@sjcrh/proteinpaint-client 2.190.2 → 2.191.0
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.
- package/dist/2dmaf-3D2KTSAN.js +1373 -0
- package/dist/AIProjectAdmin-IGPLMREH.js +829 -0
- package/dist/AppHeader-WT5AXGLC.js +835 -0
- package/dist/BoxPlot-AUFITBDB.js +1217 -0
- package/dist/CorrelationVolcano-4AZ6Y42O.js +619 -0
- package/dist/DE-MWYRMM47.js +95 -0
- package/dist/DEinput-F3JFK4HF.js +301 -0
- package/dist/DifferentialAnalysis-ZAVYUYOL.js +245 -0
- package/dist/Disco-Q3O3A2CU.js +3237 -0
- package/dist/Disco.UI-QIKPQKTY.js +245 -0
- package/dist/DmrPlot-D7TPJXWH.js +642 -0
- package/dist/GB-K57ZGFLA.js +1130 -0
- package/dist/GeneExpInput-7UYFJHSX.js +366 -0
- package/dist/HicApp-HPIHJDLQ.js +2250 -0
- package/dist/NumBinaryEditor-ENHACYTK.js +270 -0
- package/dist/NumBinaryEditor.unit.spec-TNIRFCTU.js +286 -0
- package/dist/NumContEditor-Y4CDFJM2.js +107 -0
- package/dist/NumContEditor.unit.spec-KES6AJHN.js +169 -0
- package/dist/NumCustomBinEditor-TRXZ52MH.js +38 -0
- package/dist/NumCustomBinEditor.unit.spec-2V5X5YK4.js +284 -0
- package/dist/NumDiscreteEditor-RXXL3AQ4.js +179 -0
- package/dist/NumDiscreteEditor.unit.spec-EAFEI66P.js +202 -0
- package/dist/NumRegularBinEditor-KHIFP2L7.js +38 -0
- package/dist/NumRegularBinEditor.unit.spec-ADRNCEAV.js +227 -0
- package/dist/NumSplineEditor-33SUCGNJ.js +197 -0
- package/dist/NumSplineEditor.unit.spec-7KTMNABP.js +199 -0
- package/dist/NumericDensity-PWWJBZUA.js +38 -0
- package/dist/NumericDensity.unit.spec-V5C43FCP.js +221 -0
- package/dist/NumericHandler-A6QSQAPT.js +39 -0
- package/dist/NumericHandler.unit.spec-SRFEDFCC.js +219 -0
- package/dist/ProteomeInput-BOI2634T.js +396 -0
- package/dist/RunChart2-DJNWYZ5C.js +758 -0
- package/dist/SC-ADKHO4MP.js +936 -0
- package/dist/Volcano-4GJU2666.js +1379 -0
- package/dist/WSIViewer-JQKGSN3D.js +48475 -0
- package/dist/WsiSamplesPlot-PSVYIYI7.js +165 -0
- package/dist/adSandbox-AFYF5ULQ.js +38 -0
- package/dist/app-5KDQSFDE.js +49 -0
- package/dist/app-PZ5KGBCR.js +37 -0
- package/dist/app.js +13 -13
- package/dist/bam-AYX4HVPY.js +860 -0
- package/dist/barchart-2BMDZGPJ.js +47 -0
- package/dist/barchart.data-I33D7SQC.js +22 -0
- package/dist/barchart.events-Z5AL6NU6.js +47 -0
- package/dist/barchart.integration.spec-JG7OWI6G.js +1974 -0
- package/dist/barchart.integration.spec-JG7OWI6G.js.map +7 -0
- package/dist/barchart2-KFMUPMVS.js +311 -0
- package/dist/block-7UW7QCRX.js +6202 -0
- package/dist/block.init-CZWCEEID.js +38 -0
- package/dist/block.mds.expressionrank-2JJYKI2C.js +359 -0
- package/dist/block.mds.geneboxplot-NU45ZP4J.js +828 -0
- package/dist/block.mds.junction-UVSKHUFR.js +1545 -0
- package/dist/block.mds.svcnv-6JXI63CC.js +6801 -0
- package/dist/block.svg-KAMDKUQX.js +164 -0
- package/dist/block.tk.aicheck-WEKHCRXC.js +283 -0
- package/dist/block.tk.ase-MGDGSUQN.js +365 -0
- package/dist/block.tk.bam-MB2DAFD7.js +1906 -0
- package/dist/block.tk.bedgraphdot-VUSURZ6N.js +384 -0
- package/dist/block.tk.bigwig.ui-WQTN44VK.js +212 -0
- package/dist/block.tk.hicstraw-T2JXNKWD.js +823 -0
- package/dist/block.tk.junction-2JXABLIG.js +2364 -0
- package/dist/block.tk.junction.textmatrixui-EEB3JUNU.js +199 -0
- package/dist/block.tk.ld-JZBL73US.js +99 -0
- package/dist/block.tk.menu-VQEPTCE6.js +1029 -0
- package/dist/block.tk.pgv-PYOPQDYL.js +944 -0
- package/dist/brainImaging-SYJZZN3K.js +423 -0
- package/dist/chunk-26XX7RVV.js +129 -0
- package/dist/chunk-2QWELHBX.js +54 -0
- package/dist/chunk-3MGF2FZ2.js +1179 -0
- package/dist/chunk-3S7ZWGND.js +95 -0
- package/dist/chunk-4VCBJC3B.js +203 -0
- package/dist/chunk-53WLN75I.js +50 -0
- package/dist/chunk-5GOZWJ7S.js +263 -0
- package/dist/chunk-5WKIMNGG.js +148 -0
- package/dist/chunk-5WM3CC5O.js +117 -0
- package/dist/chunk-6FF5VLGO.js +20745 -0
- package/dist/chunk-6FF5VLGO.js.map +7 -0
- package/dist/chunk-6FOKZFIT.js +613 -0
- package/dist/chunk-6FOKZFIT.js.map +7 -0
- package/dist/chunk-6GI6MDYV.js +1210 -0
- package/dist/chunk-6XOZ4DWL.js +222 -0
- package/dist/chunk-6XOZ4DWL.js.map +7 -0
- package/dist/chunk-7BOPMRFX.js +482 -0
- package/dist/chunk-7C76SLOH.js +1275 -0
- package/dist/chunk-7C76SLOH.js.map +7 -0
- package/dist/chunk-BYOIIMNZ.js +2327 -0
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- package/dist/chunk-JTMU3F2Q.js +184 -0
- package/dist/chunk-JTMU3F2Q.js.map +7 -0
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- package/dist/chunk-QMI2X23H.js +339 -0
- package/dist/chunk-QOE7MB4X.js +454 -0
- package/dist/chunk-QSMU6K5D.js +34 -0
- package/dist/chunk-RBIBHQTL.js +54 -0
- package/dist/chunk-RG5ABFA2.js +368 -0
- package/dist/chunk-RRJGFE2S.js +407 -0
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- package/dist/chunk-T2CG7BVN.js +205 -0
- package/dist/chunk-TVADJLMF.js +317 -0
- package/dist/chunk-TVADJLMF.js.map +7 -0
- package/dist/chunk-U3DKYKV7.js +293 -0
- package/dist/chunk-UQHM3F6B.js +37 -0
- package/dist/chunk-VXKO2ONI.js +534 -0
- package/dist/chunk-W3MCIBAP.js +272 -0
- package/dist/chunk-WH236OZ6.js +736 -0
- package/dist/chunk-WMELUFVS.js +254 -0
- package/dist/chunk-WS3NUPNV.js +119 -0
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- package/dist/chunk-YRQ5V7DQ.js +302 -0
- package/dist/chunk-ZK226W6V.js +194 -0
- package/dist/chunk-ZTOABVVA.js +55 -0
- package/dist/chunk-ZUTPAYSS.js +477 -0
- package/dist/condition-SZZS77TK.js +332 -0
- package/dist/controls-ZBDTHWOT.js +41 -0
- package/dist/controls.config-MTBN2XPW.js +39 -0
- package/dist/correlation-DHEH5FT4.js +99 -0
- package/dist/cuminc-TM3SMOJ2.js +1149 -0
- package/dist/cuminc.integration.spec-NEBXRMKB.js +678 -0
- package/dist/customdata.inputui-5ZEKFWYV.js +289 -0
- package/dist/dataDownload-XZ4AC6QY.js +330 -0
- package/dist/dataDownload.integration.spec-O4YQKAOJ.js +193 -0
