From a3723d98cbbbc22f00184135de4af6d8739b5033 Mon Sep 17 00:00:00 2001 From: Fran McDade Date: Tue, 21 Nov 2023 12:56:47 +1000 Subject: [PATCH 1/5] feat: display withdrawn project page (#3695) --- explorer/.gitignore | 1 + .../components/EntityGuard/common/entities.ts | 9 +++ .../EntityDeprecated/entityDeprecated.tsx | 69 ++++++++++++++++ .../EntityWithdrawn/entityWithdrawn.tsx | 64 +++++++++++++++ .../EntityGuard/entityGuard.styles.ts | 31 +++++++ .../components/EntityGuard/entityGuard.tsx | 38 +++++++++ .../projectMapper/projectEdits/entities.ts | 9 +-- .../app/viewModelBuilders/common/entities.ts | 9 +++ .../files/hca-dcp/build-hca-dcp-overrides.ts | 14 ++++ explorer/files/package.json | 7 +- .../pages/[entityListType]/[...params].tsx | 81 +++++++++++++++++++ .../hca-dcp/dev/index/projectsEntityConfig.ts | 1 + 12 files changed, 323 insertions(+), 10 deletions(-) create mode 100644 explorer/app/components/Detail/components/EntityGuard/common/entities.ts create mode 100644 explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx create mode 100644 explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx create mode 100644 explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts create mode 100644 explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx create mode 100644 explorer/files/hca-dcp/build-hca-dcp-overrides.ts diff --git a/explorer/.gitignore b/explorer/.gitignore index 3c2c70cb8..3550db0d4 100644 --- a/explorer/.gitignore +++ b/explorer/.gitignore @@ -50,5 +50,6 @@ _templates /public/favicons/* /files/anvil-catalog/out/ +/files/hca-dcp/out/ /files/ncpi-catalog/out/ /files/ncpi-catalog-dug/out/ diff --git a/explorer/app/components/Detail/components/EntityGuard/common/entities.ts b/explorer/app/components/Detail/components/EntityGuard/common/entities.ts new file mode 100644 index 000000000..e3b5df5ce --- /dev/null +++ b/explorer/app/components/Detail/components/EntityGuard/common/entities.ts @@ -0,0 +1,9 @@ +/** + * Set of entity status. + */ +export enum ENTITY_STATUS { + DEPRECATED = "DEPRECATED", + INGEST_IN_PROGRESS = "INGEST_IN_PROGRESS", + LIVE = "LIVE", + WITHDRAWN = "WITHDRAWN", +} diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx b/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx new file mode 100644 index 000000000..6326ab5ad --- /dev/null +++ b/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx @@ -0,0 +1,69 @@ +import { ButtonPrimary } from "@clevercanary/data-explorer-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary"; +import { AlertIcon } from "@clevercanary/data-explorer-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon"; +import { SectionActions } from "@clevercanary/data-explorer-ui/lib/components/common/Section/section.styles"; +import { + PRIORITY, + StatusIcon, +} from "@clevercanary/data-explorer-ui/lib/components/common/StatusIcon/statusIcon"; +import { + TEXT_BODY_LARGE_400, + TEXT_HEADING_XLARGE, +} from "@clevercanary/data-explorer-ui/lib/theme/common/typography"; +import { Link as MLink, Typography } from "@mui/material"; +import Link from "next/link"; +import { useRouter } from "next/router"; +import React from "react"; +import { Override } from "../../../../../../viewModelBuilders/common/entities"; +import { Notice, Section, SectionContent } from "../../entityGuard.styles"; + +interface EntityDeprecatedProps { + override: Override; +} + +export const EntityDeprecated = ({ + override, +}: EntityDeprecatedProps): JSX.Element => { + const router = useRouter(); + const { supersededBy } = override || {}; + const title = supersededBy + ? "Project Relocated" + : "Project Permanently Removed"; + return ( + +
+ + + + {title} + + + {supersededBy ? ( + <> + The project you are requesting has been permanently moved and + may be accessed{" "} + { + router.push({ + pathname: router.pathname, + query: { ...router.query, params: [supersededBy] }, + }); + }} + > + here + + . + + ) : ( + <>The project you are requesting has been permanently removed. + )} + + + + + To Homepage + + +
