Changelog

All notable changes to SODA for SPARC will be documented in this file.

15.2.1

Feature additions:

• Removed the ability to import empty folders and files into SODA.

Bug fixes:

• Fixed an issue preventing users with pre-2.0 Pennsieve agent versions from being able to update.

15.2.0

Feature additions:

• An accounts page is accessible through the sidebar. This page allows users to more easily manage their Pennsieve account(s) that have been connected to SODA.
• It is now possible to upload a dataset to Pennsieve in End-to-End Curation mode without first adding a banner image. This is useful for users who do not have a banner image prepared. Note that before your dataset can be published you will need to add a banner image.
• It is now possible to upload a dataset to Pennsieve in End-to-End Curation mode without first assigning a Principal Investigator (PI). Note that before your dataset can be published you will need to assign a PI.

Bug fixes:

• Fixed an issue causing the Verify Files feature to freeze when verifying large datasets.
• Fixed issues in Advanced features that made it difficult to add a banner image using the Upload a banner image feature.

15.1.0

Feature additions:

• Removed all Pennsieve Agent/log in requirements from the start up processes and added checks within both curation modes to assist users with Pennsieve account/agent requirements.
• Added a new feature in the Advanced Features tab that allows users tp compare their local and Pennsieve datasets for differences in file structure.
• Added a new feature in Prepare Datasets Step-by-Step that allows a user to verify the integrity of the files they uploaded to Pennsieve.

Bug fixes:

• Fixed an issue that caused the UI to navigate to the homepage after generating a manifest file in the Advanced Features tab.
• Fixed an issue that would cause the progress bar to hang during some dataset uploads.
• Fixed an issue in Advanced Features that would cause validation of a Pennsieve dataset to fail.
• Fixed an issue in Advanced Features that would cause some valid SDS datasets to fail to be imported in the local manifest file generation feature.

15.0.2

Bug fixes:

• Fixed an issue where uploads fail for fresh Pennsieve Agent installs.
• Fixed an issue where the manifest generation in Advanced Features fails.

v15.0.1

Bug fixes:

• Fixed an issue where uploads fail for fresh Pennsieve Agent installs.
• Fixed an issue where react components were not reinitializing and old values were not reset in the UI.

v14.1.0

Feature Additions:

• SODA disallows '.,\' in dataset titles.
• SODA tracks int_ids as well as dataset ids so that we can track a dataset once it has been published to SPARC.Science.

Bug fixes:

• SODA returns more informative error messages from the Pennsieve API when an error occurs in the curation pipeline.
• SODA shows and hides the Return and Exit buttons that appear when a dataset upload fails in the 'Upload Dataset' feature.

v14.0.0

Feature Additions:

• The SODA user interface has been updated to be more intuitive for new and existing users.

v13.1.3

Feature Additions:

• Announcements have been redesigned to convey updates and fixes clearly.
• Added the ability to generate a copy of a dataset's manifest files locally within the organize datasets feature.
• Updated the UI for GM/FFM subject metadata Species, Strain, and RRID selection, and changed the API endpoint to use SciCrunch's public API to search for RRIDs.

Bug fixes:

• Fixed an issue in the Organize datasets feature when creating a new Pennsieve dataset that prevented SODA from finding the dataset in some cases.
• Banner image selection popup has been patched to overlay above entire app.
• TLS/SSL Certificates have been updated to be current on build time.

v.13.1.2

Bug fixes:

• Fixed issue that caused an error message to appear when a user tried to connect their Pennsieve API Key and Secret to SODA during the startup flow.
• Fixed an issue preventing SODA from importing large datasets from Pennsieve due to the cached API token becoming stale before the import was complete.

v.13.1.1

Bug fixes:

• Fixed issue preventing users from importing their datasets if they have access to a large amount of datasets on Pennsieve.

v.13.1.0

Feature Additions:

• Users can generate datasets on their computer/local device in Guided Mode without having to sign in with a Pennsieve account.
• Pennsieve API Key names are more unique to resolve myriad of issues that come from having multiple users on one computer and from having one user with acccounts across multiple computers.
• Switching workspaces resets FFM UI to default state.

Bug fixes:

• Fixed issue preventing users from generating metadata files locally without a Pennsieve account in Free Form Mode.

v.13.0.0

Feature Additions:

• SODA added the ability for users to generate a local copy of their datasets for review to Guided Mode. This should assist users in ensuring their dataset is organized per their criteria before commiting to uploading their dataset to Pennsieve.
• SODA has been converted to ESM and is using Electron-Vite for bundling.

v.12.5.0

Feature Additions:

• SODA will help resolve certain issues with starting the Pennsieve Agent that some users experience.
• SODA will show high level folders in Guided Mode and Free Form mode file structure review. These folders are expandable to show the rest of the dataset structure.
• SODA tracks the size and amount of metadadta files created in Guided Mode more granularly.

v.12.4.2

Bug fixes:

• Fixed Pennsieve login bug for accounts with Emails containing periods.

v.12.4.1

Feature Additions:

• Added a method to bypass Pennsieve agent updates when a platform specific release is not able to be found.

v.12.4.0

Feature Additions:

• Added a new feature to Guided Mode that allows you to import subjects, pools, and samples from an external spreadsheet.

v.12.3.3

Bug fixes:

• If multiple Pennsieve Agents are installed on a user's system the most current Pennsieve Agent is started.

v.12.3.2

Bug fixes:

• Updated urllib3 and request versions to fix issues with the back-end processing responses from Pennsieve API.
• Modified the request to retrieve a list of datasets by utilizing Pennsieve's dataset pagination endpoint. This change was implemented to address an issue that was affecting users with a large number of datasets.
• Migrated the notarization tool from alttool to notarytool.
• SODA for SPARC launches the Pennsieve Agent for OS X Ventura.
• Duplicate files were being created when uploading a dataset through Organize Datasets and selecting the 'skip' existing files option. The 'skip' option now works as intended. Local files that exist on a Pennsieve dataset are no longer duplicated.

