fairdataihub/soda-for-sparc

Simplifying data curation for researchers funded by the NIH SPARC initiative

soda-for-sparc's Issues

[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

[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

Testing issue report

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 '....'
4. See error

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

Screenshots
If applicable, add screenshots to help explain your problem.

Operating system used:

• OS: [e.g. Windows 10 Pro]

Additional context
Add any other context about the problem here.

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

[JOSS Review] Use declared constants

Please use declared PENNSIEVE_URL everywhere else (e.g. 2 3 4). Duplicated constant PENNSIEVE_URL makes code untestable in local dev/integration test environment.

JOSS Review

[JOSS Review] Update the documentation portal link in README

Update link our dedicated webpage under documentation section of README.

JOSS Review

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:

1. Run SODA for the first time.
2. Program runs until connecting to server, then crashes.
3. 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

Rate-Limited

These updates are currently rate-limited. Click on a checkbox below to force their creation now.

• chore(deps): update dependency @rollup/plugin-commonjs to v25.0.8
• fix(deps): update dependency @yaireo/dragsort to v1.3.2
• fix(deps): update dependency cropperjs to v1.6.2
• fix(deps): update dependency doi-regex to v0.1.14
• fix(deps): update dependency dragselect to v3.0.5
• fix(deps): update dependency ini to v4.1.3
• fix(deps): update dependency jimp to v0.22.12
• chore(deps): update dependency @vitejs/plugin-react to v4.3.0
• chore(deps): update dependency electron-builder to v24.13.3
• chore(deps): update dependency eslint to v8.57.0
• chore(deps): update dependency eslint-plugin-react to v7.34.1
• chore(deps): update dependency prettier to v3.2.5
• chore(deps): update react monorepo to v18.3.1 (react, react-dom)
• fix(deps): update dependency axios to v1.7.2
• fix(deps): update dependency convert-csv-to-json to v2.47.0
• fix(deps): update dependency electron-updater to v6.2.1
• fix(deps): update dependency jspreadsheet to v10.9.11
• fix(deps): update dependency sweetalert2 to v11.11.0
• fix(deps): update dependency validator to v13.12.0
• chore(deps): update actions/checkout action to v3
• chore(deps): update apple-actions/import-codesign-certs action to v3
• chore(deps): update chromaui/action action to v10
• chore(deps): update codespell-project/actions-codespell action to v2
• chore(deps): update conda-incubator/setup-miniconda action to v3
• chore(deps): update dependency @electron-toolkit/eslint-config-prettier to v2
• chore(deps): update dependency electron to v30
• chore(deps): update dependency electron-vite to v2
• chore(deps): update dependency eslint to v9
• chore(deps): update dependency vite to v5
• chore(deps): update wearerequired/lint-action action to v2
• fix(deps): update dependency @electron-toolkit/preload to v3
• fix(deps): update dependency @electron-toolkit/utils to v3
• fix(deps): update dependency @fortawesome/fontawesome-free to v6
• fix(deps): update dependency bootbox to v6
• fix(deps): update dependency bootstrap to v5
• fix(deps): update dependency electron-context-menu to v4
• fix(deps): update dependency jspreadsheet to v11
• 🔐 Create all rate-limited PRs at once 🔐

Pending Status Checks

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• fix(deps): update dependency esbuild to v0.21.5
• fix(deps): update mantine monorepo to v7.10.2 (@mantine/core, @mantine/hooks)
• fix(deps): update dependency @tabler/icons-react to v3.6.0
• chore(deps): update dependency @rollup/plugin-commonjs to v26
• chore(deps): update github/codeql-action action to v3
• fix(deps): update dependency uuid to v10

Open

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

• chore(deps): update dependency vite to v4.5.3
• fix(deps): update dependency bootbox to v5.5.3
• fix(deps): update dependency @yaireo/tagify to v4.26.5
• fix(deps): update dependency bootstrap to v4.6.2
• fix(deps): update dependency bootstrap-icons to v1.11.3
• fix(deps): update dependency electron-log to v5.1.4
• fix(deps): update dependency jquery to v3.7.1
• chore(deps): update actions/checkout action to v4
• chore(deps): update actions/setup-node action to v4
• chore(deps): update actions/setup-python action to v5
• Click on this checkbox to rebase all open PRs at once

Ignored or Blocked

These are blocked by an existing closed PR and will not be recreated unless you click a checkbox below.

• 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
• @fortawesome/fontawesome-free ^5.15.4
• @mantine/core ^7.7.1
• @mantine/hooks ^7.7.1
• @popperjs/core ^2.11.8
• @rollup/plugin-inject ^5.0.5
• @rollup/plugin-node-resolve ^15.2.3
• @tabler/icons-react ^3.1.0
• @tarekraafat/autocomplete.js ^10.2.7
• @toast-ui/editor ^3.2.2
• @types/jstree ^3.3.45
• @yaireo/dragsort ^1.3.1
• @yaireo/tagify ^4.17.9
• accordion-js ^3.3.4
• animate.css 4.1.1
• 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
• convert-excel-to-json ^1.7.0
• cropperjs ^1.6.1
• doi-regex ^0.1.13
• dragselect ^3.0.4
• electron-context-menu ^3.6.1
• electron-log ^5.0.1
• electron-notarize ^1.2.2
• electron-updater ^6.1.7
• esbuild ^0.21.3
• excel4node ^1.8.2
• find-free-port ^2.0.0
• fomantic-ui ^2.9.3
• fs-extra ^11.1.1
• image-data-uri ^2.0.1
• immer ^10.0.4
• ini ^4.1.1
• intro.js ^7.2.0
• jimp ^0.22.10
• jquery 3.6.0
• jspreadsheet ^10.3.3
• jstree ^3.3.16
• lottie-web ^5.12.2
• module ^1.2.5
• mv ^2.1.1
• node-localstorage ^3.0.5
• notyf ^3.10.0
• select2 ^4.1.0-rc.0
• sweetalert2 ^11.9.0
• tippy.js ^6.3.7
• tui-date-picker ^4.3.3
• uuid ^9.0.1
• v8-compile-cache ^2.4.0
• validator ^13.11.0
• vite-plugin-commonjs-externals ^0.1.3
• xlsx ^0.18.5
• zustand ^4.5.2
• @electron-toolkit/eslint-config ^1.0.1
• @electron-toolkit/eslint-config-prettier ^1.0.1
• @rollup/plugin-commonjs ^25.0.7
• @vitejs/plugin-react ^4.0.4
• electron 19.0.0
• electron-builder ^24.6.3
• electron-vite ^1.0.27
• eslint ^8.47.0
• eslint-plugin-react ^7.33.2
• postcss ^8.4.38
• postcss-preset-mantine ^1.14.0
• postcss-simple-vars ^7.0.1
• 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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