Update fence helm chart to work with root and non-root users. #470

nss10 · 2025-12-12T21:22:44Z

Link to JIRA ticket if there is one: PD-77

New Features

Breaking Changes

Bug Fixes

Improvements

Update fence deployments and usersync cron jobs to work when run either root and non-root users.
Remove unused volume mounts for usersync cron job

Dependency updates

Deployment changes

github-actions · 2025-12-12T22:46:30Z

Failed to Prepare CI environment

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… not allowed. Change temp mount path to /tmp

github-actions · 2025-12-13T00:00:19Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_dicom_viewer.py	4	0	4
tests/test_centralized_auth.py	16	0	16
tests/test_graph_submit_and_query.py	13	1	14
tests/test_gen3_workflow.py	11	0	11
tests/test_pfb_export.py	1	0	1
tests/test_audit_service.py	3	3	6
tests/test_guppy_service.py	8	0	8
tests/test_data_upload.py	8	1	9
tests/test_dbgap.py	4	1	5
tests/test_presigned_url.py	7	0	7
tests/test_drs_endpoint.py	4	0	4
tests/test_requestor.py	5	0	5
tests/test_study_viewer.py	3	0	3
tests/test_user_token.py	5	0	5
tests/test_user_data_library.py	2	1	3
tests/test_login_page.py	2	0	2
tests/test_oidc_client.py	2	0	2
tests/test_client_credentials.py	1	0	1
tests/test_gen3client.py	1	0	1
tests/test_manifest_service.py	1	0	1
tests/test_discoverypage.py	1	0	1
tests/test_register_user.py	2	0	2
tests/test_workspace.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_google_data_access.py	1	0	1
tests/test_homepage.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
tests/test_gen3ff_landing_page.py	0	2	2
TOTAL	123	14	137

Please find the detailed integration test report here

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github-actions · 2025-12-13T01:57:51Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_dicom_viewer.py	4	0	0	4
tests/test_centralized_auth.py	16	0	0	16
tests/test_graph_submit_and_query.py	13	0	1	14
tests/test_gen3_workflow.py	11	0	0	11
tests/test_pfb_export.py	1	0	0	1
tests/test_audit_service.py	3	0	3	6
tests/test_data_upload.py	7	1	1	9
tests/test_guppy_service.py	8	0	0	8
tests/test_dbgap.py	4	0	1	5
tests/test_presigned_url.py	7	0	0	7
tests/test_user_token.py	3	2	0	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_user_data_library.py	2	0	1	3
tests/test_study_viewer.py	3	0	0	3
tests/test_requestor.py	5	0	0	5
tests/test_oidc_client.py	2	0	0	2
tests/test_login_page.py	2	0	0	2
tests/test_register_user.py	2	0	0	2
tests/test_google_data_access.py	1	0	0	1
tests/test_workspace.py	1	0	0	1
tests/test_gen3client.py	1	0	0	1
tests/test_homepage.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
tests/test_aggregate_mds.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
tests/test_env_sanity.py	0	0	1	1
tests/test_gen3ff_landing_page.py	0	0	2	2
tests/test_etl.py	0	0	1	1
tests/test_discoverypage.py	0	1	0	1
TOTAL	119	4	14	137

Please find the detailed integration test report here

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github-actions · 2025-12-15T16:04:19Z

Failed to Prepare CI environment

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…ectories not allowed. Change temp mount path to /tmp" This reverts commit 67c6e78.

github-actions · 2025-12-15T17:29:56Z

Failed to Prepare CI environment

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github-actions · 2025-12-15T23:01:36Z

