-  padding-top: 0px;
-  border-radius: 8px;
-  max-width: 300px;
-  width: 100%;
-  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-}
-
-.header {
-  display:flex;
-  justify-content: center;
-}
-
-.title {
-  display: flex;
-  justify-content: space-evenly;
-}
-.description {
-  display: flex;
-  justify-content: space-evenly;
-  height: 50px;
-  margin-top: 10px;
-}
-
-.submit {
-  display: flex;
-  justify-content: end;
-  margin-top: 5px;
-}
-
-.submitButton {
-  background-color: #aa94d1;
-  color: #000;
-  border: none;
-  cursor: pointer;
-  padding: 5px 10px;
-  border-radius: 4px;
-  font-size: 15px;
-  transition: background-color 0.3s ease;
-}
-
-.submitButton:hover {
-  opacity: 0.9;
-}
-
-.cancelButton {
-  background-color: #ccc;
-  color: #000;
-  border: none;
-  cursor: pointer;
-  padding: 5px 10px;
-  border-radius: 4px;
-  font-size: 15px;
-  transition: background-color 0.3s ease;
-}
-
-.cancelButton:hover {
-  opacity: 0.9;
-}
diff --git a/app/components/ReproChecklist/Modal/Modal.js b/app/components/ReproChecklist/Modal/Modal.js
deleted file mode 100644
index 343f248..0000000
--- a/app/components/ReproChecklist/Modal/Modal.js
+++ /dev/null
@@ -1,46 +0,0 @@
-import React from 'react';
-import PropTypes from 'prop-types';
-import styles from './Modal.css';
-import { Modal } from '@mui/material';
-
-function AttachModal(props) {
-  const { isOpen, onClose, onSubmit, title, component } = props;
-  return (
-    <Modal
-          open={isOpen}
-          onClose={onClose}
-          aria-labelledby="modal-title"
-          aria-describedby="modal-description"
-          className={styles.modal}
-    >
-      <form onSubmit = {onSubmit} className={styles.form}>
-          <div className={styles.header}>
-            <h3>Attach {title}</h3>
-          </div>
-          {component}
-          <div className={styles.title}>
-            <label htmlFor="title">Title:</label>
-            <input type="text" id="title" name="title" required/>
-          </div>
-          <div className={styles.description}>
-            <label htmlFor="description">Description:</label>
-            <textarea id="description" name="description" required/>
-          </div>
-          <div className={styles.submit}>
-            <button type="submit" className={styles.submitButton}>Submit</button>
-            <button type="button" className={styles.cancelButton} onClick = {onClose}>Cancel</button>
-          </div>
-        </form>
-    </Modal>
-  );
-}
-
-AttachModal.propTypes = {
-  isOpen: PropTypes.bool.isRequired,
-  onClose: PropTypes.func.isRequired,
-  onSubmit: PropTypes.func.isRequired,
-  title: PropTypes.string.isRequired,
-  component: PropTypes.element.isRequired,
-};
-
-export default AttachModal;
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index b0659c4..a229920 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -2,6 +2,7 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ReproChecklist.css';
 import ChecklistItem from './ChecklistItem';
+import Constants from '../../constants/constants';
 import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { SaveAlt } from '@mui/icons-material';
 import pdfMake from 'pdfmake/build/pdfmake';
@@ -62,7 +63,7 @@ const dependencies = {};
 const imageAssets = {};
 
 function findAssetLanguagesAndDependencies(asset) {
-  if (asset.type === 'file' && asset.contentTypes.includes('code') ) {
+  if (asset.type === Constants.AssetType.FILE && asset.contentTypes.includes(Constants.AssetContentType.CODE) ) {
     const lastSep = asset.uri.lastIndexOf(path.sep);
     const fileName = asset.uri.substring(lastSep + 1);
     const ext = fileName.split('.').pop();
@@ -85,15 +86,6 @@ function findAssetLanguagesAndDependencies(asset) {
   };
 }
 
-function findImageAssets(asset) {
-  if (asset.type === 'file' && asset.contentTypes.includes('image')) {
-    imageAssets[asset.uri] = true;
-  }
-  if (asset.children) {
-    asset.children.forEach(findImageAssets);
-  }
-};
-
 function findChecklistNotes(notes) {
   const checklistNotes = {};
   notes.forEach((note) => {
@@ -151,15 +143,12 @@ function convertImageToBase64(filePath) {
 function ReproChecklist(props) {
   const { project, checklist, error, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
   const [checklistItems, setChecklistItems] = useState(checklist);
-  const [allImages, setAllImages] = useState([]);
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
   useEffect(() => {
     if (project) {
       if(project.assets) {
         findAssetLanguagesAndDependencies(project.assets);
-        findImageAssets(project.assets);
-        setAllImages(Object.keys(imageAssets));
       }
       if(project.notes){
         const checklistNotes = findChecklistNotes(project.notes);
@@ -416,7 +405,6 @@ function ReproChecklist(props) {
           key={item.id}
           item={item}
           project={project}
-          imageAssets={allImages}
           onUpdatedNote={onUpdatedNote}
           onDeletedNote={onDeletedNote}
           onAddedNote={onAddedNote}
diff --git a/app/constants/constants.js b/app/constants/constants.js
index dd8c2ea..bdb3884 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -17,6 +17,7 @@ module.exports = {
     DIRECTORY: 'directory',
     FOLDER: 'directory', // 'DIRECTORY' is the preferred name, but we know we'll use this sometimes
     FILE: 'file',
+    URL: 'url',
     GENERIC: 'generic',
 
     // These are not a real asset types, but are used in our various controls

From 7edd4385f954abce470721d1df75977c15e1a56c Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 12 Oct 2024 19:53:23 +0530
Subject: [PATCH 27/43] proper content rendering on checklist tab

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/ReproChecklist/ReproChecklist.css |  9 +++++++++
 app/components/ReproChecklist/ReproChecklist.js  | 15 +++++++++++----
 app/containers/ProjectPage/ProjectPage.js        |  1 -
 app/services/checklist.js                        |  9 +++++----
 4 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/app/components/ReproChecklist/ReproChecklist.css b/app/components/ReproChecklist/ReproChecklist.css
index 6c30d4b..de475d1 100644
--- a/app/components/ReproChecklist/ReproChecklist.css
+++ b/app/components/ReproChecklist/ReproChecklist.css
@@ -1,3 +1,12 @@
+.empty {
+  padding: 8px;
+  border-radius: 6px;
+  background-color: #eee;
+  border: solid 1px gray;
+  font-style: italic;
+  margin-top: 15px;
+}
+
 .downloadContainer {
   position: fixed;
   bottom: 10px;
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index a229920..0d5b88f 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -2,6 +2,7 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ReproChecklist.css';
 import ChecklistItem from './ChecklistItem';
+import Error from '../Error/Error';
 import Constants from '../../constants/constants';
 import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { SaveAlt } from '@mui/icons-material';
@@ -146,7 +147,7 @@ function ReproChecklist(props) {
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
   useEffect(() => {
-    if (project) {
+    if (project && checklist && !error) {
       if(project.assets) {
         findAssetLanguagesAndDependencies(project.assets);
       }
@@ -396,7 +397,10 @@ function ReproChecklist(props) {
     setOpenExportDialog(false);
   };
 
-  return (
+  let content = <div className={styles.empty}>No checklists configured.</div>;
+
+  if (checklist) {
+    content =
     <div>
       <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklist</Typography>
       <br />
@@ -441,9 +445,12 @@ function ReproChecklist(props) {
           </Button>
         </DialogActions>
       </Dialog>
-
     </div>
-  );
+  } else if (error) {
+    content = <Error>There was an error loading the project checklist: {error}</Error>;
+  }
+
+  return <div>{content}</div>;
 }
 
 ReproChecklist.propTypes = {
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index 9dcf1e6..ca40702 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -206,7 +206,6 @@ class ProjectPage extends Component {
     }
 
     if (this.state.selectedProject && response.projectId === this.state.selectedProject.id) {
-      console.log('ProjectPage.handleLoadProjectChecklistResponse: ', response);
       this.setState({ selectedProjectChecklist: response });
     }
   }
diff --git a/app/services/checklist.js b/app/services/checklist.js
index ab9c242..29ad2b1 100644
--- a/app/services/checklist.js
+++ b/app/services/checklist.js
@@ -1,6 +1,7 @@
 import Constants from '../constants/constants';
 
 const fs = require('fs');
+const os = require('os');
 const path = require('path');
 
 export default class ChecklistService {
@@ -10,12 +11,12 @@ export default class ChecklistService {
     }
 
     const checklistFilePath = path.join(
-      projectPath,
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
       Constants.StatWrapFiles.CHECKLIST,
     );
 
-    fs.writeFileSync(checklistFilePath, JSON.stringify(checklist, null, 2), 'utf-8');
+    fs.writeFileSync(checklistFilePath, JSON.stringify(checklist));
   }
 
   loadChecklists(projectPath, callback) {
@@ -25,7 +26,7 @@ export default class ChecklistService {
     }
 
     const checklistFilePath = path.join(
-      projectPath,
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
       Constants.StatWrapFiles.CHECKLIST,
     );
@@ -36,7 +37,7 @@ export default class ChecklistService {
     }
 
     try {
-      const data = fs.readFileSync(checklistFilePath, 'utf-8');
+      const data = fs.readFileSync(checklistFilePath);
       const checklists = JSON.parse(data);
       callback(null, checklists);
     } catch (err) {

From 9c9eebfd7acde2f8dd22bc0676d6666017320d14 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 12 Oct 2024 19:57:31 +0530
Subject: [PATCH 28/43] follow folder-structure convention

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ReproChecklist/{ => ChecklistItem}/ChecklistItem.css  | 0
 .../ReproChecklist/{ => ChecklistItem}/ChecklistItem.js   | 8 ++++----
 app/components/ReproChecklist/ReproChecklist.js           | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename app/components/ReproChecklist/{ => ChecklistItem}/ChecklistItem.css (100%)
 rename app/components/ReproChecklist/{ => ChecklistItem}/ChecklistItem.js (98%)

diff --git a/app/components/ReproChecklist/ChecklistItem.css b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.css
similarity index 100%
rename from app/components/ReproChecklist/ChecklistItem.css
rename to app/components/ReproChecklist/ChecklistItem/ChecklistItem.css
diff --git a/app/components/ReproChecklist/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
similarity index 98%
rename from app/components/ReproChecklist/ChecklistItem.js
rename to app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index 50f23b4..73a1879 100644
--- a/app/components/ReproChecklist/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -1,13 +1,13 @@
 import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
-import NoteEditor from '../NoteEditor/NoteEditor';
+import NoteEditor from '../../NoteEditor/NoteEditor';
 import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
 import { IconButton, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { FaFolderOpen, FaFolderMinus, FaChevronUp, FaChevronDown } from 'react-icons/fa';
-import AssetTree from '../AssetTree/AssetTree';
-import AssetUtil from '../../utils/asset';
-import Constants from '../../constants/constants';
+import AssetTree from '../../AssetTree/AssetTree';
+import AssetUtil from '../../../utils/asset';
+import Constants from '../../../constants/constants';
 
 const { v4: uuidv4 } = require('uuid');
 
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index 0d5b88f..dea9a9f 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -1,7 +1,7 @@
 import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ReproChecklist.css';
-import ChecklistItem from './ChecklistItem';
+import ChecklistItem from './ChecklistItem/ChecklistItem';
 import Error from '../Error/Error';
 import Constants from '../../constants/constants';
 import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';

From 41c84ac37647c6ea8a0f3a15340bc31156082394 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 12 Oct 2024 20:41:18 +0530
Subject: [PATCH 29/43] checklistItems validation before mapping

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/ReproChecklist/ReproChecklist.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index dea9a9f..5d57274 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -397,14 +397,14 @@ function ReproChecklist(props) {
     setOpenExportDialog(false);
   };
 
-  let content = <div className={styles.empty}>No checklists configured.</div>;
+  let content = <div className={styles.empty}>Checklist not configured.</div>;
 
   if (checklist) {
     content =
     <div>
       <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklist</Typography>
       <br />
-      {checklistItems.map(item => (
+      {checklistItems?.map(item => (
         <ChecklistItem
           key={item.id}
           item={item}

From 832077bb049e344d5972dbb81211dfcb2360d407 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sun, 13 Oct 2024 01:59:55 +0530
Subject: [PATCH 30/43] minor fixes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/ReproChecklist/ReproChecklist.js | 4 ++--
 app/containers/ProjectPage/ProjectPage.js       | 8 ++++++--
 app/main.dev.js                                 | 8 +++-----
 app/services/checklist.js                       | 2 +-
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index 5d57274..bdd3cb9 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -399,12 +399,12 @@ function ReproChecklist(props) {
 
   let content = <div className={styles.empty}>Checklist not configured.</div>;
 
-  if (checklist) {
+  if (checklist && checklistItems) {
     content =
     <div>
       <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklist</Typography>
       <br />
-      {checklistItems?.map(item => (
+      {checklistItems.map(item => (
         <ChecklistItem
           key={item.id}
           item={item}
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index ca40702..70ac5c3 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -68,6 +68,7 @@ class ProjectPage extends Component {
     this.handleUpdateProjectResponse = this.handleUpdateProjectResponse.bind(this);
     this.handleLoadProjectLogResponse = this.handleLoadProjectLogResponse.bind(this);
     this.handleRefreshProjectLog = this.handleRefreshProjectLog.bind(this);
+    this.handleRefreshProjectChecklist = this.handleRefreshProjectChecklist.bind(this);
     this.handleLoadProjectChecklistResponse =this.handleLoadProjectChecklistResponse.bind(this);
     this.handleScanAssetDynamicDetailsResponse =
       this.handleScanAssetDynamicDetailsResponse.bind(this);
@@ -92,7 +93,7 @@ class ProjectPage extends Component {
     ipcRenderer.on(Messages.WRITE_PROJECT_LOG_RESPONSE, this.handleRefreshProjectLog);
 
     ipcRenderer.on(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, this.handleLoadProjectChecklistResponse);
-    ipcRenderer.on(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectLog);
+    ipcRenderer.on(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectChecklist);
 
     ipcRenderer.on(
       Messages.SCAN_ASSET_DYNAMIC_DETAILS_RESPONSE,
@@ -130,7 +131,7 @@ class ProjectPage extends Component {
     );
     ipcRenderer.removeListener(Messages.WRITE_PROJECT_LOG_RESPONSE, this.handleRefreshProjectLog);
     ipcRenderer.removeListener(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, this.handleLoadProjectChecklistResponse);
-    ipcRenderer.removeListener(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectLog);
+    ipcRenderer.removeListener(Messages.WRITE_PROJECT_CHECKLIST_RESPONSE, this.handleRefreshProjectChecklist);
     ipcRenderer.removeListener(
       Messages.SCAN_ASSET_DYNAMIC_DETAILS_RESPONSE,
       this.handleScanAssetDynamicDetailsResponse,
@@ -168,6 +169,9 @@ class ProjectPage extends Component {
 
   handleRefreshProjectLog() {
     ipcRenderer.send(Messages.LOAD_PROJECT_LOG_REQUEST, this.state.selectedProject);
+  }
+
+  handleRefreshProjectChecklist() {
     ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, this.state.selectedProject);
   }
 
diff --git a/app/main.dev.js b/app/main.dev.js
index 9202760..24b46fa 100644
--- a/app/main.dev.js
+++ b/app/main.dev.js
@@ -688,7 +688,7 @@ ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
     return;
   }
 
-  checklistService.loadChecklists(project.path, (error, checklist) =>{
+  checklistService.loadChecklist(project.path, (error, checklist) =>{
     if (error || !checklist) {
       response.error = true;
       response.errorMessage = `There was an error reading the project checklist ${error}`;
@@ -696,10 +696,8 @@ ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
       return;
     }
 
-    (async () => {
-      response.checklist = checklist;
-      event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
-    })();
+    response.checklist = checklist;
+    event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
   });
 });
 
diff --git a/app/services/checklist.js b/app/services/checklist.js
index 29ad2b1..8025d8a 100644
--- a/app/services/checklist.js
+++ b/app/services/checklist.js
@@ -19,7 +19,7 @@ export default class ChecklistService {
     fs.writeFileSync(checklistFilePath, JSON.stringify(checklist));
   }
 
-  loadChecklists(projectPath, callback) {
+  loadChecklist(projectPath, callback) {
     if (!projectPath) {
       callback('The project path must be specified', null);
       return;

From 97bd52cae775b5b2306eb109f0cda2c1772168e9 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 15 Oct 2024 01:37:43 +0530
Subject: [PATCH 31/43] seeds empty checklist for existing projects, handles
 writing to checklist file on update...

