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Prod push #354

Merged
merged 48 commits into from
May 14, 2024
Merged

Prod push #354

merged 48 commits into from
May 14, 2024

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HadleyKing
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HadleyKing added 30 commits April 3, 2024 21:11
@HadleyKing
Fix for get_published_bco
5f2a372 
needed to modify how a published BCO is read
Changes to be committed:
	modified:   client/src/slices/bcoSlice.js
	modified:   server/users/apis.py
@HadleyKing
Remove generate ETag functionality from Portal
f177bd5 
Changes to be committed:
	modified:   client/src/components/builder/index.js
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Update Prefix functions for new APIs
6282751 
Changes to be committed:
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
Update to search page and results.
126eeca 
Changes to be committed:
	modified:   client/src/components/bcodbs/SearchOptions.js
	modified:   client/src/components/bcodbs/SearchResults.js
	modified:   client/src/slices/searchSlice.js
@HadleyKing
Update local data prefixes
41816a2 
Changes to be committed:
	modified:   server/config/fixtures/local_data.json
@HadleyKing
Modifications to Prefix Registry:
db32e21 
support new Prefix Model
Changes to be committed:
	modified:   client/package-lock.json
	modified:   client/package.json
	modified:   client/src/App.css
	new file:   client/src/components/prefix/PrefixModify.js
	deleted:    client/src/components/prefix/PrefixResults.js
	modified:   client/src/components/prefix/PrefixSearch.js
	modified:   client/src/components/prefix/index.js
	modified:   client/src/components/prefix/prefixRegister.js
	modified:   client/src/routes.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
Change Public to a checkbox
afa01fc 
Changes to be committed:
	modified:   src/components/account/Profile.js
@HadleyKing
Prefix Registry UI changes
6286182 
Dialogue box for prefix modify and add user permissions
Changes to be committed:
	modified:   client/src/components/NotificationBox.js
	modified:   client/src/components/prefix/PrefixModify.js
	modified:   client/src/components/prefix/PrefixSearch.js
	modified:   client/src/components/prefix/index.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
Update Prefix model
f500344 
Added a `Public` and `public_hostname` to model