+ + ); +}; diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx b/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx new file mode 100644 index 000000000..8f2cb22d2 --- /dev/null +++ b/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx @@ -0,0 +1,64 @@ +import { ButtonPrimary } from "@clevercanary/data-explorer-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary"; +import { AlertIcon } from "@clevercanary/data-explorer-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon"; +import { SectionActions } from "@clevercanary/data-explorer-ui/lib/components/common/Section/section.styles"; +import { + PRIORITY, + StatusIcon, +} from "@clevercanary/data-explorer-ui/lib/components/common/StatusIcon/statusIcon"; +import { ANCHOR_TARGET } from "@clevercanary/data-explorer-ui/lib/components/Links/common/entities"; +import { + TEXT_BODY_LARGE_400, + TEXT_HEADING_XLARGE, +} from "@clevercanary/data-explorer-ui/lib/theme/common/typography"; +import { Link as MLink, Typography } from "@mui/material"; +import Link from "next/link"; +import React from "react"; +import { Override } from "../../../../../../viewModelBuilders/common/entities"; +import { Notice, Section, SectionContent } from "../../entityGuard.styles"; + +interface EntityWithdrawnProps { + override: Override; +} + +export const EntityWithdrawn = ({ + override, +}: EntityWithdrawnProps): JSX.Element => { + const { redirectUrl } = override || {}; + return ( + +
+ + + + Project Withdrawn + + +

+ The project you are requesting has been withdrawn from the HCA + Data Portal due to a GDPR request. +

+ {redirectUrl && ( + <> +

+ The project can now be accessed at:{" "} + + {redirectUrl} + +

+ + )} + + + + + To Homepage + + +
+ + ); +}; diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts b/explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts new file mode 100644 index 000000000..53f0de502 --- /dev/null +++ b/explorer/app/components/Detail/components/EntityGuard/entityGuard.styles.ts @@ -0,0 +1,31 @@ +import { Section as DXSection } from "@clevercanary/data-explorer-ui/lib/components/common/Section/section.styles"; +import { mediaTabletUp } from "@clevercanary/data-explorer-ui/lib/styles/common/mixins/breakpoints"; +import styled from "@emotion/styled"; + +export const Notice = styled.div` + margin: 0 auto; + max-width: 648px; + padding: 40px 20px; + width: 100%; +`; + +export const Section = styled(DXSection)` + align-items: center; + padding: 0; + + ${mediaTabletUp} { + padding: 0; + } +`; + +export const SectionContent = styled.div` + text-align: center; + + .MuiTypography-text-heading-xlarge { + margin-top: -8px; + } + + .MuiLink-root { + cursor: pointer; + } +`; diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx new file mode 100644 index 000000000..8c22044d3 --- /dev/null +++ b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx @@ -0,0 +1,38 @@ +import React, { Fragment } from "react"; +import { Override } from "../../../../viewModelBuilders/common/entities"; +import { ENTITY_STATUS } from "./common/entities"; +import { EntityDeprecated } from "./components/EntityDeprecated/entityDeprecated"; +import { EntityWithdrawn } from "./components/EntityWithdrawn/entityWithdrawn"; + +interface EntityGuardProps { + override: Override; +} + +export const EntityGuard = ({ override }: EntityGuardProps): JSX.Element => { + const viewMode = getEntityViewMode(override); + return ( + + {viewMode === ENTITY_STATUS.DEPRECATED && ( + + )} + {viewMode === ENTITY_STATUS.WITHDRAWN && ( + + )} + + ); +}; + +/** + * Return the view mode for the entity, depending on its current status. + * @param override - Override. + * @returns view mode. + */ +function getEntityViewMode(override: Override): ENTITY_STATUS { + if (override.deprecated) { + return ENTITY_STATUS.DEPRECATED; + } + if (override.withdrawn) { + return ENTITY_STATUS.WITHDRAWN; + } + return ENTITY_STATUS.LIVE; +} diff --git a/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts b/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts index 9297ddaca..0cc2dc019 100644 --- a/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts +++ b/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts @@ -3,6 +3,7 @@ import { ContributorResponse, PublicationResponse, } from "../../../../../../apis/azul/hca-dcp/common/entities"; +import { Override } from "../../../../../common/entities"; /** * Set of analysis portal names. @@ -25,18 +26,12 @@ export interface AnalysisPortal { url: string; } -export interface ProjectEdit { +export interface ProjectEdit extends Override { analysisPortals?: AnalysisPortal[]; contributors?: Partial[]; - deprecated?: boolean; - duplicateOf?: string; - entryId: string; projectShortname?: string; publications?: Pick< PublicationResponse, "publicationTitle" | "publicationUrl" >[]; - redirectUrl?: string; - supersededBy?: string; - withdrawn?: boolean; } diff --git a/explorer/app/viewModelBuilders/common/entities.ts b/explorer/app/viewModelBuilders/common/entities.ts index c81403721..74e6865eb 100644 --- a/explorer/app/viewModelBuilders/common/entities.ts +++ b/explorer/app/viewModelBuilders/common/entities.ts @@ -1,2 +1,11 @@ // eslint-disable-next-line @typescript-eslint/no-explicit-any -- type is unused and therefore possibly unknown. export type Unused = any; + +export interface Override { + deprecated?: boolean; + duplicateOf?: string; + entryId: string; + redirectUrl?: string; + supersededBy?: string; + withdrawn?: boolean; +} diff --git a/explorer/files/hca-dcp/build-hca-dcp-overrides.ts b/explorer/files/hca-dcp/build-hca-dcp-overrides.ts new file mode 100644 index 000000000..40bc8685e --- /dev/null +++ b/explorer/files/hca-dcp/build-hca-dcp-overrides.ts @@ -0,0 +1,14 @@ +import { projectEdits } from "../../app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants"; +import { writeAsJSON } from "../common/utils"; + +console.log("Building HCA Data Portal Overrides"); +export {}; + +async function buildOverrides(): Promise { + await writeAsJSON( + "hca-dcp/out/overrides.json", + Object.fromEntries(projectEdits.entries()) + ); +} + +buildOverrides(); diff --git a/explorer/files/package.json b/explorer/files/package.json index 2567c4876..10f05019b 100644 --- a/explorer/files/package.json +++ b/explorer/files/package.json @@ -6,11 +6,12 @@ "scripts": { "test": "echo \"Error: no test specified\" && exit 1", "build-anvil-db": "esrun anvil-catalog/build-anvil-catalog.ts", - "build-ncpi-db": "esrun ncpi-catalog/build-ncpi-catalog.ts", + "build-hca-dcp-overrides": "esrun hca-dcp/build-hca-dcp-overrides.ts", "build-dug-db": "esrun ncpi-catalog-dug/build-ncpi-catalog-dug.ts", - "update-crdc-source": "esrun ncpi-catalog/update-crdc-source.ts", - "update-bdc-source": "esrun ncpi-catalog/update-bdc-source.ts", + "build-ncpi-db": "esrun ncpi-catalog/build-ncpi-catalog.ts", "update-anvil-source": "esrun ncpi-catalog/update-anvil-source.ts", + "update-bdc-source": "esrun ncpi-catalog/update-bdc-source.ts", + "update-crdc-source": "esrun ncpi-catalog/update-crdc-source.ts", "update-kfdrc-source": "esrun ncpi-catalog/update-kfdrc-source.ts", "update-all-ncpi-sources": "npm run update-crdc-source && npm run update-bdc-source && npm run update-anvil-source && npm run update-kfdrc-source" }, diff --git a/explorer/pages/[entityListType]/[...params].tsx b/explorer/pages/[entityListType]/[...params].tsx index 21180c3e3..7db980f01 100644 --- a/explorer/pages/[entityListType]/[...params].tsx +++ b/explorer/pages/[entityListType]/[...params].tsx @@ -12,7 +12,9 @@ import { config } from "app/config/config"; import { GetStaticPaths, GetStaticProps, GetStaticPropsContext } from "next"; import { ParsedUrlQuery } from "querystring"; import React from "react"; +import { EntityGuard } from "../../app/components/Detail/components/EntityGuard/entityGuard"; import { readFile } from "../../app/utils/tsvParser"; +import { Override } from "../../app/viewModelBuilders/common/entities"; interface PageUrl extends ParsedUrlQuery { entityListType: string; @@ -21,6 +23,7 @@ interface PageUrl extends ParsedUrlQuery { export interface EntityDetailPageProps extends AzulEntityStaticResponse { entityListType: string; + override?: Override; } /** @@ -31,9 +34,57 @@ export interface EntityDetailPageProps extends AzulEntityStaticResponse { */ const EntityDetailPage = (props: EntityDetailPageProps): JSX.Element => { if (!props.entityListType) return <>; + if (props.override) return ; return ; }; +/** + * Returns a list of overrides from the override file. + * @param entityConfig - Entity config. + * @returns a list of overrides. + */ +const getOverrides = async function getOverrides( + entityConfig: EntityConfig +): Promise { + const { overrideFile } = entityConfig; + if (!overrideFile) { + return []; + } + const rawData = await readFile(overrideFile); + if (!rawData) { + return []; + } + const overrides = JSON.parse(rawData.toString()); + return (Object.values(overrides) || []) as unknown as Override[]; +}; + +/** + * Returns the override for the given entity ID. + * @param overrides - Overrides. + * @param entityId - Entity ID. + * @returns returns the override for the given entity ID. + */ +function findOverride( + overrides: Override[], + entityId?: string +): Override | undefined { + if (!entityId) { + return; + } + return overrides.find(({ entryId }) => entryId === entityId); +} + +/** + * Returns true if the entity is a special case e.g. an "override". + * @param override - Override. + * @returns true if the entity is an override. + */ +function isOverride(override: Override): boolean { + return Boolean( + override.deprecated || override.supersededBy || override.withdrawn + ); +} + /** * Seed database. * @param entityListType - Entity list type. @@ -105,6 +156,21 @@ export const getStaticPaths: GetStaticPaths = async () => { }); }); } + + // process entity overrides + if (entityConfig.overrideFile) { + const overrides = await getOverrides(entityConfig); + for (const override of overrides) { + if (isOverride(override)) { + resultParams.push({ + params: { + entityListType: entityConfig.route, + params: [override.entryId], + }, + }); + } + } + } return resultParams; }) ); @@ -135,6 +201,21 @@ export const getStaticProps: GetStaticProps = async ({ const props: EntityDetailPageProps = { entityListType: entityListType }; + // If there is a corresponding override for the given page, grab the override values from the override file and return as props. + if (entityConfig.overrideFile) { + const overrides = await getOverrides(entityConfig); + const override = findOverride( + overrides, + params?.params?.