- package/dist/databrowser.ui-V4HQMZ4X.js +433 -0
- package/dist/dictionary-RAHC3OA7.js +111 -0
- package/dist/dnaMethylation-ZUHHG7Q2.js +38 -0
- package/dist/dnaMethylation.integration.spec-JZ6ZSF5L.js +203 -0
- package/dist/dofetch-77N4NDDM.js +51 -0
- package/dist/e2pca-K7IFKNTZ.js +350 -0
- package/dist/ep-4OIFIMZH.js +1256 -0
- package/dist/expclust.gdc.spec-OJD7ENKA.js +307 -0
- package/dist/facet-SZAF3QW6.js +521 -0
- package/dist/forms2-TBRF2RI5.js +534 -0
- package/dist/gb-I5J74SHP.js +88 -0
- package/dist/geneExpClustering-OSS4OCN6.js +249 -0
- package/dist/geneExpression-IHVMJGOG.js +38 -0
- package/dist/geneExpression-WKYVSE45.js +313 -0
- package/dist/geneExpression.unit.spec-QP6CLYHP.js +102 -0
- package/dist/geneORA-65PHOTHN.js +278 -0
- package/dist/geneRanking-XCU3NX4J.js +551 -0
- package/dist/geneVariant-CZM3XP7X.js +39 -0
- package/dist/geneVariant-IMDFPV2L.js +41 -0
- package/dist/geneVariant.integration.spec-FOONVTYD.js +198 -0
- package/dist/genefusion.ui-UZM2YGIR.js +309 -0
- package/dist/geneset-IGG77MNZ.js +208 -0
- package/dist/genomeBrowser.spec-CN2XNZQF.js +281 -0
- package/dist/grin2-367QGSOU.js +1560 -0
- package/dist/grin2-S46IRWIP.js +821 -0
- package/dist/grin2-S46IRWIP.js.map +7 -0
- package/dist/gsea-RJ767G5U.js +47 -0
- package/dist/hierCluster-3D425AUU.js +63 -0
- package/dist/hierCluster-GIIB6OEC.js +59 -0
- package/dist/hierCluster.config-ENEOWYOS.js +40 -0
- package/dist/hierCluster.integration.spec-IOA3PVAN.js +395 -0
- package/dist/hierCluster.interactivity-VITUF5RM.js +54 -0
- package/dist/hierCluster.renderers-G3274UYA.js +21 -0
- package/dist/imagePlot-7VH7VFWD.js +163 -0
- package/dist/importPlot-OKOYX2NU.js +8 -0
- package/dist/isoformExpression-4SJQZFLP.js +40 -0
- package/dist/isoformExpression.unit.spec-3MQQZEPZ.js +208 -0
- package/dist/launch.adhoc-MQKVVUV7.js +42 -0
- package/dist/leftlabel.sample-JPE6CXZU.js +260 -0
- package/dist/lollipop-DMM3QYKI.js +171 -0
- package/dist/maf-TQKKVLNR.js +452 -0
- package/dist/maftimeline-BXBAXKAI.js +593 -0
- package/dist/matrix-AWVEEUKZ.js +58 -0
- package/dist/matrix-N3YUJXLP.js +63 -0
- package/dist/matrix.cells-E3LEVA7U.js +28 -0
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- package/dist/matrix.groups-BGMZZ6CM.js +27 -0
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- package/dist/matrix.interactivity-LKLF5ZQN.js +42 -0
- package/dist/matrix.layout-ORYBQUKT.js +44 -0
- package/dist/matrix.legend-RJAFOZHQ.js +22 -0
- package/dist/matrix.renderers-TLZSYHZR.js +38 -0
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- package/dist/mds.fimo-MHPHQB4X.js +518 -0
- package/dist/mds.samplescatterplot-LRL5SXJ5.js +1550 -0
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- package/dist/numericDictTermCluster-OMXIURRD.js +72 -0
- package/dist/oncomatrix-FA3ELKNE.js +295 -0
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- package/dist/polar2-WABGZYEV.js +226 -0
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- package/dist/profileForms-LYWVFIVQ.js +441 -0
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- package/dist/proteinView-ATZI5LXA.js +1320 -0
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- package/dist/qualitative-VNY32ONL.js +43 -0
- package/dist/radar2-YVHLSCAM.js +321 -0
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- /package/dist/{summary.integration.spec-54HA7BC2.js.map → summary.integration.spec-KJPNP7X2.js.map} +0 -0
- /package/dist/{summaryInput-4RLZT6RW.js.map → summaryInput-47JBGPNE.js.map} +0 -0
- /package/dist/{sunburst-SMKD45XD.js.map → sunburst-PUZYZZGK.js.map} +0 -0
- /package/dist/{survival-YQNA3WP7.js.map → survival-LGJBYXFR.js.map} +0 -0
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- /package/dist/{svgraph-5Z7VAIVR.js.map → svgraph-GWDKHIDQ.js.map} +0 -0
- /package/dist/{svmr-PHD76RV4.js.map → svmr-RRA6OUVP.js.map} +0 -0
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- /package/dist/{termCollection-MEBY34TJ.js.map → termCollection-4OVZAKYZ.js.map} +0 -0
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- /package/dist/{tp.ui-XV7CL7CA.js.map → tp.ui-TKAJ7DRO.js.map} +0 -0
- /package/dist/{tvs.dt-U6SIZTXW.js.map → tvs.dt-6NDINORK.js.map} +0 -0
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- /package/dist/{tvs.samplelst-HVNYKHXG.js.map → tvs.samplelst-NQ5BKEGM.js.map} +0 -0
- /package/dist/{tvs.termCollection-EWGTT75Z.js.map → tvs.termCollection-HOVUO7ZH.js.map} +0 -0
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getCompInit
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// plots/matrix/hierCluster.js
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var HierCluster = class _HierCluster extends Matrix {
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static type = "hierCluster";
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constructor(opts) {
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super(opts);
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async init(appState) {
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this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
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this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
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if (clickedClusterId) {
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this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
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this.clickedClusterIds.push(clickedClusterId);
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const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
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const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