filepath	SUBTOTAL
TOTAL	0

Please find the detailed integration test report here

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… files as non-root

github-actions · 2025-12-16T01:42:59Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_dicom_viewer.py	4	0	0	4
tests/test_centralized_auth.py	16	0	0	16
tests/test_graph_submit_and_query.py	13	0	1	14
tests/test_gen3_workflow.py	11	0	0	11
tests/test_audit_service.py	3	0	3	6
tests/test_pfb_export.py	1	0	0	1
tests/test_data_upload.py	8	0	1	9
tests/test_guppy_service.py	8	0	0	8
tests/test_presigned_url.py	7	0	0	7
tests/test_dbgap.py	2	2	1	5
tests/test_requestor.py	5	0	0	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_user_token.py	5	0	0	5
tests/test_study_viewer.py	3	0	0	3
tests/test_user_data_library.py	2	0	1	3
tests/test_login_page.py	1	1	0	2
tests/test_google_data_access.py	1	0	0	1
tests/test_discoverypage.py	1	0	0	1
tests/test_homepage.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_register_user.py	2	0	0	2
tests/test_gen3client.py	1	0	0	1
tests/test_workspace.py	1	0	0	1
tests/test_oidc_client.py	2	0	0	2
tests/test_manifest_service.py	1	0	0	1
tests/test_aggregate_mds.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
tests/test_gen3ff_landing_page.py	0	0	2	2
tests/test_env_sanity.py	0	0	1	1
tests/test_etl.py	0	0	1	1
TOTAL	120	3	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-16T04:07:38Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_dicom_viewer.py	4	0	0	4
tests/test_centralized_auth.py	16	0	0	16
tests/test_graph_submit_and_query.py	13	0	1	14
tests/test_gen3_workflow.py	11	0	0	11
tests/test_audit_service.py	3	0	3	6
tests/test_pfb_export.py	1	0	0	1
tests/test_guppy_service.py	8	0	0	8
tests/test_data_upload.py	8	0	1	9
tests/test_presigned_url.py	7	0	0	7
tests/test_dbgap.py	2	2	1	5
tests/test_requestor.py	5	0	0	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_user_token.py	5	0	0	5
tests/test_study_viewer.py	3	0	0	3
tests/test_user_data_library.py	2	0	1	3
tests/test_login_page.py	2	0	0	2
tests/test_oidc_client.py	2	0	0	2
tests/test_gen3client.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
tests/test_register_user.py	2	0	0	2
tests/test_discoverypage.py	1	0	0	1
tests/test_workspace.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_aggregate_mds.py	1	0	0	1
tests/test_google_data_access.py	1	0	0	1
tests/test_homepage.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
tests/test_gen3ff_landing_page.py	0	0	2	2
tests/test_env_sanity.py	0	0	1	1
tests/test_etl.py	0	0	1	1
TOTAL	121	2	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-16T05:45:10Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_dicom_viewer.py	4	0	4
tests/test_centralized_auth.py	16	0	16
tests/test_graph_submit_and_query.py	13	1	14
tests/test_gen3_workflow.py	11	0	11
tests/test_audit_service.py	3	3	6
tests/test_pfb_export.py	1	0	1
tests/test_guppy_service.py	8	0	8
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_requestor.py	5	0	5
tests/test_drs_endpoint.py	4	0	4
tests/test_study_viewer.py	3	0	3
tests/test_user_token.py	5	0	5
tests/test_user_data_library.py	2	1	3
tests/test_register_user.py	2	0	2
tests/test_discoverypage.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_login_page.py	2	0	2
tests/test_gen3client.py	1	0	1
tests/test_manifest_service.py	1	0	1
tests/test_workspace.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_google_data_access.py	1	0	1
tests/test_homepage.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
tests/test_gen3ff_landing_page.py	0	2	2
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-16T16:39:56Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_dicom_viewer.py	4	0	4
tests/test_centralized_auth.py	16	0	16
tests/test_graph_submit_and_query.py	13	1	14
tests/test_gen3_workflow.py	11	0	11
tests/test_audit_service.py	3	3	6
tests/test_pfb_export.py	1	0	1
tests/test_guppy_service.py	8	0	8
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_requestor.py	5	0	5
tests/test_drs_endpoint.py	4	0	4
tests/test_study_viewer.py	3	0	3
tests/test_user_token.py	5	0	5
tests/test_user_data_library.py	2	1	3
tests/test_register_user.py	2	0	2
tests/test_discoverypage.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_gen3client.py	1	0	1
tests/test_manifest_service.py	1	0	1
tests/test_login_page.py	2	0	2
tests/test_workspace.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_google_data_access.py	1	0	1
tests/test_homepage.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
tests/test_gen3ff_landing_page.py	0	2	2
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-17T15:07:40Z

Failed to Prepare CI environment

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github-actions · 2025-12-17T17:43:35Z

filepath	SUBTOTAL
TOTAL	0

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-17T18:58:17Z

Failed to Prepare CI environment

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github-actions · 2025-12-17T19:57:25Z

Failed to Prepare CI environment

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github-actions · 2025-12-17T21:13:16Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_dicom_viewer.py	4	0	0	4
tests/test_centralized_auth.py	16	0	0	16
tests/test_graph_submit_and_query.py	13	0	1	14
tests/test_gen3_workflow.py	11	0	0	11
tests/test_pfb_export.py	1	0	0	1
tests/test_data_upload.py	8	0	1	9
tests/test_audit_service.py	3	0	3	6
tests/test_guppy_service.py	8	0	0	8
tests/test_dbgap.py	4	0	1	5
tests/test_presigned_url.py	7	0	0	7
tests/test_drs_endpoint.py	4	0	0	4
tests/test_requestor.py	5	0	0	5
tests/test_user_token.py	5	0	0	5
tests/test_study_viewer.py	3	0	0	3
tests/test_register_user.py	2	0	0	2
tests/test_user_data_library.py	2	0	1	3
tests/test_gen3client.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
tests/test_oidc_client.py	2	0	0	2
tests/test_discoverypage.py	1	0	0	1
tests/test_aggregate_mds.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_google_data_access.py	1	0	0	1
tests/test_homepage.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
tests/test_gen3ff_landing_page.py	0	0	2	2
tests/test_env_sanity.py	0	0	1	1
tests/test_etl.py	0	0	1	1
tests/test_login_page.py	0	2	0	2
tests/test_workspace.py	0	1	0	1
TOTAL	120	3	14	137