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             |  3 +
 .../ChecklistItem/ChecklistItem.js            | 30 ++++++--
 .../ReproChecklist/ReproChecklist.js          | 76 +++++--------------
 app/constants/constants.js                    | 11 ++-
 .../CreateProjectDialog.js                    | 48 +-----------
 app/containers/ProjectPage/ProjectPage.js     | 14 ++++
 app/main.dev.js                               |  2 +-
 app/services/checklist.js                     |  2 +-
 app/utils/checklist.js                        | 20 +++++
 9 files changed, 95 insertions(+), 111 deletions(-)
 create mode 100644 app/utils/checklist.js

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index d21d267..ecbcb43 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -688,6 +688,7 @@ class Project extends Component<Props> {
             project={this.props.project}
             checklist={this.props.checklist.checklist}
             error={this.props.checklist.errorMessage}
+            onUpdated={this.props.onChecklistUpdated}
             onAddedNote={this.projectUpsertNoteHandler}
             onUpdatedNote={this.projectUpsertNoteHandler}
             onDeletedNote={this.projectDeleteNoteHandler}
@@ -763,6 +764,7 @@ Project.propTypes = {
   classes: PropTypes.object,
   onUpdated: PropTypes.func,
   onAssetSelected: PropTypes.func,
+  onChecklistUpdated: PropTypes.func,
   // This object has the following structure:
   // {
   //   logs: array<string>   - the actual log data
@@ -785,6 +787,7 @@ Project.defaultProps = {
   classes: null,
   onUpdated: null,
   onAssetSelected: null,
+  onChecklistUpdated: null,
   logs: null,
   checklist: null,
   configuration: null,
diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index 73a1879..1aa832f 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -135,17 +135,23 @@ function ChecklistItem(props) {
           <button
             className={item.answer ? styles.yesset : styles.yes}
             onClick={() => {
-              const updatedItem = { ...item, answer: true };
-              onItemUpdate(updatedItem);
+              const oldAnswer = item.answer;
+              if (oldAnswer === false) {
+                const updatedItem = { ...item, answer: true };
+                onItemUpdate(updatedItem);
+              }
             }}
           >
             {'Yes'}
           </button>
           <button
-            className={item.answer  ? styles.no : styles.noset}
+            className={item.answer ? styles.no : styles.noset}
             onClick={() => {
-              const updatedItem = { ...item, answer: false };
-              onItemUpdate(updatedItem);
+              const oldAnswer = item.answer;
+              if (oldAnswer == true) {
+                const updatedItem = { ...item, answer: false };
+                onItemUpdate(updatedItem);
+              }
             }}
           >
             {'No'}
@@ -331,13 +337,17 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.yesset : styles.yes}
                         onClick={() => {
+                          let oldAnswer = false;
                           const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
                             if (sub.id === subCheck.id) {
+                              oldAnswer = sub.answer;
                               return { ...sub, answer: true };
                             }
                             return sub;
                           })};
-                          onItemUpdate(updatedItem);
+                          if (oldAnswer === false) {
+                            onItemUpdate(updatedItem);
+                          }
                         }}
                       >
                         {'Yes'}
@@ -345,13 +355,17 @@ function ChecklistItem(props) {
                       <button
                         className={subCheck.answer ? styles.no : styles.noset}
                         onClick={() => {
+                          let oldAnswer = true;
                           const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
                             if (sub.id === subCheck.id) {
+                              oldAnswer = sub.answer;
                               return { ...sub, answer: false };
                             }
                             return sub;
                           })};
-                          onItemUpdate(updatedItem);
+                          if (oldAnswer === true) {
+                            onItemUpdate(updatedItem);
+                          }
                         }}
                       >
                         {'No'}
@@ -413,6 +427,8 @@ ChecklistItem.propTypes = {
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
+  onItemUpdate: PropTypes.func.isRequired,
+  onSelectedAsset: PropTypes.func.isRequired,
 };
 
 export default ChecklistItem;
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index bdd3cb9..08fc5b4 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -15,50 +15,6 @@ const path = require('path');
 const fs = require('fs');
 const AssetsConfig = require('../../constants/assets-config');
 
-const reproducibilityChecklist = [
-  {
-    id: '1',
-    statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
-    answer: true,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist: [],
-  },
-  {
-    id: '2',
-    statement: 'Second checklist item statement.',
-    answer: false,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist: [],
-  },
-  {
-    id: '3',
-    statement: 'List of all the languages used and the dependencies of the project.',
-    answer: true,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist:[
-      {
-        id: '3.1',
-        statement: 'Are all the languages used in the project listed?',
-        answer: true,
-      },
-      {
-        id: '3.2',
-        statement: 'Are all the dependencies of the project listed?',
-        answer: false,
-      },
-    ],
-  }
-];
-
 const languages = {};
 const dependencies = {};
 const imageAssets = {};
@@ -81,7 +37,7 @@ function findAssetLanguagesAndDependencies(asset) {
     asset.children.forEach(findAssetLanguagesAndDependencies);
   }
 
-  reproducibilityChecklist[2].scanResult = {
+  return {
     languages: Object.keys(languages),
     dependencies: Object.keys(dependencies)
   };
@@ -142,18 +98,18 @@ function convertImageToBase64(filePath) {
 
 
 function ReproChecklist(props) {
-  const { project, checklist, error, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
-  const [checklistItems, setChecklistItems] = useState(checklist);
+  const { project, checklist, error, onUpdated, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
   useEffect(() => {
     if (project && checklist && !error) {
       if(project.assets) {
-        findAssetLanguagesAndDependencies(project.assets);
+        const scanResult1 = findAssetLanguagesAndDependencies(project.assets);
+        checklist[0].scanResult = scanResult1;
       }
       if(project.notes){
         const checklistNotes = findChecklistNotes(project.notes);
-        const updatedChecklistItems = checklistItems.map((item) => {
+        const updatedChecklist = checklist.map((item) => {
           if (checklistNotes[item.id]) {
             return {
               ...item,
@@ -162,16 +118,16 @@ function ReproChecklist(props) {
           }
           return item;
         });
-        setChecklistItems(updatedChecklistItems);
+        // tbd
       }
     }
   }, [project]);
 
   const handleItemUpdate = (updatedItem) => {
-    const updatedChecklistItems = checklistItems.map(item =>
+    const updatedChecklist = checklist.map(item =>
       item.id === updatedItem.id ? updatedItem : item
     );
-    setChecklistItems(updatedChecklistItems);
+    onUpdated(project, updatedChecklist);
   };
 
   const handleReportGeneration = (exportNotes) => {
@@ -231,7 +187,7 @@ function ReproChecklist(props) {
             },
           ],
         },
-        ...checklistItems.map((item, index) => {
+        ...checklist.map((item, index) => {
           const maxWidth = 450;
           let subChecklist = [];
           if (item.subChecklist && item.subChecklist.length > 0) {
@@ -399,12 +355,12 @@ function ReproChecklist(props) {
 
   let content = <div className={styles.empty}>Checklist not configured.</div>;
 
-  if (checklist && checklistItems) {
+  if (checklist && checklist.length > 0) {
     content =
     <div>
       <Typography variant='h5' align='center' marginTop='10px'>Reproducibility Checklist</Typography>
       <br />
-      {checklistItems.map(item => (
+      {checklist.map(item => (
         <ChecklistItem
           key={item.id}
           item={item}
@@ -457,6 +413,7 @@ ReproChecklist.propTypes = {
   project: PropTypes.object.isRequired,
   checklist: PropTypes.arrayOf(PropTypes.object),
   error: PropTypes.string,
+  onUpdated: PropTypes.func.isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
   onAddedNote: PropTypes.func.isRequired,
@@ -464,7 +421,14 @@ ReproChecklist.propTypes = {
 };
 
 ReproChecklist.defaultProps = {
-  checklist: reproducibilityChecklist,
+  project: null,
+  checklist: null,
+  error: null,
+  onUpdated: null,
+  onUpdatedNote: null,
+  onDeletedNote: null,
+  onAddedNote: null,
+  onSelectedAsset: null,
 };
 
 export default ReproChecklist;
diff --git a/app/constants/constants.js b/app/constants/constants.js
index bdb3884..fcfbc2f 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -37,7 +37,7 @@ module.exports = {
   StatWrapFiles: {
     BASE_FOLDER: '.statwrap',
     LOG: '.statwrap.log',
-    CHECKLIST: '.statwrap.checklist',
+    CHECKLIST: '.statwrap-checklist.json',
   },
 
   ActionType: {
@@ -95,4 +95,13 @@ module.exports = {
   },
 
   MAX_GRAPH_LABEL_LENGTH: 31,
+
+  CHECKLIST_STATEMENTS: [
+    'All the software dependencies for the project are documented.',
+    'All the data file(s) used in the project are documented.',
+    'Clearly indicates which file(s) are used to run analysis.',
+    'Includes all necessary project documentation.',
+    'Are there multiple versions of a file? If yes, specify the versions.',
+    'Avoids using absolute paths in the code.',
+  ],
 };
diff --git a/app/containers/CreateProjectDialog/CreateProjectDialog.js b/app/containers/CreateProjectDialog/CreateProjectDialog.js
index 30d90c9..5f1119d 100644
--- a/app/containers/CreateProjectDialog/CreateProjectDialog.js
+++ b/app/containers/CreateProjectDialog/CreateProjectDialog.js
@@ -15,6 +15,7 @@ import NewDirectory from '../../components/NewDirectory/NewDirectory';
 import CloneDirectory from './CloneDirectory/CloneDirectory';
 import Error from '../../components/Error/Error';
 import UserContext from '../../contexts/User';
+import ChecklistUtil from '../../utils/checklist';
 
 import styles from './CreateProjectDialog.css';
 import Messages from '../../constants/messages';
@@ -27,50 +28,6 @@ function PaperComponent(props) {
   );
 }
 
-const reproducibilityChecklist = [
-  {
-    id: '1',
-    statement: 'First checklist item statement. Now, I am just trying to make this statement a bit longer to see how it looks in the UI, without making any sense.',
-    answer: true,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist: [],
-  },
-  {
-    id: '2',
-    statement: 'Second checklist item statement.',
-    answer: false,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist: [],
-  },
-  {
-    id: '3',
-    statement: 'List of all the languages used and the dependencies of the project.',
-    answer: true,
-    scanResult: {},
-    userNotes: [],
-    attachedImages: [],
-    attachedURLs: [],
-    subChecklist:[
-      {
-        id: '3.1',
-        statement: 'Are all the languages used in the project listed?',
-        answer: true,
-      },
-      {
-        id: '3.2',
-        statement: 'Are all the dependencies of the project listed?',
-        answer: false,
-      },
-    ],
-  }
-];
-
 class CreateProjectDialog extends Component {
   static validateProjectDirectory(step, directory, name) {
     const hasDirectory = directory && directory !== '';
@@ -204,10 +161,11 @@ class CreateProjectDialog extends Component {
           'info',
           this.context,
         );
+        const projectChecklist = ChecklistUtil.initializeChecklist();
         ipcRenderer.send(
           Messages.WRITE_PROJECT_CHECKLIST_REQUEST,
           response.project.path,
-          reproducibilityChecklist,
+          projectChecklist,
         )
       }
       this.props.onClose(true);
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index 70ac5c3..3a9e9e9 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -12,6 +12,7 @@ import styles from './ProjectPage.css';
 import UserContext from '../../contexts/User';
 
 import Messages from '../../constants/messages';
+import ChecklistUtil from '../../utils/checklist';
 
 class ProjectPage extends Component {
   constructor(props) {
@@ -175,6 +176,10 @@ class ProjectPage extends Component {
     ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, this.state.selectedProject);
   }
 
+  handleChecklistUpdate(project, checklist) {
+    ipcRenderer.send(Messages.WRITE_PROJECT_CHECKLIST_REQUEST, project.path, checklist);
+  }
+
   /**
    * Called when a project log is loaded.
    *
@@ -209,6 +214,14 @@ class ProjectPage extends Component {
       return;
     }
 
+    // Initialize the checklist file if it doesn't exist, for all the already existing projects
+    const projectChecklist = ChecklistUtil.initializeChecklist();
+    if (response.checklist && response.checklist.length === 0) {
+      // response only returns project id, we need to get the project path
+      const project = this.state.projects.find((p) => p.id === response.projectId);
+      ipcRenderer.send(Messages.WRITE_PROJECT_CHECKLIST_REQUEST, project.path, projectChecklist);
+    }
+
     if (this.state.selectedProject && response.projectId === this.state.selectedProject.id) {
       this.setState({ selectedProjectChecklist: response });
     }
@@ -378,6 +391,7 @@ class ProjectPage extends Component {
             checklist={this.state.selectedProjectChecklist}
             onUpdated={this.handleProjectUpdate}
             onAssetSelected={this.handleAssetSelected}
+            onChecklistUpdated={this.handleChecklistUpdate}
             configuration={{ assetAttributes: this.state.assetAttributes }}
             assetDynamicDetails={this.state.assetDynamicDetails}
           />
diff --git a/app/main.dev.js b/app/main.dev.js
index 24b46fa..863b9cc 100644
--- a/app/main.dev.js
+++ b/app/main.dev.js
@@ -689,7 +689,7 @@ ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
   }
 
   checklistService.loadChecklist(project.path, (error, checklist) =>{
-    if (error || !checklist) {
+    if (error && !checklist) {
       response.error = true;
       response.errorMessage = `There was an error reading the project checklist ${error}`;
       event.sender.send(Messages.LOAD_PROJECT_CHECKLIST_RESPONSE, response);
diff --git a/app/services/checklist.js b/app/services/checklist.js
index 8025d8a..d3b1463 100644
--- a/app/services/checklist.js
+++ b/app/services/checklist.js
@@ -32,7 +32,7 @@ export default class ChecklistService {
     );
 
     if (!fs.existsSync(checklistFilePath)) {
-      callback('Checklist file not found', null);
+      callback('Checklist file not found', []);
       return;
     }
 
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
new file mode 100644
index 0000000..2732443
--- /dev/null
+++ b/app/utils/checklist.js
@@ -0,0 +1,20 @@
+import Constants from '../constants/constants';
+
+export default class ChecklistUtil {
+  static initializeChecklist() {
+    const checklist = [];
+    Constants.CHECKLIST_STATEMENTS.forEach((statement, index) => {
+      checklist.push({
+        id: index + 1,
+        statement: statement,
+        answer: false,
+        scanResult: {},
+        userNotes: [],
+        attachedImages: [],
+        attachedURLs: [],
+        subChecklist: [],
+      });
+    });
+    return checklist;
+  }
+}

From 33b8c99cd88f4d5de3d4f91dfc4204f058ad7219 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 15 Oct 2024 02:03:14 +0530
Subject: [PATCH 32/43] validate checklist item

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ChecklistItem/ChecklistItem.js            | 496 +++++++++---------
 1 file changed, 250 insertions(+), 246 deletions(-)

diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index 1aa832f..82897dd 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -125,260 +125,264 @@ function ChecklistItem(props) {
   };
 
