@sjcrh/proteinpaint-client 2.170.21 → 2.170.23

package/dist/{violin.integration.spec-P5J3S26X.js → violin.integration.spec-6AFHD3SD.js}

@@ -7,44 +7,44 @@ import {
 } from "./chunk-3YJYBZIJ.js";
 import {
   getRunPp
-} from "./chunk-JUAB6AWT.js";
+} from "./chunk-VMNJ3CBS.js";
 import {
   detectGte,
   detectLst,
   detectOne,
   sleep,
   whenVisible
-} from "./chunk-XENPVHIO.js";
+} from "./chunk-M7MBFGEA.js";
 import {
   require_tape
 } from "./chunk-EFPC6YYT.js";
-import "./chunk-ULFFSC6N.js";
-import "./chunk-CA5LLXPV.js";
-import "./chunk-L2XKBMRK.js";
-import "./chunk-MWGHZ2OR.js";
-import "./chunk-JZJJOLHH.js";
-import "./chunk-IMCHIQT2.js";
+import "./chunk-XDBGOZED.js";
+import "./chunk-3KMTDBZT.js";
+import "./chunk-RVZ6M5MM.js";
+import "./chunk-2Y7E546M.js";
+import "./chunk-LRFMJ4EE.js";
+import "./chunk-HTNDG4VX.js";
 import "./chunk-MKAF2BHB.js";
 import "./chunk-DONWY7TP.js";
-import "./chunk-XG4HJBT5.js";
+import "./chunk-XULJ2UUC.js";
 import "./chunk-PRZWSBMA.js";
 import {
   fillTermWrapper,
   filterJoin,
   getFilterItemByTag
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-DXDHMTY7.js";
+import "./chunk-PZ7WCWYR.js";
 import "./chunk-OGVY5ALW.js";
-import "./chunk-QIE5DTBW.js";
+import "./chunk-ABMFFNR4.js";
 import "./chunk-YJWWWCJ6.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-CY52TN75.js";
-import "./chunk-PFBEIJLF.js";
-import "./chunk-VGLPN6PS.js";
+import "./chunk-7UR62HW6.js";
+import "./chunk-WQENZXSN.js";
+import "./chunk-KZBB7S6A.js";
 import "./chunk-LSEFWW72.js";
 import "./chunk-DQC5FFGV.js";
 import "./chunk-YCLN3A4F.js";
@@ -1426,4 +1426,4 @@ async function testViolinByCount(test, violinDiv, count) {
   const groups = await detectLst({ elem: violinDiv.node(), selector: "path.sjpp-vp-path", count: count * 2 });
   test.ok(groups, `Detected ${count} violin <path class=sjpp-vp-path>`);
 }
-//# sourceMappingURL=violin.integration.spec-P5J3S26X.js.map
+//# sourceMappingURL=violin.integration.spec-6AFHD3SD.js.map

package/dist/{violin.interactivity-VN3O6BAP.js → violin.interactivity-LDD54ACO.js}

@@ -1,19 +1,19 @@
 import {
   setInteractivity
-} from "./chunk-JFWEYCVW.js";
-import "./chunk-CTRQJ6M4.js";
+} from "./chunk-7CDMJ2DF.js";
+import "./chunk-IKXK6WW5.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-DXDHMTY7.js";
+import "./chunk-PZ7WCWYR.js";
 import "./chunk-OGVY5ALW.js";
-import "./chunk-QIE5DTBW.js";
+import "./chunk-ABMFFNR4.js";
 import "./chunk-YJWWWCJ6.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-CY52TN75.js";
-import "./chunk-PFBEIJLF.js";
-import "./chunk-VGLPN6PS.js";
+import "./chunk-7UR62HW6.js";
+import "./chunk-WQENZXSN.js";
+import "./chunk-KZBB7S6A.js";
 import "./chunk-LSEFWW72.js";
 import "./chunk-DQC5FFGV.js";
 import "./chunk-YCLN3A4F.js";
@@ -30,4 +30,4 @@ import "./chunk-HFNDKYVF.js";
 export {
   setInteractivity
 };
-//# sourceMappingURL=violin.interactivity-VN3O6BAP.js.map
+//# sourceMappingURL=violin.interactivity-LDD54ACO.js.map

package/dist/{violin.renderer-7Z5QGC2C.js → violin.renderer-6IGRXYNY.js}

@@ -1,20 +1,20 @@
 import {
   createNumericScale,
   setViolinRenderer
-} from "./chunk-ZQ5QFLEC.js";
-import "./chunk-CTRQJ6M4.js";
+} from "./chunk-Y4QM3UWA.js";
+import "./chunk-IKXK6WW5.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-DXDHMTY7.js";
+import "./chunk-PZ7WCWYR.js";
 import "./chunk-OGVY5ALW.js";
-import "./chunk-QIE5DTBW.js";
+import "./chunk-ABMFFNR4.js";
 import "./chunk-YJWWWCJ6.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-CY52TN75.js";
-import "./chunk-PFBEIJLF.js";
-import "./chunk-VGLPN6PS.js";
+import "./chunk-7UR62HW6.js";
+import "./chunk-WQENZXSN.js";
+import "./chunk-KZBB7S6A.js";
 import "./chunk-LSEFWW72.js";
 import "./chunk-DQC5FFGV.js";
 import "./chunk-YCLN3A4F.js";
@@ -32,4 +32,4 @@ export {
   createNumericScale,
   setViolinRenderer as default
 };
-//# sourceMappingURL=violin.renderer-7Z5QGC2C.js.map
+//# sourceMappingURL=violin.renderer-6IGRXYNY.js.map

