gramene-search 1.6.45 → 1.6.47

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (23) hide show
  1. package/.parcel-cache/83e7562660f7cc15-BundleGraph +0 -0
  2. package/.parcel-cache/9a0d07555444f4da-AssetGraph +0 -0
  3. package/.parcel-cache/d3a1b9507cb44047-AssetGraph +0 -0
  4. package/.parcel-cache/data.mdb +0 -0
  5. package/.parcel-cache/dc1da35000e13623-RequestGraph +0 -0
  6. package/.parcel-cache/lock.mdb +0 -0
  7. package/.parcel-cache/snapshot-dc1da35000e13623.txt +2 -2
  8. package/dist/index.js +756 -212
  9. package/dist/index.js.map +1 -1
  10. package/package.json +2 -1
  11. package/src/bundles/api.js +39 -49
  12. package/src/bundles/docs.js +1 -0
  13. package/src/bundles/views.js +1 -1
  14. package/src/components/results/Expression.js +24 -10
  15. package/src/components/results/GeneAttribs.js +11 -6
  16. package/src/components/results/StatsByGroup.js +387 -0
  17. package/src/components/results/Study.js +17 -3
  18. package/src/components/results/UserGeneLists.js +35 -24
  19. package/src/components/results/details/Expression.js +2 -2
  20. package/src/components/results/details/VEP.js +2 -1
  21. package/src/rice.html +1 -1
  22. package/dist/Study.826d318c.js +0 -137
  23. package/dist/Study.826d318c.js.map +0 -1
package/dist/index.js CHANGED
@@ -1,13 +1,16 @@
1
1
  require("./index.css");
2
+ var $gXNCa$reactjsxruntime = require("react/jsx-runtime");
3
+ var $gXNCa$react = require("react");
4
+ var $gXNCa$reduxbundlerreact = require("redux-bundler-react");
5
+ var $gXNCa$aggridreact = require("ag-grid-react");
6
+ require("ag-grid-community/styles/ag-grid.css");
7
+ require("ag-grid-community/styles/ag-theme-quartz.css");
2
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  var $gXNCa$reduxbundler = require("redux-bundler");
3
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  var $gXNCa$lodash = require("lodash");
4
10
  var $gXNCa$gramenebinsclient = require("gramene-bins-client");
5
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  var $gXNCa$gramenetreesclient = require("gramene-trees-client");
6
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  var $gXNCa$gramenetaxonomywithgenomes = require("gramene-taxonomy-with-genomes");
7
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  var $gXNCa$reactga4 = require("react-ga4");
8
- var $gXNCa$reactjsxruntime = require("react/jsx-runtime");
9
- var $gXNCa$reduxbundlerreact = require("redux-bundler-react");
10
- var $gXNCa$react = require("react");
11
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  var $gXNCa$reactbootstrap = require("react-bootstrap");
12
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  var $gXNCa$reactswitch = require("react-switch");
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  var $gXNCa$reacticonsio5 = require("react-icons/io5");
@@ -22,9 +25,6 @@ var $gXNCa$lodashget = require("lodash/get");
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  var $gXNCa$lodashisEqual = require("lodash/isEqual");
23
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  var $gXNCa$flattonested = require("flat-to-nested");
24
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  var $gXNCa$reactsimpletreemenu = require("react-simple-tree-menu");
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- var $gXNCa$aggridreact = require("ag-grid-react");
26
- require("ag-grid-community/styles/ag-grid.css");
27
- require("ag-grid-community/styles/ag-theme-quartz.css");
28
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  require("@fortawesome/fontawesome-free/css/all.min.css");
29
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  var $gXNCa$gramenedbxrefs = require("gramene-dbxrefs");
30
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  var $gXNCa$reacticonsai = require("react-icons/ai");
@@ -33,6 +33,10 @@ var $gXNCa$numeral = require("numeral");
33
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  var $gXNCa$firebaseauth = require("firebase/auth");
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34
 
35
35
 
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+ function $parcel$defineInteropFlag(a) {
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+ Object.defineProperty(a, '__esModule', {value: true, configurable: true});
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+ }
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+
36
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  function $parcel$export(e, n, v, s) {
37
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  Object.defineProperty(e, n, {get: v, set: s, enumerable: true, configurable: true});
38
42
  }
@@ -74,8 +78,133 @@ if (parcelRequire == null) {
74
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  }
75
79
 