   return (
-    <div className={styles.item}>
-      <div className={styles.statementHeader}>
-        <button className={styles.expandButton}>
-          {expanded ? <FaChevronUp className={styles.chevron} onClick={() => setExpanded(false)} /> : <FaChevronDown  className={styles.chevron} onClick={() => setExpanded(true)} />}
-        </button>
-        <span className={styles.statement}>{item.id}. {item.statement}</span>
-        <div className={styles.buttonContainer}>
-          <button
-            className={item.answer ? styles.yesset : styles.yes}
-            onClick={() => {
-              const oldAnswer = item.answer;
-              if (oldAnswer === false) {
-                const updatedItem = { ...item, answer: true };
-                onItemUpdate(updatedItem);
-              }
-            }}
-          >
-            {'Yes'}
-          </button>
-          <button
-            className={item.answer ? styles.no : styles.noset}
-            onClick={() => {
-              const oldAnswer = item.answer;
-              if (oldAnswer == true) {
-                const updatedItem = { ...item, answer: false };
-                onItemUpdate(updatedItem);
-              }
-            }}
-          >
-            {'No'}
-          </button>
-        </div>
-      </div>
-      {expanded && <div className={styles.details}>
-        <div className={styles.scanResult}>
-          {item.scanResult &&
-            Object.keys(item.scanResult).map((key) => {
-              return (
-              <div key={key}>
-                <span className={styles.scanKey}>{key}</span>
-                <ul className={styles.scanList}>
-                  {item.scanResult[key].length ? (
-                    item.scanResult[key].map((answer) => (
-                      <li key={answer}>{answer}</li>
-                    ))
-                  ) : (
-                    <li>No answers available</li>
-                  )}
-                </ul>
-              </div>
-            )})}
-        </div>
-        <NoteEditor
-          notes={item.userNotes}
-          onEditingComplete={handleNoteUpdate}
-          onDelete={handleNoteDelete}
-        />
-        <div>
-          <button className={styles.addUrlsButton} onClick={() => setAddAsset(true)}>
-            Add Asset Reference
-          </button>
-        </div>
-        <Dialog open={addAsset} onClose={() => setAddAsset(false)}>
-          <DialogTitle className={styles.dialogTitle}>Add Asset Reference</DialogTitle>
-          <DialogContent className={styles.dialogContent}>
-            <div className={styles.tree}>
-              <div className={styles.toolbar}>
-                <IconButton
-                  onClick={() => treeRef.current.setExpandAll(true)}
-                  className={styles.toolbarButton}
-                  aria-label="expand all tree items"
-                  fontSize="small"
-                >
-                  <FaFolderOpen fontSize="small" /> &nbsp;Expand
-                </IconButton>
-                <IconButton
-                  className={styles.toolbarButton}
-                  aria-label="collapse all tree items"
-                  fontSize="small"
-                  onClick={() => treeRef.current.setExpandAll(false)}
-                >
-                  <FaFolderMinus fontSize="small" /> &nbsp;Collapse
-                </IconButton>
-              </div>
-              <AssetTree
-                assets={project.assets}
-                ref={treeRef}
-                onSelectAsset={handleSelectAsset}
-                selectedAsset={selectedAsset}
-              />
-            </div>
-            <div className={styles.form}>
-              <div className={styles.title}>
-                <label htmlFor="title">Title:</label>
-                <input
-                  type="text"
-                  id="title"
-                  name="title"
-                  value={assetTitle}
-                  onChange={(e) => setAssetTitle(e.target.value)}
-                  required
-                />
-              </div>
-              <div className={styles.description}>
-                <label htmlFor="description">Description:</label>
-                <input
-                  id="description"
-                  name="description"
-                  value={assetDescription}
-                  onChange={(e) => setAssetDescription(e.target.value)}
-                />
-              </div>
-            </div>
-          </DialogContent>
-          <DialogActions>
-            <button onClick={() => handleAddAsset()} className={styles.submitButton}>
-              Add
-            </button>
-            <button onClick={() => setAddAsset(false)} className={styles.cancelButton} autoFocus>
-              Cancel
+    <div>
+      {item && (
+        <div className={styles.item}>
+          <div className={styles.statementHeader}>
+            <button className={styles.expandButton}>
+              {expanded ? <FaChevronUp className={styles.chevron} onClick={() => setExpanded(false)} /> : <FaChevronDown  className={styles.chevron} onClick={() => setExpanded(true)} />}
             </button>
-          </DialogActions>
-        </Dialog>
-        {item.attachedURLs.length > 0 && (
-          <div className={styles.urls}>
-            <div className={styles.headerWithButton}>
-              <h4>Attached URLs:</h4>
-              <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
-                {showURLs ? 'Hide' : 'Show'}
+            <span className={styles.statement}>{item.id}. {item.statement}</span>
+            <div className={styles.buttonContainer}>
+              <button
+                className={item.answer ? styles.yesset : styles.yes}
+                onClick={() => {
+                  const oldAnswer = item.answer;
+                  if (oldAnswer === false) {
+                    const updatedItem = { ...item, answer: true };
+                    onItemUpdate(updatedItem);
+                  }
+                }}
+              >
+                {'Yes'}
               </button>
-            </div>
-            <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
-              <ul>
-                {item.attachedURLs.map((url) => (
-                  <div key={url.id}>
-                    <div>
-                      <li className={styles.url}>
-                        <div className={styles.urlHeader}>
-                          <span className={styles.urlText}>{url.title}</span>
-                          <div>
-                            {copiedUrlId === url.id ? (
-                              <Done className={styles.doneButton} />
-                            ) : (
-                              <ContentCopy
-                                className={styles.copyButton}
-                                onClick={() => handleCopy(url.id, url.hyperlink)}
-                              />
-                            )}
-                            <Delete
-                              className={styles.delButton}
-                              onClick={() => handleDeleteUrl(url.id)}
-                            />
-                          </div>
-                        </div>
-                        <a href={url.hyperlink} target="">
-                          {url.hyperlink}
-                        </a>
-                        <p>{url.description}</p>
-                      </li>
-                    </div>
-                    <hr />
-                  </div>
-                ))}
-              </ul>
-            </div>
-          </div>
-        )}
-        {item.attachedImages.length > 0 && (
-          <div className={styles.images}>
-            <div className={styles.headerWithButton}>
-              <h4>Attached Images:</h4>
-              <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
-                {showImages ? 'Hide' : 'Show'}
+              <button
+                className={item.answer ? styles.no : styles.noset}
+                onClick={() => {
+                  const oldAnswer = item.answer;
+                  if (oldAnswer == true) {
+                    const updatedItem = { ...item, answer: false };
+                    onItemUpdate(updatedItem);
+                  }
+                }}
+              >
+                {'No'}
               </button>
             </div>
-            <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
-              <ul>
-                {item.attachedImages.map((image) => (
-                  <li key={image} className={styles.image}>
-                    <div className={styles.imageHeader}>
-                      <span className={styles.imageText}>{image.title}</span>
-                      <Delete
-                        className={styles.delButton}
-                        onClick={() => handleDeleteImage(image.id)}
-                      />
-                    </div>
-                    <img src={image.uri} alt="attached"/>
-                    <p>{image.description}</p>
-                  </li>
-                ))}
-              </ul>
-            </div>
           </div>
-        )}
-        {item.subChecklist.length > 0 && (
-          <div className={styles.subChecklist}>
-            <div className={styles.headerWithButton}>
-              <h4>Sub-Checklist:</h4>
-              <button className={styles.dropdownButton} onClick={() => setShowSubChecks(!showSubChecks)}>
-                {showSubChecks ? 'Hide' : 'Show'}
+          {expanded && <div className={styles.details}>
+            <div className={styles.scanResult}>
+              {item.scanResult &&
+                Object.keys(item.scanResult).map((key) => {
+                  return (
+                  <div key={key}>
+                    <span className={styles.scanKey}>{key}</span>
+                    <ul className={styles.scanList}>
+                      {item.scanResult[key].length ? (
+                        item.scanResult[key].map((answer) => (
+                          <li key={answer}>{answer}</li>
+                        ))
+                      ) : (
+                        <li>No answers available</li>
+                      )}
+                    </ul>
+                  </div>
+                )})}
+            </div>
+            <NoteEditor
+              notes={item.userNotes}
+              onEditingComplete={handleNoteUpdate}
+              onDelete={handleNoteDelete}
+            />
+            <div>
+              <button className={styles.addUrlsButton} onClick={() => setAddAsset(true)}>
+                Add Asset Reference
               </button>
             </div>
-            <div className={`${styles.subChecksContent} ${showSubChecks ? styles.show : ''}`}>
-              <ul>
-                {item.subChecklist.map((subCheck) => (
-                  <li key={subCheck.id}>
-                  <div className={styles.header}>
-                    <span>{subCheck.statement}</span>
-                    <div className={styles.buttonContainer}>
-                      <button
-                        className={subCheck.answer ? styles.yesset : styles.yes}
-                        onClick={() => {
-                          let oldAnswer = false;
-                          const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
-                            if (sub.id === subCheck.id) {
-                              oldAnswer = sub.answer;
-                              return { ...sub, answer: true };
-                            }
-                            return sub;
-                          })};
-                          if (oldAnswer === false) {
-                            onItemUpdate(updatedItem);
-                          }
-                        }}
-                      >
-                        {'Yes'}
-                      </button>
-                      <button
-                        className={subCheck.answer ? styles.no : styles.noset}
-                        onClick={() => {
-                          let oldAnswer = true;
-                          const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
-                            if (sub.id === subCheck.id) {
-                              oldAnswer = sub.answer;
-                              return { ...sub, answer: false };
-                            }
-                            return sub;
-                          })};
-                          if (oldAnswer === true) {
-                            onItemUpdate(updatedItem);
-                          }
-                        }}
-                      >
-                        {'No'}
-                      </button>
-                    </div>
+            <Dialog open={addAsset} onClose={() => setAddAsset(false)}>
+              <DialogTitle className={styles.dialogTitle}>Add Asset Reference</DialogTitle>
+              <DialogContent className={styles.dialogContent}>
+                <div className={styles.tree}>
+                  <div className={styles.toolbar}>
+                    <IconButton
+                      onClick={() => treeRef.current.setExpandAll(true)}
+                      className={styles.toolbarButton}
+                      aria-label="expand all tree items"
+                      fontSize="small"
+                    >
+                      <FaFolderOpen fontSize="small" /> &nbsp;Expand
+                    </IconButton>
+                    <IconButton
+                      className={styles.toolbarButton}
+                      aria-label="collapse all tree items"
+                      fontSize="small"
+                      onClick={() => treeRef.current.setExpandAll(false)}
+                    >
+                      <FaFolderMinus fontSize="small" /> &nbsp;Collapse
+                    </IconButton>
                   </div>
-                  </li>
-                ))}
-              </ul>
-            </div>
-          </div>
-        )}
-      </div>}
+                  <AssetTree
+                    assets={project.assets}
+                    ref={treeRef}
+                    onSelectAsset={handleSelectAsset}
+                    selectedAsset={selectedAsset}
+                  />
+                </div>
+                <div className={styles.form}>
+                  <div className={styles.title}>
+                    <label htmlFor="title">Title:</label>
+                    <input
+                      type="text"
+                      id="title"
+                      name="title"
+                      value={assetTitle}
+                      onChange={(e) => setAssetTitle(e.target.value)}
+                      required
+                    />
+                  </div>
+                  <div className={styles.description}>
+                    <label htmlFor="description">Description:</label>
+                    <input
+                      id="description"
+                      name="description"
+                      value={assetDescription}
+                      onChange={(e) => setAssetDescription(e.target.value)}
+                    />
+                  </div>
+                </div>
+              </DialogContent>
+              <DialogActions>
+                <button onClick={() => handleAddAsset()} className={styles.submitButton}>
+                  Add
+                </button>
+                <button onClick={() => setAddAsset(false)} className={styles.cancelButton} autoFocus>
+                  Cancel
+                </button>
+              </DialogActions>
+            </Dialog>
+            {item.attachedURLs.length > 0 && (
+              <div className={styles.urls}>
+                <div className={styles.headerWithButton}>
+                  <h4>Attached URLs:</h4>
+                  <button className={styles.dropdownButton} onClick={() => setShowURLs(!showURLs)}>
+                    {showURLs ? 'Hide' : 'Show'}
+                  </button>
+                </div>
+                <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
+                  <ul>
+                    {item.attachedURLs.map((url) => (
+                      <div key={url.id}>
+                        <div>
+                          <li className={styles.url}>
+                            <div className={styles.urlHeader}>
+                              <span className={styles.urlText}>{url.title}</span>
+                              <div>
+                                {copiedUrlId === url.id ? (
+                                  <Done className={styles.doneButton} />
+                                ) : (
+                                  <ContentCopy
+                                    className={styles.copyButton}
+                                    onClick={() => handleCopy(url.id, url.hyperlink)}
+                                  />
+                                )}
+                                <Delete
+                                  className={styles.delButton}
+                                  onClick={() => handleDeleteUrl(url.id)}
+                                />
+                              </div>
+                            </div>
+                            <a href={url.hyperlink} target="">
+                              {url.hyperlink}
+                            </a>
+                            <p>{url.description}</p>
+                          </li>
+                        </div>
+                        <hr />
+                      </div>
+                    ))}
+                  </ul>
+                </div>
+              </div>
+            )}
+            {item.attachedImages.length > 0 && (
+              <div className={styles.images}>
+                <div className={styles.headerWithButton}>
+                  <h4>Attached Images:</h4>
+                  <button className={styles.dropdownButton} onClick={() => setShowImages(!showImages)}>
+                    {showImages ? 'Hide' : 'Show'}
+                  </button>
+                </div>
+                <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
+                  <ul>
+                    {item.attachedImages.map((image) => (
+                      <li key={image} className={styles.image}>
+                        <div className={styles.imageHeader}>
+                          <span className={styles.imageText}>{image.title}</span>
+                          <Delete
+                            className={styles.delButton}
+                            onClick={() => handleDeleteImage(image.id)}
+                          />
+                        </div>
+                        <img src={image.uri} alt="attached"/>
+                        <p>{image.description}</p>
+                      </li>
+                    ))}
+                  </ul>
+                </div>
+              </div>
+            )}
+            {item.subChecklist.length > 0 && (
+              <div className={styles.subChecklist}>
+                <div className={styles.headerWithButton}>
+                  <h4>Sub-Checklist:</h4>
+                  <button className={styles.dropdownButton} onClick={() => setShowSubChecks(!showSubChecks)}>
+                    {showSubChecks ? 'Hide' : 'Show'}
+                  </button>
+                </div>
+                <div className={`${styles.subChecksContent} ${showSubChecks ? styles.show : ''}`}>
+                  <ul>
+                    {item.subChecklist.map((subCheck) => (
+                      <li key={subCheck.id}>
+                      <div className={styles.header}>
+                        <span>{subCheck.statement}</span>
+                        <div className={styles.buttonContainer}>
+                          <button
+                            className={subCheck.answer ? styles.yesset : styles.yes}
+                            onClick={() => {
+                              let oldAnswer = false;
+                              const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
+                                if (sub.id === subCheck.id) {
+                                  oldAnswer = sub.answer;
+                                  return { ...sub, answer: true };
+                                }
+                                return sub;
+                              })};
+                              if (oldAnswer === false) {
+                                onItemUpdate(updatedItem);
+                              }
+                            }}
+                          >
+                            {'Yes'}
+                          </button>
+                          <button
+                            className={subCheck.answer ? styles.no : styles.noset}
+                            onClick={() => {
+                              let oldAnswer = true;
+                              const updatedItem = { ...item, subChecklist: item.subChecklist.map((sub) => {
+                                if (sub.id === subCheck.id) {
+                                  oldAnswer = sub.answer;
+                                  return { ...sub, answer: false };
+                                }
+                                return sub;
+                              })};
+                              if (oldAnswer === true) {
+                                onItemUpdate(updatedItem);
+                              }
+                            }}
+                          >
+                            {'No'}
+                          </button>
+                        </div>
+                      </div>
+                      </li>
+                    ))}
+                  </ul>
+                </div>
+              </div>
+            )}
+          </div>}
+        </div>
+      )}
     </div>
   );
 }

From 3ceb3e72fbc3d1cb4ee2034df62ff0cdca9318d4 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 15 Oct 2024 20:58:39 +0530
Subject: [PATCH 33/43] adds checklist-note handling, renamed some checklist
 fields for consistency, adds checklist-name field

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             | 69 ++++++++++++++++---
 .../ChecklistItem/ChecklistItem.js            | 35 +++++-----
 .../ReproChecklist/ReproChecklist.js          | 52 +++-----------
 app/constants/constants.js                    | 12 ++--
 app/containers/ProjectPage/ProjectPage.js     |  2 +-
 app/utils/checklist.js                        |  9 +--
 6 files changed, 99 insertions(+), 80 deletions(-)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index ecbcb43..a9f8537 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -289,7 +289,7 @@ class Project extends Component<Props> {
       // TODO - fix bug here - should be failing
       assetsCopy.push(newAsset);
     } else {
-      this.upsertNoteHandler(existingAsset, 'asset', asset.uri, action, text, note);
+      this.upsertNoteHandler(existingAsset, EntityType.ASSET, asset.uri, action, text, note);
     }
     project.assets = assetsCopy;
     if (this.props.onUpdated) {
@@ -305,6 +305,35 @@ class Project extends Component<Props> {
     }
   };
 
+  checklistUpsertNoteHandler = (checklistItem, text, note) => {
+    if (this.unchangedNote(note,text)) {
+      return;
+    }
+
+    const currentProject = { ...this.props.project };
+    const action = { type: '', title: '', description: '', details: null };
+    this.upsertNoteHandler(
+      checklistItem,
+      EntityType.CHECKLIST,
+      checklistItem.name,
+      action,
+      text,
+      note
+    );
+    const updatedChecklist = this.props.checklistResponse.checklist.map(x => {
+      if (x.id === checklistItem.id) {
+        return checklistItem;
+      }
+      return x;
+    });
+    if (this.props.onChecklistUpdated) {
+      this.props.onChecklistUpdated(
+        currentProject,
+        updatedChecklist
+      );
+    }
+  }
+
   /**
    * More generic handler to implement the common delete functions needed for asset and project notes
    * @param {object} entity The entity assumed to have a `notes` collection that the note should be upserted into
@@ -447,6 +476,28 @@ class Project extends Component<Props> {
     }
   };
 
+  checklistDeleteNoteHandler = (checklistItem, note) => {
+    const currentProject = { ...this.props.project };
+    const actionDescription = this.deleteNoteHandler(
+      checklistItem,
+      EntityType.CHECKLIST,
+      checklistItem.name,
+      note
+    );
+    const updatedChecklist = this.props.checklistResponse.checklist.map(x => {
+      if (x.id === checklistItem.id) {
+        return checklistItem;
+      }
+      return x;
+    });
+    if (this.props.onChecklistUpdated) {
+      this.props.onChecklistUpdated(
+        currentProject,
+        updatedChecklist
+      );
+    }
+  }
+
   deletePersonHandler = person => {
     const currentProject = { ...this.props.project };
 
@@ -683,15 +734,15 @@ class Project extends Component<Props> {
         ) : null;
 
       const checklist =
-        this.props.project && this.props.checklist ? (
+        this.props.project && this.props.checklistResponse ? (
           <ReproChecklist
             project={this.props.project}
-            checklist={this.props.checklist.checklist}
-            error={this.props.checklist.errorMessage}
+            checklist={this.props.checklistResponse.checklist}
+            error={this.props.checklistResponse.errorMessage}
             onUpdated={this.props.onChecklistUpdated}
-            onAddedNote={this.projectUpsertNoteHandler}
-            onUpdatedNote={this.projectUpsertNoteHandler}
-            onDeletedNote={this.projectDeleteNoteHandler}
+            onAddedNote={this.checklistUpsertNoteHandler}
+            onUpdatedNote={this.checklistUpsertNoteHandler}
+            onDeletedNote={this.checklistDeleteNoteHandler}
             onSelectedAsset={this.assetSelectedHandler}
           />
         ) : null;
@@ -777,7 +828,7 @@ Project.propTypes = {
   // This object has the following structure:
   // {
   // }
-  checklist: PropTypes.object,
+  checklistResponse: PropTypes.object,
   configuration: PropTypes.object,
   assetDynamicDetails: PropTypes.object
 };
@@ -789,7 +840,7 @@ Project.defaultProps = {
   onAssetSelected: null,
   onChecklistUpdated: null,
   logs: null,
-  checklist: null,
+  checklistResponse: null,
   configuration: null,
   assetDynamicDetails: null
 };
diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index 82897dd..ac0f953 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -63,16 +63,16 @@ function ChecklistItem(props) {
 
     if (selectedAsset.type === Constants.AssetType.FILE) {
       if(selectedAsset.contentTypes.includes(Constants.AssetContentType.IMAGE)) {
-        const updatedItem = { ...item, attachedImages: [...item.attachedImages, {id: uuidv4(), uri: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
+        const updatedItem = { ...item, images: [...item.images, {id: uuidv4(), uri: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
         onItemUpdate(updatedItem);
         setShowImages(true);
       } else {
-        const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, {id: uuidv4(), hyperlink: AssetUtil.absoluteToRelativePath(project.path, selectedAsset), title: assetTitle, description: assetDescription}] };
+        const updatedItem = { ...item, urls: [...item.urls, {id: uuidv4(), hyperlink: AssetUtil.absoluteToRelativePath(project.path, selectedAsset), title: assetTitle, description: assetDescription}] };
         onItemUpdate(updatedItem);
         setShowURLs(true);
       }
     } else if (selectedAsset.type === Constants.AssetType.URL) {
-      const updatedItem = { ...item, attachedURLs: [...item.attachedURLs, {id: uuidv4(), hyperlink: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
+      const updatedItem = { ...item, urls: [...item.urls, {id: uuidv4(), hyperlink: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
       onItemUpdate(updatedItem);
       setShowURLs(true);
     }
@@ -90,12 +90,12 @@ function ChecklistItem(props) {
   };
 
   const handleDeleteUrl = (urlId) => {
-    const updatedItem = { ...item, attachedURLs: item.attachedURLs.filter((url) => url.id !== urlId) };
+    const updatedItem = { ...item, urls: item.urls.filter((url) => url.id !== urlId) };
     onItemUpdate(updatedItem);
   };
 
   const handleDeleteImage = (imageId) => {
-    const updatedItem = { ...item, attachedImages: item.attachedImages.filter((image) => image.id !== imageId) };
+    const updatedItem = { ...item, images: item.images.filter((image) => image.id !== imageId) };
     onItemUpdate(updatedItem);
   };
 
