gramene-search 2.36.1 → 2.37.0

package/README.md

@@ -77,6 +77,31 @@ iframe to <code>dev.gramene.org/static/atlasWidget.html</code>.
   band shows its factor values, sample id, replicates and TPM.
 - **eFP Browser** (where BAR has the species): the eFP image for the chosen study.
 
+**Download.** Paralogs and EBI Studies have a *Download* button among the heatmap's controls, and JGI Studies one in
+the grid's toolbar. It opens a dialog that asks for a **file name** (prefilled, focused and selected) and a
+**format**: *Tab-delimited text (.tsv)*, selected each time the dialog opens, or *JSON (.json)*. *Download* (or
+Enter) saves the data the widget shows under that name, with the format's extension added unless the name already
+has it, once however often it is clicked; *Cancel* saves nothing. The name is sanitised so that the browser saves the
+file under exactly the name the dialog shows (path separators, <code>: * ? " &lt; &gt; |</code>, control and invisible
+format characters and a leading <code>~</code> are removed, and it is cut to 200 bytes) and *Download* is disabled
+while it is blank. When the heatmap shows no data ("No data match your filtering criteria…"), the dialog says there is
+nothing to download and saves nothing.
+
+| Sub-tab | Suggested file name | Saved |
+| --- | --- | --- |
+| Paralogs | <code>&lt;gene&gt;-paralogs-&lt;experiment&gt;</code> | the heatmap's rows (the paralogs) and columns as shown: after its filters and ordering, and only the columns in view while zoomed in |
+| EBI Studies | <code>&lt;gene&gt;-ebi-studies</code> | the same, one row per study (the JGI rows are left out, as on the page) |
+| JGI Studies | <code>&lt;gene&gt;-&lt;JGI accession&gt;</code> | every sample of the study for the gene, one per line, whatever the grid's axes: gene, study, the study's factors, sample id, replicates and TPM |
+
+<code>&lt;gene&gt;</code> is the id the tab queries (the gene's <code>atlas_id</code>, or its id). The TSV of a heatmap
+starts with <code>#</code> comment lines (page URL, time, query or experiment, unit), then a header line of column
+labels and a line per row; the grid's TSV is a plain table. The JSON has the same data with ids, units and
+<code>null</code> for no data, and credits the data to their source: <code>Expression Atlas</code> for EBI studies,
+<code>phytozome-next.jgi.doe.gov</code> for a JGI study drawn in Paralogs (see gramene-atlas-heatmap's README,
+*Downloads*). For an EBI experiment the dialog of a Paralogs heatmap also links to the *Full experiment data on
+Expression Atlas* (EBI's download, formerly the "All data" menu item); JGI studies have no such download, so it is
+left out for them.
+
 Details:
 - <code>atlasUrl</code> in the site configuration names the gramene-swagger <code>/gxa/</code> instance to query,
   e.g. <code>'https://data.sorghumbase.org/sorghum_v11/gxa/'</code>. Unset, the tab queries
@@ -89,21 +114,25 @@ Details:
 - EBI Studies and JGI Studies send the gene's <code>atlas_id</code> (or its id).
 - Links open in a new tab. <code>resolveUrl</code> in <code>Expression.js</code> points row, experiment,
   "more information", Expression Atlas and download links at EBI, because gramene-swagger returns
-  relative gene links and an empty <code>geneQuery</code>; JGI studies keep their Phytozome links.
+  relative gene links and an empty <code>geneQuery</code>; JGI studies keep their Phytozome links. For
+  <code>'download'</code> it returns <code>null</code> when the experiment is a JGI study (a <code>source: 'JGI'</code>
+  study of the species, or a download URL at <code>jgi.doe.gov</code>, whose payload names Phytozome's genome page as
+  its download), which drops the dialog's full data link.
 - The chosen sub-tab, Paralogs experiment, JGI study and the grid's axes per JGI study
   (<code>jgiExperiment</code>, <code>jgiAxes</code>) are kept in <code>uiViewState.byGene[geneId].expression</code> and
   saved with shared views.
 - Styles are injected at runtime; Bootstrap 5 CSS and react-bootstrap 2 come from the host.
 