Changes to be committed:
	modified:   server/.secrets.example
	modified:   server/config/fixtures/local_data.json
	new file:   server/prefix/migrations/0002_prefix_public_prefix_public_hostname.py
	modified:   server/prefix/models.py
	modified:   server/prefix/selectors.py
@HadleyKing
Prefix Modify Dialog Box
fc0cf2e 
Changes to be committed:
	modified:   client/src/components/prefix/PrefixModify.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
Prefix Modify Box Part II
cbe5cc1 
Changes to be committed:
	modified:   client/src/components/prefix/PrefixModify.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
UI fixes
816a908 
- Commit 6fc3b4c
- Fix colors on NavBar for links
Changes to be committed:
	modified:   client/src/App.css
	modified:   client/src/components/quickSearch.js
	modified:   client/src/components/resources/Citations.js
	modified:   client/src/components/resources/Galaxy.js
	modified:   client/src/components/resources/Hive.js
	modified:   client/src/layouts/MainNavBar.js
@HadleyKing
Message handeling for Prefix registry
272fdb2 
Changes to be committed:
	modified:   client/src/components/prefix/PrefixModify.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
PRefix registry sync with User DB
42fcb6b 
Changes to be committed:
	modified:   client/src/components/prefix/PrefixModify.js
	modified:   client/src/components/prefix/index.js
	modified:   client/src/components/prefix/prefixRegister.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
@HadleyKing
Prefix db synch with registry UI
e7a121a 
Changes to be committed:
	modified:   server/bcodb/apis.py
	modified:   server/prefix/apis.py
	modified:   server/prefix/services.py
@HadleyKing
Fix create BCO response handeling
3baebb9 
Changes to be committed:
	modified:   .gitignore
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Add user search feature for Prefix Registry
60746e9 
Changes to be committed:
	modified:   client/src/components/builder/provenanceDomain.js
	modified:   client/src/components/prefix/PrefixModify.js
	new file:   client/src/components/prefix/UserSearch.js
	modified:   client/src/services/auth.service.js
	modified:   client/src/services/prefix.service.js
	modified:   client/src/slices/prefixSlice.js
	modified:   client/src/slices/searchSlice.js
@HadleyKing
Move UserSearch content to PrefixModify
7d930cb 
Changes to be committed:
	modified:   client/src/components/prefix/PrefixModify.js
	deleted:    client/src/components/prefix/UserSearch.js
@HadleyKing
Fix for Google OAuth CSRF Token issue
6ff6f00 
Fix #336 #321 #297
    Changes to be committed:
	modified:   src/services/auth.service.js
@HadleyKing
Adjust registry variables for rendering
9740dc5 
Changes to be committed:
	modified:   client/src/components/prefix/index.js
	modified:   client/src/components/prefix/prefixRegister.js
@HadleyKing
Fix for Annon search (no login)
0fb00a5 
Changes to be committed:
	modified:   client/src/components/bcodbs/SearchOptions.js
	modified:   client/src/services/auth.service.js
@HadleyKing
BCO validation fix
0c42828 
Changes to be committed:
	modified:   client/src/slices/bcoSlice.js
	modified:   server/users/apis.py
@HadleyKing
Update validate function submission
c2f9775 
Changes to be committed:
	modified:   client/src/components/account/Profile.js
	modified:   client/src/components/auth/Login.js
	modified:   client/src/services/bco.service.js
	modified:   server/config/settings.py
@HadleyKing
Update to "Add BCODB"
3d1f3b4 
Changes to be committed:
	modified:   server/authentication/services.py
	modified:   server/bcodb/apis.py
	new file:   server/bcodb/migrations/0008_remove_bcodb_group_permissions.py
	modified:   server/bcodb/models.py
@HadleyKing
Update testing data fixtures
d05ff6d 
Changes to be committed:
	modified:   server/config/fixtures/local_data.json
	modified:   server/config/fixtures/test_portal.json
@HadleyKing
Change public host name in test data
9e5e144 
Changes to be committed:
	modified:   server/config/fixtures/test_portal.json
@HadleyKing
Fixes for Publish BCO rerouting.
e038f77 
Changes to be committed:
	deleted:    client/src/components/builder/indexOld.js
	modified:   client/src/components/builder/provenanceDomain.js
	modified:   client/src/components/viewer/index.js
	modified:   client/src/layouts/objectSideBar.js
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Hide Groups button
c1da446 
Changes to be committed:
	modified:   client/src/components/account/Servers.js
@HadleyKing
Fixes for login
21a77e5 
Changes to be committed:
	modified:   client/.env.example
	modified:   client/src/components/bcodbs/SearchOptions.js
	modified:   server/bcodb/services.py
	modified:   server/tests/fixtures/testing_data.json
	modified:   server/users/apis.py
@HadleyKing
Published BCO Rendering
3c49f09 
Changes to be committed:
	modified:   client/src/components/viewer/cardViews.js
	modified:   client/src/components/viewer/index.js
	modified:   server/bcodb/services.py
HadleyKing added 17 commits May 6, 2024 09:56
@HadleyKing
Ui fixes
30904f9 
Changes to be committed:
	modified:   client/src/App.css
	new file:   client/src/components/About.js
	new file:   client/src/components/FullWidthBox.js
	new file:   client/src/components/Home.js
	new file:   client/src/components/Resources.js
	new file:   client/src/components/ThirdBox.js
	deleted:    client/src/components/about/About.js
	deleted:    client/src/components/about/BCOnexus.js
	deleted:    client/src/components/about/HorizontalHeading.js
	deleted:    client/src/components/about/MeetOurTeam.js
	deleted:    client/src/components/about/MemberInfo.js
	deleted:    client/src/components/about/MemberInfoCard.js
	deleted:    client/src/components/about/OurTeam.js
	deleted:    client/src/components/about/Overview.js
	deleted:    client/src/components/about/SB.js
	deleted:    client/src/components/about/Story.js
	deleted:    client/src/components/about/head.js
	deleted:    client/src/components/about/index.js
	deleted:    client/src/components/home/BcoDb.js
	deleted:    client/src/components/home/BioComputeResources.js
	deleted:    client/src/components/home/Builder.js
	deleted:    client/src/components/home/Documentation.js
	deleted:    client/src/components/home/FdaBox.js
	deleted:    client/src/components/home/Galaxy.js
	deleted:    client/src/components/home/Hive.js
	deleted:    client/src/components/home/Intro.js
	deleted:    client/src/components/home/Specification.js
	deleted:    client/src/components/home/Tsc.js
	deleted:    client/src/components/home/Workshop.js
	deleted:    client/src/components/home/index.js
	deleted:    client/src/components/resources/index.js
	modified:   client/src/routes.js
@HadleyKing
UI Cleanup
9008e30 
Changes to be committed:
	modified:   client/src/App.css
	modified:   client/src/components/About.js
	modified:   client/src/components/FullWidthBox.js
	modified:   client/src/components/Home.js
	modified:   client/src/components/Resources.js
	modified:   client/src/components/ThirdBox.js
