feat!: 15.2.2 (#665)

* chore: 🔨 update changelog for 15.2.2

* feat: ✨ docs versioned for soda for sparc

* fix: 🐛 img links

* fix: 🐛 unversioned docs link

versioned_docs/version-15.2.1/developer-documentation/changelog.md

@@ -7,6 +7,15 @@ image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Chan
 
 All notable changes to SODA for SPARC will be documented in this file.
 
+## 15.2.2
+
+## Bug fixes:
+
+- Fixed an issue with the Pennsieve agent version check not being able to detect old versions of the Pennsieve agent (The agent found at https://github.com/Pennsieve/agent).
+- Fixed an issue in how SODA reads the config.ini file that made it so that if the account name 'SODA-Pennsieve' exists it is always used for authentication with Pennsieve even when a defualt_profile key exists in the config.
+- Fixed an issue in the manifest creation and banner image upload/edit features of the `Advanced Features` tab that made it so users without Pennsieve Agents were not directed to the Pennsieve Agent download page. Instead they were told 'the pennsieve agent is not running.'
+- It was possible for an upload to fail early in 'Prepare Datasets Step-by-Step' and 'Upload Dataset' such that the catch statement referenced a variable that was not yet defined. This has been fixed.
+
 ## 15.2.1
 
 ## Feature additions:

versioned_docs/version-15.2.2/advanced-mode/_category_.json

@@ -0,0 +1,4 @@
+{
+    "label": "Advanced Features",
+    "position": 6
+}

versioned_docs/version-15.2.2/advanced-mode/compare-local-and-pennsieve-dataset.md

@@ -0,0 +1,43 @@
+---
+sidebar_position: 4
+title: Compare Local and Pennsieve Dataset
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Step%207%20-%20Preview%20dataset&description=Prepare%20Dataset&org=fairdataihub
+---
+
+This feature allows you to compare a dataset stored on Pennsieve with a dataset stored locally.
+
+## Background
+
+After uploading a dataset some users want to look at the individual files and folders on their local dataset to make sure each one is on Pennsieve. This feature allows you to
+automatically compare the files and folders in your local dataset with the files in your Pennsieve dataset.
+
+## How to
+
+To access this interface click on the `Advanced Features` at the bottom of the homepage, then click on the `Compare Local and Remote Dataset` card. Once accessed follow the onscreen
+instructions to compare the datasets. After comparing the datasets you will be presented with results.
+
+## Understanding the results
+
+Results will be displayed in tables. If the datasets are the same there will be no results and a message will be displayed saying the datasets are the same. If the datasets are different you will
+be presented with up to two tables. The first table is called `Files that are on Pennsieve and not in your local dataset` and contains a list of files and folders that are on Pennsieve but not in your local dataset.
+The second table is called `Files that are local and not in your Pennsieve dataset` and contains a list of files and folders that are in your local dataset but not on Pennsieve.
+
+## What can you do with your results?
+
+For results in the `Files that are on Pennsieve and not in your local dataset` table you can do the following:
+
+- Download the files in CSV format with the `Get File List in CSV` button so that you may manually decide what to do with these files.
+- Delete the files from Pennsieve with the `Delete Files from Pennsieve` button.
+
+For results in the `Files that are local and not in your Pennsieve dataset` you can do the following:
+
+- Download the files in CSV format with the `Get File List in CSV` button so that you may manually decide what to do with these files.
+- Upload the local files to Pennsieve with the `Upload Upload Selected Files from Pennsieve` button.
+
+:::note
+You can only upload SDS compliant files and folders using SODA. If you want to upload non-SDS compliant files and folders you will need to do so manually.
+:::
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/advanced-mode/create-manifest-files.md