[PARAMS_INDEX_UUID] + ); + if (override && isOverride(override)) { + props.override = override; + return { + props, + }; + } + } + // If the entity detail view is to be "statically loaded", we need to seed the database (for retrieval of the entity), or // fetch the entity detail from API. if (entityConfig.detail.staticLoad) { diff --git a/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts b/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts index d10c2cb1a..e017adea1 100644 --- a/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts +++ b/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts @@ -135,6 +135,7 @@ export const projectsEntityConfig: EntityConfig = { id: HCA_DCP_CATEGORY_KEY.PROJECT_TITLE, }, } as ListConfig, + overrideFile: "files/hca-dcp/out/overrides.json", route: "projects", staticLoad: false, }; From 2b39eaa5f0f7213acc18cd92300c7c9db5daa43b Mon Sep 17 00:00:00 2001 From: Fran McDade Date: Tue, 21 Nov 2023 16:55:01 +1000 Subject: [PATCH 2/5] feat: redirect on view of dupe project (#3697) --- .../components/EntityGuard/common/entities.ts | 1 + .../components/EntityGuard/entityGuard.tsx | 16 +++++++++++++++- explorer/pages/[entityListType]/[...params].tsx | 8 +++++++- 3 files changed, 23 insertions(+), 2 deletions(-) diff --git a/explorer/app/components/Detail/components/EntityGuard/common/entities.ts b/explorer/app/components/Detail/components/EntityGuard/common/entities.ts index e3b5df5ce..e1e829eff 100644 --- a/explorer/app/components/Detail/components/EntityGuard/common/entities.ts +++ b/explorer/app/components/Detail/components/EntityGuard/common/entities.ts @@ -3,6 +3,7 @@ */ export enum ENTITY_STATUS { DEPRECATED = "DEPRECATED", + DUPLICATE = "DUPLICATE", INGEST_IN_PROGRESS = "INGEST_IN_PROGRESS", LIVE = "LIVE", WITHDRAWN = "WITHDRAWN", diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx index 8c22044d3..d24d2a19b 100644 --- a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx +++ b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx @@ -1,4 +1,5 @@ -import React, { Fragment } from "react"; +import Router from "next/router"; +import React, { Fragment, useEffect } from "react"; import { Override } from "../../../../viewModelBuilders/common/entities"; import { ENTITY_STATUS } from "./common/entities"; import { EntityDeprecated } from "./components/EntityDeprecated/entityDeprecated"; @@ -9,12 +10,22 @@ interface EntityGuardProps { } export const EntityGuard = ({ override }: EntityGuardProps): JSX.Element => { + const { duplicateOf } = override; const viewMode = getEntityViewMode(override); + + // Redirect if duplicate entry. + useEffect(() => { + if (duplicateOf) { + Router.push(duplicateOf); + } + }, [duplicateOf]); + return ( {viewMode === ENTITY_STATUS.DEPRECATED && ( )} + {viewMode === ENTITY_STATUS.DUPLICATE &&
Redirecting...
} {viewMode === ENTITY_STATUS.WITHDRAWN && ( )} @@ -31,6 +42,9 @@ function getEntityViewMode(override: Override): ENTITY_STATUS { if (override.deprecated) { return ENTITY_STATUS.DEPRECATED; } + if (override.duplicateOf) { + return ENTITY_STATUS.DUPLICATE; + } if (override.withdrawn) { return ENTITY_STATUS.WITHDRAWN; } diff --git a/explorer/pages/[entityListType]/[...params].tsx b/explorer/pages/[entityListType]/[...params].tsx index 7db980f01..67ff369a4 100644 --- a/explorer/pages/[entityListType]/[...params].tsx +++ b/explorer/pages/[entityListType]/[...params].tsx @@ -81,7 +81,10 @@ function findOverride( */ function isOverride(override: Override): boolean { return Boolean( - override.deprecated || override.supersededBy || override.withdrawn + override.deprecated || + override.duplicateOf || + override.supersededBy || + override.withdrawn ); } @@ -210,6 +213,9 @@ export const getStaticProps: GetStaticProps = async ({ ); if (override && isOverride(override)) { props.override = override; + if (override.duplicateOf) { + props.override.duplicateOf = `/${entityListType}/${override.duplicateOf}`; + } return { props, }; From e0f37f641c0cd0d54bf00fa95235d4d569e02dec