From 0ed5b25889267f319d0848721e0a007acd626eca Mon Sep 17 00:00:00 2001 From: Howie Motenko Date: Mon, 8 Jan 2024 22:15:43 -0500 Subject: [PATCH 1/3] KANBAN-457: Add 'Data Preservation to About menu --- apps/main-app/src/constants.js | 157 +++++++++++++++++++-------------- 1 file changed, 90 insertions(+), 67 deletions(-) diff --git a/apps/main-app/src/constants.js b/apps/main-app/src/constants.js index 37743146d..19b39b66d 100644 --- a/apps/main-app/src/constants.js +++ b/apps/main-app/src/constants.js @@ -4,7 +4,8 @@ export const LARGE_COL_CLASS = 'col-md-8 col-12'; export const SMALL_COL_CLASS = 'col-md-4 col-12'; /* Wordpress REST API connection setting */ -export const WORDPRESS_REST_API_BASE = 'https://public-api.wordpress.com/wp/v2/sites/alliancegenome.wordpress.com'; +export const WORDPRESS_REST_API_BASE = + 'https://public-api.wordpress.com/wp/v2/sites/alliancegenome.wordpress.com'; export const WORDPRESS_PAGE_BASE_URL = WORDPRESS_REST_API_BASE + '/pages?slug='; export const WORDPRESS_POST_BASE_URL = WORDPRESS_REST_API_BASE + '/posts'; export const WORDPRESS_POST_URL = WORDPRESS_POST_BASE_URL + '?slug='; @@ -14,7 +15,7 @@ export const WARNING_BANNER_SLUG = 'warning-banner'; export const CATEGORIES = [ { name: 'all', - displayName: 'All' + displayName: 'All', }, { name: 'gene', @@ -24,7 +25,7 @@ export const CATEGORIES = [ { name: 'go', displayName: 'Gene Ontology', - displayFields: ['primaryKey', 'collapsible_synonyms', 'branch'] + displayFields: ['primaryKey', 'collapsible_synonyms', 'branch'], }, { name: 'disease', @@ -34,17 +35,25 @@ export const CATEGORIES = [ { name: 'allele', displayName: 'Allele/Variant', - displayFields: ['primaryKey','genes', 'synonyms','variantType','molecularConsequence', 'diseases', 'variantName'], + displayFields: [ + 'primaryKey', + 'genes', + 'synonyms', + 'variantType', + 'molecularConsequence', + 'diseases', + 'variantName', + ], }, { name: 'model', displayName: 'Model', - displayFields: ['primaryKey','synonyms'], + displayFields: ['primaryKey', 'synonyms'], }, { name: 'dataset', displayName: 'HTP Dataset Index', - displayFields: ['dataProviderNote', 'idCollection', 'tags', 'summary'] + displayFields: ['dataProviderNote', 'idCollection', 'tags', 'summary'], }, ]; @@ -57,14 +66,11 @@ export const NON_HIGHLIGHTED_FIELDS = [ 'primaryKey', 'orthologs', 'homologs.symbol', - 'homologs.panther_family' + 'homologs.panther_family', ]; //show these fields in both the highlight section and their normal spot -export const DUPLICATE_HIGHLIGHTED_FIELDS = [ - 'crossReferences', - 'synonyms' -]; +export const DUPLICATE_HIGHLIGHTED_FIELDS = ['crossReferences', 'synonyms']; export const NAV_MENU = [ { @@ -100,8 +106,8 @@ export const NAV_MENU = [ label: 'JBrowse', route: '/jbrowse/?data=data%2FHomo%20sapiens', external: true, - } - ] + }, + ], }, { label: 'Members', @@ -109,57 +115,57 @@ export const NAV_MENU = [ { label: 'FlyBase', shortLabel: 'FlyBase', - route: '/members/flybase' + route: '/members/flybase', }, { label: 'Mouse Genome Database', shortLabel: 'MGD', - route: '/members/mgd' + route: '/members/mgd', }, { label: 'Rat Genome Database', shortLabel: 'RGD', - route: '/members/rgd' + route: '/members/rgd', }, { label: 'Saccharomyces Genome Database', shortLabel: 'SGD', - route: '/members/sgd' + route: '/members/sgd', }, { label: 'WormBase', shortLabel: 'WormBase', - route: '/members/wormbase' + route: '/members/wormbase', }, { label: 'Xenbase', shortLabel: 'Xenbase', - route: '/members/xenbase' + route: '/members/xenbase', }, { label: 'Zebrafish Information Network', shortLabel: 'ZFIN', - route: '/members/zfin' + route: '/members/zfin', }, { label: 'Gene Ontology Consortium', shortLabel: 'GOC', - route: '/members/goc' - } - ] + route: '/members/goc', + }, + ], }, { label: 'News', sub: [ { label: 'News and Events', - route: '/news' + route: '/news', }, { label: 'Release Notes', - route: '/release-notes' - } - ] + route: '/release-notes', + }, + ], }, { label: 'About', @@ -170,21 +176,21 @@ export const NAV_MENU = [ }, { label: 'Funding', - route: '/funding' + route: '/funding', }, { - label: 'Organization and Governance', - route: '/organization-and-governance' + label: 'Publications', + route: '/publications', }, { - label: 'Privacy, Warranty, and Licensing', - route: '/privacy-warranty-licensing' + label: 'Organization and Governance', + route: '/organization-and-governance', }, { - label: 'Publications', - route: '/publications', - } - ] + label: 'Privacy, Warranty, Licensing, and Data Preservation Commitment', + route: '/privacy-warranty-licensing', + }, + ], }, { label: 'Working Groups', @@ -195,21 +201,21 @@ export const NAV_MENU = [ sub: [ { label: 'FAQ / Known Issues', - route: '/faq' + route: '/faq', }, { label: 'Glossary', - route: '/glossary' + route: '/glossary', }, { label: 'Tutorials', - route: '/tutorials' + route: '/tutorials', }, { label: 'User Documentation', - route: '/help' + route: '/help', }, - ] + ], }, { label: 'Community', @@ -223,8 +229,8 @@ export const NAV_MENU = [ label: 'Twitter', route: 'https://twitter.com/alliancegenome', external: true, - } - ] + }, + ], }, { label: 'Contact Us', @@ -233,7 +239,7 @@ export const NAV_MENU = [ { label: 'Cite Us', route: '/cite-us', - } + }, ]; export const DEFAULT_TABLE_STATE = { @@ -251,9 +257,11 @@ export const SPECIES = [ apolloName: 'human', apolloTrack: '/All%20Genes/', jBrowseName: 'Homo sapiens', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/human/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/human/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -265,9 +273,11 @@ export const SPECIES = [ apolloName: 'mouse', apolloTrack: '/All%20Genes/', jBrowseName: 'Mus musculus', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/MGI/mouse/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/MGI/mouse/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -279,9 +289,11 @@ export const SPECIES = [ apolloName: 'rat', apolloTrack: '/All%20Genes/', jBrowseName: 'Rattus norvegicus', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/RGD/rat/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/RGD/rat/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -293,9 +305,11 @@ export const SPECIES = [ apolloName: 'x_laevis', apolloTrack: '/All%20Genes/', jBrowseName: 'Xenopus laevis', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_laevis/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_laevis/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: true, @@ -307,9 +321,11 @@ export const SPECIES = [ apolloName: 'x_tropicalis', apolloTrack: '/All%20Genes/', jBrowseName: 'Xenopus tropicalis', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_tropicalis/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_tropicalis/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: true, @@ -321,9 +337,11 @@ export const SPECIES = [ apolloName: 'zebrafish', apolloTrack: '/All%20Genes/', jBrowseName: 'Danio rerio', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/zfin/zebrafish-11/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/zfin/zebrafish-11/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -335,9 +353,11 @@ export const SPECIES = [ apolloName: 'fly', apolloTrack: '/All%20Genes/', jBrowseName: 'Drosophila melanogaster', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/FlyBase/fruitfly/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/FlyBase/fruitfly/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -349,9 +369,11 @@ export const SPECIES = [ apolloName: 'worm', apolloTrack: '/All%20Genes/', jBrowseName: 'Caenorhabditis