@@ -0,0 +1,52 @@
+---
+sidebar_position: 1
+title: Create Manifest files
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Create%20Manifest%20Files&description=Prepare%20Metadata&org=fairdataihub
+---
+
+## Background
+
+Manifest files are mandatory for all datasets. To learn more about this metadata file please refer to our corresponding "
+[How to](../how-to/how-to-structure-the-manifest-metadata-file)" page.
+
+This section will allow you to generate manifest files for your pre-existing datasets stored locally and on Pennsieve.
+
+:::tip
+If you do not have pre-existing datasets SODA allows you to create a new dataset and generate manifest files at the same time.  
+[Instructions are provided here](../upload-dataset/organize-dataset).
+:::
+
+## How to
+
+To access this interface click on the `Advanced Features` button on the bottom of the homepage, then click on the on the `Create manifest.xlsx` card.
+
+1. You can start by either choosing to generate a manifest.xlsx file for a pre-existing dataset stored on your local computer or on Pennsieve.
+
+2. Select where the manifest.xlsx files will be generated.
+
+   - For local datasets user the `Browse here` input to point SODA to your dataset's location.
+
+   - For Pennsieve datasets use the dropdown to select which Pennsieve dataset you would like to create Manifest files for.
+
+3. A tree structure of your dataset will appear to demonstrate the Manifest files that will be generated. You can click `Continue` to move forward.
+
+4. (Optional) After clicking `Continue` you can edit SODA-generated manifest files by clicking on the `manifest.xlsx` file of the high level folder you would like to edit. If you do not wish to do so, simply click `No, generate now` to start generating the manifest files.
+
+   - When editing manifest files you may edit the `Description` or `Additional Metadata` columns in your dataset's manifest files before generating them to the desired destination.
+   - When editing manifest files you can also add or remove custom columns using the `Context Menu`. To do this select a column header and then right click on it to activate the `Context Menu`.
+
+   :::info
+   If the dataset contains manifest.xlsx files, SODA will load the existing manifest files for your edits. Note that at this moment, only the manifest.xlsx files are supported by SODA (not any other manifest file types).  
+   :::
+
+   ![](https://github.com/fairdataihub/SODA-for-SPARC/raw/main/docs/documentation/Prepare-metadata/Manifest/manifest-editor-context-menu.png?raw=true)
+
+5. After you finish editing the manifest files at Step 3, click `Generate now`.
+
+:::tip
+When you are in the manifest file's editing interface, click on the arrow symbol next to a folder to expand it.  
+:::
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/advanced-mode/upload-a-banner-image.md

@@ -0,0 +1,35 @@
+---
+sidebar_position: 2
+title: Upload a banner image
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Upload%20a%20banner%20image&description=Manage%20Dataset&org=fairdataihub
+---
+
+## Background
+
+All SPARC datasets must have the following metadata on Pennsieve: subtitle, description, banner image, license, and tags. This interface allows you to easily add a banner image to your Pennsieve dataset. This image will be associated with the dataset and used as a thumbnail once the dataset is published on the [SPARC data portal](https://sparc.science/).
+
+:::caution
+Only .PNG, .JPEG, and .TIFF images are allowed to be used as a banner.
+:::
+
+## How to
+
+To access this interface click on the `Advanced Features` at the bottom of the homepage, then click on the `Upload a banner image` card.
+
+1. Select/confirm your Pennsieve account and dataset. If you have not connected your Pennsieve account with SODA yet, [use the instructions available here](../connecting-to-pennsieve/connecting-with-username-password). Any existing banner image for your Pennsieve dataset will be automatically imported in the interface.
+2. Select/confirm your Workspace. Learn more about workspaces [here](../how-to/how-to-use-workspaces).
+3. Click on `Edit banner image`
+4. Click on `Import image` in the new pop-up window.
+5. Select the image file you want to use as a banner image.
+6. Crop the file as desired.
+
+   :::info
+   All banner images must be square, have a minimum display size of _512x512 px_ (_1024x1024 px_ preferred), and have a maximum size of _2048x2048 px_.
+   If the image exceeds in dimensions SODA can scale the image down automatically.
+   :::
+
+7. Click on `Save changes`. The newly added banner image will be displayed in the interface.
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/advanced-mode/validate-your-dataset.md