@@ -106,21 +106,21 @@ function ChecklistItem(props) {
     }
     if (note) {
       if (onUpdatedNote) {
-        onUpdatedNote(project, `Checklist ${item.id}: ` + text, note);
+        onUpdatedNote(item, text, note);
       }
     } else {
       if (onAddedNote) {
-        onAddedNote(project, `Checklist ${item.id}: ` + text);
+        onAddedNote(item, text);
       }
     }
   };
 
   const handleNoteDelete = (note) => {
     if (onDeletedNote) {
-      onDeletedNote(project, note);
+      onDeletedNote(item, note);
     }
 
-    const updatedItem = { ...item, userNotes: item.userNotes.filter((n) => n.id !== note.id) };
+    const updatedItem = { ...item, notes: item.notes.filter((n) => n.id !== note.id) };
     onItemUpdate(updatedItem);
   };
 
@@ -180,7 +180,7 @@ function ChecklistItem(props) {
                 )})}
             </div>
             <NoteEditor
-              notes={item.userNotes}
+              notes={item.notes}
               onEditingComplete={handleNoteUpdate}
               onDelete={handleNoteDelete}
             />
@@ -250,7 +250,7 @@ function ChecklistItem(props) {
                 </button>
               </DialogActions>
             </Dialog>
-            {item.attachedURLs.length > 0 && (
+            {item.urls.length > 0 && (
               <div className={styles.urls}>
                 <div className={styles.headerWithButton}>
                   <h4>Attached URLs:</h4>
@@ -260,7 +260,7 @@ function ChecklistItem(props) {
                 </div>
                 <div className={`${styles.urlContent} ${showURLs ? styles.show : ''}`}>
                   <ul>
-                    {item.attachedURLs.map((url) => (
+                    {item.urls.map((url) => (
                       <div key={url.id}>
                         <div>
                           <li className={styles.url}>
@@ -294,7 +294,7 @@ function ChecklistItem(props) {
                 </div>
               </div>
             )}
-            {item.attachedImages.length > 0 && (
+            {item.images.length > 0 && (
               <div className={styles.images}>
                 <div className={styles.headerWithButton}>
                   <h4>Attached Images:</h4>
@@ -304,7 +304,7 @@ function ChecklistItem(props) {
                 </div>
                 <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
                   <ul>
-                    {item.attachedImages.map((image) => (
+                    {item.images.map((image) => (
                       <li key={image} className={styles.image}>
                         <div className={styles.imageHeader}>
                           <span className={styles.imageText}>{image.title}</span>
@@ -390,12 +390,13 @@ function ChecklistItem(props) {
 ChecklistItem.propTypes = {
   item: PropTypes.shape({
     id: PropTypes.string.isRequired,
+    name: PropTypes.string.isRequired,
     statement: PropTypes.string.isRequired,
     answer: PropTypes.bool.isRequired,
     scanResult: PropTypes.objectOf(
       PropTypes.arrayOf(PropTypes.string)
     ),
-    userNotes: PropTypes.arrayOf(
+    notes: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         author: PropTypes.string.isRequired,
@@ -403,7 +404,7 @@ ChecklistItem.propTypes = {
         content: PropTypes.string.isRequired,
       })
     ),
-    attachedImages: PropTypes.arrayOf(
+    images: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         uri: PropTypes.string.isRequired,
@@ -411,7 +412,7 @@ ChecklistItem.propTypes = {
         description: PropTypes.string.isRequired,
       })
     ),
-    attachedURLs: PropTypes.arrayOf(
+    urls: PropTypes.arrayOf(
       PropTypes.shape({
         id: PropTypes.string.isRequired,
         hyperlink: PropTypes.string.isRequired,
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index 08fc5b4..4bc36c7 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -43,27 +43,6 @@ function findAssetLanguagesAndDependencies(asset) {
   };
 }
 
-function findChecklistNotes(notes) {
-  const checklistNotes = {};
-  notes.forEach((note) => {
-    if (note.content.startsWith('Checklist') && note.content.includes(':')) {
-      const id = note.content.split(':')[0].split(' ')[1];
-      if (!checklistNotes[id]) {
-        checklistNotes[id] = [];
-      }
-      const checklistNote = {
-        id: note.id,
-        author: note.author,
-        updated: note.updated,
-        content: note.content.split(':')[1].trim(),
-      };
-      checklistNotes[id].push(checklistNote);
-    }
-  });
-  return checklistNotes;
-}
-
-
 function convertImageToBase64(filePath) {
   try {
     const file = fs.readFileSync(filePath);
@@ -98,7 +77,7 @@ function convertImageToBase64(filePath) {
 
 
 function ReproChecklist(props) {
-  const { project, checklist, error, onUpdated, onUpdatedNote, onDeletedNote, onAddedNote, onSelectedAsset} = props;
+  const { project, checklist, error, onUpdated, onAddedNote, onUpdatedNote, onDeletedNote, onSelectedAsset} = props;
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
   useEffect(() => {
@@ -107,19 +86,6 @@ function ReproChecklist(props) {
         const scanResult1 = findAssetLanguagesAndDependencies(project.assets);
         checklist[0].scanResult = scanResult1;
       }
-      if(project.notes){
-        const checklistNotes = findChecklistNotes(project.notes);
-        const updatedChecklist = checklist.map((item) => {
-          if (checklistNotes[item.id]) {
-            return {
-              ...item,
-              userNotes: checklistNotes[item.id],
-            };
-          }
-          return item;
-        });
-        // tbd
-      }
     }
   }, [project]);
 
@@ -216,8 +182,8 @@ function ReproChecklist(props) {
           }
 
           let notes = [];
-          if (exportNotes && item.userNotes && item.userNotes.length > 0) {
-            notes = item.userNotes.map((note, noteIndex) => ({
+          if (exportNotes && item.notes && item.notes.length > 0) {
+            notes = item.notes.map((note, noteIndex) => ({
               text: `${noteIndex + 1}. ${note.content}`,
               margin: [20, 2],
               width: maxWidth,
@@ -226,8 +192,8 @@ function ReproChecklist(props) {
 
           let images = [];
           const imageWidth = 135;
-          if(item.attachedImages && item.attachedImages.length > 0){
-            images = item.attachedImages.map((image) => {
+          if(item.images && item.images.length > 0){
+            images = item.images.map((image) => {
               const base64Image = convertImageToBase64(image.uri);
               if (base64Image) {
                 return {
@@ -256,8 +222,8 @@ function ReproChecklist(props) {
           }
 
           let urls = [];
-          if(item.attachedURLs && item.attachedURLs.length > 0){
-            urls = item.attachedURLs.map((url, urlIndex) => {
+          if(item.urls && item.urls.length > 0){
+            urls = item.urls.map((url, urlIndex) => {
               return {
                 unbreakable: true,
                 columns: [
@@ -414,9 +380,9 @@ ReproChecklist.propTypes = {
   checklist: PropTypes.arrayOf(PropTypes.object),
   error: PropTypes.string,
   onUpdated: PropTypes.func.isRequired,
+  onAddedNote: PropTypes.func.isRequired,
   onUpdatedNote: PropTypes.func.isRequired,
   onDeletedNote: PropTypes.func.isRequired,
-  onAddedNote: PropTypes.func.isRequired,
   onSelectedAsset: PropTypes.func.isRequired,
 };
 
@@ -425,9 +391,9 @@ ReproChecklist.defaultProps = {
   checklist: null,
   error: null,
   onUpdated: null,
+  onAddedNote: null,
   onUpdatedNote: null,
   onDeletedNote: null,
-  onAddedNote: null,
   onSelectedAsset: null,
 };
 
diff --git a/app/constants/constants.js b/app/constants/constants.js
index fcfbc2f..1e48b0b 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -97,11 +97,11 @@ module.exports = {
   MAX_GRAPH_LABEL_LENGTH: 31,
 
   CHECKLIST_STATEMENTS: [
-    'All the software dependencies for the project are documented.',
-    'All the data file(s) used in the project are documented.',
-    'Clearly indicates which file(s) are used to run analysis.',
-    'Includes all necessary project documentation.',
-    'Are there multiple versions of a file? If yes, specify the versions.',
-    'Avoids using absolute paths in the code.',
+    ['Dependency', 'All the software dependencies for the project are documented.'],
+    ['Data', 'All the data file(s) used in the project are documented.'],
+    ['Entrypoint', 'Clearly indicates which file(s) are used to run analysis.'],
+    ['Documentation', 'Includes all necessary project documentation.'],
+    ['Organization', 'Are there multiple versions of a file? If yes, specify the versions.'],
+    ['Portability', 'Avoids using absolute paths in the code.'],
   ],
 };
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index 3a9e9e9..0a0304e 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -388,7 +388,7 @@ class ProjectPage extends Component {
           <Project
             project={this.state.selectedProject}
             logs={this.state.selectedProjectLogs}
-            checklist={this.state.selectedProjectChecklist}
+            checklistResponse={this.state.selectedProjectChecklist}
             onUpdated={this.handleProjectUpdate}
             onAssetSelected={this.handleAssetSelected}
             onChecklistUpdated={this.handleChecklistUpdate}
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index 2732443..095b907 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -6,12 +6,13 @@ export default class ChecklistUtil {
     Constants.CHECKLIST_STATEMENTS.forEach((statement, index) => {
       checklist.push({
         id: index + 1,
-        statement: statement,
+        name: statement[0],
+        statement: statement[1],
         answer: false,
         scanResult: {},
-        userNotes: [],
-        attachedImages: [],
-        attachedURLs: [],
+        notes: [],
+        images: [],
+        urls: [],
         subChecklist: [],
       });
     });

From c8cba8109ba75fc96aa886c9dba46640f04abe67 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Tue, 15 Oct 2024 21:11:14 +0530
Subject: [PATCH 34/43] change constant name to more generic

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/constants/constants.js | 2 +-
 app/utils/checklist.js     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/constants/constants.js b/app/constants/constants.js
index 1e48b0b..b03af26 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -96,7 +96,7 @@ module.exports = {
 
   MAX_GRAPH_LABEL_LENGTH: 31,
 
-  CHECKLIST_STATEMENTS: [
+  CHECKLIST: [
     ['Dependency', 'All the software dependencies for the project are documented.'],
     ['Data', 'All the data file(s) used in the project are documented.'],
     ['Entrypoint', 'Clearly indicates which file(s) are used to run analysis.'],
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index 095b907..ffd2463 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -3,7 +3,7 @@ import Constants from '../constants/constants';
 export default class ChecklistUtil {
   static initializeChecklist() {
     const checklist = [];
-    Constants.CHECKLIST_STATEMENTS.forEach((statement, index) => {
+    Constants.CHECKLIST.forEach((statement, index) => {
       checklist.push({
         id: index + 1,
         name: statement[0],

From 0b05b174ccac9b7cddc2caf504891f3c87b852a6 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 15:32:20 +0530
Subject: [PATCH 35/43] adds clarification regarding checklist-note updates

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index a9f8537..119f7d4 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -320,12 +320,15 @@ class Project extends Component<Props> {
       text,
       note
     );
+    // Once the checklist item is updated, we must also update the entire checklist linked to the project.
     const updatedChecklist = this.props.checklistResponse.checklist.map(x => {
       if (x.id === checklistItem.id) {
         return checklistItem;
       }
       return x;
     });
+    // Updates the checklist linked to the current project and saves the changes to the checklist file.
+    // Note that the checklist object is not directly attached to the project object, as opposed to the asset and person objects.
     if (this.props.onChecklistUpdated) {
       this.props.onChecklistUpdated(
         currentProject,
@@ -484,12 +487,15 @@ class Project extends Component<Props> {
       checklistItem.name,
       note
     );
+    // Once the checklist item is updated, we must also update the entire checklist linked to the project.
     const updatedChecklist = this.props.checklistResponse.checklist.map(x => {
       if (x.id === checklistItem.id) {
         return checklistItem;
       }
       return x;
     });
+    // Updates the checklist linked to the current project and saves the changes to the checklist file.
+    // Note that the checklist object is not directly attached to the project object, as opposed to the asset and person objects.
     if (this.props.onChecklistUpdated) {
       this.props.onChecklistUpdated(
         currentProject,

From 810f45948b73c79d93df404010f1a54e1125ede2 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 15:34:12 +0530
Subject: [PATCH 36/43] refactors code adding utility classes, and some minor
 fixes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ChecklistItem/ChecklistItem.js            |  6 +-
 .../ReproChecklist/ReproChecklist.js          | 72 ++-----------------
 app/utils/checklist.js                        | 29 ++++++++
 app/utils/general.js                          | 34 +++++++++
 4 files changed, 72 insertions(+), 69 deletions(-)

diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index ac0f953..e15d9f2 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -78,6 +78,8 @@ function ChecklistItem(props) {
     }
 
     setAddAsset(false);
+    setAssetTitle('');
+    setAssetDescription('');
   }
 
   const handleCopy = (urlId, hyperlink) => {
@@ -305,7 +307,7 @@ function ChecklistItem(props) {
                 <div className={`${styles.imageContent} ${showImages ? styles.show : ''}`}>
                   <ul>
                     {item.images.map((image) => (
-                      <li key={image} className={styles.image}>
+                      <li key={image.id} className={styles.image}>
                         <div className={styles.imageHeader}>
                           <span className={styles.imageText}>{image.title}</span>
                           <Delete
@@ -389,7 +391,7 @@ function ChecklistItem(props) {
 
 ChecklistItem.propTypes = {
   item: PropTypes.shape({
-    id: PropTypes.string.isRequired,
+    id: PropTypes.number.isRequired,
     name: PropTypes.string.isRequired,
     statement: PropTypes.string.isRequired,
     answer: PropTypes.bool.isRequired,
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index 4bc36c7..ed24559 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -3,78 +3,16 @@ import PropTypes from 'prop-types';
 import styles from './ReproChecklist.css';
 import ChecklistItem from './ChecklistItem/ChecklistItem';
 import Error from '../Error/Error';
-import Constants from '../../constants/constants';
 import { Typography, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { SaveAlt } from '@mui/icons-material';
 import pdfMake from 'pdfmake/build/pdfmake';
 import pdfFonts from 'pdfmake/build/vfs_fonts';
+import GeneralUtil from '../../utils/general';
+import ChecklistUtil from '../../utils/checklist';
 
 pdfMake.vfs = pdfFonts.pdfMake.vfs;
 
 const path = require('path');
-const fs = require('fs');
-const AssetsConfig = require('../../constants/assets-config');
-
-const languages = {};
-const dependencies = {};
-const imageAssets = {};
-
-function findAssetLanguagesAndDependencies(asset) {
-  if (asset.type === Constants.AssetType.FILE && asset.contentTypes.includes(Constants.AssetContentType.CODE) ) {
-    const lastSep = asset.uri.lastIndexOf(path.sep);
-    const fileName = asset.uri.substring(lastSep + 1);
-    const ext = fileName.split('.').pop();
-    if(ext){
-      AssetsConfig.contentTypes.forEach((contentType) => {
-        if(contentType.extensions.includes(ext)) {
-          languages[contentType.name] = true;
-        }
-      });
-    }
-  }
-
-  if(asset.children){
-    asset.children.forEach(findAssetLanguagesAndDependencies);
-  }
-
-  return {
-    languages: Object.keys(languages),
-    dependencies: Object.keys(dependencies)
-  };
-}
-
-function convertImageToBase64(filePath) {
-  try {
-    const file = fs.readFileSync(filePath);
-    const ext = path.extname(filePath).toLowerCase();
-    let mimeType;
-    switch (ext) {
-      case '.jpg':
-      case '.jpeg':
-        mimeType = 'image/jpeg';
-        break;
-      case '.png':
-        mimeType = 'image/png';
-        break;
-      case '.gif':
-        mimeType = 'image/gif';
-        break;
-      case '.webp':
-        mimeType = 'image/webp';
-        break;
-      case '.svg':
-        mimeType = 'image/svg+xml';
-        break;
-      default:
-        mimeType = 'application/octet-stream';
-    }
-    return `data:${mimeType};base64,${file.toString('base64')}`;
-  } catch (error) {
-    console.error('Error converting image to Base64:', error);
-    return null;
-  }
-};
-
 
 function ReproChecklist(props) {
   const { project, checklist, error, onUpdated, onAddedNote, onUpdatedNote, onDeletedNote, onSelectedAsset} = props;
@@ -83,7 +21,7 @@ function ReproChecklist(props) {
   useEffect(() => {
     if (project && checklist && !error) {
       if(project.assets) {
-        const scanResult1 = findAssetLanguagesAndDependencies(project.assets);
+        const scanResult1 = ChecklistUtil.findAssetLanguagesAndDependencies(project.assets);
         checklist[0].scanResult = scanResult1;
       }
     }
@@ -97,8 +35,8 @@ function ReproChecklist(props) {
   };
 
   const handleReportGeneration = (exportNotes) => {
-    const checkedIcon = convertImageToBase64(path.join(__dirname, 'images/yes.png'));
-    const statWrapLogo = convertImageToBase64(path.join(__dirname, 'images/banner.png'));
+    const checkedIcon = GeneralUtil.convertImageToBase64(path.join(__dirname, 'images/yes.png'));
+    const statWrapLogo = GeneralUtil.convertImageToBase64(path.join(__dirname, 'images/banner.png'));
 
