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Fix config specs
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@rtitle
rtitle committed Nov 22, 2022
1 parent e7ece34 commit 49917a4
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2 changes: 1 addition & 1 deletion http/src/test/scala/org/broadinstitute/dsde/workbench/leonardo/config/ConfigSpec.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@ final class ConfigSpec extends AnyFlatSpec with Matchers {
true,
DbPassword("replace-me"),
GalaxyOrchUrl("https://firecloud-orchestration.dsde-dev.broadinstitute.org/api/"),
GalaxyDrsUrl("https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3"),
GalaxyDrsUrl("https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve"),
5,
3
)
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4 changes: 2 additions & 2 deletions http/src/test/scala/org/broadinstitute/dsde/workbench/leonardo/util/GKEInterpreterSpec.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ class GKEInterpreterSpec extends AnyFlatSpecLike with TestComponent with Leonard

res.mkString(
","
) shouldBe """nfs.storageClass.name=nfs-app1-galaxy-rls,cvmfs.repositories.cvmfs-gxy-data-app1-galaxy-rls=data.galaxyproject.org,cvmfs.cache.alienCache.storageClass=nfs-app1-galaxy-rls,galaxy.persistence.storageClass=nfs-app1-galaxy-rls,galaxy.cvmfs.galaxyPersistentVolumeClaims.data.storageClassName=cvmfs-gxy-data-app1-galaxy-rls,galaxy.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,nfs.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.configs.job_conf\.yml.runners.k8s.k8s_node_selector=cloud.google.com/gke-nodepool: pool1,galaxy.postgresql.master.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.ingress.path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-from=https://1455694897.jupyter.firecloud.org,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-to=https://leo,galaxy.ingress.hosts[0].host=1455694897.jupyter.firecloud.org,galaxy.ingress.hosts[0].paths[0].path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.tls[0].hosts[0]=1455694897.jupyter.firecloud.org,galaxy.ingress.tls[0].secretName=tls-secret,galaxy.configs.galaxy\[email protected],galaxy.configs.galaxy\[email protected],galaxy.terra.launch.workspace=test-workspace,galaxy.terra.launch.namespace=dsp-leo-test1,galaxy.terra.launch.apiURL=https://firecloud-orchestration.dsde-dev.broadinstitute.org/api/,galaxy.terra.launch.drsURL=https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3,galaxy.jobs.maxLimits.memory=6,galaxy.jobs.maxLimits.cpu=4,galaxy.jobs.maxRequests.memory=1,galaxy.jobs.maxRequests.cpu=1,galaxy.serviceAccount.create=false,galaxy.serviceAccount.name=app1-galaxy-ksa,rbac.serviceAccount=app1-galaxy-ksa,persistence.nfs.name=ns-nfs-disk,persistence.nfs.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1,persistence.nfs.size=250Gi,persistence.postgres.name=ns-postgres-disk,galaxy.postgresql.galaxyDatabasePassword=replace-me,persistence.postgres.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1-gxy-postres-disk,persistence.postgres.size=10Gi,nfs.persistence.existingClaim=ns-nfs-disk-pvc,nfs.persistence.size=250Gi,galaxy.postgresql.persistence.existingClaim=ns-postgres-disk-pvc,galaxy.persistence.size=200Gi,configs.WORKSPACE_NAME=test-workspace,extraEnv[0].name=WORKSPACE_NAME,extraEnv[0].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[0].valueFrom.configMapKeyRef.key=WORKSPACE_NAME,configs.WORKSPACE_BUCKET=gs://test-bucket,extraEnv[1].name=WORKSPACE_BUCKET,extraEnv[1].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[1].valueFrom.configMapKeyRef.key=WORKSPACE_BUCKET,configs.WORKSPACE_NAMESPACE=dsp-leo-test1,extraEnv[2].name=WORKSPACE_NAMESPACE,extraEnv[2].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[2].valueFrom.configMapKeyRef.key=WORKSPACE_NAMESPACE"""
