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Simplifying data curation for researchers funded by the NIH SPARC initiative

Home Page: https://fairdataihub.org/sodaforsparc

License: MIT License

CSS 5.76% HTML 14.35% JavaScript 69.71% Python 7.74% Jupyter Notebook 2.37% MDX 0.07%

windows mac ubuntu curation sparc-dataset

soda-for-sparc's Introduction

Keep Calm and Curate!

Your one-stop tool for curating and submitting SPARC datasets
By SPARC investigators, for SPARC investigators

Explore our documentation »

Report Issue · Submit feedback

About

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 investigators according to the FAIR SPARC data curation guidelines. 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.

A screenshot of the user interface of SODA.

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 to download the version suitable for your operating system.

All our releases are also accessible in the releases tab.

Documentation

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. Provide adequate information (operating system, steps leading to error, screenshots) so we can help you efficiently. Alternatively, you could also use our feedback form. The feedback form is also accessible directly in the user interface of SODA.

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 section of our documentation.

License

SODA is distributed under the MIT License. See LICENSE for more information.

Privacy Policy

SODA uses Kombucha Analytics for tracking. Tracking is anonymous and no identifying personal information is collected. Tracking is implemented as part of our agreement with the SPARC program to report usage statistics for SODA. Tracking is also used to identify errors and subsequently improve user experience. To learn more about what is tracked and how we use Kombucha Analytics within SODA, please read our Privacy Policy.

Acknowledgements

NIH SPARC Initiative
Blackfynn Team
SPARC Dataset Curation Team
Our beta testers, including:
- Natalia Biscola (Icahn School of Medicine at Mount Sinai)
- John Dawson (UC Davis)
- Clara Huesing (Pennington Biomedical Research Center)
- Scott John (UCLA)
- Muriel Larauche (Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UCLA)
- Madelyn Lorenz (Washington University in St. Louis)
- Kun-Han Lu (Weldon School of Biomedical Engineering, Purdue University)
- Alison Moss (Thomas Jefferson University)
- Anna Rietsch (Cleveland Clinic, Cleveland OH)
- Joseph Sassoon (Integrated Medical Systems Laboratory - New York Institute of Technology)

Citing

If you use SODA for SPARC to curate your dataset, please cite the following references:

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
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
Marroquin, C., Clark, J., Portillo, D., Soundarajan, S., Ngo, T., & Patel, B., (2024). SODA (Software to Organize Data Automatically) for SPARC. Zenodo. 10.5281/zenodo.12774826

soda-for-sparc's People

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Stargazers

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hsorby guestaccount76 megasanjay jacobiclark bendichter slugb0t yarikoptic aaronm-2112

soda-for-sparc's Issues

[JOSS Review] Authentication guards for flask_restx APIs

How is the flask_restx APIs under api folder protected. Unless I am missing something, I don't see authentication or authorisation enforced on these API operations and this could be a security risk.

JOSS Review

[JOSS Review] Inconsistent use of HTTP status code

Inconsistent use of HTTP status code particularly in Flask authentication and authorisation.

A few examples:

Using 400 (bad request) instead of 401 (unauthorized) 1

Using 500 (Internal Server Error) instead of 400 (bad request) 1

Translating 400(bad request) into 409 (conflict) 1

JOSS Review

DOI Tweaks for JOSS submission

Hello JOSS editor here - thanks for fixing up the DOIs, there is one final tweak needed on this line:

https://github.com/fairdataihub/SODA-for-SPARC/blob/f51ab22d0174b0e0c3b65b0af00864be78b6b3b1/paper/paper.bib#L75C40-L75C41

Need to drop the close parenthesis at the end of the DOI.

  doi = {10.12688/f1000research.75071.1)}

Our paper compiling tests should pass once that is through

openjournals/joss-reviews#5952

FAIR Compliance Dashboard

Check the FAIRness of your software

This issue is your repository's dashboard for all things FAIR. Keep it open as making and keeping software FAIR is a continuous process that evolves along with the software. You can read the documentation to learn more.