76
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  var parcelRegister = parcelRequire.register;
77
- parcelRegister("7u0Mi", function(module, exports) {
78
- module.exports = Promise.resolve(require("./Study.826d318c.js")).then(()=>parcelRequire('7zuJ6'));
81
+ parcelRegister("7zuJ6", function(module, exports) {
82
+
83
+ $parcel$defineInteropFlag(module.exports);
84
+
85
+ $parcel$export(module.exports, "default", () => $5833a2eeefc77457$export$2e2bcd8739ae039);
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+
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+
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+
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+
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+
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+
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+ const $5833a2eeefc77457$var$metaRenderer = (params)=>{
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+ if (params.value.ontology) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
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+ href: `http://purl.obolibrary.org/obo/${params.value.id.replace(":", "_")}`,
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+ target: "_blank",
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+ children: params.value.label
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+ });
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+ return params.value.label;
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+ };
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+ const $5833a2eeefc77457$var$sampleRenderer = (params)=>{
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+ const sampleMeta = params.value;
102
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("label", {
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+ children: [
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
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+ type: "checkbox",
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+ checked: params.desiredSamples.hasOwnProperty(sampleMeta._id),
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+ onChange: ()=>params.doToggleExpressionSample(sampleMeta._id)
108
+ }),
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+ "\xa0",
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+ sampleMeta.experiment,
111
+ "-",
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+ sampleMeta.group
113
+ ]
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+ });
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+ // return JSON.stringify(sampleMeta,null,2);
116
+ };
117
+ const $5833a2eeefc77457$var$connectedSampleRenderer = (0, $gXNCa$reduxbundlerreact.connect)('selectDesiredSamples', 'doToggleExpressionSample', $5833a2eeefc77457$var$sampleRenderer);
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+ const $5833a2eeefc77457$var$Study = (props)=>{
119
+ let samples = props.expressionSamples[props.id];
120
+ let sampleMetadata = [];
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+ let metadataFields = [
122
+ {
123
+ field: "sampleId",
124
+ cellRenderer: $5833a2eeefc77457$var$connectedSampleRenderer
125
+ }
126
+ ];
127
+ let isFactor = {};
128
+ samples.forEach((sample, idx)=>{
129
+ if (idx === 0) {
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+ let factors = {
131
+ headerName: 'Experimental Variables',
132
+ children: []
133
+ };
134
+ sample.factor.forEach((factor)=>{
135
+ factors.children.push({
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+ field: factor.type,
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+ cellRenderer: $5833a2eeefc77457$var$metaRenderer
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+ });
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+ isFactor[factor.type] = true;
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+ });
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+ metadataFields.push(factors);
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+ let characteristics = {
143
+ headerName: 'Sample Characteristics',
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+ children: []
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+ };
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+ sample.characteristic.forEach((ch)=>{
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+ if (!isFactor[ch.type]) characteristics.children.push({
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+ field: ch.type,
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+ cellRenderer: $5833a2eeefc77457$var$metaRenderer
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+ });
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+ });
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+ metadataFields.push(characteristics);
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+ }
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+ let s_info = {
155
+ sampleId: sample
156
+ };
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+ sample.factor.forEach((factor)=>{
158
+ s_info[factor.type] = {
159
+ label: factor.label
160
+ };
161
+ if (factor.ontology) {
162
+ s_info[factor.type]['ontology'] = factor.ontology;
163
+ s_info[factor.type]['id'] = factor.id;
164
+ }
165
+ });
166
+ sample.characteristic.forEach((ch)=>{
167
+ s_info[ch.type] = {
168
+ label: ch.label
169
+ };
170
+ if (ch.ontology) {
171
+ s_info[ch.type]['ontology'] = ch.ontology;
172
+ s_info[ch.type]['id'] = ch.id;
173
+ }
174
+ });
175
+ sampleMetadata.push(s_info);
176
+ });
177
+ const [rowData, setRowData] = (0, $gXNCa$react.useState)(sampleMetadata);
178
+ const [colDefs, setColDefs] = (0, $gXNCa$react.useState)(metadataFields);
179
+ const defaultColDef = (0, $gXNCa$react.useMemo)(()=>{
180
+ return {
181
+ filter: true
182
+ };
183
+ }, []);
184
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
185
+ children: [
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
187
+ className: "ag-theme-quartz",
188
+ style: {
189
+ height: `${44 * (samples.length + 2)}px`
190
+ },
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+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
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+ rowData: rowData,
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+ columnDefs: colDefs,
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+ defaultColDef: defaultColDef
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+ })
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+ }),
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+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
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+ href: `https://www.ebi.ac.uk/gxa/experiments/${props.id}`,
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+ children: [
200
+ "EBI Atlas Experiment: ",
201
+ props.id
202
+ ]
203
+ })
204
+ ]
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+ });
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+ };
207
+ var $5833a2eeefc77457$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectExpressionSamples', $5833a2eeefc77457$var$Study);
79
208
 
80
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  });
81
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@@ -95,10 +224,11 @@ $parcel$export(module.exports, "Views", () => $693dd8c7a5607c3a$export$5cb791131
95
224
 