Known Issues:

• The Organize dataset feature will not create duplicate folders in the expected manner.
• The Organize dataset feature will not skip folders in the expected manner.

v.12.3.1

Bug fixes:

• Fixed a bug allowing subjects and samples to be created without a name.

v.12.3.0

Feature Additions:

• SODA for SPARC returns more informative and useful error messages to the client when a service that it depends on is unavailable or behaving unexpectedly.
• A button for gathering the user's Kombucha Analytics client ID is available in the 'Contact Us' page in the sidebar. This eases the user's burden when making a request to view/delete their analytics data as per GDPR.
• SODA for SPARC now uploads files/folders to existing datasets on an average of 47% faster than before!
• SODA for SPARC also uploads new SODA created datasets onto Pennsieve are also on average 48% faster than before!
• Importing datasets from Pennsieve have been slightly improved on average by 10%.
• Enhanced the user experience when importing folders and files into SODA.

Bug fixes:

• Fixed an issue where announcements for new SODA for SPARC features did not display on a fresh install or after an auto update.
• Fixed an issue in Free Form Mode's standalone dataset validator wherein the validation table would display even when validation failed to complete.
• Fixed a UI issue with moving groups of items from the file explorer.
• Manifest files generated by SODA for SPARC now have the correct file name when files are renamed within the virtual file explorer.
• Tippy popovers have been added to the Share with Curation Team button along with the Create Manifests button in Free Form Mode's Prepare Metadata section and Disseminate section.
• Error message on upload provided links and are now opened in another window rather than within SODA for SPARC.
• Curate and Share button's icon has been updated to be more intuitive. Changing color when it is selected.
• Return to progress button that appears in the nav bar will correctly update the navigation menu depending where the user navigates.
• Move item pop up has a max height preventing users from endlessly scrolling to confirm their move.
• Disseminate calender does not hide anymore when checkbox to awknowledge sharing with the curation team. (Should only be modified by the embargo checkbox)
• Sweet alert icons for Prepare Metadata -> No 'metadata' file found in root directory will all be the same icon.

v.12.2.2

Bug fixes:

• Fixed an issue where switching workspaces in Free Form Mode and Guided Mode would sometimes disallow access to the target workspace for up to a minute.

v.12.2.1

Bug fixes:

• Free Form Mode's Standalone Validator feature no longer shows a validation results table when validation fails due to a user missing required metadata files.
• Linking your ORCID ID with Pennsieve through SODA for SPARC no longer fails to authenticate when given a valid user profile.

v.12.2.0

Feature Additions:

• Windows builds are created with the ASAR flag set to true. This allows for the application to be packaged as a single file. This will speed up the installation process for Windows users.
• Analytics for SODA have been converted to Kombucha. Fully replacing Google Analytics.
• usersCreated field added to the Kombucha User ID. This will allow us to track when a new user is created in SODA.

Bug fixes:

• Showing confirm button for workspace selection in Free Form Mode (Step 6) after the first upload.
• Kombucha User ID is being correctly stored in the user's local storage.

v.12.1.1 - 2023-07-25

Feature Additions:

• Implemented access token caching for improved request performance

Bug fixes:

• Fixed an issue when importing duplicate folders and files into the file explorer
• Fixed an issue where the SODA server would sometimes crash on MAC due to too many import/upload status requests being made to the server

v.12.1.0

Feature Additions:

• Dataset Description Metadata updated from SDS 2.0.0 -> 2.1.0
• Submission Metadata updated from SDS 2.0.0 -> 2.1.0
• Files Explorer can now move files in Guided Mode (patched for Free Form Mode)

Bug fixes:

• Fixed an issue causing the server to not connect for Window's users
• Fixed an issue where moving files in the File Explorer did not remove files from their original location

v.12.0.2

Bug fixes:

• Fixed an issue causing the server to not connect for Window's users

v.12.0.1

Feature Additions:

• Removed calls to analytics in order to prepare for our new analytics platform
• Updated pre_flight_checks to give better error messages and allow the user to restart the checks.

Bug fixes:

• The file explorer can now import hidden files that are within a folder.
• Dataset is locked pop up will wait for user to confirm pop up before continuing processes.
• Local dataset upload throw "Dataset is Locked" pop up when trying to upload to a dataset that is locked.

v.12.0.0

Feature Additions:

• RE-JOIN support: All workflows in End to End Curation and Free Form Mode allow for viewing, modifying, creating, and uploading RE-JOIN datasets.
• Multiple workspace support: Users can switch between their available workspaces in End to End Curation and Free Form Mode to perform curation tasks.
• Updated Pre-Publishing Support: End to End Curation and Free Form Mode implement the new process for submitting a dataset to the Curation Team for pre-publishing review.
• DOI Reservation is now available in End to End Curation after uploading.
• Free Form Mode's Create a dataset section now shows an animation upon successful creation of a dataset.
• Auto generate Manifest’s section in Free Form Mode now has a loading spinner when generating manifests. This lets users know that SODA is working on the task when large datasets may take time to create manifests.
• Protocols.io support has been fully removed from SODA.
• Local upload errors will now only be shown in the form of a pop up rather than both a popup and on the local dataset upload section page.
• Icon for Curate and Share was updated.
• Removed End to End Curation pages requiring duplicate data entry streamlining the Pennsieve metadata process

Bug fixes:

