[issue_tracker] Add attachments to issues

CHANGELOG.md

@@ -16,6 +16,7 @@ changes in the following format: PR #1234***
 - Very old instrument relying on QuickForm may have issues due to code changes (PR #4928)
 
 #### Modules 
+- The issue_tracker module now has the feature of uploading attachments to new or existing issues.
 
 ##### Battery Manager
  - New module created to manage the entries in the test_battery table of the database.

SQL/0000-00-00-schema.sql

@@ -2091,3 +2091,17 @@ CREATE TABLE `publication_users_edit_perm_rel` (
   CONSTRAINT `FK_publication_users_edit_perm_rel_PublicationID` FOREIGN KEY (`PublicationID`) REFERENCES `publication` (`PublicationID`),
   CONSTRAINT `FK_publication_users_edit_perm_rel_UserID` FOREIGN KEY (`UserID`) REFERENCES `users` (`ID`)
 ) ENGINE=InnoDB DEFAULT CHARSET='utf8';
+
+CREATE TABLE `issues_attachments` (
+    `ID` int NOT NULL AUTO_INCREMENT,
+    `issueID` int(11) NOT NULL,
+    `file_hash` varchar(64) NOT NULL,
+    `date_added` timestamp NOT NULL DEFAULT current_timestamp(),
+    `file_name` varchar(255) NOT NULL DEFAULT '',
+    `deleted` tinyint(1) NOT NULL DEFAULT 0,
+    `user` varchar(255) NOT NULL DEFAULT '',
+    `description` text DEFAULT NULL,
+    `file_size` int(20) DEFAULT NULL,
+    `mime_type` varchar(255) NOT NULL DEFAULT '',
+    PRIMARY KEY (`ID`)
+) DEFAULT CHARSET=utf8mb4;

SQL/0000-00-03-ConfigTables.sql

@@ -25,8 +25,8 @@ CREATE TABLE `Config` (
   KEY `fk_Config_1_idx` (`ConfigID`),
   CONSTRAINT `fk_Config_1`
   FOREIGN KEY (`ConfigID`)
-    REFERENCES `ConfigSettings` (`ID`) 
-    ON DELETE CASCADE 
+    REFERENCES `ConfigSettings` (`ID`)
+    ON DELETE CASCADE
     ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
@@ -124,6 +124,9 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPrivate', 'Private Key for Google reCAPTCHA', 1, 0, 'text', ID, 'reCAPTCHA Private Key', 2 FROM ConfigSettings WHERE Name="APIKeys";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'reCAPTCHAPublic', 'Public Key for Google reCaptcha', 1, 0, 'text', ID, 'reCAPTCHA Public Key', 3 FROM ConfigSettings WHERE Name="APIKeys";
 
+-- Issue_Tracker attachments for issues.
+INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`) VALUES (106, 'IssueTrackerDataPath', 'Path to Issue Tracker data files', 1, 0, 'web_path', 26, 'Issue Tracker Data Path', 8);
+
 -- Loris-MRI/Imaging Pipeline options from the $profile (commonly "prod") file
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('imaging_pipeline', 'Imaging Pipeline settings', 1, 0, 'Imaging Pipeline', 12);
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataDirBasepath', 'Base Path to the data directory of Loris-MRI', 1, 0, 'text', ID, 'Loris-MRI Data Directory', 1 FROM ConfigSettings WHERE Name="imaging_pipeline";
@@ -254,3 +257,5 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, 't1'    FROM ConfigSettings WHER
 INSERT INTO Config (ConfigID, Value) SELECT ID, 't2'    FROM ConfigSettings WHERE Name="modalities_to_deface";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 'pd'    FROM ConfigSettings WHERE Name="modalities_to_deface";
 INSERT INTO Config (ConfigID, Value) SELECT ID, 'false'  FROM ConfigSettings WHERE Name="usePwnedPasswordsAPI";
+
+INSERT INTO `Config` (`ID`, `ConfigID`, `Value`) VALUES (106, 106, '/data/issue_tracker/');