LICENSE ✔️

A LICENSE file is found at the root level of the repository.

Metadata ✔️

A CITATION.cff and a codemeta.json file are found in the repository. They may need to be updated over time as new people are contributing to the software, etc.

Issue with program crashing upon startup

Describe the issue
I'm having an issue with the program crashing. The program crashes when it tries to connect to the servers, and then doesn't start after that until I restart my computer, where it then crashes again if it tries to connect. It appears that the application in C:\Users______\AppData\Local\Programs\SODA for SPARC\resources\app\pyflaskdist
is still running after the crash. When I run the program again, there are multiple instances of this application running.

To Reproduce
Steps that leads to the issue:

Run SODA for the first time.
Program runs until connecting to server, then crashes.
Run SODA for a second time, crashes immediately.

Expected behavior
I expect the program to not crash upon connecting to the server.

Screenshots
None

Operating system used:
Windows 10

Additional context
I have tried restarting my computer, reinstalling SODA in different locations, and running as administrator.

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Warning

These dependencies are deprecated:

Datasource	Name	Replacement PR?
npm	`electron-notarize`

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chore(deps): update dependency postcss to v8.4.39
fix(deps): update dependency zustand to v4.5.4
chore(deps): update github/codeql-action action to v3

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These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

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chore(deps): update dependency electron to v19.1.9

Detected dependencies

github-actions

.github/workflows/Build-and-deploy-linux.yml

actions/checkout v3

actions/setup-python v2

conda-incubator/setup-miniconda v2

actions/setup-node v4

.github/workflows/Build-and-deploy-mac.yml

actions/checkout v3

actions/setup-python v2

conda-incubator/setup-miniconda v2

actions/setup-node v4

apple-actions/import-codesign-certs v1

.github/workflows/Build-and-deploy-win.yml

actions/checkout v3

actions/setup-python v4

conda-incubator/setup-miniconda v2

actions/setup-node v4

.github/workflows/check-misspellings.yml

actions/checkout v2

.github/workflows/chromatic.yml

actions/checkout v1

chromaui/action v1

.github/workflows/codeql-analysis.yml

actions/checkout v2

github/codeql-action v1

github/codeql-action v1

github/codeql-action v1

.github/workflows/codespell.yml

actions/checkout v3

codespell-project/actions-codespell v1

.github/workflows/gitlab-sync.yml

actions/checkout v2

wangchucheng/git-repo-sync v0.1.0

.github/workflows/lint-check.yml

actions/checkout v2

actions/setup-node v1

wearerequired/lint-action v1

actions/setup-python v1

wearerequired/lint-action v1

.github/workflows/release-on-zenodo.yml

actions/setup-node v3

megasanjay/upload-to-zenodo v2.0.1

html

index.html

animate.css 4.1.1

npm

package.json

@electron-toolkit/preload ^2.0.0

@electron-toolkit/utils ^2.0.0

@fairdataihub/config ^2.2.3

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axios ^1.6.0

bootbox 5.5.2

bootstrap 4.0.0

bootstrap-icons 1.5.0

bootstrap-select ^1.13.18

check-disk-space ^3.4.0

convert-csv-to-json ^2.0.0

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cropperjs ^1.6.1

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electron-context-menu ^3.6.1

electron-log ^5.0.1

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esbuild ^0.21.3

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fomantic-ui ^2.9.3

fs-extra ^11.1.1

image-data-uri ^2.0.1

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ini ^4.1.1

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jquery 3.6.0

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uuid ^9.0.1

v8-compile-cache ^2.4.0

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vite-plugin-commonjs-externals ^0.1.3

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@electron-toolkit/eslint-config ^1.0.1

@electron-toolkit/eslint-config-prettier ^1.0.1

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@vitejs/plugin-react ^4.0.4

electron 19.0.0

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prettier ^3.0.2

react ^18.2.0

react-dom ^18.2.0

rollup-plugin-copy ^3.5.0

vite ^4.4.9

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Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
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Operating system used:

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Additional context
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