	modified:   client/src/components/account/Profile.js
	modified:   client/src/components/account/Servers.js
	modified:   client/src/components/account/index.js
	modified:   client/src/components/account/passwordReset.js
	modified:   client/src/components/quickSearch.js
	new file:   client/src/images/cgc2.png
	modified:   client/src/routes.js
@HadleyKing
Reimplement token reset for bcodb
cb750d9 
Changes to be committed:
	modified:   client/src/components/account/Servers.js
	modified:   client/src/services/auth.service.js
	modified:   client/src/slices/accountSlice.js
	modified:   server/bcodb/apis.py
	modified:   server/bcodb/services.py
	modified:   server/bcodb/urls.py
@HadleyKing
Revamp About, Home, and Resources pages
5b43275 
Changes to be committed:
	deleted:    client/src/components/account/bcodbGroups/dbInfo.js
	deleted:    client/src/components/account/bcodbGroups/editGroup.js
	deleted:    client/src/components/account/bcodbGroups/groups.js
	deleted:    client/src/components/account/bcodbGroups/index.js
	deleted:    client/src/components/account/bcodbGroups/permissions.js
	deleted:    client/src/components/resources/Builder.js
	deleted:    client/src/components/resources/CGC.js
	deleted:    client/src/components/resources/Citations.js
	deleted:    client/src/components/resources/DNAnexus.js
	deleted:    client/src/components/resources/Galaxy.js
	deleted:    client/src/components/resources/Hive.js
	deleted:    client/src/components/resources/Packages.js
	deleted:    client/src/components/resources/Tsc.js
	new file:   client/src/images/swagger.png
	renamed:    client/src/components/About.js -> client/src/pages/About.js
	renamed:    client/src/components/Home.js -> client/src/pages/Home.js
	renamed:    client/src/components/Resources.js -> client/src/pages/Resources.js
	modified:   client/src/routes.js
@HadleyKing
Update MUI
8e75bb7 
Changes to be committed:
	modified:   client/src/components/auth/Login.js
	modified:   client/src/components/auth/PasswordReset.js
	modified:   client/src/components/auth/Register.js
	modified:   client/src/components/bcodbs/SearchOptions.js
	modified:   client/src/components/bcodbs/index.js
	modified:   client/src/components/builder/components.js
	modified:   client/src/components/builder/contibutor.js
	modified:   client/src/components/builder/descriptionDomain.js
	modified:   client/src/components/builder/errorDomain.js
	modified:   client/src/components/builder/executionDomain.js
	modified:   client/src/components/builder/extensionDomain.js
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/builder/ioDomain.js
	modified:   client/src/components/builder/parametricDomain.js
	modified:   client/src/components/builder/preview.js
	modified:   client/src/components/builder/provenanceDomain.js
	modified:   client/src/components/builder/rawJson.js
	modified:   client/src/components/builder/reviewer.js
	modified:   client/src/components/builder/specialFeilds.js
	modified:   client/src/components/builder/treeView.js
	modified:   client/src/components/builder/usabilityDomain.js
	modified:   client/src/components/prefix/PrefixSearch.js
	modified:   client/src/components/prefix/index.js
	modified:   client/src/components/viewer/cardViews.js
	modified:   client/src/components/viewer/index.js
	modified:   client/src/layouts/ObjectNavBar.js
	modified:   client/src/layouts/objectSideBar.js
	modified:   client/src/layouts/shared/AppDropDown.js
	modified:   client/src/layouts/shared/DocDropDown.js
	modified:   client/src/layouts/shared/HelpDropDown.js
	modified:   client/src/layouts/shared/ToolsDropDown.js
@HadleyKing
update profile
a5b3616
@HadleyKing
Fix Builder display
ae05fa4 
Changes to be committed:
	modified:   client/src/components/builder/index.js
@HadleyKing
Changes to accomidate BCO Score
54a289c 
Changes to be committed:
	modified:   client/src/components/builder/executionDomain.js
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/viewer/cardViews.js
	modified:   client/src/layouts/shared/ToolsDropDown.js
	modified:   client/src/pages/Bcodbs.js
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Align left for citations
a16fd56 
Changes to be committed:
	modified:   client/src/App.css
@HadleyKing
Fixes for Publishing and validating
ab0f61d 
Changes to be committed:
	modified:   client/src/components/builder/executionDomain.js
	modified:   client/src/layouts/objectSideBar.js
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Add funding sources to about pages
548e9c8 
Changes to be committed:
	modified:   client/src/App.css
	modified:   client/src/pages/About.js
@HadleyKing
Add loading components
6ed76cf 
Changes to be committed:
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/viewer/index.js
	new file:   client/src/images/biocomputing.gif
@HadleyKing
Add loading card for BCOs
2477c7b 
Changes to be committed:
	modified:   client/src/components/builder/components.js
	modified:   client/src/components/builder/errorDomain.js
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/builder/rawJson.js
	modified:   client/src/slices/bcoSlice.js
@HadleyKing
Add loading to bcodb page
4a774ac 
also fixed Execution Domain formatting
Changes to be committed:
	modified:   client/src/components/builder/executionDomain.js
	modified:   client/src/pages/Bcodbs.js
@HadleyKing
Update quickSearch for loading function
00e5eb8 
Changes to be committed:
	modified:   client/src/components/quickSearch.js
@HadleyKing
Login Notice
5982ca9 
Changes to be committed:
	modified:   client/package-lock.json
	modified:   client/package.json
	modified:   client/src/components/account/index.js
	modified:   client/src/components/auth/Login.js
	modified:   client/src/components/auth/PasswordReset.js
	modified:   client/src/components/auth/Register.js
	modified:   client/src/components/builder/index.js
	modified:   client/src/components/prefix/index.js
	modified:   client/src/components/quickSearch.js
	modified:   client/src/components/viewer/index.js
	modified:   client/src/layouts/MainLayout.js
	modified:   client/src/layouts/MainNavBar.js
	modified:   client/src/layouts/ObjectNavBar.js
	modified:   client/src/layouts/ObjectViewLayout.js
	modified:   client/src/pages/Bcodbs.js
	modified:   client/src/routes.js
	modified:   client/src/slices/accountSlice.js
	modified:   client/src/slices/searchSlice.js
@HadleyKing
Expired JWT implemented
c1089bc 
Changes to be committed:
	modified:   client/package-lock.json
	modified:   client/package.json
	modified:   client/src/App.js
	modified:   client/src/components/quickSearch.js
	modified:   client/src/pages/Bcodbs.js
	modified:   client/src/routes.js
	modified:   client/src/slices/accountSlice.js
	modified:   client/src/slices/searchSlice.js
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gitguardian bot commented May 14, 2024 •
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⚠️ GitGuardian has uncovered 7 secrets following the scan of your pull request.