• The sign on process no longer creates Duplicate Pennsieve API Keys.
• Manifest generation no longer fails when processing datasets with non-SPARC folders at the root of the dataset.
• Locked datasets can no longer be edited through SODA in any case.
• The ‘Loading dataset details’ message appears after selecting a Pennsieve dataset and does not disappear until loading has completed.
• The ‘Confirm’ and ‘Generate’ buttons in Free Form Mode’s Prepare Metadata section have been standardized.
• The popup that appears when importing a data deliverables document in Free Form Mode’s Prepare Metadata section was not closeable.
• In Free Form Mode’s standalone manifest generator, the option to ‘Preview Manifest Files Locally’ would prevent further manifest edits before completion of the workflow. This has been resolved. It is now possible to create a local preview and then make further edits.
• Free Form Mode’s collection editing feature no longer shows a success message when an error occurs.
• The error message that appears when a user tries to edit a locked dataset has been made clearer.
• Free Form Mode’s Permissions Section’s “Can’t find PI Owner?” help box dynamically aligns with page resizing.
• 0KB Files warning popup has been made scrollable for when large amounts of files are listed.
• Organize Datasets -> Select high level folder -> Derivatives folder onclick being misshapen has been fixed.
• Free Form Mode’s License and Permissions fetching data when dataset selected as None has been patched.
• Links to SODA’s documentation have been updated as the file structure has been updated on SODA’s doc site.
• Locked dataset popup will wait for the user’s response before continuing other processes.
• When a dataset is pre-selected and a user tries to modify their dataset, they will get a locked error message throughout freeform mode.
• Added a Guided Mode Sweet Alert that notifies the user as to why a page fails to open.

Known Issues:

• After submitting a dataset for pre-publishing review it is not possible to edit the dataset permissions within SODA’s UIs.

v.11.1.0

Bug fixes:

• Fixed an issue allowing pre-release Pennsieve agents to be required for users
• GM: Removed the ability to add forbidden characters to dataset names

Feature Additions:

• Simplified the home page by narrowing down the flow to two buttons: End to End and Free Form curation
• Simplified the share with curation team flow

v.11.0.0 - 2023-03-29

Bug fixes:

• GM: Sharing with the Curation Team has been modified to notify the Curation Team. -GM: For the file explorer the right click menu has been aligned with the mouse position.

• FFM: Prepare Metadata -> dataset_description.xlsx text was being modified and has been patched to display fields as the user originally wrote it.

• FFM: Imported metadata files not resetting upon changing a dataset has been patched.

• The ability for deleting all files selected has been fixed.

• Taxonomy endpoint has been patched to look up names and return response corrently.

Feature Additions:

• SODA for SPARC's home page has been updated to be minimal and easier to navigate. Free form mode and Guided mode have been merged to one location: Curate and Share.
• GM: Ability to reserve a DOI after uploading.

v.10.0.5 - 2023-03-20

Feature Additions:

• GM: Contributor names in the dataset_description file will now always upload as "Last name, First name"
• FFM: Contributors table emulates Guided Mode's contributors table
• FFM: Removed the "Corresponding Authors" metadata field from dataset_description as it is no longer required per the SPARC dataset structure
• FFM: Bug fixed causing ORCIDs to not get pulled into the dataset_description contributors UI

v.10.0.4 - 2023-02-24

Bug fixes:

• Imported datasets with manifests that carry incorrect headers for the standard columns (filename, timestamp, description, file type, Additional Metadata) will be preserved as extra columns.
• Auto generating manifests will preserve column headers for each individual high level folder rather than giving the same headers to all manifests.

v.10.0.3 - 2023-02-14

Feature additions:

• Removed AirTable support. A future version will allow users to store data that was stored on AirTable locally.

Bug fixes:

• SODA for SPARC returns the correct Pennsieve Agent output log file instead of the outdated out.log file in the Gather Logs feature.
• Fixed an issue with non-standard manifest file headers not being imported properly.

v.10.0.2

Bug fixes:

• Fixed an issue causing Guided Mode dataset imports to reject when proper criteria are met.
• Fixed an issue causing the Pennsieve Agent to not start up properly
• Fixed an issue on Mac and Linux where importing a dataset with manifest files present would cause the import to fail.
• Fixed an issue on Mac and Linux where importing metadata files would fail.

v.10.0.0

Feature additions:

• SODA for SPARC imports users' non-standard manifest columns (file name, timestamp, description, file type, additional metadata) app wide.
• SODA for SPARC has new file standards for uploading to match the SDS.
• SODA for SPARC uses the new Pennsieve Agent for uploading dataset files.
• SODA for SPARC uses the Pennsieve API for communication with Pennsieve.
• Manifest files are now edited through a new window rather than a pop up.
• Manifests files have a new template styling that matches the SDS.
• SODA for SPARC's tree view displays of users' dataset structures now list folders first then files alphanumerically.
• Freeform Mode: The Organize Datasets feature's manifest file generator has been overhauled.
• Guided Mode: Added the ability to edit an existing dataset on Pennsieve.
• Guided Mode: Banner Images can be drag and dropped to be imported.
• Guided Mode: File navigation is now only showing user file structure necessary to them rather the entire dataset structure.

Bug fixes:

• Lazy Loading was added to editable manifest for large datasets.
• Lazy Loading was added to editable manifest for large datasets.
• Guided Mode: Fixed subjects and samples metadata not properly copying over when extra fields were added.
• Lazy Loading was added to editable manifest for large datasets to prevent slowing down SODA.