-<code>gramene-atlas-heatmap</code> is a dependency (<code>^6.2.0</code>, which adds <code>filterRows</code> and
-<code>ExpressionFactorGrid</code>) and brings in <code>gramene-anatomogram</code>. To try unreleased fork changes,
+<code>gramene-atlas-heatmap</code> is a dependency (<code>^6.3.0</code>: 6.2.0 added <code>filterRows</code> and
+<code>ExpressionFactorGrid</code>, 6.3.0 the Download dialog and <code>downloadFileName</code>) and brings in
+<code>gramene-anatomogram</code>. To try unreleased fork changes,
 install packed tarballs of both packages over the registry versions (not <code>npm link</code> or
 <code>file:</code>, which load a second React); the next <code>npm install</code> puts the registry versions back.
 ```bash
 cd ../anatomogram && npm run pack:local      # gramene-anatomogram-3.0.0.tgz
-cd ../atlas-heatmap && npm run pack:local    # gramene-atlas-heatmap-6.2.0.tgz
+cd ../atlas-heatmap && npm run pack:local    # gramene-atlas-heatmap-6.3.0.tgz
 cd ../gramene-search && npm install --no-save ../anatomogram/gramene-anatomogram-3.0.0.tgz \
-  ../atlas-heatmap/gramene-atlas-heatmap-6.2.0.tgz && rm -rf .parcel-cache*
+  ../atlas-heatmap/gramene-atlas-heatmap-6.3.0.tgz && rm -rf .parcel-cache*
 ```
 Run the sorghum demo against another atlas instance (<code>ATLAS_URL</code>) and data release
 (<code>GRAMENE_DATA</code>, default <code>https://data.sorghumbase.org/sorghum_v10b</code>); sorghum_v11 has the