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this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
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}
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delete this.clickedLeftClusterIds;
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} else this.plotDendrogramHclust("top");
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});
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this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
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const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
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if (clickedLeftClusterId) {
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this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
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this.clickedLeftClusterIds.push(clickedLeftClusterId);
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const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
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const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
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}
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if (this.clickedClusterIds) {
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} else this.plotDendrogramHclust("left");
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});
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}
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async setHierClusterData(_data = {}) {
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this.prevServerData = this.currServerData;
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this.currServerData = structuredClone(d);
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if (!deepEqual(this.prevServerData, this.currServerData)) {
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}
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if (!d.clustering) {
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if (d.gene) {
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}
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}
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this.hierClusterData = d;
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samples[column.name] = { sample: column.name };
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for (const [j, row] of c.row.order.entries()) {
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const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
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samples[column.name][tw.$id] = {
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{
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label: s.termGroupName,
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value
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}
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]
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};
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}
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}
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this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : this.config.dataType === NUMERIC_DICTIONARY_TERM ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
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if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
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this.hcTermSorter = (a, b) => {
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const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
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const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
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if (i == -1 && j == -1) return 0;
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if (i == -1) return 1;
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if (j == -1) return -1;
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return i - j;
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};
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this.hcSampleNameOrder = c.col.order.map((col) => col.name);
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this.hcSampleSorter = (a, b) => {
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const i = this.hcSampleNameOrder.indexOf(a.sample);
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const j = this.hcSampleNameOrder.indexOf(b.sample);
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if (i == -1 && j == -1) return 0;
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if (i == -1) return 1;
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if (j == -1) return -1;
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return i - j;
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};
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const byTermId = {};
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for (const tw of twlst) {
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if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
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}
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this.hierClusterSamples = {
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refs: { byTermId, bySampleId: d.bySampleId },
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lst: c.col.order.map((c2) => samples[c2.name]),
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samples,
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removedHierClusterTerms: d.removedHierClusterTerms
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};
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}