Known Issues:

• Freeform Mode:
  • The transition to the generate step in the Organize Datasets feature is slowed when working with large datasets.
  • Uploading large amounts of very small files ( <= 1kb ) will sometimes cause the upload to pause or crash. It is best to restart the upload when this happens.
• When working with large datasets and trying to auto generate manifest files to edit. It can take some time and with no status indicator on the progress. (To be added)

v.9.4.0

Feature additions:

• ORCID ID's are validated when adding contributors in guided mode
• At the final step in guided mode permissions will be indicated next to the names chosen by the user along with minor text changes.
• Guided Mode: Added a sidebar to allow users to easily navigate through pages that have already been completed.
• Guided Mode: Added the ability to progress through the protocol page if the user does not have protocols prepared.
• Guided Mode: Condensed PI owner selection + dataset permissions into one page to simplify the process for users.

Bug fixes:

• Airtable keys are validated to ensure the API keys are still valid for use. If not they will be prompted again for an API key when necessary.
• Guided Mode -> Before getting started page: tool tips were fixed to normalize across the app
• Free form tool tips normalized with guided mode tool tips
• SPARC Consortium Organization modified to only say SPARC Organization

v.9.3.3

Feature additions:

• Documentation was added for non-SPARC data curation.
• Updated link to the Pennsieve agent. Link to the first agent will say that the agent is deprecated (ignore when downloading).
• Homepage styling added lotties to the home page.

v.9.3.2

Bug fixes:

• Patched announcements to not cause error on auto update.

v.9.3.1

Bug fixes:

• Accounts failing to pass consortium check has been patched.
• Guided Mode: When Pennsieve link is copied a a notyf was created. Sometimes multiple notyfs were created at once and has been patched to only do so once.
• Prepare Metadata -> Dataset description -> Edit protocols: Duplicate protocols will not be allowed and when editing a protocol the current name can accepted again.
• Prepare Metadata -> Dataset description -> Click here to select my dataset from Pennsieve: would hide the page after selecting a dataset. Has been patched to behave accordingly.

v.9.3.0

Feature additions:

• Guided Mode: Added a new page to let users know what accounts and documents they will be needing to curate a dataset.
• Guided Mode: Manifest files now automatically update when changes are made to a dataset's structure.
• Guided Mode: Contributor addition flow upgraded to make AirTable contributor importation more intuitive.
• Guided Mode: dataset upload error alerts now give a clearer reason as to why the dataset upload failed and what can be done to remedy the issue.
• Guided Mode: simplified the UI for selecting a SPARC award.

Bug fixes:

• Announcements should launch on auto-updates moving forward now!

v.9.2.3

Bug fixes:

• Guided Mode: Manifest files - Auto-generated manifest files no longer include their high level folder in their path.

v.9.2.2

Bug fixes:

• Prepare Metadata - Create manifest.xlsx: Manifest files created from large datasets will no longer be 0KB or fail to be created.
• Prepare Metadata - Create manifest.xlsx: An issue for Windows users that prevents the file explorer from immediately opening after creating manifest files has been corrected. Windows users will now be able to see their manifest files in the explorer post creation to check them for correctness.
• Prepare Metadata - Create manifest.xlsx: Users will no longer have to wait to get feedback that their manifest files are being generated for large datasets.

Known issues:

• Guided Mode - Manifest file entries created with guided mode include their high level SPARC folder in the file name column.

v.9.2.1

Bug fixes:

• Fixed an issue where medium and large datasets were not being imported in Organize Datasets or the Create manifest.xlsx feature on Darwin.

v.9.2.0

Feature additions:

• An announcements system has been added to give the user updates on recents changes/additions to SODA.
• Guided Mode: Added the ability to retry uploading a dataset if an upload in progress fails.

Bug fixes:

• In organize dataset: When moving files/folders to another location there will be a check if any duplicates are there already.
• On startup the server will try to connect continuosly. (backOff was replaced)
• Organize dataset: import dataset will correctly check manifest details.
• Guided Mode: Fixed the automatically generated headers for manifest files
• Guided Mode: Changed the generated filepath from the filepath on the user's local machine to the path relative to the SPARC dataset structure

v.9.1.0

• An announcements system has been added to give the user updates on recents changes/additions to SODA.
• Tags throughout SODA are now sortable. (Ex: Dataset tags, milestone tags, etc.)
• Prepare Metadata - Create manifest.xlsx: Automated synchronization between manifest files and their Pennsieve dataset. E.g., if a file is removed from a dataset, the file's corresponding manifest file entry will be removed.
• Prepare Metadata - Create manifest.xlsx: Empty columns are dropped from manifest files once the user generates their files locally or on Pennsieve.
• Prepare Metadata - Create manifest.xlsx: Preview manifest files locally before they are uploaded to Pennsieve.
• Prepare Metadata - Create manifest.xlsx: Generate manfiest files locally in your directory of choice.
• Guided Mode - added the ability to edit auto-generated manifest files in a spreadsheet like UI.
• Freeform Mode - Ability to add your dataset to a collection has been added. Intended to better group datasets.
• Image optimzation for banner images. Image sizes that exceed over 2048 x 2048 will be prompted to scale the image accordingly for upload.

Bug fixes:

• In Organize datasets, when importing files/folders the loading screen's z-index was higher than the duplicate alert popup. The issue has been resolved by lowering the loading screen's z-index.
• When uploading a dataset "Preparing list of files to upload" would verify files from Pennsieve individually. For datasets with large files this would cause a long wait time during this step. Another method of verifying files was created to verify files by retrieving the information folder by folder, reducing wait time significantly.
• Manifest files generated in SODA include timestamps following the designated SPARC format.
• Prepare Metadata - Create manifest.xlsx: The manifest editor's 'Save' and 'Cancel' buttons now are always viewable without having to scroll to the bottom of the manifest file.

Known Issues:

• When a user has a large amount of files the step "Creating folder structure" can take a good amount of time.

v.9.0.1

Bug fixes:

• Fixed an issue that caused the Organize Dataset feature to break when switching from Free Form Mode to Guided Mode and back.