     const documentDefinition = {
       content: [
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index ffd2463..dd4ffb5 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -1,4 +1,6 @@
 import Constants from '../constants/constants';
+import AssetsConfig from '../constants/assets-config';
+const path = require('path');
 
 export default class ChecklistUtil {
   static initializeChecklist() {
@@ -18,4 +20,31 @@ export default class ChecklistUtil {
     });
     return checklist;
   }
+
+  static findAssetLanguagesAndDependencies(asset, languages = {}, dependencies = {}) {
+    if (asset.type === Constants.AssetType.FILE && asset.contentTypes.includes(Constants.AssetContentType.CODE) ) {
+      const lastSep = asset.uri.lastIndexOf(path.sep);
+      const fileName = asset.uri.substring(lastSep + 1);
+      const ext = fileName.split('.').pop();
+
+      if(ext){
+        AssetsConfig.contentTypes.forEach((contentType) => {
+          if(contentType.extensions.includes(ext)) {
+            languages[contentType.name] = true;
+          }
+        });
+      }
+    }
+
+    if(asset.children){
+      asset.children.forEach(child => {
+        this.findAssetLanguagesAndDependencies(child, languages, dependencies);
+      });
+    }
+
+    return {
+      languages: Object.keys(languages),
+      dependencies: Object.keys(dependencies)
+    };
+  }
 }
diff --git a/app/utils/general.js b/app/utils/general.js
index 7c5ca40..6624528 100644
--- a/app/utils/general.js
+++ b/app/utils/general.js
@@ -1,5 +1,7 @@
 /* eslint-disable no-underscore-dangle */
 const DefaultDisplayName = '(empty)';
+const path = require('path');
+const fs = require('fs');
 
 export default class GeneralUtil {
   static formatDateTime(date) {
@@ -152,4 +154,36 @@ export default class GeneralUtil {
       };
     }, []);
   }
+
+  static convertImageToBase64(filePath) {
+    try {
+      const file = fs.readFileSync(filePath);
+      const ext = path.extname(filePath).toLowerCase();
+      let mimeType;
+      switch (ext) {
+        case '.jpg':
+        case '.jpeg':
+          mimeType = 'image/jpeg';
+          break;
+        case '.png':
+          mimeType = 'image/png';
+          break;
+        case '.gif':
+          mimeType = 'image/gif';
+          break;
+        case '.webp':
+          mimeType = 'image/webp';
+          break;
+        case '.svg':
+          mimeType = 'image/svg+xml';
+          break;
+        default:
+          mimeType = 'application/octet-stream';
+      }
+      return `data:${mimeType};base64,${file.toString('base64')}`;
+    } catch (error) {
+      console.error('Error converting image to Base64:', error);
+      return null;
+    }
+  };
 }

From 444079c52a93a35d4a4eee47d8852b90abb57aeb Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 15:34:49 +0530
Subject: [PATCH 37/43] adds unit testing for checklist util

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 test/utils/checklist.spec.js | 113 +++++++++++++++++++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 test/utils/checklist.spec.js

diff --git a/test/utils/checklist.spec.js b/test/utils/checklist.spec.js
new file mode 100644
index 0000000..46b40ce
--- /dev/null
+++ b/test/utils/checklist.spec.js
@@ -0,0 +1,113 @@
+import ChecklistUtil from "../../app/utils/checklist";
+import Constants from "../../app/constants/constants";
+
+describe('utils', () => {
+  describe('ChecklistUtil', () => {
+    describe('findAssetLanguagesAndDependencies', () => {
+      it('should return empty result when asset is null or undefined', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies(null)).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies(undefined)).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
+      it('should return correct languages and dependencies for valid code assets', () => {
+        const languages = {'R': ['r', 'rmd', 'rnw', 'snw'], 'Python': ['py', 'py3', 'pyi'], 'SAS': ['sas'], 'Stata': ['do', 'ado', 'mata'], 'HTML': ['htm', 'html']};
+        Object.keys(languages).forEach((lang) => {
+          languages[lang].forEach((ext) => {
+            expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+              type: Constants.AssetType.FILE,
+              contentTypes: [Constants.AssetContentType.CODE],
+              uri: `path/to/file.${ext}`,
+            })).toEqual({
+              languages: [lang],
+              dependencies: [],
+            });
+          });
+        });
+      });
+
+      it('should return empty result for non-code assets (data, documentation)', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.DATA],
+          uri: 'path/to/file.csv',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
+      it('should return empty result for directory/folder type assets', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.DIRECTORY,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/directory/',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
+      it('should not identify malformed URIs', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/malformed-uri.',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
+      it('should ignore random/unknown extensions that are not in the content types', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/file.cmd',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
+      it('should handle nested assets and recurse properly', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FOLDER,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/folder',
+          children: [
+            {
+              type: Constants.AssetType.FILE,
+              contentTypes: [Constants.AssetContentType.CODE],
+              uri: 'path/to/folder/file1.py',
+            },
+            {
+              type: Constants.AssetType.FILE,
+              contentTypes: [Constants.AssetContentType.CODE],
+              uri: 'path/to/folder/file2.r',
+            }
+          ],
+        })).toEqual({
+          languages: ['Python', 'R'], // don't change the languages ordering in this array
+          dependencies: [],
+        });
+      });
+
+      it('should not crash when asset has no extension in its URI', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/file',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+    });
+  });
+});

From 819ea68bfa01870d2dd0cafd8caecbecb2ae991f Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 15:35:01 +0530
Subject: [PATCH 38/43] adds unit testing for checklist service

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 test/services/checklist.spec.js | 104 ++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 test/services/checklist.spec.js

diff --git a/test/services/checklist.spec.js b/test/services/checklist.spec.js
new file mode 100644
index 0000000..af73e70
--- /dev/null
+++ b/test/services/checklist.spec.js
@@ -0,0 +1,104 @@
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+const process = require('process');
+
+import ChecklistService from '../../app/services/checklist';
+import Constants from '../../app/constants/constants';
+
+jest.mock('fs');
+jest.mock('os');
+
+const TEST_USER_HOME_PATH = process.platform === 'win32' ? 'C:\\Users\\test' : '/User/test';
+os.homedir.mockReturnValue(TEST_USER_HOME_PATH);
+const TEST_PROJECT_PATH = process.platform === 'win32' ? 'C:\\testProject' : '~/testProject';
+
+describe('services', () => {
+  describe('ChecklistService', () => {
+    const mockProjectPath = TEST_PROJECT_PATH;
+    const resolvedProjectPath = path.join(TEST_USER_HOME_PATH, 'testProject', Constants.StatWrapFiles.BASE_FOLDER, Constants.StatWrapFiles.CHECKLIST);
+    const checklistData = [{ id: 1, name: 'Dependency', statement: 'All the software dependencies for the project are documented.', answer: true }];
+
+    const checklistService = new ChecklistService();
+
+    beforeEach(() => {
+      jest.clearAllMocks();
+    });
+
+    describe('writeChecklist', () => {
+      it('should throw an error if projectPath is null or undefined', () => {
+        expect(() => checklistService.writeChecklist(null, checklistData)).toThrow('Invalid project path or checklist data');
+        expect(() => checklistService.writeChecklist(undefined, checklistData)).toThrow('Invalid project path or checklist data');
+      });
+
+      it('should throw an error if checklist data is null or undefined', () => {
+        expect(() => checklistService.writeChecklist(mockProjectPath, null)).toThrow('Invalid project path or checklist data');
+        expect(() => checklistService.writeChecklist(mockProjectPath, undefined)).toThrow('Invalid project path or checklist data');
+      });
+
+      it('should correctly resolve the project path and write checklist data to a file', () => {
+        fs.writeFileSync = jest.fn();
+
+        checklistService.writeChecklist(mockProjectPath, checklistData);
+
+        expect(fs.writeFileSync).toHaveBeenCalledWith(
+          resolvedProjectPath,
+          JSON.stringify(checklistData)
+        );
+      });
+
+      it('should handle errors thrown during file write', () => {
+        fs.writeFileSync = jest.fn(() => {
+          throw new Error('Write failed');
+        });
+
+        expect(() => checklistService.writeChecklist(mockProjectPath, checklistData)).toThrow('Write failed');
+      });
+    });
+
+    describe('loadChecklist', () => {
+      it('should return an error if projectPath is null or undefined', (done) => {
+        checklistService.loadChecklist(null, (err, result) => {
+          expect(err).toBe('The project path must be specified');
+          expect(result).toBeNull();
+          done();
+        });
+      });
+
+      it('should return an error if checklist file does not exist', (done) => {
+        fs.existsSync = jest.fn().mockReturnValue(false);
+
+        checklistService.loadChecklist(mockProjectPath, (err, result) => {
+          expect(err).toBe('Checklist file not found');
+          expect(result).toEqual([]);
+          done();
+        });
+      });
+
+      it('should correctly read and parse checklist data from the file', (done) => {
+        fs.existsSync = jest.fn().mockReturnValue(true);
+        fs.readFileSync = jest.fn().mockReturnValue(JSON.stringify(checklistData));
+
+        checklistService.loadChecklist(mockProjectPath, (err, result) => {
+          expect(err).toBeNull();
+          expect(result).toEqual(checklistData);
+          expect(fs.readFileSync).toHaveBeenCalledWith(resolvedProjectPath);
+          done();
+        });
+      });
+
+      it('should return an error if file read or parsing fails', (done) => {
+        fs.existsSync = jest.fn().mockReturnValue(true);
+        fs.readFileSync = jest.fn(() => {
+          throw new Error('Read failed');
+        });
+
+        checklistService.loadChecklist(mockProjectPath, (err, result) => {
+          expect(err).toBe('Error reading or parsing checklist file');
+          expect(result).toBeNull();
+          done();
+        });
+      });
+    });
+  });
+});

From 61611323d097d9c58b211873d03e76b12795ba8f Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 20:08:04 +0530
Subject: [PATCH 39/43] replaces all instances of the project literal with its
 stored constant

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/constants/constants.js                   |  1 +
 app/services/assets/handlers/file.js         |  2 +-
 app/services/project.js                      | 21 ++++++++++----------
 test/services/assets/handlers/file.spec.js   |  3 ++-
 test/services/assets/handlers/python.spec.js |  3 ++-
 test/services/assets/handlers/r.spec.js      |  3 ++-
 test/services/assets/handlers/sas.spec.js    |  3 ++-
 test/services/assets/handlers/stata.spec.js  |  3 ++-
 test/services/project.spec.js                | 20 +++++++++----------
 test/utils/asset.spec.js                     |  2 +-
 test/utils/general.spec.js                   |  2 +-
 test/utils/note.spec.js                      |  2 +-
 test/utils/workflow.spec.js                  |  2 +-
 13 files changed, 36 insertions(+), 31 deletions(-)

diff --git a/app/constants/constants.js b/app/constants/constants.js
index b03af26..97e9e87 100644
--- a/app/constants/constants.js
+++ b/app/constants/constants.js
@@ -36,6 +36,7 @@ module.exports = {
 
   StatWrapFiles: {
     BASE_FOLDER: '.statwrap',
+    PROJECT: '.statwrap-project.json',
     LOG: '.statwrap.log',
     CHECKLIST: '.statwrap-checklist.json',
   },
diff --git a/app/services/assets/handlers/file.js b/app/services/assets/handlers/file.js
index 59c2322..4331363 100644
--- a/app/services/assets/handlers/file.js
+++ b/app/services/assets/handlers/file.js
@@ -13,7 +13,7 @@ const FILE_IGNORE_LIST = [
   '.DS_Store',
   'Thumbs.db',
   '.keep', // We use these within our template projects
-  '.statwrap-project.json', // ProjectService DefaultProjectFile -- circular dependency, so we need to use literal
+  Constants.StatWrapFiles.PROJECT,
   StatWrapFiles.LOG,
   StatWrapFiles.BASE_FOLDER,
   '.git',
diff --git a/app/services/project.js b/app/services/project.js
index 62f8128..9fbf1db 100644
--- a/app/services/project.js
+++ b/app/services/project.js
@@ -13,11 +13,10 @@ const fs = require('fs');
 const os = require('os');
 const path = require('path');
 
-const DefaultProjectFile = '.statwrap-project.json';
 const ProjectFileFormatVersion = '1';
 const MaximumFolderNameLength = 255;
 
-export { DefaultProjectFile, ProjectFileFormatVersion };
+export { ProjectFileFormatVersion };
 
 export default class ProjectService {
   /**
@@ -89,9 +88,9 @@ export default class ProjectService {
 
   lockProjectFile(projectPath) {
     const filePath = path.join(
-      projectPath.replace('~', os.homedir),
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
-      DefaultProjectFile,
+      Constants.StatWrapFiles.PROJECT,
     );
 
     lockfile.lockSync(filePath);
@@ -99,9 +98,9 @@ export default class ProjectService {
 
   unlockProjectFile(projectPath) {
     const filePath = path.join(
-      projectPath.replace('~', os.homedir),
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
-      DefaultProjectFile,
+      Constants.StatWrapFiles.PROJECT,
     );
 
     lockfile.unlockSync(filePath);
@@ -112,9 +111,9 @@ export default class ProjectService {
   // name should not be specified as part of projectPath.
   loadProjectFile(projectPath) {
     const filePath = path.join(
-      projectPath.replace('~', os.homedir),
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
-      DefaultProjectFile,
+      Constants.StatWrapFiles.PROJECT,
     );
 
     try {
@@ -174,7 +173,7 @@ export default class ProjectService {
     // This will handle if someone is trying to configure what they think is a new project,
     // but it actually already exists
     const configFolderPath = path.join(
-      projectPath.replace('~', os.homedir),
+      projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
     );
     try {
@@ -183,7 +182,7 @@ export default class ProjectService {
       fs.mkdirSync(configFolderPath, { recursive: true });
     }
 
-    const filePath = path.join(configFolderPath, DefaultProjectFile);
+    const filePath = path.join(configFolderPath, Constants.StatWrapFiles.PROJECT);
     fs.writeFileSync(filePath, JSON.stringify(this.stripExtraProjectData(project)));
   }
 
@@ -233,7 +232,7 @@ export default class ProjectService {
         // appended to the root folder.
         const sanitizedName = this.sanitizeFolderName(project.name);
         const projectDirectory = path.join(
-          project.directory.replace('~', os.homedir),
+          project.directory.replace('~', os.homedir()),
           sanitizedName,
         );
         validationReport.project.name = project.name;
diff --git a/test/services/assets/handlers/file.spec.js b/test/services/assets/handlers/file.spec.js
index 631ddf8..f78aa6e 100644
--- a/test/services/assets/handlers/file.spec.js
+++ b/test/services/assets/handlers/file.spec.js
@@ -1,5 +1,6 @@
 import fs from 'fs';
 import FileHandler from '../../../../app/services/assets/handlers/file';
+import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
 jest.mock('os');
@@ -30,7 +31,7 @@ describe('services', () => {
         const handler = new FileHandler();
         expect(handler.includeFile('/User/test/Project/.DS_Store')).toBeFalsy();
         expect(handler.includeFile('C:/test/Project/Thumbs.db')).toBeFalsy();
-        expect(handler.includeFile('.statwrap-project.json')).toBeFalsy();
+        expect(handler.includeFile(Constants.StatWrapFiles.PROJECT)).toBeFalsy();
       });
 
       it('should include allowable files and folders', () => {
diff --git a/test/services/assets/handlers/python.spec.js b/test/services/assets/handlers/python.spec.js
index cb85e7b..7b3f0d8 100644
--- a/test/services/assets/handlers/python.spec.js
+++ b/test/services/assets/handlers/python.spec.js
@@ -1,5 +1,6 @@
 import fs from 'fs';
 import PythonHandler from '../../../../app/services/assets/handlers/python';
+import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
 jest.mock('os');
@@ -30,7 +31,7 @@ describe('services', () => {
         const handler = new PythonHandler();
         expect(handler.includeFile('/User/test/Project/python')).toBeFalsy();
         expect(handler.includeFile('C:/test/Project/Thumbs.db')).toBeFalsy();
-        expect(handler.includeFile('.statwrap-project.json')).toBeFalsy();
+        expect(handler.includeFile(Constants.StatWrapFiles.PROJECT)).toBeFalsy();
       });
 
       it('should exclude where Python extension exists but is not the last', () => {
diff --git a/test/services/assets/handlers/r.spec.js b/test/services/assets/handlers/r.spec.js
index 09f313a..843aada 100644
--- a/test/services/assets/handlers/r.spec.js
+++ b/test/services/assets/handlers/r.spec.js
@@ -1,5 +1,6 @@
 import fs from 'fs';
 import RHandler from '../../../../app/services/assets/handlers/r';
+import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
 jest.mock('os');
@@ -30,7 +31,7 @@ describe('services', () => {
         const handler = new RHandler();
         expect(handler.includeFile('/User/test/Project/r')).toBeFalsy();
         expect(handler.includeFile('C:/test/Project/Thumbs.db')).toBeFalsy();
-        expect(handler.includeFile('.statwrap-project.json')).toBeFalsy();
+        expect(handler.includeFile(Constants.StatWrapFiles.PROJECT)).toBeFalsy();
       });
 
       it('should exclude where R extension exists but is not the last', () => {
diff --git a/test/services/assets/handlers/sas.spec.js b/test/services/assets/handlers/sas.spec.js
index 235cbd9..f2bb43d 100644
--- a/test/services/assets/handlers/sas.spec.js
+++ b/test/services/assets/handlers/sas.spec.js
@@ -1,5 +1,6 @@
 import fs from 'fs';
 import SASHandler from '../../../../app/services/assets/handlers/sas';
+import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
 jest.mock('os');
@@ -30,7 +31,7 @@ describe('services', () => {
         const handler = new SASHandler();
         expect(handler.includeFile('/User/test/Project/sas')).toBeFalsy();
         expect(handler.includeFile('C:/test/Project/Thumbs.db')).toBeFalsy();
-        expect(handler.includeFile('.statwrap-project.json')).toBeFalsy();
+        expect(handler.includeFile(Constants.StatWrapFiles.PROJECT)).toBeFalsy();
       });
 
