merged in staging changes v6.0.0

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @megasanjay @aaronm-2112

.github/workflows/check-misspellings.yml

@@ -26,5 +26,5 @@ jobs:
       - uses: peter-evans/create-pull-request@main
         with:
           token: ${{ secrets.BOT_ACTIONS }}
-          commit-message: "Fixes by misspell-fixer"
-          title: "Typos fix by misspell-fixer"
+          commit-message: "fix(typo): 🐛 typo fixes by misspell-fixer"
+          title: "fix(typo): 🐛 typo fixes by misspell-fixer"

.github/workflows/lint-check.yml

@@ -33,6 +33,7 @@ jobs:
         with:
           prettier: true
           prettier_extensions: "css,html,js,json,jsx,md,sass,scss,ts,tsx,vue"
+          commit_message: "style: 🎨 fix code style issues with ${linter}"
           auto_fix: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
           git_email: "[email protected]"
@@ -51,6 +52,7 @@ jobs:
         with:
           black: true
           black_dir: "./src/pysoda"
+          commit_message: "style: 🎨 fix code style issues with ${linter}"
           auto_fix: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
           git_email: "[email protected]"

.zenodo.json

@@ -1,13 +1,9 @@
 {
   "upload_type": "software",
   "title": "SODA (Software to Organize Data Automatically) for SPARC",
-  "publication_date": "2022-04-01",
+  "publication_date": "2022-05-18",
   "creators": [
-    {
-      "name": "Patel, Bhavesh",
-      "affiliation": "FAIR Data Innovations Hub",
-      "orcid": "0000-0002-0307-262X"
-    },
+    { "name": "Patel, Bhavesh", "affiliation": "FAIR Data Innovations Hub" },
     { "name": "Ngo, Tram", "affiliation": "FAIR Data Innovations Hub" },
     {
       "name": "Soundarajan, Sanjay",
@@ -33,5 +29,5 @@
     "ubuntu",
     "windows"
   ],
-  "version": "5.3.2"
+  "version": "6.0.0"
 }

CHANGELOG.md

@@ -5,11 +5,44 @@ All notable changes to SODA will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v.6.0.0 - 2022-05-17
+
+### 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.
+
 ## v.5.4.0 - 2022-04-25
 
+### NOTE: This version of SODA was not officially released.
+
 ### Feature additions:
 
-- In Organize Dataset: Lazy loading is now a feature when viewing all imported items in a dataset. This will ease performance when datasets are large (over 500+ items) and can cause issues when rendering on older machines.
+- 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.
 

CITATION.cff

@@ -7,7 +7,6 @@ authors:
   email: [email protected]
   family-names: Patel
   given-names: Bhavesh
-  orcid: 0000-0002-0307-262X
 - affiliation: FAIR Data Innovations Hub
   email: [email protected]
   family-names: Ngo
@@ -29,7 +28,11 @@ authors:
   family-names: Portillo
   given-names: Dorian
 cff-version: 1.2.0
-date-released: '2022-04-01T20:39:04.395Z'
+date-released: '2022-05-18'
+identifiers:
+- description: DOI for this software's record on Zenodo
+  type: doi
+  value: https://doi.org/10.5281/zenodo.5565455
 keywords:
 - SPARC
 - FAIR
@@ -46,4 +49,5 @@ repository-code: https://github.com/fairdataihub/SODA-for-SPARC
 title: SODA (Software to Organize Data Automatically) for SPARC
 type: software
 url: https://fairdataihub.org/
-version: 5.3.2
+version: 6.0.0
+

README.md

@@ -2,7 +2,17 @@
 [![Stargazers][stars-shield]][stars-url]
 [![Issues][issues-shield]][issues-url]
 [![MIT License][license-shield]][license-url]
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5639796.svg)](https://doi.org/10.5281/zenodo.5639796)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5565455.svg)](https://doi.org/10.5281/zenodo.5565455)
+[![Curated with FAIRshare](https://raw.githubusercontent.com/fairdataihub/FAIRshare/main/badge.svg)](https://fairdataihub.org/fairshare)
+
+[contributors-shield]: https://img.shields.io/github/contributors/fairdataihub/SODA-for-SPARC.svg?style=flat-square
+[contributors-url]: https://github.com/fairdataihub/SODA-for-SPARC/graphs/contributors
+[stars-shield]: https://img.shields.io/github/stars/fairdataihub/SODA-for-SPARC.svg?style=flat-square
+[stars-url]: https://github.com/fairdataihub/SODA-for-SPARC/stargazers
+[issues-shield]: https://img.shields.io/github/issues/fairdataihub/SODA-for-SPARC.svg?style=flat-square
+[issues-url]: https://github.com/fairdataihub/SODA-for-SPARC/issues
+[license-shield]: https://img.shields.io/github/license/fairdataihub/SODA-for-SPARC.svg?style=flat-square
+[license-url]: https://github.com/fairdataihub/SODA-for-SPARC/blob/main/LICENSE
 
