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chore(iatlas): import iatlas-api from GitLab with `nx import` #2929

Merged

tschaffter merged 1,215 commits into Sage-Bionetworks:main from tschaffter:iatlas/import-api

Nov 27, 2024

Member

tschaffter commented Nov 27, 2024 •

edited by jira bot

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Contributes to ARCH-339

Nx says to not squash merge when merging to main:

 NX   Merging these changes into main

MERGE these changes when merging these changes.
Do NOT squash these commits when merging these changes.
If you rebase, make sure to use "--rebase-merges" to preserve merge commits.
To UNDO these changes, run "git reset HEAD~1 --hard"

However, I'm going to squash merge this PR because that's how we manage our PRs to keep its git history clean. I will then evaluate the impact on accessing the git history of the imported files.

The command used to import the project:

nx import https://gitlab.com/cri-iatlas/iatlas-api.git apps/iatlas/api-gitlab

andrewelamb and others added 30 commits

April 27, 2021 14:46


          removed genesbytag query

5e08d63


          patch/tooling: [#176502085] Removed the aws credentials files and try…

2dc036b

… to update directly with aws ecs update-service.


          Merge branch 'feature/pivotal_176502085' into 'staging'

db91c6a

patch/tooling: [#176502085] Removed the aws credentials files and try to...

See merge request cri-iatlas/iatlas-api!217


          patch/tooling: [#176502085] No need for the aws region in this script.

15654ca


          Merge branch 'feature/pivotal_176502085' into 'staging'

e1b0b6b

patch/tooling: [#176502085] No need for the aws region in this script.

See merge request cri-iatlas/iatlas-api!218


          temp_commit

44045b2


          update nodes to use new paging limits

ed8e793


          Merge branch 'staging' into add_paging_to_genes

00c09eb


          added ability to change genes query limit based on wetaher samples ar…

5d3ac74

…e requested or not


          refactored testing code to include common query builder

821169c


          Merge branch 'add_paging_to_genes' into 'staging'

d135b5e

Add paging to genes

See merge request cri-iatlas/iatlas-api!219


          temp commit not working

43d1c68


          added cohort db models


          temp commit

486a096


          features pagination working

007ad14


          removed uneeded queries

7eaf740


          Merge branch 'add_paging_to_features' into 'staging'

81c8fe1

Add paging to features

See merge request cri-iatlas/iatlas-api!220


          resolve merge conflict

16583d2


          all cohort db tests working

6d37587


          added cohort queries

7b0d92f


          temp commit

ba45b39


          features tests working, a few others failing

394da73


          removed logging

eaec73e


          added feature_values query, fixed teets in other queries

073060b


          all tests passing

b331fcb


          patch/tooling: [#176502085] Added clearer comments. Removed tools tha…

7006cf6

…t are unneeded in the build.


          Merge branch 'feature/pivotal_176502085' into 'staging'

580c1bd

patch/tooling: [#176502085] Added clearer comments. Removed tools that are unneeded in the build.

See merge request cri-iatlas/iatlas-api!221


          added cohorts to genes query, genes tests working, others failing

929f8ac


          Merge branch 'staging' into use_cohorts_in_features

e859712


          Merge branch 'staging' into add_cohort_queries

6c6f494

jonryser and others added 21 commits

May 7, 2024 18:22


          Update .gitlab-ci.yml file (commented out tests!!!!)

0d6d9dc


          Update .gitlab-ci.yml file (Still no tests!!)

dbc1cf9


          Update .gitlab-ci.yml file (Commented out test stages)

e42e7d3


          Merge branch 'no-tests' into 'staging'

f817978

Update .gitlab-ci.yml file (commented out tests!!!!)