Mon Sep 17 00:00:00 2001 From: Fran McDade Date: Tue, 21 Nov 2023 17:08:38 +1000 Subject: [PATCH 3/5] feat: overrides json file relocated (#3695) --- explorer/.gitignore | 1 - .../files/hca-dcp/build-hca-dcp-overrides.ts | 2 +- explorer/files/hca-dcp/overrides.json | 1893 +++++++++++++++++ .../hca-dcp/dev/index/projectsEntityConfig.ts | 2 +- 4 files changed, 1895 insertions(+), 3 deletions(-) create mode 100644 explorer/files/hca-dcp/overrides.json diff --git a/explorer/.gitignore b/explorer/.gitignore index 3550db0d4..3c2c70cb8 100644 --- a/explorer/.gitignore +++ b/explorer/.gitignore @@ -50,6 +50,5 @@ _templates /public/favicons/* /files/anvil-catalog/out/ -/files/hca-dcp/out/ /files/ncpi-catalog/out/ /files/ncpi-catalog-dug/out/ diff --git a/explorer/files/hca-dcp/build-hca-dcp-overrides.ts b/explorer/files/hca-dcp/build-hca-dcp-overrides.ts index 40bc8685e..e3675028d 100644 --- a/explorer/files/hca-dcp/build-hca-dcp-overrides.ts +++ b/explorer/files/hca-dcp/build-hca-dcp-overrides.ts @@ -6,7 +6,7 @@ export {}; async function buildOverrides(): Promise { await writeAsJSON( - "hca-dcp/out/overrides.json", + "hca-dcp/overrides.json", Object.fromEntries(projectEdits.entries()) ); } diff --git a/explorer/files/hca-dcp/overrides.json b/explorer/files/hca-dcp/overrides.json new file mode 100644 index 000000000..49015c9d3 --- /dev/null +++ b/explorer/files/hca-dcp/overrides.json @@ -0,0 +1,1893 @@ +{ + "0": { + "entryId": "f8aa201c-4ff1-45a4-890e-840d63459ca2", + "publications": [ + { + "publicationTitle": "Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease", + "publicationUrl": "https://www.sciencedirect.com/science/article/pii/S0092867418311681?via%3Dihub" + } + ] + }, + "1": { + "entryId": "091cf39b-01bc-42e5-9437-f419a66c8a45", + "publications": [ + { + "publicationTitle": "Characterization of cell fate probabilities in single-cell data with Palantir", + "publicationUrl": "https://www.nature.com/articles/s41587-019-0068-4" + } + ] + }, + "2": { + "analysisPortals": [ + { + "icon": "/images/icons/cellxgene.svg", + "label": "CELLxGENE", + "name": "CELLXGENE", + "url": "https://cellxgene.cziscience.com/collections/4d74781b-8186-4c9a-b659-ff4dc4601d91" + }, + { + "icon": "/images/icons/ucsc-cell.svg", + "label": "UCSC Cell Browser", + "name": "CELL_BROWSER", + "url": "https://tissue-stability.cells.ucsc.edu" + } + ], + "contributors": [ + { + "contactName": "Sarah,A,Teichmann", + "projectRole": "Co-investigator" + } + ], + "entryId": "c4077b3c-5c98-4d26-a614-246d12c2e5d7", + "publications": [ + { + "publicationTitle": "scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation", + "publicationUrl": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1906-x" + } + ] + }, + "3": { + "analysisPortals": [ + { + "icon": "/images/icons/cellxgene.svg", + "label": "CELLxGENE", + "name": "CELLXGENE", + "url": "https://cellxgene.cziscience.com/collections/a9254216-6cd8-4186-b32c-349363777584" + }, + { + "icon": "/images/icons/ucsc-cell.svg", + "label": "UCSC Cell Browser", + "name": "CELL_BROWSER", + "url": "https://placenta-decidua.cells.ucsc.edu" + }, + { + "icon": "/images/icons/ucsc-genome.svg", + "label": "Genome Browser", + "name": "GENOME_BROWSER", + "url": "https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=placentaVentoTormo&position=default" + } + ], + "entryId": "f83165c5-e2ea-4d15-a5cf-33f3550bffde", + "publications": [ + { + "publicationTitle": "Single-cell reconstruction of the early maternal–fetal interface in humans", + "publicationUrl": "https://www.nature.com/articles/s41586-018-0698-6" + } + ] + }, + "4": { + "analysisPortals": [ + { + "icon": 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"files/hca-dcp/out/overrides.json", + overrideFile: "files/hca-dcp/overrides.json", route: "projects", staticLoad: false, }; From be6d96b888f335f038a580d058dd5a169f13be6e Mon Sep 17 00:00:00 2001 From: Fran McDade Date: Wed, 22 Nov 2023 17:22:07 +1000 Subject: [PATCH 4/5] feat: updated overrides (#3695) --- .../EntityDeprecated/entityDeprecated.tsx | 2 +- .../EntityWithdrawn/entityWithdrawn.tsx | 2 +- .../components/EntityGuard/entityGuard.tsx | 2 +- .../projectMapper/projectEdits/entities.ts | 2 +- .../app/viewModelBuilders/common/entities.ts | 9 - .../files/hca-dcp/build-hca-dcp-overrides.ts | 14 - explorer/files/hca-dcp/overrides.json | 1893 ----------------- .../pages/[entityListType]/[...params].tsx | 36 +- .../hca-dcp/dev/index/projectsEntityConfig.ts | 3 +- 9 files changed, 14 insertions(+), 1949 deletions(-) delete mode 100644 explorer/files/hca-dcp/build-hca-dcp-overrides.ts delete mode 100644 explorer/files/hca-dcp/overrides.json diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx b/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx index 6326ab5ad..d15c4f78c 100644 --- a/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx +++ b/explorer/app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx @@ -5,6 +5,7 @@ import { PRIORITY, StatusIcon, } from "@clevercanary/data-explorer-ui/lib/components/common/StatusIcon/statusIcon"; +import { Override } from "@clevercanary/data-explorer-ui/lib/config/entities"; import { TEXT_BODY_LARGE_400, TEXT_HEADING_XLARGE, @@ -13,7 +14,6 @@ import { Link as MLink, Typography } from "@mui/material"; import Link from "next/link"; import { useRouter } from "next/router"; import React from "react"; -import { Override } from "../../../../../../viewModelBuilders/common/entities"; import { Notice, Section, SectionContent } from "../../entityGuard.styles"; interface EntityDeprecatedProps { diff --git a/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx b/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx index 8f2cb22d2..b70e8f5aa 100644 --- a/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx +++ b/explorer/app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx @@ -6,6 +6,7 @@ import { StatusIcon, } from "@clevercanary/data-explorer-ui/lib/components/common/StatusIcon/statusIcon"; import { ANCHOR_TARGET } from "@clevercanary/data-explorer-ui/lib/components/Links/common/entities"; +import { Override } from "@clevercanary/data-explorer-ui/lib/config/entities"; import { TEXT_BODY_LARGE_400, TEXT_HEADING_XLARGE, @@ -13,7 +14,6 @@ import { import { Link as MLink, Typography } from "@mui/material"; import Link from "next/link"; import React from "react"; -import { Override } from "../../../../../../viewModelBuilders/common/entities"; import { Notice, Section, SectionContent } from "../../entityGuard.styles"; interface EntityWithdrawnProps { diff --git a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx index d24d2a19b..4a4c75fed 100644 --- a/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx +++ b/explorer/app/components/Detail/components/EntityGuard/entityGuard.tsx @@ -1,6 +1,6 @@ +import { Override } from "@clevercanary/data-explorer-ui/lib/config/entities"; import Router from "next/router"; import React, { Fragment, useEffect } from "react"; -import { Override } from "../../../../viewModelBuilders/common/entities"; import { ENTITY_STATUS } from "./common/entities"; import { EntityDeprecated } from "./components/EntityDeprecated/entityDeprecated"; import { EntityWithdrawn } from "./components/EntityWithdrawn/entityWithdrawn"; diff --git a/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts b/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts index 0cc2dc019..592b1f947 100644 --- a/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts +++ b/explorer/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts @@ -1,9 +1,9 @@ import { StaticImageProps } from "@clevercanary/data-explorer-ui/lib/components/common/StaticImage/staticImage"; +import { Override } from "@clevercanary/data-explorer-ui/lib/config/entities"; import { ContributorResponse, PublicationResponse, } from "../../../../../../apis/azul/hca-dcp/common/entities"; -import { Override } from "../../../../../common/entities"; /** * Set of analysis portal names. diff --git a/explorer/app/viewModelBuilders/common/entities.ts b/explorer/app/viewModelBuilders/common/entities.ts index 74e6865eb..c81403721 100644 --- a/explorer/app/viewModelBuilders/common/entities.ts +++ b/explorer/app/viewModelBuilders/common/entities.ts @@ -1,11 +1,2 @@ // eslint-disable-next-line @typescript-eslint/no-explicit-any -- type is unused and therefore possibly unknown. export type Unused = any; - -export interface Override { - deprecated?: boolean; - duplicateOf?: string; - entryId: string; - redirectUrl?: string; - supersededBy?: string; - withdrawn?: boolean; -} diff --git a/explorer/files/hca-dcp/build-hca-dcp-overrides.ts b/explorer/files/hca-dcp/build-hca-dcp-overrides.ts deleted file mode 100644 index e3675028d..000000000 --- a/explorer/files/hca-dcp/build-hca-dcp-overrides.ts +++ /dev/null @@ -1,14 +0,0 @@ -import { projectEdits } from "../../app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants"; -import { writeAsJSON } from "../common/utils"; - -console.log("Building HCA Data Portal Overrides"); -export {}; - -async function buildOverrides(): Promise { - await writeAsJSON( - "hca-dcp/overrides.json", - Object.fromEntries(projectEdits.entries()) - ); -} - -buildOverrides(); diff --git a/explorer/files/hca-dcp/overrides.json b/explorer/files/hca-dcp/overrides.json deleted file mode 100644 index 