 <!-- HEADER -->
 <br />
@@ -18,7 +28,7 @@
    <i> By SPARC investigators, for SPARC investigators </i>
     <br />
     <br />
-    <a href="https://fairdataihub.org/sodaforsparc/docs/getting-started/User-Interface"><strong>Explore our documentation »</strong></a>
+    <a href="https://docs.sodaforsparc.io/"><strong>Explore our documentation »</strong></a>
     <br />
     <br />
     <a href="https://github.com/fairdataihub/SODA-for-SPARC/issues">Report Issue</a>
@@ -33,17 +43,17 @@
 
 - [About](#about)
 - [Downloading SODA](#Downloading-soda)
-- [Using SODA](#Using-SODA)
 - [Full Documentation](#Full-Documentation)
 - [Issues and Feedback](#Issues-and-Feedback)
-- [Using the Source Code](#Using-the-Source-Code)
+- [Contributing](#Contributing)
 - [License](#license)
-- [Privacy Policy](#Privacy-Policy)
+- [Privacy Policy](https://docs.sodaforsparc.io/docs/privacypolicy)
 - [Acknowledgements](#acknowledgements)
+- [Citing](#Citing)
 
 ## About
 
-SODA (Software to Organize Data Automatically) for SPARC is a desktop software intended to facilitate the data organization and submission process for [SPARC](https://commonfund.nih.gov/sparc) investigators and thus promote the [FAIR Data Principles](https://www.go-fair.org/fair-principles/). The idea for a computer software that assists researchers in curating and sharing their data originated during the SPARC Hackathon in December 2018, where it won the Public's Choice Award, before receiving support from the National Institutes of Health (NIH) for further development. SODA for SPARC is designed such that users can accomplish all the [requirements to submit a SPARC dataset](https://docs.google.com/presentation/d/1EQPn1FmANpPsFt3CguU-JOQVMMlJsNXluQAK_gb2qVg/edit?usp=sharing) rapidly through a single interface. Moreover, requirements have been broken down into easy-to-perform steps and automation has been integrated to reduce users' effort to a bare minimum during each step, often to just a few clicks.
+SODA (Software to Organize Data Automatically) for SPARC is an open-source and free cross-platform desktop software intended to facilitate the data organization and submission process for [SPARC](https://commonfund.nih.gov/sparc) investigators according to the [FAIR SPARC data curation guidelines](https://sparc.science/help/7k8nEPuw3FjOq2HuS8OVsd#top). The idea for a computer software that assists researchers in curating and sharing their data originated during the SPARC Hackathon in December 2018, where it won the Public's Choice Award, before receiving support from the National Institutes of Health (NIH) for further development. SODA for SPARC is designed such that users can accomplish all the requirements to submit a SPARC dataset rapidly through a single interface. Moreover, requirements have been broken down into easy-to-perform steps and automation has been integrated to reduce users' effort to a bare minimum during each step, often to just a few clicks.
 
 <p align="center">
   <img src="https://github.com/fairdataihub/SODA-for-SPARC/blob/main/docs/documentation/Landing-page/UserInterface.PNG" alt="interface" width="600">
@@ -54,42 +64,21 @@ SODA (Software to Organize Data Automatically) for SPARC is a desktop software i
 
 ## Downloading SODA
 
-SODA is distributed as an easy-to-install application for Windows, Mac OS, and Ubuntu. Follow the instructions provided in [our dedicated documentation](https://fairdataihub.org/sodaforsparc/docs/getting-started/Download-Soda) to download the version suitable for your operating system.
+SODA is distributed as an easy-to-install application for Windows, Mac OS, and Ubuntu. Follow the instructions provided in [our dedicated documentation](https://docs.sodaforsparc.io/docs/getting-started/download-soda) to download the version suitable for your operating system.
 
 All our releases are also accessible in the [releases tab](https://github.com/fairdataihub/SODA-for-SPARC/releases/latest).
 