SQL/New_patches/2019-10-29_adding_issues_attachments_table.sql

@@ -0,0 +1,21 @@
+CREATE TABLE `issues_attachments` (
+    `ID` int NOT NULL AUTO_INCREMENT,
+    `issueID` int(11) NOT NULL,
+    `file_hash` varchar(64) NOT NULL,
+    `date_added` timestamp NOT NULL DEFAULT current_timestamp(),
+    `file_name` varchar(255) NOT NULL DEFAULT '',
+    `deleted` tinyint(1) NOT NULL DEFAULT 0,
+    `user` varchar(255) NOT NULL DEFAULT '',
+    `description` text DEFAULT NULL,
+    `file_size` int(20) DEFAULT NULL,
+    `mime_type` varchar(255) NOT NULL DEFAULT '',
+    PRIMARY KEY (`ID`)
+) DEFAULT CHARSET=utf8mb4;
+
+INSERT INTO `ConfigSettings` (`ID`, `Name`, `Description`, `Visible`, `AllowMultiple`, `DataType`, `Parent`, `Label`, `OrderNumber`)
+VALUES
+(106, 'IssueTrackerDataPath', 'Path to Issue Tracker data files', 1, 0, 'web_path', 26, 'Issue Tracker Data Path', 8);
+
+INSERT INTO `Config` (`ID`, `ConfigID`, `Value`)
+VALUES
+(106, 106, '/data/issue_tracker/');

modules/issue_tracker/README.md

@@ -1,11 +1,11 @@
 # Issue Tracker
 
 ## Purpose
-The Issues Module allows users to track issues they have with data, or with their LORIS instance itself. A form with pre-defined fields is provided for users to submit issues, and a filter-form gives a sortable and filterable table view of issues viewable by the user.
+The Issues Module allows users to track issues they have with data, or with their LORIS instance itself. A form with pre-defined fields is provided for users to submit issues, upload attachments and a filter-form gives a sortable and filterable table view of issues viewable by the user.
 
 ## Permissions
-- `issue_tracker_reporter` permission allows adding an issue, editing issues created by the user, and commenting on all issues for the site. 
-- `issue_tracker_developer` permission allows to do the same, as well as closing an issue or editing any field of a submitted issue for the site. 
+- `issue_tracker_reporter` permission allows adding an issue, editing issues created by the user, download issue attachments and commenting on all issues for the site.
+- `issue_tracker_developer` permission allows to do the same, as well as closing an issue or editing any field of a submitted issue for the site.
 - `view_all_sites` permission allows a user to view issues relevant to data from other sites. 
 
 Most of the permissions are controlled in `IssueForm.js`, dependent on values returned in `editIssue.php`.

modules/issue_tracker/ajax/EditIssue.php

@@ -28,6 +28,9 @@
  */
 require_once "Email.class.inc";
 
+use LORIS\Data\Filters\HasAnyPermissionOrUserSiteMatch;
+use LORIS\issue_tracker\Provisioners\AttachmentProvisioner;
+
 //TODO: or split it into two files... :P
 if ($_SERVER['REQUEST_METHOD'] === "GET") {
     echo json_encode(getIssueFields());
@@ -112,6 +115,19 @@ function editIssue()
     updateHistory($historyValues, $issueID);
     updateComments($_POST['comment'], $issueID);
 
+    // Attachment for new issue.
+    if (isset($_FILES['file'])) {
+        $attachment = new \LORIS\issue_tracker\UploadHelper();
+        $attachment->setupUploading(
+            $user,
+            $_FILES,
+            array(
+                'fileDescription' => '',
+                'issueID'         => $issueID,
+            )
+        );
+    }
+
     // Adding new assignee to watching
     if (isset($issueValues['assignee'])) {
         $nowWatching = array(
@@ -662,12 +678,24 @@ function getIssueFields()
         $issueID   = $_GET['issueID'];
         $issueData = getIssueData($issueID);
 