       it('should exclude where SAS extension exists but is not the last', () => {
diff --git a/test/services/assets/handlers/stata.spec.js b/test/services/assets/handlers/stata.spec.js
index 44a9945..1856c2e 100644
--- a/test/services/assets/handlers/stata.spec.js
+++ b/test/services/assets/handlers/stata.spec.js
@@ -1,5 +1,6 @@
 import fs from 'fs';
 import StataHandler from '../../../../app/services/assets/handlers/stata';
+import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
 jest.mock('os');
@@ -30,7 +31,7 @@ describe('services', () => {
         const handler = new StataHandler();
         expect(handler.includeFile('/User/test/Project/stata')).toBeFalsy();
         expect(handler.includeFile('C:/test/Project/Thumbs.db')).toBeFalsy();
-        expect(handler.includeFile('.statwrap-project.json')).toBeFalsy();
+        expect(handler.includeFile(Constants.StatWrapFiles.PROJECT)).toBeFalsy();
       });
 
       it('should exclude where Stata extension exists but is not the last', () => {
diff --git a/test/services/project.spec.js b/test/services/project.spec.js
index fa2183c..6a865c5 100644
--- a/test/services/project.spec.js
+++ b/test/services/project.spec.js
@@ -56,7 +56,7 @@ describe('services', () => {
         const project = new ProjectService().loadProjectFile('~/Test/Path');
         expect(project).not.toBeNull();
         expect(fs.readFileSync).toHaveBeenCalledWith(
-          `${TEST_USER_HOME_PATH}Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/.statwrap-project.json`,
+          `${TEST_USER_HOME_PATH}Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/${Constants.StatWrapFiles.PROJECT}`,
         );
       });
       it.onWindows('should resolve the ~ home path', () => {
@@ -64,7 +64,7 @@ describe('services', () => {
         const project = new ProjectService().loadProjectFile('~\\Test\\Path');
         expect(project).not.toBeNull();
         expect(fs.readFileSync).toHaveBeenCalledWith(
-          `${TEST_USER_HOME_PATH}Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\.statwrap-project.json`,
+          `${TEST_USER_HOME_PATH}Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\${Constants.StatWrapFiles.PROJECT}`,
         );
       });
       it.onMac('should return the project details', () => {
@@ -72,7 +72,7 @@ describe('services', () => {
         const project = new ProjectService().loadProjectFile('/Test/Path');
         expect(project).not.toBeNull();
         expect(fs.readFileSync).toHaveBeenCalledWith(
-          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/.statwrap-project.json`,
+          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/${Constants.StatWrapFiles.PROJECT}`,
         );
       });
       it.onWindows('should return the project details', () => {
@@ -80,7 +80,7 @@ describe('services', () => {
         const project = new ProjectService().loadProjectFile('C:\\Test\\Path');
         expect(project).not.toBeNull();
         expect(fs.readFileSync).toHaveBeenCalledWith(
-          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\.statwrap-project.json`,
+          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\${Constants.StatWrapFiles.PROJECT}`,
         );
       });
       it('should throw an exception if the JSON is invalid', () => {
@@ -127,28 +127,28 @@ describe('services', () => {
       it.onMac('should resolve the ~ home path', () => {
         new ProjectService().saveProjectFile('~/Test/Path', { id: '1' });
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `${TEST_USER_HOME_PATH}Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/.statwrap-project.json`,
+          `${TEST_USER_HOME_PATH}Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
       it.onWindows('should resolve the ~ home path', () => {
         new ProjectService().saveProjectFile('~\\Test\\Path', { id: '1' });
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `${TEST_USER_HOME_PATH}Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\.statwrap-project.json`,
+          `${TEST_USER_HOME_PATH}Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
       it.onMac('should save the project details', () => {
         new ProjectService().saveProjectFile('/Test/Path', { id: '1' });
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/.statwrap-project.json`,
+          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
       it.onWindows('should save the project details', () => {
         new ProjectService().saveProjectFile('C:\\Test\\Path', { id: '1' });
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\.statwrap-project.json`,
+          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
@@ -166,7 +166,7 @@ describe('services', () => {
           { recursive: true },
         );
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/.statwrap-project.json`,
+          `/Test/Path/${Constants.StatWrapFiles.BASE_FOLDER}/${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
@@ -184,7 +184,7 @@ describe('services', () => {
           { recursive: true },
         );
         expect(fs.writeFileSync).toHaveBeenCalledWith(
-          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\.statwrap-project.json`,
+          `C:\\Test\\Path\\${Constants.StatWrapFiles.BASE_FOLDER}\\${Constants.StatWrapFiles.PROJECT}`,
           '{"id":"1"}',
         );
       });
diff --git a/test/utils/asset.spec.js b/test/utils/asset.spec.js
index 07596d2..d093b5b 100644
--- a/test/utils/asset.spec.js
+++ b/test/utils/asset.spec.js
@@ -1,7 +1,7 @@
 import AssetUtil from '../../app/utils/asset';
 import Constants from '../../app/constants/constants';
 
-describe('services', () => {
+describe('utils', () => {
   describe('AssetUtil', () => {
     describe('getHandlerMetadata', () => {
       it('should return null when there is no metadata', () => {
diff --git a/test/utils/general.spec.js b/test/utils/general.spec.js
index 8c068e9..ab34754 100644
--- a/test/utils/general.spec.js
+++ b/test/utils/general.spec.js
@@ -1,7 +1,7 @@
 /* eslint-disable prettier/prettier */
 import GeneralUtil from '../../app/utils/general';
 
-describe('services', () => {
+describe('utils', () => {
   describe('GeneralUtil', () => {
     describe('formatDateTime', () => {
       it('returns an empty string for an empty date parameter', () => {
diff --git a/test/utils/note.spec.js b/test/utils/note.spec.js
index 3c68a45..cfc6605 100644
--- a/test/utils/note.spec.js
+++ b/test/utils/note.spec.js
@@ -1,6 +1,6 @@
 import AssetUtil from '../../app/utils/note';
 
-describe('services', () => {
+describe('utils', () => {
   describe('NoteUtil', () => {
     describe('createNote', () => {
       it('creates the note', () => {
diff --git a/test/utils/workflow.spec.js b/test/utils/workflow.spec.js
index 56d7f76..66ef576 100644
--- a/test/utils/workflow.spec.js
+++ b/test/utils/workflow.spec.js
@@ -2,7 +2,7 @@
 import WorkflowUtil from '../../app/utils/workflow';
 import Constants from '../../app/constants/constants';
 
-describe('services', () => {
+describe('utils', () => {
   describe('WorkwlowUtil', () => {
     describe('getAllDependencies', () => {
       it('should handle empty/invalid inputs', () => {

From 4757eef168f10ec06eb637f30bff089ac94dfb3f Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Thu, 17 Oct 2024 20:42:46 +0530
Subject: [PATCH 40/43] minor fixes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/services/assets/handlers/file.js         | 2 +-
 app/utils/checklist.js                       | 6 ++++++
 test/services/assets/asset.spec.js           | 1 -
 test/services/assets/handlers/file.spec.js   | 1 -
 test/services/assets/handlers/python.spec.js | 1 -
 test/services/assets/handlers/r.spec.js      | 1 -
 test/services/assets/handlers/sas.spec.js    | 1 -
 test/services/assets/handlers/stata.spec.js  | 1 -
 8 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/app/services/assets/handlers/file.js b/app/services/assets/handlers/file.js
index 4331363..50b195b 100644
--- a/app/services/assets/handlers/file.js
+++ b/app/services/assets/handlers/file.js
@@ -13,7 +13,7 @@ const FILE_IGNORE_LIST = [
   '.DS_Store',
   'Thumbs.db',
   '.keep', // We use these within our template projects
-  Constants.StatWrapFiles.PROJECT,
+  StatWrapFiles.PROJECT,
   StatWrapFiles.LOG,
   StatWrapFiles.BASE_FOLDER,
   '.git',
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index dd4ffb5..47c5b28 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -22,6 +22,12 @@ export default class ChecklistUtil {
   }
 
   static findAssetLanguagesAndDependencies(asset, languages = {}, dependencies = {}) {
+    if (!asset) {
+      return {
+        languages: [],
+        dependencies: []
+      };
+    }
     if (asset.type === Constants.AssetType.FILE && asset.contentTypes.includes(Constants.AssetContentType.CODE) ) {
       const lastSep = asset.uri.lastIndexOf(path.sep);
       const fileName = asset.uri.substring(lastSep + 1);
diff --git a/test/services/assets/asset.spec.js b/test/services/assets/asset.spec.js
index 209aed6..edc9143 100644
--- a/test/services/assets/asset.spec.js
+++ b/test/services/assets/asset.spec.js
@@ -4,7 +4,6 @@ import path from 'path';
 import AssetService from '../../../app/services/assets/asset';
 
 jest.mock('fs');
-jest.mock('os');
 
 class DummyHandler {
   _id = 'Dummy';
diff --git a/test/services/assets/handlers/file.spec.js b/test/services/assets/handlers/file.spec.js
index f78aa6e..4c798fe 100644
--- a/test/services/assets/handlers/file.spec.js
+++ b/test/services/assets/handlers/file.spec.js
@@ -3,7 +3,6 @@ import FileHandler from '../../../../app/services/assets/handlers/file';
 import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
-jest.mock('os');
 
 describe('services', () => {
   describe('FileHandler', () => {
diff --git a/test/services/assets/handlers/python.spec.js b/test/services/assets/handlers/python.spec.js
index 7b3f0d8..6db97b9 100644
--- a/test/services/assets/handlers/python.spec.js
+++ b/test/services/assets/handlers/python.spec.js
@@ -3,7 +3,6 @@ import PythonHandler from '../../../../app/services/assets/handlers/python';
 import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
-jest.mock('os');
 
 describe('services', () => {
   describe('PythonHandler', () => {
diff --git a/test/services/assets/handlers/r.spec.js b/test/services/assets/handlers/r.spec.js
index 843aada..385717e 100644
--- a/test/services/assets/handlers/r.spec.js
+++ b/test/services/assets/handlers/r.spec.js
@@ -3,7 +3,6 @@ import RHandler from '../../../../app/services/assets/handlers/r';
 import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
-jest.mock('os');
 
 describe('services', () => {
   describe('RHandler', () => {
diff --git a/test/services/assets/handlers/sas.spec.js b/test/services/assets/handlers/sas.spec.js
index f2bb43d..6bd6627 100644
--- a/test/services/assets/handlers/sas.spec.js
+++ b/test/services/assets/handlers/sas.spec.js
@@ -3,7 +3,6 @@ import SASHandler from '../../../../app/services/assets/handlers/sas';
 import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
-jest.mock('os');
 
 describe('services', () => {
   describe('SASHandler', () => {
diff --git a/test/services/assets/handlers/stata.spec.js b/test/services/assets/handlers/stata.spec.js
index 1856c2e..24f2719 100644
--- a/test/services/assets/handlers/stata.spec.js
+++ b/test/services/assets/handlers/stata.spec.js
@@ -3,7 +3,6 @@ import StataHandler from '../../../../app/services/assets/handlers/stata';
 import Constants from '../../../../app/constants/constants';
 
 jest.mock('fs');
-jest.mock('os');
 
 describe('services', () => {
   describe('StataHandler', () => {

From 2b2bc0c04359ffd6f325d91ef139aaee8cd23b4c Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 18 Oct 2024 19:52:32 +0530
Subject: [PATCH 41/43] adds a few more tests and fixes some of the existing
 ones

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 .../ChecklistItem/ChecklistItem.js            |  8 +++++++-
 app/utils/checklist.js                        |  2 +-
 test/services/checklist.spec.js               |  8 ++++++--
 test/utils/checklist.spec.js                  | 20 +++++++++++++++++++
 4 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index e15d9f2..62a51d8 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -80,6 +80,7 @@ function ChecklistItem(props) {
     setAddAsset(false);
     setAssetTitle('');
     setAssetDescription('');
+    setSelectedAsset(null);
   }
 
   const handleCopy = (urlId, hyperlink) => {
@@ -247,7 +248,12 @@ function ChecklistItem(props) {
                 <button onClick={() => handleAddAsset()} className={styles.submitButton}>
                   Add
                 </button>
-                <button onClick={() => setAddAsset(false)} className={styles.cancelButton} autoFocus>
+                <button onClick={() => {
+                  setAddAsset(false);
+                  setAssetTitle('');
+                  setAssetDescription('');
+                  setSelectedAsset(null);
+                }} className={styles.cancelButton} autoFocus>
                   Cancel
                 </button>
               </DialogActions>
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index 47c5b28..aefc28d 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -35,7 +35,7 @@ export default class ChecklistUtil {
 
       if(ext){
         AssetsConfig.contentTypes.forEach((contentType) => {
-          if(contentType.extensions.includes(ext)) {
+          if(contentType.categories.includes(Constants.AssetContentType.CODE) && contentType.extensions.includes(ext)) {
             languages[contentType.name] = true;
           }
         });
diff --git a/test/services/checklist.spec.js b/test/services/checklist.spec.js
index af73e70..ef14740 100644
--- a/test/services/checklist.spec.js
+++ b/test/services/checklist.spec.js
@@ -11,7 +11,7 @@ jest.mock('os');
 
 const TEST_USER_HOME_PATH = process.platform === 'win32' ? 'C:\\Users\\test' : '/User/test';
 os.homedir.mockReturnValue(TEST_USER_HOME_PATH);
-const TEST_PROJECT_PATH = process.platform === 'win32' ? 'C:\\testProject' : '~/testProject';
+const TEST_PROJECT_PATH = process.platform === 'win32' ? `${TEST_USER_HOME_PATH}\\testProject` : '~/testProject';
 
 describe('services', () => {
   describe('ChecklistService', () => {
@@ -61,8 +61,12 @@ describe('services', () => {
         checklistService.loadChecklist(null, (err, result) => {
           expect(err).toBe('The project path must be specified');
           expect(result).toBeNull();
-          done();
         });
+        checklistService.loadChecklist(undefined, (err, result) => {
+          expect(err).toBe('The project path must be specified');
+          expect(result).toBeNull();
+        });
+        done();
       });
 
       it('should return an error if checklist file does not exist', (done) => {
diff --git a/test/utils/checklist.spec.js b/test/utils/checklist.spec.js
index 46b40ce..c173033 100644
--- a/test/utils/checklist.spec.js
+++ b/test/utils/checklist.spec.js
@@ -42,6 +42,26 @@ describe('utils', () => {
         });
       });
 
+      it('should return empty result for unmatching content type and asset type', () => {
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.DATA],
+          uri: 'path/to/file.py',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+
+        expect(ChecklistUtil.findAssetLanguagesAndDependencies({
+          type: Constants.AssetType.FILE,
+          contentTypes: [Constants.AssetContentType.CODE],
+          uri: 'path/to/file.csv',
+        })).toEqual({
+          languages: [],
+          dependencies: [],
+        });
+      });
+
       it('should return empty result for directory/folder type assets', () => {
         expect(ChecklistUtil.findAssetLanguagesAndDependencies({
           type: Constants.AssetType.DIRECTORY,

From 338806a7210771b41443cb815683ed13da7ec0a5 Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Fri, 18 Oct 2024 21:21:14 +0530
Subject: [PATCH 42/43] adds comments and updates checklist docs, enabling
 decent documentation all around the project, and some minor fixes

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/components/Project/Project.js             | 21 ++++++----
 .../ChecklistItem/ChecklistItem.js            | 42 +++++++++----------
 .../ReproChecklist/ReproChecklist.js          | 10 ++++-
 .../CreateProjectDialog.js                    |  1 +
 app/containers/ProjectPage/ProjectPage.js     | 12 ++++--
 app/main.dev.js                               | 11 ++++-
 app/services/checklist.js                     | 15 +++++++
 app/utils/checklist.js                        | 12 ++++++
 app/utils/general.js                          |  5 +++
 docs/ReproducibilityChecklists-DataModels.md  | 24 +++++------
 10 files changed, 106 insertions(+), 47 deletions(-)

diff --git a/app/components/Project/Project.js b/app/components/Project/Project.js
index 119f7d4..9c56014 100644
--- a/app/components/Project/Project.js
+++ b/app/components/Project/Project.js
@@ -305,6 +305,14 @@ class Project extends Component<Props> {
     }
   };
 
+  /**
+   * General handler to either insert a new note for a checklist item or update an existing note for
+   * a checklist item.  It figures out the appropriate action to take depending on if the note parameter
+   * is provided or not. It also updates the entire checklist linked to the project.
+   * @param {object} checklistItem The checklist item for which the note should be added/updated
+   * @param {string} text The note text
+   * @param {object} note Optional parameter if there is an existing note being updated.  If not provided, a new note is assumed.
+   */
   checklistUpsertNoteHandler = (checklistItem, text, note) => {
     if (this.unchangedNote(note,text)) {
       return;
@@ -424,12 +432,6 @@ class Project extends Component<Props> {
     }
   };
 
-  assetSelectedHandler = asset => {
-    if (this.props.onAssetSelected) {
-      this.props.onAssetSelected(asset);
-    }
-  };
-
   projectDeleteNoteHandler = (project, note) => {
     const currentProject = { ...this.props.project };
     if (currentProject.id !== project.id) {
@@ -479,6 +481,11 @@ class Project extends Component<Props> {
     }
   };
 
