From 5c972dab8d0beffc633c6da6686a043234d53af2 Mon Sep 17 00:00:00 2001 From: PlanXCyborg <38964842+PlanXCyborg@users.noreply.github.com> Date: Wed, 16 Feb 2022 13:09:37 -0600 Subject: [PATCH 1/5] apply version 2022.02 to qa-niaid.planx-pla.net --- qa-niaid.planx-pla.net/manifest.json | 46 ++++++++++++++-------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/qa-niaid.planx-pla.net/manifest.json b/qa-niaid.planx-pla.net/manifest.json index 29e4f38fc..26dc45a06 100644 --- a/qa-niaid.planx-pla.net/manifest.json +++ b/qa-niaid.planx-pla.net/manifest.json @@ -7,29 +7,29 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:3.2.0", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2021.09", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.02", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.02", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2021.09", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2021.09", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2021.09", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2021.09", - "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2021.09", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2021.09", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2021.09", - "sower": "quay.io/cdis/sower:master", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.19.3", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2021.09", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.02", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.02", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.02", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.02", + "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.02", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.02", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.02", + "sower": "quay.io/cdis/sower:2022.02", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2022.02", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.02", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2021.09", - "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:1.5.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2021.09", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2021.09", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.02", + "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2022.02", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.02", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.02", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2021.09", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2021.09", - "manifestservice": "quay.io/cdis/manifestservice:master", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2021.09" + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.02", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.02", + "manifestservice": "quay.io/cdis/manifestservice:2022.02", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.02" }, "arborist": { "deployment_version": "2" @@ -39,7 +39,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2021.09" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.02" } }, "global": { @@ -89,7 +89,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2021.09", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.02", "pull_policy": "Always", "env": [ { @@ -161,4 +161,4 @@ "restart_policy": "Never" } ] -} +} \ No newline at end of file From a6d8344931e54dea68c54d8824e7881e8cb5faf1 Mon Sep 17 00:00:00 2001 From: PlanXCyborg <38964842+PlanXCyborg@users.noreply.github.com> Date: Wed, 16 Feb 2022 13:09:38 -0600 Subject: [PATCH 2/5] apply version 2022.02 to qa-niaid.planx-pla.net --- .../manifests/hatchery/hatchery.json | 94 +++++++++---------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json b/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json index 7215be2eb..ad1d11675 100644 --- a/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json +++ b/qa-niaid.planx-pla.net/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2021.09", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.02", "env": { "NAMESPACE": "qa-niaid", "HOSTNAME": "qa-niaid.planx-pla.net" @@ -25,51 +25,51 @@ ] }, "containers": [ - { - "target-port": 8787, - "cpu-limit": "1.0", - "memory-limit": "1024Mi", - "name": "R Studio", - "image": "quay.io/cdis/rstudio:master", - "env": { - "DISABLE_AUTH": "true" - }, - "args": [], - "path-rewrite": "/", - "use-tls": "false", - "ready-probe": "/", - "user-volume-location": "/home/rstudio/pd", - "fs-gid": 100 + { + "target-port": 8787, + "cpu-limit": "1.0", + "memory-limit": "1024Mi", + "name": "R Studio", + "image": "quay.io/cdis/rstudio:master", + "env": { + "DISABLE_AUTH": "true" }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "1024Mi", - "name": "Jupyter (Python 3.9.5, R 4.1.0)", - "image": "quay.io/cdis/jupyter-6.4.0-with-base-packages:latest", - "env": { - "NAMESPACE": "qa-niaid", - "FRAME_ANCESTORS": "https://qa-niaid.planx-pla.net/" - }, - "args": [ - "--NotebookApp.base_url=/lw-workspace/proxy/", - "--NotebookApp.password=''", - "--NotebookApp.token=''" - ], - "command": [ - "start-notebook.sh" - ], - "path-rewrite": "/lw-workspace/proxy/", - "use-tls": "false", - "ready-probe": "/lw-workspace/proxy/", - "lifecycle-post-start": [ - "/bin/sh", - "-c", - "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true" - ], - "user-uid": 1000, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd" - } + "args": [], + "path-rewrite": "/", + "use-tls": "false", + "ready-probe": "/", + "user-volume-location": "/home/rstudio/pd", + "fs-gid": 100 + }, + { + "target-port": 8888, + "cpu-limit": "1.0", + "memory-limit": "1024Mi", + "name": "Jupyter (Python 3.9.5, R 4.1.0)", + "image": "quay.io/cdis/jupyter-6.4.0-with-base-packages:latest", + "env": { + "NAMESPACE": "qa-niaid", + "FRAME_ANCESTORS": "https://qa-niaid.planx-pla.net/" + }, + "args": [ + "--NotebookApp.base_url=/lw-workspace/proxy/", + "--NotebookApp.password=''", + "--NotebookApp.token=''" + ], + "command": [ + "start-notebook.sh" + ], + "path-rewrite": "/lw-workspace/proxy/", + "use-tls": "false", + "ready-probe": "/lw-workspace/proxy/", + "lifecycle-post-start": [ + "/bin/sh", + "-c", + "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true" + ], + "user-uid": 1000, + "fs-gid": 100, + "user-volume-location": "/home/jovyan/pd" + } ] -} +} \ No newline at end of file From 26db67dbb4949024e3e88694c4feb0c1886405d4 Mon Sep 17 00:00:00 2001 From: Atharva Rane Date: Wed, 16 Feb 2022 14:26:06 -0500 Subject: [PATCH 3/5] fixing the sower version --- qa-niaid.planx-pla.net/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-niaid.planx-pla.net/manifest.json b/qa-niaid.planx-pla.net/manifest.json index 26dc45a06..608709b47 100644 --- a/qa-niaid.planx-pla.net/manifest.json +++ b/qa-niaid.planx-pla.net/manifest.json @@ -17,7 +17,7 @@ "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.02", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.02", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.02", - "sower": "quay.io/cdis/sower:2022.02", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.02", "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2022.02", "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.02", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", From 6253bf40aba9c261e13adb6f6b2d9ac12cce59a9 Mon Sep 17 00:00:00 2001 From: Atharva Rane <41084525+atharvar28@users.noreply.github.com> Date: Mon, 21 Feb 2022 10:46:08 -0500 Subject: [PATCH 4/5] updating the portal version to latest release --- qa-niaid.planx-pla.net/manifest.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qa-niaid.planx-pla.net/manifest.json b/qa-niaid.planx-pla.net/manifest.json index 608709b47..f202d7804 100644 --- a/qa-niaid.planx-pla.net/manifest.json +++ b/qa-niaid.planx-pla.net/manifest.json @@ -18,7 +18,7 @@ "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.02", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.02", "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.02", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2022.02", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.20.0", "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.02", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.02", @@ -161,4 +161,4 @@ "restart_policy": "Never" } ] -} \ No newline at end of file +} From 846de59222a1756acc5682b8c866d6aac4c19d5d Mon Sep 17 00:00:00 2001 From: Atharva Rane <41084525+atharvar28@users.noreply.github.com> Date: Tue, 22 Feb 2022 16:38:29 -0500 Subject: [PATCH 5/5] update portal service --- qa-niaid.planx-pla.net/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qa-niaid.planx-pla.net/manifest.json b/qa-niaid.planx-pla.net/manifest.json index f202d7804..a973e551d 100644 --- a/qa-niaid.planx-pla.net/manifest.json +++ b/qa-niaid.planx-pla.net/manifest.json @@ -18,7 +18,7 @@ "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.02", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.02", "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.02", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.20.0", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.19.3", "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.02", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.02",