Known Issues:

• There is a bug when switching to Guided Mode before uploading Dataset Metadata in Free Form mode and then switching back to Free Form Mode. This will be addressed in the next update
• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.
• In the Organize Dataset feature, if a dataset is large enough and being uploaded to Pennsieve it will not pass the file and folder integrity check. This is a separate issue from those that were fixed as part of the bug fixes section outlined in v.8.0.1. Users should find more large datasets are uploadable to Pennsieve than in the previous release. Note as well this does not apply to the Upload Local Dataset feature, which has a very high upper bound for the amount of files that can be uploaded to Pennsieve as of the current release.

v.9.0.0

Feature additions:

• Guided Mode, a new dataset curation mode, is now available. Guided Mode streamlines the SPARC data curation process by guiding users step-by-step through the entire process. Currently, it only supports curating new datasets from scratch.
• The SODA server will run on a free port if the default port is not available.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.
• In the Organize Dataset feature, if a dataset is large enough and being uploaded to Pennsieve it will not pass the file and folder integrity check. This is a separate issue from those that were fixed as part of the bug fixes section outlined in v.8.0.1. Users should find more large datasets are uploadable to Pennsieve than in the previous release. Note as well this does not apply to the Upload Local Dataset feature, which has a very high upper bound for the amount of files that can be uploaded to Pennsieve as of the current release.

v.8.0.1

Bug fixes:

• Fixed an issue that prevented large datasets from being uploaded to Pennsieve or generated locally in Organize Dataset and Upload a Local Dataset to Pennsieve feature.
• Fixed an issue that prevented manifest files from being generated/uploaded to Pennsieve for large datasets in the stand alone manifest file feature found under Prepare Metadata - Create manifest.xlsx.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.
• In the Organize Dataset feature, if a dataset is large enough and being uploaded to Pennsieve it will not pass the file and folder integrity check. This is a separate issue from those that were fixed as part of the bug fixes section. Users should find more large datasets are uploadable to Pennsieve than in the previous release. Note as well this does not apply to the Upload Local Dataset feature, which has a very high upper bound for the amount of files that can be uploaded to Pennsieve as of the current release.

Version 8.0.0

Feature additions:

• Updated Electron to version 19.0.0.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.

Version 7.0.1

Bug fixes:

• Fixed an issue where SODA will exit on startup if the Pennsieve Agent is installed but there is not a configuration file or .pennsieve folder.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.

Version 7.0.0

Feature additions:

• The evolving SPARC Dataset Structure (SDS) all SPARC datasets must follow now includes additional mandatory metadata files. As such, in step 4 of the Organize dataset feature, found in the Prepare Datasets tab, the README.txt file is now mandatory.
• Layout of the Prepare Metadata tab has been changed. Buttons are spread out more evenly and the Manifest files button received an icon change.
• The Overview page has been overhauled to be more informative and visually stimulating.
• Documentation and Contact Us tabs added to the navigation bar.
• Contact Us tab will provide user information on how to reach out to the team for any issues or suggestions. As well as providing a Gather Logs button for the user to provide in an email for the team to look at any issues in depth.
• Visual overhaul for the prompts that allow users to connect their Pennsieve account with SODA.
• Simplified UI for adding a URL or DOI to a dataset_description.xlsx in the Prepare Metadata tab.
• Converted the SODA server from Zerorpc to Flask.

Bug fixes:

• The option to upload duplicate files to an existing Pennsieve dataset through the Organize Datasets feature no longer causes an error while uploading.
• Hidden files can now be imported except .DS_Store and Thumbs.db files.
• The input for renaming or creating a new dataset no longer references undefined function in its HTML.
• The navigation buttons in each individual Prepare Metadata section have been updated to match the perceived flow from the Prepare Metadata tab.
• The Add/edit subtitle feature has been updated so that the chracter limit matches the SDS 2.0 specification. This fixes a bug that would cause an error if a user met the character limit enforced by SODA and then tried to add or edit their subtitle.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.

Version 6.0.0

Feature additions:

• In Organize Dataset: Lazy loading is now a feature when viewing all imported items in a dataset. This will increase performance when rendering large datasets (over 500+ items).
• Importing a local dataset will now be handled on the python end to increase performance. A progress bar is also included to show details about import to user.
• In the Organize Datasets section importing files/folders will cause a toast to display on the bottom right to notify the user of a successful import.
• SODA for SPARC now uses onefile builds for all OS!
• SODA for SPARC uses .asar formatting for Mac and Linux builds!
• Added the "Unknown" option for the "Sex" field in the subjects file generator.

Bug fixes:

• Fixed bug under Step 3 - Organize datasets when users click Next to get to subsequent steps, and when they go back to this step, they cannot navigate in and out the high-level folders anymore.
• Added a SweetAlert loading popup for when users move a large number of files/folders under Step 3 - Organize datasets.
• Fixed bug related to the false warning of "The dataset does not contain valid SPARC folders" due to wrongly saved local dataset paths.
• Fixed UI bug related to the manifest file generator where the live spreadsheet is auto-opened without being prompted to open.
• Fixed bug with illegally formatted metadata files being dropped in Step 4: Metadata files.
• Fixed UI bug where tooltips in the Prepare Metadata section receive a top and a right message on hover.
• Fixed bug in Organize Datasets Step 3 where dragging and dropping folders with non-allowed characters would prevent further navigation.
• Fixed bug in Organize Datasets where files and folders would not keep their white space values once inserted into the UI.
• Fixed issue with drag and dropping folders with non-allowed characters being replaced/removed

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.
• The Create manifest.xlsx feature will spawn an error while generating manifest files for a local dataset if there are hidden files in the dataset directory. SODA will not tell the user the cause is the presence of the hidden files.

