From 9dfbf6f44e8d2dece1784a731c9737011e1f8120 Mon Sep 17 00:00:00 2001 From: Atharva Rane Date: Fri, 29 Sep 2023 16:04:08 -0400 Subject: [PATCH 1/4] Deploying GWAS to jenkins-new --- .secrets.baseline | 8 +++--- jenkins-new.planx-pla.net/manifest.json | 4 ++- .../manifests/argo/argo.json | 11 ++++++++ jenkins-new.planx-pla.net/portal/gitops.json | 26 ++++++++++++++++++- 4 files changed, 43 insertions(+), 6 deletions(-) create mode 100644 jenkins-new.planx-pla.net/manifests/argo/argo.json diff --git a/.secrets.baseline b/.secrets.baseline index 9e56bf50b..7265d561a 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -325,21 +325,21 @@ "filename": "jenkins-new.planx-pla.net/manifest.json", "hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865", "is_verified": false, - "line_number": 83 + "line_number": 85 }, { "type": "Secret Keyword", "filename": "jenkins-new.planx-pla.net/manifest.json", "hashed_secret": "0447a636536df0264b2000403fbefd69f603ceb1", "is_verified": false, - "line_number": 251 + "line_number": 253 }, { "type": "Secret Keyword", "filename": "jenkins-new.planx-pla.net/manifest.json", "hashed_secret": "ca253d1c9dece2da0d6fb24ded7bdb849a475966", "is_verified": false, - "line_number": 257 + "line_number": 259 } ], "jenkins-niaid.planx-pla.net/manifest.json": [ @@ -7620,5 +7620,5 @@ } ] }, - "generated_at": "2023-09-25T17:46:20Z" + "generated_at": "2023-09-29T20:03:58Z" } diff --git a/jenkins-new.planx-pla.net/manifest.json b/jenkins-new.planx-pla.net/manifest.json index f8a1f407e..2d62a3182 100644 --- a/jenkins-new.planx-pla.net/manifest.json +++ b/jenkins-new.planx-pla.net/manifest.json @@ -32,7 +32,9 @@ "dashboard": "quay.io/cdis/gen3-statics:master", "requestor": "quay.io/cdis/requestor:master", "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master", - "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master" + "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master", + "argo-wrapper": "quay.io/cdis/argo-wrapper:master", + "cohort-middleware": "quay.io/cdis/cohort-middleware:master" }, "arborist": { "deployment_version": "2" diff --git a/jenkins-new.planx-pla.net/manifests/argo/argo.json b/jenkins-new.planx-pla.net/manifests/argo/argo.json new file mode 100644 index 000000000..8e34dc71c --- /dev/null +++ b/jenkins-new.planx-pla.net/manifests/argo/argo.json @@ -0,0 +1,11 @@ +{ + "scaling_groups": { + "default": "{{workflow.name}}", + "custom": { + } + }, + "bucket": "second-argo-bucket", + "internal-s3-bucket": "gen3-argo-707767160287-devplanetv1", + "indexd_admin_user": "fence", + "environment": "jenkins-new" +} \ No newline at end of file diff --git a/jenkins-new.planx-pla.net/portal/gitops.json b/jenkins-new.planx-pla.net/portal/gitops.json index 15b3e1bdf..dde2bad55 100644 --- a/jenkins-new.planx-pla.net/portal/gitops.json +++ b/jenkins-new.planx-pla.net/portal/gitops.json @@ -1,5 +1,6 @@ { "gaTrackingId": "UA-119127212-3", + "argoTemplate": "gwas-template", "graphql": { "boardCounts": [ ], @@ -32,6 +33,12 @@ "label": "Explore data", "color": "#035C94" }, + { + "icon": "analysis", + "link": "/analysis", + "color": "#a2a2a2", + "name": "Apps" + }, { "name": "Analyze Data", "icon": "anvil-analyze", @@ -79,6 +86,12 @@ "color": "#035C94", "name": "Exploration" }, + { + "icon": "analysis", + "link": "/analysis", + "color": "#a2a2a2", + "name": "Apps" + }, { "icon": "workspace", "link": "/workspace", @@ -107,8 +120,19 @@ "explorer": true, "discovery": true, "discoveryUseAggMDS": true, - "studyRegistration": true + "studyRegistration": true, + "analysis": true }, + "analysisTools": [ + { + "title": "OHDSI Atlas", + "description": "Use this App for cohort creation. These will be automatically populated in the Gen3 GWAS App", + "applicationUrl": "https://atlas.qa-mickey.planx-pla.net/atlas/", + "image": "/custom/sponsors/gitops-sponsors/atlas-logo.png" + }, + "GWASUIApp", + "GWASResults" + ], "discoveryConfig": { "features": { "advSearchFilters": { From 0eeb33ee71470a5378fd8a6339e0466a4a235cb9 Mon Sep 17 00:00:00 2001 From: Atharva Rane <41084525+atharvar28@users.noreply.github.com> Date: Mon, 16 Oct 2023 11:11:28 -0400 Subject: [PATCH 2/4] Delete jenkins-new.planx-pla.net/manifests/argo/argo.json --- jenkins-new.planx-pla.net/manifests/argo/argo.json | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 jenkins-new.planx-pla.net/manifests/argo/argo.json diff --git a/jenkins-new.planx-pla.net/manifests/argo/argo.json b/jenkins-new.planx-pla.net/manifests/argo/argo.json deleted file mode 100644 index 8e34dc71c..000000000 --- a/jenkins-new.planx-pla.net/manifests/argo/argo.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "scaling_groups": { - "default": "{{workflow.name}}", - "custom": { - } - }, - "bucket": "second-argo-bucket", - "internal-s3-bucket": "gen3-argo-707767160287-devplanetv1", - "indexd_admin_user": "fence", - "environment": "jenkins-new" -} \ No newline at end of file From 59d30c1147123f44103a6dc57bcb03ad3e5c1492 Mon Sep 17 00:00:00 2001 From: Atharva Rane <41084525+atharvar28@users.noreply.github.com> Date: Mon, 16 Oct 2023 12:27:39 -0400 Subject: [PATCH 3/4] Update Jenkinsfile to run the GWASUI Tests --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 23005e239..73e550ad3 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,5 +1,5 @@ #!groovy -@Library('cdis-jenkins-lib@master') _ +@Library('cdis-jenkins-lib@test/skip_secrets_setup') _ testPipeline { MANIFEST = "True" } From 56682ce4df56b823e735fef373ab938e5f234438 Mon Sep 17 00:00:00 2001 From: Atharva Rane <41084525+atharvar28@users.noreply.github.com> Date: Tue, 17 Oct 2023 11:16:19 -0400 Subject: [PATCH 4/4] Update Jenkinsfile --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 73e550ad3..23005e239 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,5 +1,5 @@ #!groovy -@Library('cdis-jenkins-lib@test/skip_secrets_setup') _ +@Library('cdis-jenkins-lib@master') _ testPipeline { MANIFEST = "True" }