96
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  const $9d9aeaf9299e61a1$var$facets = [
97
226
  "{!facet.limit='300' facet.mincount='1' key='taxon_id'}taxon_id",
98
- "{!facet.limit='100' facet.mincount='1' key='genetree'}gene_tree",
99
- "{!facet.limit='100' facet.mincount='1' key='pathways'}pathways__ancestors",
100
- "{!facet.limit='100' facet.mincount='1' key='domains'}domain_roots",
101
- "{!facet.limit='-1' facet.mincount='1' key='fixed_1000__bin'}fixed_1000__bin"
227
+ // "{!facet.limit='100' facet.mincount='1' key='genetree'}gene_tree",
228
+ // "{!facet.limit='100' facet.mincount='1' key='pathways'}pathways__ancestors",
229
+ // "{!facet.limit='100' facet.mincount='1' key='domains'}domain_roots",
230
+ "{!facet.limit='-1' facet.mincount='1' key='fixed_1000__bin'}fixed_1000__bin",
231
+ "{!facet.limit='100' facet.mincount='0' key='AED' type='range' start=0 end=1.0 gap=0.01}MAKER__AED__attr_f"
102
232
  ];
103
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  const $9d9aeaf9299e61a1$var$genomesOfInterest = '(taxon_id:2769) OR (taxon_id:3055) OR (taxon_id:3218) OR (taxon_id:3702) OR (taxon_id:3847) OR (taxon_id:4555) OR (taxon_id:4558) OR (taxon_id:4577) OR (taxon_id:13333) OR (taxon_id:15368) OR (taxon_id:29760) OR (taxon_id:39947) OR (taxon_id:55577) OR (taxon_id:88036) OR (taxon_id:214687)';
104
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  const $9d9aeaf9299e61a1$var$sites = [
@@ -314,138 +444,80 @@ $9d9aeaf9299e61a1$var$grameneGermplasm.reactGrameneGermplasm = (0, $gXNCa$reduxb
314
444
  // }
315
445
  // }
316
446
  // );
317
- const $9d9aeaf9299e61a1$var$attribFacetFields = [
318
- "{!facet.limit='10' facet.mincount='1' key='age'}panset_age_attr_s",
319
- "{!facet.limit='100' facet.mincount='1' key='taxa'}panset_ntaxa_attr_i",
320
- "{!facet.limit='100' facet.mincount='1' key='AED' type='range' start=0 end=1.0 gap=0.25}MAKER_AED_attr_f",
321
- "{!facet.limit='100' facet.mincount='1' key='QI2' type='range' start=0 end=1.0 gap=0.25}MAKER_QI2_attr_f",
322
- "{!facet.limit='100' facet.mincount='1' key='QI3' type='range' start=0 end=1.0 gap=0.25}MAKER_QI3_attr_f",
323
- "{!facet.limit='100' facet.mincount='1' key='QI4' type='range' start=0 end=1.0 gap=0.25}MAKER_QI4_attr_f",
324
- "{!facet.limit='100' facet.mincount='1' key='QI5' type='range' start=0 end=1.0 gap=0.25}MAKER_QI5_attr_f",
325
- "{!facet.limit='100' facet.mincount='1' key='QI6' type='range' start=0 end=1.0 gap=0.25}MAKER_QI6_attr_f"
447
+ const $9d9aeaf9299e61a1$var$MAKERAttribs = [
448
+ 'MAKER__AED__attr_f',
449
+ 'MAKER__QI1__attr_i',
450
+ 'MAKER__QI2__attr_f',
451
+ 'MAKER__QI3__attr_f',
452
+ 'MAKER__QI4__attr_f',
453
+ 'MAKER__QI5__attr_f',
454
+ 'MAKER__QI6__attr_f',
455
+ 'MAKER__QI7__attr_i',
456
+ 'MAKER__QI8__attr_i',
457
+ 'MAKER__QI9__attr_i'
326
458
  ];
327
- const $9d9aeaf9299e61a1$var$attribFacets = {
328
- "age": {
329
- "type": "terms",
330
- "field": "panset_age_attr_s"
331
- },
332
- "nTaxa": {
333
- "type": "terms",
334
- "field": "panset_ntaxa_attr_i",
335
- "limit": 100
336
- },
337
- "AED": {
338
- "type": "range",
339
- "field": "MAKER_AED_attr_f",
340
- "start": 0.0,
341
- "end": 1.0,
342
- "gap": 0.25
343
- },
344
- "QI2": {
345
- "type": "range",
346
- "field": "MAKER_QI2_attr_f",
347
- "start": 0.0,
348
- "end": 1.0,
349
- "gap": 0.25
350
- },
351
- "QI3": {
352
- "type": "range",
353
- "field": "MAKER_QI3_attr_f",
354
- "start": 0.0,
355
- "end": 1.0,
356
- "gap": 0.25
357
- },
358
- "QI4": {
359
- "type": "range",
360
- "field": "MAKER_QI4_attr_f",
361
- "start": 0.0,
362
- "end": 1.0,
363
- "gap": 0.25
364
- },
365
- "QI5": {
366
- "type": "range",
367
- "field": "MAKER_QI5_attr_f",
368
- "start": 0.0,
369
- "end": 1.0,
370
- "gap": 0.25
371
- },
372
- "QI6": {
373
- "type": "range",
374
- "field": "MAKER_QI6_attr_f",
375
- "start": 0.0,
376
- "end": 1.0,
377
- "gap": 0.25
378
- },
379
- "byAge": {
380
- "type": "terms",
381
- "field": "panset_age_attr_s",
382
- "facet": {
383
- "nTaxa": {
384
- "type": "terms",
385
- "field": "panset_ntaxa_attr_i",
386
- "limit": 100
387
- },
388
- "AED": {
389
- "type": "range",
390
- "field": "MAKER_AED_attr_f",
391
- "start": 0.0,
392
- "end": 1.0,
393
- "gap": 0.25
394
- },
395
- "QI2": {
396
- "type": "range",
397
- "field": "MAKER_QI2_attr_f",
398
- "start": 0.0,
399
- "end": 1.0,
400
- "gap": 0.25
401
- },
402
- "QI3": {
403
- "type": "range",
404
- "field": "MAKER_QI3_attr_f",
405
- "start": 0.0,
406
- "end": 1.0,
407
- "gap": 0.25
408
- },
409
- "QI4": {
410
- "type": "range",
411
- "field": "MAKER_QI4_attr_f",
412
- "start": 0.0,
413
- "end": 1.0,
414
- "gap": 0.25
415
- },
416
- "QI5": {
417
- "type": "range",
418
- "field": "MAKER_QI5_attr_f",
419
- "start": 0.0,
420
- "end": 1.0,
421
- "gap": 0.25
422
- },
423
- "QI6": {
424
- "type": "range",
425
- "field": "MAKER_QI6_attr_f",
426
- "start": 0.0,
427
- "end": 1.0,
428
- "gap": 0.25
429
- }
459
+ const $9d9aeaf9299e61a1$var$geneAttribs = {
460
+ "MAKER transcript metrics": [
461
+ {
462
+ name: "AED",
463
+ description: "Annotation Edit Distance",
464
+ dtype: "f",
465
+ fieldName: "MAKER__AED__attr_f"
466
+ },
467
+ {
468
+ name: "QI1",
469
+ description: "Length of the 5' UTR",
470
+ dtype: "i",
471
+ fieldName: "MAKER__QI1__attr_i"
472
+ },
473
+ {
474
+ name: "QI2",
475
+ description: "Fraction of splice sites confirmed by an EST alignment",
476
+ dtype: "f",
477
+ fieldName: "MAKER__QI2__attr_f"
478
+ },
479
+ {
480
+ name: "QI3",
481
+ description: "Fraction of exons that overlap an EST alignment",
482
+ dtype: "f",
483
+ fieldName: "MAKER__QI3__attr_f"
484
+ },
485
+ {
486
+ name: "QI4",
487
+ description: "Fraction of exons that overlap EST or Protein alignments",
488
+ dtype: "f",
489
+ fieldName: "MAKER__QI4__attr_f"
490
+ },
491
+ // { name: "QI5", description: "Fraction of splice sites confirmed by a SNAP prediction", dtype: "f", fieldName: "MAKER__QI5__attr_f" },