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async requestData() {
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const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
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const twlst = this.hcTermGroup.lst;
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const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
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return [data, twlst];
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}
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-
getHCRequestBody(state) {
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|
-
this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
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const s = state.config.settings.hierCluster;
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const dictionaryLegendFilter = {
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type: "tvslst",
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in: true,
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join: "and",
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lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
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|
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};
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168
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-
const terms = this.getClusterRowTermsAsParameter();
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if (!terms.length) throw "no data";
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if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
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|
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if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
|
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const body = {
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genome: state.vocab.genome,
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|
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dslabel: state.vocab.dslabel,
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|
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dataType: state.config.dataType,
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|
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clusterMethod: s.clusterMethod,
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177
|
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distanceMethod: s.distanceMethod,
|
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178
|
-
zScoreTransformation: s.zScoreTransformation,
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179
|
-
terms,
|
|
180
|
-
filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
|
|
181
|
-
filter0: state.filter0
|
|
182
|
-
};
|
|
183
|
-
if (state.config.dataType == "proteomeAbundance") {
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|
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|
-
body.proteomeDetails = {
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|
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|
-
organism: state.config.proteomeDetails?.organism,
|
|
186
|
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assay: state.config.proteomeDetails?.assay,
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|
187
|
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cohort: state.config.proteomeDetails?.cohort
|
|
188
|
-
};
|
|
189
|
-
}
|
|
190
|
-
return body;
|
|
191
|
-
}
|
|
192
|
-
combineData() {
|
|
193
|
-
if (!this.hierClusterSamples) return;
|
|
194
|
-
const d = this.data;
|
|
195
|
-
const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
|
|
196
|
-
const samples = {};
|
|
197
|
-
const lst = [];
|
|
198
|
-
for (const sampleId in this.hierClusterSamples.samples) {
|
|
199
|
-
const s = this.hierClusterSamples.samples[sampleId];
|
|
200
|
-
samples[sampleId] = s;
|
|
201
|
-
lst.push(s);
|
|
202
|
-
if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
|
|
203
|
-
const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
|
|
204
|
-
if (!s._ref_) s._ref_ = _ref_;
|
|
205
|
-
else Object.assign(s._ref_, _ref_);
|
|
206
|
-
}
|
|
207
|
-
const t = this.hierClusterSamples.refs.byTermId;
|
|
208
|
-
for (const $id of Object.keys(t)) {
|
|
209
|
-
d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
|
|
210
|
-
}
|
|
211
|
-
this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
|
|
212
|
-
}
|
|
213
|
-
setHierColorScale(c) {
|
|
214
|
-
const hc = this.settings.hierCluster;
|
|
215
|
-
const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
|
|
216
|
-
const globalMinMaxes = [];
|
|
217
|
-
for (const row of c.matrix) {
|
|
218
|
-
globalMinMaxes.push(...extent(row));
|
|
219
|
-
}
|
|
220
|
-
const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
|
|
221
|
-
const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
|
|
222
|
-
this.hierClusterValues = { scale, min, max };
|
|
223
|
-
}
|
|
224
|
-
getValueColor(value) {
|
|
225
|
-
const hc = this.settings.hierCluster;
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const zScoreCap = this.settings.hierCluster.zScoreCap;
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return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
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return this.hierClusterValues.scale(value / this.hierClusterValues.max);
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}
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}
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/* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
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request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