Please consider investigating the findings and remediating the incidents. Failure to do so may lead to compromising the associated services or software components.

🔎 Detected hardcoded secrets in your pull request
GitGuardian id GitGuardian status Secret Commit Filename
4444564 Triggered Generic High Entropy Secret 0fb00a5 client/src/components/bcodbs/SearchOptions.js View secret
4444564 Triggered Generic High Entropy Secret 21a77e5 client/src/components/bcodbs/SearchOptions.js View secret
5477444 Triggered Generic High Entropy Secret 9e5e144 server/config/fixtures/test_portal.json View secret
8266999 Triggered Generic High Entropy Secret 9e5e144 server/config/fixtures/test_portal.json View secret
8267000 Triggered Generic High Entropy Secret 9e5e144 server/config/fixtures/test_portal.json View secret
8267001 Triggered Generic High Entropy Secret 9e5e144 server/config/fixtures/test_portal.json View secret
8474558 Triggered Generic High Entropy Secret 9e5e144 server/config/fixtures/test_portal.json View secret
🛠 Guidelines to remediate hardcoded secrets
  1. Understand the implications of revoking this secret by investigating where it is used in your code.
  2. Replace and store your secrets safely. Learn here the best practices.
  3. Revoke and rotate these secrets.
  4. If possible, rewrite git history. Rewriting git history is not a trivial act. You might completely break other contributing developers' workflow and you risk accidentally deleting legitimate data.

To avoid such incidents in the future consider

🦉 GitGuardian detects secrets in your source code to help developers and security teams secure the modern development process. You are seeing this because you or someone else with access to this repository has authorized GitGuardian to scan your pull request.

@HadleyKing HadleyKing merged commit 641ea89 into 24.04 May 14, 2024
0 of 2 checks passed
@HadleyKing HadleyKing deleted the prod_push branch May 14, 2024 01:30
@HadleyKing HadleyKing restored the prod_push branch May 14, 2024 01:33
@HadleyKing HadleyKing mentioned this pull request May 14, 2024
Merged
@HadleyKing HadleyKing deleted the prod_push branch May 14, 2024 01:48
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@HadleyKing