From 54c3537201cb579e4a64d1f49d5936cdbbf61975 Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Thu, 10 Mar 2022 10:02:33 -0600 Subject: [PATCH 1/3] Deploy multiple paymodels branches to BRH --- brh.data-commons.org/manifest.json | 26 ++-- .../manifests/hatchery/hatchery.json | 145 ++---------------- 2 files changed, 23 insertions(+), 148 deletions(-) diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index b99c715c91..825eb6d13d 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -9,20 +9,20 @@ "versions": { "ambassador": "quay.io/datawire/ambassador:1.4.2", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1", - "arborist": "quay.io/cdis/arborist:2021.11", - "dashboard": "quay.io/cdis/gen3-statics:2021.11", - "fence": "quay.io/cdis/fence:2021.11", + "arborist": "quay.io/cdis/arborist:2022.03", + "dashboard": "quay.io/cdis/gen3-statics:2022.03", + "fence": "quay.io/cdis/fence:2022.03", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch", - "hatchery": "quay.io/cdis/hatchery:feat_default_pay_model", - "indexd": "quay.io/cdis/indexd:2021.11", - "metadata": "quay.io/cdis/metadata-service:1.6.2", - "portal": "quay.io/cdis/data-portal:3.17.4", - "peregrine": "quay.io/cdis/peregrine:2021.11", - "pidgin": "quay.io/cdis/pidgin:2021.11", - "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1", - "manifestservice": "quay.io/cdis/manifestservice:2021.11", - "wts": "quay.io/cdis/workspace-token-service:2021.11", - "sheepdog": "quay.io/cdis/sheepdog:2021.11" + "hatchery": "quay.io/cdis/hatchery:feat_multiple_paymodels", + "indexd": "quay.io/cdis/indexd:2022.03", + "metadata": "quay.io/cdis/metadata-service:1.6.4", + "portal": "quay.io/cdis/portal:feat_multiple_paymodels", + "peregrine": "quay.io/cdis/peregrine:2022.03", + "pidgin": "quay.io/cdis/pidgin:2022.03", + "revproxy": "quay.io/cdis/nginx:2022.03", + "manifestservice": "quay.io/cdis/manifestservice:2022.03", + "wts": "quay.io/cdis/workspace-token-service:2022.03", + "sheepdog": "quay.io/cdis/sheepdog:2022.03" }, "arborist": { "deployment_version": "2" diff --git a/brh.data-commons.org/manifests/hatchery/hatchery.json b/brh.data-commons.org/manifests/hatchery/hatchery.json index 10839ebd3a..56e3123976 100755 --- a/brh.data-commons.org/manifests/hatchery/hatchery.json +++ b/brh.data-commons.org/manifests/hatchery/hatchery.json @@ -3,14 +3,15 @@ "sub-dir": "/lw-workspace", "user-volume-size": "10Gi", "default-pay-model": { - "aws_account_id": "354484406138", - "name": "brhworkspaces", + "account_id": "354484406138", + "workspace_type": "brhworkspaces", "region": "us-east-1" }, + "pay-models-dynamodb-table": "bmh-admin-portal-backend-bmhworkspacetableD4D73E43-34AAJOR7A5AG", "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:fix_no_exit", + "image": "quay.io/cdis/ecs-ws-sidecar:feat_datamounting", "env": { "NAMESPACE": "default", "HOSTNAME": "brh.data-commons.org" @@ -34,13 +35,14 @@ "target-port": 8888, "cpu-limit": "1.0", "memory-limit": "2Gi", - "name": "(Generic) Jupyter Notebook with R Kernel", - "image": "quay.io/cdis/jupyter-superslim-r:master", + "name": "(Generic) Jupyter Lab Notebook with R Kernel", + "image": "quay.io/cdis/jupyter-superslim-r:1.0.1", "env": { "FRAME_ANCESTORS": "https://brh.data-commons.org" }, "args": [ "--NotebookApp.base_url=/lw-workspace/proxy/", + "--NotebookApp.default_url=/lab", "--NotebookApp.password=''", "--NotebookApp.token=''", "--NotebookApp.ip='*'", @@ -132,141 +134,14 @@ "target-port": 8888, "cpu-limit": "1.0", "memory-limit": "2Gi", - "name": "(Tutorial) JCOIN Tracking Opioid Stigma Notebook", - "image": "quay.io/cdis/heal-notebooks:jcoin__177f89f0fab8a13c606c68bab0b953aa3fed4b71", - "env": { - "FRAME_ANCESTORS": "https://brh.data-commons.org" - }, - "args": [ - "--NotebookApp.base_url=/lw-workspace/proxy/", - "--NotebookApp.password=''", - "--NotebookApp.token=''", - "--NotebookApp.shutdown_no_activity_timeout=5400", - "--NotebookApp.quit_button=False" - ], - "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/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" - ], - "user-uid": 1000, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "(Tutorial) BACPAC Synthetic Data Analysis