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Fix code style issues with Prettier
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7 changes: 3 additions & 4 deletions .github/ISSUE_TEMPLATE/feature_request.md
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---
name: Feature request
about: Suggest a feature you would like us to integrate in SODA
title: ''
labels: ''
assignees: ''

title: ""
labels: ""
assignees: ""
---

**Is your feature request related to a problem? Please describe.**
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11 changes: 6 additions & 5 deletions .github/ISSUE_TEMPLATE/report-issue.md
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---
name: Report issue
about: Let us know of any issue you encounter while using SODA
title: ''
labels: ''
assignees: ''

title: ""
labels: ""
assignees: ""
---

**Describe the issue**
A clear and concise description of what the issue is.

**To Reproduce**
Steps that leads to the issue:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
Expand All @@ -24,7 +24,8 @@ A clear and concise description of what you expected to happen.
If applicable, add screenshots to help explain your problem.

**Operating system used:**
- OS: [e.g. Windows 10 Pro]

- OS: [e.g. Windows 10 Pro]

**Additional context**
Add any other context about the problem here.
2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### 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 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:
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26 changes: 13 additions & 13 deletions CODE_OF_CONDUCT.md
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Expand Up @@ -14,22 +14,22 @@ appearance, race, religion, or sexual identity and orientation.
Examples of behavior that contributes to creating a positive environment
include:

* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
- Using welcoming and inclusive language
- Being respectful of differing viewpoints and experiences
- Gracefully accepting constructive criticism
- Focusing on what is best for the community
- Showing empathy towards other community members

Examples of unacceptable behavior by participants include:

* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
- The use of sexualized language or imagery and unwelcome sexual attention or
advances
- Trolling, insulting/derogatory comments, and personal or political attacks
- Public or private harassment
- Publishing others' private information, such as a physical or electronic
address, without explicit permission
- Other conduct which could reasonably be considered inappropriate in a
professional setting

## Our Responsibilities

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4 changes: 2 additions & 2 deletions CONTRIBUTING.md
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Expand Up @@ -4,7 +4,7 @@ We love contributions from everyone.
By participating in this project,
you agree to abide by the thoughtbot [code of conduct].

[code of conduct]: https://thoughtbot.com/open-source-code-of-conduct
[code of conduct]: https://thoughtbot.com/open-source-code-of-conduct

We expect everyone to follow the code of conduct
anywhere in thoughtbot's project codebases,
Expand All @@ -21,7 +21,7 @@ Mention how your changes affect the project to other developers and users in the

Push to your fork. Write a [good commit message][commit]. Submit a pull request.

[commit]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
[commit]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html

Others will give constructive feedback.
This is a time for discussion and improvements,
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74 changes: 40 additions & 34 deletions README.md
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Expand Up @@ -28,21 +28,22 @@
</p>

<!-- TABLE OF CONTENTS -->

## Table of Contents

* [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)
* [License](#license)
* [Privacy Policy](#Privacy-Policy)
* [Acknowledgements](#acknowledgements)
- [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)
- [License](#license)
- [Privacy Policy](#Privacy-Policy)
- [Acknowledgements](#acknowledgements)

## 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 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.

<p align="center">
<img src="https://github.com/fairdataihub/SODA-for-SPARC/blob/main/docs/documentation/Landing-page/UserInterface.PNG" alt="interface" width="600">
Expand All @@ -52,11 +53,13 @@ SODA (Software to Organize Data Automatically) for SPARC is a desktop software i
</p>

## 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/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).

## Using SODA

Click on the image below and watch our video to quickly familiarize yourself with the user interface of SODA:

<p align="center">
Expand All @@ -67,49 +70,51 @@ Click on the image below and watch our video to quickly familiarize yourself wit

Please see our [suggested workflow for preparing and submitting your SPARC dataset](https://fairdataihub.org/sodaforsparc/docs/Organize-and-submit-a-new-SPARC-dataset-with-SODA) rapidly and accurately with SODA.

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.


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/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.

## 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>
</p>

## Using the Source Code

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 manual](https://github.com/fairdataihub/SODA-for-SPARC/wiki) of our documentation.

## License

SODA is distributed under the MIT License. See [LICENSE](https://github.com/fairdataihub/SODA-for-SPARC/blob/main/LICENSE) for more information.

## Privacy Policy

SODA uses Google Analytics to track user interactions with the application. 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 indentify errors and subsequently improve user experience. To learn more about what is tracked and how we use Google Analytics within SODA, please read our [Privacy Policy](https://github.com/fairdataihub/SODA-for-SPARC#Privacy-Policy).

## Acknowledgements
* [NIH SPARC Initiative](https://commonfund.nih.gov/sparc)
* [Blackfynn Team](https://www.blackfynn.com/)
* [SPARC Dataset Curation Team](https://github.com/SciCrunch/sparc-curation)
* 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](https://scholar.google.com/citations?user=lo1TkqwAAAAJ&hl=en&oi=ao) (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)

- [NIH SPARC Initiative](https://commonfund.nih.gov/sparc)
- [Blackfynn Team](https://www.blackfynn.com/)
- [SPARC Dataset Curation Team](https://github.com/SciCrunch/sparc-curation)
- 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](https://scholar.google.com/citations?user=lo1TkqwAAAAJ&hl=en&oi=ao) (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)

[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
Expand All @@ -121,8 +126,9 @@ SODA uses Google Analytics to track user interactions with the application. Trac
[license-url]: https://github.com/fairdataihub/SODA-for-SPARC/blob/main/LICENSE

## Developers
* 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)

- 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)
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