Version 5.4.0

Feature additions:

• In Organize Dataset: Lazy loading is now a feature when viewing all imported items in a dataset. This will increase performance when datasets are large (over 500+ items) and fix issues with rendering files/folders on older machines.
• Importing a local dataset will now be handled on the python end to increase performance. A progress bar is also included to show details about import to user.
• On success of importing files/folders there will be a toast display on the bottom right to give user a notification.

Bug fixes:

• Fixed bug under Step 3 - Organize datasets when users click Next to get to subsequent steps, and when they go back to this step, they cannot navigate in and out the high-level folders anymore.
• Added a SweetAlert loading popup for when users move a large number of files/folders under Step 3 - Organize datasets.
• Fixed bug related to the false warning of "The dataset does not contain valid SPARC folders" due to wrongly saved local dataset paths.
• Fixed UI bug related to the manifest file generator where the live spreadsheet is auto-opened without being prompted to open.
• Fixed bug with illegally formatted metadata files being dropped in Step 4: Metadata files.
• Fixed UI bug where tooltips in the Prepare Metadata section receive a top and a right message on hover.

Known Issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.
• The Organize Datasets option to upload duplicate files to Pennsieve uploads some duplicates but does not upload all.
• When using the Create manifest.xlsx feature any custom columns added to a manifest file stored on Pennsieve will not be imported for editing.

Version 5.3.3

Bug fixes:

• Uploading a local dataset to a new Pennsieve dataset through the Organize Dataset feature no longer pauses indefinitely before the upload begins.

Known issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.

Version 5.3.2

Feature additions:

• When Editing Manifest files generated through SODA a user may now utilize a Context Menu to add or remove new columns to the manifest file.
• A user may now import existing manifest files from local datasets.
• A user will have the option to perform other curation tasks after starting a dataset upload/generation. Upon doing so they will see a upload progress bar in the navigation bar.
• User can upload large folders( 1k+ files ) through SODA to Pennsieve.

Known issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.
• When uploading a dataset through Upload Local Dataset or Organize Dataset feature to Pennsieve the upload will sometimes freeze. When this occurs it is best to reset the upload and ensure the Pennsieve Agent has been stopped before attempting to upload again. It is also necessary to verify the integrity of uploaded files up to that point. This can be done by simply ensuring all files from folders that have been uploaded are included in the Pennsieve dataset.

Version 5.3.1

Bug fixes:

• Drag and drop functionality in Organize Datasets now correctly imports multi-selected files and folders.
• Updated the mac SODA for SPARC application icon.

Known issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.3.0

Feature additions:

• A stand-alone manifest file generation feature has been added. For this feature, users can now generate manifest files for their datasets stored locally or on Pennsieve.
• When importing files/folders duplicates will now prompt user if they would like to skip, replace, or rename them accordingly.

Bug fixes:

• Fixed issue wherein Submission.xlsx files are not uploaded to Pennsieve in the Prepare Metadata section.
• Fixed issue that prevented dataset_description.xlsx protocols from being editable within the Prepare Metadata section.

Known issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.2.1

Bug fixes:

• Fixed issue where file uploads to Pennsieve would sometimes fail because of an uncleared Pennsieve Client file upload queue.

Known issues:

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.2.0

Feature additions:

• Users can hover over their account and dataset text to edit the selected dataset/account in the account and dataset details card throughout SODA for SPARC.
• Users can submit their dataset to the SPARC Curation Team for pre-publishing review.
• Users can exclude high level metadata files from publishing from within the pre-publishing review process.
• Users can choose to place their dataset under embargo so that after being published their dataset is not immediately made public.
• Users can withdraw their dataset from pre-publishing review.
• Users can link their Pennsieve account to their ORCID iD from within the pre-publishing review process.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.1.0

Feature additions

• Users can upload and edit descriptive digital metadata tags to their dataset. By SPARC guidelines tags are now required before a researcher can publish a dataset.
• Updated the add/edit description digital metadata feature to be more intuitive for users.
• Updated the add/edit digital metadata buttons to distinguish between metadata addition and editing.
• Updated the loading and confirmation Sweet Alert messages to give the user a better idea of the background processes taking place.
• Added interfaces for creating the (optional) CHANGES.txt and README.txt files in SODA.
• Added the functionality to generate metadata files directly on Pennsieve.
• Added the functionality to edit metadata files imported directly from Pennsieve.
• Added interface to import code-related metadata files in SODA.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.0.2

Bug fixes

• Edited documentation links according to the new changes made to SODA's documentation website.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.0.1

Bug fixes

• Fixed bug caused by external bug from protocols.io. HTTPs request returning insufficient information was fixed by protocols.io. We integrated the fix on our side.
• Fixed bug that caused "Generate" buttons in the prepare metadata sections from creating tooltips on hover.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 5.0.0

Feature additions

• Updated Prepare metadata section to adapt to new SDS 2.0.0 version.
• Added the feature to import existing dataset_description.xlsx file for edits in SODA.
• Added onboarding for submission file.

Bug fixes

• Fixed subjects and samples file generation bug with extra optional column added.

Known issues

• Temporarily removed support for Protocols.io integration due to code change from Protocols.io.
• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.8.0

Feature additions

• Added onboarding for subjects and samples tables.
• Added validation checks for verifying the backend and front end app versions.
• Refactored large parts of the code performance improvements.
• Added onboarding for step 3 of the Organize dataset process.