Please find the detailed integration test report here

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github-actions · 2025-12-17T21:42:21Z

filepath	passed	skipped	SUBTOTAL
tests/test_dbgap.py	4	1	5
TOTAL	4	1	5

Please find the detailed integration test report here

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github-actions · 2025-12-18T00:37:02Z

filepath	passed	skipped	SUBTOTAL
tests/test_dbgap.py	4	1	5
TOTAL	4	1	5

Please find the detailed integration test report here

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…ore/fence_non_root_pem

github-actions · 2025-12-18T14:26:14Z

Failed to Prepare CI environment

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github-actions · 2025-12-18T21:55:26Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_dicom_viewer.py	4	0	0	4
tests/test_centralized_auth.py	16	0	0	16
tests/test_graph_submit_and_query.py	13	0	1	14
tests/test_gen3_workflow.py	10	1	0	11
tests/test_pfb_export.py	1	0	0	1
tests/test_data_upload.py	8	0	1	9
tests/test_audit_service.py	3	0	3	6
tests/test_guppy_service.py	8	0	0	8
tests/test_dbgap.py	4	0	1	5
tests/test_presigned_url.py	7	0	0	7
tests/test_drs_endpoint.py	4	0	0	4
tests/test_requestor.py	5	0	0	5
tests/test_user_token.py	5	0	0	5
tests/test_study_viewer.py	3	0	0	3
tests/test_user_data_library.py	2	0	1	3
tests/test_oidc_client.py	2	0	0	2
tests/test_login_page.py	1	1	0	2
tests/test_gen3client.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
tests/test_register_user.py	2	0	0	2
tests/test_discoverypage.py	1	0	0	1
tests/test_aggregate_mds.py	1	0	0	1
tests/test_workspace.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_google_data_access.py	1	0	0	1
tests/test_homepage.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
tests/test_gen3ff_landing_page.py	0	0	2	2
tests/test_env_sanity.py	0	0	1	1
tests/test_etl.py	0	0	1	1
TOTAL	121	2	14	137

Please find the detailed integration test report here

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github-actions · 2025-12-18T22:27:10Z

filepath	passed	SUBTOTAL
tests/test_login_page.py	2	2
TOTAL	2	2

Please find the detailed integration test report here

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Update fence helm chart to work with readonly private key

2e7c472

Change symlink to simple cp since symlink on root owned directories…

67c6e78

… not allowed. Change temp mount path to /tmp

Eliminate unused volume mount

5b9a0eb

revert readonly changes to test with securityContext

9e01ce7

Revert "Change symlink to simple cp since symlink on root owned dir…

466474d

…ectories not allowed. Change temp mount path to /tmp" This reverts commit 67c6e78.

Remove dockerrun.sh

8d092f2

nss10 added 2 commits December 15, 2025 17:57

Update paramiko path in usersync job and look into running other /etc…

b02bbab

… files as non-root

Update dnsPolicy in usersync-cron

2e07a09

Run usersync as root

50e8551

nss10 added 3 commits December 15, 2025 22:29

fetch location of pkey.py in image dynamically

965408c

Remove extra line

4ea4010

Get PKEY path dynamically using python

3f0a7b4

nss10 added 2 commits December 16, 2025 09:41

Merge branch 'master' into chore/fence_non_root_pem

57a2cf3

Bump gen3 chart for lint check

7e92468

nss10 marked this pull request as ready for review December 16, 2025 16:22

Remove extra commands

4bb7362

nss10 requested review from EliseCastle23 and jawadqur and removed request for EliseCastle23 December 16, 2025 16:48

nss10 added 3 commits December 17, 2025 07:26

Change usersync to run with non-root user

7d01bba

Update SecurityContext and change file mount locations for non-gen3 user

ad3645b

Merge branch 'master' into chore/fence_non_root_pem

28e95af

BAckwards compatible way to mount fence-ssh-keys

3901862

nss10 added 2 commits December 17, 2025 14:08

Update volume mounts in Container

ba644d8

remove runAsUser for usersync

d570066

nss10 added the TestDbgap label Dec 17, 2025

Ensure ssh dir exists before moving ssh keys

b89f918

Remove unused volumeMounts in initContainers

6b49276

nss10 changed the title ~~Update fence helm chart to work with readonly private key~~ Update fence helm chart to work with root and non-root users. Dec 18, 2025

nss10 added 3 commits December 18, 2025 07:56

Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into ch…

2788aac

…ore/fence_non_root_pem

Update common chart version fence

3aa3631

Gen3 chart version bump

edf46cd

nss10 added 2 commits December 18, 2025 14:57

Merge branch 'master' into chore/fence_non_root_pem

406ebcf

Update gen3 chart version -- Lint check

71c341e

nss10 removed the TestDbgap label Dec 18, 2025

PlanXCyborg added the TestLoginPage label Dec 18, 2025

jawadqur approved these changes Dec 18, 2025

View reviewed changes

nss10 merged commit adfdd99 into master Dec 19, 2025
3 of 4 checks passed

nss10 deleted the chore/fence_non_root_pem branch December 19, 2025 02:25

Update fence helm chart to work with root and non-root users. #470

Update fence helm chart to work with root and non-root users. #470

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nss10 commented Dec 12, 2025 •

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