@@ -0,0 +1,41 @@
+---
+sidebar_position: 3
+title: Standalone Validator
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Step%207%20-%20Preview%20dataset&description=Prepare%20Dataset&org=fairdataihub
+---
+
+This feature allows you to validate one of your organized datasets stored locally or on Pennsieve. This can save you time by allowing you to avoid stepping
+through `Organize dataset` in `Upload Dataset` or `Prepare Dataset Step-by-Step` UIs when validating your dataset is your only goal.
+
+## Background
+
+All SPARC datasets must conform to the SPARC Dataset Structure format described [here](https://docs.sparc.science/docs/overview-of-sparc-dataset-format).
+It is recommended that, when possible, you resolve any validation errors before submitting your dataset to the SPARC Curation Team for review.
+
+## How to
+
+To access this interface click on the `Advanced Features` at the bottom of the homepage, then click on the `Validate dataset` card.
+
+- First choose which validation workflow you will perform:
+  - Pennsieve validation: For validating a dataset stored on Pennsieve.
+  - Local validation: For validating a dataset stored on your computer or a local drive.
+- Pennsieve validation workflow:
+  - Select which dataset you would like to validate from the dropdown menu.
+  - Click `Confirm` to import the dataset.
+  - Once imported, click the `Validate Dataset` button to begin the validation process.
+  - Once validation is complete you will be presented with a table of results with two columns.
+    - Path: The `Path` column will contain the path to the file, folder, or field that was validated.
+    - Message: The `Message` column will contain the message informing you what was determined to be invalid about the file, folder, or field specified in the `Path` column.
+  - To fix your errors, simply alter your dataset to correct the given error messages then re-run validation for confirmation.
+- Local validation workflow:
+  - Select the location of the local dataset you would like to validate.
+  - Click `Confirm` to finalize your selection.
+  - Click `Validate Dataset` to begin the validation process.
+  - Once validation is complete you will be presented with a table of results with two columns.
+    - Path: The `Path` column will contain the path to the file, folder, or field that was validated.
+    - Message: The `Message` column will contain the message informing you what was determined to be invalid about the file, folder, or field specified in the `Path` column.
+  - To fix your errors, simply alter your dataset to correct the given error messages then re-run validation for confirmation.
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/common-errors/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Common errors and their solutions",
+  "position": 6
+}

versioned_docs/version-15.2.2/common-errors/api-version-mismatch.md

@@ -0,0 +1,27 @@
+---
+sidebar_position: 6
+title: API Version Mismatch
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=API%20Version%20Mismatch&description=Common%20errors%20and%20their%20solutions&org=fairdataihub
+---
+
+## Issue Background
+
+Upon downloading/auto-updating the old server was never replaced by the most up to date server.
+
+## Solution
+
+**This solution is for Linux users only.**
+
+1. Check if there is a server running in the background by typing `app` in the `System Monitor` and ending this process.
+2. Uninstall/remove the SODA AppImage by deleting it.
+3. Download and reinstall [SODA](https://github.com/fairdataihub/SODA-for-SPARC/releases/download/v12.2.0/SODA-for-SPARC-12.2.0.AppImage)
+
+Sometimes upon following this process and reinstalling SODA the same issue appears. This can happen when the `app` process does not appear in the System Monitor even though
+it is running in the background. If this happens you can use the following terminal commands in lieu of step 1 to find the `app` process and end it before completing steps 2 and 3:
+
+1. Check for the server by running this command in the terminal: `lsof -i:4242`
+   - If there is a result ( not an empty console ) then end the 'app' service by running this command in the terminal: `kill -9 <pid>`
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/common-errors/deleting-pennsieve-config-files.md

@@ -0,0 +1,32 @@
+---
+sidebar_position: 8
+title: Deleting your Pennsieve account config
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Deleting%20Pennsieve%20config%20files&description=&org=fairdataihub
+---
+
+## Issue Background
+
+There is a known issue where the Pennsieve Agent fails to start due to more than one profile using the same name. To alleviate this issue, please view the steps below.
+
+## For Windows
+
+1. Open the Windows file explorer
+2. Navigate to: 'C:\Users\<your-user-name&gt\.pennsieve' (If you can't see it, press 'Command' + 'h' to display hidden files)
+3. Delete all the files and folders inside the ".pennsieve" folder.
+
+## For MacOS
+
+1. Open the Finder application
+2. Navigate to: /Users/&ltyour-user-name&gt/.pennsieve (If you can't see it, press 'Command' + 'Shift' + '.' to display hidden files)
+3. Delete all the files and folders inside the ".pennsieve" folder.
+
+## For Linux
+
+1. Open Nautilus/your default file explorer
+2. Navigate to the Home directory
+3. Open the .pennsieve folder (If you can't find it, press 'ctrl+h' to display hidden files)
+4. Delete all the files and folders inside the ".pennsieve" folder.
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/common-errors/installing-the-pennsieve-agent.md

@@ -0,0 +1,17 @@
+---
+sidebar_position: 1
+title: Installing the Pennsieve agent
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Installing%20the%20Pennsieve%20agent&description=Common%20errors%20and%20their%20solutions&org=fairdataihub
+---
+
+## Issue Background
+
+**Name 'AgentInstallationError'** issue happens when SODA detects that you have not installed the Pennsieve agent. The Pennsieve agent is necessary for the dataset upload process.
+
+## Solution
+
+You can follow the [instructions provided here](https://docs.pennsieve.io/docs/installing-the-pennsieve-agent-1) to install the Pennsieve agent. For any other questions, please visit the dedicated [Pennsieve Documentation](https://docs.pennsieve.io/docs).
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/common-errors/issues-regarding-hidden-files-or-folders.md