Bug fixes

• Importing subjects + samples files have been adapted to new strain/species UI change
• Changed the activation point for illegal character checks.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.7.1

Bug fixes

• Fixed Airtable Base ID bug for the Airtable login function.
• Added checks more illegal characters for folder names.
• Fixed Contributor Role suggestion dropdown bug that only showed a maximum of 5 items.
• Fixed Start over functions for subjects and samples files to adapt to the new Add strains and Add species UI change.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.7.0

Feature additions

• Changed user interface for Prepare metadata - Create submission.xlsx file. This user interface was changed to be even more user-friendly and consistent with the user interface of Prepare metadata - Create dataset_description.xlsx file.
• Added user onboarding tutorials to help first time users of the app understand Step 3 of Organizing datasets better.
• Changed strain and species retrieval under Create subjects.xlsx and Create samples.xlsx from input search to button clicks.
• Changed all of the remaining status elements into Sweetalert popups for consistency in the app.
• Added an option to replace metadata files when generating if one already exists at the destination folder.
• Added restrictions to the folder creation user interface to be more in line with the requirements from Pennsieve.

Bug fixes

• Switched popover libraries to ensure that hyperlinks are clickable when required.
• Changed table tooltip (Edit/Copy/Delete a subject or sample) in the features Create subjects.xlsx and Create samples.xlsx to be text-based for clearer instructions for users.
• Fixed a bug with samples file generation where copying fields would cause an error when generating the final file.
• Fixed an issue where libraries were being loaded out of order leading to errors when opening SODA for the first time.
• When uploading a dataset, we have now locked the sidebar to prevent accidental clicks that would take you out of the UI.
• Fixed a bug where loading an award from Airtable would require two attempts.
• Fixed a bug where macOS version of SODA would run the pre-check message everytime the app lost focus.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.6.2

Bug fixes

• Changed the way SODA populated the dataset_description file - protocols, originating articles/DOIs, and additional links options. Protocols and Originating articles/DOIs DO NOT have a description. Only additional links does. Changed the backend and frontend accordingly to enforce this change.
• Added a warning whenever users import another existing metadata file (subjects, samples, dataset_description) onto SODA.
• Fixed margin bug for Details display (Prepare dataset -> Step 3).
• Added warning for when a user imports an existing metadata file. If any values from the file does not follow SPARC standard values, they will be ignored and not imported onto SODA for edits.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.6.1

Bug fixes

• Fixed a bug where manifest file data wasn't being pulled down correctly on Windows.
• Fixed a bug where .tiff images were not being converted by SODA.
• Fixed an issue where multiple sample id imports from the primary folder would not work.
• Fixed a bug where the import primary folder button would dissapear when starting over.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.6.0

Feature additions

• You can now create your subjects.xlsx and samples.xlsx files directly through SODA.
• Added additional navigation buttons that should allow a user to not have to return to the main menu when a certain function is complete. This workflow follows the step by step guide found here.
• Added a new warning when uploading a banner image.
• Transformed the existing user interface for the dataset_description.xlsx file. This new interface is changed to be consistent with the newly added subjects.xlsx and samples.xlsx interfaces.

Bug fixes

• Fixed a bug where the footer of the app could be mispositioned sometimes.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.5.1

Bug fixes

• Fixed a bug where trying to connect to Pennsieve with an API key alone would return an error.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.5.0

Feature additions

• All input and message boxes should now follow the call to action button ordering that is specified in their OS application guidelines.
• Added additional navigation buttons that should allow a user to not have to return to the main menu when a certain function is complete. This workflow follows the step by step guide found here.

Bug fixes

• Fixed a bug where certain message input boxes would take accidental clicks outside the clickable area and clear the input
• The dataset_description file will no longer enforce a 5 keyword limit.
• Fixed a bug where the siebar would open up when exiting a datset curation workflow.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.4.0

Feature additions

• Added support for more stringent file check with regards to metadata files. This should prevent you from importing files that are not valid.
• Added a button to paste your API keys into the application more easily.
• Added better warnings for when a backend module fails. This should give you more information about the status of SODA and if a restart of the app maybe necessary.
• Adjusted the ordering of message box buttons to better follow OS specific guidelines for Human Interface Design.

Bug fixes

• Fixed a potential bug where misspelled high level folders could cause SODA to not pull the correct information from Pennsieve.
• Fixed a bug where launching SODA could randomly cause step 7 of 'Organize Datasets' to not show up when generating a dataset.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.3.0

Feature additions

• Added support for toast style notifications to better show relevant information. When you open the app, SODA will run through a checklist of items so that you can see if you are missing any components required for the workflow. This includes checking for Pennsieve agent updates and SODA application updates as well.
• You can now use your Pennsieve login details to connect your Pennsieve account to SODA. This will replace the default API key based login. The original login method with API key will remain as a secondary login alternative.
• Added better warning messages to functions that were not descriptive enough so now you will have a better idea of what they do.
• You can now add line breaks for your dataset descriptions when created through SODA.
• SODA now uses a new visual look for showing message boxes and alerts. This would make SODA's UI more consistent.

Bug fixes

• Fixed a bug where SODA was unable to update on macOS through the built in buttons. The new update notification will be less intrusive and take up less space on your screen.
• When you request a database from Pennsieve, SODA will now generate a timestamp that is inline with the curation team's requirements.
• Fixed a visual bug where users would have been able to continue through certain datasets on a dataset that did not have a valid name.
• Fixed a visual bug where right clicking on an item in 'Step 3' of our organize datasets would show the context menu in the wrong position.
• Fixed a minor bug where .jpeg files were not requesting their proper icon in the UI.
• Added minor bug fixes with new Pennsieve APIs. As we go forward, performance of key SODA-Pennseive elements should improve.

Known issues

• There is a bug with removing dataset permissions using both SODA and Pennsieve. If you want to remove your own permission from a dataset, another user with either 'Manager' or 'Owner' permissions must remove you from the dataset. This is an issue with Pennsieve's backend system and will be updated soon.

