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craigrbarnescmlsnsnyk-botShawn O'Connorocshawn
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Chore/update 0.11.11 (#25)
* fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (#84) * update to @gen3/ff 0.10.85 (#85) * Update README.md (#86) add unrelated-histories information * Fix docker start (#88) * fix Docker not starting * fix Docker not starting * update env files (#89) * Release 0.10.89 (#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (#93) * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * update to 0.10.91 (uc-cdis#96) * fix version to 0.10.91 (uc-cdis#97) * update to 0.10.92 (uc-cdis#104) * update to node 22.11, gen3FF 0.10.94 (uc-cdis#107) * update git node version * update gen3 to 0.11.11 * add favicon (uc-cdis#109) * add favicon * add favicon --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Add Datadog/remove faro (uc-cdis#105) * add Datadog/remove faro * remove Grafana * first update * update package-lock * first update * update explorer config --------- Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com>
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‎.env.development‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
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NEXT_PUBLIC_GEN3_API=https://qa-vpodc.planx-pla.net
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NEXT_PUBLIC_GEN3_API=https://localhost:3010
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NEXT_PUBLIC_DATACOMMONS="vpodc_data_commons"

‎.env.production‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
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NEXT_PUBLIC_DATACOMMONS="vpodc_data_commons"

‎.github/workflows/ci.yaml‎

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- uses: actions/checkout@v2
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- uses: actions/setup-node@v4.1.0
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with:
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node-version: 20.17.0
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node-version: 22.11.0
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- name: Get Version
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run: npm -v
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- name: Install modules

‎.nvmrc‎

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v20.17.0
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v22.11.0

‎Dockerfile‎

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# docker build -t ff .
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# docker run -p 3000:3000 -it ff
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# Build stage
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FROM node:20-slim AS builder
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FROM node:22-slim AS builder
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WORKDIR /gen3
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npm run build
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# Production stage
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FROM node:20-slim AS runner
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FROM node:22-slim AS runner
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WORKDIR /gen3
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‎config/gen3/explorer.json‎

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[
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{
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"tabTitle": "Patients",
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"tabTitle": "Cases",
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"charts": {},
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"filters": {
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"tabs": [
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{
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"title": "Demographic",
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"fields": [
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"project_id",
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"Days_To_Birth",
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"Days_To_Death",
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"DeceasedFlag",
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"Ethnicity",
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"Gender",
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"Race"
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]
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},
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{
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"title": "ActionableMutations",
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"fields": [
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"project_id",
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"ActionableMutations.Lab",
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"ActionableMutations.Gene",
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"ActionableMutations.DaysFromAnchorDateToBxDate"
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]
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},
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{
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"title": "Oncology Primary",
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"fields": [
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"project_id",
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"Oncology_Primary.Multiplicitycounter",
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"Oncology_Primary.ICDOSite",
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"Oncology_Primary.Radiation",
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"Oncology_Primary.Chemotherapy",
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"Oncology_Primary.DaysFromAnchorDateToDiagnosisDate",
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"Oncology_Primary.Gradedifferentiation",
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"Oncology_Primary.Laterality",
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"Oncology_Primary.Stagegroupbest",
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"Oncology_Primary.RadiationsurgerySequence",
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"Oncology_Primary.Histologyicdo3X",
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"Oncology_Primary.Lymphvascularinvasionl",
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"Oncology_Primary.SeerSummaryStage2000",
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"Oncology_Primary.PhysiciansStage",
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"Oncology_Primary.DaysFromAnchorDateToMostdefinitivesurgDate",
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"Oncology_Primary.ChemotherapyFac",
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"Oncology_Primary.TumorSize",
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"Oncology_Primary.SequenceNumber"
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"project_id"
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]
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}
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]
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},
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"buttons": [
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{
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"enabled": false,
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"type": "manifest",
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"title": "Download Manifest",
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"leftIcon": "datafile",
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"rightIcon": "download",
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"fileName": "manifest.json"
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}
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],
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"table": {
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"enabled": true,
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"fields": [
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"project_id",
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"Race",
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"Ethnicity",
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"Gender",
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"ActionableMutations.Lab",
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"Oncology_Primary.Multiplicitycounter",
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"Oncology_Primary.ICDOSite"
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"_case_id",
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"submitter_id"
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]
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},
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"guppyConfig": {
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"dataType": "patients",
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"nodeCountTitle": "Patients",
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"dataType": "case",
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"nodeCountTitle": "Case",
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"fieldMapping": [],
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"manifestMapping": {
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"resourceIndexType": "file",
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"resourceIdField": "object_id",
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"referenceIdFieldInResourceIndex": "case_id",
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"referenceIdFieldInDataIndex": "Chicago_ID"
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"resourceIndexType": "data_file",
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"resourceIdField": "_imaging_file_id",
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"referenceIdFieldInResourceIndex": "_case_id",
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"referenceIdFieldInDataIndex": "_case_id"
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}
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}
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},
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{
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"title": "Files",
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"fields": [
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"project_id",
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"data_type",
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"data_category",
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"data_format",
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"file_size"
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"data_type",
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"program_name",
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"project_code",
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"project_id"
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]
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}
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]
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},
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"buttons": [
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{
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"enabled": false,
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"type": "file-manifest",
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"title": "Download Manifest",
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"leftIcon": "datafile",
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"rightIcon": "download",
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"fileName": "manifest.json"
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}
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],
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"table": {
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"enabled": true,
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"fields": [
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"submitter_id",
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"data_type",
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"_case_id",
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"_imaging_file_id",
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"data_category",
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"data_format",
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"data_type",
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"file_name",
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"file_size",
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"object_id"
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"md5sum",
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"program_name",
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"project_code",
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"project_id",
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"submitter_id"
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]
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},
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"guppyConfig": {
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"dataType": "file",
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"nodeCountTitle": "Files",
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"dataType": "data_file",
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"nodeCountTitle": "File",
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"fieldMapping": [],
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"manifestMapping": {
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"resourceIndexType": "file",
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"resourceIdField": "object_id",
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"referenceIdFieldInResourceIndex": "object_id",
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"referenceIdFieldInDataIndex": "Chicago_ID"
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"resourceIndexType": "case",
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"resourceIdField": "_imaging_file_id",
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"referenceIdFieldInResourceIndex": "_case_id",
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"referenceIdFieldInDataIndex": "_imaging_file_id"
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}
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}
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}

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