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Fix/export pfb options anvil fix #4065

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merged 4 commits into from
Jan 25, 2022
Merged

Fix/export pfb options anvil fix #4065

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df1e156
apply version 2022.01 to staging.theanvil.io
PlanXCyborg Jan 14, 2022
0154cb7
apply version 2022.01 to staging.theanvil.io
PlanXCyborg Jan 14, 2022
d1dbb86
Configure export-to-files and export to SB
mpingram Jan 21, 2022
01d9507
Deploy portal branch with fix
mpingram Jan 24, 2022
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114 changes: 91 additions & 23 deletions staging.theanvil.io/manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,29 +7,29 @@
"autodeploy": "yes"
},
"versions": {
"access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2021.11",
"arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2021.11",
"audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2021.11",
"access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2022.01",
"arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.01",
"audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.01",
"aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
"fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2021.11",
"fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.01",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
"guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2021.11",
"hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2021.11",
"guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.01",
"hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.01",
"ambassador": "quay.io/datawire/ambassador:1.4.2",
"indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2021.11",
"manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2021.11",
"peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2021.11",
"pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2021.11",
"portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2021.11",
"revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2021.11",
"sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2021.11",
"sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2021.11",
"spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2021.11",
"tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2021.11",
"ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2021.11",
"wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2021.11",
"dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2021.11",
"metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2021.11"
"indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.01",
"manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.01",
"peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.01",
"pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.01",
"portal": "quay.io/cdis/data-portal:feat_export-file-pfb-to-url",
"revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.01",
"sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.01",
"sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.01",
"spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.01",
"tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.01",
"ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.01",
"wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.01",
"dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.01",
"metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.01"
},
"indexd": {
"arborist": "true"
Expand Down Expand Up @@ -60,7 +60,7 @@
"action": "export",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2021.11",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.01",
"pull_policy": "Always",
"env": [
{
Expand Down Expand Up @@ -122,14 +122,82 @@
}
],
"restart_policy": "Never"
},
{
"name": "pelican-export-files",
"action": "export-files",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.01",
"pull_policy": "Always",
"env": [
{
"name": "DICTIONARY_URL",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "dictionary_url"
}
}
},
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
},
{
"name": "ROOT_NODE",
"value": "file"
},
{
"name": "EXTRA_NODES",
"value": ""
}
],
"volumeMounts": [
{
"name": "pelican-creds-volume",
"readOnly": true,
"mountPath": "/pelican-creds.json",
"subPath": "config.json"
},
{
"name": "peregrine-creds-volume",
"readOnly": true,
"mountPath": "/peregrine-creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "12Gi"
},
"volumes": [
{
"name": "pelican-creds-volume",
"secret": {
"secretName": "pelicanservice-g3auto"
}
},
{
"name": "peregrine-creds-volume",
"secret": {
"secretName": "peregrine-creds"
}
}
],
"restart_policy": "Never"
}
],
"google": {
"enabled": "yes"
},
"ssjdispatcher": {
"job_images": {
"indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2021.11"
"indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.01"
}
},
"arborist": {
Expand Down Expand Up @@ -208,4 +276,4 @@
"targetCpu": 40
}
}
}
}
4 changes: 2 additions & 2 deletions staging.theanvil.io/manifests/hatchery/hatchery.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"sidecar": {
"cpu-limit": "1.0",
"memory-limit": "512Mi",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2021.08",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.01",
"env": {
"NAMESPACE": "default",
"HOSTNAME": "staging.theanvil.io"
Expand Down Expand Up @@ -172,4 +172,4 @@
"fs-gid": 100
}
]
}
}
38 changes: 33 additions & 5 deletions staging.theanvil.io/portal/gitops.json
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Original file line number Diff line number Diff line change
Expand Up @@ -222,23 +222,23 @@
{
"enabled": true,
"type": "export-pfb-to-url",
"targetURLTemplate": "https://cgc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc",
"targetURLTemplate": "https://cgc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to CGC",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
},
{
"enabled": true,
"type": "export-pfb-to-url",
"targetURLTemplate": "https://cav-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc",
"targetURLTemplate": "https://cav-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to CAVATICA",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
},
{
"enabled": true,
"type": "export-pfb-to-url",
"targetURLTemplate": "https://bdc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=bdc",
"targetURLTemplate": "https://bdc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to BDC (Seven Bridges)",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
Expand Down Expand Up @@ -373,7 +373,36 @@
"accessibleValidationField": "project_id",
"downloadAccessor": "object_id"
},
"dropdowns": {
"sevenBridges": {
"title": "Export to Seven Bridges"
}
},
"buttons": [
{
"enabled": true,
"type": "export-file-pfb-to-url",
"targetURLTemplate": "https://cgc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to CGC",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
},
{
"enabled": true,
"type": "export-file-pfb-to-url",
"targetURLTemplate": "https://cav-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to CAVATICA",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
},
{
"enabled": true,
"type": "export-file-pfb-to-url",
"targetURLTemplate": "https://bdc-interop-vayu.sbgenomics.com/import/pfb?URL={{PRESIGNED_URL}}&source=anvil",
"title": "Export to BDC (Seven Bridges)",
"rightIcon": "external-link",
"dropdownId": "sevenBridges"
},
{
"enabled": true,
"type": "export-files-to-workspace",
Expand All @@ -399,8 +428,7 @@
"enableLimitedFilePFBExport": {
"sourceNodeField": "source_node"
},
"terraExportURL": "https://anvil.terra.bio/#import-data",
"dropdowns": {}
"terraExportURL": "https://anvil.terra.bio/#import-data"
},
{
"tabTitle": "Downloadable",
Expand Down