diff --git a/staging.theanvil.io/etlMapping.yaml b/staging.theanvil.io/etlMapping.yaml index 963a9fb0c5..a5def221a7 100644 --- a/staging.theanvil.io/etlMapping.yaml +++ b/staging.theanvil.io/etlMapping.yaml @@ -40,6 +40,14 @@ mappings: path: samples src: original_material_type fn: set + - name: sample_submitter_id + path: samples + src: submitter_id + fn: set + - name: sequencing_assay_submitter_id + path: samples.sequencings + src: submitter_id + fn: set - name: exome_capture_platform path: samples.sequencings src: exome_capture_platform @@ -104,6 +112,8 @@ mappings: - name: project_id - name: submitter_id - name: object_id + - name: drs_id + src: object_id - name: md5sum - name: file_name - name: file_size @@ -161,3 +171,13 @@ mappings: - name: phenotype_group src: phenotype_group fn: set + sample: + props: + - name: sample_submitter_id + src: submitter_id + fn: set + sequencing: + props: + - name: sequencing_assay_submitter_id + src: submitter_id + fn: set diff --git a/staging.theanvil.io/manifest.json b/staging.theanvil.io/manifest.json index 7763a8f8f7..ab8b53f4da 100644 --- a/staging.theanvil.io/manifest.json +++ b/staging.theanvil.io/manifest.json @@ -7,29 +7,29 @@ "autodeploy": "yes" }, "versions": { - "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2022.03", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.03", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.03", + "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2022.05", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.05", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.05", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.03", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.05", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.03", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.03", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.05", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.05", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.03", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.03", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.03", - "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.03", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.22.1", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.03", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.03", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.03", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.03", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:0.6.5", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.03", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.03", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.03", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.03" + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.05", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.05", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.05", + "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.05", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2022.05", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.05", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.05", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.05", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.05", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.05", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.05", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.05", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.05", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.05" }, "indexd": { "arborist": "true" @@ -38,7 +38,7 @@ "environment": "anvilstaging", "hostname": "staging.theanvil.io", "revproxy_arn": "arn:aws:acm:us-east-1:474789003679:certificate/9fd731e3-3366-4bd0-a3ef-0453dc07289a", - "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/2.3.2/schema.json", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/2.3.6/schema.json", "portal_app": "gitops", "kube_bucket": "kube-anvilstaging-gen3", "logs_bucket": "logs-anvilstaging-gen3", @@ -60,7 +60,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.03", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.05", "pull_policy": "Always", "env": [ { @@ -128,7 +128,7 @@ "action": "export-files", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.03", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.05", "pull_policy": "Always", "env": [ { @@ -152,10 +152,6 @@ { "name": "ROOT_NODE", "value": "file" - }, - { - "name": "EXTRA_NODES", - "value": "" } ], "volumeMounts": [ @@ -197,7 +193,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.03" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.05" } }, "arborist": { diff --git a/staging.theanvil.io/manifests/hatchery/hatchery.json b/staging.theanvil.io/manifests/hatchery/hatchery.json index c1117fde56..4c59ff95d5 100644 --- a/staging.theanvil.io/manifests/hatchery/hatchery.json +++ b/staging.theanvil.io/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "512Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.03", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.05", "env": { "NAMESPACE": "default", "HOSTNAME": "staging.theanvil.io" @@ -172,4 +172,4 @@ "fs-gid": 100 } ] -} \ No newline at end of file +}