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ocshawncmlsnsnyk-botShawn O'Connorcraigrbarnes
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Chore/upstreem sync (#58)
* 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 * update gen3 to 0.11.18 * update gen3 to 0.11.19 and add footer links * update to Gen3 FEF 0.11.43 (uc-cdis#127) * add GradioApp support (uc-cdis#128) * add GradioApp support * fix default * update dependencies * update more dependencies * update more dependencies * add the hugging face apps (uc-cdis#129) * update tailwind paths for Gen3/frontend (uc-cdis#136) * fix default * update package-lock * fix build error * remove gradio * remove older tailwind path * update gen3 version and package lock * update gen3 to 0.11.47 * update gen3 to 0.11.48 remove unneeded cookies-next * place favicon back '' * fix build errors * fix build errors by sorting out dependencies --------- 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: Craig Barnes <craig.barnes@intelligentlight.com>
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‎.env.development‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=vpodcqa
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NEXT_PUBLIC_GEN3_API=https://qa-vpodc.planx-pla.net
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NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010
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NEXT_PUBLIC_DATACOMMONS="vpodc_data_commons"

‎Dockerfile‎

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@@ -12,7 +12,7 @@ COPY ./public ./public
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COPY ./config ./config
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COPY ./start.sh ./
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COPY ./next-custom-image-loader.js ./
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RUN npm install @swc/core@1.13.5 @napi-rs/magic-string && \
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RUN npm install @swc/core @napi-rs/magic-string && \
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npm run build
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# Production stage

‎config/vpodcprod/dataLibrary.json‎

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{
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"useAPI": false,
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"actions": [
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{
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"id": "exportTerra",
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"label": "Export: Terra",
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"rightIcon" : "gen3:send",
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"buttonLabel" : "Export",
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"actionFunction" : "export-pfb-to-url",
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"parameters" : {
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"targetURLTemplate" : "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc"
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},
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"itemRules": [
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{
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"field": "type",
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"operator": "equals",
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"value": "GA4GH_DRS",
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"errorMessage": "file type must be GA4GH_DRS"
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}
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],
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"groupRules": [
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{
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"field": "type",
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"operator": "count",
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"value": "GA4GH_DRS",
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"total": 1,
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"errorMessage": "Only 1 GA4GH_DRS can be selected"
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}
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]
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},
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{
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"id": "exportTo7Bridges",
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"label": "Export: Seven Bridges",
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"rightIcon" : "gen3:send",
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"buttonLabel" : "Export",
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"actionFunction" : "export-pfb-to-url",
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"parameters" : {
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"targetURLTemplate" : "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc"
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},
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"itemRules": [
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{
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"field": "type",
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"operator": "equals",
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"value": "GA4GH_DRS",
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"errorMessage": "file type must be GA4GH_DRS"
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}
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],
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"groupRules": [
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{
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"field": "type",
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"operator": "count",
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"value": "GA4GH_DRS",
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"total": 1,
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"errorMessage": "only 1 GA4GH_DRS can be selected"
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}
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]
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}
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]
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}

‎config/vpodcprod/modals.json‎

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"DATA USE AGREEMENT – COMMERCIAL USE PERMITTED",
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"This Data Use Agreement (this “Agreement”) is by and between you or the entity you represent (“you”) and the University of Chicago (the “University”) and governs your access to and use of the deidentified imaging and associated demographic and clinical data provided to you by the University. By accessing, using, or downloading any data, you are agreeing to be bound by the terms and conditions of this Agreement. If you are entering into this Agreement for an entity, such as the company you work for, you represent and warrant that you have legal authority to bind that entity",
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"1. The University may terminate this Agreement at any time upon notice to you. The University shall have no liability in the event of any such termination. Upon such termination, the University may direct that you immediately return or destroy all copies of any data and, upon the University’s request, you will certify the foregoing to the University in writing."
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]
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],
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"className" : "text-base-contrast-max"
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},
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"expireDays": 365,
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"showOnlyOnLogin": true
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"showOnlyOnLogin": false
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}
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}

‎config/vpodcqa/dataLibrary.json‎

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{
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"useAPI": false,
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"actions": [
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{
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"id": "exportTerra",
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"label": "Export: Terra",
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"rightIcon" : "gen3:send",
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"buttonLabel" : "Export",
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"actionFunction" : "export-pfb-to-url",
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"parameters" : {
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"targetURLTemplate" : "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc"
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},
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"itemRules": [
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{
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"field": "type",
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"operator": "equals",
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"value": "GA4GH_DRS",
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"errorMessage": "file type must be GA4GH_DRS"
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}
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],
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"groupRules": [
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{
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"field": "type",
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"operator": "count",
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"value": "GA4GH_DRS",
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"total": 1,
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"errorMessage": "Only 1 GA4GH_DRS can be selected"
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}
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]
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},
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{
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"id": "exportTo7Bridges",
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"label": "Export: Seven Bridges",
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"rightIcon" : "gen3:send",
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"buttonLabel" : "Export",
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"actionFunction" : "export-pfb-to-url",
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"parameters" : {
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"targetURLTemplate" : "https://platform.sb.biodatacatalyst.nhlbi.nih.gov/import/pfb?URL={{PRESIGNED_URL}}&source=bdc"
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},
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"itemRules": [
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{
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"field": "type",
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"operator": "equals",
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"value": "GA4GH_DRS",
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"errorMessage": "file type must be GA4GH_DRS"
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}
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],
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"groupRules": [
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{
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"field": "type",
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"operator": "count",
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"value": "GA4GH_DRS",
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"total": 1,
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"errorMessage": "only 1 GA4GH_DRS can be selected"
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}
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]
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}
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]
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}

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