492
+ // { name: "QI6", description: "Fraction of exons that overlap a SNAP prediction", dtype: "f", fieldName: "MAKER__QI6__attr_f" },
493
+ {
494
+ name: "QI7",
495
+ description: "Number of exons in the mRNA",
496
+ dtype: "i",
497
+ fieldName: "MAKER__QI7__attr_i"
498
+ },
499
+ {
500
+ name: "QI8",
501
+ description: "Length of the 3' UTR",
502
+ dtype: "i",
503
+ fieldName: "MAKER__QI8__attr_i"
504
+ },
505
+ {
506
+ name: "QI9",
507
+ description: "Length of the protein sequence produced by the mRNA",
508
+ dtype: "i",
509
+ fieldName: "MAKER__QI9__attr_i"
430
510
  }
431
- }
511
+ ]
432
512
  };
513
+ const $9d9aeaf9299e61a1$var$statsFields = $9d9aeaf9299e61a1$var$geneAttribs['MAKER transcript metrics'].map(// (f) => `stats.field={!min=true max=true count=true mean=true stddev=true percentiles='20,40,60,80,90,95,99'}${f}`
514
+ (f)=>`stats.field={!min=true max=true count=true mean=true stddev=true percentiles='10,20,30,40,50,60,70,80,90,99.99'}${f.fieldName}`);
433
515
  const $9d9aeaf9299e61a1$var$grameneGeneAttribs = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
434
516
  name: 'grameneGeneAttribs',
435
517
  actionBaseType: 'GRAMENE_GENE_ATTRIBS',
436
518
  persist: false,
437
519
  getPromise: ({ store: store })=>{
438
- const g = store.selectGrameneGenomes();
439
- const taxa = Object.keys(g.active);
440
- let fq = '';
441
- if (taxa.length) {
442
- console.log('search add a fq for ', taxa);
443
- fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;
444
- }
445
- return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&json.facet=${JSON.stringify($9d9aeaf9299e61a1$var$attribFacets)}&rows=0${fq}`)// return fetch(`${store.selectGrameneAPI()}/search?rows=1&q=MAKER_AED_attr_f:*&json.facet=${JSON.stringify(attribFacets)}`)
446
- .then((res)=>res.json()).then((res)=>{
447
- return res.facets;
448
- });
520
+ return fetch(`${store.selectGrameneAPI()}/geneAttributes`).then((res)=>$9d9aeaf9299e61a1$var$geneAttribs);
449
521
  }
450
522
  });
451
523
  $9d9aeaf9299e61a1$var$grameneGeneAttribs.reactGrameneGeneAttribs = (0, $gXNCa$reduxbundler.createSelector)('selectGrameneGeneAttribsShouldUpdate', 'selectGrameneFiltersStatus', 'selectGrameneViews', (shouldUpdate, status, views)=>{
@@ -470,7 +542,7 @@ const $9d9aeaf9299e61a1$var$grameneSearch = (0, $gXNCa$reduxbundler.createAsyncR
470
542
  console.log('search add a fq for ', taxa);
471
543
  fq = `&fq=taxon_id:(${taxa.join(' OR ')})`;
472
544
  }
473
- return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&facet.field=${$9d9aeaf9299e61a1$var$facets}&rows=${rows}&start=${offset}${fq}`).then((res)=>res.json()).then((res)=>{
545
+ return fetch(`${store.selectGrameneAPI()}/search?q=${store.selectGrameneFiltersQueryString()}&facet.field=${$9d9aeaf9299e61a1$var$facets}&rows=${rows}&start=${offset}${fq}&stats=true&${$9d9aeaf9299e61a1$var$statsFields.join('&')}`).then((res)=>res.json()).then((res)=>{
474
546
  res.response.docs.forEach((d)=>{
475
547
  d.can_show = {};
476
548
  d.capabilities.forEach((c)=>{
@@ -603,9 +675,11 @@ const $9d9aeaf9299e61a1$var$grameneParalogs = {
603
675
  });
604
676
  const API = store.selectGrameneAPI();
605
677
  const q = supertree ? `supertree_attr_s:${supertree}` : `homology__within_species_paralog:${geneId}`;
606
- fetch(`${API}/search?q=${q}&rows=100&fq=taxon_id:${taxon_id}`).then((res)=>res.json()).then((res)=>{
678
+ fetch(`${API}/search?q=${q}&rows=1000&fq=taxon_id:${taxon_id}`).then((res)=>res.json()).then((res)=>{
607
679
  let newParalogs = {};
608
- newParalogs[geneId] = res.response.docs.map((d)=>d.id);
680
+ newParalogs[geneId] = res.response.numFound > 0 ? res.response.docs.map((d)=>d.id) : [
681
+ geneId
682
+ ];
609
683
  dispatch({
610
684
  type: 'GRAMENE_PARALOGS_RECEIVED',
611
685
  payload: newParalogs
@@ -671,6 +745,7 @@ var // function selectFacetIDs(store, field) {
671
745
  $9d9aeaf9299e61a1$export$2e2bcd8739ae039 = [
672
746
  $9d9aeaf9299e61a1$var$grameneSuggestions,
673
747
  $9d9aeaf9299e61a1$var$grameneSearch,
748
+ $9d9aeaf9299e61a1$var$grameneGeneAttribs,
674
749
  $9d9aeaf9299e61a1$var$grameneMaps,
675
750
  $9d9aeaf9299e61a1$var$grameneTaxonomy,
676
751
  $9d9aeaf9299e61a1$var$grameneTaxDist,
@@ -678,7 +753,6 @@ $9d9aeaf9299e61a1$export$2e2bcd8739ae039 = [
678
753
  $9d9aeaf9299e61a1$var$grameneParalogs,
679
754
  $9d9aeaf9299e61a1$var$curatedGenes,
680
755
  $9d9aeaf9299e61a1$var$grameneGermplasm,
681
- $9d9aeaf9299e61a1$var$grameneGeneAttribs,
682
756
  $9d9aeaf9299e61a1$var$expressionSamples,
683
757
  $9d9aeaf9299e61a1$var$expressionStudies
684
758
  ];
@@ -1370,7 +1444,7 @@ const $24971af0a229e0e3$var$grameneViews = {
1370
1444
  {
1371
1445
  id: 'attribs',
1372
1446
  name: 'Gene attributes',
1373
- show: 'disabled',
1447
+ show: 'off',
1374
1448
  shouldScroll: false
1375
1449
  }
1376
1450
  ]
@@ -1556,6 +1630,7 @@ const $671312b287158a8a$var$grameneDocs = {
1556
1630
  else newState.desiredSamples[payload] = {
1557
1631
  status: 'need'
1558
1632
  };
1633
+ return newState;
1559
1634
  }
1560
1635
  return state;
1561
1636
  };
@@ -2390,7 +2465,7 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
2390
2465
  // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {
2391
2466
  // paralogs = gene.homology.homologous_genes.within_species_paralog;
2392
2467
  // }
2393
- if (paralogs.length > 1 && atlasExperiment) paralogs_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
2468
+ if (paralogs.length > 0 && atlasExperiment) paralogs_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
2394
2469
  return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tabs), {
2395
2470
  activeKey: activeTab,
2396
2471
  onSelect: (k)=>setActiveTab(k),
@@ -3483,7 +3558,8 @@ var $54c74a4689d5a778$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
3483
3558
 
