Feat: helm for OHDSI webapi service #459

pieterlukasse · 2025-12-04T22:36:55Z

Link to JIRA ticket if there is one: https://ctds-planx.atlassian.net/browse/VPODC-206

New Features

adding helm charts for OHDSI WebAPI (the backend for OHDSI Atlas)

github-actions · 2025-12-04T23:20:20Z

filepath	passed	failed	error	SUBTOTAL
tests/test_oauth2.py	7	8	0	15
tests/test_user_token.py	2	3	0	5
tests/test_study_viewer.py	0	3	1	4
tests/test_discoverypage.py	0	1	1	2
tests/test_workspace.py	0	1	0	1
tests/test_aggregate_mds.py	0	1	0	1
tests/test_presigned_url.py	0	0	7	7
tests/test_drs_endpoint.py	0	0	4	4
TOTAL	9	17	13	39

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-05T21:45:21Z

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_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	4	0	1	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_requestor.py	5	0	0	5
tests/test_study_viewer.py	3	0	0	3
tests/test_user_token.py	5	0	0	5
tests/test_user_data_library.py	2	0	1	3
tests/test_register_user.py	1	1	0	2
tests/test_oidc_client.py	2	0	0	2
tests/test_client_credentials.py	1	0	0	1
tests/test_gen3client.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
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_google_data_access.py	1	0	0	1
tests/test_login_page.py	2	0	0	2
tests/test_homepage.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_etl.py	0	0	1	1
tests/test_gen3ff_landing_page.py	0	0	2	2
TOTAL	122	1	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

helm/ohdsi-webapi/templates/ohdsi-webapi-client-create-job.yaml

...according to cloud-automation version

... as well as auto creation of fence client entry.

github-actions · 2025-12-09T22:45:51Z

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_data_upload.py	8	1	9
tests/test_guppy_service.py	8	0	8
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
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_register_user.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_oidc_client.py	2	0	2
tests/test_discoverypage.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_workspace.py	1	0	1
tests/test_google_data_access.py	1	0	1
tests/test_login_page.py	2	0	2
tests/test_homepage.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_gen3ff_landing_page.py	0	2	2
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-12-10T20:19:46Z

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_user_token.py	5	0	5
tests/test_study_viewer.py	3	0	3
tests/test_user_data_library.py	2	1	3
tests/test_login_page.py	2	0	2
tests/test_google_data_access.py	1	0	1
tests/test_discoverypage.py	1	0	1
tests/test_register_user.py	2	0	2
tests/test_homepage.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_manifest_service.py	1	0	1
tests/test_workspace.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_aggregate_mds.py	1	0	1
tests/test_gen3client.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_gen3ff_landing_page.py	0	2	2
tests/test_etl.py	0	1	1
tests/test_env_sanity.py	0	1	1
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

…g it ...and also ensure the secret exists before patching it

github-actions · 2025-12-11T22:58:21Z

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_user_token.py	5	0	5
tests/test_study_viewer.py	3	0	3
tests/test_user_data_library.py	2	1	3
tests/test_login_page.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_register_user.py	2	0	2
tests/test_discoverypage.py	1	0	1
tests/test_workspace.py	1	0	1
tests/test_oidc_client.py	2	0	2
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_gen3ff_landing_page.py	0	2	2
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

helm/ohdsi-webapi/templates/ohdsi-webapi-client-create-job.yaml

github-actions · 2025-12-17T21:54:10Z

filepath	passed	failed	error	skipped	SUBTOTAL
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_gen3_workflow.py	10	1	0	0	11
tests/test_guppy_service.py	8	0	0	0	8
tests/test_audit_service.py	3	0	0	3	6
tests/test_presigned_url.py	7	0	0	0	7
tests/test_data_upload.py	8	0	2	1	11
tests/test_requestor.py	5	0	0	0	5
tests/test_drs_endpoint.py	4	0	0	0	4
tests/test_dbgap.py	4	0	0	1	5
tests/test_study_viewer.py	3	0	0	0	3
tests/test_user_token.py	5	0	0	0	5
tests/test_user_data_library.py	2	0	0	1	3
tests/test_register_user.py	1	1	0	0	2
tests/test_oidc_client.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	1	1	0	0	2
tests/test_aggregate_mds.py	1	0	0	0	1
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_env_sanity.py	0	0	0	1	1
tests/test_etl.py	0	0	0	1	1
tests/test_gen3ff_landing_page.py	0	0	0	2	2
tests/test_pfb_export.py	0	1	0	0	1
tests/test_discoverypage.py	0	1	0	0	1
tests/test_workspace.py	0	1	0	0	1
TOTAL	117	6	2	14	139

Please find the detailed integration test report here

Please find the Github Action logs here

…ce client

github-actions · 2025-12-19T21:07:15Z

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_guppy_service.py	8	0	8
tests/test_presigned_url.py	7	0	7
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_dbgap.py	4	1	5
tests/test_requestor.py	5	0	5
tests/test_user_token.py	5	0	5
tests/test_drs_endpoint.py	4	0	4
tests/test_user_data_library.py	2	1	3
tests/test_study_viewer.py	3	0	3
tests/test_login_page.py	2	0	2
tests/test_discoverypage.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_workspace.py	1	0	1
tests/test_gen3client.py	1	0	1
tests/test_register_user.py	2	0	2
tests/test_manifest_service.py	1	0	1
tests/test_google_data_access.py	1	0	1
tests/test_aggregate_mds.py	1	0	1
tests/test_homepage.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_gen3ff_landing_page.py	0	2	2
tests/test_env_sanity.py	0	1	1
tests/test_etl.py	0	1	1
TOTAL	123	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

