├── .circleci ├── config.yml └── initdb.sql ├── .dockerignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── 1-bug_report.yml │ ├── 2-feature_request.yml │ ├── 3-documentation_request.yml │ └── config.yml ├── pull_request_template.md └── workflows │ └── main.yml ├── .gitignore ├── .sonarcloud.properties ├── .travis.yml ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── ROADMAP.md ├── SECURITY.md ├── WALKTHROUGH.md ├── apps ├── .eslintrc.js ├── .gitignore ├── .prettierignore ├── .prettierrc.js ├── .turboignore ├── README.md ├── aggregates │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── src │ │ ├── App.vue │ │ ├── interfaces │ │ │ └── types.ts │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ └── index.ts │ │ └── views │ │ │ └── view-dashboard.vue │ ├── tsconfig.json │ └── vite.config.js ├── audit-ci.jsonc ├── build.gradle ├── cat.env-sample ├── catalogue │ ├── .env-sample │ ├── .gitignore │ ├── Dockerfile │ ├── README.md │ ├── __screenshots__ │ │ ├── should-show-the-alt-logo.spec.ts │ │ │ └── should-show-the-alt-logo-1.png │ │ └── theme.spec.ts │ │ │ ├── landing-page-aumc-1.png │ │ │ ├── landing-page-molgenis-1.png │ │ │ └── landing-page-umcg-1.png │ ├── app │ │ ├── app.vue │ │ ├── components │ │ │ ├── AppWrapper.vue │ │ │ ├── BottomModal.vue │ │ │ ├── ButtonGroup.vue │ │ │ ├── CatalogueItemList.vue │ │ │ ├── CatalogueListItem.vue │ │ │ ├── CategoriesTree.vue │ │ │ ├── CodeBlock.vue │ │ │ ├── CollectionEventDisplay.vue │ │ │ ├── ContactCard.vue │ │ │ ├── ContactCardList.vue │ │ │ ├── ContactForm.vue │ │ │ ├── DatasetDisplay.vue │ │ │ ├── FilterWell.vue │ │ │ ├── HamburgerMenu.vue │ │ │ ├── HorizontalScrollHelper.vue │ │ │ ├── HyperLink.vue │ │ │ ├── ListCollapsible.vue │ │ │ ├── ListCollapsibleItemChild.vue │ │ │ ├── ListCollapsibleItemParent.vue │ │ │ ├── ListTree.vue │ │ │ ├── ListTreeItem.vue │ │ │ ├── MainNavigation.vue │ │ │ ├── NavigationIconsMobile.vue │ │ │ ├── NetworkCard.vue │ │ │ ├── OrganisationCard.vue │ │ │ ├── OrganizationSideContent.vue │ │ │ ├── ReferenceCard.vue │ │ │ ├── ReferenceCardList.vue │ │ │ ├── ResourceCard.vue │ │ │ ├── SearchBar.vue │ │ │ ├── SearchResults.vue │ │ │ ├── SearchResultsCount.vue │ │ │ ├── SearchResultsList.vue │ │ │ ├── SearchResultsViewTabs.vue │ │ │ ├── SearchResultsViewTabsMobile.vue │ │ │ ├── SettingsMessage.vue │ │ │ ├── SideNavigation.vue │ │ │ ├── SubpopulationDisplay.vue │ │ │ ├── VariableCard.vue │ │ │ ├── VariableDisplay.vue │ │ │ ├── content │ │ │ │ ├── ContentBlockCatalogues.vue │ │ │ │ ├── ContentBlockCollectionEvents.vue │ │ │ │ ├── ContentBlockContact.vue │ │ │ │ ├── ContentBlockData.vue │ │ │ │ ├── ContentBlockIntro.vue │ │ │ │ ├── ContentBlockNetwork.vue │ │ │ │ ├── ContentBlockOrganisations.vue │ │ │ │ ├── ContentBlockPartners.vue │ │ │ │ ├── ContentBlockPublications.vue │ │ │ │ ├── ContentBlockSubpopulations.vue │ │ │ │ ├── ContentBlockVariables.vue │ │ │ │ ├── Mapped.vue │ │ │ │ ├── Ontology.vue │ │ │ │ ├── TreeNode.vue │ │ │ │ └── cohort │ │ │ │ │ └── GeneralDesign.vue │ │ │ ├── filter │ │ │ │ ├── Container.vue │ │ │ │ ├── List.vue │ │ │ │ ├── Ontology.vue │ │ │ │ └── Sidebar.vue │ │ │ ├── footer │ │ │ │ └── FooterVersion.vue │ │ │ ├── harmonisation │ │ │ │ ├── HarmonisationGridPerVariable.vue │ │ │ │ ├── HarmonisationLegend.vue │ │ │ │ ├── HarmonisationLegendDetailed.vue │ │ │ │ ├── HarmonisationLegendMatrix.vue │ │ │ │ ├── HarmonisationListPerVariable.vue │ │ │ │ ├── HarmonisationStatus.vue │ │ │ │ ├── HarmonisationStatusIcon.vue │ │ │ │ ├── HarmonisationTable.vue │ │ │ │ ├── HarmonisationTableCell.vue │ │ │ │ ├── HarmonisationTableCellAvailableIcon.vue │ │ │ │ ├── HarmonisationTableCellStatusIcon.vue │ │ │ │ └── VariableDetails.vue │ │ │ ├── header │ │ │ │ ├── Catalogue.vue │ │ │ │ └── Global.vue │ │ │ ├── landing │ │ │ │ ├── CardPrimary.vue │ │ │ │ ├── CardSecondary.vue │ │ │ │ ├── Central.vue │ │ │ │ ├── CohortsOnly.vue │ │ │ │ ├── Primary.vue │ │ │ │ └── Secondary.vue │ │ │ ├── layouts │ │ │ │ ├── DetailPage.vue │ │ │ │ ├── LandingPage.vue │ │ │ │ └── SearchPage.vue │ │ │ ├── notification │ │ │ │ └── NotificationModal.vue │ │ │ ├── store │ │ │ │ ├── HeaderButton.vue │ │ │ │ ├── Modal.vue │ │ │ │ ├── ModalResourceList.vue │ │ │ │ └── ModalResourceListItem.vue │ │ │ └── table │ │ │ │ ├── Content.vue │ │ │ │ └── Sticky.vue │ │ ├── composables │ │ │ ├── assetLoader.ts │ │ │ ├── fetchGql.ts │ │ │ ├── fetchMetadata.ts │ │ │ ├── fetchOntology.ts │ │ │ ├── fetchSetting.ts │ │ │ ├── sendContactForm.ts │ │ │ ├── useBannerData.ts │ │ │ ├── useGqlFetch.ts │ │ │ ├── useHeaderData.ts │ │ │ ├── useQueryParams.ts │ │ │ └── useTheme.ts │ │ ├── error.vue │ │ ├── gql │ │ │ ├── collectionEvent.js │ │ │ ├── collectionEvents.js │ │ │ ├── datasetDetails.js │ │ │ ├── datasets.js │ │ │ ├── fragments │ │ │ │ ├── file.js │ │ │ │ ├── mappings.js │ │ │ │ └── ontology.js │ │ │ ├── metadata.js │ │ │ ├── resource.js │ │ │ ├── resources.js │ │ │ ├── subpopulation.js │ │ │ ├── subpopulations.js │ │ │ ├── variable.ts │ │ │ └── variables.js │ │ ├── pages │ │ │ ├── [catalogue] │ │ │ │ ├── [resourceType] │ │ │ │ │ ├── [resource] │ │ │ │ │ │ ├── collection-events │ │ │ │ │ │ │ └── [collectionevent].vue │ │ │ │ │ │ ├── index.vue │ │ │ │ │ │ ├── subpopulations │ │ │ │ │ │ │ └── [subpopulation].vue │ │ │ │ │ │ └── variables │ │ │ │ │ │ │ └── [variable].vue │ │ │ │ │ └── index.vue │ │ │ │ ├── about.vue │ │ │ │ ├── index.vue │ │ │ │ └── variables │ │ │ │ │ ├── [variable].vue │ │ │ │ │ └── index.vue │ │ │ ├── about.vue │ │ │ ├── index.vue │ │ │ └── tables.vue │ │ ├── plugins │ │ │ ├── analytics.client.ts │ │ │ └── scrollPosition.client.ts │ │ ├── stores │ │ │ └── useDatasetStore.ts │ │ └── utils │ │ │ ├── buildQueryFilter.test.ts │ │ │ ├── buildQueryFilter.ts │ │ │ ├── dateUtils.ts │ │ │ ├── debugUtils.ts │ │ │ ├── errorLogger.test.ts │ │ │ ├── errorLogger.ts │ │ │ ├── filterUtils.test.ts │ │ │ ├── filterUtils.ts │ │ │ ├── harmonisation.ts │ │ │ ├── headingUtils.test.ts │ │ │ ├── headingUtils.ts │ │ │ ├── ontologyUtils.test.ts │ │ │ ├── ontologyUtils.ts │ │ │ ├── treeHelpers.ts │ │ │ ├── urlHelpers.test.ts │ │ │ ├── urlHelpers.ts │ │ │ └── variableUtils.ts │ ├── graphql.config.json │ ├── interfaces │ │ ├── catalogue.ts │ │ └── types.ts │ ├── nuxt.config.ts │ ├── package.json │ ├── playwright.config.ts │ ├── public │ │ └── _nuxt-styles │ │ │ ├── css │ │ │ └── main.css │ │ │ ├── fonts │ │ │ ├── BebasNeue-Regular.woff2 │ │ │ ├── IBMPlexSans-Bold.woff2 │ │ │ ├── IBMPlexSans-BoldItalic.woff2 │ │ │ ├── IBMPlexSans-Italic.woff2 │ │ │ └── IBMPlexSans-Regular.woff2 │ │ │ ├── img │ │ │ ├── aumc.ico │ │ │ ├── hdsu.ico │ │ │ ├── molgenis-logo-blue-small.svg │ │ │ ├── molgenis.ico │ │ │ └── umcg.ico │ │ │ └── logos │ │ │ ├── HDSU-logo-voor-in-presentaties-1536x188.png │ │ │ ├── HDSU-logo.svg │ │ │ ├── UMCG_Logo_2025_blauw.svg │ │ │ └── UMCGkort.woordbeeld.svg │ ├── router.options.ts │ ├── sample-docker-run.sh │ ├── sample-nginx.conf │ ├── tailwind-config.ts │ ├── tests │ │ ├── about-link-visibility.spec.ts │ │ ├── aggregates-url.spec.ts │ │ ├── catalogue-description.spec.ts │ │ ├── catalogue-test_1.spec.ts │ │ ├── dataset-details.spec.ts │ │ ├── harmonization-status-show-on-variable-detail-page.spec.ts │ │ ├── header-items.spec.ts │ │ ├── keep-filter-on-pagination-change.spec.ts │ │ ├── navigate-to-next-page-on-cohorts-list-page.spec.ts │ │ ├── network-of-networks.spec.ts │ │ ├── network-resource-list-item-detail-link.spec.ts │ │ ├── reset-page-on-filter-change.spec.ts │ │ ├── retain-filter-state.spec.ts │ │ ├── search-results-count.spec.ts │ │ ├── should-show-the-alt-logo.spec.ts │ │ ├── show-landing-page.spec.ts │ │ ├── sitemap.spec.ts │ │ ├── theme.spec.ts │ │ └── variable-cohort-filter.spec.ts │ ├── tsconfig.json │ └── vitest.config.js ├── central │ ├── .gitignore │ ├── README.md │ ├── favicon.ico │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── Groups.vue │ │ │ ├── LastUpdateField.vue │ │ │ ├── SchemaCreateModal.vue │ │ │ ├── SchemaDeleteModal.vue │ │ │ ├── SchemaEditModal.vue │ │ │ └── admin │ │ │ │ ├── Admin.vue │ │ │ │ ├── EditTemplate.vue │ │ │ │ ├── ManagePrivacyPolicy.vue │ │ │ │ ├── ManageSettings.vue │ │ │ │ ├── ManageTemplates.vue │ │ │ │ ├── ManageUsers.vue │ │ │ │ └── TemplateEditButton.vue │ │ └── main.js │ └── vite.config.js ├── cranio-provider │ ├── README.md │ ├── index.html │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── banner-about.png │ │ │ ├── banner-diagnoses.jpg │ │ │ ├── ern-cranio-logo.png │ │ │ ├── example-provider-header.jpg │ │ │ ├── favicon.ico │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── AppFooter.vue │ │ │ ├── DashboardChartLayout.vue │ │ │ ├── LoadingBlock.vue │ │ │ ├── ProviderDashboard.vue │ │ │ ├── ProviderSidebar.vue │ │ │ └── ValueShowcase.vue │ │ ├── data │ │ │ └── props.js │ │ ├── main.ts │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── types │ │ │ ├── app.ts │ │ │ ├── index.ts │ │ │ └── schema.ts │ │ ├── utils │ │ │ ├── clpUtils.ts │ │ │ ├── csSurgicalUtils.ts │ │ │ ├── generateAxisTicks.ts │ │ │ ├── generateColorPalette.ts │ │ │ ├── getCranioSchemaNames.ts │ │ │ ├── getDashboardData.ts │ │ │ ├── getGeneticHearingLossData.ts │ │ │ ├── getOrganisation.ts │ │ │ ├── getSchemaName.ts │ │ │ ├── index.ts │ │ │ └── parseChartTitle.ts │ │ └── views │ │ │ ├── cleft_lip_palate │ │ │ ├── all_centers.vue │ │ │ └── your_center.vue │ │ │ ├── craniosynostosis │ │ │ ├── all_centers │ │ │ │ ├── general.vue │ │ │ │ └── surgical.vue │ │ │ └── your_center │ │ │ │ ├── general.vue │ │ │ │ └── surgical.vue │ │ │ ├── genetic_hearing_loss │ │ │ ├── all_centers.vue │ │ │ └── your_center.vue │ │ │ ├── provider-overview.vue │ │ │ └── view-404.vue │ ├── tests │ │ ├── generateAxisTicks.test.ts │ │ ├── index.test.ts │ │ └── parseChartTitle.test.ts │ ├── tsconfig.json │ └── vite.config.js ├── cranio-public │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── banner-about.png │ │ │ ├── banner-diagnoses.jpg │ │ │ ├── ern-cranio-logo.png │ │ │ ├── example-provider-header.jpg │ │ │ ├── favicon.ico │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── AppFooter.vue │ │ │ └── breadcrumbs.vue │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ └── views │ │ │ ├── view-about.vue │ │ │ ├── view-documents.vue │ │ │ ├── view-home.vue │ │ │ ├── view-providers.vue │ │ │ └── view-public-dashboard.vue │ └── vite.config.js ├── dev-proxy.config.js ├── directory │ ├── .babelrc │ ├── .eslintrc.cjs │ ├── .gitignore │ ├── README.md │ ├── dev-index.html │ ├── index.html │ ├── package.json │ ├── playwright.config.ts │ ├── public │ │ ├── bbmri-darkmode-favicon.ico │ │ ├── bbmri-lightmode-favicon.ico │ │ └── img │ │ │ ├── bacteria.jpg │ │ │ ├── bacterial-blue.png │ │ │ ├── bbmri-eric-logo.png │ │ │ ├── bbmri-nl-logo.png │ │ │ ├── blood-sample-blue.png │ │ │ ├── brain-blue.png │ │ │ ├── coronavirus-blue.png │ │ │ ├── heart-blue.png │ │ │ ├── infected-blue.png │ │ │ ├── lab.jpg │ │ │ ├── lab2.jpg │ │ │ ├── metabolism-blue.png │ │ │ ├── microscope.jpg │ │ │ ├── pediatrics-blue.png │ │ │ ├── ribbon-blue.png │ │ │ ├── statistics-blue.png │ │ │ └── work-programme.