elegans', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/WormBase/c_elegans_PRJNA13758/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/WormBase/c_elegans_PRJNA13758/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -363,9 +385,11 @@ export const SPECIES = [ apolloName: 'yeast', apolloTrack: '/All%20Genes/', jBrowseName: 'Saccharomyces cerevisiae', - jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/SGD/yeast/', + jBrowsenclistbaseurl: + 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/SGD/yeast/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz', + jBrowsefastaurl: + 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -382,12 +406,12 @@ export const SPECIES = [ enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: false, geneSynopsisProvider: 'UniProt', - } + }, ]; -export const TAXON_ORDER = SPECIES.map(s => s.taxonId); +export const TAXON_ORDER = SPECIES.map((s) => s.taxonId); -export const SPECIES_NAME_ORDER = SPECIES.map(s => s.fullName); +export const SPECIES_NAME_ORDER = SPECIES.map((s) => s.fullName); export const GA_PROPERTY_ID_UA = 'UA-98765810-1'; export const GA_PROPERTY_ID_GA4 = 'G-H3F65KGJDR'; @@ -400,6 +424,5 @@ export const GA_EVENT_CATEGORY = { export const GA_EVENT_ACTION = { GO_TO_PAGE: 'Go to page', GO_TO_SEARCH_RESULTS: 'Go to search results', - SET_PAGE_SIZE: 'Set page size' + SET_PAGE_SIZE: 'Set page size', }; - From 104ab156f077de37f144176271d1a9a1a90f2e57 Mon Sep 17 00:00:00 2001 From: Howie Motenko Date: Thu, 18 Jan 2024 10:20:30 -0500 Subject: [PATCH 2/3] Revert "KANBAN-457: Add 'Data Preservation to About menu" This reverts commit 0ed5b25889267f319d0848721e0a007acd626eca. --- apps/main-app/src/constants.js | 157 ++++++++++++++------------------- 1 file changed, 67 insertions(+), 90 deletions(-) diff --git a/apps/main-app/src/constants.js b/apps/main-app/src/constants.js index 19b39b66d..37743146d 100644 --- a/apps/main-app/src/constants.js +++ b/apps/main-app/src/constants.js @@ -4,8 +4,7 @@ export const LARGE_COL_CLASS = 'col-md-8 col-12'; export const SMALL_COL_CLASS = 'col-md-4 col-12'; /* Wordpress REST API connection setting */ -export const WORDPRESS_REST_API_BASE = - 'https://public-api.wordpress.com/wp/v2/sites/alliancegenome.wordpress.com'; +export const WORDPRESS_REST_API_BASE = 'https://public-api.wordpress.com/wp/v2/sites/alliancegenome.wordpress.com'; export const WORDPRESS_PAGE_BASE_URL = WORDPRESS_REST_API_BASE + '/pages?slug='; export const WORDPRESS_POST_BASE_URL = WORDPRESS_REST_API_BASE + '/posts'; export const WORDPRESS_POST_URL = WORDPRESS_POST_BASE_URL + '?slug='; @@ -15,7 +14,7 @@ export const WARNING_BANNER_SLUG = 'warning-banner'; export const CATEGORIES = [ { name: 'all', - displayName: 'All', + displayName: 'All' }, { name: 'gene', @@ -25,7 +24,7 @@ export const CATEGORIES = [ { name: 'go', displayName: 'Gene Ontology', - displayFields: ['primaryKey', 'collapsible_synonyms', 'branch'], + displayFields: ['primaryKey', 'collapsible_synonyms', 'branch'] }, { name: 'disease', @@ -35,25 +34,17 @@ export const CATEGORIES = [ { name: 'allele', displayName: 'Allele/Variant', - displayFields: [ - 'primaryKey', - 'genes', - 'synonyms', - 'variantType', - 'molecularConsequence', - 'diseases', - 'variantName', - ], + displayFields: ['primaryKey','genes', 'synonyms','variantType','molecularConsequence', 'diseases', 'variantName'], }, { name: 'model', displayName: 'Model', - displayFields: ['primaryKey', 'synonyms'], + displayFields: ['primaryKey','synonyms'], }, { name: 'dataset', displayName: 'HTP Dataset Index', - displayFields: ['dataProviderNote', 'idCollection', 'tags', 'summary'], + displayFields: ['dataProviderNote', 'idCollection', 'tags', 'summary'] }, ]; @@ -66,11 +57,14 @@ export const NON_HIGHLIGHTED_FIELDS = [ 'primaryKey', 'orthologs', 'homologs.symbol', - 'homologs.panther_family', + 'homologs.panther_family' ]; //show these fields in both the highlight section