3484
3559
 
3485
3560
  const $283508ffcf8a47c4$var$ggURL = {
3486
- IRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',
3561
+ xIRRI: 'https://gringlobal.irri.org/gringlobal/accessiondetail?id=',
3562
+ IRRI: 'https://www.irri.org/genesys-rice#/a/',
3487
3563
  ARS: 'https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=',
3488
3564
  ICRISAT: 'https://genebank.icrisat.org/IND/PassportSummary?ID=',
3489
3565
  sorbmutdb: 'https://www.depts.ttu.edu/igcast/sorbmutdb.php',
@@ -5492,21 +5568,461 @@ var $b36244140732570a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
5492
5568
 
5493
5569
 
5494
5570
 
5571
+
5572
+
5573
+ function $dbdedae66c619d9b$export$2e2bcd8739ae039({ groups: groups, stats: stats }) {
5574
+ const fields = stats?.stats_fields || {};
5575
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
5576
+ style: {
5577
+ fontFamily: "system-ui, -apple-system, Segoe UI, Roboto, sans-serif",
5578
+ lineHeight: 1.35
5579
+ },
5580
+ children: Object.entries(groups).map(([groupName, attrs])=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$GroupTable, {
5581
+ groupName: groupName,
5582
+ attributes: attrs,
5583
+ fields: fields
5584
+ }, groupName))
5585
+ });
5586
+ }
5587
+ function $dbdedae66c619d9b$var$GroupTable({ groupName: groupName, attributes: attributes, fields: fields }) {
5588
+ const hasAny = attributes?.some((a)=>fields[a.fieldName]);
5589
+ const columns = (0, $gXNCa$react.useMemo)(()=>[
5590
+ {
5591
+ key: "attr",
5592
+ label: "Attribute",
5593
+ min: 120
5594
+ },
5595
+ {
5596
+ key: "desc",
5597
+ label: "Description",
5598
+ min: 380,
5599
+ flex: true
5600
+ },
5601
+ {
5602
+ key: "mean",
5603
+ label: "Mean",
5604
+ min: 100
5605
+ },
5606
+ {
5607
+ key: "stddev",
5608
+ label: "Std Dev",
5609
+ min: 110
5610
+ },
5611
+ {
5612
+ key: "min",
5613
+ label: "Min",
5614
+ min: 90
5615
+ },
5616
+ {
5617
+ key: "max",
5618
+ label: "Max",
5619
+ min: 90
5620
+ },
5621
+ {
5622
+ key: "count",
5623
+ label: "Count",
5624
+ min: 90
5625
+ },
5626
+ {
5627
+ key: "dist",
5628
+ label: "Distribution",
5629
+ min: 220
5630
+ }
5631
+ ], []);
5632
+ const initial = (0, $gXNCa$react.useMemo)(()=>columns.map((c)=>c.flex ? Math.max(380, c.min) : c.min), [
5633
+ columns
5634
+ ]);
5635
+ const { colWidths: colWidths, startResize: startResize, resizing: resizing } = $dbdedae66c619d9b$var$useResizableColumns({
5636
+ initialWidths: initial,
5637
+ minWidths: columns.map((c)=>c.min || 60)
5638
+ });
5639
+ const nfInt = (0, $gXNCa$react.useMemo)(()=>new Intl.NumberFormat("en-US", {
5640
+ maximumFractionDigits: 0
5641
+ }), []);
5642
+ const nfFloat = (0, $gXNCa$react.useMemo)(()=>new Intl.NumberFormat("en-US", {
5643
+ minimumFractionDigits: 0,
5644
+ maximumFractionDigits: 3
5645
+ }), []);
5646
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("section", {
5647
+ style: {
5648
+ marginBottom: 24
5649
+ },
5650
+ children: [
5651
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("header", {
5652
+ style: {
5653
+ display: "flex",
5654
+ alignItems: "baseline",
5655
+ gap: 12,
5656
+ marginBottom: 8
5657
+ },
5658
+ children: [
5659
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h2", {
5660
+ style: {
5661
+ margin: 0,
5662
+ fontSize: 18
5663
+ },
5664
+ children: groupName
5665
+ }),
5666
+ !hasAny && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
5667
+ style: {
5668
+ fontSize: 12,
5669
+ color: "#666"
5670
+ },
5671
+ children: "No stats available for this group."
5672
+ })
5673
+ ]
5674
+ }),
5675
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
5676
+ style: {
5677
+ overflowX: "auto",
5678
+ border: "1px solid #eee",
5679
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5680
+ boxShadow: "0 1px 2px rgba(0,0,0,0.04)"
5681
+ },
5682
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("table", {
5683
+ style: $dbdedae66c619d9b$var$tableStyle,
5684
+ children: [
5685
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("colgroup", {
5686
+ children: colWidths.map((w, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("col", {
5687
+ style: {
5688
+ width: w
5689
+ }
5690
+ }, i))
5691
+ }),
5692
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
5693
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tr", {
5694
+ children: columns.map((col, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$ResizableTh, {
5695
+ label: col.label,
5696
+ index: i,
5697
+ onResizeStart: startResize
5698
+ }, col.key))
5699
+ })
5700
+ }),
5701
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
5702
+ children: attributes.map((a)=>{
5703
+ const s = fields[a.fieldName] || {};
5704
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
5705
+ children: [
5706
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5707
+ mono: true,
5708
+ title: a.fieldName,
5709
+ children: a.name
5710
+ }),
5711
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5712
+ title: a.description,
5713
+ children: a.description
5714
+ }),
5715
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5716
+ align: "right",
5717
+ children: $dbdedae66c619d9b$var$fmtValue(s.mean, a.dtype, true, nfInt, nfFloat)
5718
+ }),
5719
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5720
+ align: "right",
5721
+ children: $dbdedae66c619d9b$var$fmtValue(s.stddev, a.dtype, true, nfInt, nfFloat)
5722
+ }),
5723
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5724
+ align: "right",
5725
+ children: $dbdedae66c619d9b$var$fmtValue(s.min, a.dtype, false, nfInt, nfFloat)
5726
+ }),
5727
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5728
+ align: "right",
5729
+ children: $dbdedae66c619d9b$var$fmtValue(s.max, a.dtype, false, nfInt, nfFloat)
5730
+ }),
5731
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5732
+ align: "right",
5733
+ children: $dbdedae66c619d9b$var$fmtCount(s.count, nfInt)
5734
+ }),
5735
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$Td, {
5736
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$PercentileHeatmapNormalized, {
5737
+ percentilesArr: s.percentiles,
5738
+ min: s.min,
5739
+ max: s.max
5740
+ })
5741
+ })
5742
+ ]
5743
+ }, a.fieldName);
5744
+ })
5745
+ })
5746
+ ]
5747
+ })
5748
+ }),
5749
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
5750
+ style: {
5751
+ marginTop: 6,
5752
+ fontSize: 12,
5753
+ color: "#666"
5754
+ },
5755
+ children: [
5756
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
5757
+ children: "Tip:"
5758
+ }),
5759
+ " Drag the divider at the right edge of any header to resize.",
5760
+ resizing && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
5761
+ style: {
5762
+ marginLeft: 8,
5763
+ color: "#999"
5764
+ },
5765
+ children: "(resizing\u2026)"
5766
+ })
5767
+ ]
5768
+ })
5769
+ ]
5770
+ });
5771
+ }
5772
+ /* ===================== Percentiles / Heatmap ===================== */ /**
5773
+ * Convert alternating array into ordered pairs: [["10.0", v10], ["20.0", v20], ...]
5774
+ * - Preserves the exact order provided by Solr
5775
+ */ function $dbdedae66c619d9b$var$percentilesArrayToPairs(arr) {
5776
+ if (!Array.isArray(arr)) return [];
5777
+ const out = [];
5778
+ for(let i = 0; i < arr.length - 1; i += 2)out.push([
5779
+ String(arr[i]),
5780
+ arr[i + 1]
5781
+ ]);
5782
+ return out;
5783
+ }
5784
+ function $dbdedae66c619d9b$var$normalizeBetween(value, min, max) {
5785
+ if (!isFinite(min) || !isFinite(max) || max <= min || !isFinite(value)) return null;
5786
+ return (value - min) / (max - min);
5787
+ }
5788
+ // White -> Blue (0 -> 1)
5789
+ function $dbdedae66c619d9b$var$rgbWhiteToBlue(vNorm) {