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── Button.vue │ │ │ ├── Card.vue │ │ │ ├── CardItem.vue │ │ │ ├── CheckBox.vue │ │ │ ├── Error.vue │ │ │ ├── ImageCard.vue │ │ │ ├── Tabs.vue │ │ │ ├── biobankcards-components │ │ │ │ ├── BiobankCard.vue │ │ │ │ ├── CollectionsSection.vue │ │ │ │ ├── HeaderSection.vue │ │ │ │ ├── MatchesOn.vue │ │ │ │ ├── OrganizationSection.vue │ │ │ │ ├── PaginationBar.vue │ │ │ │ ├── ResultHeader.vue │ │ │ │ ├── Service.vue │ │ │ │ └── ServiceSection.vue │ │ │ ├── cart │ │ │ │ ├── CartItem.vue │ │ │ │ └── NegotiatorSelection.vue │ │ │ ├── checkout-components │ │ │ │ ├── CheckOut.vue │ │ │ │ └── CollectionSelector.vue │ │ │ ├── configuration │ │ │ │ ├── DiffEditor.vue │ │ │ │ ├── FilterConfigUI.vue │ │ │ │ ├── FilterEditor.vue │ │ │ │ ├── JsonEditor.vue │ │ │ │ └── LandingpageEditor.vue │ │ │ ├── filters │ │ │ │ ├── CheckboxFilter.vue │ │ │ │ ├── OntologyFilter.vue │ │ │ │ ├── SearchFilter.vue │ │ │ │ ├── ServiceFilter.vue │ │ │ │ ├── ToggleFilter.vue │ │ │ │ └── base │ │ │ │ │ ├── CheckboxComponent.vue │ │ │ │ │ ├── MatchTypeRadiobutton.vue │ │ │ │ │ ├── StringFilter.vue │ │ │ │ │ ├── TreeBranchComponent.vue │ │ │ │ │ └── TreeComponent.vue │ │ │ ├── generators │ │ │ │ ├── ViewGenerator.vue │ │ │ │ └── view-components │ │ │ │ │ ├── Subcollection.vue │ │ │ │ │ ├── array.vue │ │ │ │ │ ├── hyperlink.vue │ │ │ │ │ ├── longtext.vue │ │ │ │ │ ├── mref.vue │ │ │ │ │ ├── quality.vue │ │ │ │ │ └── string.vue │ │ │ ├── landingpage-components │ │ │ │ ├── LandingpageBiobankSpotlight.vue │ │ │ │ ├── LandingpageCallToAction.vue │ │ │ │ ├── LandingpageCollectionSpotlight.vue │ │ │ │ ├── LandingpageHeader.vue │ │ │ │ └── LandingpageSearch.vue │ │ │ ├── partial-views │ │ │ │ ├── ApplicationHeaderPartialView.vue │ │ │ │ ├── BiobankCardsPartialView.vue │ │ │ │ ├── README.md │ │ │ │ └── ServiceDetails.vue │ │ │ ├── report-components │ │ │ │ ├── CollapseComponent.vue │ │ │ │ ├── CollectionReportInfoCard.vue │ │ │ │ ├── CollectionTitle.vue │ │ │ │ ├── CollectionsHeader.vue │ │ │ │ ├── ContactInformation.vue │ │ │ │ ├── FactsTable.vue │ │ │ │ ├── ReportCollectionDetails.vue │ │ │ │ ├── ReportDescription.vue │ │ │ │ ├── ReportDetailsList.vue │ │ │ │ ├── ReportStudyDetails.vue │ │ │ │ ├── ReportTitle.vue │ │ │ │ ├── StudyReportInfoCard.vue │ │ │ │ └── reportInterfaces.ts │ │ │ └── tables │ │ │ │ └── QualityColumn.vue │ │ ├── composables │ │ │ └── errorHandler.ts │ │ ├── dev-assets │ │ │ └── mg-bbmri-eric-4.css │ │ ├── filter-config │ │ │ ├── facetConfigurator.ts │ │ │ ├── filterOptions.ts │ │ │ └── initialFilterFacets.ts │ │ ├── functions │ │ │ ├── applyFiltersToQuery.js │ │ │ ├── bioschemasMapper.js │ │ │ ├── bookmarkMapper.ts │ │ │ ├── extractValue.js │ │ │ ├── flattenOntologyBranch.test.ts │ │ │ ├── flattenOntologyBranch.ts │ │ │ ├── getPropertyByPath.js │ │ │ ├── sorting.ts │ │ │ ├── trackMatomoEvent.ts │ │ │ ├── viewmodelMapper.js │ │ │ └── viewmodelMapper.test.ts │ │ ├── i18n │ │ │ └── i18n.js │ │ ├── interfaces │ │ │ ├── directory.ts │ │ │ ├── interfaces.ts │ │ │ └── matomo.ts │ │ ├── main.ts │ │ ├── property-config │ │ │ ├── contactInfoColumns.ts │ │ │ ├── headInfoColumns.ts │ │ │ ├── initialBiobankColumns.ts │ │ │ ├── initialBiobankReportColumns.js │ │ │ ├── initialCollectionColumns.js │ │ │ ├── initialLandingpage.js │ │ │ └── initialStudyColumns.js │ │ ├── router │ │ │ └── index.js │ │ ├── stores │ │ │ ├── biobanksStore.ts │ │ │ ├── checkoutStore.ts │ │ │ ├── collectionStore.js │ │ │ ├── filtersStore.ts │ │ │ ├── networkStore.ts │ │ │ ├── qualitiesStore.js │ │ │ ├── settingsStore.js │ │ │ └── studyStore.ts │ │ └── views │ │ │ ├── AboutView.vue │ │ │ ├── BiobankReport.vue │ │ │ ├── CollectionReport.vue │ │ │ ├── ConfigurationScreen.vue │ │ │ ├── HomeView.vue │ │ │ ├── Landingpage.vue │ │ │ ├── NetworkReport.vue │ │ │ ├── ServiceReport.vue │ │ │ └── StudyReport.vue │ ├── tests │ │ ├── add-remove-from-service-detail.spec.ts │ │ ├── diseases-filter-tree.spec.ts │ │ ├── getAppRoute.ts │ │ ├── hello-world.spec.ts │ │ ├── select-all-buttons.spec.ts │ │ ├── set-filters-on-refresh-or-back-button.spec.ts │ │ ├── show-no-service-message.spec.ts │ │ ├── show-services-on-biobank-detail.spec.ts │ │ ├── signin.ts │ │ ├── test-error-state.spec.ts │ │ └── view-biobank-services.spec.ts │ ├── tsconfig.json │ ├── vite.config.js │ └── vitest.config.js ├── emx2-analytics │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── package.json │ ├── src │ │ ├── App.vue │ │ ├── lib │ │ │ ├── analytics.ts │ │ │ └── providers │ │ │ │ └── siteImprove.ts │ │ ├── main.ts │ │ ├── style.css │ │ ├── types │ │ │ ├── Provider.ts │ │ │ └── Trigger.ts │ │ └── vite-env.d.ts │ ├── tsconfig.app.json │ ├── tsconfig.json │ ├── tsconfig.node.json │ └── vite.config.ts ├── ern-genturis │ ├── index.html │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── bkg-image-dashboard.jpg │ │ │ ├── bkg-image-documents.jpg │ │ │ ├── en-funded-by-the-eu-neg.png │ │ │ ├── en-funded-by-the-eu-pantone.png │ │ │ ├── en-funded-by-the-eu-pos.png │ │ │ ├── ern-funded-by-eu.svg │ │ │ ├── genturis-carousel.jpg │ │ │ ├── genturis-disease-groups.png │ │ │ ├── genturis-logo-crab.jpg │ │ │ ├── genturis-logo-crab.svg │ │ │ ├── genturis-registry-logo-bg-white.png │ │ │ ├── genturis-registry-logo.png │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── Address.vue │ │ │ ├── AppFooter.vue │ │ │ └── QuickLinks.vue │ │ ├── main.ts │ │ ├── router │ │ │ └── router.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ └── utils.ts │ │ └── views │ │ │ ├── view-about.vue │ │ │ ├── view-contact.vue │ │ │ ├── view-disclaimer.vue │ │ │ ├── view-documents.vue │ │ │ ├── view-governance.vue │ │ │ ├── view-home.vue │ │ │ ├── view-members.vue │ │ │ ├── view-privacy.vue │ │ │ └── view-public-dashboard.vue │ ├── tsconfig.json │ └── vite.config.js ├── ern-ithaca │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── ern-ithaca-buildings.jpg │ │ │ ├── ern-ithaca-header.jpg │ │ │ ├── ern-ithaca-logo-white.png │ │ │ ├── ern-ithaca-logo.png │ │ │ ├── favicon.ico │ │ │ ├── molgenis-logo-blue-text.png │ │ │ └── molgenis-logo-blue-white.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ └── AppFooter.vue │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ └── utils.js │ │ └── views │ │ │ ├── view-about.vue │ │ │ ├── view-dashboard.vue │ │ │ ├── view-documents.vue │ │ │ ├── view-home.vue │ │ │ └── view-transparency.vue │ └── vite.config.js ├── ern-reconnet │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ ├── favicon.ico │ │ └── img │ │ │ ├── ern-funded-by-eu.svg │ │ │ ├── ern-reconnet-about-header.jpg │ │ │ ├── ern-reconnet-dashboard-header.jpg │ │ │ ├── ern-reconnet-docs-header.jpg │ │ │ ├── ern-reconnet-header.jpg │ │ │ ├── ern-reconnet-logo.png │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ └── AppFooter.vue │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ └── index.scss │ │ └── views │ │ │ ├── about-page.vue │ │ │ ├── dashboard-page.vue │ │ │ ├── documents-page.vue │ │ │ └── home-page.vue │ └── vite.config.js ├── ern-skin │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── app-header-background.png │ │ │ ├── ern-funded-by-eu.svg │ │ │ ├── ern-logo.png │ │ │ ├── ern-skin-about-header.jpg │ │ │ ├── ern-skin-erdri.png │ │ │ ├── ern-skin-funding.png │ │ │ ├── ern-skin-groups.png │ │ │ ├── ern-skin-logo.png │ │ │ ├── erras-header.jpg │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── AppFooter.vue │ │ │ ├── CustomPageHeader.vue │ │ │ ├── PrivateFiles.vue │ │ │ ├── Publications.vue │ │ │ └── Studies.vue │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ └── utils.ts │ │ └── views │ │ │ ├── view-about.vue │ │ │ ├── view-documents.vue │ │ │ ├── view-home.vue │ │ │ ├── view-public-dashboard.vue │ │ │ └── view-studies.vue │ └── vite.config.js ├── gportal │ ├── .env │ ├── README.md │ ├── index.html │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── bkg-beacon.jpg │ │ │ ├── bkg-datasets.jpg │ │ │ ├── gdi-logo.png │ │ │ ├── gdi-portal.jpg │ │ │ └── molgenis-logo-blue-text.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── AppFooter.vue │ │ │ └── CheckBoxSearch.vue │ │ ├── interfaces │ │ │ ├── beacon.ts │ │ │ └── datasets.ts │ │ ├── main.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ ├── beacon.ts │ │ │ └── index.ts │ │ └── views │ │ │ ├── search-beacon.vue │ │ │ ├── search-dataset.vue │ │ │ ├── view-get-started.vue │ │ │ └── view-home.vue │ ├── tsconfig.json │ └── vite.config.js ├── graphql-playground │ ├── .gitignore │ ├── README.md │ ├── eslint.config.js │ ├── index.html │ ├── package.json │ ├── public │ │ └── vite.svg │ ├── src │ │ ├── App.jsx │ │ ├── assets │ │ │ └── react.svg │ │ ├── main.jsx │ │ └── style.css │ └── vite.config.js ├── helloworld │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── HelloWorld.vue │ │ │ └── SomeQuery.vue │ │ └── main.js │ └── vite.config.js ├── metadata-utils │ ├── package.json │ ├── src │ │ ├── IQueryMetaData.ts │ │ ├── fieldHelpers.ts │ │ ├── index.ts │ │ ├── tableQuery.ts │ │ ├── toFormData.ts │ │ └── types.ts │ ├── test │ │ ├── tableQuery.test.ts │ │ └── test-resources │ │ │ └── metadata.ts │ ├── tsconfig.json │ └── vite.config.ts ├── molgenis-components │ ├── .gitignore │ ├── README.md │ ├── assets │ │ └── img │ │ │ ├── molgenis_logo.png │ │ │ └── molgenis_logo_white.png │ ├── docs-plugin.js │ ├── index.html │ ├── jsconfig.json │ ├── lib │ │ └── main.js │ ├── package.json │ ├── public │ │ ├── assets │ │ │ └── img │ │ │ │ ├── molgenis_logo.png │ │ │ │ └── molgenis_logo_white.png │ │ ├── favicon.ico │ │ └── theme.css │ ├── src │ │ ├── App.vue │ │ ├── ClientView.vue │ │ ├── DemoItem.vue │ │ ├── Interfaces │ │ │ ├── IError.ts │ │ │ ├── IRow.ts │ │ │ └── MenuItem.ts │ │ ├── Sidebar.vue │ │ ├── client │ │ │ ├── IClient.ts │ │ │ ├── client.ts │ │ │ ├── queryBuilder.test.ts │ │ │ └── queryBuilder.ts │ │ ├── components │ │ │ ├── account │ │ │ │ ├── Interfaces.ts │ │ │ │ ├── LocaleSwitch.vue │ │ │ │ ├── MolgenisAccount.vue │ │ │ │ ├── MolgenisSession.vue │ │ │ │ ├── MolgenisSignin.vue │ │ │ │ ├── MolgenisSignup.vue │ │ │ │ └── TokenManager.vue │ │ │ ├── constants.ts │ │ │ ├── display │ │ │ │ ├── ContactDisplay.vue │ │ │ │ ├── GridBlock.vue │ │ │ │ ├── ImageCard.vue │ │ │ │ ├── ImageDisplay.vue │ │ │ │ ├── KeyValueBlock.vue │ │ │ │ ├── LinksList.vue │ │ │ │ ├── PageHeader.vue │ │ │ │ ├── PersonDetails.vue │ │ │ │ └── TableDisplay.vue │ │ │ ├── filters │ │ │ │ ├── BooleanFilter.vue │ │ │ │ ├── DateFilter.vue │ │ │ │ ├── DateTimeFilter.vue │ │ │ │ ├── DecimalFilter.vue │ │ │ │ ├── FilterContainer.vue │ │ │ │ ├── FilterInput.vue │ │ │ │ ├── FilterSidebar.vue │ │ │ │ ├── FilterWell.vue │ │ │ │ ├── FilterWells.vue │ │ │ │ ├── IntegerFilter.vue │ │ │ │ ├── LongFilter.vue │ │ │ │ ├── OntologyFilter.vue │ │ │ │ ├── RefListFilter.vue │ │ │ │ └── StringFilter.vue │ │ │ ├── forms │ │ │ │ ├── ArrayInput.vue │ │ │ │ ├── ButtonAction.vue │ │ │ │ ├── ButtonAlt.vue │ │ │ │ ├── ButtonDanger.vue │ │ │ │ ├── ButtonDropdown.vue │ │ │ │ ├── ButtonOutline.vue │ │ │ │ ├── ButtonSubmit.vue │ │ │ │ ├── ConfirmModal.vue │ │ │ │ ├── EditModal.vue │ │ │ │ ├── FormGroup.vue │ │ │ │ ├── FormInput.vue │ │ │ │ ├── FormMolgenis.vue │ │ │ │ ├── HtmlDropdown.vue │ │ │ │ ├── IconAction.vue │ │ │ │ ├── IconBar.vue │ │ │ │ ├── IconDanger.vue │ │ │ │ ├── Info.vue │ │ │ │ ├── InfoPopover.vue │ │ │ │ ├── InlineInput.vue │ │ │ │ ├── InputBoolean.vue │ │ │ │ ├── InputCheckbox.vue │ │ │ │ ├── InputDate.vue │ │ │ │ ├── InputDateTime.vue │ │ │ │ ├── InputDecimal.vue │ │ │ │ ├── InputEmail.vue │ │ │ │ ├── InputFile.vue │ │ │ │ ├── InputGroup.vue │ │ │ │ ├── InputHeading.vue │ │ │ │ ├── InputHyperlink.vue │ │ │ │ ├── InputInt.vue │ │ │ │ ├── InputJson.vue │ │ │ │ ├── InputLong.vue │ │ │ │ ├── InputOntology.vue │ │ │ │ ├── InputOntologySubtree.vue │ │ │ │ ├── InputPassword.vue │ │ │ │ ├── InputRadio.vue │ │ │ │ ├── InputRangeDate.vue │ │ │ │ ├── InputRangeDateTime.vue │ │ │ │ ├── InputRangeDecimal.vue │ │ │ │ ├── InputRangeInt.vue │ │ │ │ ├── InputRangeLong.vue │ │ │ │ ├── InputRefBack.vue │ │ │ │ ├── InputRefItem.vue │ │ │ │ ├── InputRefList.vue │ │ │ │ ├── InputRefSelect.vue │ │ │ │ ├── InputSearch.vue │ │ │ │ ├── InputSelect.vue │ │ │ │ ├── InputSelectInplace.vue │ │ │ │ ├── InputString.vue │ │ │ │ ├── InputText.vue │ │ │ │ ├── InputTextLocalized.vue │ │ │ │ ├── MessageError.vue │ │ │ │ ├── MessageSuccess.vue │ │ │ │ ├── MessageWarning.vue │ │ │ │ ├── RowEdit.vue │ │ │ │ ├── RowEditFooter.vue │ │ │ │ ├── Tooltip.vue │ │ │ │ ├── TooltipComponent.vue │ │ │ │ ├── baseInputs │ │ │ │ │ ├── BaseInput.vue │ │ │ │ │ ├── BaseInputDate.vue │ │ │ │ │ ├── BaseInputDecimal.vue │ │ │ │ │ ├── BaseInputInt.vue │ │ │ │ │ ├── BaseInputLong.vue │ │ │ │ │ └── BaseInputProps.ts │ │ │ │ └── formUtils │ │ │ │ │ ├── formUtils.test.ts │ │ │ │ │ └── formUtils.ts │ │ │ ├── layout │ │ │ │ ├── Breadcrumb.vue │ │ │ │ ├── CookieWall.vue │ │ │ │ ├── GTag.vue │ │ │ │ ├── LayoutCard.vue │ │ │ │ ├── LayoutForm.vue │ │ │ │ ├── LayoutModal.vue │ │ │ │ ├── Molgenis.test.ts │ │ │ │ ├── Molgenis.vue │ │ │ │ ├── MolgenisFooter.vue │ │ │ │ ├── MolgenisMenu.vue │ │ │ │ ├── ReadMore.vue │ │ │ │ ├── ShowMore.vue │ │ │ │ ├── SimpleModal.vue │ │ │ │ ├── Spinner.vue │ │ │ │ ├── Tabs.vue │ │ │ │ └── VueTemplate.vue │ │ │ ├── mockDatasets.js │ │ │ ├── tables │ │ │ │ ├── AggregateTable.vue │ │ │ │ ├── DataDisplayCell.vue │ │ │ │ ├── IAggregateData.ts │ │ │ │ ├── Pagination.vue │ │ │ │ ├── RecordCards.vue │ │ │ │ ├── RefSideModal.vue │ │ │ │ ├── RefTable.vue │ │ │ │ ├── RenderValue.vue │ │ │ │ ├── RoutedTableExplorer.vue │ │ │ │ ├── RowButton.vue │ │ │ │ ├── RowButtonAdd.vue │ │ │ │ ├── RowButtonClone.vue │ │ │ │ ├── RowButtonDelete.vue │ │ │ │ ├── RowButtonEdit.vue │ │ │ │ ├── RowCard.vue │ │ │ │ ├── SelectionBox.vue │ │ │ │ ├── ShowHide.vue │ │ │ │ ├── SideModal.vue │ │ │ │ ├── TableExplorer.vue │ │ │ │ ├── TableMolgenis.vue │ │ │ │ ├── TableRow.vue │ │ │ │ ├── TableSearch.vue │ │ │ │ ├── TableSettings.vue │ │ │ │ ├── TableSimple.vue │ │ │ │ ├── TableStickyHeaders.vue │ │ │ │ └── cellTypes │ │ │ │ │ ├── EmailDisplay.vue │ │ │ │ │ ├── FileDisplay.vue │ │ │ │ │ ├── HyperlinkDisplay.vue │ │ │ │ │ ├── ListDisplay.vue │ │ │ │ │ ├── ObjectDisplay.vue │ │ │ │ │ ├── StringDisplay.vue │ │ │ │ │ └── TextDisplay.vue │ │ │ ├── task │ │ │ │ ├── ITask.ts │ │ │ │ ├── SubTask.vue │ │ │ │ ├── Task.vue │ │ │ │ ├── TaskList.vue │ │ │ │ └── TaskManager.vue │ │ │ ├── utils.test.ts │ │ │ └── utils.ts │ │ ├── main.js │ │ └── queryEmx2 │ │ │ ├── queryEMX2.test.ts │ │ │ └── queryEmx2.ts │ ├── tsconfig.json │ └── vite.config.js ├── molgenis-viz │ ├── .gitignore │ ├── .prettierignore │ ├── README.md │ ├── docs │ │ ├── components │ │ │ ├── Accordion.md │ │ │ ├── ActionLink.md │ │ │ ├── AppPage.md │ │ │ ├── BarChart.md │ │ │ ├── ButtonSearch.md │ │ │ ├── ChartLegend.md │ │ │ ├── ColumnChart.md │ │ │ ├── Dashboard.md │ │ │ ├── DashboardBox.md │ │ │ ├── DataHighlights.md │ │ │ ├── DataTable.md │ │ │ ├── GaugeChart.md │ │ │ ├── GeoMercator.md │ │ │ ├── GroupedColumnChart.md │ │ │ ├── InfoCard.md │ │ │ ├── InputLabel.md │ │ │ ├── InputSearch.md │ │ │ ├── LinkCard.md │ │ │ ├── LoadingScreen.md │ │ │ ├── MessageBox.md │ │ │ ├── PageFooter.md │ │ │ ├── PageFooterMeta.md │ │ │ ├── PageForm.md │ │ │ ├── PageFormSection.md │ │ │ ├── PageHeader.md │ │ │ ├── PageSection.md │ │ │ ├── PieChart.md │ │ │ ├── PieChart2.md │ │ │ ├── ProgressMeter.md │ │ │ ├── ScatterPlot.md │ │ │ ├── UnorderedList.md │ │ │ └── breadcrumbs-ui.md │ │ └── index.html │ ├── index.html │ ├── jsconfig.json │ ├── lib │ │ └── main.js │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── bar-chart-header.jpg │ │ │ ├── chris-fuller-unsplash.jpg │ │ │ ├── column-chart-header.jpg │ │ │ ├── demo-dashboard-header.jpg │ │ │ ├── gauge-chart-header.jpg │ │ │ ├── grouped-column-chart-header.jpg │ │ │ ├── header-image.jpg │ │ │ ├── highlights-header.jpg │ │ │ ├── home-header.jpg │ │ │ ├── legend-header.jpg │ │ │ ├── map-header.jpg │ │ │ ├── pie-chart-header.jpg │ │ │ ├── scatter-plot-header.jpg │ │ │ └── table-header.jpg │ ├── src │ │ ├── App.vue │ │ ├── app-components │ │ │ ├── breadcrumbs.vue │ │ │ ├── settings_chart_type_selector.vue │ │ │ └── settings_new_chart.vue │ │ ├── assets │ │ │ ├── molgenis-logo-blue-small.png │ │ │ ├── molgenis-logo-blue-small.svg │ │ │ └── molgenis-logo-blue.jpg │ │ ├── components │ │ │ ├── display │ │ │ │ ├── Accordion.vue │ │ │ │ ├── ActionLink.vue │ │ │ │ ├── FileList.vue │ │ │ │ ├── InfoCard.vue │ │ │ │ ├── LinkCard.vue │ │ │ │ ├── LoadingScreen.vue │ │ │ │ ├── MessageBox.vue │ │ │ │ ├── MolgenisLogo.vue │ │ │ │ ├── QuickLinks.vue │ │ │ │ └── UnorderedList.vue │ │ │ ├── forms │ │ │ │ ├── ButtonSearch.vue │ │ │ │ ├── InputLabel.vue │ │ │ │ └── InputSearch.vue │ │ │ ├── icons │ │ │ │ ├── ChatBubble.vue │ │ │ │ ├── CheckCircle.vue │ │ │ │ ├── Cog.vue │ │ │ │ ├── ExclaimationCircle.vue │ │ │ │ ├── ExclaimationTriangle.vue │ │ │ │ ├── ExternalLink.vue │ │ │ │ ├── MagnifyingGlassCircle.vue │ │ │ │ ├── viz-bar-chart.vue │ │ │ │ ├── viz-column-chart.vue │ │ │ │ ├── viz-pie-chart.vue │ │ │ │ └── viz-scatter-plot.vue │ │ │ ├── layouts │ │ │ │ ├── Dashboard.vue │ │ │ │ ├── DashboardChart.vue │ │ │ │ ├── DashboardRow.vue │ │ │ │ ├── Page.vue │ │ │ │ ├── PageFooter.vue │ │ │ │ ├── PageFooterMeta.vue │ │ │ │ ├── PageFooterMolgenisCitation.vue │ │ │ │ ├── PageForm.vue │ │ │ │ ├── PageFormSection.vue │ │ │ │ ├── PageHeader.vue │ │ │ │ └── PageSection.vue │ │ │ └── viz │ │ │ │ ├── BarChart.vue │ │ │ │ ├── BarChartEmx.vue │ │ │ │ ├── ChartLegend.vue │ │ │ │ ├── ColumnChart.vue │ │ │ │ ├── ColumnChartEmx.vue │ │ │ │ ├── DataHighlights.vue │ │ │ │ ├── DataTable.vue │ │ │ │ ├── DataTableEmx.vue │ │ │ │ ├── GaugeChart.vue │ │ │ │ ├── GeoMercator.vue │ │ │ │ ├── GeoMercatorEmx.vue │ │ │ │ ├── GroupedColumnChart.vue │ │ │ │ ├── GroupedColumnChartEmx.vue │ │ │ │ ├── PieChart.vue │ │ │ │ ├── PieChart2.vue │ │ │ │ ├── PieChart2Emx.vue │ │ │ │ ├── ProgressMeter.vue │ │ │ │ ├── ScatterPlot.vue │ │ │ │ └── ScatterPlotEmx.vue │ │ ├── data │ │ │ └── world.geo.json │ │ ├── gql │ │ │ └── schema.ts │ │ ├── interfaces │ │ │ ├── schema.ts │ │ │ └── viz.ts │ │ ├── main.js │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── heightwidth.scss │ │ │ ├── mixins.scss │ │ │ ├── padding.scss │ │ │ ├── palettes.scss │ │ │ ├── resets.scss │ │ │ ├── textPosition.scss │ │ │ └── variables.scss │ │ ├── utils │ │ │ ├── defaults.ts │ │ │ ├── emxViz.ts │ │ │ ├── graphql.ts │ │ │ ├── index.ts │ │ │ ├── useFetch.ts │ │ │ └── utils.js │ │ └── views │ │ │ ├── charts-builder.vue │ │ │ ├── charts-home.vue │ │ │ ├── view-home.vue │ │ │ ├── viz-bar-chart.vue │ │ │ ├── viz-chart-legend.vue │ │ │ ├── viz-column-chart.vue │ │ │ ├── viz-data-highlights.vue │ │ │ ├── viz-datatable.vue │ │ │ ├── viz-demo.vue │ │ │ ├── viz-geo-mercator.vue │ │ │ ├── viz-grouped-column-chart.vue │ │ │ ├── viz-pie-chart-2.vue │ │ │ ├── viz-pie-chart.vue │ │ │ ├── viz-progress-charts.vue │ │ │ └── viz-scatter-plot.vue │ ├── tsconfig.json │ ├── vite.config.js │ └── vuese.config.js ├── nestor-public │ ├── README.md │ ├── index.html │ ├── package.json │ ├── public │ │ └── img │ │ │ ├── bg-dashboard.jpg │ │ │ ├── bg-documents.jpg │ │ │ ├── kwf_supported_by_logo.png │ │ │ ├── molgenis-logo-blue-text.png │ │ │ └── nestor-logo.png │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── Address.vue │ │ │ ├── AppFooter.vue │ │ │ └── QuickLinks.vue │ │ ├── data │ │ │ └── nl.geo.json │ │ ├── graphql │ │ │ └── gqlOrganisations.js │ │ ├── main.ts │ │ ├── pages │ │ │ ├── view-about.vue │ │ │ ├── view-contact.vue │ │ │ ├── view-dashboard.vue │ │ │ ├── view-disclaimer.vue │ │ │ ├── view-documents.vue │ │ │ ├── view-governance.vue │ │ │ ├── view-home.vue │ │ │ └── view-privacy.vue │ │ ├── router │ │ │ └── index.js │ │ ├── styles │ │ │ ├── index.scss │ │ │ └── variables.scss │ │ ├── types │ │ │ ├── index.ts │ │ │ └── schema.ts │ │ └── utils │ │ │ ├── generateAxisTicks.ts │ │ │ └── utils.ts │ ├── tsconfig.json │ └── vite.config.js ├── package-lock.json ├── package.json ├── pages │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── assets │ │ │ └── logo.png │ │ ├── components │ │ │ ├── EditPage.vue │ │ │ ├── ListPages.vue │ │ │ └── ViewPage.vue │ │ ├── main.js │ │ └── utils │ │ │ ├── generateHtmlPreview.js │ │ │ ├── getPageSetting.js │ │ │ └── newPageContentObject.js │ └── vite.config.js ├── pnpm-lock.yaml ├── pnpm-workspace.yaml ├── projectmanager │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── PersonPlanning.vue │ │ │ └── ProjectPlanning.vue │ │ ├── gql │ │ │ ├── persons.js │ │ │ ├── projects.js │ │ │ └── schemaName.js │ │ ├── interfaces │ │ │ └── props.ts │ │ └── main.js │ ├── tsconfig.json │ └── vite.config.js ├── reports │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── ListReports.vue │ │ │ └── ViewEditReport.vue │ │ └── main.js │ └── vite.config.js ├── schema │ ├── favicon.ico │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── src │ │ ├── App.vue │ │ ├── columnTypes.js │ │ ├── components │ │ │ ├── ColumnDefinition.vue │ │ │ ├── ColumnEditModal.vue │ │ │ ├── ColumnView.vue │ │ │ ├── NomnomDiagram.vue │ │ │ ├── OntologyView.vue │ │ │ ├── PrintViewList.vue │ │ │ ├── PrintViewTable.vue │ │ │ ├── ProfileManager.vue │ │ │ ├── Schema.vue │ │ │ ├── SchemaDiagram.vue │ │ │ ├── SchemaToc.vue │ │ │ ├── SchemaView.vue │ │ │ ├── TableEditModal.vue │ │ │ └── TableView.vue │ │ ├── main.js │ │ └── utils.ts │ ├── tsconfig.json │ └── vite.config.js ├── settings │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── ChangelogViewer.vue │ │ │ ├── Members.vue │ │ │ ├── MenuDesign.vue │ │ │ ├── MenuManager.vue │ │ │ ├── PageManager.vue │ │ │ ├── SettingsManager.vue │ │ │ └── Theme.vue │ │ └── main.js │ └── vite.config.js ├── tables │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── assets │ │ │ └── logo.png │ │ ├── components │ │ │ ├── ListTables.vue │ │ │ ├── TablesTable.vue │ │ │ └── ViewTable.vue │ │ └── main.js │ └── vite.config.js ├── tailwind-components │ ├── .eslintrc.js │ ├── .gitignore │ ├── .pa11yci │ ├── README.md │ ├── app │ │ ├── DemoDataControls.vue │ │ ├── PlaygroundNavBar.vue │ │ ├── app.vue │ │ ├── assets │ │ │ ├── css │ │ │ │ ├── main.css │ │ │ │ ├── plugins │ │ │ │ │ ├── datepicker.css │ │ │ │ │ ├── font.css │ │ │ │ │ ├── popper.css │ │ │ │ │ └── tailwind.css │ │ │ │ └── theme │ │ │ │ │ ├── aumc.css │ │ │ │ │ ├── dark.css │ │ │ │ │ ├── hdsu.css │ │ │ │ │ ├── molgenis.css │ │ │ │ │ └── umcg.css │ │ │ ├── fonts │ │ │ │ ├── BebasNeue-Regular.woff2 │ │ │ │ ├── IBMPlexSans-Bold.woff2 │ │ │ │ ├── IBMPlexSans-BoldItalic.woff2 │ │ │ │ ├── IBMPlexSans-Italic.woff2 │ │ │ │ └── IBMPlexSans-Regular.woff2 │ │ │ ├── icons │ │ │ │ ├── Add Circle.svg │ │ │ │ ├── Arrow down.svg │ │ │ │ ├── Arrow left.svg │ │ │ │ ├── Arrow right.svg │ │ │ │ ├── Arrow up.svg │ │ │ │ ├── Caret down.svg │ │ │ │ ├── Caret left.svg │ │ │ │ ├── Caret right.svg │ │ │ │ ├── Caret up.svg │ │ │ │ ├── Check.svg │ │ │ │ ├── Checklist.svg │ │ │ │ ├── Clinical.svg │ │ │ │ ├── Collapsible ListItem.svg │ │ │ │ ├── Collapsible ListItemSub.svg │ │ │ │ ├── Colorize.svg │ │ │ │ ├── Columns.svg │ │ │ │ ├── Completed.svg │ │ │ │ ├── Copy.svg │ │ │ │ ├── Cross.svg │ │ │ │ ├── Database.svg │ │ │ │ ├── Dataset linked.svg │ │ │ │ ├── Dataset.svg │ │ │ │ ├── Edit.svg │ │ │ │ ├── Exclamation.svg │ │ │ │ ├── External link.svg │ │ │ │ ├── Filter alt off.svg │ │ │ │ ├── Filter alt.svg │ │ │ │ ├── Filter.svg │ │ │ │ ├── Format Align Left.svg │ │ │ │ ├── Globe.svg │ │ │ │ ├── Handshake.svg │ │ │ │ ├── Hub.svg │ │ │ │ ├── Image Data Warehouse.svg │ │ │ │ ├── Image Diagram.svg │ │ │ │ ├── Image Lightbulb.svg │ │ │ │ ├── Image Link.svg │ │ │ │ ├── Image Table.svg │ │ │ │ ├── Info.svg │ │ │ │ ├── Left Panel Open.svg │ │ │ │ ├── Menu Open.svg │ │ │ │ ├── Menu.svg │ │ │ │ ├── Moon.svg │ │ │ │ ├── Mouse.svg │ │ │ │ ├── Patient list.svg │ │ │ │ ├── People.svg │ │ │ │ ├── Percent.svg │ │ │ │ ├── Plus.svg │ │ │ │ ├── ProgressActivity.svg │ │ │ │ ├── Right Panel Open.svg │ │ │ │ ├── Schedule.svg │ │ │ │ ├── Search.svg │ │ │ │ ├── Shopping Cart Add.svg │ │ │ │ ├── Shopping Cart.svg │ │ │ │ ├── Star solid.svg │ │ │ │ ├── Star.svg │ │ │ │ ├── Sun.svg │ │ │ │ ├── Trash.svg │ │ │ │ ├── University.svg │ │ │ │ ├── Upload file.svg │ │ │ │ ├── User.svg │ │ │ │ ├── View compact.svg │ │ │ │ ├── View normal.svg │ │ │ │ ├── View table.svg │ │ │ │ ├── demography.svg │ │ │ │ ├── double arrow left.svg │ │ │ │ ├── double arrow right.svg │ │ │ │ ├── equal.svg │ │ │ │ ├── groups.svg │ │ │ │ ├── harmonised variables.svg │ │ │ │ ├── image Diagram 2.svg │ │ │ │ ├── institution.svg │ │ │ │ ├── list.svg │ │ │ │ └── person.svg │ │ │ └── img │ │ │ │ ├── aumc.ico │ │ │ │ ├── hdsu.ico │ │ │ │ ├── molgenis-logo-blue-small.svg │ │ │ │ ├── molgenis.ico │ │ │ │ └── umcg.ico │ │ ├── components │ │ │ ├── Accordion.vue │ │ │ ├── BackgroundGradient.vue │ │ │ ├── Banner.vue │ │ │ ├── BaseIcon.vue │ │ │ ├── BreadCrumbs.vue │ │ │ ├── Button.vue │ │ │ ├── ButtonBar.vue │ │ │ ├── CardList.vue │ │ │ ├── CardListItem.vue │ │ │ ├── ColorTile.vue │ │ │ ├── Container.vue │ │ │ ├── ContentReadMore.vue │ │ │ ├── CustomTooltip.vue │ │ │ ├── DefinitionList.vue │ │ │ ├── DefinitionListDefinition.vue │ │ │ ├── DefinitionListTerm.vue │ │ │ ├── FooterComponent.vue │ │ │ ├── Header.vue │ │ │ ├── HeaderButton.vue │ │ │ ├── HeaderButtonMobile.vue │ │ │ ├── Input.vue │ │ │ ├── Logo.vue │ │ │ ├── LogoMobile.vue │ │ │ ├── Message.vue │ │ │ ├── Modal.vue │ │ │ ├── Navigation.vue │ │ │ ├── PageHeader.vue │ │ │ ├── Pagination.vue │ │ │ ├── ShowMore.vue │ │ │ ├── SideModal.vue │ │ │ ├── SourceCode.vue │ │ │ ├── Story.vue │ │ │ ├── Tab.vue │ │ │ ├── Table.vue │ │ │ ├── TableCell.vue │ │ │ ├── TableHead.vue │ │ │ ├── TableHeadRow.vue │ │ │ ├── TableRow.vue │ │ │ ├── ThemeSwitch.vue │ │ │ ├── button │ │ │ │ ├── Dropdown.vue │ │ │ │ ├── FilterWellContainer.vue │ │ │ │ ├── IconButton.vue │ │ │ │ └── Text.vue │ │ │ ├── content │ │ │ │ ├── ContentAdded.vue │ │ │ │ ├── ContentBlock.vue │ │ │ │ ├── ContentBlockAttachedFiles.vue │ │ │ │ ├── ContentBlockDescription.vue │ │ │ │ ├── ContentBlockModal.vue │ │ │ │ ├── ContentBlocks.vue │ │ │ │ ├── ContentGenericItem.vue │ │ │ │ ├── ContentGenericItemList.vue │ │ │ │ ├── EMX2Section.vue │ │ │ │ ├── FileDocumentCard.vue │ │ │ │ ├── FileImageCard.vue │ │ │ │ ├── FileList.vue │ │ │ │ └── type │ │ │ │ │ ├── ContentTypeHyperLink.vue │ │ │ │ │ ├── ContentTypeOntologyArray.vue │ │ │ │ │ ├── ContentTypeRefBack.vue │ │ │ │ │ ├── ContentTypeString.vue │ │ │ │ │ └── ContentTypeText.vue │ │ │ ├── display │ │ │ │ ├── List.vue │ │ │ │ ├── ListItem.vue │ │ │ │ └── Record.vue │ │ │ ├── editor │ │ │ │ ├── CodeEditor.vue │ │ │ │ └── HtmlPreview.vue │ │ │ ├── field │ │ │ │ └── Set.vue │ │ │ ├── filter │ │ │ │ └── Search.vue │ │ │ ├── form │ │ │ │ ├── DeleteModal.vue │ │ │ │ ├── EditModal.vue │ │ │ │ ├── Error.vue │ │ │ │ ├── Field.vue │ │ │ │ ├── Fields.vue │ │ │ │ ├── Form.vue │ │ │ │ ├── Legend.vue │ │ │ │ ├── Message.vue │ │ │ │ ├── NextSectionNav.vue │ │ │ │ ├── PreviousSectionNav.vue │ │ │ │ ├── RequiredInfoSection.vue │ │ │ │ └── legend │ │ │ │ │ ├── ErrorCounter.vue │ │ │ │ │ └── Header.vue │ │ │ ├── global │ │ │ │ └── icons │ │ │ │ │ ├── AddCircle.vue │ │ │ │ │ ├── ArrowDown.vue │ │ │ │ │ ├── ArrowLeft.vue │ │ │ │ │ ├── ArrowRight.vue │ │ │ │ │ ├── ArrowUp.vue │ │ │ │ │ ├── CaretDown.vue │ │ │ │ │ ├── CaretLeft.vue │ │ │ │ │ ├── CaretRight.vue │ │ │ │ │ ├── CaretUp.vue │ │ │ │ │ ├── Check.vue │ │ │ │ │ ├── Checklist.vue │ │ │ │ │ ├── Clinical.vue │ │ │ │ │ ├── CollapsibleListItem.vue │ │ │ │ │ ├── CollapsibleListItemSub.vue │ │ │ │ │ ├── Colorize.vue │ │ │ │ │ ├── Columns.vue │ │ │ │ │ ├── Completed.vue │ │ │ │ │ ├── Copy.vue │ │ │ │ │ ├── Cross.vue │ │ │ │ │ ├── Database.vue │ │ │ │ │ ├── Dataset.vue │ │ │ │ │ ├── DatasetLinked.vue │ │ │ │ │ ├── Demography.vue │ │ │ │ │ ├── DoubleArrowLeft.vue │ │ │ │ │ ├── DoubleArrowRight.vue │ │ │ │ │ ├── Edit.vue │ │ │ │ │ ├── Equal.vue │ │ │ │ │ ├── Exclamation.vue │ │ │ │ │ ├── ExternalLink.vue │ │ │ │ │ ├── Filter.vue │ │ │ │ │ ├── FilterAlt.vue │ │ │ │ │ ├── FilterAltOff.vue │ │ │ │ │ ├── FormatAlignLeft.vue │ │ │ │ │ ├── Globe.vue │ │ │ │ │ ├── Groups.vue │ │ │ │ │ ├── Handshake.vue │ │ │ │ │ ├── HarmonisedVariables.vue │ │ │ │ │ ├── Hub.vue │ │ │ │ │ ├── ImageDataWarehouse.vue │ │ │ │ │ ├── ImageDiagram.vue │ │ │ │ │ ├── ImageDiagram2.vue │ │ │ │ │ ├── ImageLightbulb.vue │ │ │ │ │ ├── ImageLink.vue │ │ │ │ │ ├── ImageTable.vue │ │ │ │ │ ├── Info.vue │ │ │ │ │ ├── Institution.vue │ │ │ │ │ ├── LeftPanelOpen.vue │ │ │ │ │ ├── List.vue │ │ │ │ │ ├── Menu.vue │ │ │ │ │ ├── MenuOpen.vue │ │ │ │ │ ├── Moon.vue │ │ │ │ │ ├── Mouse.vue │ │ │ │ │ ├── PatientList.vue │ │ │ │ │ ├── People.vue │ │ │ │ │ ├── Percent.vue │ │ │ │ │ ├── Person.vue │ │ │ │ │ ├── Plus.vue │ │ │ │ │ ├── ProgressActivity.vue │ │ │ │ │ ├── RestartAlt.vue │ │ │ │ │ ├── RightPanelOpen.vue │ │ │ │ │ ├── Schedule.vue │ │ │ │ │ ├── Search.vue │ │ │ │ │ ├── ShoppingCart.vue │ │ │ │ │ ├── ShoppingCartAdd.vue │ │ │ │ │ ├── Star.vue │ │ │ │ │ ├── StarSolid.vue │ │ │ │ │ ├── Sun.vue │ │ │ │ │ ├── Trash.vue │ │ │ │ │ ├── University.vue │ │ │ │ │ ├── UploadFile.vue │ │ │ │ │ ├── User.vue │ │ │ │ │ ├── ViewCompact.vue │ │ │ │ │ ├── ViewNormal.vue │ │ │ │ │ └── ViewTable.vue │ │ │ ├── input │ │ │ │ ├── Array.vue │ │ │ │ ├── Boolean.vue │ │ │ │ ├── Checkbox.vue │ │ │ │ ├── CheckboxGroup.vue │ │ │ │ ├── CheckboxIcon.vue │ │ │ │ ├── Date.vue │ │ │ │ ├── DateTime.vue │ │ │ │ ├── Decimal.vue │ │ │ │ ├── File.vue │ │ │ │ ├── GUIDELINES.md │ │ │ │ ├── InputGroupContainer.vue │ │ │ │ ├── Int.vue │ │ │ │ ├── Label.vue │ │ │ │ ├── List.vue │ │ │ │ ├── Listbox.vue │ │ │ │ ├── Long.vue │ │ │ │ ├── Ontology.vue │ │ │ │ ├── PlaceHolder.vue │ │ │ │ ├── Radio.vue │ │ │ │ ├── RadioGroup.vue │ │ │ │ ├── RadioIcon.vue │ │ │ │ ├── Ref.vue │ │ │ │ ├── RefBack.vue │ │ │ │ ├── RefSelect.vue │ │ │ │ ├── RefSelect │ │ │ │ │ ├── Container.vue │ │ │ │ │ ├── InputOption.vue │ │ │ │ │ ├── Toggle.vue │ │ │ │ │ └── Toolbar.vue │ │ │ │ ├── Search.vue │ │ │ │ ├── Select.vue │ │ │ │ ├── String.vue │ │ │ │ ├── Switch.vue │ │ │ │ ├── TestContainer.vue │ │ │ │ ├── TextArea.vue │ │ │ │ ├── Tree.vue │ │ │ │ ├── TreeNode.vue │ │ │ │ ├── listbox │ │ │ │ │ ├── ListItem.vue │ │ │ │ │ └── Toggle.vue │ │ │ │ └── ref │ │ │ │ │ └── ListItem.vue │ │ │ ├── label │ │ │ │ └── DraftLabel.vue │ │ │ ├── story │ │ │ │ └── ComponentOutput.vue │ │ │ ├── table │ │ │ │ ├── CellEMX2.vue │ │ │ │ ├── TableEMX2.vue │ │ │ │ ├── TableHeadCell.vue │ │ │ │ ├── TableHeaderAction.vue │ │ │ │ ├── control │ │ │ │ │ └── Columns.vue │ │ │ │ └── modal │ │ │ │ │ └── TableModalRef.vue │ │ │ ├── text │ │ │ │ ├── Hyperlink.vue │ │ │ │ └── NoResultsMessage.vue │ │ │ ├── transition │ │ │ │ └── SlideUp.vue │ │ │ ├── value │ │ │ │ ├── Bool.vue │ │ │ │ ├── Date.vue │ │ │ │ ├── DateTime.vue │ │ │ │ ├── Decimal.vue │ │ │ │ ├── EMX2.vue │ │ │ │ ├── Email.vue │ │ │ │ ├── File.vue │ │ │ │ ├── Hyperlink.vue │ │ │ │ ├── Int.vue │ │ │ │ ├── List.vue │ │ │ │ ├── Long.vue │ │ │ │ ├── Object.vue │ │ │ │ ├── Ref.vue │ │ │ │ ├── RefBack.vue │ │ │ │ ├── String.vue │ │ │ │ └── Text.vue │ │ │ └── viz │ │ │ │ ├── ChartLegend.vue │ │ │ │ └── ChartLegendMarker.vue │ │ ├── composables │ │ │ ├── fetchGraphql.ts │ │ │ ├── fetchMetadata.ts │ │ │ ├── fetchRowData.ts │ │ │ ├── fetchRowPrimaryKey.ts │ │ │ ├── fetchTableData.ts │ │ │ ├── fetchTableMetadata.ts │ │ │ ├── useForm.ts │ │ │ ├── useSession.ts │ │ │ └── useSettings.ts │ │ ├── layouts │ │ │ ├── default.vue │ │ │ ├── focus.vue │ │ │ └── fullPage.vue │ │ ├── pages │ │ │ ├── Accordion.story.vue │ │ │ ├── Banner.story.vue │ │ │ ├── BreadCrumbs.story.vue │ │ │ ├── Button.story.vue │ │ │ ├── ButtonBar.story.vue │ │ │ ├── ButtonDropdown.story.vue │ │ │ ├── CustomTooltip.story.vue │ │ │ ├── DataFetch.other.vue │ │ │ ├── DisplayList.story.vue │ │ │ ├── FilterSearch.story.vue │ │ │ ├── FooterComponent.story.vue │ │ │ ├── Form.story.vue │ │ │ ├── FormField.story.vue │ │ │ ├── Header.story.vue │ │ │ ├── Icons.story.vue │ │ │ ├── Legend.story.vue │ │ │ ├── Logo.story.vue │ │ │ ├── LogoMobile.story.vue │ │ │ ├── Message.story.vue │ │ │ ├── Modal.story.vue │ │ │ ├── Navigation.story.vue │ │ │ ├── PageHeader.story.vue │ │ │ ├── Pagination.story.vue │ │ │ ├── Session.story.vue │ │ │ ├── ShowMore.story.vue │ │ │ ├── SideModal.story.vue │ │ │ ├── Styles.other.vue │ │ │ ├── ThemeSwitch.story.vue │ │ │ ├── form │ │ │ │ ├── AddModal.story.vue │ │ │ │ ├── EditModal.story.vue │ │ │ │ ├── Error.story.vue │ │ │ │ └── RequiredInfoSection.story.vue │ │ │ ├── index.vue │ │ │ ├── input │ │ │ │ ├── Array.story.vue │ │ │ │ ├── Boolean.story.vue │ │ │ │ ├── CheckboxGroup.story.vue │ │ │ │ ├── Date.story.vue │ │ │ │ ├── DateTime.story.vue │ │ │ │ ├── Decimal.story.vue │ │ │ │ ├── Email.story.vue │ │ │ │ ├── File.story.vue │ │ │ │ ├── Hyperlink.story.vue │ │ │ │ ├── Int.story.vue │ │ │ │ ├── Label.story.vue │ │ │ │ ├── List.story.vue │ │ │ │ ├── Listbox.story.vue │ │ │ │ ├── Long.story.vue │ │ │ │ ├── Ontology.story.vue │ │ │ │ ├── RadioGroup.story.vue │ │ │ │ ├── Ref.story.vue │ │ │ │ ├── RefBack.story.vue │ │ │ │ ├── RefSelect.story.vue │ │ │ │ ├── Search.story.vue │ │ │ │ ├── Select.story.vue │ │ │ │ ├── String.story.vue │ │ │ │ ├── Switch.story.vue │ │ │ │ ├── TextArea.story.vue │ │ │ │ └── Tree.story.vue │ │ │ ├── label │ │ │ │ └── Draft.story.vue │ │ │ ├── samples │ │ │ │ ├── data │ │ │ │ │ └── cohort-table-metadata.js │ │ │ │ ├── formModal.vue │ │ │ │ └── rowEdit.vue │ │ │ ├── table │ │ │ │ ├── EMX2.story.vue │ │ │ │ └── modal │ │ │ │ │ └── Ref.story.vue │ │ │ ├── text │ │ │ │ └── Hyperlink.story.vue │ │ │ ├── transition │ │ │ │ └── SlideUp.story.vue │ │ │ └── viz │ │ │ │ └── ChartLegend.story.vue │ │ ├── plugins │ │ │ ├── clearSession.client.ts │ │ │ ├── onFirstView.ts │ │ │ ├── whenInView.ts │ │ │ └── whenOverlapsWithTopOfContainer.ts │ │ └── utils │ │ │ ├── Pages.ts │ │ │ ├── errorToMessage.ts │ │ │ ├── flattenObject.ts │ │ │ ├── generateSourceMap.js │ │ │ ├── getPrimaryKey.ts │ │ │ ├── logger.ts │ │ │ ├── moduleToString.ts │ │ │ ├── openReAuthenticationWindow.ts │ │ │ ├── rowToString.ts │ │ │ ├── scrollTools.ts │ │ │ ├── sessionExpiredError.ts │ │ │ ├── sortColumns.ts │ │ │ └── typeUtils.ts │ ├── nuxt.config.ts │ ├── package.json │ ├── playwright.config.ts │ ├── public │ │ └── favicon.ico │ ├── scripts │ │ ├── create_vue_components_from_icons.cjs │ │ └── pa11y_update_urls.js │ ├── server │ │ ├── routes │ │ │ ├── [schema] │ │ │ │ ├── api │ │ │ │ │ ├── file │ │ │ │ │ │ └── [...].ts │ │ │ │ │ └── trigger.ts │ │ │ │ └── graphql.ts │ │ │ └── graphql.ts │ │ └── tsconfig.json │ ├── svgo.config.cjs │ ├── tailwind.config.js │ ├── tests │ │ ├── e2e │ │ │ ├── auth.setup.ts │ │ │ ├── buttonBar.spec.ts │ │ │ └── components │ │ │ │ ├── form │ │ │ │ ├── addModal.spec.ts │ │ │ │ ├── edit-mode.spec.ts │ │ │ │ ├── editModal.spec.ts │ │ │ │ ├── formInteraction.spec.ts │ │ │ │ ├── inputEmail.spec.ts │ │ │ │ ├── inputHyperlink.spec.ts │ │ │ │ ├── performance.spec.ts │ │ │ │ └── renderForm.spec.ts │ │ │ │ ├── input │ │ │ │ ├── listbox.spec.ts │ │ │ │ ├── ontology.spec.ts │ │ │ │ ├── textarea.spec.ts │ │ │ │ └── tree.spec.ts │ │ │ │ └── table │ │ │ │ ├── admin.tableEMX2.spec.ts │ │ │ │ └── draftStatus.spec.ts │ │ └── vitest │ │ │ ├── components │ │ │ ├── Button.spec.ts │ │ │ ├── PageHeader.spec.ts │ │ │ ├── Pagination.spec.ts │ │ │ ├── __snapshots__ │ │ │ │ └── Pagination.spec.ts.snap │ │ │ ├── form │ │ │ │ └── Error.spec.ts │ │ │ ├── input │ │ │ │ ├── Boolean.spec.ts │ │ │ │ ├── CheckboxGroup.spec.ts │ │ │ │ ├── Listbox.spec.ts │ │ │ │ └── RadioGroup.spec.ts │ │ │ └── text │ │ │ │ └── Hyperlink.spec.ts │ │ │ ├── composables │ │ │ └── useForm.spec.ts │ │ │ └── utils │ │ │ ├── flattenObject.spec.ts │ │ │ ├── rowToString.spec.ts │ │ │ └── typeUtils.spec.ts │ ├── tsconfig.json │ ├── types │ │ ├── listbox.ts │ │ └── types.ts │ └── vitest.config.ts ├── tasks │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ │ └── favicon.ico │ ├── src │ │ ├── App.vue │ │ ├── components │ │ │ ├── ListJobs.vue │ │ │ ├── ListScripts.vue │ │ │ ├── SubmitButton.vue │ │ │ └── TaskViewButton.vue │ │ └── main.js │ └── vite.config.js ├── turbo.json ├── ui │ ├── .gitignore │ ├── app │ │ ├── app.vue │ │ ├── components │ │ │ ├── DeleteUserConfirmation.vue │ │ │ ├── EditUserModal.vue │ │ │ ├── NewUserModal.vue │ │ │ └── TokenManagement.vue │ │ ├── layouts │ │ │ └── default.vue │ │ ├── middleware │ │ │ └── adminOnly.ts │ │ ├── pages │ │ │ ├── [schema] │ │ │ │ ├── [table] │ │ │ │ │ └── index.vue │ │ │ │ ├── analytics.vue │ │ │ │ ├── index.vue │ │ │ │ └── pages │ │ │ │ │ ├── [page] │ │ │ │ │ ├── edit.vue │ │ │ │ │ └── index.vue │ │ │ │ │ └── index.vue │ │ │ ├── account.vue │ │ │ ├── admin.vue │ │ │ ├── admin │ │ │ │ ├── settings.vue │ │ │ │ └── users.vue │ │ │ ├── index.vue │ │ │ ├── login.vue │ │ │ └── reauthenticated.vue │ │ ├── stores │ │ │ └── metaStore.ts │ │ └── util │ │ │ └── adminUtils.ts │ ├── nuxt.config.ts │ ├── package.json │ ├── playwright.config.ts │ ├── public │ │ └── favicon.ico │ ├── server │ │ └── routes │ │ │ ├── [schema] │ │ │ └── api │ │ │ │ └── trigger │ │ │ │ ├── [trigger].ts │ │ │ │ └── index.ts │ │ │ └── oidc-login.get.ts │ ├── tests │ │ └── e2e │ │ │ ├── admin-page.spec.ts │ │ │ ├── crud-users.spec.ts │ │ │ ├── crud.spec.ts │ │ │ ├── explorer-ref-columns.spec.ts │ │ │ ├── login-.spec.ts │ │ │ ├── re-authtest.spec.ts │ │ │ └── wcag-html-lang.spec.ts │ └── tsconfig.json └── updownload │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── jsconfig.json │ ├── package.json │ ├── public │ └── favicon.ico │ ├── src │ ├── App.vue │ ├── assets │ │ └── logo.png │ ├── components │ │ └── Import.vue │ └── main.js │ └── vite.config.js ├── azure-pipelines.yml ├── backend ├── build.gradle ├── molgenis-emx2-analytics │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── analytics │ │ │ ├── model │ │ │ ├── Trigger.java │ │ │ └── actions │ │ │ │ ├── CreateTriggerAction.java │ │ │ │ ├── DeleteTriggerAction.java │ │ │ │ └── UpdateTriggerAction.java │ │ │ ├── repository │ │ │ ├── TriggerRepository.java │ │ │ └── TriggerRepositoryImpl.java │ │ │ └── service │ │ │ ├── AnalyticsService.java │ │ │ └── AnalyticsServiceImpl.java │ │ └── test │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── analytics │ │ ├── repository │ │ └── TriggerRepositoryTest.java │ │ └── service │ │ └── TestAnalyticsService.java ├── molgenis-emx2-beacon-v2 │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── beaconv2 │ │ │ ├── BeaconSpec.java │ │ │ ├── EntryType.java │ │ │ ├── QueryBuilder.java │ │ │ ├── QueryEntryType.java │ │ │ ├── Templates.java │ │ │ ├── common │ │ │ ├── Meta.java │ │ │ ├── Schemas.java │ │ │ ├── SecurityLevel.java │ │ │ └── misc │ │ │ │ ├── Granularity.java │ │ │ │ ├── Handover.java │ │ │ │ ├── HandoverType.java │ │ │ │ ├── IncludedResultsetResponses.java │ │ │ │ └── NCITToGSSOSexMapping.java │ │ │ ├── endpoints │ │ │ ├── ColumnPath.java │ │ │ ├── Configuration.java │ │ │ ├── EntryTypes.java │ │ │ ├── FilteringTerms.java │ │ │ ├── Info.java │ │ │ ├── Map.java │ │ │ ├── OntologyTerm.java │ │ │ ├── datasets │ │ │ │ ├── DatasetsMeta.java │ │ │ │ ├── Pagination.java │ │ │ │ ├── ReceivedRequestSummary.java │ │ │ │ └── ResponseSummary.java │ │ │ ├── filteringterms │ │ │ │ ├── FilteringTerm.java │ │ │ │ └── FilteringTermsFetcher.java │ │ │ └── genomicvariants │ │ │ │ ├── CaseLevelData.java │ │ │ │ ├── ClinicalInterpretations.java │ │ │ │ ├── GenomicVariant.java │ │ │ │ ├── Position.java │ │ │ │ ├── SortByPosition.java │ │ │ │ └── VariantLevelData.java │ │ │ ├── filter │ │ │ ├── Filter.java │ │ │ ├── FilterConceptVP.java │ │ │ ├── FilterParser.java │ │ │ ├── FilterParserFactory.java │ │ │ ├── FilterParserVP.java │ │ │ ├── FilterType.java │ │ │ ├── GenomicQueryType.java │ │ │ ├── RegularFilterParser.java │ │ │ └── VariantFilterParser.java │ │ │ └── requests │ │ │ ├── BeaconQuery.java │ │ │ ├── BeaconRequestBody.java │ │ │ ├── BeaconRequestMeta.java │ │ │ ├── BeaconRequestParameters.java │ │ │ └── Similarity.java │ │ └── resources │ │ ├── entry-types │ │ ├── analyses.jslt │ │ ├── biosamples.jslt │ │ ├── catalogs.jslt │ │ ├── cohorts.jslt │ │ ├── datasets.jslt │ │ ├── g_variants.jslt │ │ ├── individuals.jslt │ │ └── runs.jslt │ │ ├── info.jslt │ │ ├── informational │ │ ├── configuration.jslt │ │ ├── entry_types.jslt │ │ ├── info.jslt │ │ └── map.jslt │ │ ├── meta.jslt │ │ ├── ontology.jslt │ │ ├── range.jslt │ │ └── response_summary.jslt ├── molgenis-emx2-cafevariome │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── cafevariome │ │ ├── CafeVariomeQuery.java │ │ ├── Granularity.java │ │ ├── QueryRecord.java │ │ ├── Range.java │ │ ├── response │ │ ├── RecordIndexResponse.java │ │ └── RecordResponse.java │ │ ├── test.http │ │ ├── test_match_all.http │ │ └── test_record_index.http ├── molgenis-emx2-datamodels │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ ├── datamodels │ │ │ ├── BiobankDirectoryLoader.java │ │ │ ├── DashboardLoader.java │ │ │ ├── DataModels.java │ │ │ ├── DirectoryLoader.java │ │ │ ├── PatientRegistryDemoLoader.java │ │ │ ├── ProjectManagerLoader.java │ │ │ ├── UiDashboardLoader.java │ │ │ ├── profiles │ │ │ │ ├── CreateSchemas.java │ │ │ │ ├── PostProcessProfiles.java │ │ │ │ ├── ProfileDocGen.java │ │ │ │ ├── Profiles.java │ │ │ │ ├── ResourceListing.java │ │ │ │ ├── RetrieveAllProfiles.java │ │ │ │ └── SchemaFromProfile.java │ │ │ ├── test │ │ │ │ ├── ArrayTypeTestExample.java │ │ │ │ ├── CrossSchemaReferenceExample.java │ │ │ │ ├── JobsModel.java │ │ │ │ ├── JsonLdExample.java │ │ │ │ ├── ProductComponentPartsExample.java │ │ │ │ ├── RefAndRefArrayTestExample.java │ │ │ │ └── SimpleTypeTestExample.java │ │ │ └── util │ │ │ │ └── CompareTools.java │ │ │ └── io │ │ │ ├── ImportDataModelTask.java │ │ │ └── ImportProfileTask.java │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── datamodels │ │ │ ├── CatalogueTest.java │ │ │ ├── DashboardTest.java │ │ │ ├── DirectoryTest.java │ │ │ ├── PagesTest.java │ │ │ ├── PatientRegistryTest.java │ │ │ ├── TestLoaders.java │ │ │ ├── TestProfileDocGen.java │ │ │ ├── beacon │ │ │ ├── BeaconConfigurationTest.java │ │ │ ├── BeaconEntryTypesTest.java │ │ │ ├── BeaconInfoTest.java │ │ │ ├── BeaconMapTest.java │ │ │ ├── BeaconTestUtil.java │ │ │ ├── entrytypes │ │ │ │ ├── BeaconAnalysisTest.java │ │ │ │ ├── BeaconAuthorityTests.java │ │ │ │ ├── BeaconBiosamplesTests.java │ │ │ │ ├── BeaconCohortsTests.java │ │ │ │ ├── BeaconGenomicVariantTest.java │ │ │ │ ├── BeaconGranularityTests.java │ │ │ │ ├── BeaconIndividualsTests.java │ │ │ │ ├── BeaconPaginationTests.java │ │ │ │ └── BeaconRunsTests.java │ │ │ └── vp │ │ │ │ ├── BeaconVpEntryTypesTest.java │ │ │ │ └── BeaconVpMapTest.java │ │ │ └── cafevarime │ │ │ └── QueryRecordTest.java │ │ └── resources │ │ ├── TestIncludeProfile.yaml │ │ ├── TestProfileWithError.yaml │ │ └── student │ │ ├── courses.csv │ │ ├── enrollment.csv │ │ ├── molgenis.csv │ │ └── students.csv ├── molgenis-emx2-email │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── email │ │ │ ├── EmailMessage.java │ │ │ ├── EmailService.java │ │ │ ├── EmailSettings.java │ │ │ └── EmailValidator.java │ │ └── test │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── email │ │ ├── EmailServiceTest.java │ │ └── EmailValidatorTest.java ├── molgenis-emx2-fairdatapoint │ └── src │ │ └── main │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── fairdatapoint │ │ └── Queries.java ├── molgenis-emx2-graphql │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ ├── graphql │ │ │ ├── GraphqlAdminFieldFactory.java │ │ │ ├── GraphqlApiFactory.java │ │ │ ├── GraphqlApiMutationResult.java │ │ │ ├── GraphqlApiMutationResultWithToken.java │ │ │ ├── GraphqlConstants.java │ │ │ ├── GraphqlCustomExceptionHandler.java │ │ │ ├── GraphqlCustomTypes.java │ │ │ ├── GraphqlDatabaseFieldFactory.java │ │ │ ├── GraphqlException.java │ │ │ ├── GraphqlManifesFieldFactory.java │ │ │ ├── GraphqlSchemaFieldFactory.java │ │ │ ├── GraphqlSessionFieldFactory.java │ │ │ ├── GraphqlSessionHandlerInterface.java │ │ │ └── GraphqlTableFieldFactory.java │ │ │ ├── json │ │ │ ├── Column.java │ │ │ ├── JsonExceptionMapper.java │ │ │ ├── JsonUtil.java │ │ │ ├── LanguageValue.java │ │ │ ├── Schema.java │ │ │ ├── Setting.java │ │ │ └── Table.java │ │ │ └── settings │ │ │ ├── ReportUtils.java │ │ │ └── SettingsDataModel.java │ │ └── test │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── graphql │ │ ├── TestGraphQLCompositeKeys.java │ │ ├── TestGraphqlAdminFields.java │ │ ├── TestGraphqlCrossSchemaRefs.java │ │ ├── TestGraphqlDatabaseFields.java │ │ ├── TestGraphqlSchemaFields.java │ │ ├── TestSumQuery.java │ │ ├── TestTableQueriesWithInheritance.java │ │ └── TestTokenBasedAccess.java ├── molgenis-emx2-io │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── io │ │ │ ├── FileUtils.java │ │ │ ├── ImportCsvZipTask.java │ │ │ ├── ImportDataTask.java │ │ │ ├── ImportDirectoryTask.java │ │ │ ├── ImportExcelTask.java │ │ │ ├── ImportMetadataTask.java │ │ │ ├── ImportSchemaTask.java │ │ │ ├── ImportTableTask.java │ │ │ ├── MolgenisIO.java │ │ │ ├── emx1 │ │ │ ├── Emx1.java │ │ │ ├── Emx1Attribute.java │ │ │ └── Emx1Entity.java │ │ │ ├── emx2 │ │ │ ├── Emx2.java │ │ │ ├── Emx2Files.java │ │ │ ├── Emx2Members.java │ │ │ ├── Emx2Settings.java │ │ │ └── Emx2Tables.java │ │ │ ├── readers │ │ │ ├── CsvTableReader.java │ │ │ ├── CsvTableWriter.java │ │ │ ├── RowReaderApacheCommons.java.backup │ │ │ ├── RowReaderFlatmapper.java.backup │ │ │ ├── RowReaderJackson.java │ │ │ └── RowReaderUnivocity.java.backup │ │ │ └── tablestore │ │ │ ├── AutoCloseableIterable.java │ │ │ ├── RowProcessor.java │ │ │ ├── TableAndFileStore.java │ │ │ ├── TableStore.java │ │ │ ├── TableStoreForCsvFile.java │ │ │ ├── TableStoreForCsvFilesClasspath.java │ │ │ ├── TableStoreForCsvFilesDirectory.java │ │ │ ├── TableStoreForCsvInMemory.java │ │ │ ├── TableStoreForCsvInZipFile.java │ │ │ └── TableStoreForXlsxFile.java │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── io │ │ │ ├── AUtil.java │ │ │ ├── RowReaderCsvTest.java.backup │ │ │ ├── TestColumnTypeIsFile.java │ │ │ ├── TestCsvTableReader.java │ │ │ ├── TestEmx2Roles.java │ │ │ ├── TestEmx2Settings.java │ │ │ ├── TestExcelStore.java │ │ │ ├── TestExtends.java │ │ │ ├── TestImportEmptyAutoId.java │ │ │ ├── TestImportExportAllExamples.java │ │ │ ├── TestImportExportEmx2DataAndMetadata.java │ │ │ ├── TestImportTableTask.java │ │ │ ├── TestLegacyImport.java │ │ │ ├── TestOntologyMetadataExport.java │ │ │ ├── TestReadWriteStores.java │ │ │ ├── TestRenameAndDelete.java │ │ │ ├── TestSettingsAndMembersLoading.java │ │ │ ├── TestTypesImport.java │ │ │ ├── readers │ │ │ └── CsvTableReaderTest.java │ │ │ └── tablestore │ │ │ └── TableStoreForCsvFilesClasspathTest.java │ │ └── resources │ │ ├── Book3.xlsx │ │ ├── CatalogueCentralCollections.xlsx │ │ ├── CatalogueCentralDictionaries.xlsx │ │ ├── CatalogueCentralOntologies.xlsx │ │ ├── CatalogueLocalHarmonizedVariables.xlsx │ │ ├── CatalogueLocalMappings.xlsx │ │ ├── CatalogueLocalSourceVariables.xlsx │ │ ├── DateExample.xlsx │ │ ├── HealthDataCatalogue.xlsx │ │ ├── TestImportEmptyAutoId.xlsx │ │ ├── TestImportTableDelete │ │ ├── DeleteWithError │ │ │ └── Category.csv │ │ ├── delete │ │ │ ├── Category.csv │ │ │ └── Pet.csv │ │ └── insert │ │ │ ├── Category.csv │ │ │ └── Pet.csv │ │ ├── TestImportTableMissingKey │ │ ├── molgenis.csv │ │ └── test.csv │ │ ├── TestImportTableTask │ │ ├── molgenis.csv │ │ └── test.csv │ │ ├── TestLargeNumeric.xlsx │ │ ├── TypeTest.csv │ │ ├── TypeTest.tsv │ │ ├── TypeTest.xlsx │ │ ├── TypeTestSemiColon.csv │ │ ├── attributes1.txt │ │ ├── attributes_typetest.csv │ │ ├── bbmri-nl-complete.zip │ │ ├── bbmri-nl-complete │ │ ├── attributes.csv │ │ ├── bbmri_nl_age_types.csv │ │ ├── bbmri_nl_biobanks.csv │ │ ├── bbmri_nl_body_parts.csv │ │ ├── bbmri_nl_cohorts.csv │ │ ├── bbmri_nl_collection_types.csv │ │ ├── bbmri_nl_countries.csv │ │ ├── bbmri_nl_data_category_types.csv │ │ ├── bbmri_nl_disease_types.csv │ │ ├── bbmri_nl_exp_data_types.csv │ │ ├── bbmri_nl_imaging_data.csv │ │ ├── bbmri_nl_juristic_persons.csv │ │ ├── bbmri_nl_material_types.csv │ │ ├── bbmri_nl_modalities.csv │ │ ├── bbmri_nl_persons.csv │ │ ├── bbmri_nl_podium.csv │ │ ├── bbmri_nl_publications.csv │ │ ├── bbmri_nl_sample_collections.csv │ │ ├── bbmri_nl_sample_size_types.csv │ │ ├── bbmri_nl_sequences.csv │ │ ├── bbmri_nl_sex_types.csv │ │ ├── bbmri_nl_staff_size_types.csv │ │ ├── entities.csv │ │ ├── packages.csv │ │ └── tags.csv │ │ ├── csv-with-empty-lines.csv │ │ ├── molgenis1 │ │ └── molgenis.csv │ │ ├── profile │ │ └── imagetest.csv │ │ ├── settings_and_members.xlsx │ │ ├── test1.txt │ │ ├── testRenameWhenRefs.csv │ │ └── test_array_with_commas.csv ├── molgenis-emx2-nonparallel-tests │ ├── build.gradle │ └── src │ │ └── test │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ ├── graphql │ │ └── TestGraphqlAggregatePermission.java │ │ └── sql │ │ └── TestMigration.java ├── molgenis-emx2-rdf │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── rdf │ │ │ ├── BasicIRI.java │ │ │ ├── ColumnTypeRdfMapper.java │ │ │ ├── DefaultNamespace.java │ │ │ ├── IriGenerator.java │ │ │ ├── PrimaryKey.java │ │ │ ├── RdfMapData.java │ │ │ ├── RdfRootService.java │ │ │ ├── RdfSchemaService.java │ │ │ ├── RdfSchemaValidationService.java │ │ │ ├── RdfService.java │ │ │ ├── RdfUtils.java │ │ │ ├── config │ │ │ ├── RdfConfig.java │ │ │ └── RdfConfigReader.java │ │ │ ├── generators │ │ │ ├── Emx2RdfGenerator.java │ │ │ ├── RdfApiGenerator.java │ │ │ ├── RdfApiGeneratorFactory.java │ │ │ ├── RdfGenerator.java │ │ │ ├── RdfRowsGenerator.java │ │ │ ├── RootRdfGenerator.java │ │ │ └── SemanticRdfGenerator.java │ │ │ ├── mappers │ │ │ ├── NamespaceMapper.java │ │ │ └── OntologyIriMapper.java │ │ │ ├── shacl │ │ │ ├── ShaclSelector.java │ │ │ └── ShaclSet.java │ │ │ └── writers │ │ │ ├── RdfModelWriter.java │ │ │ ├── RdfStreamWriter.java │ │ │ ├── RdfWriter.java │ │ │ ├── ShaclResultWriter.java │ │ │ └── WriterFactory.java │ │ ├── test │ │ ├── java │ │ │ └── org │ │ │ │ └── molgenis │ │ │ │ └── emx2 │ │ │ │ └── rdf │ │ │ │ ├── ColumnTypeRdfMapperTest.java │ │ │ │ ├── InMemoryRDFHandlerTest.java │ │ │ │ ├── IriGeneratorTest.java │ │ │ │ ├── OntologyTableSemantics.java │ │ │ │ ├── PrimaryKeyTest.java │ │ │ │ ├── RDFTest.java │ │ │ │ ├── RdfUtilsTest.java │ │ │ │ ├── config │ │ │ │ └── RdfConfigReaderTest.java │ │ │ │ ├── mappers │ │ │ │ ├── NamespaceMapperTest.java │ │ │ │ └── OntologyIriMapperTest.java │ │ │ │ └── shacl │ │ │ │ ├── ShaclSelectorTest.java │ │ │ │ └── ShaclSetTest.java │ │ └── resources │ │ │ ├── OntologyTableSemanticsTestFile.csv │ │ │ ├── _shacl │ │ │ └── pet_store_simple │ │ │ │ └── shacl.ttl │ │ │ ├── hpo_patients.xlsx │ │ │ ├── rdf_files │ │ │ └── rdf_api │ │ │ │ └── pet_store │ │ │ │ ├── emx2 │ │ │ │ └── schema.ttl │ │ │ │ └── semantic │ │ │ │ ├── ontology_tag.ttl │ │ │ │ ├── row_fire_ant.ttl │ │ │ │ ├── schema.ttl │ │ │ │ └── table_user.ttl │ │ │ ├── shacl_files │ │ │ └── pet_store │ │ │ │ └── simple │ │ │ │ ├── output_emx2.ttl │ │ │ │ └── output_semantic.ttl │ │ │ └── testfiles │ │ │ └── molgenis.png │ │ └── testFixtures │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── rdf │ │ ├── CustomAssertions.java │ │ ├── InMemoryRDFHandler.java │ │ ├── RdfParser.java │ │ └── RdfValidator.java ├── molgenis-emx2-run │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ └── RunMolgenisEmx2Full.java ├── molgenis-emx2-sql │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── molgenis │ │ │ │ └── emx2 │ │ │ │ └── sql │ │ │ │ ├── AToolToCleanDatabase.java │ │ │ │ ├── ChangeLogExecutor.java │ │ │ │ ├── ChangeLogUtils.java │ │ │ │ ├── JWTgenerator.java │ │ │ │ ├── JooqTransaction.java │ │ │ │ ├── MetadataUtils.java │ │ │ │ ├── MetadataUtils2.java │ │ │ │ ├── MetadataUtils2.java.backup │ │ │ │ ├── Migrations.java │ │ │ │ ├── SqlColumnExecutor.java │ │ │ │ ├── SqlColumnRefArrayExecutor.java │ │ │ │ ├── SqlColumnRefExecutor.java │ │ │ │ ├── SqlDatabase.java │ │ │ │ ├── SqlDatabaseExecutor.java │ │ │ │ ├── SqlMolgenisException.java │ │ │ │ ├── SqlQuery.java │ │ │ │ ├── SqlQueryBuilderHelpers.java │ │ │ │ ├── SqlQueryException.java │ │ │ │ ├── SqlRawQueryForSchema.java │ │ │ │ ├── SqlRow.java │ │ │ │ ├── SqlSchema.java │ │ │ │ ├── SqlSchemaMetadata.java │ │ │ │ ├── SqlSchemaMetadataExecutor.java │ │ │ │ ├── SqlTable.java │ │ │ │ ├── SqlTableMetadata.java │ │ │ │ ├── SqlTableMetadataExecutor.java │ │ │ │ ├── SqlTypeUtils.java │ │ │ │ ├── SqlUserAwareConnectionProvider.java │ │ │ │ └── TestDatabaseFactory.java │ │ └── resources │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── sql │ │ │ ├── migration1.sql │ │ │ ├── migration10.sql │ │ │ ├── migration11.sql │ │ │ ├── migration12.sql │ │ │ ├── migration13.sql │ │ │ ├── migration14.sql │ │ │ ├── migration15.sql │ │ │ ├── migration16.sql │ │ │ ├── migration17.sql │ │ │ ├── migration18.sql │ │ │ ├── migration19.sql │ │ │ ├── migration2.sql │ │ │ ├── migration20.sql │ │ │ ├── migration21.sql │ │ │ ├── migration22.sql │ │ │ ├── migration23.sql │ │ │ ├── migration24.sql │ │ │ ├── migration25.sql │ │ │ ├── migration26.sql │ │ │ ├── migration27.sql │ │ │ ├── migration28.sql │ │ │ ├── migration29.sql │ │ │ ├── migration3.sql │ │ │ ├── migration4.sql │ │ │ ├── migration5.sql │ │ │ ├── migration8.sql │ │ │ └── migration9.sql │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── sql │ │ │ ├── Benchmark.java │ │ │ ├── ChangeLogExecutorTest.java │ │ │ ├── ChangeLogUtilsTest.java │ │ │ ├── InitDatabase.java │ │ │ ├── SnowflakeIdGeneratorTest.java │ │ │ ├── SqlDatabaseTest.java │ │ │ ├── SqlQueryBuilderHelpersTest.java │ │ │ ├── SqlQueryWithRefTests.java │ │ │ ├── SqlSchemaTest.java │ │ │ ├── TestAddColumnUpdateSearchTrigger.java │ │ │ ├── TestAggregatePermission.java │ │ │ ├── TestBatchRequestsForSpeed.java │ │ │ ├── TestChangelog.java │ │ │ ├── TestCompositeForeignKeys.java │ │ │ ├── TestComputedOrDefaultValue.java │ │ │ ├── TestConditionalRequired.java │ │ │ ├── TestCopy.java │ │ │ ├── TestCreateArrayDataTypes.java │ │ │ ├── TestCreateBasicDataColumnTypeColumns.java │ │ │ ├── TestCreateForeignKeys.java │ │ │ ├── TestCreateForeignKeysArrays.java │ │ │ ├── TestCreateForeignKeysCascadeDelete.java │ │ │ ├── TestCreateMREF_old.java │ │ │ ├── TestCreateMref.java │ │ │ ├── TestCreateTransactionForMultipleOperations.java │ │ │ ├── TestCrossSchemaForeignKeysAndInheritance.java │ │ │ ├── TestDeferConstrainChecksToEndOfTransaction.java │ │ │ ├── TestEvaluateExpressions.java │ │ │ ├── TestFileType.java │ │ │ ├── TestFullTextSearch.java │ │ │ ├── TestGrantRolesToUsers.java │ │ │ ├── TestInherits.java │ │ │ ├── TestMergeAlter.java │ │ │ ├── TestMergeDrop.java │ │ │ ├── TestMetaDataIsStoredForNextSessions.java │ │ │ ├── TestMgColumns.java │ │ │ ├── TestOntologyQueries.java │ │ │ ├── TestOntologyTableIsGenerated.java │ │ │ ├── TestOrderByWithCollation.java │ │ │ ├── TestQuery.java │ │ │ ├── TestQueryExpandIntoReferences.java │ │ │ ├── TestQueryJsonGraph.java │ │ │ ├── TestQueryOntologySearchQueryExpansion.java │ │ │ ├── TestReadonly.java │ │ │ ├── TestRefBack.java │ │ │ ├── TestRefBackChangeCascade.java │ │ │ ├── TestRowLevelSecurity.java │ │ │ ├── TestSchemaCreateDestroy.java │ │ │ ├── TestSchemaUpdate.java │ │ │ ├── TestSettings.java │ │ │ ├── TestSqlQueryContainsOperator.java │ │ │ ├── TestSqlRawQueryForSchema.java │ │ │ ├── TestSqlTypeUtils.java │ │ │ ├── TestTableAndColumnMetadataNotTestedElseWhere.java │ │ │ ├── TestTransaction.java │ │ │ ├── TestTruncate.java │ │ │ ├── TestUpdateWithPartialFields.java │ │ │ ├── TestUsersAndPermissions.java │ │ │ └── TestValidation.java │ │ └── resources │ │ └── testfiles │ │ └── molgenis.png ├── molgenis-emx2-tasks │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── tasks │ │ │ ├── ScriptTableListener.java │ │ │ ├── ScriptTask.java │ │ │ ├── ScriptType.java │ │ │ ├── Task.java │ │ │ ├── TaskChangedHandler.java │ │ │ ├── TaskService.java │ │ │ ├── TaskServiceInDatabase.java │ │ │ ├── TaskServiceInMemory.java │ │ │ ├── TaskServiceScheduler.java │ │ │ └── TaskStatus.java │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── tasks │ │ │ ├── DummyTask.java │ │ │ ├── TestScriptTask.java │ │ │ ├── TestTask.java │ │ │ ├── TestTaskServiceDatabaseBacked.java │ │ │ └── TestTaskServiceScheduler.java │ │ └── resources │ │ └── TestScriptTask │ │ ├── Scripts.csv │ │ └── _files │ │ ├── data.csv │ │ ├── extrafiles.zip │ │ └── venv.zip ├── molgenis-emx2-typescript │ ├── build.gradle │ ├── catalogue.ts │ └── src │ │ ├── main │ │ └── java │ │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── typescript │ │ │ ├── AToolToGenerateTypeScriptTypes.java │ │ │ └── Generator.java │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── typescript │ │ │ ├── AToolToGenerateTypeScriptTypesTest.java │ │ │ └── GeneratorTest.java │ │ └── resources │ │ ├── expected-types.ts │ │ └── expected-typetest-types.ts ├── molgenis-emx2-webapi │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── org │ │ │ │ └── molgenis │ │ │ │ └── emx2 │ │ │ │ ├── RunMolgenisEmx2.java │ │ │ │ └── web │ │ │ │ ├── AnalyticsApi.java │ │ │ │ ├── ApplicationCachePerUser.java │ │ │ │ ├── BeaconApi.java │ │ │ │ ├── BootstrapThemeService.java │ │ │ │ ├── CafeVariomeApi.java │ │ │ │ ├── Constants.java │ │ │ │ ├── CsvApi.java │ │ │ │ ├── DownloadApiUtils.java │ │ │ │ ├── ExcelApi.java │ │ │ │ ├── FileApi.java │ │ │ │ ├── GraphqlApi.java │ │ │ │ ├── JavaScriptBindings.java │ │ │ │ ├── JavalinCustomHttpActionAdapter.java │ │ │ │ ├── JsonApi.java │ │ │ │ ├── JsonYamlApi.java │ │ │ │ ├── MessageApi.java │ │ │ │ ├── MolgenisSessionHandler.java │ │ │ │ ├── MolgenisWebservice.java │ │ │ │ ├── OpenApiUiFactory.java │ │ │ │ ├── OpenApiYamlGenerator.java │ │ │ │ ├── PodiumApi.java │ │ │ │ ├── ProfilesApi.java │ │ │ │ ├── RDFApi.java │ │ │ │ ├── SecurityConfigFactory.java │ │ │ │ ├── SiteMapService.java │ │ │ │ ├── StaticFileMapper.java │ │ │ │ ├── TaskApi.java │ │ │ │ ├── TaskReference.java │ │ │ │ ├── ZipApi.java │ │ │ │ ├── actions │ │ │ │ └── SendMessageAction.java │ │ │ │ ├── controllers │ │ │ │ ├── MetricsController.java │ │ │ │ └── OIDCController.java │ │ │ │ ├── response │ │ │ │ ├── ResponseStatus.java │ │ │ │ └── Status.java │ │ │ │ ├── service │ │ │ │ ├── CatalogueSiteMap.java │ │ │ │ └── PodiumService.java │ │ │ │ ├── transformers │ │ │ │ └── ActionTransformer.java │ │ │ │ └── util │ │ │ │ ├── EncodingHelpers.java │ │ │ │ ├── EnvHelpers.java │ │ │ │ └── HttpHeaderUtils.java │ │ └── resources │ │ │ ├── public_html │ │ │ ├── apps │ │ │ │ └── resources │ │ │ │ │ └── webfonts │ │ │ │ │ ├── fa-brands-400.eot │ │ │ │ │ ├── fa-brands-400.svg │ │ │ │ │ ├── fa-brands-400.ttf │ │ │ │ │ ├── fa-brands-400.woff │ │ │ │ │ ├── fa-brands-400.woff2 │ │ │ │ │ ├── fa-regular-400.eot │ │ │ │ │ ├── fa-regular-400.svg │ │ │ │ │ ├── fa-regular-400.ttf │ │ │ │ │ ├── fa-regular-400.woff │ │ │ │ │ ├── fa-regular-400.woff2 │ │ │ │ │ ├── fa-solid-900.eot │ │ │ │ │ ├── fa-solid-900.svg │ │ │ │ │ ├── fa-solid-900.ttf │ │ │ │ │ ├── fa-solid-900.woff │ │ │ │ │ └── fa-solid-900.woff2 │ │ │ └── js │ │ │ │ └── expressions │ │ │ │ └── 0.21.2 │ │ │ │ └── expressions.js │ │ │ └── theme │ │ │ ├── bootstrap46 │ │ │ ├── _alert.scss │ │ │ ├── _badge.scss │ │ │ ├── _breadcrumb.scss │ │ │ ├── _button-group.scss │ │ │ ├── _buttons.scss │ │ │ ├── _card.scss │ │ │ ├── _carousel.scss │ │ │ ├── _close.scss │ │ │ ├── _code.scss │ │ │ ├── _custom-forms.scss │ │ │ ├── _dropdown.scss │ │ │ ├── _forms.scss │ │ │ ├── _functions.scss │ │ │ ├── _grid.scss │ │ │ ├── _images.scss │ │ │ ├── _input-group.scss │ │ │ ├── _jumbotron.scss │ │ │ ├── _list-group.scss │ │ │ ├── _media.scss │ │ │ ├── _mixins.scss │ │ │ ├── _modal.scss │ │ │ ├── _nav.scss │ │ │ ├── _navbar.scss │ │ │ ├── _pagination.scss │ │ │ ├── _popover.scss │ │ │ ├── _print.scss │ │ │ ├── _progress.scss │ │ │ ├── _reboot.scss │ │ │ ├── _root.scss │ │ │ ├── _spinners.scss │ │ │ ├── _tables.scss │ │ │ ├── _toasts.scss │ │ │ ├── _tooltip.scss │ │ │ ├── _transitions.scss │ │ │ ├── _type.scss │ │ │ ├── _utilities.scss │ │ │ ├── _variables.scss │ │ │ ├── bootstrap-grid.scss │ │ │ ├── bootstrap-reboot.scss │ │ │ ├── bootstrap.scss │ │ │ ├── mixins │ │ │ │ ├── _alert.scss │ │ │ │ ├── _background-variant.scss │ │ │ │ ├── _badge.scss │ │ │ │ ├── _border-radius.scss │ │ │ │ ├── _box-shadow.scss │ │ │ │ ├── _breakpoints.scss │ │ │ │ ├── _buttons.scss │ │ │ │ ├── _caret.scss │ │ │ │ ├── _clearfix.scss │ │ │ │ ├── _deprecate.scss │ │ │ │ ├── _float.scss │ │ │ │ ├── _forms.scss │ │ │ │ ├── _gradients.scss │ │ │ │ ├── _grid-framework.scss │ │ │ │ ├── _grid.scss │ │ │ │ ├── _hover.scss │ │ │ │ ├── _image.scss │ │ │ │ ├── _list-group.scss │ │ │ │ ├── _lists.scss │ │ │ │ ├── _nav-divider.scss │ │ │ │ ├── _pagination.scss │ │ │ │ ├── _reset-text.scss │ │ │ │ ├── _resize.scss │ │ │ │ ├── _screen-reader.scss │ │ │ │ ├── _size.scss │ │ │ │ ├── _table-row.scss │ │ │ │ ├── _text-emphasis.scss │ │ │ │ ├── _text-hide.scss │ │ │ │ ├── _text-truncate.scss │ │ │ │ ├── _transition.scss │ │ │ │ └── _visibility.scss │ │ │ ├── utilities │ │ │ │ ├── _align.scss │ │ │ │ ├── _background.scss │ │ │ │ ├── _borders.scss │ │ │ │ ├── _clearfix.scss │ │ │ │ ├── _display.scss │ │ │ │ ├── _embed.scss │ │ │ │ ├── _flex.scss │ │ │ │ ├── _float.scss │ │ │ │ ├── _interactions.scss │ │ │ │ ├── _overflow.scss │ │ │ │ ├── _position.scss │ │ │ │ ├── _screenreaders.scss │ │ │ │ ├── _shadows.scss │ │ │ │ ├── _sizing.scss │ │ │ │ ├── _spacing.scss │ │ │ │ ├── _stretched-link.scss │ │ │ │ ├── _text.scss │ │ │ │ └── _visibility.scss │ │ │ └── vendor │ │ │ │ └── _rfs.scss │ │ │ ├── fontawesom5153 │ │ │ ├── _animated.scss │ │ │ ├── _bordered-pulled.scss │ │ │ ├── _core.scss │ │ │ ├── _fixed-width.scss │ │ │ ├── _icons.scss │ │ │ ├── _larger.scss │ │ │ ├── _list.scss │ │ │ ├── _mixins.scss │ │ │ ├── _rotated-flipped.scss │ │ │ ├── _screen-reader.scss │ │ │ ├── _shims.scss │ │ │ ├── _stacked.scss │ │ │ ├── _variables.scss │ │ │ ├── brands.scss │ │ │ ├── fontawesome.scss │ │ │ ├── regular.scss │ │ │ ├── solid.scss │ │ │ └── v4-shims.scss │ │ │ └── theme.scss │ │ └── test │ │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ └── web │ │ │ ├── JavalinCustomHttpActionAdapterTest.java │ │ │ ├── PerformanceTest.java │ │ │ ├── RunWebApi.java │ │ │ ├── StaticFileMapperTest.java │ │ │ ├── TestOpenApi.java │ │ │ ├── TestUtils.java │ │ │ ├── TestValidationWithJavaScriptBindings.java │ │ │ ├── WebApiSmokeTests.java │ │ │ ├── service │ │ │ ├── CatalogueSiteMapTest.java │ │ │ └── PodiumServiceTest.java │ │ │ ├── test.json │ │ │ └── util │ │ │ ├── EncodingHelpersTest.java │ │ │ ├── EnvHelpersTest.java │ │ │ └── HttpHeaderUtilsTest.java │ │ └── resources │ │ ├── index.html │ │ └── test.txt └── molgenis-emx2 │ ├── build.gradle │ └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── molgenis │ │ │ └── emx2 │ │ │ ├── Binary.java │ │ │ ├── BinaryFileWrapper.java │ │ │ ├── Change.java │ │ │ ├── Column.java │ │ │ ├── ColumnType.java │ │ │ ├── Constants.java │ │ │ ├── Database.java │ │ │ ├── DatabaseListener.java │ │ │ ├── Filter.java │ │ │ ├── FilterBean.java │ │ │ ├── HasLabelsDescriptionsAndSettings.java │ │ │ ├── HasSettings.java │ │ │ ├── HasSettingsInterface.java │ │ │ ├── LastUpdate.java │ │ │ ├── Member.java │ │ │ ├── MolgenisException.java │ │ │ ├── MutationType.java │ │ │ ├── Operator.java │ │ │ ├── Order.java │ │ │ ├── Privileges.java │ │ │ ├── Query.java │ │ │ ├── QueryBean.java │ │ │ ├── Reference.java │ │ │ ├── Row.java │ │ │ ├── Schema.java │ │ │ ├── SchemaInfo.java │ │ │ ├── SchemaMetadata.java │ │ │ ├── SelectColumn.java │ │ │ ├── Sort.java │ │ │ ├── Table.java │ │ │ ├── TableListener.java │ │ │ ├── TableMetadata.java │ │ │ ├── TableType.java │ │ │ ├── Transaction.java │ │ │ ├── User.java │ │ │ ├── Version.java │ │ │ ├── beans │ │ │ ├── ColumnAnnotation.java │ │ │ ├── Mapper.java │ │ │ └── SortBean.java │ │ │ └── utils │ │ │ ├── ColumnSort.java │ │ │ ├── EnvironmentProperty.java │ │ │ ├── JavaScriptUtils.java │ │ │ ├── MolgenisExceptionDetail.java │ │ │ ├── MolgenisObjectMapper.java │ │ │ ├── PeriodConverter.java │ │ │ ├── RandomString.java │ │ │ ├── StopWatch.java │ │ │ ├── TableSort.java │ │ │ ├── TypeUtils.java │ │ │ ├── URIUtils.java │ │ │ ├── URLUtils.java │ │ │ └── generator │ │ │ ├── IdGenerator.java │ │ │ ├── IdGeneratorImpl.java │ │ │ └── SnowflakeIdGenerator.java │ └── resources │ │ └── log4j2.xml │ ├── test │ └── java │ │ └── org │ │ └── molgenis │ │ └── emx2 │ │ ├── TestColumn.java │ │ ├── TestColumnTypeValidation.java │ │ ├── TestGetSetAllTypesOnRows.java │ │ ├── TestMapPojoToTable.java │ │ ├── TestRows.java │ │ ├── TestTableColumnLabels.java │ │ ├── TestTableMetadata.java │ │ ├── TestTypeUtils.java │ │ ├── TestUser.java │ │ ├── beans │ │ ├── PersonBean.java │ │ └── TypeTestBean.java │ │ └── utils │ │ ├── TestJavaScriptUtils.java │ │ └── URLUtilsTest.java │ └── testFixtures │ └── java │ └── org │ └── molgenis │ └── emx2 │ └── TestResourceLoader.java ├── changelog-notes.tpl ├── ci-build-images └── Dockerfile ├── ci-build-packages ├── SCRIPTS │ ├── after-install.sh │ ├── after-remove.sh │ ├── before-install.sh │ └── before-remove.sh ├── create-nightly-release.sh ├── create-packages.sh ├── create-stable-release.sh ├── log4j2.xml └── molgenis-emx2.service ├── ci ├── create_or_update_k8s-azure.sh └── set_kubectl_config-azure.sh ├── data ├── _Design decisions.md ├── __init__.py ├── _demodata │ ├── applications │ │ ├── datacatalogue │ │ │ ├── Agents.csv │ │ │ ├── Collection events.csv │ │ │ ├── Contacts.csv │ │ │ ├── Dataset mappings.csv │ │ │ ├── Datasets.csv │ │ │ ├── Documentation.csv │ │ │ ├── Endpoint.csv │ │ │ ├── External identifiers.csv │ │ │ ├── Internal identifiers.csv │ │ │ ├── Linkages.csv │ │ │ ├── Organisations.csv │ │ │ ├── Profiles.csv │ │ │ ├── Publications.csv │ │ │ ├── Resource counts.csv │ │ │ ├── Resource mappings.csv │ │ │ ├── Resources.csv │ │ │ ├── Reused variables.csv │ │ │ ├── Samplesets.csv │ │ │ ├── Subpopulation counts.csv │ │ │ ├── Subpopulations.csv │ │ │ ├── Variable mappings.csv │ │ │ ├── Variable values.csv │ │ │ ├── Variables.csv │ │ │ ├── Version.csv │ │ │ └── _files │ │ │ │ ├── 1433a47ade624a84b23167b2021ed410.jpg │ │ │ │ ├── 17a9dab7e7274b51a7d9c4371194bad8.jpg │ │ │ │ ├── 49a688823ceb44069e16b921c6b0ddae.jpg │ │ │ │ ├── 653af6b84ed94a6fbec96f811df4299b.jpg │ │ │ │ ├── 742c473e39e64ba397f07d0e9a6d84da.jpg │ │ │ │ ├── 7ae000c0426946209404493371e33377.jpg │ │ │ │ ├── 7c5a586c66744471b2b3c610cc1dfc9e.jpg │ │ │ │ ├── 9e9be3caf2284bd38889c4075320f62b.jpg │ │ │ │ ├── bb2e0096f12a4ea1a92b6682345263e3.jpg │ │ │ │ ├── cc3cbe18cd164188962e956ddc3308a7.jpg │ │ │ │ ├── d11622fcde214ade936ce9ef80e8914d.jpg │ │ │ │ ├── d4b566a3ca814f75a75f7410b7f456f8.jpg │ │ │ │ ├── f1618ae223d443619561102558321969.jpg │ │ │ │ └── ff8595905e194f769a76eb0757debc46.jpg │ │ ├── datacatalogue_aggregates │ │ │ ├── Collections.csv │ │ │ └── FORCE_NEN patients.csv │ │ ├── datacatalogue_cohortstaging │ │ │ ├── Collection events.csv │ │ │ ├── Contacts.csv │ │ │ ├── Dataset mappings.csv │ │ │ ├── Datasets.csv │ │ │ ├── Documentation.csv │ │ │ ├── External identifiers.csv │ │ │ ├── Organisations.csv │ │ │ ├── Publications.csv │ │ │ ├── Resources.csv │ │ │ ├── Subpopulation counts.csv │ │ │ ├── Subpopulations.csv │ │ │ ├── Variable mappings.csv │ │ │ ├── Variable values.csv │ │ │ └── Variables.csv │ │ ├── datacatalogue_networkstaging │ │ │ ├── Collection events.csv │ │ │ ├── Contacts.csv │ │ │ ├── Datasets.csv │ │ │ ├── Documentation.csv │ │ │ ├── Resources.csv │ │ │ ├── Subpopulations.csv │ │ │ ├── Variable values.csv │ │ │ └── Variables.csv │ │ ├── imagetest │ │ │ ├── User.csv │ │ │ └── _files │ │ │ │ └── e019a97346d1416f91ba56fe842f44c6.jpg │ │ ├── pages │ │ │ ├── Dependencies CSS.csv │ │ │ └── Developer page.csv │ │ ├── patient_registry │ │ │ ├── Agents.csv │ │ │ ├── Clinical measurements.csv │ │ │ ├── Clinical observations.csv │ │ │ ├── Consent documents.csv │ │ │ ├── Contacts.csv │ │ │ ├── Disease history.csv │ │ │ ├── Endpoint.csv │ │ │ ├── Experiments OGM.csv │ │ │ ├── Experiments RNA.csv │ │ │ ├── Experiments lrGS.csv │ │ │ ├── Experiments srDNA.csv │ │ │ ├── File locations.csv │ │ │ ├── File storage location.csv │ │ │ ├── Files.csv │ │ │ ├── Genomic variants.csv │ │ │ ├── Individual consent.csv │ │ │ ├── Individuals.csv │ │ │ ├── Interpretation consensus.csv │ │ │ ├── Pedigree members.csv │ │ │ ├── Pedigree.csv │ │ │ ├── Phenotype observations.csv │ │ │ ├── Resources.csv │ │ │ ├── Variant interpretation analyses.csv │ │ │ └── Variant interpretations.csv │ │ └── petstore │ │ │ ├── Category.csv │ │ │ ├── Order.csv │ │ │ ├── Pet.csv │ │ │ ├── User.csv │ │ │ └── _files │ │ │ └── 65c0628c9e94414d877e4a51cf5dc3ac.jpg │ └── shared-examples │ │ ├── Agent.csv │ │ ├── Catalog.csv │ │ ├── Cohorts.csv │ │ ├── ContactPersons.csv │ │ ├── Contacts.csv │ │ ├── Container.csv │ │ ├── Datasets.csv │ │ ├── Endpoint.csv │ │ ├── Organisations.csv │ │ └── Resources.csv ├── _models │ ├── shared │ │ ├── Agents.csv │ │ ├── Collection events.csv │ │ ├── Consent documents.csv │ │ ├── Contacts.csv │ │ ├── Dataset mappings.csv │ │ ├── Datasets.csv │ │ ├── Documentation.csv │ │ ├── Endpoint.csv │ │ ├── External identifiers.csv │ │ ├── Genomic variants.csv │ │ ├── Individuals.csv │ │ ├── Internal identifiers.csv │ │ ├── Linkages.csv │ │ ├── Materials.csv │ │ ├── Organisations.csv │ │ ├── Pedigree.csv │ │ ├── Processes.csv │ │ ├── Profiles.csv │ │ ├── Publications.csv │ │ ├── Resource counts.csv │ │ ├── Resource mappings.csv │ │ ├── Resources.csv │ │ ├── Reused variables.csv │ │ ├── Samplesets.csv │ │ ├── Subpopulation counts.csv │ │ ├── Subpopulations.csv │ │ ├── Variable mappings.csv │ │ ├── Variable values.csv │ │ ├── Variables.csv │ │ ├── Variant interpretations.csv │ │ └── Version.csv │ └── specific │ │ ├── Catalogue aggregates.csv │ │ ├── CatalogueOntologies │ │ └── molgenis.csv │ │ ├── Pages.csv │ │ ├── RD3.csv │ │ ├── dev │ │ └── DataCatalogueFlat.csv │ │ ├── imagetest.csv │ │ ├── petstore.csv │ │ └── typetest.csv ├── _ontologies │ ├── ATC.csv │ ├── Access rights.csv │ ├── Age groups at onset.csv │ ├── Age groups.csv │ ├── AgeGroups.csv │ ├── Agent types.csv │ ├── Allow recontacting.csv │ ├── Analyses performed.csv │ ├── Anatomical location.csv │ ├── Ancestry.csv │ ├── Areas of information cohorts.csv │ ├── Areas of information ds.csv │ ├── CatalogueTypes.csv │ ├── Chromosomes.csv │ ├── Clinical study types.csv │ ├── Cohort collection types.csv │ ├── Cohort designs.csv │ ├── Cohort study types.csv │ ├── Consent document types.csv │ ├── Consent representative.csv │ ├── Contribution types.csv │ ├── Countries.csv │ ├── DAP information.csv │ ├── DCMITypes.csv │ ├── Data access conditions.csv │ ├── Data categories.csv │ ├── Data use conditions.csv │ ├── Data use modifiers.csv │ ├── Data use permissions.csv │ ├── Dataset types.csv │ ├── Datasource types.csv │ ├── Disease stage.csv │ ├── Disease status.csv │ ├── Diseases-DUPLICATE.csv │ ├── Diseases.csv │ ├── DistributionType.csv │ ├── Document types.csv │ ├── External identifier types.csv │ ├── Family relations.csv │ ├── File formats.csv │ ├── File storage locations.csv │ ├── Formats.csv │ ├── Funding types.csv │ ├── Gender at birth.csv │ ├── Gender identity.csv │ ├── Genes.csv │ ├── Genome accessions.csv │ ├── Genotypic sex.csv │ ├── ICDO morphologies.csv │ ├── ICDO topologies.csv │ ├── INN.csv │ ├── Inclusion Exclusion Criteria.csv │ ├── InclusionCriteria.csv │ ├── Individual analysis consensus.csv │ ├── Individual status.csv │ ├── Informed consent required.csv │ ├── Informed consent types.csv │ ├── Inheritance pattern.csv │ ├── Internal identifier types.csv │ ├── Keywords.csv │ ├── Languages-DUPLICATE.csv │ ├── Languages.csv │ ├── Legislations.csv │ ├── Library layout.csv │ ├── Library source.csv │ ├── Linkage strategies.csv │ ├── Mapping status.csv │ ├── MedDRA.csv │ ├── Medical history.csv │ ├── Medication.csv │ ├── Medicine brand names.csv │ ├── Metabolomic analysis type.csv │ ├── Metabolomic assay type.csv │ ├── Metabolomic processing type.csv │ ├── Month of the year.csv │ ├── Months.csv │ ├── Network features.csv │ ├── Network types.csv │ ├── NoYesUnknown.csv │ ├── Observation targets.csv │ ├── Off study reasons.csv │ ├── Organisation features.csv │ ├── Organisation roles.csv │ ├── Organisation types.csv │ ├── Organisations.csv │ ├── Pathological state.csv │ ├── Phenotypes.csv │ ├── Population entry.csv │ ├── Population exit.csv │ ├── Population of interest.csv │ ├── Refresh periods.csv │ ├── Regions.csv │ ├── Release types.csv │ ├── Resource types.csv │ ├── Resources.csv │ ├── Sample availability.csv │ ├── Sample categories.csv │ ├── Sample type.csv │ ├── Sample types.csv │ ├── Sequencing enrichment kits.csv │ ├── Sequencing instrument models.csv │ ├── Sequencing methods.csv │ ├── Sequencing platforms.csv │ ├── Severity.csv │ ├── Sex.csv │ ├── Standardized tools.csv │ ├── Status details.csv │ ├── Status.csv │ ├── Storage conditions.csv │ ├── Study datasource types.csv │ ├── Study design classification.csv │ ├── Study features.csv │ ├── Study funding.csv │ ├── Study quality marks.csv │ ├── Study requirements.csv │ ├── Study scopes.csv │ ├── Study status.csv │ ├── Study topics.csv │ ├── Study trial regulatory scopes.csv │ ├── Study types.csv │ ├── StudyDesign.csv │ ├── Tag.csv │ ├── Themes.csv │ ├── Time periods.csv │ ├── Tissue type.csv │ ├── Titles.csv │ ├── Tumor sites.csv │ ├── Units.csv │ ├── Variable repeat units.csv │ ├── Variant classifications.csv │ ├── Variant origin.csv │ ├── Variant types.csv │ ├── Variation category.csv │ ├── Visit type.csv │ ├── Vocabularies.csv │ ├── Web fetch priority.csv │ ├── Web languages.csv │ ├── Years.csv │ ├── Zygosity.csv │ └── _semantics.csv ├── _profiles │ ├── CohortsStaging.yaml │ ├── DataCatalogue.yaml │ ├── DataCatalogueAggregates.yaml │ ├── FAIRGenomes.yaml │ ├── INTEGRATECohorts.yaml │ ├── ImageTest.yaml │ ├── NetworksStaging.yaml │ ├── Pages.yaml │ ├── PatientRegistry.yaml │ ├── PetStore.yaml │ ├── RWEStaging.yaml │ ├── SharedStaging.yaml │ ├── StudiesStaging.yaml │ ├── TypeTest.yaml │ ├── UMCGCohortsStaging.yaml │ └── UMCUCohorts.yaml ├── _settings │ ├── datacatalogue │ │ └── molgenis_settings.csv │ ├── datacatalogue_sharedstaging │ │ └── molgenis_members.csv │ ├── gdi │ │ └── placeholder.csv │ ├── patient_registry │ │ ├── molgenis_members.csv │ │ └── molgenis_settings.csv │ └── petstore │ │ ├── molgenis_members.csv │ │ └── molgenis_settings.csv ├── _shacl │ ├── dcat-ap │ │ └── v3.0.0 │ │ │ ├── imports.ttl │ │ │ ├── mdr-vocabularies.shape.ttl │ │ │ ├── mdr_imports.ttl │ │ │ ├── range.ttl │ │ │ ├── shapes.ttl │ │ │ └── shapes_recommended.ttl │ ├── ejp_rd_vp_level_1 │ │ └── 01-08-2024 │ │ │ ├── biobank.shacl │ │ │ ├── catalog.shacl │ │ │ ├── data-service.shacl │ │ │ ├── dataset.shacl │ │ │ ├── distribution.shacl │ │ │ ├── guideline.shacl │ │ │ ├── patient-registry.shacl │ │ │ └── resource.shacl │ ├── fair_data_point │ │ └── v1.2 │ │ │ ├── CatalogShape.ttl │ │ │ └── FAIRDataPointShape.ttl │ ├── health-ri │ │ ├── v1.0.0 │ │ │ ├── Catalog.ttl │ │ │ ├── DataService.ttl │ │ │ ├── Dataset.ttl │ │ │ ├── DatasetSeries.ttl │ │ │ ├── Distribution.ttl │ │ │ └── Resource.ttl │ │ ├── v2.0.0 │ │ │ └── HRI-Datamodel-shapes.ttl │ │ └── v2.0.2 │ │ │ └── HRI-Datamodel-shapes.ttl │ └── sets.yaml ├── biobank-directory │ ├── demo │ │ ├── AlsoKnownIn.csv │ │ ├── Biobanks.csv │ │ ├── CollectionFacts.csv │ │ ├── Collections.csv │ │ ├── NationalNodes.csv │ │ ├── Networks.csv │ │ ├── Persons.csv │ │ ├── QualityInfoBiobanks.csv │ │ ├── QualityInfoCollections.csv │ │ ├── QualityInfoServices.csv │ │ ├── Services.csv │ │ ├── Studies.csv │ │ ├── molgenis_members.csv │ │ └── molgenis_settings.csv │ ├── molgenis.csv │ ├── ontologies │ │ ├── AccessTypes.csv │ │ ├── AgeRanges.csv │ │ ├── AgeUnits.csv │ │ ├── AssessmentLevels.csv │ │ ├── BodyParts.csv │ │ ├── Categories.csv │ │ ├── CollectionTypes.csv │ │ ├── CommonNetworkElements.csv │ │ ├── Countries.csv │ │ ├── DataCategories.csv │ │ ├── DataRefreshTypes.csv │ │ ├── DataUseOntologies.csv │ │ ├── DiseaseTypes.csv │ │ ├── ImageDatasetTypes.csv │ │ ├── ImagingModalities.csv │ │ ├── MaterialTypes.csv │ │ ├── QualityStandards.csv │ │ ├── SOPs.csv │ │ ├── SampleSizes.csv │ │ ├── ServiceCategories.csv │ │ ├── ServiceTypes.csv │ │ ├── SexTypes.csv │ │ ├── StorageTemperatureTypes.csv │ │ ├── TRLs.csv │ │ └── molgenis.csv │ └── stagingArea │ │ ├── demo │ │ ├── AlsoKnownIn.csv │ │ ├── Biobanks.csv │ │ ├── CollectionFacts.csv │ │ ├── Collections.csv │ │ ├── Networks.csv │ │ ├── Persons.csv │ │ ├── Services.csv │ │ └── Studies.csv │ │ └── molgenis.csv ├── dashboard │ ├── demodata │ │ ├── datasets │ │ │ ├── dataproviders.csv │ │ │ └── statistics.csv │ │ └── ontologies │ │ │ ├── components.csv │ │ │ └── organisations.csv │ └── molgenis.csv ├── datacatalogue │ ├── .gitignore │ ├── Cohorts_CoreVariables.xlsx │ ├── Cohorts_SourceVariablesAndMappings.xlsx │ ├── EMA_3.8 │ │ └── molgenis.csv │ ├── RWEcatalogue │ │ ├── AgeGroups.csv │ │ ├── CareSettings.csv │ │ ├── Contacts.csv │ │ ├── Countries.csv │ │ ├── Counts.csv │ │ ├── DAPs.csv │ │ ├── Data sources.csv │ │ ├── DatabankFamilies.csv │ │ ├── FundingTypes.csv │ │ ├── InformedConsents.csv │ │ ├── InstitutionRoles.csv │ │ ├── InstitutionTypes.csv │ │ ├── Languages.csv │ │ ├── LinkageStrategies.csv │ │ ├── Linked resources.csv │ │ ├── Months.csv │ │ ├── Organisations.csv │ │ ├── Regions.csv │ │ ├── ResourceTypes.csv │ │ ├── StudyFeatures.csv │ │ ├── StudyFunding.csv │ │ ├── StudyTypes.csv │ │ └── Vocabularies.csv │ ├── _datacatalogue_schema.xlsx │ ├── model-update-procedure.md │ ├── molgenis_settings.csv │ └── stagingRWE │ │ └── molgenis.csv ├── patient_registry_demo │ ├── data │ │ ├── components.csv │ │ ├── dataproviders.csv │ │ ├── followUpSubject.csv │ │ ├── historyStatistics.csv │ │ ├── statistics.csv │ │ └── subject.csv │ ├── molgenis.csv │ └── ontologies │ │ ├── Icd10.csv │ │ ├── InclusionStatus.csv │ │ ├── SequencingMethods.csv │ │ ├── acmg.csv │ │ ├── activeLesionsBSA.csv │ │ ├── affectedSiblings.csv │ │ ├── allelicState.csv │ │ ├── allocateSufferingConditions.csv │ │ ├── anatomicalSources.csv │ │ ├── arthritis.csv │ │ ├── biologicalDiagnosis.csv │ │ ├── biospecimenTypes.csv │ │ ├── cancer.csv │ │ ├── cancerForm.csv │ │ ├── cockayneSyndromeType.csv │ │ ├── codesystemType.csv │ │ ├── complementationGroup1.csv │ │ ├── complementationGroup2.csv │ │ ├── complementationGroup3.csv │ │ ├── complementationGroup4.csv │ │ ├── complementationGroup5.csv │ │ ├── countries.csv │ │ ├── countryEU.csv │ │ ├── cultureType.csv │ │ ├── currentAcne.csv │ │ ├── deformitiesExtremities.csv │ │ ├── diseaseGroup.csv │ │ ├── extracutaneousOrgans.csv │ │ ├── eyeColor.csv │ │ ├── familyMembers.csv │ │ ├── fitzpatrickTypes.csv │ │ ├── genderAtBirth.csv │ │ ├── genderIdentity.csv │ │ ├── gene.csv │ │ ├── geneticTestingDone.csv │ │ ├── goodBadUnknown.csv │ │ ├── grades.csv │ │ ├── hairColor.csv │ │ ├── hematologicalType.csv │ │ ├── hpo.csv │ │ ├── icf.csv │ │ ├── inheritance.csv │ │ ├── medicalImage.csv │ │ ├── mobility.csv │ │ ├── modeOfInheritance.csv │ │ ├── mucosalInvolvement.csv │ │ ├── onsetType.csv │ │ ├── ordo.csv │ │ ├── organisations.csv │ │ ├── otherCancerEB.csv │ │ ├── otherFamilyConditions.csv │ │ ├── painNAS.csv │ │ ├── positiveNegativeUnknown.csv │ │ ├── remainingLesionsBSA.csv │ │ ├── responseToTreatment.csv │ │ ├── sampleType.csv │ │ ├── score1.csv │ │ ├── score2.csv │ │ ├── skinColor.csv │ │ ├── skinManifestations.csv │ │ ├── subgroupGenodermatosis.csv │ │ ├── subgroupsDNA.csv │ │ ├── transport.csv │ │ ├── typeHurleyStage.csv │ │ ├── typeOfEB.csv │ │ ├── typeOfInflammatoryBowelDisease.csv │ │ ├── weekMonth.csv │ │ ├── weekspreg.csv │ │ ├── yesNo.csv │ │ ├── yesNoMultiple.csv │ │ ├── yesNoNotReported.csv │ │ ├── yesNoUnknown.csv │ │ ├── yesNoWheelchair.csv │ │ └── yesNotReported.csv ├── projectmanager │ ├── data │ │ ├── PanamaExport.csv │ │ ├── Persons.csv │ │ ├── Planning.csv │ │ ├── ProjectUnits.csv │ │ └── Projects.csv │ └── molgenis.csv ├── scripts │ ├── .gitignore │ ├── __init__.py │ ├── catalogue │ │ ├── .env_example │ │ ├── README │ │ ├── __init__.py │ │ ├── catalogue_util │ │ │ ├── __init__.py │ │ │ ├── client.py │ │ │ └── zip_handling.py │ │ ├── new_run.py │ │ ├── publish │ │ │ └── publish_resources.py │ │ ├── requirements.txt │ │ ├── run.py │ │ ├── run_old.py │ │ └── update │ │ │ ├── __init__.py │ │ │ ├── spaces_for_3x.py │ │ │ ├── update_2_9.py │ │ │ ├── update_3_10.py │ │ │ ├── update_3_11.py │ │ │ ├── update_3_7.py │ │ │ ├── update_3_8.py │ │ │ ├── update_3_x.py │ │ │ ├── update_5_x.py │ │ │ ├── update_5_x_old.py │ │ │ └── update_7_x.py │ ├── catalogue_portals_merge.py │ ├── feat_flat_catalogue_model.py │ ├── merge_models.py │ └── util │ │ ├── __init__.py │ │ ├── client.py │ │ ├── update_client.py │ │ └── zip_handling.py └── ui_dashboards │ ├── demodata │ ├── Chart data.csv │ ├── Chart palette.csv │ ├── Charts.csv │ └── Dashboard pages.csv │ ├── molgenis.csv │ └── ontologies │ ├── Chart types.csv │ ├── Legend positions.csv │ └── Time intervals.csv ├── docker-compose.yml ├── docs ├── .nojekyll ├── README.md ├── _footer.md ├── _navbar.md ├── _sidebar.md ├── armadillo │ ├── README.md │ ├── _sidebar.md │ ├── data_cohort-data-manager.md │ └── data_researcher.md ├── build.gradle ├── catalogue │ ├── README.md │ ├── _sidebar.md │ ├── cat_admin.md │ ├── cat_data-manager.md │ └── cat_researcher.md ├── directory │ ├── README.md │ ├── _sidebar.md │ └── directory_admin.md ├── img │ ├── cat_armadillo-lifecycle-login.png │ ├── cat_catalogue-landing-page.png │ ├── cat_cohort-harmonised-variable.png │ ├── cat_collections-list.png │ ├── cat_databases.png │ ├── cat_detailed-harmonised-variable-view.png │ ├── cat_federated-analysis.png │ ├── cat_filters-collections.png │ ├── cat_harmonisation-specifications.png │ ├── cat_homepage-variables.png │ ├── cat_homepage.png │ ├── cat_keywords-sheet.png │ ├── cat_project-variables.png │ ├── cat_resource-information-page.png │ ├── cat_rstudio-login.png │ ├── cat_search-and-filters.png │ ├── cat_search-variables.png │ ├── cat_tables-in-catalogue.png │ ├── cat_tables-in-cohort-catalogue.png │ ├── cat_target-collection-events-sheet.png │ ├── cat_target-release-sheet.png │ ├── cat_target-repeated-variable-sheet.png │ ├── cat_target-subcohorts-sheet.png │ ├── cat_target-tables-sheet.png │ ├── cat_target-variable-sheet.png │ ├── cat_target-variables-sheet.png │ ├── cat_variable-mapping.png │ ├── cat_variable-open.png │ ├── cat_variables-search-bar.png │ ├── molgenis_logo_white.png │ ├── semantics.png │ ├── start-change-password.png │ ├── start-create-database-next.png │ ├── start-create-database.png │ ├── start-database-list.png │ ├── start-download-excel.png │ ├── start-download.png │ ├── start-hi-admin.png │ ├── start-import.png │ ├── start-schema-edit-example.png │ ├── start-schema-edit.png │ ├── start-tables-example.png │ ├── start-tables.png │ └── start-welcome.png ├── index.html ├── install.md ├── intro.md ├── molgenis │ ├── CSV.md │ ├── README.md │ ├── _sidebar.md │ ├── dev.md │ ├── dev_apps.md │ ├── dev_architecture.md │ ├── dev_basics.md │ ├── dev_batchapi.md │ ├── dev_beaconv2.md │ ├── dev_cafevariome.md │ ├── dev_graphql.md │ ├── dev_guidelines.md │ ├── dev_messageapi.md │ ├── dev_migrations.md │ ├── dev_principles.md │ ├── dev_profiles.md │ ├── dev_quickstart.md │ ├── dev_rdf.md │ ├── dev_technologies.md │ ├── dev_troubleshooting.md │ ├── run.md │ ├── run_backup.md │ ├── run_docker.md │ ├── run_helm.md │ ├── run_java.md │ ├── run_systemd.md │ ├── run_updates.md │ ├── semantics.md │ ├── use.md │ ├── use_analytics.md │ ├── use_database.md │ ├── use_database_settings.md │ ├── use_forms.md │ ├── use_global_settings.md │ ├── use_permissions.md │ ├── use_quickstart.md │ ├── use_reports.md │ ├── use_schema.md │ ├── use_scripts_jobs.md │ ├── use_tables.md │ ├── use_tokens.md │ ├── use_updownload.md │ ├── use_usingapis.md │ └── use_usingpyclient.md └── resources │ ├── BBMRI-NL_catalogue_form.docx │ ├── Dictionary.xlsx │ ├── Dictionary_testCohort.xlsx │ ├── Dictionary_testNetwork.xlsx │ ├── FairDataPointTemplate.xlsx │ ├── Mappings.xlsx │ ├── Mappings_testCohort.xlsx │ └── reflink_example1739203151994.zip ├── e2e ├── README.md ├── __screenshots__ │ └── catalogue │ │ └── should-show-the-alt-logo.spec.ts │ │ └── should-show-the-alt-logo-1.png ├── manual-tests │ ├── README.md │ └── catalogue │ │ ├── catalogue-test_1.md │ │ ├── catalogue-test_10.md │ │ ├── catalogue-test_11.md │ │ ├── catalogue-test_12.md │ │ ├── catalogue-test_13.md │ │ ├── catalogue-test_2.md │ │ ├── catalogue-test_4.md │ │ ├── catalogue-test_5.md │ │ ├── catalogue-test_6.md │ │ ├── catalogue-test_7.md │ │ ├── catalogue-test_8.md │ │ └── catalogue-test_9.md ├── package.json ├── playwright.config.ts ├── settings.gradle └── tests │ ├── admin!example.spec.ts │ ├── auth.setup.spec.ts │ ├── central │ ├── admin!create-database.spec.ts │ ├── set-custom-central-menu.spec.ts │ └── toggle-oidc-login.spec.ts │ ├── example.spec.ts │ └── molgenis-components │ └── forms │ └── input-select.spec.ts ├── gradle.properties ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── helm-chart ├── Chart.yaml ├── README.md ├── questions.yaml ├── templates │ ├── _helpers.tpl │ ├── deployment.yaml │ ├── ingress.yaml │ ├── postgres-config.yml │ ├── pvc.yaml │ ├── secret-oidc.yaml │ ├── secret-postgres.yaml │ ├── secret.yaml │ └── svc.yaml └── values.yaml ├── pre-commit-format-apply ├── renovate.json ├── settings.gradle └── tools ├── README.md ├── build.gradle ├── directory ├── .coveragerc ├── .gitignore ├── .isort.cfg ├── .pre-commit-config.yaml ├── AUTHORS.md ├── CHANGELOG.md ├── LICENSE.txt ├── Pipfile ├── Pipfile.lock ├── README.md ├── bump-version.sh ├── dev │ ├── .env_example │ └── dev.py ├── pyproject.toml ├── setup.cfg ├── setup.py ├── src │ └── molgenis_emx2 │ │ └── directory_client │ │ ├── __init__.py │ │ ├── categories.py │ │ ├── directory.py │ │ ├── directory_client.py │ │ ├── errors.py │ │ ├── model.py │ │ ├── model_fitting.py │ │ ├── pid_manager.py │ │ ├── pid_service.py │ │ ├── printer.py │ │ ├── publication_preparer.py │ │ ├── publisher.py │ │ ├── stager.py │ │ ├── transformer.py │ │ ├── utils.py │ │ └── validation.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── resources │ │ ├── __init__.py │ │ ├── also_known.json │ │ ├── biobanks.json │ │ ├── collections.json │ │ ├── facts.json │ │ ├── networks.json │ │ ├── persons.json │ │ ├── services.json │ │ └── studies.json │ ├── test_categories.py │ ├── test_directory.py │ ├── test_errors.py │ ├── test_model.py │ ├── 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