Version 4.2.1

Bug fixes

• Updated Pennsieve python packages to support minor bugfixes and performance improvements.
• Fixed a minor bug in how dataset statistics were being recorded.
• Fixed a bug where the contact person could not be changed when creating the dataset_description metadata file.

Version 4.2.0

Feature additions

• SODA now supports Pennsieve.
  • With the transition from Blackfynn to Pennsieve complete, SODA now uses the Pennsieve platform as the backend of the app.
  • For the user, the changes should be integrated in with no downtime. All pre-existing functionality of Blackfynn is now supported within SODA. You will only need new API keys for using SODA as well as the Pennsieve agent.

Bug fixes

• When creating the manifest files for local review, SODA will now ignore deleted files and folders before creating the manifest file.
• When you rename a file with more than one extension, SODA will correctly identify the name portion of the file and allow you to rename your file accordingly.
• For long file names or files with long paths, the user interface will break the text to control text clipping boundaries.
• Fixed a bug where manifest files with the 'strict Open XML' format and .xlsx extensions were being read incorrectly. SODA will now ignore manifest files that are not saved in the right format and warn you about this issue when you pull a dataset from Pennsieve.
• When uploading on macOS, hidden files like .DS_STORE will currently break the Pennsieve agent upload. To combat this if your folder has these hidden files, SODA will block the upload when you use the 'Manage Datasets - Upload a local folder' feature. If you import a folder, that has these files, within the 'Organize Dataset' process, SODA will filter out these files automatically.
• When showing popups for users, the messages now don't unintentionally move other content out of the way. This should make SODA to be more consistent to use.
• Added a bug fix for the dataset subtitle character count

Version 4.1.0

Feature additions

• Complete UI overhaul for the Manage Datasets, Prepare Metadata and Disseminate Dataset features to bring the SODA's visuals to be consistent across all features.
• Organize a local dataset
  • You are now able to import and organize dataset folders and files directly from your local file system.
  • After organizing the dataset and including your metadata files, you can push your dataset directly to Blackfynn for storage and publishing or save it on your computer for future use.
• Organize a Blackfynn dataset
  • You are now able to import a dataset, directly from Blaackfynn and rename, move and delete files directly from SODA.
  • Support for importing pre-existing manifest files and metadata files has been included.
  • You will be able to import new files from your computer and deposit it within your Blackfynn dataset as well.
• Save your progress
  • If you are in the middle of organizing a dataset and have to leave the process at any time, you can now save all your current progress and restart from the exact same point at a later time.
• Organize dataset
  • You can now start over the dataset organization process at any point from step 3 onward by clicking the Start over button (located next to the Back button).
  • You can now move files and folders to another folder by right-clicking on the items and select Move to.
  • SODA now allows multiple selections of files and folders for manipulation. This can be achieved by dragging your mouse pointers over several items or pressing and holding the Ctrl button and select the items.
  • Blackfynn has updated how their backend systems handle file names when you upload to their platform. SODA will take care of all the file names and generate your manifest files accordingly.
  • When you organize a dataset, you can now generate your manifest files locally to verify their accuracy before you upload them to Blackfynn.
  • A preview step is added to the dataset organization process that gives users a preview of their dataset structure, generate options, and options to edit if applicable. The dataset structure at this step will be shown in a tree view for an easy and convenient file track.
• Unshare with the Curation team
  • If you have already shared your dataset with the Curation team, you can now remove it from this state with a click of just one button
• Unshare with the SPARC Consortium
  • If you have already shared your dataset with the SPARC consortium, you can now remove it from this state with a click of just one button
• Search dropdowns
  • Multiple dropdowns throughout SODA are now searchable. These dropdowns include the dataset list, PI owner/user/team list, and SPARC award list.
• Updated account management
  • SODA now restricts you to have only one valid account at a time. This account has to be within the SPARC Consortium organization. If you have any Blackfynn API keys from an unsupported organization they will be removed and SODA will prompt you to regenerate a new key set that is within the SPARC Consortium organization.
• Adding Permissions for users
  • Within the dropdowns for selecting users within the SPARC organization, you will now see their email for better clarity.
• Added support for TIFF banner images
  • If you wanted your TIFF image to be the banner image of your dataset, you can now use SODA to automatically convert and set your banner image.
• Added support for in-app updating on macOS

Bug fixes

• When uploading a local dataset to an existing Blackfynn folder, the 'skip' folders option now correctly uploads files that were not meant to be skipped.
• Creating a new local folder as your dataset destination now renames the generated folder correctly if a duplicate folder has to be created.
• Squashed a bug where files uploaded to Blackfynn were sometimes not renamed.
• Create dataset_description.xlsx file Fixed bug where a contributor's affiliations have a comma.
• Fixed a bug where when you would upload files to Blackfynn, it would create a duplicate and not replace your old files.
• Added support for files with more than one extension. This fixes a bug where the manifest file was providing the incorrect file type.

Version 3.0.1

Feature additions

• Full file organization interface with lower-level folder support (1)
• Revised User Interface for the Prepare dataset -> Organize dataset feature aiming to make it more user-friendly and the curation process easier to follow through (2)
• Added in-app updating for Windows and Linux (Ubuntu)

Further notes

• Feature (1) further explained Extended the previous interface such that users can create virtual subfolder structures within high-level SPARC folders and specify files to be included in each of them.
• Feature (2) further explained Changed user interface for the Organize dataset feature such that there are fewer texts and more easy-to-follow steps. It now follows the question-by-question format that guides users through the curation steps. This change aims at creating better interactions between SODA and users, thus making the curation process quicker and easier.

Major bug fixes

• Updated Airtable SPARC's table name to reflect the change initiated by SPARC. Prior to the fix, SODA could not connect to the SPARC award data sheet, thus raising an error when users utilize the Prepare metadata feature.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

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