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IGVF-1883 Add sample summary to analysis-set displays #614

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merged 3 commits into from
Oct 1, 2024
Merged

IGVF-1883 Add sample summary to analysis-set displays #614

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120c7da
IGVF-1883-update-analysis-set-npm
forresttanaka Aug 28, 2024
e355054
IGVF-1883-update-analysis-set-npm
forresttanaka Sep 30, 2024
0ce7777
IGVF-1883-update-analysis-set-npm
forresttanaka Sep 30, 2024
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4 changes: 4 additions & 0 deletions components/file-table.js
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,10 @@ const filesColumns = [
title: "Content Type",
sorter: (item) => item.content_type.toLowerCase(),
},
{
id: "summary",
title: "Summary",
},
{
id: "lab",
title: "Lab",
Expand Down
9 changes: 3 additions & 6 deletions components/search/__tests__/list-renderer.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -1429,13 +1429,13 @@ describe("Test the AnalysisSet component", () => {
expect(uniqueId).toHaveTextContent(/IGVFDS3099XPLN$/);

const title = screen.getByTestId("search-list-item-title");
expect(title).toHaveTextContent(/^primary analysis$/);
expect(title).toHaveTextContent(/^primary analysis of data$/);

const meta = screen.queryByTestId("search-list-item-meta");
expect(meta).toHaveTextContent("J. Michael Cherry, Stanford");

const supplement = screen.getByTestId("search-list-item-supplement");
expect(supplement).toHaveTextContent("primary analysis of data");
expect(supplement).toHaveTextContent("Alternate Accessions");

const status = screen.getByTestId("search-list-item-quality");
expect(status).toHaveTextContent("released");
Expand Down Expand Up @@ -1469,14 +1469,11 @@ describe("Test the AnalysisSet component", () => {
expect(uniqueId).toHaveTextContent(/IGVFDS0390NOLS$/);

const title = screen.getByTestId("search-list-item-title");
expect(title).toHaveTextContent(/^primary analysis$/);
expect(title).toHaveTextContent(/^primary analysis of data$/);

const meta = screen.queryByTestId("search-list-item-meta");
expect(meta).toHaveTextContent(/^J. Michael Cherry, Stanford/);

const supplement = screen.queryByTestId("search-list-item-supplement");
expect(supplement).toHaveTextContent("primary analysis of data");

const status = screen.getByTestId("search-list-item-quality");
expect(status).toHaveTextContent("released");
});
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28 changes: 22 additions & 6 deletions components/search/list-renderer/analysis-set.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,28 +8,44 @@ import {
SearchListItemQuality,
SearchListItemSupplement,
SearchListItemSupplementAlternateAccessions,
SearchListItemSupplementSummary,
SearchListItemSupplementContent,
SearchListItemSupplementLabel,
SearchListItemSupplementSection,
SearchListItemTitle,
SearchListItemType,
SearchListItemUniqueId,
} from "./search-list-item";

export default function AnalysisSet({ item: analysisSet }) {
const isSupplementsVisible =
analysisSet.alternate_accessions?.length > 0 || analysisSet.sample_summary;

return (
<SearchListItemContent>
<SearchListItemMain>
<SearchListItemUniqueId>
<SearchListItemType item={analysisSet} />
{analysisSet.accession}
</SearchListItemUniqueId>
<SearchListItemTitle>{analysisSet.file_set_type}</SearchListItemTitle>
<SearchListItemTitle>{analysisSet.summary}</SearchListItemTitle>
<SearchListItemMeta>
<span key="lab">{analysisSet.lab.title}</span>
</SearchListItemMeta>
<SearchListItemSupplement>
<SearchListItemSupplementAlternateAccessions item={analysisSet} />
<SearchListItemSupplementSummary item={analysisSet} />
</SearchListItemSupplement>
{isSupplementsVisible && (
<SearchListItemSupplement>
<SearchListItemSupplementAlternateAccessions item={analysisSet} />
{analysisSet.sample_summary && (
<SearchListItemSupplementSection>
<SearchListItemSupplementLabel>
Samples
</SearchListItemSupplementLabel>
<SearchListItemSupplementContent>
{analysisSet.sample_summary}
</SearchListItemSupplementContent>
</SearchListItemSupplementSection>
)}
</SearchListItemSupplement>
)}
</SearchListItemMain>
<SearchListItemQuality item={analysisSet} />
</SearchListItemContent>
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2 changes: 1 addition & 1 deletion lib/__tests__/common-requests.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -314,7 +314,7 @@ describe("Test all the common requests", () => {
request
);
expect(mockFunction).toBeCalledWith(
"/search/?field=@type&field=accession&field=content_type&field=creation_timestamp&field=file_format&field=file_size&field=file_set&field=flowcell_id&field=href&field=illumina_read_type&field=index&field=lab.title&field=lane&field=seqspecs&field=sequencing_platform&field=sequencing_run&field=status&field=upload_status&@id=/sequence-files/IGVFFI4067OVRO/&@id=/sequence-files/IGVFFI1165AJSO/&limit=2",
"/search/?field=@type&field=accession&field=content_type&field=creation_timestamp&field=file_format&field=file_size&field=file_set&field=flowcell_id&field=href&field=illumina_read_type&field=index&field=lab.title&field=lane&field=seqspecs&field=sequencing_platform&field=sequencing_run&field=status&field=summary&field=upload_status&@id=/sequence-files/IGVFFI4067OVRO/&@id=/sequence-files/IGVFFI1165AJSO/&limit=2",
expect.anything()
);
expect(result).toHaveLength(2);
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1 change: 1 addition & 0 deletions lib/common-requests.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,7 @@ export async function requestFiles(
"sequencing_platform",
"sequencing_run",
"status",
"summary",
"upload_status",
])
).unwrap_or([]);
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,6 @@
"prettier": "^3.0.3",
"prettier-plugin-tailwindcss": "^0.6.5",
"pretty-format": "^29.5.0",
"tailwindcss": "^3.1.8"
"tailwindcss": "^3.4.10"
}
}
31 changes: 27 additions & 4 deletions pages/analysis-sets/[id].js
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Original file line number Diff line number Diff line change
Expand Up @@ -128,9 +128,36 @@ export default function AnalysisSet({
</DataItemList>
</>
)}
{analysisSet.sample_summary && (
<>
<DataItemLabel>Samples</DataItemLabel>
<DataItemValue>{analysisSet.sample_summary}</DataItemValue>
</>
)}
{analysisSet.protocols?.length > 0 && (
<>
<DataItemLabel>Protocols</DataItemLabel>
<DataItemList isCollapsible isUrlList>
{analysisSet.protocols.map((protocol) => (
<a
href={protocol}
key={protocol}
target="_blank"
rel="noopener noreferrer"
>
{protocol}
</a>
))}
</DataItemList>
</>
)}
</DataArea>
</DataPanel>

{files.length > 0 && (
<FileTable files={files} fileSet={analysisSet} isDownloadable />
)}

{analysisSet.samples?.length > 0 && (
<SampleTable
samples={analysisSet.samples}
Expand Down Expand Up @@ -174,10 +201,6 @@ export default function AnalysisSet({
/>
)}

{files.length > 0 && (
<FileTable files={files} fileSet={analysisSet} isDownloadable />
)}

{documents.length > 0 && <DocumentTable documents={documents} />}
<Attribution attribution={attribution} />
</JsonDisplay>
Expand Down
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