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ambassador:
enabled: true
image:
repository: quay.io/datawire/ambassador
tag: 1.4.2
arborist:
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist
tag: "2025.07"
externalSecrets:
dbcreds: qa-midrc-arborist-creds
audit:
enabled: true
externalSecrets:
auditG3auto: qa-midrc-audit-g3auto
dbcreds: qa-midrc-audit-creds
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service
tag: master
aws-es-proxy:
enabled: true
image:
repository: quay.io/cdis/aws-es-proxy
tag: v1.3.1
esEndpoint: vpc-devplanetv2-gen3-metadata-2-xkwr2f3gbxua5mqqi7rhnat4la.us-east-1.es.amazonaws.com
awshelper:
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper
tag: "2025.07"
dashboard:
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics
tag: "2025.07"
ohif-viewer:
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer
tag: gen3-v3.9.3
orthanc:
enabled: true
externalSecrets:
orthancS3G3Auto: qa-midrc-orthanc-s3-g3auto
dbcreds: qa-midrc-orthanc-s3-creds
dicom-server:
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-orthanc
tag: gen3-0.1.2
externalSecrets:
orthancG3Auto: qa-midrc-orthanc-g3auto
dbcreds: qa-midrc-orthanc-creds
fence:
usersync:
usersync: true
userYamlS3Path: s3://cdis-gen3-users/qa/user.yaml
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
externalSecrets:
createK8sGoogleAppSecrets: false
fenceConfig: qa-midrc-fence-config
fenceGoogleAppCredsSecret: qa-midrc-fence-google-app-creds
fenceGoogleStorageCredsSecret: qa-midrc-fence-google-storage-creds
fenceJwtKeys: qa-midrc-fence-jwt
dbcreds: qa-midrc-fence-creds
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence
tag: "2025.07"
fluentd:
enabled: true
image:
repository: fluent/fluentd-kubernetes-daemonset
tag: v1.15.3-debian-cloudwatch-1.0
gen3-workflow:
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-workflow
tag: test_plugin-support-with-logs
global:
crossplane:
enabled: true
oidcProviderUrl: "oidc.eks.us-east-1.amazonaws.com/id/F057519C0E32B7DE2580904C4007BB21"
accountId: "707767160287"
aws:
account: "707767160287"
awsEsProxyRole: devplanetv2--qa-midrc--es-access
enabled: true
secretStoreServiceAccount:
enabled: true
# roleArn: arn:aws:iam::707767160287:role/qa-midrc-external-secrets-sa
# temporarily using shared role
roleArn: arn:aws:iam::707767160287:role/devplanetv2-external-secrets-sa
wafv2:
enabled: true
wafAclArn: "arn:aws:wafv2:us-east-1:707767160287:regional/webacl/devplanetv2-waf/30660590-f707-4ecf-aeae-ddfbe381f388"
dev: false
dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.3.9/schema.json
dispatcherJobNum: "10"
environment: devplanetv2
externalSecrets:
deploy: true
hostname: qa-midrc.planx-pla.net
manifestGlobalExtraValues:
kube_bucket: kube-qaplanetv2-gen3
logs_bucket: logs-qaplanetv2-gen3
publicDataSets: true
tierAccessLevel: libre
tierAccessLimit: "2"
portalApp: gitops
postgres:
dbCreate: false
revproxyArn: arn:aws:acm:us-east-1:707767160287:certificate/520ede2f-fc82-4bb9-af96-4b4af7deabbd
guppy:
esEndpoint: http://elasticsearch:9200
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
authFilterField: auth_resource_path
configIndex: midrc_array-config
indices:
- index: midrc_case
type: case
- index: midrc_measurement
type: measurement
- index: midrc_annotation
type: annotation
- index: midrc_data_file
type: data_file
- index: midrc_imaging_study
type: imaging_study
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy
tag: "2025.07"
indexd:
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
externalSecrets:
serviceCreds: qa-midrc-indexd-service-creds
dbcreds: qa-midrc-indexd-creds
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd
tag: "2025.07"
manifestservice:
enabled: true
externalSecrets:
manifestserviceG3auto: qa-midrc-manifestservice-g3auto
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice
tag: "2025.07"
metadata:
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
externalSecrets:
metadataG3auto: qa-midrc-metadata-g3auto
dbcreds: qa-midrc-metadata-creds
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service
tag: "2025.07"
peregrine:
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
image:
repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine
tag: "2025.07"
portal:
autoscaling:
enabled: true
maxReplicas: 4
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
gitops:
css: |
:root {
--primary-color: #421C52;
--secondary-color: #421C52;
--primary-color_light: #B7474D;
--secondary-color_light: #90799b;
--g3-color__bg-cloud: #F5F5F5;
--g3-color__bg-coal: #4A4A4A;
--g3-color__gray: #606060;
--g3-color__lightgray: #9B9B9B;
--g3-color__smoke: #D1D1D1;
--g3-color__silver: #E7E7E7;
--g3-color__black: #000000;
--g3-color__white: #FFFFFF;
--g3-primary-btn__color: var(--g3-color__white);
--g3-primary-btn__bg-color: var(--secondary-color);
--g3-primary-btn__bg-color--hover: var(--secondary-color_light);
--g3-primary-btn__border-color: var(--g3-color__lightgray);
--g3-primary-btn__border-color--hover: var(--g3-color__gray);
--g3-primary-btn__border-color--active: var(--g3-color__lightgray);
--g3-secondary-btn__color: var(--g3-color__white);
--g3-secondary-btn__bg-color: var(--secondary-color);
--g3-secondary-btn__bg-color--hover: var(--secondary-color_light);
--g3-secondary-btn__border-color: var(--g3-color__lightgray);
--g3-secondary-btn__border-color--hover: var(--g3-color__gray);
--g3-secondary-btn__border-color--active: var(--g3-color__lightgray);
--g3-default-btn__color: var(--g3-color__gray);
--g3-default-btn__color--hover: var(--g3-color__black);
--g3-default-btn__color--active: var(--g3-color_lightgray);
--g3-default-btn__bg-color: var(--g3-color__white);
--g3-default-btn__border-color: var(--g3-color__gray);
--g3-default-btn__border-color--hover: var(--g3-color__black);
--g3-disabled-btn__color: var(--g3-color__lightgray);
--g3-disabled-btn__bg-color: var(--g3-color__white);
--g3-disabled-btn__border-color: var(--g3-color__silver);
--g3-dropdown-item__bg-color: var(--g3-color__gray);
--g3-dropdown-item__color: var(--g3-color__white);
--g3-dropdown-menu__border-color: var(--g3-color__gray);
--g3-footer-color: var(--g3-color__bg-coal);
--g3-font__medium-weight: 500;
--g3-font__semi-bold-weight: 600;
}
/* Buttons */
.data-dictionary__switch-button--active,
.popup__title {
background-color: var(--primary-color);
}
/* Nav Bars and Footer */
.top-bar,
.top-bar__header,
.top-icon-button.body-typo {
background-color: var(--secondary-color);
}
.top-bar__link {
border-right: 2px solid #fff;
}
.nav-button:hover,
.button-active {
border-bottom: 3px solid var(--primary-color);
}
.nav-bar__link--right,
.nav-bar__link--right:last-child {
border: none;
}
.footer-container {
background-color: var(--secondary-color);
}
.footer__nav {
background-color: var(--secondary-color);
align-items: center;
}
.footer__version-area {
width: 300px;
}
.footer__logo-area {
order: -1;
width: auto;
}
/* Data Explorer */
.aggregation-card .bucket-item .bucket-count {
color: var(--secondary-color);
}
.aggregation-card input[type='checkbox']:checked {
background: var(--secondary-color);
}
.g3-single-select-filter__checkbox:checked {
background: var(--primary-color);
}
/* .input-range__track--active,
.rc-slider-track,
.g3-single-select-filter__count .g3-icon--under {
background-color: var(--primary-color);
} */
/* Charts */
tspan.special-number,
.special-number,
.form-special-number {
color: var(--primary-color);
}
.special-number {
fill: var(--primary-color);
}
.data-explorer__charts tspan.special-number,
.data-explorer__charts .special-number,
.data-explorer__charts .form-special-number {
color: var(--secondary-color);