and their normal spot -export const DUPLICATE_HIGHLIGHTED_FIELDS = ['crossReferences', 'synonyms']; +export const DUPLICATE_HIGHLIGHTED_FIELDS = [ + 'crossReferences', + 'synonyms' +]; export const NAV_MENU = [ { @@ -106,8 +100,8 @@ export const NAV_MENU = [ label: 'JBrowse', route: '/jbrowse/?data=data%2FHomo%20sapiens', external: true, - }, - ], + } + ] }, { label: 'Members', @@ -115,57 +109,57 @@ export const NAV_MENU = [ { label: 'FlyBase', shortLabel: 'FlyBase', - route: '/members/flybase', + route: '/members/flybase' }, { label: 'Mouse Genome Database', shortLabel: 'MGD', - route: '/members/mgd', + route: '/members/mgd' }, { label: 'Rat Genome Database', shortLabel: 'RGD', - route: '/members/rgd', + route: '/members/rgd' }, { label: 'Saccharomyces Genome Database', shortLabel: 'SGD', - route: '/members/sgd', + route: '/members/sgd' }, { label: 'WormBase', shortLabel: 'WormBase', - route: '/members/wormbase', + route: '/members/wormbase' }, { label: 'Xenbase', shortLabel: 'Xenbase', - route: '/members/xenbase', + route: '/members/xenbase' }, { label: 'Zebrafish Information Network', shortLabel: 'ZFIN', - route: '/members/zfin', + route: '/members/zfin' }, { label: 'Gene Ontology Consortium', shortLabel: 'GOC', - route: '/members/goc', - }, - ], + route: '/members/goc' + } + ] }, { label: 'News', sub: [ { label: 'News and Events', - route: '/news', + route: '/news' }, { label: 'Release Notes', - route: '/release-notes', - }, - ], + route: '/release-notes' + } + ] }, { label: 'About', @@ -176,21 +170,21 @@ export const NAV_MENU = [ }, { label: 'Funding', - route: '/funding', - }, - { - label: 'Publications', - route: '/publications', + route: '/funding' }, { label: 'Organization and Governance', - route: '/organization-and-governance', + route: '/organization-and-governance' }, { - label: 'Privacy, Warranty, Licensing, and Data Preservation Commitment', - route: '/privacy-warranty-licensing', + label: 'Privacy, Warranty, and Licensing', + route: '/privacy-warranty-licensing' }, - ], + { + label: 'Publications', + route: '/publications', + } + ] }, { label: 'Working Groups', @@ -201,21 +195,21 @@ export const NAV_MENU = [ sub: [ { label: 'FAQ / Known Issues', - route: '/faq', + route: '/faq' }, { label: 'Glossary', - route: '/glossary', + route: '/glossary' }, { label: 'Tutorials', - route: '/tutorials', + route: '/tutorials' }, { label: 'User Documentation', - route: '/help', + route: '/help' }, - ], + ] }, { label: 'Community', @@ -229,8 +223,8 @@ export const NAV_MENU = [ label: 'Twitter', route: 'https://twitter.com/alliancegenome', external: true, - }, - ], + } + ] }, { label: 'Contact Us', @@ -239,7 +233,7 @@ export const NAV_MENU = [ { label: 'Cite Us', route: '/cite-us', - }, + } ]; export const DEFAULT_TABLE_STATE = { @@ -257,11 +251,9 @@ export const SPECIES = [ apolloName: 'human', apolloTrack: '/All%20Genes/', jBrowseName: 'Homo sapiens', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/human/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/human/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -273,11 +265,9 @@ export const SPECIES = [ apolloName: 'mouse', apolloTrack: '/All%20Genes/', jBrowseName: 'Mus musculus', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/MGI/mouse/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/MGI/mouse/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -289,11 +279,9 @@ export const SPECIES = [ apolloName: 'rat', apolloTrack: '/All%20Genes/', jBrowseName: 'Rattus norvegicus', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/RGD/rat/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/RGD/rat/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -305,11 +293,9 @@ export const SPECIES = [ apolloName: 'x_laevis', apolloTrack: '/All%20Genes/', jBrowseName: 'Xenopus