package/dist/{vocabulary-SIJORF5B.js → vocabulary-YBNE26CP.js}

@@ -2,19 +2,19 @@ import {
   getVocabFromSamplesArray,
   q_to_param,
   vocabInit
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-DXDHMTY7.js";
+import "./chunk-PZ7WCWYR.js";
 import "./chunk-OGVY5ALW.js";
-import "./chunk-QIE5DTBW.js";
+import "./chunk-ABMFFNR4.js";
 import "./chunk-YJWWWCJ6.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
 import "./chunk-ITJ2SXU5.js";
 import "./chunk-FN5XPUPH.js";
-import "./chunk-CY52TN75.js";
-import "./chunk-PFBEIJLF.js";
-import "./chunk-VGLPN6PS.js";
+import "./chunk-7UR62HW6.js";
+import "./chunk-WQENZXSN.js";
+import "./chunk-KZBB7S6A.js";
 import "./chunk-LSEFWW72.js";
 import "./chunk-DQC5FFGV.js";
 import "./chunk-YCLN3A4F.js";
@@ -33,4 +33,4 @@ export {
   q_to_param,
   vocabInit
 };
-//# sourceMappingURL=vocabulary-SIJORF5B.js.map
+//# sourceMappingURL=vocabulary-YBNE26CP.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-client",
-  "version": "2.170.21",
+  "version": "2.170.23",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "type": "module",
   "main": "dist/app.js",