See merge request cri-iatlas/iatlas-api!276


          fix tests

6a98e9c


          fix tests

9abaa39


          removed test that was crashing

cf99a0d


          Merge branch 'fix_tests' into 'staging'

9175a59

fix tests

See merge request cri-iatlas/iatlas-api!277


          add features to cells query

ddd53ee


          Merge branch 'add_cells_query' into 'staging'

84b8062

add features to cells query

See merge request cri-iatlas/iatlas-api!278


          fix paging

6f3139b


          Merge branch 'add_cells_query' into 'staging'

4df6cd0

fix paging

See merge request cri-iatlas/iatlas-api!279


          fix features query using cohorts

8a9d024


          fix features query using cohorts

a5e5b6b


          Merge branch 'add_cells_query' into 'staging'

827313f

fix features query using cohorts

See merge request cri-iatlas/iatlas-api!280


          Merge branch 'master' into 'staging'

ed1eae1

Master

See merge request cri-iatlas/iatlas-api!281


          fix sampels test

c0883e7


          Merge branch 'add_cells_query' into 'staging'

8de859e

fix sampels test

See merge request cri-iatlas/iatlas-api!282


          small change to test file to trigger workflow

4761b0f


          Merge branch 'fix_test' into 'staging'

fc74590

small change to test file to trigger workflow

See merge request cri-iatlas/iatlas-api!284


          feat(repo): merge staging from https://gitlab.com/cri-iatlas/iatlas-a…

4f17ff9

…pi.git

tschaffter self-assigned this

tschaffter had a problem deploying to sonar

November 27, 2024 19:36

— with

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tschaffter marked this pull request as ready for review

November 27, 2024 19:41


          move files to apps/iatlas/api and remove selected files

576892d

tschaffter had a problem deploying to sonar

November 27, 2024 21:30

— with

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github-advanced-security bot found potential problems

View reviewed changes

apps/iatlas/api/requirements.txt

@@ @@ -0,0 +1,13 @@ @@
+              ariadne==0.13.0
+              click==7.1.2
+              Flask==1.1.2

Check failure

Code scanning / Trivy

flask: Possible disclosure of permanent session cookie due to missing Vary: Cookie header High

Package: Flask
Installed Version: 1.1.2
Vulnerability CVE-2023-30861
Severity: HIGH
Fixed Version: 2.3.2, 2.2.5
Link: CVE-2023-30861

apps/iatlas/api/requirements.txt

+              MarkupSafe==1.1.1
+              psycopg2-binary==2.8.5
+              SQLAlchemy==1.3.17
+              starlette==0.13.4

Check failure

Code scanning / Trivy

There MultipartParser usage in Encode's Starlette python framework bef ... High

Package: starlette
Installed Version: 0.13.4
Vulnerability CVE-2023-30798
Severity: HIGH
Fixed Version: 0.25.0
Link: CVE-2023-30798

apps/iatlas/api/requirements.txt

+              MarkupSafe==1.1.1
+              psycopg2-binary==2.8.5
+              SQLAlchemy==1.3.17
+              starlette==0.13.4

Check failure

Code scanning / Trivy

starlette: Starlette Denial of service (DoS) via multipart/form-data High

Package: starlette
Installed Version: 0.13.4
Vulnerability CVE-2024-47874
Severity: HIGH
Fixed Version: 0.40.0
Link: CVE-2024-47874

apps/iatlas/api/requirements.txt

+              SQLAlchemy==1.3.17
+              starlette==0.13.4
+              typing-extensions==3.7.4.2
+              Werkzeug==1.0.1

Check failure

Code scanning / Trivy

python-werkzeug: high resource usage when parsing multipart form data with many fields High

Package: Werkzeug
Installed Version: 1.0.1
Vulnerability CVE-2023-25577
Severity: HIGH
Fixed Version: 2.2.3
Link: CVE-2023-25577

apps/iatlas/api/requirements.txt

+              SQLAlchemy==1.3.17
+              starlette==0.13.4
+              typing-extensions==3.7.4.2
+              Werkzeug==1.0.1

Check failure

Code scanning / Trivy

python-werkzeug: user may execute code on a developer's machine High

Package: Werkzeug
Installed Version: 1.0.1
Vulnerability CVE-2024-34069
Severity: HIGH
Fixed Version: 3.0.3
Link: CVE-2024-34069

tschaffter merged commit b873d15 into Sage-Bionetworks:main

12 of 14 checks passed

tschaffter deleted the iatlas/import-api branch

November 27, 2024 21:40

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