…ientId and secret into webapi config

pieterlukasse · 2025-12-19T21:13:18Z

helm/ohdsi-webapi/templates/ohdsi-webapi-reverse-proxy-config.yaml

+    }
+    http {
+      server {
+          listen       80;


github-actions · 2025-12-19T22:20:42Z

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_guppy_service.py	8	0	0	8
tests/test_audit_service.py	3	0	3	6
tests/test_data_upload.py	8	0	1	9
tests/test_presigned_url.py	7	0	0	7
tests/test_requestor.py	5	0	0	5
tests/test_dbgap.py	4	0	1	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_user_token.py	4	1	0	5
tests/test_user_data_library.py	2	0	1	3
tests/test_study_viewer.py	3	0	0	3
tests/test_oidc_client.py	2	0	0	2
tests/test_discoverypage.py	1	0	0	1
tests/test_register_user.py	2	0	0	2
tests/test_login_page.py	2	0	0	2
tests/test_workspace.py	1	0	0	1
tests/test_manifest_service.py	1	0	0	1
tests/test_client_credentials.py	1	0	0	1
tests/test_gen3client.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	122	1	14	137

Please find the detailed integration test report here

Please find the Github Action logs here

...and fix the $hostname issue in webapi config

pieterlukasse · 2025-12-19T22:44:17Z

helm/ohdsi-webapi/templates/ohdsi-webapi-client-create-job.yaml

+      volumes:
+        - name: config-volume
+          secret:
+            secretName: "fence-config" # TODO does not seem to be used anywhere....instead "fence-dbcreds" is used...


pieterlukasse · 2025-12-19T22:45:31Z

helm/ohdsi-webapi/templates/ohdsi-webapi-config.yaml

+metadata:
+  name: ohdsi-webapi-config
+type: Opaque
+stringData: # TODO - should this be data (base64)??


@AidanHilt please advise

pieterlukasse · 2025-12-19T22:47:13Z

helm/ohdsi-webapi/values.yaml

+    # -- (bool) Will use ExternalSecret resources to pull secrets from Secrets Manager instead of creating them locally. Be cautious as this will override any fence secrets you have deployed.
+    deploy: false
+  # -- (string) Hostname for the deployment.
+  hostname: localhost


maybe not a good default...?

pieterlukasse · 2025-12-19T22:48:40Z

helm/ohdsi-webapi/values.yaml

+# -- (bool) Whether to automatically create a OIDC a client in Fence.
+createFenceClientJobEnabled: true
+# Service account for accessing webapi secrets and updating with OIDC client ID created in Fence (set to "default" if testing locally):
+webapiSecretsServiceAccountName: "webapi-secrets"


@AidanHilt where is the step that creates a service account with this "webapi-secrets" name? I think this is inherited from the previous kubernetes config, but not sure if these same service accounts are still present or if there should be a template adding the service account?

github-actions · 2025-12-19T23:01:15Z

filepath	SUBTOTAL
TOTAL	0

Please find the detailed integration test report here

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github-actions · 2026-01-03T03:06:02Z

Failed to Prepare CI environment

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pieterlukasse changed the title ~~Feat/healm for ohdsi services~~ Feat: helm for OHDSI services Dec 4, 2025

pieterlukasse requested a review from AidanHilt December 9, 2025 21:26

pieterlukasse commented Dec 9, 2025

View reviewed changes

helm/ohdsi-webapi/templates/ohdsi-webapi-client-create-job.yaml Outdated Show resolved Hide resolved

pieterlukasse marked this pull request as ready for review December 9, 2025 21:35

pieterlukasse added 6 commits December 9, 2025 16:36

feat: initial commit ohdsi-webapi helm chart

789032e

feat: adjusted ohdsi-webapi helm chart

e591678

...according to cloud-automation version

feat: add "create fence client" step for ohdsi-webapi

9674d1d

feat: improvements to default repo and naming

8a9d4a8

feat: add config options for DB connection and arborist

a089fca

... as well as auto creation of fence client entry.

feat: improve comments in values.yaml

eb4aeaa

pieterlukasse force-pushed the feat/healm_for_ohdsi_services branch from 7967a64 to eb4aeaa Compare December 9, 2025 21:36

pieterlukasse changed the title ~~Feat: helm for OHDSI services~~ Feat: helm for OHDSI webapi service Dec 9, 2025

feat: added config for allowing an external secret

bf28306

feat: ensure existing atlas client (if any) is removed before creatin…

61d4b66

…g it ...and also ensure the secret exists before patching it

fix: add nginx config and DB port config

7cd3c89

AidanHilt approved these changes Dec 17, 2025

View reviewed changes

helm/ohdsi-webapi/templates/ohdsi-webapi-client-create-job.yaml Outdated Show resolved Hide resolved

feat: workfing version of add-fence-client which adds WebAPI as a Fen…

7435ed8

…ce client

feat: working version of update-webapi-config step that adds Fence cl…

a3c7ec2

…ientId and secret into webapi config

pieterlukasse commented Dec 19, 2025

View reviewed changes

helm/ohdsi-webapi/templates/ohdsi-webapi-reverse-proxy-config.yaml

}

http {

server {

listen 80;

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pieterlukasse Dec 19, 2025

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review?

fix: fix linter issue in webapiSecretsServiceAccountName

40dc222

feat: add instructions to get the secret patching step working locally

2343fbb

...and fix the $hostname issue in webapi config

pieterlukasse commented Dec 19, 2025

View reviewed changes

pieterlukasse added 2 commits January 2, 2026 17:01

feat: add a values_local.yaml for local testing of the chart

9660c9c

fix: use Values.fenceUrl

094b8af

Feat: helm for OHDSI webapi service #459

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pieterlukasse commented Dec 4, 2025 •

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