5790
+ const t = $dbdedae66c619d9b$var$clamp01(vNorm);
5791
+ const rg = Math.round(255 * (1 - t));
5792
+ return `rgb(${rg}, ${rg}, 255)`;
5793
+ }
5794
+ function $dbdedae66c619d9b$var$clamp01(x) {
5795
+ if (typeof x !== "number" || !isFinite(x)) return 0;
5796
+ return Math.max(0, Math.min(1, x));
5797
+ }
5798
+ function $dbdedae66c619d9b$var$fmtFloat(v) {
5799
+ if (v == null || !isFinite(v)) return "n/a";
5800
+ return v.toFixed(3);
5801
+ }
5802
+ /**
5803
+ * PercentileHeatmapNormalized
5804
+ * - Infers bins from percentilesArr (order preserved)
5805
+ * - Colors normalized by row min/max
5806
+ */ function $dbdedae66c619d9b$var$PercentileHeatmapNormalized({ percentilesArr: percentilesArr, min: min, max: max }) {
5807
+ const pairs = (0, $gXNCa$react.useMemo)(()=>$dbdedae66c619d9b$var$percentilesArrayToPairs(percentilesArr), [
5808
+ percentilesArr
5809
+ ]);
5810
+ const n = pairs.length || 1; // avoid zero columns
5811
+ const validScale = isFinite(min) && isFinite(max) && max > min;
5812
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
5813
+ style: {
5814
+ ...$dbdedae66c619d9b$var$heatRowDynamic,
5815
+ gridTemplateColumns: `repeat(${n}, 1fr)`
5816
+ },
5817
+ children: pairs.map(([pStr, raw], idx)=>{
5818
+ const rawNum = typeof raw === "number" && isFinite(raw) ? raw : null;
5819
+ const norm = rawNum == null ? null : validScale ? $dbdedae66c619d9b$var$normalizeBetween(rawNum, min, max) : null;
5820
+ const bg = norm == null ? "#f2f2f2" : $dbdedae66c619d9b$var$rgbWhiteToBlue(norm);
5821
+ const label = `${pStr} \u{2192} raw ${$dbdedae66c619d9b$var$fmtFloat(rawNum)} (norm ${$dbdedae66c619d9b$var$fmtFloat(norm)})`;
5822
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($dbdedae66c619d9b$var$HeatCell, {
5823
+ background: bg,
5824
+ label: label
5825
+ }, `${pStr}-${idx}`);
5826
+ })
5827
+ });
5828
+ }
5829
+ function $dbdedae66c619d9b$var$HeatCell({ background: background, label: label }) {
5830
+ const [hover, setHover] = (0, $gXNCa$react.useState)(false);
5831
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
5832
+ style: {
5833
+ ...$dbdedae66c619d9b$var$heatCell,
5834
+ background: background
5835
+ },
5836
+ onMouseEnter: ()=>setHover(true),
5837
+ onMouseLeave: ()=>setHover(false),
5838
+ title: label,
5839
+ children: hover && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
5840
+ style: $dbdedae66c619d9b$var$popover,
5841
+ children: label
5842
+ })
5843
+ });
5844
+ }
5845
+ /* ===================== Resizable columns ===================== */ function $dbdedae66c619d9b$var$useResizableColumns({ initialWidths: initialWidths, minWidths: minWidths }) {
5846
+ const [colWidths, setColWidths] = (0, $gXNCa$react.useState)(initialWidths);
5847
+ const [resizing, setResizing] = (0, $gXNCa$react.useState)(false);
5848
+ const activeRef = (0, $gXNCa$react.useRef)(null); // { index, startX, startW }
5849
+ (0, $gXNCa$react.useEffect)(()=>{
5850
+ if (initialWidths?.length) setColWidths(initialWidths);
5851
+ }, [
5852
+ initialWidths?.length
5853
+ ]); // eslint-disable-line react-hooks/exhaustive-deps
5854
+ const onMouseMove = (e)=>{
5855
+ if (!activeRef.current) return;
5856
+ const { index: index, startX: startX, startW: startW } = activeRef.current;
5857
+ const dx = e.clientX - startX;
5858
+ const next = [
5859
+ ...colWidths
5860
+ ];
5861
+ const minW = minWidths?.[index] ?? 60;
5862
+ next[index] = Math.max(minW, startW + dx);
5863
+ setColWidths(next);
5864
+ };
5865
+ const endResize = ()=>{
5866
+ activeRef.current = null;
5867
+ setResizing(false);
5868
+ document.body.style.cursor = "";
5869
+ document.body.style.userSelect = "";
5870
+ window.removeEventListener("mousemove", onMouseMove);
5871
+ window.removeEventListener("mouseup", endResize);
5872
+ };
5873
+ const startResize = (index, ev)=>{
5874
+ const startX = ev.clientX;
5875
+ const startW = colWidths[index];
5876
+ activeRef.current = {
5877
+ index: index,
5878
+ startX: startX,
5879
+ startW: startW
5880
+ };
5881
+ setResizing(true);
5882
+ document.body.style.cursor = "col-resize";
5883
+ document.body.style.userSelect = "none";
5884
+ window.addEventListener("mousemove", onMouseMove);
5885
+ window.addEventListener("mouseup", endResize);
5886
+ };
5887
+ (0, $gXNCa$react.useEffect)(()=>{
5888
+ return ()=>{
5889
+ window.removeEventListener("mousemove", onMouseMove);
5890
+ window.removeEventListener("mouseup", endResize);
5891
+ };
5892
+ }, []); // eslint-disable-line react-hooks/exhaustive-deps
5893
+ return {
5894
+ colWidths: colWidths,
5895
+ setColWidths: setColWidths,
5896
+ startResize: startResize,
5897
+ resizing: resizing
5898
+ };
5899
+ }
5900
+ function $dbdedae66c619d9b$var$ResizableTh({ label: label, index: index, onResizeStart: onResizeStart }) {
5901
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5909
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
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5933
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5935
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5944
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5947
+ });
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5950
+ width: "100%",
5951
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+ };
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+ const $dbdedae66c619d9b$var$heatRowDynamic = {
5981
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+ gap: 2,
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+ alignItems: "center",
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+ width: "100%",
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+ const $dbdedae66c619d9b$var$heatCell = {
5988
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+ borderRadius: 3,
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+ boxShadow: "inset 0 0 0 1px rgba(0,0,0,0.06)"
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+ };
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5994
+ position: "absolute",
5995
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6000
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6001
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6002
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6003
+ whiteSpace: "nowrap",
6004
+ pointerEvents: "none"
6005
+ };
6006
+
6007
+
5495
6008
  class $67bf5a43401bffdc$var$GeneAttribs extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
5496
6009
  constructor(props){
5497
6010
  super(props);
5498
6011
  this.state = {};
5499
6012
  }
5500
6013
  render() {
5501
- return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
5502
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5503
- children: this.props.grameneGeneAttribs && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("pre", {
5504
- children: "hi"
5505
- })
5506
- });
6014
+ if (this.props.grameneGeneAttribs && this.props.grameneSearch) {
6015
+ const groups = this.props.grameneGeneAttribs;
6016
+ const stats = this.props.grameneSearch.stats;
6017
+ return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $dbdedae66c619d9b$export$2e2bcd8739ae039), {
6018
+ groups: groups,
6019
+ stats: stats
6020
+ });
6021
+ }
6022
+ return null;
5507
6023
  }
5508
6024
  }
5509
- var $67bf5a43401bffdc$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneGeneAttribs', $67bf5a43401bffdc$var$GeneAttribs);
6025
+ var $67bf5a43401bffdc$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneSearch', 'selectGrameneGeneAttribs', $67bf5a43401bffdc$var$GeneAttribs);
5510
6026
 
