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DCF PROD RELEASE Q3 1596041133 #1889

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merged 7 commits into from
Aug 3, 2020
Merged

DCF PROD RELEASE Q3 1596041133 #1889

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530457b
copying manifest.json to nci-crdc.datacommons.io
themarcelor Jul 29, 2020
53582b4
copying manifests/fence/fence-config-public.yaml to nci-crdc.datacomm…
themarcelor Jul 29, 2020
b1c57c1
copying portal/gitops.json to nci-crdc.datacommons.io
themarcelor Jul 29, 2020
4f5c975
setting fence 2020.07
Jul 29, 2020
fe80b9d
restore original set of fence buckets
Jul 29, 2020
27f81cb
duplicate cred in fence config
Jul 29, 2020
7fef6ae
fix service accounts
Jul 30, 2020
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32 changes: 16 additions & 16 deletions nci-crdc.datacommons.io/manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,19 +7,19 @@
"autodeploy": "yes"
},
"versions": {
"fence": "quay.io/cdis/fence:2020.06",
"arborist": "quay.io/cdis/arborist:2020.06",
"google-sa-validation": "placeholder:2020.06",
"indexd": "quay.io/cdis/indexd:2020.06",
"peregrine": "quay.io/cdis/peregrine:2020.06",
"pidgin": "quay.io/cdis/pidgin:2020.06",
"revproxy": "quay.io/cdis/nginx:2020.06",
"sheepdog": "quay.io/cdis/sheepdog:2020.06",
"portal": "quay.io/cdis/data-portal:2020.06",
"sower": "quay.io/cdis/sower:2020.06",
"fence": "quay.io/cdis/fence:2020.07",
"arborist": "quay.io/cdis/arborist:2020.07",
"google-sa-validation": "placeholder:2020.07",
"indexd": "quay.io/cdis/indexd:2020.07",
"peregrine": "quay.io/cdis/peregrine:2020.07",
"pidgin": "quay.io/cdis/pidgin:2020.07",
"revproxy": "quay.io/cdis/nginx:2020.07",
"sheepdog": "quay.io/cdis/sheepdog:2020.07",
"portal": "quay.io/cdis/data-portal:2020.07",
"sower": "quay.io/cdis/sower:2020.07",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
"ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.06",
"metadata": "quay.io/cdis/metadata-service:2020.06"
"ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.07",
"metadata": "quay.io/cdis/metadata-service:2020.07"
},
"arborist": {
"deployment_version": "2"
Expand All @@ -35,7 +35,7 @@
},
"ssjdispatcher": {
"job_images": {
"indexing": "quay.io/cdis/indexs3client:2020.06"
"indexing": "quay.io/cdis/indexs3client:2020.07"
}
},
"sower": [
Expand All @@ -46,7 +46,7 @@
"serviceAccountName": "jobs-nci-crdc-datacommons-io",
"container": {
"name": "job-task",
"image": "quay.io/cdis/manifest-indexing:1.1.6",
"image": "quay.io/cdis/manifest-indexing:2.0.0",
"pull_policy": "Always",
"env": [
{
Expand Down Expand Up @@ -87,7 +87,7 @@
"serviceAccountName": "jobs-nci-crdc-datacommons-io",
"container": {
"name": "job-task",
"image": "quay.io/cdis/download-indexd-manifest:1.1.6",
"image": "quay.io/cdis/download-indexd-manifest:2.0.0",
"pull_policy": "Always",
"env": [
{
Expand Down Expand Up @@ -127,7 +127,7 @@
"hostname": "nci-crdc.datacommons.io",
"revproxy_arn": "arn:aws:acm:us-east-1:584476192960:certificate/4173b316-0510-4216-8043-3f9234570475",
"dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json",
"portal_app": "dev",
"portal_app": "gitops",
"kube_bucket": "kube-dcfprod-gen3",
"logs_bucket": "logs-dcfprod-gen3",
"sync_from_dbgap": "True",
Expand Down
282 changes: 282 additions & 0 deletions nci-crdc.datacommons.io/portal/gitops.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,282 @@
{
"gaTrackingId": "undefined",
"graphql": {
"boardCounts": [
{
"graphql": "_case_count",
"name": "Case",
"plural": "Cases"
},
{
"graphql": "_experiment_count",
"name": "Experiment",
"plural": "Experiments"
},
{
"graphql": "_aliquot_count",
"name": "Aliquot",
"plural": "Aliquots"
}
],
"chartCounts": [
{
"graphql": "_case_count",
"name": "Case"
},
{
"graphql": "_experiment_count",
"name": "Experiment"
},
{
"graphql": "_aliquot_count",
"name": "Aliquot"
}
],
"projectDetails": "boardCounts"
},
"components": {
"appName": "NCI Data Commons Framework Services",
"index": {
"introduction": {
"heading": "Data Commons",
"text": "The NCI Data Commons Framework Services supports the management, analysis and sharing of data for the research community.",
"link": "/submission"
},
"buttons": [
{
"name": "Define Data Field",
"icon": "data-field-define",
