Add integration tests for multi-user support and other funnel regression bugs by nss10 · Pull Request #489 · uc-cdis/gen3-code-vigil

nss10 · 2026-03-04T01:01:38Z

Link to JIRA ticket if there is one: MIDRC-1166

New Features

Breaking Changes

Bug Fixes

Improvements

Dependency updates

Deployment changes

github-actions · 2026-03-04T01:35:21Z

Failed to Prepare CI environment

Please find the Github Action logs here

github-actions · 2026-03-04T02:09:09Z

Failed to Prepare CI environment

Please find the Github Action logs here

github-actions · 2026-03-04T03:57:41Z

Test summary after running integration tests

filepath	passed	failed	error	skipped	SUBTOTAL
tests/test_gen3_workflow.py	0	0	16	0	16
tests/test_oauth2.py	15	0	0	0	15
tests/test_dicom_viewer.py	4	0	0	0	4
tests/test_centralized_auth.py	16	0	0	0	16
tests/test_graph_submit_and_query.py	13	0	0	1	14
tests/test_audit_service.py	3	0	0	3	6
tests/test_pfb_export.py	1	0	0	0	1
tests/test_guppy_service.py	8	0	0	0	8
tests/test_presigned_url.py	7	0	0	0	7
tests/test_data_upload.py	8	0	0	1	9
tests/test_dbgap.py	4	0	0	1	5
tests/test_requestor.py	5	0	0	0	5
tests/test_drs_endpoint.py	4	0	0	0	4
tests/test_user_token.py	5	0	0	0	5
tests/test_user_data_library.py	2	0	0	1	3
tests/test_study_viewer.py	3	0	0	0	3
tests/test_register_user.py	2	0	0	0	2
tests/test_client_credentials.py	1	0	0	0	1
tests/test_gen3client.py	1	0	0	0	1
tests/test_manifest_service.py	1	0	0	0	1
tests/test_login_page.py	2	0	0	0	2
tests/test_oidc_client.py	2	0	0	0	2
tests/test_google_data_access.py	1	0	0	0	1
tests/test_homepage.py	1	0	0	0	1
tests/test_ras_authn.py	0	0	0	3	3
tests/test_gen3ff_landing_page.py	0	0	0	2	2
tests/test_env_sanity.py	0	0	0	1	1
tests/test_etl.py	0	0	0	1	1
tests/test_discoverypage.py	0	1	0	0	1
tests/test_workspace.py	0	1	0	0	1
tests/test_aggregate_mds.py	0	1	0	0	1
TOTAL	109	3	16	14	142

Test summary after rerunning failed integration tests

filepath	passed	failed	SUBTOTAL
tests/test_gen3_workflow.py	10	6	16
tests/test_discoverypage.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_workspace.py	0	1	1
TOTAL	12	7	19

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here

github-actions · 2026-03-04T05:35:37Z

Failed to Prepare CI environment

Please find the Github Action logs here

github-actions · 2026-03-04T15:38:23Z

Failed to Prepare CI environment

Please find the Github Action logs here

github-actions · 2026-03-04T17:14:43Z

Test summary after running integration tests

filepath	passed	failed	SUBTOTAL
tests/test_gen3_workflow.py	14	2	16
TOTAL	14	2	16

Test summary after rerunning failed integration tests

filepath	failed	SUBTOTAL
tests/test_gen3_workflow.py	2	2
TOTAL	2	2

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here

…ses in TODO

github-actions · 2026-03-04T18:22:24Z

Test summary after running integration tests

filepath	passed	failed	SUBTOTAL
tests/test_gen3_workflow.py	15	1	16
TOTAL	15	1	16

Test summary after rerunning failed integration tests

filepath	failed	SUBTOTAL
tests/test_gen3_workflow.py	1	1
TOTAL	1	1

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here

nss10 · 2026-03-04T19:43:55Z

+            },
+        ]
+
+        for test_case in test_cases:


Can speed this up by creating all tasks in parallel, and polling them simultaneously. We can use* this design to combine more regression test cases and test them in parallel.

can we not use pytest parametrize mark? - https://docs.pytest.org/en/stable/how-to/parametrize.html

github-actions · 2026-03-04T19:57:57Z

Test summary after running integration tests

filepath	passed	failed	SUBTOTAL
tests/test_gen3_workflow.py	15	1	16
TOTAL	15	1	16

Test summary after rerunning failed integration tests

filepath	passed	SUBTOTAL
tests/test_gen3_workflow.py	1	1
TOTAL	1	1

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here

paulineribeyre · 2026-03-04T22:53:38Z

+                "command": ["echo 'This will fail' && exit 1"],
+                "expected_exit_code": 1,
+                "expected_state": "EXECUTOR_ERROR",
+            },
+            {
+                "command": ["False"],


Could you clarify in comments or the docstring the difference between the 2 cases, why does the TES server behave differently

In case of a command like False, we get a K8s error --

This is the cause of the System Error

paulineribeyre · 2026-03-05T19:40:32Z

+    # TODO:
+    # * Test the POST /ga4gh/tes/v1/tasks:cancel with a task id that is not present in the system, and expect a 404 from gen3-workflow


Nice! there's a ticket for the next tests https://ctds-planx.atlassian.net/browse/MIDRC-1230

Are these just the ones you could think of off the top of your head, or did you go through the list on the OHSU slack board?

Are these just the ones you could think of off the top of your head.