package/dist/index.js

@@ -8158,39 +8158,43 @@ const $9e29a4f60318db7a$var$editSearch = (url, edit)=>{
 // (genes/<id>) that only some instances redirect to EBI, and atlasUrl itself is
 // not a browsable page, so point the heatmap's links at EBI's Expression Atlas.
 // JGI studies link to Phytozome, which takes no geneQuery. undefined keeps the
-// heatmap's own URL.
-const $9e29a4f60318db7a$var$resolveUrl = (kind, url, context)=>{
-    const genes = $9e29a4f60318db7a$var$genesOf(context);
-    const withGenes = (params)=>{
-        if (genes.length) params.set('geneQuery', JSON.stringify(genes.map((value)=>({
-                value: value
-            }))));
+// heatmap's own URL, null drops the link. isJgiExperiment(accession) tells the
+// JGI studies apart: they have no full data download (their payload's download
+// URL is Phytozome's page for the genome), so the Download dialog of a Paralogs
+// heatmap drawn from one leaves out "Full experiment data on Expression Atlas".
+const $9e29a4f60318db7a$var$isJgiUrl = (url)=>/^https?:\/\/([^/]+\.)?jgi\.doe\.gov\//i.test(url);
+const $9e29a4f60318db7a$var$makeResolveUrl = (isJgiExperiment)=>(kind, url, context)=>{
+        const genes = $9e29a4f60318db7a$var$genesOf(context);
+        const withGenes = (params)=>{
+            if (genes.length) params.set('geneQuery', JSON.stringify(genes.map((value)=>({
+                    value: value
+                }))));
+        };
+        switch(kind){
+            case 'row':
+                {
+                    const uri = context.row && context.row.uri;
+                    return uri && !/^https?:/i.test(uri) ? new URL(uri, $9e29a4f60318db7a$var$EBI_GXA).href : undefined;
+                }
+            case 'atlas':
+                return $9e29a4f60318db7a$var$EBI_GXA;
+            case 'experiment':
+                return $9e29a4f60318db7a$var$isEbiUrl(url) ? $9e29a4f60318db7a$var$editSearch(url, withGenes) : undefined;
+            case 'moreInformation':
+                if (context.experiment) return $9e29a4f60318db7a$var$isEbiUrl(url) ? $9e29a4f60318db7a$var$editSearch(url, withGenes) : undefined;
+                return genes.length ? `${$9e29a4f60318db7a$var$EBI_GXA}genes/${encodeURIComponent(genes[0])}` : undefined;
+            case 'download':
+                if (isJgiExperiment(context.experiment) || $9e29a4f60318db7a$var$isJgiUrl(url)) return null;
+                return $9e29a4f60318db7a$var$editSearch(url, (params)=>params.delete('geneQuery'));
+            default:
+                return undefined;
+        }
     };
-    switch(kind){
-        case 'row':
-            {
-                const uri = context.row && context.row.uri;
-                return uri && !/^https?:/i.test(uri) ? new URL(uri, $9e29a4f60318db7a$var$EBI_GXA).href : undefined;
-            }
-        case 'atlas':
-            return $9e29a4f60318db7a$var$EBI_GXA;
-        case 'experiment':
-            return $9e29a4f60318db7a$var$isEbiUrl(url) ? $9e29a4f60318db7a$var$editSearch(url, withGenes) : undefined;
-        case 'moreInformation':
-            if (context.experiment) return $9e29a4f60318db7a$var$isEbiUrl(url) ? $9e29a4f60318db7a$var$editSearch(url, withGenes) : undefined;
-            return genes.length ? `${$9e29a4f60318db7a$var$EBI_GXA}genes/${encodeURIComponent(genes[0])}` : undefined;
-        case 'download':
-            return $9e29a4f60318db7a$var$editSearch(url, (params)=>params.delete('geneQuery'));
-        default:
-            return undefined;
-    }
-};
 const $9e29a4f60318db7a$var$HEATMAP_OPTIONS = {
     showAnatomogram: true,
     isWidget: true,
     showControlMenu: true,
-    linkTarget: '_blank',
-    resolveUrl: $9e29a4f60318db7a$var$resolveUrl
+    linkTarget: '_blank'
 };
 const $9e29a4f60318db7a$var$studyLabel = (e)=>`${e.type}:${e.description || e._id}`;
 const $9e29a4f60318db7a$var$jgiStudyLabel = (e)=>e.description ? `${e.name || e._id}: ${e.description}` : e.name || e._id;
@@ -8326,6 +8330,13 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
     }, [
         allJgiKey
     ]);
+    // A new resolveUrl does not redraw a heatmap: it asks the latest one for its links.
+    const resolveUrl = (0, $gXNCa$react.useMemo)(()=>{
+        const accessions = new Set(allJgiStudies.map((e)=>e._id));
+        return $9e29a4f60318db7a$var$makeResolveUrl((accession)=>accessions.has(accession));
+    }, [
+        allJgiKey
+    ]);
     // The EBI Studies heatmap waits for the studies list, which names the JGI
     // studies its filter drops: drawn before the list is in (a first visit; the
     // list is persisted), it would show the JGI rows and then redraw without
@@ -8388,9 +8399,11 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                     }),
                     activeTab === "paralogs" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$grameneatlasheatmap.ExpressionAtlasHeatmap), {
                         ...$9e29a4f60318db7a$var$HEATMAP_OPTIONS,
+                        resolveUrl: resolveUrl,
                         atlasUrl: atlasUrl,
                         query: paralogsQuery,
-                        experiment: atlasExperiment
+                        experiment: atlasExperiment,
+                        downloadFileName: `${geneQuery}-paralogs-${atlasExperiment}`
                     }, `${atlasUrl} ${atlasExperiment} ${paralogQuery}`)
                 ]
             }, "gxaparalogs"),
@@ -8406,10 +8419,12 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                     }),
                     activeTab === "gene" && studiesSettled && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$grameneatlasheatmap.ExpressionAtlasHeatmap), {
                         ...$9e29a4f60318db7a$var$HEATMAP_OPTIONS,
+                        resolveUrl: resolveUrl,
                         atlasUrl: atlasUrl,
                         query: allStudiesQuery,
                         experiment: false,
-                        filterRows: filterRows
+                        filterRows: filterRows,
+                        downloadFileName: `${geneQuery}-ebi-studies`
                     }, `${atlasUrl} all ${geneQuery}`)
                 ]
             }, "gxa"),
@@ -8453,8 +8468,9 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                         rowFactor: jgiAxesOfStudy.rowFactor,
                         columnFactor: jgiAxesOfStudy.columnFactor,
                         onChangeFactors: setJgiAxes,
+                        downloadFileName: `${geneQuery}-${jgiExperiment}`,
                         linkTarget: "_blank",
-                        resolveUrl: $9e29a4f60318db7a$var$resolveUrl
+                        resolveUrl: resolveUrl
                     }, `${atlasUrl} ${jgiExperiment} ${geneQuery}`)
                 ]
             }, "jgi"),