"body": "The Data Commons define the data in a general way. Please study the dictionary before you start browsing.",
"link": "/DD",
"label": "Learn more"
},
{
"name": "Explore Data",
"icon": "data-explore",
"body": "The Exploration Page gives you insights and a clear overview under selected factors.",
"link": "/explorer",
"label": "Explore data"
},
{
"name": "Access Data",
"icon": "data-access",
"body": "Use our selected tool to filter out the data you need.",
"link": "/query",
"label": "Query data"
},
{
"name": "Submit Data",
"icon": "data-submit",
"body": "Submit Data based on the dictionary.",
"link": "/submission",
"label": "Submit data"
}
]
},
"navigation": {
"title": "NCI Data Commons Framework Services",
"items": [
{
"icon": "dictionary",
"link": "/DD",
"name": "Dictionary",
"tooltip": ""
},
{
"icon": "profile",
"link": "/identity",
"name": "Profile",
"tooltip": ""
}
]
},
"topBar": {
"items": [
{
"icon": "upload",
"link": "/submission",
"name": "Submit Data"
},
{
"link": "https://gen3.org/resources/user/",
"name": "Documentation"
}
]
},
"login": {
"title": "NCI Data Commons Framework Services",
"subTitle": "Explore, Analyze, and Share Data",
"text": "The vision of DCFS is to make it easier to develop, operate, and interoperate data commons, data clouds, knowledge bases, and other resources for managing, analyzing, and sharing research data that can be part of a large data commons ecosystem.",
"contact": "If you have any questions about access or the registration process, please contact ",
"email": "support@datacommons.io"
},
"certs": {
"security_quiz": {
"title": "BloodPAC User agreement",
"description": "The agreement on what you can and need to do in a Commons.",
"questions": [
{
"name": "Things you can do after registration",
"question": "As a registered user, I can do the following things without any problem. Is it true or not:",
"options": [
"Browse public Project",
"Upload file",
"Download file",
"Invite people"
],
"answer": 0,
"hint": "Some information about this question"
},
{
"name": "Things you need to do to become the registered user",
"question": "In order to be a register user, I must do the following things otherwise:",
"options": [
"Agree the user agreement",
"Accept a consent",
"None of them",
"Both of them"
],
"answer": 2,
"hint": "Some information about this question"
},
{
"name": "Things you can do with data",
"question": "How can I share data with other people according to the policy of the commons",
"options": [
"I can not share data",
"I can only share data with BPA memebers",
"I can share data with family",
"I can share data with my wife"
],
"answer": 1,
"hint": "Some information about this question"
}
]
}
},
"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"
}
],
"privacyPolicy": {
"text": "",
"routeHref": "",
"footerHref": "",
"file": ""
}
},
"requiredCerts": [],
"featureFlags": {
"explorer": true,
"analysis": false
},
"dataExplorerConfig": {
"arrangerConfig": {
"projectId": "search",
"graphqlField": "subject",
"index": "",
"nodeCountField": "node_id"
},
"charts": {
"project": {
"chartType": "count",
"title": "Projects"
},
"study": {
"chartType": "count",
"title": "Studies"
},
"file_type": {
"chartType": "count",
"title": "File Types"
},
"ethnicity": {
"chartType": "stackedBar",
"title": "Ethnicity"
},
"gender": {
"chartType": "pie",
"title": "Gender"
},
"race": {
"chartType": "pie",
"title": "Race"
},
"vital_status": {
"chartType": "bar",
"title": "Vital Status"
}
},
"filters": {
"tabs": [
{
"title": "Project",
"fields": [
"project",
"study"
]
},
{
"title": "Subject",
"fields": [
"race",
"ethnicity",
"gender",
"vital_status"
]
},
{
"title": "File",
"fields": [
"file_type"
]
}
]
},
"buttons": [
{
"enabled": true,
"type": "data",
"title": "Download All Data",
"leftIcon": "user",
"rightIcon": "download",
"fileName": "data.json"
},
{
"enabled": true,
"type": "manifest",
"title": "Download Manifest",
"leftIcon": "datafile",
"rightIcon": "download",
"fileName": "manifest.json"
}
],
"table": {
"enabled": true,
"fields": [
"project",
"study",
"race",
"ethnicity",
"gender",
"vital_status",
"whatever_lab_result_value",
"file_count",
"file_type",
"file_format"
]
}
},
"useArboristUI": false,
"showArboristAuthzOnProfile": false,
"showFenceAuthzOnProfile": true,
"componentToResourceMapping": {}
}