|
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|
-
|
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236
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use of this function is unfortunate because:
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237
|
-
the incomplete migration of {name} to {gene} for gene-based term
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geneset edit ui is hardcoded to return {name}
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existing plot states contain {name}
|
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|
-
|
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241
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!!! migration instruction !!!
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- term.name is for display only, if a term is gene-based, it has term.gene=str
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- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
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|
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*/
|
|
246
|
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getClusterRowTermsAsParameter() {
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const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
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lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
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return lst;
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}
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};
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for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
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for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
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}
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var hierClusterInit = getCompInit(HierCluster);
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var componentInit = hierClusterInit;
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export {
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HierCluster,
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hierClusterInit,
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componentInit
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};
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//# sourceMappingURL=chunk-DYVY7D67.js.map
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package/dist/chunk-G6WVVRDA.js
DELETED
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@@ -1,339 +0,0 @@
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1
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import {
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storeInit
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} from "./chunk-OSWTQVAX.js";
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import {
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summaryInit
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} from "./chunk-S6OIEQXG.js";
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import {
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navInit
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} from "./chunk-DNM2DKYE.js";
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import {
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AppBase,
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downloadSVGsAsPdf,
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filterRxCompInit,
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14
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newSandboxDiv,
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15
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sayerror,
|
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vocabInit
|
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} from "./chunk-UK3PTE3P.js";
|
|
18
|
-
import {
|
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-
importPlot
|
|
20
|
-
} from "./chunk-IFA3COXY.js";
|
|
21
|
-
import {
|
|
22
|
-
Menu
|
|
23
|
-
} from "./chunk-HYOEWQ5P.js";
|
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import {
|
|
25
|
-
AppApi,
|
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-
getCompInit,
|
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27
|
-
multiInit
|
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-
} from "./chunk-5V43Y2RC.js";
|
|
29
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import {
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-
select_default
|
|
31
|
-
} from "./chunk-I6Y4O3RR.js";
|
|
32
|
-
|
|
33
|
-
// mass/plot.js
|
|
34
|
-
var MassPlot = class _MassPlot {
|
|
35
|
-
static type = "plot";
|
|
36
|
-
constructor(opts) {
|
|
37
|
-
this.type = _MassPlot.type;
|
|
38
|
-
setRenderers(this);
|
|
39
|
-
this.initUi(opts);
|
|
40
|
-
}
|
|
41
|
-
reactsTo(action) {
|
|
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|
-
if (action.type.includes("cache_termq")) return true;
|
|
43
|
-
if (action.type.endsWith("_group")) return true;
|
|
44
|
-
if (action.type.startsWith("plot_")) {
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|
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|
-
return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
|
|
46
|
-
}
|
|
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|
-
if (action.type.startsWith("filter")) return true;
|
|
48
|
-
if (action.type.startsWith("cohort")) return true;
|
|
49
|
-
if (action.type == "app_refresh") return true;
|
|
50
|
-
if (action.type.endsWith("customTerm")) return true;
|
|
51
|
-
}
|
|
52
|
-
// !!! NOTE: This getState() method is reused by the plot-specific recover component.