5511
6027
 
5512
6028
 
@@ -5634,7 +6150,9 @@ var $76e15aea9236bd47$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
5634
6150
 
5635
6151
 
5636
6152
 
5637
- const $261baeb81c4d4d8a$var$LazyStudy = /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).lazy(()=>(parcelRequire("7u0Mi")));
6153
+ var $7zuJ6 = parcelRequire("7zuJ6");
6154
+
6155
+ const $261baeb81c4d4d8a$var$LazyStudy = /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).lazy(()=>Promise.resolve((parcelRequire("7zuJ6"))));
5638
6156
  const $261baeb81c4d4d8a$var$StudyList = (props)=>{
5639
6157
  return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
5640
6158
  alwaysOpen: true,
@@ -5647,13 +6165,8 @@ const $261baeb81c4d4d8a$var$StudyList = (props)=>{
5647
6165
  children: study.description
5648
6166
  }),
5649
6167
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Body, {
5650
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5651
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5653
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5654
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5655
- id: study._id
5656
- })
6168
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $7zuJ6.default), {
6169
+ id: study._id
5657
6170
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5658
6171
  })
5659
6172
  ]
@@ -5665,15 +6178,21 @@ const $261baeb81c4d4d8a$var$Expression = (props)=>{
5665
6178
  let searchTaxa = {};
5666
6179
  if (props.grameneSearch) {
5667
6180
  const taxon_id_facet = props.grameneSearch.facet_counts.facet_fields.taxon_id;
5668
- taxon_id_facet.filter((tid, idx)=>idx % 2 === 0).forEach((tid)=>searchTaxa[tid] = true);
6181
+ taxon_id_facet.filter((tid, idx)=>idx % 2 === 0).forEach((tid)=>{
6182
+ if (tid > 1000000) {
6183
+ const tid2 = Math.floor(tid / 1000);
6184
+ if (props.expressionStudies[tid2]) searchTaxa[tid2] = tid;
6185
+ } else searchTaxa[tid] = tid;
6186
+ });
5669
6187
  }
5670
- const availableTaxa = Object.keys(props.expressionStudies).filter((tid)=>searchTaxa[tid] || searchTaxa[tid + '001']).sort((a, b)=>props.grameneMaps[a + '001'].left_index - props.grameneMaps[b + '001'].left_index);
6188
+ const availableTaxa = Object.keys(props.expressionStudies).filter((tid)=>searchTaxa[tid]).sort((a, b)=>props.grameneMaps[searchTaxa[a]].left_index - props.grameneMaps[searchTaxa[b]].left_index);
5671
6189
  return availableTaxa && props.grameneTaxonomy && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
5672
6190
  children: [
5673
6191
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
5674
6192
  children: [
5675
6193
  "This is where you can launch a component for the selected samples. props.desiredSamples lists them. This component can request the data from the API organize samples by factor metadata? One big table with all the studies?",
5676
6194
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Button), {
6195
+ onClick: console.log(Object.keys(props.desiredSamples)),
5677
6196
  children: [
5678
6197
  "Show Samples (",
5679
6198
  Object.keys(props.desiredSamples).length,
@@ -5686,7 +6205,8 @@ const $261baeb81c4d4d8a$var$Expression = (props)=>{
5686
6205
  alwaysOpen: true,
5687
6206
  defaultActiveKey: availableTaxa.length === 1 ? "tax_0" : undefined,
5688
6207
  children: availableTaxa.map((tid, idx)=>{
5689
- const n = props.expressionStudies[tid].length;
6208
+ const baselineStudies = props.expressionStudies[tid].filter((study)=>study.type === 'Baseline');
6209
+ const n = baselineStudies.length;
5690
6210
  return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Item, {
5691
6211
  eventKey: 'tax_' + idx,
5692
6212
  children: [
@@ -5701,7 +6221,7 @@ const $261baeb81c4d4d8a$var$Expression = (props)=>{
5701
6221
  }),
5702
6222
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5703
6223
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5704
- studies: props.expressionStudies[tid]
6224
+ studies: baselineStudies
5705
6225
  })
5706
6226
  })
5707
6227
  ]
@@ -5760,6 +6280,28 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5760
6280
  setError('Failed to fetch gene lists. Please try again later.');
5761
6281
  }
5762
6282
  };
6283
+ // Example functions for viewing and deleting lists
6284
+ const viewGeneList = (list)=>{
6285
+ alert(`Viewing gene list: ${list.label}`);
6286
+ props.addFilter({
6287
+ category: 'Gene List',
6288
+ fq_field: 'saved_search',
6289
+ fq_value: list.hash,
6290
+ name: list.label
6291
+ });
6292
+ };
6293
+ const deleteGeneList = async (api, listId)=>{
6294
+ if (window.confirm('Are you sure you want to delete this gene list?')) // Replace with the actual delete request
6295
+ try {
6296
+ await fetch(`${api}/gene_lists/${listId}`, {
6297
+ method: 'DELETE'
6298
+ });
6299
+ alert('Gene list deleted!');
6300
+ // Optionally refetch the updated list
6301
+ } catch (err) {
6302
+ alert('Failed to delete gene list.');
6303
+ }
6304
+ };
5763
6305
  // Fetch data when the component is mounted
5764
6306
  (0, $gXNCa$react.useEffect)(()=>{
5765
6307
  fetchPublicGeneLists();
@@ -5785,20 +6327,28 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5785
6327
  hover: true,
5786
6328
  className: "mt-4",
5787
6329
  children: [
5788
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
5789
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- children: [
5791
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5792
- children: "List Name"
5793
- }),
5794
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5795
- children: "Number of Genes"
5796
- }),
5797
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5798
- children: "Actions"
6330
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("thead", {
6331
+ children: [
6332
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tr", {
6333
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6334
+ colspan: 3,
6335
+ children: "My gene lists"
5799
6336
  })
5800
- ]
5801
- })
6337
+ }),
6338
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
6339
+ children: [
6340
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6341
+ children: "List Name"
6342
+ }),
6343
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6344
+ children: "Number of Genes"
6345
+ }),
6346
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6347
+ children: "Actions"
6348
+ })
6349
+ ]
6350
+ })
6351
+ ]
5802
6352
  }),
5803
6353