Yeah, these were the "might as well"s!! !

github-actions · 2026-03-13T17:23:24Z

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

github-actions · 2026-03-13T18:02:36Z

Test summary after running integration tests

filepath	passed	failed	SUBTOTAL
tests/test_gen3_workflow.py	13	3	16
TOTAL	13	3	16

Test summary after rerunning failed integration tests

filepath	failed	SUBTOTAL
tests/test_gen3_workflow.py	3	3
TOTAL	3	3

Please find the detailed integration test report here

Please find the detailed integration test report after rerunning failed tests here

Please find the Github Action logs here

…/gen3-code-vigil into chore/add_new_g3wf_tests

github-actions · 2026-03-13T21:38:32Z

filepath	passed	SUBTOTAL
tests/test_gen3_workflow.py	16	16
TOTAL	16	16

Please find the detailed integration test report here

Please find the Github Action logs here

haraprasadj · 2026-03-17T14:48:37Z

+            },
+        ]
+
+        for test_case in test_cases:


can we not use pytest parametrize mark? - https://docs.pytest.org/en/stable/how-to/parametrize.html

github-actions · 2026-03-17T16:05:27Z

filepath	error	SUBTOTAL
tests/test_gen3_workflow.py	5	5
TOTAL	5	5

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2026-03-17T16:38:07Z

filepath	passed	SUBTOTAL
tests/test_gen3_workflow.py	17	17
TOTAL	17	17

Please find the detailed integration test report here

Please find the Github Action logs here

haraprasadj

+1

Add integration tests for multi-user support

7f6453d

Add more test cases

bcc544c

nss10 changed the title ~~Add integration tests for multi-user support~~ Add integration tests for multi-user support and other funnel regression bugs Mar 4, 2026

nss10 added the TestGen3Workflow label Mar 4, 2026

Merge branch 'master' into chore/add_new_g3wf_tests

9095d52

Fix exit code; update username for other_valid_user; add more test ca…

c4ccd41

…ses in TODO

nss10 added 3 commits March 4, 2026 13:03

Update TES task States to include SYSTEM_ERROR

6455598

Add more tests in the TODO comments

d948d4c

Comments cleanup

a357d25

nss10 requested a review from paulineribeyre March 4, 2026 19:41

nss10 commented Mar 4, 2026

View reviewed changes

paulineribeyre reviewed Mar 5, 2026

View reviewed changes

Responding to PR comments

c28df6d

paulineribeyre reviewed Mar 13, 2026

View reviewed changes

Comment thread gen3-integration-tests/tests/test_gen3_workflow.py Outdated

paulineribeyre reviewed Mar 13, 2026

View reviewed changes

Comment thread gen3-integration-tests/tests/test_gen3_workflow.py Outdated

paulineribeyre reviewed Mar 13, 2026

View reviewed changes

Comment thread gen3-integration-tests/tests/test_gen3_workflow.py Outdated

Fix docstring and TODO comments

096204c

nss10 requested a review from paulineribeyre March 13, 2026 21:05

nss10 added 2 commits March 13, 2026 16:06

Merge branch 'master' into chore/add_new_g3wf_tests

ef7e428

fix import error

58f19e3

Merge branch 'chore/add_new_g3wf_tests' of https://github.com/uc-cdis…

5d52f34

…/gen3-code-vigil into chore/add_new_g3wf_tests

paulineribeyre previously approved these changes Mar 13, 2026

View reviewed changes

haraprasadj previously approved these changes Mar 17, 2026

View reviewed changes

parametrize tests

57e7cdd

nss10 dismissed stale reviews from haraprasadj and paulineribeyre via 57e7cdd March 17, 2026 15:35

Merge branch 'master' into chore/add_new_g3wf_tests

ac93980

nss10 requested review from haraprasadj and paulineribeyre March 17, 2026 15:38

fix: incorrect decorator

0194862

haraprasadj approved these changes Mar 17, 2026

View reviewed changes

nss10 merged commit fcae56d into master Mar 17, 2026
5 checks passed

nss10 deleted the chore/add_new_g3wf_tests branch March 17, 2026 16:48

		# TODO:
		# * Test the POST /ga4gh/tes/v1/tasks:cancel with a task id that is not present in the system, and expect a 404 from gen3-workflow

Conversation

nss10 commented Mar 4, 2026 • edited by atlassian bot Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

New Features

Breaking Changes

Bug Fixes

Improvements

Dependency updates

Deployment changes

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

nss10 Mar 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

haraprasadj Mar 17, 2026

Choose a reason for hiding this comment

Uh oh!

github-actions bot commented Mar 4, 2026

Uh oh!

paulineribeyre Mar 4, 2026

Choose a reason for hiding this comment

Uh oh!

nss10 Mar 12, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

paulineribeyre Mar 5, 2026

Choose a reason for hiding this comment

Uh oh!

nss10 Mar 12, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

github-actions bot commented Mar 13, 2026

Uh oh!

github-actions bot commented Mar 13, 2026

Uh oh!

Uh oh!

Uh oh!

Uh oh!

github-actions bot commented Mar 13, 2026

Uh oh!

haraprasadj Mar 17, 2026

Choose a reason for hiding this comment

Uh oh!

github-actions bot commented Mar 17, 2026

Uh oh!

github-actions bot commented Mar 17, 2026

Uh oh!

haraprasadj left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

nss10 commented Mar 4, 2026 •

edited by atlassian bot

Loading

nss10 Mar 4, 2026 •

edited

Loading