-## Using SODA
-
-Click on the image below and watch our video to quickly familiarize yourself with the user interface of SODA:
-
-<p align="center">
-<a href="https://www.youtube.com/watch?v=Fyn9R0Tk_pU" target="_blank">
-<img src="https://img.youtube.com/vi/Fyn9R0Tk_pU/0.jpg" />
-</a>
-</p>
-
-Please see our [suggested workflow for preparing and submitting your SPARC dataset](https://fairdataihub.org/sodaforsparc/docs/getting-started/Organize-and-submit-a-new-SPARC-dataset-with-SODA) rapidly and accurately with SODA.
+## Documentation
 
-Although we would highly encourage you to use SODA for the entire organization and submission process of your dataset, SODA is designed such that you are not bound to using the software for all of the steps: you can perform desired steps from SODA and others outside.
-
-## Full Documentation
-
-See the [documentation](https://fairdataihub.org/sodaforsparc/docs/getting-started/User-Interface) for our full documentation, including details about each features and how to use them as well as guidance for using and contributing to our source code.
+See the [our dedicated webpage]() for the full documentation, including details about each features and how to use them.
 
 ## Issues and Feedback
 
 To report any issues with the software, suggest improvements, or request a new feature, please open a new issue via the [Issues tab](https://github.com/fairdataihub/SODA-for-SPARC/issues). Provide adequate information (operating system, steps leading to error, screenshots) so we can help you efficiently. Alternatively, you could also use [our feedback form](https://docs.google.com/forms/d/e/1FAIpQLSfyUw2_NI1-2tlAr8oB5_JcJ_yjTB-zUDt9skfGjNU9qjITwg/viewform?ts=5e433bea). The feedback form is also accessible directly in the user interface of SODA.
 
-<p align="center">
-   <img src="https://github.com/fairdataihub/SODA-for-SPARC/blob/main/docs/documentation/Landing-page/feedbackform.PNG" alt="interface" width="600">
-  <br/>
-  <i> A screenshot of our feedback form in the user interface of SODA. </i>
-  </img>
- </p>
-
-## Using the Source Code
+## Contributing
 
-If you want to contribute, modify SODA to better suit your needs, or compile it for an operating system not mentioned above, please follow the instructions provided in the [developer manual](https://github.com/fairdataihub/SODA-for-SPARC/wiki) of our documentation.
+If you want to contribute, modify SODA to better suit your needs, or compile it for an operating system not mentioned above, please follow the instructions provided in the [developer section](https://docs.sodaforsparc.io/docs/developer-documentation/project-setup) of our documentation.
 
 ## License
 
@@ -116,19 +105,10 @@ SODA uses Google Analytics to track user interactions with the application. Trac
   - Anna Rietsch (Cleveland Clinic, Cleveland OH)
   - Joseph Sassoon (Integrated Medical Systems Laboratory - New York Institute of Technology)
 
-[contributors-shield]: https://img.shields.io/github/contributors/bvhpatel/SODA.svg?style=flat-square
-[contributors-url]: https://github.com/fairdataihub/SODA-for-SPARC/graphs/contributors
-[stars-shield]: https://img.shields.io/github/stars/bvhpatel/SODA.svg?style=flat-square
-[stars-url]: https://github.com/fairdataihub/SODA-for-SPARC/stargazers
-[issues-shield]: https://img.shields.io/github/issues/bvhpatel/SODA.svg?style=flat-square
-[issues-url]: https://github.com/fairdataihub/SODA-for-SPARC/issues
-[license-shield]: https://img.shields.io/github/license/bvhpatel/SODA.svg?style=flat-square
-[license-url]: https://github.com/fairdataihub/SODA-for-SPARC/blob/main/LICENSE
+## Citing
 
-## Developers
+If you use SODA for SPARC to curate your dataset, please cite the following references:
 
-- Bhavesh Patel (California Medical Innovations Institute)
-- Tram Ngo (California Medical Innovations Institute)
-- Sanjay Soundarajan (California Medical Innovations Institute)
-- Parya Aghasafari (UC Davis)
-- Karl Helmer (Harvard Medical School/Massachusetts General Hospital)
+1. Patel, B., Srivastava, H., Aghasafari, P., & Helmer, K. (2020). SPARC: SODA, an interactive software for curating SPARC datasets. The FASEB Journal, 34(S1), 1-1. [10.1096/fasebj.2020.34.s1.02483](https://doi.org/10.1096/fasebj.2020.34.s1.02483)
+2. Bandrowski, A., Grethe, J. S., Pilko, A., Gillespie, T., Pine, G., Patel, B., Surles-Zeigler, M., & Martone, M. E. (2021). SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data. bioRxiv. [10.1101/2021.02.10.430563](https://doi.org/10.1101/2021.02.10.430563)
+3. Patel, B., Ngo, T., Soundarajan, S., Marroquin, A., Clark, J., & Portillo, D. (2022). SODA (Software to Organize Data Automatically) for SPARC. Zenodo. [10.5281/zenodo.5565455](https://doi.org/10.5281/zenodo.5565455)