+  /**
+   * General handler to delete a note for a checklist item. It also updates the entire checklist linked to the project.
+   * @param {object} checklistItem The checklist item for which the note should be deleted
+   * @param {object} note The note to delete
+   */
   checklistDeleteNoteHandler = (checklistItem, note) => {
     const currentProject = { ...this.props.project };
     const actionDescription = this.deleteNoteHandler(
@@ -749,7 +756,7 @@ class Project extends Component<Props> {
             onAddedNote={this.checklistUpsertNoteHandler}
             onUpdatedNote={this.checklistUpsertNoteHandler}
             onDeletedNote={this.checklistDeleteNoteHandler}
-            onSelectedAsset={this.assetSelectedHandler}
+            onSelectedAsset={this.props.onAssetSelected}
           />
         ) : null;
 
diff --git a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
index 62a51d8..d84af97 100644
--- a/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
+++ b/app/components/ReproChecklist/ChecklistItem/ChecklistItem.js
@@ -2,8 +2,8 @@ import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import styles from './ChecklistItem.css';
 import NoteEditor from '../../NoteEditor/NoteEditor';
-import { AddBox, ContentCopy , Done, Delete} from '@mui/icons-material';
-import { IconButton, Button, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
+import { ContentCopy , Done, Delete} from '@mui/icons-material';
+import { IconButton, Dialog, DialogActions, DialogContent, DialogContentText, DialogTitle } from '@mui/material';
 import { FaFolderOpen, FaFolderMinus, FaChevronUp, FaChevronDown } from 'react-icons/fa';
 import AssetTree from '../../AssetTree/AssetTree';
 import AssetUtil from '../../../utils/asset';
@@ -17,15 +17,25 @@ function ChecklistItem(props) {
   const treeRef = React.useRef(null);
 
   const [expanded, setExpanded] = useState(false);
+
+  const [copiedUrlId, setCopiedUrlId] = useState(null);
+
   const [showImages, setShowImages] = useState(false);
   const [showURLs, setShowURLs] = useState(false);
   const [showSubChecks, setShowSubChecks] = useState(false);
-  const [copiedUrlId, setCopiedUrlId] = useState(null);
-  const [selectedAsset, setSelectedAsset] = useState();
+
+  const [selectedAsset, setSelectedAsset] = useState(null);
   const [addAsset, setAddAsset] = useState(false);
   const [assetTitle, setAssetTitle] = useState('');
   const [assetDescription, setAssetDescription] = useState('');
 
+  const resetAssetDialog = () => {
+    setAddAsset(false);
+    setAssetTitle('');
+    setAssetDescription('');
+    setSelectedAsset(null);
+  };
+
   const handleSelectAsset = (selAsset) => {
     let asset = selAsset;
     if (asset && (asset.contentTypes === null || asset.contentTypes === undefined)) {
@@ -38,6 +48,8 @@ function ChecklistItem(props) {
       if (asset.type === Constants.AssetType.FILE) {
         const fileName = AssetUtil.getAssetNameFromUri(asset.uri);
         setAssetTitle(fileName);
+      // Handles case for URL assets
+      // TODO: Title is currently the same as URI, some way to get a better title?
       } else if (asset.type === Constants.AssetType.URL) {
         setAssetTitle(asset.uri);
       } else {
@@ -62,10 +74,12 @@ function ChecklistItem(props) {
     }
 
     if (selectedAsset.type === Constants.AssetType.FILE) {
+      // Adds image files to checklist images
       if(selectedAsset.contentTypes.includes(Constants.AssetContentType.IMAGE)) {
         const updatedItem = { ...item, images: [...item.images, {id: uuidv4(), uri: selectedAsset.uri, title: assetTitle, description: assetDescription}] };
         onItemUpdate(updatedItem);
         setShowImages(true);
+      // Adds file as URL
       } else {
         const updatedItem = { ...item, urls: [...item.urls, {id: uuidv4(), hyperlink: AssetUtil.absoluteToRelativePath(project.path, selectedAsset), title: assetTitle, description: assetDescription}] };
         onItemUpdate(updatedItem);
@@ -77,13 +91,11 @@ function ChecklistItem(props) {
       setShowURLs(true);
     }
 
-    setAddAsset(false);
-    setAssetTitle('');
-    setAssetDescription('');
-    setSelectedAsset(null);
+    resetAssetDialog();
   }
 
   const handleCopy = (urlId, hyperlink) => {
+    // Copy the URL to the clipboard
     navigator.clipboard.writeText(hyperlink).then(() => {
       setCopiedUrlId(urlId);
       setTimeout(() => {
@@ -103,10 +115,6 @@ function ChecklistItem(props) {
   };
 
   const handleNoteUpdate = (note, text) => {
-    if (!text) {
-      console.log("Detected an empty new note - this will not be created");
-      return;
-    }
     if (note) {
       if (onUpdatedNote) {
         onUpdatedNote(item, text, note);
@@ -122,9 +130,6 @@ function ChecklistItem(props) {
     if (onDeletedNote) {
       onDeletedNote(item, note);
     }
-
-    const updatedItem = { ...item, notes: item.notes.filter((n) => n.id !== note.id) };
-    onItemUpdate(updatedItem);
   };
 
   return (
@@ -248,12 +253,7 @@ function ChecklistItem(props) {
                 <button onClick={() => handleAddAsset()} className={styles.submitButton}>
                   Add
                 </button>
-                <button onClick={() => {
-                  setAddAsset(false);
-                  setAssetTitle('');
-                  setAssetDescription('');
-                  setSelectedAsset(null);
-                }} className={styles.cancelButton} autoFocus>
+                <button onClick={() => resetAssetDialog()} className={styles.cancelButton} autoFocus>
                   Cancel
                 </button>
               </DialogActions>
diff --git a/app/components/ReproChecklist/ReproChecklist.js b/app/components/ReproChecklist/ReproChecklist.js
index ed24559..eaab298 100644
--- a/app/components/ReproChecklist/ReproChecklist.js
+++ b/app/components/ReproChecklist/ReproChecklist.js
@@ -18,15 +18,18 @@ function ReproChecklist(props) {
   const { project, checklist, error, onUpdated, onAddedNote, onUpdatedNote, onDeletedNote, onSelectedAsset} = props;
   const [openExportDialog, setOpenExportDialog] = useState(false);
 
+  // this useEffect hook is here to load the scan results for all the checklist statements
   useEffect(() => {
     if (project && checklist && !error) {
       if(project.assets) {
+        // scan result for the first checklist statement
         const scanResult1 = ChecklistUtil.findAssetLanguagesAndDependencies(project.assets);
         checklist[0].scanResult = scanResult1;
       }
     }
   }, [project]);
 
+  // Handles the update of checklist for changes in the checklist items
   const handleItemUpdate = (updatedItem) => {
     const updatedChecklist = checklist.map(item =>
       item.id === updatedItem.id ? updatedItem : item
@@ -34,7 +37,9 @@ function ReproChecklist(props) {
     onUpdated(project, updatedChecklist);
   };
 
+  // Handles the generation of the reproducibility checklist report in PDF format
   const handleReportGeneration = (exportNotes) => {
+    // pdfMake requires base64 encoded images
     const checkedIcon = GeneralUtil.convertImageToBase64(path.join(__dirname, 'images/yes.png'));
     const statWrapLogo = GeneralUtil.convertImageToBase64(path.join(__dirname, 'images/banner.png'));
 
@@ -132,7 +137,7 @@ function ReproChecklist(props) {
           const imageWidth = 135;
           if(item.images && item.images.length > 0){
             images = item.images.map((image) => {
-              const base64Image = convertImageToBase64(image.uri);
+              const base64Image = GeneralUtil.convertImageToBase64(image.uri);
               if (base64Image) {
                 return {
                   image: base64Image,
@@ -145,6 +150,8 @@ function ReproChecklist(props) {
             });
           }
 
+          // Rendering images by rows, as rendering in columns overflows the page and we can't wrap columns under each other,
+          // math for 3 images per row is as follows:
           // imageWidth*n + calumnGap*(n-1) <= maxWidth - leftMargin - rightMargin
           // 135*n + 10*(n-1) <= 450 - 20 - 0;
           // n <= 440/145 --> n = 3
@@ -297,6 +304,7 @@ function ReproChecklist(props) {
           </DialogContentText>
         </DialogContent>
         <DialogActions>
+          {/* selective export of notes */}
           <Button onClick={() => handleReportGeneration(true)} color="primary">
             Yes
           </Button>
diff --git a/app/containers/CreateProjectDialog/CreateProjectDialog.js b/app/containers/CreateProjectDialog/CreateProjectDialog.js
index 5f1119d..a244ec6 100644
--- a/app/containers/CreateProjectDialog/CreateProjectDialog.js
+++ b/app/containers/CreateProjectDialog/CreateProjectDialog.js
@@ -161,6 +161,7 @@ class CreateProjectDialog extends Component {
           'info',
           this.context,
         );
+        // Seed the project checklist with the null or falsey values
         const projectChecklist = ChecklistUtil.initializeChecklist();
         ipcRenderer.send(
           Messages.WRITE_PROJECT_CHECKLIST_REQUEST,
diff --git a/app/containers/ProjectPage/ProjectPage.js b/app/containers/ProjectPage/ProjectPage.js
index 0a0304e..ec8f41c 100644
--- a/app/containers/ProjectPage/ProjectPage.js
+++ b/app/containers/ProjectPage/ProjectPage.js
@@ -37,7 +37,7 @@ class ProjectPage extends Component {
       selectedProject: null,
       // The logs (aka Project Log) for the selected project
       selectedProjectLogs: null,
-
+      // The checklist for the selected project
       selectedProjectChecklist: null,
 
       // UI element to inform us what the popup project list menu is attached to
@@ -176,6 +176,7 @@ class ProjectPage extends Component {
     ipcRenderer.send(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, this.state.selectedProject);
   }
 
+  // This handler writes the updated checklist to the checklist file.
   handleChecklistUpdate(project, checklist) {
     ipcRenderer.send(Messages.WRITE_PROJECT_CHECKLIST_REQUEST, project.path, checklist);
   }
@@ -209,6 +210,11 @@ class ProjectPage extends Component {
     }
   }
 
+  /**
+   * Called when a project checklist is loaded.
+   * @param {object} sender The sender of the message
+   * @param {object} response Response containing a project ID and the checklist (if loaded)
+   */
   handleLoadProjectChecklistResponse(sender, response) {
     if (!response || !response.projectId) {
       return;
@@ -217,7 +223,7 @@ class ProjectPage extends Component {
     // Initialize the checklist file if it doesn't exist, for all the already existing projects
     const projectChecklist = ChecklistUtil.initializeChecklist();
     if (response.checklist && response.checklist.length === 0) {
-      // response only returns project id, we need to get the project path
+      // response only returns project id, we need to find the project path
       const project = this.state.projects.find((p) => p.id === response.projectId);
       ipcRenderer.send(Messages.WRITE_PROJECT_CHECKLIST_REQUEST, project.path, projectChecklist);
     }
@@ -234,7 +240,7 @@ class ProjectPage extends Component {
 
   handleProjectExternallyChangedResponse(sender, response) {
     // If any project externally changes - even if it's not the one we currently have selected - we want
-    // to reload the project log so we can detect changes and notify (if needed);
+    // to reload the project log and checklist, so we can detect changes and notify (if needed);
     if (response && response.projectId && this.state.projects) {
       const foundProject = this.state.projects.find((project) => project.id === response.projectId);
       if (foundProject) {
diff --git a/app/main.dev.js b/app/main.dev.js
index 863b9cc..4a16828 100644
--- a/app/main.dev.js
+++ b/app/main.dev.js
@@ -666,6 +666,9 @@ ipcMain.on(Messages.LOAD_PROJECT_LOG_REQUEST, async (event, project) => {
   });
 });
 
+/**
+ * Write the project checklist to the checklist file.
+ */
 ipcMain.on(
   Messages.WRITE_PROJECT_CHECKLIST_REQUEST,
   async (event, projectPath, checklist) => {
@@ -674,6 +677,10 @@ ipcMain.on(
   },
 );
 
+/**
+ * Load the project checklist from the checklist file.
+ * Returns response with checklist data and error message if any.
+ */
 ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
   const response = {
     projectId: project ? project.id : null,
@@ -688,7 +695,9 @@ ipcMain.on(Messages.LOAD_PROJECT_CHECKLIST_REQUEST, async (event, project) => {
     return;
   }
 
-  checklistService.loadChecklist(project.path, (error, checklist) =>{
+  checklistService.loadChecklist(project.path, (error, checklist) => {
+    // This checks for error when there is issue reading the checklist file,
+    // not when the checklist file is not found. For the latter, we return an empty array.
     if (error && !checklist) {
       response.error = true;
       response.errorMessage = `There was an error reading the project checklist ${error}`;
diff --git a/app/services/checklist.js b/app/services/checklist.js
index d3b1463..db25eb1 100644
--- a/app/services/checklist.js
+++ b/app/services/checklist.js
@@ -5,11 +5,18 @@ const os = require('os');
 const path = require('path');
 
 export default class ChecklistService {
+  /**
+   * Writes the checklist data to the checklist file
+   * @param {string} projectPath The path to the project
+   * @param {object} checklist The checklist data to write
+   * @throws {Error} If the project path or checklist data is invalid or if there is an error writing the file
+   */
   writeChecklist(projectPath, checklist) {
     if (!projectPath || !checklist) {
       throw new Error('Invalid project path or checklist data');
     }
 
+    // Unix-based paths may start with ~, which needs to be replaced with the home directory
     const checklistFilePath = path.join(
       projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
@@ -19,12 +26,18 @@ export default class ChecklistService {
     fs.writeFileSync(checklistFilePath, JSON.stringify(checklist));
   }
 
+  /**
+   * Loads the checklist data from the checklist file
+   * @param {string} projectPath The path to the project
+   * @param {function} callback The callback function to call with the loaded checklist data and error message
+   */
   loadChecklist(projectPath, callback) {
     if (!projectPath) {
       callback('The project path must be specified', null);
       return;
     }
 
+    // Unix-based paths may start with ~, which needs to be replaced with the home directory
     const checklistFilePath = path.join(
       projectPath.replace('~', os.homedir()),
       Constants.StatWrapFiles.BASE_FOLDER,
@@ -32,6 +45,8 @@ export default class ChecklistService {
     );
 
     if (!fs.existsSync(checklistFilePath)) {
+      // If the checklist file does not exist, return an empty array
+      // so that it doesn't display error in the UI for existing projects
       callback('Checklist file not found', []);
       return;
     }
diff --git a/app/utils/checklist.js b/app/utils/checklist.js
index aefc28d..9cf38dc 100644
--- a/app/utils/checklist.js
+++ b/app/utils/checklist.js
@@ -3,6 +3,10 @@ import AssetsConfig from '../constants/assets-config';
 const path = require('path');
 
 export default class ChecklistUtil {
+  /**
+   * This function initializes the checklist with the statements and seeds other properties
+   * @returns {object} The initialized checklist
+   */
   static initializeChecklist() {
     const checklist = [];
     Constants.CHECKLIST.forEach((statement, index) => {
@@ -21,6 +25,13 @@ export default class ChecklistUtil {
     return checklist;
   }
 
+  /**
+   * This function returns the languages and dependencies of an asset and its children
+   * @param {object} asset The asset to find the languages and dependencies of
+   * @param {object} languages Empty object that acts like a map to store the languages found as keys
+   * @param {object} dependencies Empty object that acts like a map to store the dependencies found as keys
+   * @returns {object} An object containing the languages and dependencies found as arrays
+   */
   static findAssetLanguagesAndDependencies(asset, languages = {}, dependencies = {}) {
     if (!asset) {
       return {
@@ -35,6 +46,7 @@ export default class ChecklistUtil {
 
       if(ext){
         AssetsConfig.contentTypes.forEach((contentType) => {
+          // Ensures both the extension and content type are for code files
           if(contentType.categories.includes(Constants.AssetContentType.CODE) && contentType.extensions.includes(ext)) {
             languages[contentType.name] = true;
           }
diff --git a/app/utils/general.js b/app/utils/general.js
index 6624528..b92a21a 100644
--- a/app/utils/general.js
+++ b/app/utils/general.js
@@ -155,6 +155,11 @@ export default class GeneralUtil {
     }, []);
   }
 
+  /**
+   * This function converts an image file to it's Base64 string
+   * @param {string} filePath The path to the image file
+   * @returns {string} The Base64 string of the image
+   */
   static convertImageToBase64(filePath) {
     try {
       const file = fs.readFileSync(filePath);
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
index 38bb94e..c45eb62 100644
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ b/docs/ReproducibilityChecklists-DataModels.md
@@ -9,14 +9,13 @@ The **Checklist Object** represents a single checklist item within the reproduci
 | Attribute          | Type       | Description                                                                                                                                               |
 | ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                     |
+| `name`             | String     | The name of the checklist item.                                                                                                                           |
 | `statement`        | String     | The statement or question associated with the checklist item.                                                                                             |
-| `type`             | String     | Indicates the type of checklist item, such as boolean or descriptive.                                                                                     |
-| `answer`           | String     | Stores the user's response to the checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                                         |
-| `userNotes`        | Array ([]Note)| An array containing user-added notes associated with the checklist item.                                                                               |
-| `attachedImages`   | Array ([]Image)| An array containing image data of images attached to the checklist item.                                                                              |
-| `attachedURLs`     | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
-| `subChecklist`    | Array ([]Sub_checklist)| An array containing sub-checklist associated with the checklist item.                                                                        |
-| `updated`          | String     | The timestamp indicating when the checklist item was last updated.                                                                                        |
+| `answer`           | Bool       | Stores the user's response to the checklist item.                                                                                                         |
+| `notes`            | Array ([]Note)| An array containing user notes attached to the checklist item.                                                                                         |
+| `images`           | Array ([]Image)| An array containing data of image files attached to the checklist item.                                                                               |
+| `urls`             | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
+| `subChecklist`     | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                        |
 
 ### Sub-Checklist Object
 
@@ -30,9 +29,7 @@ The **Sub-Checklist Object** represents a sub-item within a checklist item. It s
 | --------------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                  |
 | `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
-| `type`          | String   | Indicates the type of sub-checklist item, such as boolean or descriptive.                                                                                  |
-| `answer`        | String   | Stores the user's response to the sub-checklist item. ('yes'/'no' for boolean type, 'answer description' for descriptive type)                                                                                         |
-| `updated`       | String   | The timestamp indicating when the sub-checklist item was last updated.                                                                                     |
+| `answer`        | Bool   | Stores the user's response to the sub-checklist item.                                                                                                        |
 
 ### Note Object
 
@@ -54,22 +51,22 @@ This follows the same structure as the existing [notes data type](https://github
 
 #### About
 
-The **Image Object** stores image data of the image attached to checklist items.
+The **Image Object** stores data of the image files attached to checklist items.
 