}
.data-explorer__charts .special-number {
fill: var(--secondary-color);
}
/* MIDRC Index Changes */
.index-button-bar {
width: 100%;
background-color: var(--g3-color__white);
}
.index-button-bar__thumbnail-button {
background-color: inherit;
border: none;
}
.index-button-bar__icon {
filter: hue-rotate(45deg);
}
.index-button-bar__item, .index-button-bar__thumbnail-title {
display: none;
}
@media screen and (max-width: 1170px) {
.index-button-bar {
padding: 0 10%;
}
}
/* MIDRC Submission Page Changes */
.project-dashboard__title {
display: none;
}
.submission-header {
display: none;
}
json: |
{
"gaTrackingId": "UA-119127212-1",
"graphql": {
"boardCounts": [
{
"graphql": "_case_count",
"name": "Case",
"plural": "Cases"
},
{
"graphql": "_imaging_study_count",
"name": "Imaging Study",
"plural": "Imaging Studies"
},
{
"graphql": "_ct_series_file_count",
"name": "Computed Tomography (CT) Series",
"plural": "Computed Tomography (CT) Series"
},
{
"graphql": "_dx_series_file_count",
"name": "Digital X-ray (DX) Series",
"plural": "Digital X-ray (DX) Series"
},
{
"graphql": "_cr_series_file_count",
"name": "Computed Radiography (CR) Series",
"plural": "Computed Radiography (CR) Series"
},
{
"graphql": "_mr_series_file_count",
"name": "Magnetic Resonance (MR) Series",
"plural": "Magnetic Resonance (MR) Series"
}
],
"chartCounts": [],
"projectDetails": "boardCounts"
},
"resourceBrowser": {
"title": "Jupyter Notebook Tutorials",
"public": true,
"description": "The Jupyter notebooks contained in this notebook viewer pull data from various sources to generate and output useful tables, charts, graphs, and models. Each notebook is static, meaning the data being used by the notebooks is not updated in real time. Executable versions of these notebooks can be downloaded from <a href='https://github.com/MIDRC/tutorial_notebooks'> MIDRC's GitHub Repository</a>. If you’d like to browse the machine learning-related algorithms and code being developed by MIDRC, please visit <a href='https://midrc.org/algorithms'>the algorithms page</a> on our website.",
"resources": [
{
"title": "Cohort Building Using LOINC Terms",
"description": "This notebook demonstrates how to build a cohort of patients based on LOINC terms derived by harmonizing original DICOM study descriptions, modalities, and body parts examined using the LOINC playbook. Imaging study DICOM data element harmonization using the LOINC playbook is the result of an effort by MIDRC's Technology and Development Project 3b (TDP3b) and the Collaborative Research Project 12 (CRP-12). Links to the GitHub repository where the code for performing LOINC harmonization is maintained is included in the notebook.",
"imageUrl": "/dashboard/Public/notebooks/Cohort_Building_Using_LOINC_Terms.png",
"link": "/dashboard/Public/notebooks/Cohort_Building_Using_LOINC_Terms.html"
},
{
"title": "Build a Patient Cohort and Access Chest CT Scans and Annotations",
"description": "This notebook demonstrates how to build a cohort of MIDRC patients based on clinical and demographic data and then access all Chest CT scans and any related annotations.",
"imageUrl": "/dashboard/Public/notebooks/Chest_CT_Images_for_Cohort.png",
"link": "/dashboard/Public/notebooks/Chest_CT_Images_for_Cohort.html"
},
{
"title": "Access Files for Specific Case IDs",
"description": "This notebook demonstrates how to build a cohort of MIDRC patients based on clinical and demographic data and then obtain a file download manifest for x-ray and annotation files related to that cohort.",
"imageUrl": "/dashboard/Public/notebooks/Access_Files_for_Specific_Case_IDs.png",
"link": "/dashboard/Public/notebooks/Access_Files_for_Specific_Case_IDs.html"
},
{
"title": "Cohort Selection Using Temporal COVID-19 Test Data",