@@ -0,0 +1,21 @@
+---
+sidebar_position: 5
+title: Issues regarding hidden files or folders
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Issues%20regarding%20hidden%20files%20or%20folders&description=Common%20errors%20and%20their%20solutions&org=fairdataihub
+---
+
+## Background
+
+There are some issues related to hidden files and folders that SODA users have experienced. If you get any errors caused by hidden file(s) or folder(s) and do not know how to find them, it is very likely that such file(s) or folder(s) are hidden on your computer.
+
+## Solution
+
+To learn about how to show hidden files and folders, please visit the link below for your Operating system:
+
+- [Windows](https://support.microsoft.com/en-us/windows/view-hidden-files-and-folders-in-windows-10-97fbc472-c603-9d90-91d0-1166d1d9f4b5#:~:text=Open%20File%20Explorer%20from%20the,folders%2C%20and%20drives%20and%20OK.)
+- [macOS](https://www.ionos.com/digitalguide/server/configuration/showing-hidden-files-on-a-mac/#:~:text=Keyboard%20shortcuts%20are%20probably%20the,keys%20at%20the%20same%20time.)
+- [Ubuntu](https://help.ubuntu.com/stable/ubuntu-help/files-hidden.html.en#:~:text=If%20you%20want%20to%20see,files%20that%20are%20not%20hidden.)
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-15.2.2/common-errors/pennsieve-agent-uploads.md

@@ -0,0 +1,41 @@
+---
+sidebar_position: 3
+title: Pennsieve agent fails to upload a dataset
+image: https://kalai.fairdataihub.org/api/generate?app=soda-for-sparc&title=Pennsieve%20agent%20fails%20to%20upload%20a%20dataset&description=Common%20errors%20and%20their%20solutions&org=fairdataihub
+---
+
+## Issue Background
+
+SODA uses the Pennsieve Agent to upload datasets to Pennsieve. At the time of writing, the Pennsieve Agent will occasionally fail to upload a dataset that is composed of a very high number of files. It is important to note that datasets that take up a large amount of storage space should have no problem being uploaded; unless said datasets have a very high number of files.
+
+The error will occur in the `Prepare datasets` tab under the `Organize dataset` section or in the `Manage Datasets` tab under the `Upload a Local Dataset` section when trying to upload a dataset, and will look like this:
+
+![](https://github.com/fairdataihub/SODA-for-SPARC/blob/main/docs/documentation/Common-errors/pennsieve-agent-error.PNG?raw=true)
+
+## Solution
+
+Upload the dataset folder(s) one at a time or in smaller groups using the 'Upload Local Dataset' feature in SODA. By doing so you can eventually push all of your dataset folders up to Pennsieve. You can then use the Pennsieve File Viewer to organize your dataset if uploading using this strategy forced you to lose the dataset's folder hierarchy.
+
+Here is how to do this in more detail:
+
+1. Navigate to 'Upload a Local Dataset' under the `Manage Datasets` tab.
+2. Select the Pennsieve dataset you would like to upload your dataset files and folder to.
+3. Browse to the location of your dataset and select an individual data folder to upload.
+4. Click `Upload dataset`
+5. Repeat until all of your dataset folders are uploaded to Pennsieve.
+6. Navigate to [Pennsieve's site](https://app.pennsieve.io)
+7. Search for your dataset and select it.
+8. In the side bar select `Files`
+9. Reorganize your dataset using the File viewer interface.
+
+## Manifest File Generation
+
+If you want to create manifest files but are having trouble with the Pennsieve Agent because of the amount of files within your dataset then there is a workaround using SODA.
+
+1. Navigate to `Generate Manifest Files` under the `Prepare Metadata` tab.
+2. Select `Existing Local Dataset`
+3. Click `Generate`
+4. Navigate to [Pennsieve's site](https://app.pennsieve.io) and select your dataset.
+5. In the side bar select `Files`
+6. Use Pennsieve's `Add File` feature to upload your manifest files to Pennsieve.
+   - It can expedite the process if you navigate to the folder you would like to place the Manifest into before uploading. This is because uploading manifest files to the root of the dataset directory will add a suffix indicating file name duplication. These will have to be renamed once moved to their correct directory.