|
|
53
|
-
// When logging something within getState, it may have been called by either the plot or recover instance
|
|
54
|
-
getState(appState) {
|
|
55
|
-
const config = appState.plots.find((p) => p.id === this.id);
|
|
56
|
-
if (!config) {
|
|
57
|
-
throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
|
|
58
|
-
}
|
|
59
|
-
return {
|
|
60
|
-
termfilter: appState.termfilter,
|
|
61
|
-
config,
|
|
62
|
-
groups: appState.groups,
|
|
63
|
-
// quick fix to skip history tracking as needed
|
|
64
|
-
_scope_: appState._scope_
|
|
65
|
-
};
|
|
66
|
-
}
|
|
67
|
-
async main() {
|
|
68
|
-
this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
|
|
69
|
-
if (!this.components) await this.setComponents(this.opts);
|
|
70
|
-
}
|
|
71
|
-
async setComponents(opts) {
|
|
72
|
-
const _ = await importPlot(opts.chartType);
|
|
73
|
-
const promises = {
|
|
74
|
-
// recover: recoverInit({
|
|
75
|
-
// app: this.app,
|
|
76
|
-
// holder: this.dom.localRecoverDiv,
|
|
77
|
-
// getState: appState => this.getState(appState),
|
|
78
|
-
// reactsTo: action =>
|
|
79
|
-
// action.id == this.id &&
|
|
80
|
-
// (action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
|
|
81
|
-
// action._track_ != 'none',
|
|
82
|
-
// plot_id: this.id,
|
|
83
|
-
// maxHistoryLen: 10,
|
|
84
|
-
// hideLabel: true
|
|
85
|
-
// }),
|
|
86
|
-
chart: _.componentInit({
|
|
87
|
-
app: this.app,
|
|
88
|
-
holder: this.dom.viz,
|
|
89
|
-
header: this.dom.paneTitleDiv,
|
|
90
|
-
id: this.id,
|
|
91
|
-
plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
|
|
92
|
-
/******* reason for passing plotDiv to chart ********
|
|
93
|
-
- this plot instance may allow to launch a new plot as a persistent sandbox
|
|
94
|
-
inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
|
|
95
|
-
the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
|
|
96
|
-
thus the need to directly access plotDiv
|
|
97
|
-
- example: mds3 tk from genome browser can launch disco etc
|
|
98
|
-
- having access to plotDiv may offer flexibility for the plot to do stuff
|
|
99
|
-
|
|
100
|
-
since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
|
|
101
|
-
this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
|
|
102
|
-
*/
|
|
103
|
-
getFilterImage: async () => this.components.filter.getFilterImage()
|
|
104
|
-
})
|
|
105
|
-
};
|
|
106
|
-
if (!this.state.config.hidePlotFilter)
|
|
107
|
-
promises.filter = filterRxCompInit({
|
|
108
|
-
app: this.app,
|
|
109
|
-
vocabApi: this.app.vocabApi,
|
|
110
|
-
parentId: this.id,
|
|
111
|
-
holder: this.dom.filterDiv,
|
|
112
|
-
hideLabel: true,
|
|
113
|
-
emptyLabel: "+Add new filter",
|
|
114
|
-
callback: (filter) => {
|
|
115
|
-
this.app.dispatch({
|
|
116
|
-
id: this.id,
|
|
117
|
-
type: "plot_edit",
|
|
118
|
-
config: { filter }
|
|
119
|
-
});
|
|
120
|
-
}
|
|
121
|
-
});
|
|
122
|
-
this.components = await multiInit(promises);
|
|
123
|
-
}
|
|
124
|
-
destroy() {
|
|
125
|
-
this.dom.holder.app_div.selectAll("*").remove();
|
|
126
|
-
this.dom.holder.app_div.remove();
|
|
127
|
-
for (const key in this.dom) {
|
|
128
|
-
delete this.dom[key];
|
|
129
|
-
}
|
|
130
|
-
}
|
|
131
|
-
};
|
|
132
|
-
var plotInit = getCompInit(MassPlot);
|
|
133
|
-
function setRenderers(self) {
|
|
134
|
-
self.initUi = function(opts) {
|
|
135
|
-