"description": "This tutorial demonstrates how to use the MIDRC data commons' APIs to access imaging study and COVID-19 test data, how to use temporal properties in those data to select a cohort of COVID-19 positive imaging studies, and how to access those image files using the Gen3 SDK.",
"imageUrl": "/dashboard/Public/notebooks/Cohort_selection_Using_MIDRC_Temporal_COVID_Test_Data.png",
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"title": "Querying and Accessing MIDRC Data",
"description": "This notebook is intended to demonstrate a variety of ways to access file objects and structured data, also known as metadata, in the MIDRC Data Commons using MIDRC APIs.",
"imageUrl": "/dashboard/Public/notebooks/Querying_and_Accessing_MIDRC_Data.png",
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"title": "Exploring MIDRC CT Scans",
"description": "In this demo we will review how to import MIDRC imaging data, how to convert CT scan images from dicom (dcm) formats to png and jpeg formats, and how to view these CT scan images. This demo will also show how to extract file and patient metadata from the header of dicom (dcm) files.",
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"title": "MIDRC Open-R1 Clinical Data Analysis",
"description": "In this notebook we will visualize the distribution of subjects accross a variety demographics and their COVID-19 status in the Open-R1 dataset from The Medical Imaging and Data Resource Center.",
"imageUrl": "/dashboard/Public/notebooks/MIDRC_Clinical_Data.png",
"link": "/dashboard/Public/notebooks/MIDRC_Clinical_Data.html"
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{
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"description": "This notebook demonstrates how to build a cohort of severe COVID-19 cases using patient clinical data and AI research-based annotations in the MIDRC data commons. Our goal is to download structured data and files for 2 related cohorts: 1) severe COVID cases and 2) a control cohort of non-severe COVID cases. Additionally, we want the cohorts to be somewhat balanced and matched in terms of the demographics: age, sex, race, and ethnicity.",
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"title": "Cohort Building Using Queries of the MIDRC Data Commons",
"description": "This notebook briefly demonstrates how to use the MIDRC open APIs to build a cohort of MIDRC imaging studies using patient clinical data and AI-research-based annotations in the MIDRC data commons and then access and view the X-ray image files associated with those imaging studies.",
"imageUrl": "/dashboard/Public/notebooks/MIDRC_Cohort_Building-DLL_RSNA_2023.png",
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"12. THE MIDRC DATA IS PROVIDED ON AN ”AS IS”, “WHERE IS” BASIS. THE UNIVERSITY MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THE UNIVERSITY WILL HAVE NO LIABILITY WHATSOEVER ARISING FROM YOUR ACCESS OR USE OF THE MIDRC DATA, INCLUDING WITHOUT LIMITATION ANY LIABILITY ARISING FROM LOST PROFITS, COSTS OF PROCURING SUBSTITUTE GOODS OR SERVICES, LOST BUSINESS, ENHANCED DAMAGES FOR INTELLECTUAL PROPERTY INFRINGEMENT, OR FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL, PUNITIVE, OR OTHER SPECIAL DAMAGES SUFFERED BY YOU OR YOUR SUBLICENSEES, JOINT VENTURES, OR AFFILIATES ARISING OUT OF OR RELATED TO THE AGREEMENT AND NON-EXCLUSIVE LICENSES GRANTED THEREUNDER FOR ALL CAUSES OF ACTION OF ANY KIND (INCLUDING TORT, CONTRACT, NEGLIGENCE, STRICT LIABILITY AND BREACH OF WARRANTY) EVEN IF THE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. ALSO, UNIVERSITY WILL NOT BE LIABLE FOR ANY DIRECT DAMAGES SUFFERED BY YOU OR YOUR SUBLICENSEES, JOINT VENTURES, OR AFFILIATES ARISING OUT OF OR RELATED TO YOUR USE OF THE MIDRC DATA.",
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