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
5804
6354
  children: privateGeneLists.map((list, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
@@ -5807,18 +6357,18 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5807
6357
  children: list.label
5808
6358
  }),
5809
6359
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
5810
- children: list.hash
6360
+ children: list.n_genes || 0
5811
6361
  }),
5812
6362
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
5813
6363
  children: [
5814
6364
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
5815
6365
  variant: "info",
5816
- onClick: ()=>$0f50f369018a42ef$var$viewGeneList(list),
6366
+ onClick: ()=>viewGeneList(list),
5817
6367
  children: "View"
5818
6368
  }),
5819
6369
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
5820
6370
  variant: "danger",
5821
- onClick: ()=>$0f50f369018a42ef$var$deleteGeneList(props.api, list._id),
6371
+ onClick: ()=>deleteGeneList(props.api, list._id),
5822
6372
  className: "ml-2",
5823
6373
  children: "Delete"
5824
6374
  })
@@ -5835,20 +6385,28 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5835
6385
  hover: true,
5836
6386
  className: "mt-4",
5837
6387
  children: [
5838
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
5839
- children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
5840
- children: [
5841
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5842
- children: "List Name"
5843
- }),
5844
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5845
- children: "Number of Genes"
5846
- }),
5847
- /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
5848
- children: "Actions"
6388
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("thead", {
6389
+ children: [
6390
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tr", {
6391
+ children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6392
+ colSpan: 3,
6393
+ children: "Public gene lists"
5849
6394
  })
5850
- ]
5851
- })
6395
+ }),
6396
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
6397
+ children: [
6398
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6399
+ children: "List Name"
6400
+ }),
6401
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6402
+ children: "Number of Genes"
6403
+ }),
6404
+ /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
6405
+ children: "Actions"
6406
+ })
6407
+ ]
6408
+ })
6409
+ ]
5852
6410
  }),
5853
6411
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
5854
6412
  children: publicGeneLists.map((list, index)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
@@ -5857,18 +6415,18 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5857
6415
  children: list.label
5858
6416
  }),
5859
6417
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
5860
- children: list.hash
6418
+ children: list.n_genes || 0
5861
6419
  }),
5862
6420
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
5863
6421
  children: [
5864
6422
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
5865
6423
  variant: "info",
5866
- onClick: ()=>$0f50f369018a42ef$var$viewGeneList(list),
6424
+ onClick: ()=>viewGeneList(list),
5867
6425
  children: "View"
5868
6426
  }),
5869
6427
  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
5870
6428
  variant: "danger",
5871
- onClick: ()=>$0f50f369018a42ef$var$deleteGeneList(props.api, list._id),
6429
+ onClick: ()=>deleteGeneList(props.api, list._id),
5872
6430
  className: "ml-2",
5873
6431
  children: "Delete"
5874
6432
  })
@@ -5886,22 +6444,6 @@ const $0f50f369018a42ef$var$GeneListDisplayComponent = (props)=>{
5886
6444
  ]
5887
6445
  });
5888
6446
  };
5889
- // Example functions for viewing and deleting lists
5890
- const $0f50f369018a42ef$var$viewGeneList = (list)=>{
5891
- alert(`Viewing gene list: ${list.name}\nGenes: ${list.genes.join(', ')}`);
5892
- };
5893
- const $0f50f369018a42ef$var$deleteGeneList = async (api, listId)=>{
5894
- if (window.confirm('Are you sure you want to delete this gene list?')) // Replace with the actual delete request
5895
- try {
5896
- await fetch(`${api}/gene_lists/${listId}`, {
5897
- method: 'DELETE'
5898
- });
5899
- alert('Gene list deleted!');
5900
- // Optionally refetch the updated list
5901
- } catch (err) {
5902
- alert('Failed to delete gene list.');
5903
- }
5904
- };
5905
6447
  const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
5906
6448
  const [geneList, setGeneList] = (0, $gXNCa$react.useState)('');
5907
6449
  const [listHash, setListHash] = (0, $gXNCa$react.useState)(null);
@@ -5963,6 +6505,7 @@ const $0f50f369018a42ef$var$GeneListComponent = (props)=>{
5963
6505
  label: listName,
5964
6506
  hash: listHash,
5965
6507
  site: props.site,
6508
+ n_genes: validatedList.length,
5966
6509
  isPublic: listIsPublic
5967
6510
  };
5968
6511
  const queryString = new URLSearchParams(queryParams).toString();
@@ -6123,14 +6666,15 @@ const $0f50f369018a42ef$var$UserGeneListsComponent = (props)=>{
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  /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Col), {
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  children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($0f50f369018a42ef$var$GeneListDisplayComponent, {
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  api: props.configuration.grameneData,
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- site: props.configuration.id
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+ site: props.configuration.id,
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+ addFilter: props.doAcceptGrameneSuggestion
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  })
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  })
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  ]
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  })
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  });
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  };
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- var $0f50f369018a42ef$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectConfiguration', $0f50f369018a42ef$var$UserGeneListsComponent);
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+ var $0f50f369018a42ef$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectConfiguration', 'doAcceptGrameneSuggestion', $0f50f369018a42ef$var$UserGeneListsComponent);
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