diff --git a/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts b/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts index 90a8eba98..76a2f920c 100644 --- a/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts +++ b/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts @@ -1,7 +1,11 @@ import { ANALYSIS_PORTAL, AnalysisPortal, ProjectEdit } from "./entities"; +const azimuthIcon = "/images/icons/azimuth.png"; +const bioDataCatalystIcon = "/images/icons/bio-data-catalyst.png"; const cxgIcon = "/images/icons/cxg.png"; const genomeBrowserIcon = "/images/icons/ucsc-genome.svg"; +const jbrowseIcon = "/images/icons/jbrowse.png"; +const lcaIcon = "/images/icons/lca.png"; const lgeaIcon = "/images/icons/lgea.png"; const lungmapIcon = "/images/icons/lungmap.svg"; const shinyIcon = "/images/icons/shiny.png"; @@ -10,6 +14,24 @@ const stemCellHubIcon = "/images/icons/stem.svg"; const toppCellIcon = "/images/icons/toppcell.png"; const ucscCellBrowserIcon = "/images/icons/ucsc-cell.svg"; +/** + * Azimuth analysis portal. + */ +const AZIMUTH: Omit = { + icon: azimuthIcon, + label: "Azimuth", + name: ANALYSIS_PORTAL.AZIMUTH, +}; + +/** + * BioData Catalyst analysis portal. + */ +const BIO_DATA_CATALYST: Omit = { + icon: bioDataCatalystIcon, + label: "BioData Catalyst", + name: ANALYSIS_PORTAL.BIO_DATA_CATALYST, +}; + /** * CZ CELLxGENE analysis portal. */ @@ -28,6 +50,24 @@ const GENOME_BROWSER: Omit = { name: ANALYSIS_PORTAL.GENOME_BROWSER, }; +/** + * JBrowse analysis portal. + */ +const JBROWSE: Omit = { + icon: jbrowseIcon, + label: "JBrowse", + name: ANALYSIS_PORTAL.JBROWSE, +}; + +/** + * LCA analysis portal. + */ +const LCA: Omit = { + icon: lcaIcon, + label: "LCA", + name: ANALYSIS_PORTAL.LCA, +}; + /** * LGEA analysis portal. */ @@ -607,6 +647,10 @@ export const baseProjectEdits: ProjectEdit[] = [ }, { analysisPortals: [ + { + ...BIO_DATA_CATALYST, + url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/", + }, { ...CZ_CELLXGENE, url: "https://cellxgene.cziscience.com/collections/48d354f5-a5ca-4f35-a3bb-fa3687502252", @@ -649,6 +693,14 @@ export const baseProjectEdits: ProjectEdit[] = [ }, { analysisPortals: [ + { + ...AZIMUTH, + url: "https://app.lungmap.net/app/azimuth-mouse-lung-cellref-seed", + }, + { + ...CZ_CELLXGENE, + url: "https://app.lungmap.net/app/cellxgene-mouse-cellref", + }, { ...LGEA, url: "https://research.cchmc.org/pbge/lunggens/SCLAB.html", @@ -657,6 +709,10 @@ export const baseProjectEdits: ProjectEdit[] = [ ...LUNGMAP_APPS, url: "https://lungmap.net/breath-omics-experiment-page/?experiment_id=LMEX0000001222", }, + { + ...SHINY, + url: "https://app.lungmap.net/app/shinycell-mouse-lung-cellref", + }, ], entryId: "1bdcecde-16be-4208-88f4-78cd2133d11d", }, @@ -1671,6 +1727,14 @@ export const baseProjectEdits: ProjectEdit[] = [ }, { analysisPortals: [ + { + ...BIO_DATA_CATALYST, + url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/", + }, + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004409", + }, { ...SINGLE_CELL, url: "https://singlecell.broadinstitute.org/single_cell/study/SCP1157/bronchiolitis-obliterans-syndrome-lungmap", @@ -1685,16 +1749,21 @@ export const baseProjectEdits: ProjectEdit[] = [ { analysisPortals: [ { - ...LUNGMAP_APPS, - url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004396", + ...CZ_CELLXGENE, + url: "https://cellxgene.cziscience.com/collections/f86d6317-7215-409e-bfda-3f4ded3dadaa", + }, + { + ...JBROWSE, + // eslint-disable-next-line sonarjs/no-hardcoded-passwords -- shared session link, not a secret + url: "https://jbrowse.lungmap.net/?session=share-U7sOFrqK09&password=4cHnL", }, { ...LGEA, url: "https://research.cchmc.org/pbge/lunggens/tools/lung_at_glance.html?tab=reference&species=Human", }, { - ...CZ_CELLXGENE, - url: "https://cellxgene.cziscience.com/collections/f86d6317-7215-409e-bfda-3f4ded3dadaa", + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004396", }, { ...SHINY, @@ -1709,6 +1778,14 @@ export const baseProjectEdits: ProjectEdit[] = [ }, { analysisPortals: [ + { + ...BIO_DATA_CATALYST, + url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/", + }, + { + ...CZ_CELLXGENE, + url: "https://cellxgene.cziscience.com/collections/3a5dbf8a-9b3e-4309-b4c5-d8a024f83734", + }, { ...LUNGMAP_APPS, url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004400", @@ -1717,10 +1794,6 @@ export const baseProjectEdits: ProjectEdit[] = [ ...SHINY, url: "https://app.lungmap.net/app/shinycell-bpd", }, - { - ...CZ_CELLXGENE, - url: "https://cellxgene.cziscience.com/collections/3a5dbf8a-9b3e-4309-b4c5-d8a024f83734", - }, ], entryId: "1977dc47-8414-4263-a870-6b0f207d8ab3", }, @@ -1826,10 +1899,84 @@ export const baseProjectEdits: ProjectEdit[] = [ { analysisPortals: [ { - ...LGEA, + ...LCA, url: "https://research.cchmc.org/pbge/lunggens/LCA/LCA.html", }, + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004412", + }, ], entryId: "ccea5717-a848-4c06-8d2d-d1b694e89441", }, + { + analysisPortals: [ + { + ...CZ_CELLXGENE, + url: "https://lungcells.app.vumc.org/", + }, + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004401", + }, + { + ...SHINY, + url: "https://app.lungmap.net/app/shinycell-bpd-vanderbilt", + }, + ], + entryId: "9393acbf-e8d8-4b96-9c71-996e245e5f23", + }, + { + analysisPortals: [ + { + ...BIO_DATA_CATALYST, + url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/", + }, + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004406", + }, + ], + entryId: "834e0d16-71b6-4425-a8ab-022b5000961c", + }, + { + analysisPortals: [ + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004415", + }, + ], + entryId: "e651ac3e-03aa-46fa-9ed3-70c6fda4e440", + }, + { + analysisPortals: [ + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004407", + }, + ], + entryId: "3a02d15f-9c6a-4ef7-852b-4ddec733b70b", + }, + { + analysisPortals: [ + { + ...LUNGMAP_APPS, + url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004414", + }, + { + ...SHINY, + url: "https://app.lungmap.net/app/shinycell-iaec2", + }, + ], + entryId: "1f009151-2206-4294-929a-9c720f19a13f", + }, + { + analysisPortals: [ + { + ...LUNGMAP_APPS, + url: "https://lungmap-data-submissions.s3.us-east-1.amazonaws.com/tmp/spatial_data_new.html?name=Xenium+Pilot", + }, + ], + entryId: "e99faee2-7706-4c1a-9d28-76c68320f549", + }, ]; diff --git a/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts b/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts index 4ffd2818f..a47041d5b 100644 --- a/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts +++ b/app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts @@ -9,8 +9,12 @@ import { * Set of analysis portal names. */ export enum ANALYSIS_PORTAL { + AZIMUTH = "AZIMUTH", + BIO_DATA_CATALYST = "BIO_DATA_CATALYST", CZ_CELLXGENE = "CZ_CELLXGENE", GENOME_BROWSER = "GENOME_BROWSER", + JBROWSE = "JBROWSE", + LCA = "LCA", LGEA = "LGEA", LUNGMAP_APPS = "LUNGMAP_APPS", SHINY = "SHINY", diff --git a/public/images/icons/azimuth.png b/public/images/icons/azimuth.png new file mode 100644 index 000000000..7cbf75852 Binary files /dev/null and b/public/images/icons/azimuth.png differ diff --git a/public/images/icons/bio-data-catalyst.png b/public/images/icons/bio-data-catalyst.png new file mode 100644 index 000000000..e934b11c6 Binary files /dev/null and b/public/images/icons/bio-data-catalyst.png differ diff --git a/public/images/icons/jbrowse.png b/public/images/icons/jbrowse.png new file mode 100644 index 000000000..bc1783f88 Binary files /dev/null and b/public/images/icons/jbrowse.png differ diff --git a/public/images/icons/lca.png b/public/images/icons/lca.png new file mode 100644 index 000000000..4de713698 Binary files /dev/null and b/public/images/icons/lca.png differ