laevis', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_laevis/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_laevis/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: true, @@ -321,11 +307,9 @@ export const SPECIES = [ apolloName: 'x_tropicalis', apolloTrack: '/All%20Genes/', jBrowseName: 'Xenopus tropicalis', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_tropicalis/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/XenBase/x_tropicalis/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: true, @@ -337,11 +321,9 @@ export const SPECIES = [ apolloName: 'zebrafish', apolloTrack: '/All%20Genes/', jBrowseName: 'Danio rerio', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/zfin/zebrafish-11/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/zfin/zebrafish-11/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz', vertebrate: true, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -353,11 +335,9 @@ export const SPECIES = [ apolloName: 'fly', apolloTrack: '/All%20Genes/', jBrowseName: 'Drosophila melanogaster', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/FlyBase/fruitfly/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/FlyBase/fruitfly/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -369,11 +349,9 @@ export const SPECIES = [ apolloName: 'worm', apolloTrack: '/All%20Genes/', jBrowseName: 'Caenorhabditis elegans', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/WormBase/c_elegans_PRJNA13758/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/WormBase/c_elegans_PRJNA13758/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -385,11 +363,9 @@ export const SPECIES = [ apolloName: 'yeast', apolloTrack: '/All%20Genes/', jBrowseName: 'Saccharomyces cerevisiae', - jBrowsenclistbaseurl: - 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/SGD/yeast/', + jBrowsenclistbaseurl: 'https://s3.amazonaws.com/agrjbrowse/docker/6.0.0/SGD/yeast/', jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz', - jBrowsefastaurl: - 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz', + jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz', vertebrate: false, enableSingleCellExpressionAtlasLink: true, enableOrthologComparison: true, @@ -406,12 +382,12 @@ export const SPECIES = [ enableSingleCellExpressionAtlasLink: false, enableOrthologComparison: false, geneSynopsisProvider: 'UniProt', - }, + } ]; -export const TAXON_ORDER = SPECIES.map((s) => s.taxonId); +export const TAXON_ORDER = SPECIES.map(s => s.taxonId); -export const SPECIES_NAME_ORDER = SPECIES.map((s) => s.fullName); +export const SPECIES_NAME_ORDER = SPECIES.map(s => s.fullName); export const GA_PROPERTY_ID_UA = 'UA-98765810-1'; export const GA_PROPERTY_ID_GA4 = 'G-H3F65KGJDR'; @@ -424,5 +400,6 @@ export const GA_EVENT_CATEGORY = { export const GA_EVENT_ACTION = { GO_TO_PAGE: 'Go to page', GO_TO_SEARCH_RESULTS: 'Go to search results', - SET_PAGE_SIZE: 'Set page size', + SET_PAGE_SIZE: 'Set page size' }; + From bdfae1c0c74480409203fb7b81b7467315dd2737 Mon Sep 17 00:00:00 2001 From: Howie Motenko Date: Thu, 18 Jan 2024 10:32:58 -0500 Subject: [PATCH 3/3] Redo - Add data preservation without prettier --- apps/main-app/src/constants.js | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/apps/main-app/src/constants.js b/apps/main-app/src/constants.js index 37743146d..cb64a03c4 100644 --- a/apps/main-app/src/constants.js +++ b/apps/main-app/src/constants.js @@ -172,18 +172,18 @@ export const NAV_MENU = [ label: 'Funding', route: '/funding' }, + { + label: 'Publications', + route: '/publications', + }, { label: 'Organization and Governance', route: '/organization-and-governance' }, { - label: 'Privacy, Warranty, and Licensing', + label: 'Privacy, Warranty, Licensing, and Data Preservation Commitment', route: '/privacy-warranty-licensing' }, - { - label: 'Publications', - route: '/publications', - } ] }, {