49015c9d3..000000000 --- a/explorer/files/hca-dcp/overrides.json +++ /dev/null @@ -1,1893 +0,0 @@ -{ - "0": { - "entryId": "f8aa201c-4ff1-45a4-890e-840d63459ca2", - "publications": [ - { - "publicationTitle": "Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease", - "publicationUrl": "https://www.sciencedirect.com/science/article/pii/S0092867418311681?via%3Dihub" - } - ] - }, - "1": { - "entryId": "091cf39b-01bc-42e5-9437-f419a66c8a45", - "publications": [ - { - "publicationTitle": "Characterization of cell fate probabilities in single-cell data with Palantir", - "publicationUrl": "https://www.nature.com/articles/s41587-019-0068-4" - } - ] - }, - "2": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": "https://cellxgene.cziscience.com/collections/4d74781b-8186-4c9a-b659-ff4dc4601d91" - }, - { - "icon": "/images/icons/ucsc-cell.svg", - "label": "UCSC Cell Browser", - "name": "CELL_BROWSER", - "url": "https://tissue-stability.cells.ucsc.edu" - } - ], - "contributors": [ - { - "contactName": "Sarah,A,Teichmann", - "projectRole": "Co-investigator" - } - ], - "entryId": "c4077b3c-5c98-4d26-a614-246d12c2e5d7", - "publications": [ - { - "publicationTitle": "scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation", - "publicationUrl": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1906-x" - } - ] - }, - "3": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": "https://cellxgene.cziscience.com/collections/a9254216-6cd8-4186-b32c-349363777584" - }, - { - "icon": "/images/icons/ucsc-cell.svg", - "label": "UCSC Cell Browser", - "name": "CELL_BROWSER", - "url": "https://placenta-decidua.cells.ucsc.edu" - }, - { - "icon": "/images/icons/ucsc-genome.svg", - "label": "Genome Browser", - "name": "GENOME_BROWSER", - "url": "https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=placentaVentoTormo&position=default" - } - ], - "entryId": "f83165c5-e2ea-4d15-a5cf-33f3550bffde", - "publications": [ - { - "publicationTitle": "Single-cell reconstruction of the early maternal–fetal interface in humans", - "publicationUrl": "https://www.nature.com/articles/s41586-018-0698-6" - } - ] - }, - "4": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": "https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf" - } - ], - "entryId": "4a95101c-9ffc-4f30-a809-f04518a23803", - "publications": [ - { - "publicationTitle": "Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease", - "publicationUrl": "https://www.nature.com/articles/s41467-019-12464-3" - } - ] - }, - "5": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": "https://cellxgene.cziscience.com/collections/bd5230f4-cd76-4d35-9ee5-89b3e7475659" - }, - { - "icon": "/images/icons/ucsc-cell.svg", - "label": "UCSC Cell Browser", - "name": "CELL_BROWSER", - "url": "https://human-liver.cells.ucsc.edu" - } - ], - "contributors": [ - { - "contactName": "Jeff,C,Liu", - "projectRole": "Computational Scientist" - }, - { - "contactName": "Brendan,T,Innes", - "projectRole": "Computational Scientist" - } - ], - "entryId": "4d6f6c96-2a83-43d8-8fe1-0f53bffd4674" - }, - "6": { - "entryId": "008e40e8-66ae-43bb-951c-c073a2fa6774", - "projectShortname": "RNA-seq of human embryonic heart, lung, and cerebellum", - "redirectUrl": "https://ega-archive.org/studies/EGAS00001004375", - "withdrawn": true - }, - "7": { - "deprecated": true, - "entryId": "29f53b7e-071b-44b5-998a-0ae70d0229a4", - "projectShortname": "Profiling of CD34+ cells from human bone marrow to understand hematopoiesis", - "supersededBy": "091cf39b-01bc-42e5-9437-f419a66c8a45" - }, - "8": { - "deprecated": true, - "entryId": "dd7ada84-3f14-4765-b7ce-9b64642bb3dc", - "projectShortname": "Single-nucleus RNA-seq profiling of the human primary motor cortex in amyotrophic lateral sclerosis and frontotemporal lobar degeneration" - }, - "9": { - "duplicateOf": "a004b150-1c36-4af6-9bbd-070c06dbc17d", - "entryId": "9bab0f03-a725-4a13-9ab1-196e46cd80ed" - }, - "10": { - "duplicateOf": "504e0cee-1688-40fa-b936-361c4a831f87", - "entryId": "992aad5e-7fab-46d9-a47d-df715e8cfd24" - }, - "11": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": 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- } - ], - "entryId": "9b876d31-0739-4e96-9846-f76e6a427279" - }, - "136": { - "analysisPortals": [ - { - "icon": "/images/icons/cellxgene.svg", - "label": "CELLxGENE", - "name": "CELLXGENE", - "url": "https://cellxgene.cziscience.com/collections/f7cecffa-00b4-4560-a29a-8ad626b8ee08" - } - ], - "entryId": "8f1f653d-3ea1-4d8e-b4a7-b97dc852c2b1" - } -} diff --git a/explorer/pages/[entityListType]/[...params].tsx b/explorer/pages/[entityListType]/[...params].tsx index 67ff369a4..c9122c143 100644 --- a/explorer/pages/[entityListType]/[...params].tsx +++ b/explorer/pages/[entityListType]/[...params].tsx @@ -3,7 +3,10 @@ import { PARAMS_INDEX_TAB, PARAMS_INDEX_UUID, } from "@clevercanary/data-explorer-ui/lib/common/constants"; -import { EntityConfig } from "@clevercanary/data-explorer-ui/lib/config/entities"; +import { + EntityConfig, + Override, +} from "@clevercanary/data-explorer-ui/lib/config/entities"; import { getEntityConfig } from "@clevercanary/data-explorer-ui/lib/config/utils"; import { getEntityService } from "@clevercanary/data-explorer-ui/lib/hooks/useEntityService"; import { database } from "@clevercanary/data-explorer-ui/lib/utils/database"; @@ -14,7 +17,6 @@ import { ParsedUrlQuery } from "querystring"; import React from "react"; import { EntityGuard } from "../../app/components/Detail/components/EntityGuard/entityGuard"; import { readFile } from "../../app/utils/tsvParser"; -import { Override } from "../../app/viewModelBuilders/common/entities"; interface PageUrl extends ParsedUrlQuery { entityListType: string; @@ -38,26 +40,6 @@ const EntityDetailPage = (props: EntityDetailPageProps): JSX.Element => { return ; }; -/** - * Returns a list of overrides from the override file. - * @param entityConfig - Entity config. - * @returns a list of overrides. - */ -const getOverrides = async function getOverrides( - entityConfig: EntityConfig -): Promise { - const { overrideFile } = entityConfig; - if (!overrideFile) { - return []; - } - const rawData = await readFile(overrideFile); - if (!rawData) { - return []; - } - const overrides = JSON.parse(rawData.toString()); - return (Object.values(overrides) || []) as unknown as Override[]; -}; - /** * Returns the override for the given entity ID. * @param overrides - Overrides. @@ -161,9 +143,8 @@ export const getStaticPaths: GetStaticPaths = async () => { } // process entity overrides - if (entityConfig.overrideFile) { - const overrides = await getOverrides(entityConfig); - for (const override of overrides) { + if (entityConfig.overrides) { + for (const override of entityConfig.overrides) { if (isOverride(override)) { resultParams.push({ params: { @@ -205,10 +186,9 @@ export const getStaticProps: GetStaticProps = async ({ const props: EntityDetailPageProps = { entityListType: entityListType }; // If there is a corresponding override for the given page, grab the override values from the override file and return as props. - if (entityConfig.overrideFile) { - const overrides = await getOverrides(entityConfig); + if (entityConfig.overrides) { const override = findOverride( - overrides, + entityConfig.overrides, params?.params?.[PARAMS_INDEX_UUID] ); if (override && isOverride(override)) { diff --git a/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts b/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts index 1df96f610..32df8a2cf 100644 --- a/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts +++ b/explorer/site-config/hca-dcp/dev/index/projectsEntityConfig.ts @@ -7,6 +7,7 @@ import { import { ProjectsResponse } from "../../../../app/apis/azul/hca-dcp/common/responses"; import { getProjectId } from "../../../../app/apis/azul/hca-dcp/common/utils"; import * as C from "../../../../app/components"; +import { projectEdits } from "../../../../app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants"; import * as V from "../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders"; import { HCA_DCP_CATEGORY_KEY, HCA_DCP_CATEGORY_LABEL } from "../../category"; import { mainColumn as exportMainColumn } from "../detail/project/exportMainColumn"; @@ -135,7 +136,7 @@ export const projectsEntityConfig: EntityConfig = { id: HCA_DCP_CATEGORY_KEY.PROJECT_TITLE, }, } as ListConfig, - overrideFile: "files/hca-dcp/overrides.json", + overrides: projectEdits, route: "projects", staticLoad: false, }; From 0fe9feea60bb58a5de07dbd8b877de78c1b1d3fd Mon Sep 17 00:00:00 2001 From: Fran McDade Date: Wed, 22 Nov 2023 17:30:45 +1000 Subject: [PATCH 5/5] feat: linting (#3695) --- explorer/files/package.json | 1 - 1 file changed, 1 deletion(-) diff --git a/explorer/files/package.json b/explorer/files/package.json index 10f05019b..75c938a58 100644 --- a/explorer/files/package.json +++ b/explorer/files/package.json @@ -6,7 +6,6 @@ "scripts": { "test": "echo \"Error: no test specified\" && exit 1", "build-anvil-db": "esrun anvil-catalog/build-anvil-catalog.ts", - "build-hca-dcp-overrides": "esrun hca-dcp/build-hca-dcp-overrides.ts", "build-dug-db": "esrun ncpi-catalog-dug/build-ncpi-catalog-dug.ts", "build-ncpi-db": "esrun ncpi-catalog/build-ncpi-catalog.ts", "update-anvil-source": "esrun ncpi-catalog/update-anvil-source.ts",