) shouldBe """nfs.storageClass.name=nfs-app1-galaxy-rls,cvmfs.repositories.cvmfs-gxy-data-app1-galaxy-rls=data.galaxyproject.org,cvmfs.cache.alienCache.storageClass=nfs-app1-galaxy-rls,galaxy.persistence.storageClass=nfs-app1-galaxy-rls,galaxy.cvmfs.galaxyPersistentVolumeClaims.data.storageClassName=cvmfs-gxy-data-app1-galaxy-rls,galaxy.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,nfs.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.configs.job_conf\.yml.runners.k8s.k8s_node_selector=cloud.google.com/gke-nodepool: pool1,galaxy.postgresql.master.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.ingress.path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-from=https://1455694897.jupyter.firecloud.org,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-to=https://leo,galaxy.ingress.hosts[0].host=1455694897.jupyter.firecloud.org,galaxy.ingress.hosts[0].paths[0].path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.tls[0].hosts[0]=1455694897.jupyter.firecloud.org,galaxy.ingress.tls[0].secretName=tls-secret,galaxy.configs.galaxy\[email protected],galaxy.configs.galaxy\[email protected],galaxy.terra.launch.workspace=test-workspace,galaxy.terra.launch.namespace=dsp-leo-test1,galaxy.terra.launch.apiURL=https://firecloud-orchestration.dsde-dev.broadinstitute.org/api/,galaxy.terra.launch.drsURL=https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve,galaxy.jobs.maxLimits.memory=6,galaxy.jobs.maxLimits.cpu=4,galaxy.jobs.maxRequests.memory=1,galaxy.jobs.maxRequests.cpu=1,galaxy.serviceAccount.create=false,galaxy.serviceAccount.name=app1-galaxy-ksa,rbac.serviceAccount=app1-galaxy-ksa,persistence.nfs.name=ns-nfs-disk,persistence.nfs.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1,persistence.nfs.size=250Gi,persistence.postgres.name=ns-postgres-disk,galaxy.postgresql.galaxyDatabasePassword=replace-me,persistence.postgres.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1-gxy-postres-disk,persistence.postgres.size=10Gi,nfs.persistence.existingClaim=ns-nfs-disk-pvc,nfs.persistence.size=250Gi,galaxy.postgresql.persistence.existingClaim=ns-postgres-disk-pvc,galaxy.persistence.size=200Gi,configs.WORKSPACE_NAME=test-workspace,extraEnv[0].name=WORKSPACE_NAME,extraEnv[0].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[0].valueFrom.configMapKeyRef.key=WORKSPACE_NAME,configs.WORKSPACE_BUCKET=gs://test-bucket,extraEnv[1].name=WORKSPACE_BUCKET,extraEnv[1].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[1].valueFrom.configMapKeyRef.key=WORKSPACE_BUCKET,configs.WORKSPACE_NAMESPACE=dsp-leo-test1,extraEnv[2].name=WORKSPACE_NAMESPACE,extraEnv[2].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[2].valueFrom.configMapKeyRef.key=WORKSPACE_NAMESPACE"""
}

it should "build Galaxy override values string with restore info" in {
Expand Down Expand Up @@ -151,7 +151,7 @@ class GKEInterpreterSpec extends AnyFlatSpecLike with TestComponent with Leonard
)
result.mkString(
","
) shouldBe """nfs.storageClass.name=nfs-app1-galaxy-rls,cvmfs.repositories.cvmfs-gxy-data-app1-galaxy-rls=data.galaxyproject.org,cvmfs.cache.alienCache.storageClass=nfs-app1-galaxy-rls,galaxy.persistence.storageClass=nfs-app1-galaxy-rls,galaxy.cvmfs.galaxyPersistentVolumeClaims.data.storageClassName=cvmfs-gxy-data-app1-galaxy-rls,galaxy.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,nfs.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.configs.job_conf\.yml.runners.k8s.k8s_node_selector=cloud.google.com/gke-nodepool: pool1,galaxy.postgresql.master.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.ingress.path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-from=https://1455694897.jupyter.firecloud.org,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-to=https://leo,galaxy.ingress.hosts[0].host=1455694897.jupyter.firecloud.org,galaxy.ingress.hosts[0].paths[0].path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.tls[0].hosts[0]=1455694897.jupyter.firecloud.org,galaxy.ingress.tls[0].secretName=tls-secret,galaxy.configs.galaxy\[email protected],galaxy.configs.galaxy\[email protected],galaxy.terra.launch.workspace=test-workspace,galaxy.terra.launch.namespace=dsp-leo-test1,galaxy.terra.launch.apiURL=https://firecloud-orchestration.dsde-dev.broadinstitute.org/api/,galaxy.terra.launch.drsURL=https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3,galaxy.jobs.maxLimits.memory=6,galaxy.jobs.maxLimits.cpu=4,galaxy.jobs.maxRequests.memory=1,galaxy.jobs.maxRequests.cpu=1,galaxy.serviceAccount.create=false,galaxy.serviceAccount.name=app1-galaxy-ksa,rbac.serviceAccount=app1-galaxy-ksa,persistence.nfs.name=ns-nfs-disk,persistence.nfs.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1,persistence.nfs.size=250Gi,persistence.postgres.name=ns-postgres-disk,galaxy.postgresql.galaxyDatabasePassword=replace-me,persistence.postgres.