 #### Attributes
 
 | Attribute       | Type     | Description                                                                                                                                               |
 | --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `id`            | UUID     | A generated unique identifier for the image.                                                                                                              |
+| `uri`           | String   | The URI of the image file.                                                                                                                                |
 | `title`         | String   | The title of the image.                                                                                                                                   |
 | `description`   | String   | A brief description of the image.                                                                                                                         |
-| `updated`       | String   | The timestamp indicating when the image was last updated.                                                                                                 |
 
 ### URL Object
 
 #### About
 
-The **URL Object** stores hyperlink of the URL attached to checklist items.
+The **URL Object** stores hyperlink of the URLs attached to checklist items.
 
 #### Attributes
 
@@ -79,6 +76,5 @@ The **URL Object** stores hyperlink of the URL attached to checklist items.
 | `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
 | `title`         | String   | The title of the URL.                                                                                                                                     |
 | `description`   | String   | A brief description of the URL.                                                                                                                           |
-| `updated`       | String   | The timestamp indicating when the URL was last updated.                                                                                                   |
 
 This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.

From 8a96e60cd6910af9df21a7d88d02de7eb28288de Mon Sep 17 00:00:00 2001
From: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
Date: Sat, 19 Oct 2024 12:18:53 +0530
Subject: [PATCH 43/43] renames the checklist doc for data struct, and
 completes rename of checklists to checklist everywhere

Signed-off-by: AdiAkhileshSingh15 <adiakhilesh.singh.cse21@itbhu.ac.in>
---
 app/services/checklist.js                    |  4 +-
 docs/ReproducibilityChecklist-Planning.md    | 39 ++++++++++
 docs/ReproducibilityChecklist.md             | 80 ++++++++++++++++++++
 docs/ReproducibilityChecklists-DataModels.md | 80 --------------------
 docs/ReproducibilityChecklists-Planning.md   | 39 ----------
 5 files changed, 121 insertions(+), 121 deletions(-)
 create mode 100644 docs/ReproducibilityChecklist-Planning.md
 create mode 100644 docs/ReproducibilityChecklist.md
 delete mode 100644 docs/ReproducibilityChecklists-DataModels.md
 delete mode 100644 docs/ReproducibilityChecklists-Planning.md

diff --git a/app/services/checklist.js b/app/services/checklist.js
index db25eb1..d35ff28 100644
--- a/app/services/checklist.js
+++ b/app/services/checklist.js
@@ -53,8 +53,8 @@ export default class ChecklistService {
 
     try {
       const data = fs.readFileSync(checklistFilePath);
-      const checklists = JSON.parse(data);
-      callback(null, checklists);
+      const checklist = JSON.parse(data);
+      callback(null, checklist);
     } catch (err) {
       callback('Error reading or parsing checklist file', null);
     }
diff --git a/docs/ReproducibilityChecklist-Planning.md b/docs/ReproducibilityChecklist-Planning.md
new file mode 100644
index 0000000..ab7a2f1
--- /dev/null
+++ b/docs/ReproducibilityChecklist-Planning.md
@@ -0,0 +1,39 @@
+# Reproducible Research Checklist
+
+This document provides design guidance and general requirements for the reproducible research checklist feature in StatWrap.
+
+## Modes of Operation
+
+There are two modes of operation for the checklist:
+
+### 1. Automated information gathering / decision making (StatWrap)
+
+StatWrap will use information from project assets and user-entered metadata in order to provide information about reproducible research practices. This will be used to **inform** users, but will not make a binary indicator (yes/no) about if a practice is "reproducible" or not.
+
+StatWrap should be configured to provide information about the following categories of data. The way the data could be displayed is noted, but is not intended to limit the final implementation. For each of these, there should be a service method that is able to perform the processed logic. Unlike the actual checklist UI, these items are not configurable by the end user, they are built within StatWrap.
+
+1. **Summarize the software used** - this should include programming language(s) and dependencies. Programming languages can be inferred from file extensions. Dependencies can be inferred from specific references in code files (already processed by StatWrap), as well as dependency files used for specific languages (e.g., `requirements.txt` for Python). StatWrap does not need to determine the specific version used in any environment if it is not specified elsewhere.
+2. **Multiple versions of a file** - use a heuristic from file names to determine if the user has versioned files using a naming convention, as opposed to using source control. For example, `main_analysis.R` and `main_analysis_v2.R` or `main_analysis-jd.R`. StatWrap could use metrics other than the file name, such as similarity of file content, to further infer if the files are likely versioned. For a grouping of files that StatWrap thinks are versioned, it should check attributes to:
+
+   1. See if any of the files are marked as 'archived'.
+   2. If more than one file is marked as an 'entry point'.
+
+3. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`. If so, display these file(s)/folder(s) as the projecct documentation.
+4. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project. This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`). StatWrap should report which file(s) are using absolute paths.
+5. **Binary / proprietary file formats for data** - flag data files that are not purely text-based. This can be done from a configureable list of file extensions.
+6. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
+   1. Input data - data flagged with an attribute of "Input / Raw Data", or data contained in folders using a configurable list of folder names (e.g., `raw`, `input`)
+   2. Derived data - data flagged with an attribute of "Derived", or data contained in folders using a configurable list of folder names (e.g., `output`, `derived`)
+   3. Data (general) - data files that we cannot otherwise categorize
+7. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps. Note that a single code file may have multiple annotations:
+   1. Data acquisition - used to import / pull data. This would be flagged with an attribute of "Data acquisition".
+   2. Data processing - this would be flagged with an attribute of "Data processing"
+   3. Analysis - this would be flagged with an attribute of "Analysis"
+8. **Entry points** - StatWrap should list all code files flagged as entry points by the user. If none, and code files exist, this should also be noted ("No entry point has been specified"). This could be combined with the previous item.
+9. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data. Summarize these for the user as external assets that are being referenced.
+
+### 2. Human-entered information / decision making (user)
+
+This is more of the traditional "checklist", where the user is presented with a list of questions that they may attest to. Some of the answers may be pre-filled using data collected by StatWrap as defined in the automated information gathering (previous section).
+
+(See proposal by Adi)
diff --git a/docs/ReproducibilityChecklist.md b/docs/ReproducibilityChecklist.md
new file mode 100644
index 0000000..f6895e8
--- /dev/null
+++ b/docs/ReproducibilityChecklist.md
@@ -0,0 +1,80 @@
+## Checklist Object
+
+### About
+
+The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklist.
+
+### Attributes
+
+| Attribute      | Type                    | Description                                                             |
+| -------------- | ----------------------- | ----------------------------------------------------------------------- |
+| `id`           | UUID                    | A generated unique identifier for the checklist item.                   |
+| `name`         | String                  | The name of the checklist item.                                         |
+| `statement`    | String                  | The statement or question associated with the checklist item.           |
+| `answer`       | Bool                    | Stores the user's response to the checklist item.                       |
+| `notes`        | Array ([]Note)          | An array containing user notes attached to the checklist item.          |
+| `images`       | Array ([]Image)         | An array containing data of image files attached to the checklist item. |
+| `urls`         | Array ([]URL)           | An array containing URLs attached to the checklist item.                |
+| `subChecklist` | Array ([]Sub_checklist) | An array containing sub-checklist associated with the checklist item.   |
+
+### Sub-Checklist Object
+
+#### About
+
+The **Sub-Checklist Object** represents a sub-item within a checklist item. It shares similar attributes with the Checklist Object, except for attachments, but is nested within the parent checklist item.
+
+#### Attributes
+
+| Attribute   | Type   | Description                                                       |
+| ----------- | ------ | ----------------------------------------------------------------- |
+| `id`        | UUID   | A generated unique identifier for the sub-checklist item.         |
+| `statement` | String | The statement or question associated with the sub-checklist item. |
+| `answer`    | Bool   | Stores the user's response to the sub-checklist item.             |
+
+### Note Object
+
+#### About
+
+The **Note Object** stores user-added note associated with checklist items.
+This follows the same structure as the existing [notes data type](https://github.com/StatTag/StatWrap/blob/master/docs/Notes.md)
+
+#### Attributes
+
+| Attribute | Type   | Description                                                          |
+| --------- | ------ | -------------------------------------------------------------------- |
+| `id`      | UUID   | A generated unique identifier for the note.                          |
+| `author`  | String | A display name taken from StatWrap to indicate who created the note. |
+| `updated` | String | The timestamp indicating when the note was last updated.             |
+| `content` | String | The text content of the note.                                        |
+
+### Image Object
+
+#### About
+
+The **Image Object** stores data of the image files attached to checklist items.
+
+#### Attributes
+
+| Attribute     | Type   | Description                                  |
+| ------------- | ------ | -------------------------------------------- |
+| `id`          | UUID   | A generated unique identifier for the image. |
+| `uri`         | String | The URI of the image file.                   |
+| `title`       | String | The title of the image.                      |
+| `description` | String | A brief description of the image.            |
+
+### URL Object
+
+#### About
+
+The **URL Object** stores hyperlink of the URLs attached to checklist items.
+
+#### Attributes
+
+| Attribute     | Type   | Description                                |
+| ------------- | ------ | ------------------------------------------ |
+| `id`          | UUID   | A generated unique identifier for the URL. |
+| `hyperlink`   | String | The hyperlink associated with the URL.     |
+| `title`       | String | The title of the URL.                      |
+| `description` | String | A brief description of the URL.            |
+
+This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.
diff --git a/docs/ReproducibilityChecklists-DataModels.md b/docs/ReproducibilityChecklists-DataModels.md
deleted file mode 100644
index c45eb62..0000000
--- a/docs/ReproducibilityChecklists-DataModels.md
+++ /dev/null
@@ -1,80 +0,0 @@
-## Checklist Object
-
-### About
-
-The **Checklist Object** represents a single checklist item within the reproducibility checklist. It encompasses various attributes and sub-objects to capture different aspects such as statement, type, answer, user notes, attached images, attached URLs, and sub-checklist.
-
-### Attributes
-
-| Attribute          | Type       | Description                                                                                                                                               |
-| ------------------ | ---------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`               | UUID       | A generated unique identifier for the checklist item.                                                                                                     |
-| `name`             | String     | The name of the checklist item.                                                                                                                           |
-| `statement`        | String     | The statement or question associated with the checklist item.                                                                                             |
-| `answer`           | Bool       | Stores the user's response to the checklist item.                                                                                                         |
-| `notes`            | Array ([]Note)| An array containing user notes attached to the checklist item.                                                                                         |
-| `images`           | Array ([]Image)| An array containing data of image files attached to the checklist item.                                                                               |
-| `urls`             | Array ([]URL)| An array containing URLs attached to the checklist item.                                                                                                |
-| `subChecklist`     | Array ([]Sub_checklist)| An array containing sub-checklists associated with the checklist item.                                                                        |
-
-### Sub-Checklist Object
-
-#### About
-
-The **Sub-Checklist Object** represents a sub-item within a checklist item. It shares similar attributes with the Checklist Object, except for attachments, but is nested within the parent checklist item.
-
-#### Attributes
-
-| Attribute       | Type     | Description                                                                                                                                                |
-| --------------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the sub-checklist item.                                                                                                  |
-| `statement`     | String   | The statement or question associated with the sub-checklist item.                                                                                          |
-| `answer`        | Bool   | Stores the user's response to the sub-checklist item.                                                                                                        |
-
-### Note Object
-
-#### About
-
-The **Note Object** stores user-added note associated with checklist items.
-This follows the same structure as the existing [notes data type](https://github.com/StatTag/StatWrap/blob/master/docs/Notes.md)
-
-#### Attributes
-
-| Attribute       | Type     | Description                                                                                                                                               |
-| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the note.                                                                                                               |
-| `author`        | String   | A display name taken from StatWrap to indicate who created the note.                                                                                      |
-| `updated`       | String   | The timestamp indicating when the note was last updated.                                                                                                  |
-| `content`       | String   | The text content of the note.                                                                                                                             |
-
-### Image Object
-
-#### About
-
-The **Image Object** stores data of the image files attached to checklist items.
-
-#### Attributes
-
-| Attribute       | Type     | Description                                                                                                                                               |
-| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the image.                                                                                                              |
-| `uri`           | String   | The URI of the image file.                                                                                                                                |
-| `title`         | String   | The title of the image.                                                                                                                                   |
-| `description`   | String   | A brief description of the image.                                                                                                                         |
-
-### URL Object
-
-#### About
-
-The **URL Object** stores hyperlink of the URLs attached to checklist items.
-
-#### Attributes
-
-| Attribute       | Type     | Description                                                                                                                                               |
-| --------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `id`            | UUID     | A generated unique identifier for the URL.                                                                                                                |
-| `hyperlink`     | String   | The hyperlink associated with the URL.                                                                                                                    |
-| `title`         | String   | The title of the URL.                                                                                                                                     |
-| `description`   | String   | A brief description of the URL.                                                                                                                           |
-
-This documentation outlines the structure and attributes of various objects involved in the reproducibility checklist project.
diff --git a/docs/ReproducibilityChecklists-Planning.md b/docs/ReproducibilityChecklists-Planning.md
deleted file mode 100644
index 3220f2d..0000000
--- a/docs/ReproducibilityChecklists-Planning.md
+++ /dev/null
@@ -1,39 +0,0 @@
-# Reproducible Research Checklist
-
-This document provides design guidance and general requirements for the reproducible research checklist feature in StatWrap.
-
-## Modes of Operation
-
-There are two modes of operation for the checklist:
-
-### 1. Automated information gathering / decision making (StatWrap)
-
-StatWrap will use information from project assets and user-entered metadata in order to provide information about reproducible research practices.  This will be used to **inform** users, but will not make a binary indicator (yes/no) about if a practice is "reproducible" or not.
-
-StatWrap should be configured to provide information about the following categories of data.  The way the data could be displayed is noted, but is not intended to limit the final implementation.  For each of these, there should be a service method that is able to perform the processed logic.  Unlike the actual checklist UI, these items are not configurable by the end user, they are built within StatWrap.
-
-1. **Summarize the software used** - this should include programming language(s) and dependencies.  Programming languages can be inferred from file extensions.  Dependencies can be inferred from specific references in code files (already processed by StatWrap), as well as dependency files used for specific languages (e.g., `requirements.txt` for Python).  StatWrap does not need to determine the specific version used in any environment if it is not specified elsewhere.
-2. **Multiple versions of a file** - use a heuristic from file names to determine if the user has versioned files using a naming convention, as opposed to using source control. For example, `main_analysis.R` and `main_analysis_v2.R` or `main_analysis-jd.R`.  StatWrap could use metrics other than the file name, such as similarity of file content, to further infer if the files are likely versioned.  For a grouping of files that StatWrap thinks are versioned, it should check attributes to:
-
-    1. See if any of the files are marked as 'archived'.
-    2. If more than one file is marked as an 'entry point'.
-
-4. **Location of project documentation** - StatWrap should detect the presence of a README file (any extension), and if there is a folder named `doc`, `docs`, or `documentation`.  If so, display these file(s)/folder(s) as the projecct documentation.
-5. **Absolute paths used** - StatWrap should detect if explicit absolute paths are used within the code files within a project.  This should detect across Mac, Linux, and Windows, including multiple ways of denoting paths across OS (e.g., on Windows languages like R will let you reference `C:/test/file.csv` or `C:\test\file.csv`), as well as fully qualified network paths (e.g., `\\research\files\test.csv`).  StatWrap should report which file(s) are using absolute paths.
-6. **Binary / proprietary file formats for data** - flag data files that are not purely text-based.  This can be done from a configureable list of file extensions.
-7. **List categories of data files/folders** - using user-assigned attributes, or folder naming conventions, display the list of files associated with different categories of data:
-	1. Input data - data flagged with an attribute of "Input / Raw Data", or data contained in folders using a configurable list of folder names (e.g., `raw`, `input`)
-	2. Derived data - data flagged with an attribute of "Derived", or data contained in folders using a configurable list of folder names (e.g., `output`, `derived`)
-	3. Data (general) - data files that we cannot otherwise categorize
-8. **List categories of code files/folders** - using user-assigned attributes, or folder naming conventions, display the list of code files associated with different processing steps.  Note that a single code file may have multiple annotations:
-   1. Data acquisition - used to import / pull data. This would be flagged with an attribute of "Data acquisition".
-   2. Data processing - this would be flagged with an attribute of "Data processing"
-   3. Analysis - this would be flagged with an attribute of "Analysis"
-9. **Entry points** - StatWrap should list all code files flagged as entry points by the user.  If none, and code files exist, this should also be noted ("No entry point has been specified").  This could be combined with the previous item.
-10. **External assets** - identify references in the code to: databases, APIs, web URLs that contain data.  Summarize these for the user as external assets that are being referenced.
-
-### 2. Human-entered information / decision making (user)
-
-This is more of the traditional "checklist", where the user is presented with a list of questions that they may attest to.  Some of the answers may be pre-filled using data collected by StatWrap as defined in the automated information gathering (previous section).
-
-(See proposal by Adi)