Notebook", - "image": "quay.io/cdis/heal-notebooks:bacpac__10670ad79b4488cfa9f1b3681ce52bc3f1139b5a", - "env": { - "FRAME_ANCESTORS": "https://brh.data-commons.org" - }, - "args": [ - "--NotebookApp.base_url=/lw-workspace/proxy/", - "--NotebookApp.password=''", - "--NotebookApp.token=''", - "--NotebookApp.shutdown_no_activity_timeout=5400", - "--NotebookApp.quit_button=False" - ], - "command": [ - "start-notebook.sh" - ], - "path-rewrite": "/lw-workspace/proxy/", - "use-tls": "false", - "ready-probe": "/lw-workspace/proxy/", - "lifecycle-post-start": [ - "/bin/sh", - "-c", - "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" - ], - "user-uid": 1000, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "(Tutorial) Opioid Prevalence And Overdoses Notebook", - "image": "quay.io/cdis/heal-notebooks:cdcdea__2c94886708fbf7454b6e54f64eb844886d0c3a93", - "env": { - "FRAME_ANCESTORS": "https://brh.data-commons.org" - }, - "args": [ - "--NotebookApp.base_url=/lw-workspace/proxy/", - "--NotebookApp.password=''", - "--NotebookApp.token=''", - "--NotebookApp.shutdown_no_activity_timeout=5400", - "--NotebookApp.quit_button=False" - ], - "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/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" - ], - "user-uid": 1000, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "(Tutorial) Opioid Overdose Trajectories Notebook", - "image": "quay.io/cdis/heal-notebooks:cdcwonder__fd15dab0198c6dd0da71e6806ac690c7c8632fa7", - "env": { - "FRAME_ANCESTORS": "https://brh.data-commons.org" - }, - "args": [ - "--NotebookApp.base_url=/lw-workspace/proxy/", - "--NotebookApp.password=''", - "--NotebookApp.token=''", - "--NotebookApp.shutdown_no_activity_timeout=5400", - "--NotebookApp.quit_button=False" - ], - "command": [ - "start-notebook.sh" - ], - "path-rewrite": "/lw-workspace/proxy/", - "use-tls": "false", - "ready-probe": "/lw-workspace/proxy/", - "lifecycle-post-start": [ - "/bin/sh", - "-c", - "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true" - ], - "user-uid": 1000, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "(Tutorial) Opioid Environment Toolkit And OEPS R Notebook", - "image": "quay.io/cdis/heal-notebooks:oeps__69567adc7583405788eafc39ae8af51a6a5d7690", + "name": "(Tutorials) Example Analysis Jupyter Lab Notebooks", + "image": "quay.io/cdis/heal-notebooks:combined_tutorials__fbd5ce467b9c2a8e4d59c2d7ec49ad6c5c80312a", "env": { "FRAME_ANCESTORS": "https://brh.data-commons.org" }, "args": [ "--NotebookApp.base_url=/lw-workspace/proxy/", + "--NotebookApp.default_url=/lab", "--NotebookApp.password=''", "--NotebookApp.token=''", "--NotebookApp.shutdown_no_activity_timeout=5400", From 95634ecc120f633194bf11d1bae0415c121f6a32 Mon Sep 17 00:00:00 2001 From: jawadqur <55899496+jawadqur@users.noreply.github.com> Date: Thu, 10 Mar 2022 10:09:21 -0600 Subject: [PATCH 2/3] Update manifest.json --- brh.data-commons.org/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index 825eb6d13d..23e06de821 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -16,7 +16,7 @@ "hatchery": "quay.io/cdis/hatchery:feat_multiple_paymodels", "indexd": "quay.io/cdis/indexd:2022.03", "metadata": "quay.io/cdis/metadata-service:1.6.4", - "portal": "quay.io/cdis/portal:feat_multiple_paymodels", + "portal": "quay.io/cdis/data=portal:feat_multiple_paymodels", "peregrine": "quay.io/cdis/peregrine:2022.03", "pidgin": "quay.io/cdis/pidgin:2022.03", "revproxy": "quay.io/cdis/nginx:2022.03", From 6728a481b00aa104c30501a9e5028a1a444d8055 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Thu, 10 Mar 2022 10:31:06 -0600 Subject: [PATCH 3/3] Update brh.data-commons.org/manifest.json --- brh.data-commons.org/manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index 23e06de821..d1cf29fe5b 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -16,7 +16,7 @@ "hatchery": "quay.io/cdis/hatchery:feat_multiple_paymodels", "indexd": "quay.io/cdis/indexd:2022.03", "metadata": "quay.io/cdis/metadata-service:1.6.4", - "portal": "quay.io/cdis/data=portal:feat_multiple_paymodels", + "portal": "quay.io/cdis/data-portal:feat_multiple_paymodels", "peregrine": "quay.io/cdis/peregrine:2022.03", "pidgin": "quay.io/cdis/pidgin:2022.03", "revproxy": "quay.io/cdis/nginx:2022.03",