package/dist/chunk-2KJMSFOW.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/matrix.data.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { sample_match_termvaluesetting } from '#common/termutils'\nimport { isDictionaryType } from '#shared/terms.js'\n\nexport function mayRequireToken(tokenMessage = '') {\n\tconst message = tokenMessage || this.state.tokenVerificationMessage\n\tif (!message && this.state.hasVerifiedToken) {\n\t\tthis.dom.errdiv.style('display', 'none').html()\n\t\tthis.dom.controls.style('display', this.opts.controls ? 'inline-block' : '')\n\t\tthis.dom.svg.style('display', '')\n\t\treturn false\n\t} else {\n\t\tthis.dom.errdiv.style('display', '').html(message || 'Requires login')\n\t\tthis.dom.controls.style('display', 'none')\n\t\tthis.dom.svg.style('display', 'none')\n\t\treturn true\n\t}\n}\n\nexport function getMatrixRequestOpts(state) {\n\t/* requests data for all terms shown in matrix,\n\t\tby creating request argument for getAnnotatedSampleData and run it\n\t\tNOTE this excludes the term group used for hierCluster, as its data request is done separately\n\t\t*/\n\tconst terms = []\n\n\tconst termgroups =\n\t\tthis.chartType == 'hierCluster'\n\t\t\t? state.config.termgroups.filter(grp => grp.type != 'hierCluster')\n\t\t\t: state.config.termgroups\n\tfor (const grp of termgroups) {\n\t\tterms.push(...getNormalizedTwLstCopy(grp.lst))\n\t}\n\tif (state.config.divideBy) terms.push(normalizeTwForRequest(structuredClone(state.config.divideBy)))\n\n\t// !!! NOTE !!!\n\t// all parameters here must remove payload properties that are\n\t// not relevant to the data request, so that the dofetch and/or\n\t// browser caching would work\n\tconst opts = {\n\t\tterms,\n\t\tfilter: state.filter,\n\t\tfilter0: state.filter0,\n\t\tmaxGenes: state.config.settings.matrix.maxGenes,\n\t\t/*********** quick fix\n\t\twhen the flag is true, set artificially large number to ensure all genes are sent in one query\n\t\tthis avoids changing getAnnotatedSampleData()\n\t\tadditional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX\n\t\t*/\n\t\ttermsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1000 : 1\n\t}\n\n\tif (this.chartType == 'hierCluster') {\n\t\t/* quick fix, only needed for gdc\n\t\t\tso backend case query will know this context and pull cases with gene exp data\n\t\t\tis ignored by non-gdc datasets\n\t\t\t*/\n\t\topts.isHierCluster = 1\n\t}\n\n\treturn opts\n}\n\nfunction getNormalizedTwLstCopy(twlst) {\n\tconst lst = structuredClone(twlst)\n\tlst.forEach(normalizeTwForRequest)\n\tlst.sort(sortTwLst)\n\treturn lst\n}\n\nfunction normalizeTwForRequest(tw) {\n\tif (!tw?.term) return\n\t// These props are cohort-dependent and should be ignored like termfilter.filter0.\n\t// Note that state filter, filter0 are always sent to the server for dataset-related requests,\n\t// which indirectly covers the computed properties below that are being deleted.\n\tdelete tw.term.category2samplecount\n\t// for GDC, the term.values may not be known ahead of time\n\t// and only filled in as data comes in, should ignore this\n\t// computed value as to avoid affecting tracked state\n\n\t// for dictionary term, term.values is queryed from terms table\n\tif (isDictionaryType(tw.term.type) && tw.term.type !== 'samplelst') delete tw.term.values\n\treturn tw\n}\n\nfunction sortTwLst(twa, twb) {\n\tconst a = twa?.$id || twa.term?.id || twa?.term?.name\n\tconst b = twb?.$id || twb.term?.id || twb?.term?.name\n\treturn a < b ? -1 : 1\n}\n\nexport async function setData(_data) {\n\tconst opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state)\n\tthis.numTerms = opts.terms.length\n\topts.loadingDiv = this.chartType != 'hierCluster' && this.dom.loadingDiv\n\t// const abortCtrl = new AbortController()\n\t// opts.signal = abortCtrl.signal\n\t// opts.signal = this.api.getAbortSignal()\n\t// rely on getAnnotatedSampleData() to set a default abortSignal from `this.app.getAbortSignal()`\n\tconst data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data)\n\tthis.data = data\n\tthis.origData = structuredClone(this.data)\n\tthis.sampleIdMap = {}\n\tfor (const d of this.data.lst) {\n\t\t// mapping of sample string name to integer id\n\t\t// TODO: not able to find matching sample names between ASH and termdb?\n\t\tthis.sampleIdMap[d.sample] = d._ref_.label\n\t}\n}\n\nexport function applyLegendValueFilter() {\n\tconst self = this\n\tif (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return\n\n\tfor (const grpFilter of self.config.legendGrpFilter.lst) {\n\t\tif (grpFilter.dt) {\n\t\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\t\tfor (const oneSampleData of self.origData.lst) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\t\tconst newValues = []\n\t\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\t\tif (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {\n\t\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tgrpFilter.filteredOutCats = [...filteredOutCats]\n\t\t\tfor (const oneSampleData of Object.values(self.origData.samples)) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\t\tv => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst geneVariant$ids = Object.values(self.data.refs.byTermId)\n\t\t.filter(v => v.term?.type == 'geneVariant')\n\t\t.map(v => v.$id)\n\tconst data = { samples: {}, lst: [], refs: self.data.refs }\n\n\tconst onlyHardFilter = structuredClone(self.config.legendValueFilter)\n\tonlyHardFilter.lst = onlyHardFilter.lst.filter(\n\t\tl => !l.tvs.legendFilterType || l.tvs.legendFilterType !== 'geneVariant_soft'\n\t)\n\tfor (const row of self.origData.lst) {\n\t\tconst include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids)\n\t\tif (include || self.chartType == 'hierCluster') {\n\t\t\t// for hierCluster, should not filter out any samples by sample_match_termvaluesetting\n\t\t\t// samples are filtered out by joining legendValueFilter with filter in setHierClusterData\n\t\t\tdata.samples[row.sample] = row\n\t\t\tdata.lst.push(row)\n\t\t}\n\t}\n\n\tfor (const valFilter of self.config.legendValueFilter.lst) {\n\t\tif (valFilter.tvs.legendFilterType !== 'geneVariant_soft') continue\n\t\t// applying each soft filter\n\t\tconst tvsV = valFilter.tvs.values[0]\n\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\tfor (const oneSampleData of data.lst) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\tconst newValues = []\n\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\tif (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {\n\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tvalFilter.filteredOutCats = [...filteredOutCats]\n\t\tfor (const oneSampleData of Object.values(data.samples)) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\tv => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))\n\t\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n\tif (self.chartType !== 'hierCluster' && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == 'GDC')\n\t\tremove_empty_sample(data, geneVariant$ids)\n\tself.data = data\n}\n\n// each time gene legend soft filter or gene legend group filter is applied (when cell gene values updated), remove\n// the samples that have empty cells (not even WT or BLANK)\nfunction remove_empty_sample(data) {\n\tfor (const oneSampleData of data.lst) {\n\t\tlet removeSample = true\n\t\tfor (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {\n\t\t\tif (!annoForOneTerm.values) continue\n\t\t\tconst annoType = data.refs.byTermId[key].term.type\n\t\t\tif (annoType != 'geneVariant') continue\n\t\t\tif (annoForOneTerm.values.length) removeSample = false\n\t\t}\n\t\tif (removeSample) {\n\t\t\tdata.lst = data.lst.filter(dl => dl.sample !== oneSampleData.sample)\n\t\t\tdelete data.samples[parseInt(oneSampleData.sample)]\n\t\t}\n\t}\n\treturn data\n}\n"],
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