const holder = opts.holder;
|
|
136
|
-
opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
|
|
137
|
-
holder.header.style("padding", 0);
|
|
138
|
-
try {
|
|
139
|
-
self.dom = {
|
|
140
|
-
tip: new Menu({ padding: "0px" }),
|
|
141
|
-
holder,
|
|
142
|
-
paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
|
|
143
|
-
localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
|
|
144
|
-
filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
|
|
145
|
-
body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
|
|
146
|
-
// will hold no data notice or the page title in multichart views
|
|
147
|
-
errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
|
|
148
|
-
// dom.viz will hold the rendered view
|
|
149
|
-
viz: holder.body.append("div")
|
|
150
|
-
};
|
|
151
|
-
} catch (e) {
|
|
152
|
-
self.dom.errdiv.style("display", "none").text(e);
|
|
153
|
-
}
|
|
154
|
-
};
|
|
155
|
-
}
|
|
156
|
-
|
|
157
|
-
// mass/app.ts
|
|
158
|
-
var MassApp = class extends AppBase {
|
|
159
|
-
// expected class-specific props
|
|
160
|
-
constructor(opts, api) {
|
|
161
|
-
super(opts);
|
|
162
|
-
this.components = {};
|
|
163
|
-
this.wasDestroyed = false;
|
|
164
|
-
this.api = api;
|
|
165
|
-
if (opts.addLoginCallback) {
|
|
166
|
-
opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
|
|
167
|
-
}
|
|
168
|
-
this.type = "app";
|
|
169
|
-
this.dom = {
|
|
170
|
-
holder: opts.holder,
|
|
171
|
-
// do not modify holder style
|
|
172
|
-
topbar: opts.holder.append("div"),
|
|
173
|
-
errdiv: opts.holder.append("div"),
|
|
174
|
-
plotDiv: opts.holder.append("div")
|
|
175
|
-
};
|
|
176
|
-
this.plotIdToSandboxId = {};
|
|
177
|
-
}
|
|
178
|
-
static {
|
|
179
|
-
this.type = "app";
|
|
180
|
-
}
|
|
181
|
-
async preApiFreeze(api) {
|
|
182
|
-
try {
|
|
183
|
-
api.tip = new Menu({ padding: "5px" });
|
|
184
|
-
api.tip.d.on("keyup", (event) => {
|
|
185
|
-
if (event.key == "Escape") api.tip.hide();
|
|
186
|
-
});
|
|
187
|
-
api.printError = (e) => this.printError(e);
|
|
188
|
-
api.vocabApi = await vocabInit({
|
|
189
|
-
app: api,
|
|
190
|
-
state: { vocab: this.opts.state.vocab },
|
|
191
|
-
fetchOpts: this.opts.fetchOpts,
|
|
192
|
-
getDatasetAccessToken: this.opts.getDatasetAccessToken
|
|
193
|
-
});
|
|
194
|
-
api.hasWebGL = function() {
|
|
195
|
-
try {
|
|
196
|
-
const canvas = document.createElement("canvas");
|
|
197
|
-
return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
|
|
198
|
-
} catch (_) {
|
|
199
|
-
return false;
|
|
200
|
-
}
|
|
201
|
-
};
|
|
202
|
-
this.opts.state.vocab = api.vocabApi.vocab;
|
|
203
|
-
} catch (e) {
|
|
204
|
-
console.log(`preApiFreeze error`, e);
|
|
205
|
-
throw e;
|
|
206
|
-
}
|
|
207
|
-
}
|
|
208
|
-
async init() {
|
|
209
|
-
try {
|
|
210
|
-
const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
|
|
211
|
-
const embeddedSessionState = this.opts.embeddedSessionState;
|
|
212
|
-
if (embeddedSessionState) {
|
|
213
|
-
Object.assign(this.opts.state, embeddedSessionState);
|
|
214
|
-
}
|
|
215
|
-
this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
|
|
216
|
-
this.state = await this.store.copyState();
|
|
217
|
-
this.components = {};
|
|
218
|
-
if (this.state.nav.header_mode != "hidden") {
|
|
219
|
-
this.components.nav = await navInit({
|
|
220
|
-
app: this.api,
|
|
221
|
-
