diff --git a/components/AtlasTable.tsx b/components/AtlasTable.tsx index 3a03d08..f664a07 100644 --- a/components/AtlasTable.tsx +++ b/components/AtlasTable.tsx @@ -25,123 +25,77 @@ interface IAtlasTableProps { filteredBiospecimens: Entity[]; } -const MinervaStoryViewerLink = (props: { url: string; count: number }) => ( - - - {props.count < 100 && '\u00A0'} - {props.count < 10 && '\u00A0'} - {props.count}{' '} - - +const ViewerLink = (props: { url: string; tooltip: string; children: React.ReactNode }) => ( + + + {props.children} + + ); + +// Create specific ViewerLink components +const MinervaStoryViewerLink = (props: { url: string }) => ( + +
+ +
+
); -const AutoMinervaViewerLink = (props: { url: string; count: number }) => ( - - - {props.count < 100 && '\u00A0'} - {props.count < 10 && '\u00A0'} - {props.count}{' '} - - - +const AutoMinervaViewerLink = (props: { url: string }) => ( + + + ); -const CBioPortalViewerLink = (props: { url: string; count: number }) => ( - - - {props.count < 100 && '\u00A0'} - {props.count < 10 && '\u00A0'} - {props.count}{' '} - - - +const CBioPortalViewerLink = (props: { url: string }) => ( + +
+ +
+
); -const CellxgeneViewerLink = (props: { url: string; count: number }) => ( - - - {props.count < 100 && '\u00A0'} - {props.count < 10 && '\u00A0'} - {props.count}{' '} - - - +const CellxgeneViewerLink = (props: { url: string }) => ( + +
+ +
+
); -const BroadSingleCellPortalViewerLink = (props: { - url: string; - count: number; -}) => ( - - - {props.count < 100 && '\u00A0'} - {props.count < 10 && '\u00A0'} - {props.count}{' '} - - - +const BroadSingleCellPortalViewerLink = (props: { url: string }) => ( + + + ); - type AtlasTableData = AtlasX & { isSelected: boolean }; @observer @@ -196,30 +150,32 @@ export default class AtlasTable extends React.Component { get columns() { return [ { - name: 'Project Title', - selector: (atlas: AtlasX) => atlas.atlas_name, - grow: 1.25, + name: 'Project', + selector: (atlas: AtlasX) => ( + + {atlas.atlas_name} + + ), + grow: 2, wrap: true, sortable: true, }, { - name: 'Project ID', - selector: (atlas: AtlasX) => atlas.atlas_id, - wrap: true, - sortable: false, - }, - { - name: 'Lead Research Teams', + name: 'Investigator', selector: (atlas: AtlasX) => atlas.team_name, grow: 1.25, wrap: true, sortable: true, }, { - name: 'Status', + name: 'Project Status', selector: (atlas: AtlasX) => atlas.status, - grow: 1, - wrap: true, + grow: 1.5, + wrap: false, sortable: true, }, // We don't have multiple publications per project yet @@ -227,15 +183,15 @@ export default class AtlasTable extends React.Component { name: 'Publication', selector: 'publication', cell: (atlas: AtlasX) => ( - atlas.publication? <> : '' + atlas.publication? <> : '' ), - grow: 0.75, + grow: 1, wrap: true, sortable: true, }, // TODO include names of datasets { - name: 'Dataset Accessions', + name: 'Data Types', selector: '', cell: (atlas: AtlasX) => { return ( @@ -247,7 +203,7 @@ export default class AtlasTable extends React.Component { sortable: false, }, { - name: 'Cases', + name: 'Patients', grow: 0.5, selector: 'num_cases', cell: (atlas: AtlasX) => ( @@ -267,26 +223,7 @@ export default class AtlasTable extends React.Component { sortable: true, }, { - name: 'Biospecimens', - selector: 'num_biospecimens', - cell: (atlas: AtlasX) => ( - - {this.shouldShowFilteredFractions - ? `${ - ( - this.filteredBiospecimensByAtlas[ - atlas.atlas_id - ] || [] - ).length - }/` - : ''} - {atlas.num_biospecimens} - - ), - sortable: true, - }, - { - name: 'Viewers', + name: 'External Tools', selector: 'atlas_id', // dummy selector - you need to put something or else nothing will render grow: 1.5, cell: (atlas: AtlasX) => { @@ -297,13 +234,11 @@ export default class AtlasTable extends React.Component { url={ 'https://cellxgene.cziscience.com/collections/99f1515b-46a2-4bc4-94c3-f62659dc1eb4' } - count={1} /> ); @@ -313,7 +248,6 @@ export default class AtlasTable extends React.Component { url={ 'https://triage.cbioportal.mskcc.org/study/summary?id=ovarian_drapkin_2022' } - count={1} /> ); } else if (atlas.atlas_id === 'syn52047509') { @@ -322,7 +256,6 @@ export default class AtlasTable extends React.Component { url={ 'https://triage.cbioportal.mskcc.org/study/summary?id=brca_ellisen_2022' } - count={1} /> ); } else { diff --git a/components/ExploreSummary.tsx b/components/ExploreSummary.tsx index 15f5b0c..d03de01 100644 --- a/components/ExploreSummary.tsx +++ b/components/ExploreSummary.tsx @@ -21,10 +21,6 @@ export const ExploreSummary: React.FunctionComponent = ( props.getGroupsByPropertyFiltered[AttributeNames.AtlasName] ).length; - const organCount = _.keys( - props.getGroupsByPropertyFiltered[AttributeNames.TissueorOrganofOrigin] - ).length; - const cancerTypeCount = _.keys( props.getGroupsByPropertyFiltered[AttributeNames.PrimaryDiagnosis] ).length; @@ -43,9 +39,7 @@ export const ExploreSummary: React.FunctionComponent = (
{pluralize('Team', atlasCount, true)}
-
{pluralize('Organ', organCount, true)}
-
{pluralize('Cancer Type', cancerTypeCount, true)}
-
{pluralize('Case', props.filteredCaseCount, true)}
+
{pluralize('Patient', props.filteredCaseCount, true)}
{props.filteredBiospecimenCount === 1 ? 'Biospecimen' diff --git a/components/FileTable.tsx b/components/FileTable.tsx index 070825a..5c58eb6 100644 --- a/components/FileTable.tsx +++ b/components/FileTable.tsx @@ -389,17 +389,6 @@ export default class FileTable extends React.Component { wrap: true, sortable: true, }, - { - name: 'Organ', - selector: (file: Entity) => { - return _.uniq( - file.diagnosis.map((d) => d.TissueorOrganofOrigin) - ).join(', '); - }, - cell: truncatedTableCell, - wrap: true, - sortable: true, - }, { name: 'Diagnosis', selector: (file: Entity) => { diff --git a/components/PortalNavbar.tsx b/components/PortalNavbar.tsx index a19791e..f4891a8 100644 --- a/components/PortalNavbar.tsx +++ b/components/PortalNavbar.tsx @@ -25,8 +25,8 @@ const PortalNavbar = () => ( HTAN Data Portal diff --git a/components/filter/FilterControls.tsx b/components/filter/FilterControls.tsx index 3ea45e5..0e43879 100644 --- a/components/filter/FilterControls.tsx +++ b/components/filter/FilterControls.tsx @@ -65,7 +65,6 @@ const FilterControls: React.FunctionComponent = observer( const selectOptions = [ AttributeNames.AtlasName, - AttributeNames.TissueorOrganofOrigin, AttributeNames.PrimaryDiagnosis, AttributeNames.assayName, AttributeNames.Level, @@ -125,34 +124,6 @@ const FilterControls: React.FunctionComponent = observer(
-
-
- - - - - -
-
-
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"@types/react" "^16.9.11" + "@types/react" ">=16.9.11" invariant "^2.2.4" react-lifecycles-compat "^3.0.4" +undici-types@~5.26.4: + version "5.26.5" + resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" + integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== + unfetch@^4.1.0: version "4.2.0" resolved "https://registry.yarnpkg.com/unfetch/-/unfetch-4.2.0.tgz#7e21b0ef7d363d8d9af0fb929a5555f6ef97a3be" @@ -3330,21 +3329,14 @@ update-notifier@4.1.0: url-parse-lax@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/url-parse-lax/-/url-parse-lax-3.0.0.tgz#16b5cafc07dbe3676c1b1999177823d6503acb0c" - integrity sha1-FrXK/Afb42dsGxmZF3gj1lA6yww= + integrity sha512-NjFKA0DidqPa5ciFcSrXnAltTtzz84ogy+NebPvfEgAck0+TNg4UJ4IN+fB7zRZfbgUf0syOo9MDxFkDSMuFaQ== dependencies: prepend-http "^2.0.0" -use-subscription@1.5.1: - version "1.5.1" - resolved "https://registry.yarnpkg.com/use-subscription/-/use-subscription-1.5.1.tgz#73501107f02fad84c6dd57965beb0b75c68c42d1" - integrity sha512-Xv2a1P/yReAjAbhylMfFplFKj9GssgTwN7RlcTxBujFQcloStWNDQdc4g4NRWH9xS4i/FDk04vQBptAXoF3VcA== - dependencies: - object-assign "^4.1.1" - util-deprecate@^1.0.1, util-deprecate@~1.0.1: version "1.0.2" resolved "https://registry.yarnpkg.com/util-deprecate/-/util-deprecate-1.0.2.tgz#450d4dc9fa70de732762fbd2d4a28981419a0ccf" - integrity sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8= + integrity sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw== validate-npm-package-license@^3.0.1: version "3.0.4" @@ -3355,15 +3347,15 @@ validate-npm-package-license@^3.0.1: spdx-expression-parse "^3.0.0" vercel@^21.1.0: - version "21.1.0" - resolved "https://registry.yarnpkg.com/vercel/-/vercel-21.1.0.tgz#dd118bb89b1c2eee078437eac7f6f71ff4f80ea9" - integrity sha512-01NKN1V7oAq4oxkm7OPw/SNMsnF+UPX2OTgq5SxUKyZlz34aqvj+LvEjs4KWNGXFzTAelmuFze7VOObvmB7mug== - dependencies: - "@vercel/build-utils" "2.7.0" - "@vercel/go" "1.1.7" - "@vercel/node" "1.9.0" - "@vercel/python" "1.2.4" - "@vercel/ruby" "1.2.5" + version "21.3.3" + resolved "https://registry.yarnpkg.com/vercel/-/vercel-21.3.3.tgz#22af77308cf612699c652ad49ecedc60eaa0b38f" + integrity sha512-NhxhAmpUoymKQp2WT0PR+NgFPcoVRuhYJ7HSSPKP+S0UCQtZNhy9YCeMkbBzooAw9rrb8gEH+ODEbhK0u5YlFg== + dependencies: + "@vercel/build-utils" "2.10.1" + "@vercel/go" "1.2.2" + "@vercel/node" "1.9.1" + "@vercel/python" "2.0.1" + "@vercel/ruby" "1.2.6" update-notifier "4.1.0" warning@^4.0.0, warning@^4.0.3: @@ -3373,10 +3365,23 @@ warning@^4.0.0, warning@^4.0.3: dependencies: loose-envify "^1.0.0" +webidl-conversions@^3.0.0: + version "3.0.1" + resolved "https://registry.yarnpkg.com/webidl-conversions/-/webidl-conversions-3.0.1.tgz#24534275e2a7bc6be7bc86611cc16ae0a5654871" + integrity sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ== + +whatwg-url@^5.0.0: + version "5.0.0" + resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-5.0.0.tgz#966454e8765462e37644d3626f6742ce8b70965d" + integrity sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw== + dependencies: + tr46 "~0.0.3" + webidl-conversions "^3.0.0" + which@1.2.x: version "1.2.14" resolved "https://registry.yarnpkg.com/which/-/which-1.2.14.tgz#9a87c4378f03e827cecaf1acdf56c736c01c14e5" - integrity sha1-mofEN48D6CfOyvGs31bHNsAcFOU= + integrity sha512-16uPglFkRPzgiUXYMi1Jf8Z5EzN1iB4V0ZtMXcHZnwsBtQhhHeCqoWw7tsUY42hJGNDWtUsVLTjakIa5BgAxCw== dependencies: isexe "^2.0.0" @@ -3420,7 +3425,7 @@ wrap-ansi@^7.0.0: wrappy@1: version "1.0.2" resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f" - integrity sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8= + integrity sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ== write-file-atomic@^3.0.0: version "3.0.3" @@ -3445,7 +3450,7 @@ y18n@^5.0.5: yallist@^2.1.2: version "2.1.2" resolved "https://registry.yarnpkg.com/yallist/-/yallist-2.1.2.tgz#1c11f9218f076089a47dd512f93c6699a6a81d52" - integrity sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI= + integrity sha512-ncTzHV7NvsQZkYe1DW7cbDLm0YpzHmZF5r/iyP3ZnQtMiJ+pjzisCiMNI+Sj+xQF5pXhSHxSB3uDbsBTzY/c2A== yallist@^4.0.0: version "4.0.0" @@ -3453,9 +3458,9 @@ yallist@^4.0.0: integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A== yaml@^1.7.2: - version "1.10.0" - resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.0.tgz#3b593add944876077d4d683fee01081bd9fff31e" - integrity sha512-yr2icI4glYaNG+KWONODapy2/jDdMSDnrONSjblABjD9B4Z5LgiircSt8m8sRZFNi08kG9Sm0uSHtEmP3zaEGg== + version "1.10.2" + resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b" + integrity sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg== yargs-parser@^20.2.3: version "20.2.9" @@ -3468,9 +3473,9 @@ yargs-parser@^21.1.1: integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== yargs@^17.2.1: - version "17.7.1" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.1.tgz#34a77645201d1a8fc5213ace787c220eabbd0967" - integrity sha512-cwiTb08Xuv5fqF4AovYacTFNxk62th7LKJ6BL9IGUpTJrWoU7/7WdQGTP2SjKf1dUNBGzDd28p/Yfs/GI6JrLw== + version "17.7.2" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" + integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== dependencies: cliui "^8.0.1" escalade "^3.1.1"