-        $desc       = $db->pselect(
+        $desc = $db->pselect(
             "SELECT issueComment
 FROM issues_comments WHERE issueID=:i
 ORDER BY dateAdded LIMIT 1",
             array('i' => $issueID)
         );
+
+        $filter      = new HasAnyPermissionOrUserSiteMatch(
+            array(
+                'issue_tracker_reporter',
+                'issue_tracker_developer'
+            )
+        );
+        $provisioner = (new AttachmentProvisioner($issueID))->filter($filter);
+        $attachments = (new \LORIS\Data\Table())
+            ->withDataFrom($provisioner)
+            ->toArray($user);
+
         $isWatching = $db->pselectOne(
             "SELECT userID, issueID FROM issues_watching
             WHERE issueID=:issueID AND userID=:userID",
@@ -681,7 +709,10 @@ function getIssueFields()
         } else {
             $issueData['watching'] = "Yes";
         }
+        $username = $user->getUsername();
         $issueData['commentHistory'] = getComments($issueID);
+        $issueData['attachments']    = $attachments;
+        $issueData['whoami']         = $username;
         $issueData['othersWatching'] = getWatching($issueID);
         $issueData['desc']           = $desc[0]['issueComment'] ?? '';
     }

modules/issue_tracker/help/issue_tracker.md

@@ -1,11 +1,11 @@
 # Issue Tracker
 
-This module allows you to submit, edit, view, and track issues.
+This module allows you to submit, edit, view, upload and track issues.
 
 Use the *Selection Filter* section to search for specific issues, if desired. In the data table, you can navigate between different tabs—**All Issues**, **Active Issues**, **Closed Issues**, and **My Issues**—to further narrow your results. 
 
 In the table, in the *Title* column, you can click on any issue name to edit its details. 
 
-Click **New Issue** if you wish to add a new issue. Then, populate the fields and click **Submit Issue**.
+Click **New Issue** if you wish to add a new issue. Then, populate the fields and click **Submit Issue**. You may also upload an attachment for the issue.
 
 Note that you can add users to the "Watching" list - this will send email notifications to the selected users when the issue is created and updated. If you are the author of an issue, and you add yourself as Watching, you won't be sent notifications about your own updates. 

modules/issue_tracker/jsx/CommentList.js

@@ -19,10 +19,6 @@ class CommentList extends Component {
   }
 
   render() {
-    const btnCommentsLabel = (this.state.collapsed ?
-      'Show Comment History' :
-      'Hide Comment History');
-
     const changes = this.props.commentHistory.reduce(function(carry, item) {
       let label = item.dateAdded.concat(' - ', item.addedBy);
       if (!carry[label]) {
@@ -59,18 +55,9 @@ class CommentList extends Component {
     }, this);
 
     return (
-      <div>
-        <div className='btn btn-primary'
-             onClick={this.toggleCollapsed}
-             data-toggle='collapse'
-             data-target='#comment-history'
-             style={{margin: '10px 0'}}
-        >
-          {btnCommentsLabel}
-        </div>
-        <div id='comment-history' className='collapse'>
-          {history}
-        </div>
+      <div id='comment-history'>
+        <h3>Comment History</h3>
+        {history}
       </div>
     );
   }

modules/issue_tracker/jsx/IssueForm.js

@@ -1,5 +1,8 @@
 import Loader from 'Loader';
+import Modal from 'jsx/Modal';
 import CommentList from './CommentList';
+import IssueUploadAttachmentForm from './attachments/uploadForm';
+import AttachmentsList from './attachments/attachmentsList';
 
 /**
  * Issue add/edit form
@@ -25,6 +28,7 @@ class IssueForm extends Component {
       isLoaded: false,
       isNewIssue: false,
       issueID: 0,
+      showAttachmentUploadModal: false,
     };
 