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1-gxy-postres,persistence.postgres.size=10Gi,nfs.persistence.existingClaim=ns-nfs-disk-pvc,nfs.persistence.size=250Gi,galaxy.postgresql.persistence.existingClaim=ns-postgres-disk-pvc,galaxy.persistence.size=200Gi,configs.WORKSPACE_NAME=test-workspace,extraEnv[0].name=WORKSPACE_NAME,extraEnv[0].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[0].valueFrom.configMapKeyRef.key=WORKSPACE_NAME,configs.WORKSPACE_BUCKET=gs://test-bucket,extraEnv[1].name=WORKSPACE_BUCKET,extraEnv[1].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[1].valueFrom.configMapKeyRef.key=WORKSPACE_BUCKET,configs.WORKSPACE_NAMESPACE=dsp-leo-test1,extraEnv[2].name=WORKSPACE_NAMESPACE,extraEnv[2].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[2].valueFrom.configMapKeyRef.key=WORKSPACE_NAMESPACE,restore.persistence.nfs.galaxy.pvcID=galaxy-pvc-id,restore.persistence.nfs.cvmfsCache.pvcID=cvmfs-pvc-id,galaxy.persistence.existingClaim=app1-galaxy-rls-galaxy-pvc,cvmfs.cache.alienCache.existingClaim=app1-galaxy-rls-cvmfs-alien-cache-pvc""".stripMargin
) shouldBe """nfs.storageClass.name=nfs-app1-galaxy-rls,cvmfs.repositories.cvmfs-gxy-data-app1-galaxy-rls=data.galaxyproject.org,cvmfs.cache.alienCache.storageClass=nfs-app1-galaxy-rls,galaxy.persistence.storageClass=nfs-app1-galaxy-rls,galaxy.cvmfs.galaxyPersistentVolumeClaims.data.storageClassName=cvmfs-gxy-data-app1-galaxy-rls,galaxy.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,nfs.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.configs.job_conf\.yml.runners.k8s.k8s_node_selector=cloud.google.com/gke-nodepool: pool1,galaxy.postgresql.master.nodeSelector.cloud\.google\.com/gke-nodepool=pool1,galaxy.ingress.path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-from=https://1455694897.jupyter.firecloud.org,galaxy.ingress.annotations.nginx\.ingress\.kubernetes\.io/proxy-redirect-to=https://leo,galaxy.ingress.hosts[0].host=1455694897.jupyter.firecloud.org,galaxy.ingress.hosts[0].paths[0].path=/proxy/google/v1/apps/dsp-leo-test1/app1/galaxy,galaxy.ingress.tls[0].hosts[0]=1455694897.jupyter.firecloud.org,galaxy.ingress.tls[0].secretName=tls-secret,galaxy.configs.galaxy\[email protected],galaxy.configs.galaxy\[email protected],galaxy.terra.launch.workspace=test-workspace,galaxy.terra.launch.namespace=dsp-leo-test1,galaxy.terra.launch.apiURL=https://firecloud-orchestration.dsde-dev.broadinstitute.org/api/,galaxy.terra.launch.drsURL=https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve,galaxy.jobs.maxLimits.memory=6,galaxy.jobs.maxLimits.cpu=4,galaxy.jobs.maxRequests.memory=1,galaxy.jobs.maxRequests.cpu=1,galaxy.serviceAccount.create=false,galaxy.serviceAccount.name=app1-galaxy-ksa,rbac.serviceAccount=app1-galaxy-ksa,persistence.nfs.name=ns-nfs-disk,persistence.nfs.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1,persistence.nfs.size=250Gi,persistence.postgres.name=ns-postgres-disk,galaxy.postgresql.galaxyDatabasePassword=replace-me,persistence.postgres.persistentVolume.extraSpec.gcePersistentDisk.pdName=disk1-gxy-postres,persistence.postgres.size=10Gi,nfs.persistence.existingClaim=ns-nfs-disk-pvc,nfs.persistence.size=250Gi,galaxy.postgresql.persistence.existingClaim=ns-postgres-disk-pvc,galaxy.persistence.size=200Gi,configs.WORKSPACE_NAME=test-workspace,extraEnv[0].name=WORKSPACE_NAME,extraEnv[0].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[0].valueFrom.configMapKeyRef.key=WORKSPACE_NAME,configs.WORKSPACE_BUCKET=gs://test-bucket,extraEnv[1].name=WORKSPACE_BUCKET,extraEnv[1].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[1].valueFrom.configMapKeyRef.key=WORKSPACE_BUCKET,configs.WORKSPACE_NAMESPACE=dsp-leo-test1,extraEnv[2].name=WORKSPACE_NAMESPACE,extraEnv[2].valueFrom.configMapKeyRef.name=app1-galaxy-rls-galaxykubeman-configs,extraEnv[2].valueFrom.configMapKeyRef.key=WORKSPACE_NAMESPACE,restore.persistence.nfs.galaxy.pvcID=galaxy-pvc-id,restore.persistence.nfs.cvmfsCache.pvcID=cvmfs-pvc-id,galaxy.persistence.existingClaim=app1-galaxy-rls-galaxy-pvc,cvmfs.cache.alienCache.existingClaim=app1-galaxy-rls-cvmfs-alien-cache-pvc""".stripMargin
}

it should "build Cromwell override values string" in {
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