     // Bind component instance to custom methods
@@ -33,12 +37,30 @@ class IssueForm extends Component {
     this.setFormData = this.setFormData.bind(this);
     this.isValidForm = this.isValidForm.bind(this);
     this.showAlertMessage = this.showAlertMessage.bind(this);
+    this.closeAttachmentUploadModal = this.closeAttachmentUploadModal.bind(this);
+    this.openAttachmentUploadModal = this.openAttachmentUploadModal.bind(this);
   }
 
   componentDidMount() {
     this.getFormData();
   }
 
+  openAttachmentUploadModal(e) {
+    e.preventDefault();
+    this.setState({showAttachmentUploadModal: true});
+  }
+  closeAttachmentUploadModal() {
+    this.setState({
+      upload: {
+        formData: {
+          fileType: '',
+          fileDescription: '',
+        },
+      },
+      showAttachmentUploadModal: false,
+    });
+  }
+
   render() {
     // If error occurs, return a message.
     // XXX: Replace this with a UI component for 500 errors.
@@ -64,6 +86,8 @@ class IssueForm extends Component {
     let submitButtonValue;
     let commentLabel;
     let isWatching = this.state.issueData.watching;
+    let attachmentUploadBtn = null;
+    let attachmentFileElement = null;
 
     if (this.state.isNewIssue) {
       headerText = 'Create New Issue';
@@ -72,15 +96,36 @@ class IssueForm extends Component {
       dateCreated = 'Sometime Soon!';
       submitButtonValue = 'Submit Issue';
       commentLabel = 'Description';
+      attachmentFileElement = (
+        <FileElement
+          name='file'
+          label='Attachment for issue'
+          onUserInput={this.setFormData}
+          errorMessage={this.state.errorMessage}
+          value={this.state.formData.file}
+        />
+      );
     } else {
       headerText = 'Edit Issue #' + this.state.issueData.issueID;
       lastUpdateValue = this.state.issueData.lastUpdate;
       lastUpdatedByValue = this.state.issueData.lastUpdatedBy;
       dateCreated = this.state.issueData.dateCreated;
       submitButtonValue = 'Update Issue';
       commentLabel = 'New Comment';
+      attachmentUploadBtn = (
+        <ButtonElement
+          onUserInput={this.openAttachmentUploadModal}
+          label={'Add Attachment'}
+        />
+      );
     }
 
+    const fileCollection = this.state.isNewIssue || (
+      <AttachmentsList issue={this.props.issue}
+                       attachments={this.state.issueData['attachments']}
+      />
+    );
+
     const commentHistory = this.state.isNewIssue || (
       <CommentList commentHistory={this.state.issueData.commentHistory} />
     );
@@ -137,6 +182,15 @@ class IssueForm extends Component {
 
     return (
       <div>
+        <Modal
+          title='Attachment for Issue'
+          onClose={this.closeAttachmentUploadModal}
+          show={this.state.showAttachmentUploadModal}
+        >
+          <IssueUploadAttachmentForm
+            issue={this.props.issue}
+          />
+        </Modal>
         <FormElement
           name='issueEdit'
           onSubmit={this.handleSubmit}
@@ -248,8 +302,11 @@ class IssueForm extends Component {
             onUserInput={this.setFormData}
             value={this.state.formData.comment}
           />
+          {attachmentFileElement}
           <ButtonElement label={submitButtonValue}/>
+          {attachmentUploadBtn}
         </FormElement>
+        {fileCollection}
         {commentHistory}
       </div>
     );
@@ -439,6 +496,8 @@ class IssueForm extends Component {
 IssueForm.propTypes = {
   DataURL: PropTypes.string.isRequired,
   action: PropTypes.string.isRequired,
+  issue: PropTypes.string.isRequired,
+  whoami: PropTypes.string.isRequired,
 };
 
 export default IssueForm;