holder: this.dom.topbar,
|
|
222
|
-
header_mode: this.state && this.state.nav && this.state.nav.header_mode,
|
|
223
|
-
vocab: this.state.vocab,
|
|
224
|
-
massSessionDuration: this.state.termdbConfig.massSessionDuration,
|
|
225
|
-
// this.opts.massSessionDuration
|
|
226
|
-
pkgver: this.opts.pkgver,
|
|
227
|
-
downloadPlots: () => {
|
|
228
|
-
this.downloadPlots();
|
|
229
|
-
}
|
|
230
|
-
});
|
|
231
|
-
}
|
|
232
|
-
this.components.plots = {};
|
|
233
|
-
if (this.opts.app?.doNotAwaitInitRender) {
|
|
234
|
-
this.api.dispatch();
|
|
235
|
-
} else {
|
|
236
|
-
await this.api.dispatch();
|
|
237
|
-
}
|
|
238
|
-
} catch (e) {
|
|
239
|
-
this.printError(e);
|
|
240
|
-
throw e;
|
|
241
|
-
}
|
|
242
|
-
}
|
|
243
|
-
async main() {
|
|
244
|
-
await this.api.vocabApi.main();
|
|
245
|
-
this.dom.plotDiv?.style(
|
|
246
|
-
"display",
|
|
247
|
-
this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
|
|
248
|
-
);
|
|
249
|
-
const newPlots = {};
|
|
250
|
-
let sandbox;
|
|
251
|
-
for (const plot of this.state.plots) {
|
|
252
|
-
if (plot.parentId) continue;
|
|
253
|
-
if (this.components.plots && !(plot.id in this.components.plots)) {
|
|
254
|
-
sandbox = newSandboxDiv(this.dom.plotDiv, {
|
|
255
|
-
close: () => {
|
|
256
|
-
this.api.dispatch({
|
|
257
|
-
type: "plot_delete",
|
|
258
|
-
id: plot.id
|
|
259
|
-
});
|
|
260
|
-
},
|
|
261
|
-
plotId: plot.id,
|
|
262
|
-
beforePlotId: plot.insertBefore || null,
|
|
263
|
-
style: {
|
|
264
|
-
width: "98.5%"
|
|
265
|
-
}
|
|
266
|
-
});
|
|
267
|
-
if (plot.chartType == "summary")
|
|
268
|
-
newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
|
|
269
|
-
else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
|
|
270
|
-
}
|
|
271
|
-
}
|
|
272
|
-
const numNewPlots = Object.keys(newPlots).length;
|
|
273
|
-
if (numNewPlots) {
|
|
274
|
-
await Promise.all(Object.values(newPlots));
|
|
275
|
-
for (const plotId in newPlots) {
|
|
276
|
-
this.components.plots[plotId] = await newPlots[plotId];
|
|
277
|
-
}
|
|
278
|
-
}
|
|
279
|
-
for (const plotId in this.components.plots) {
|
|
280
|
-
if (!this.state.plots.find((p) => p.id === plotId)) {
|
|
281
|
-
this.components.plots[plotId].destroy();
|
|
282
|
-
delete this.components.plots[plotId];
|
|
283
|
-
}
|
|
284
|
-
}
|
|
285
|
-
}
|
|
286
|
-
printError(e) {
|
|
287
|
-
const errdiv = e.errdiv || this.dom.errdiv;
|
|
288
|
-
if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
|
|
289
|
-
sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
|
|
290
|
-
if (e.stack) console.log(e.stack);
|
|
291
|
-
this.bus.emit("error");
|
|
292
|
-
if (this.opts?.debug) {
|
|
293
|
-
console.groupCollapsed("Stack trace from MassApp.printError() call.");
|
|
294
|
-
console.trace();
|
|
295
|
-
console.groupEnd();
|
|
296
|
-
}
|
|
297
|
-
}
|
|
298
|
-
skipPrevActionAbort(action) {
|
|
299
|
-
if (!action) return false;
|
|
300
|
-
if (action.type.startsWith("filter")) return false;
|
|
301
|
-
if (action.type.startsWith("cohort")) return false;
|
|
302
|
-
if (action.type == "app_refresh") {
|
|
303
|
-
if (action.subactions) {
|
|
304
|
-
return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
|
|
305
|
-
}
|
|
306
|
-
}
|
|
307
|
-
return true;
|
|
308
|
-
}
|
|
309
|
-
async downloadPlots() {
|
|
310
|
-
const chartImagesAll = [];
|
|
311
|
-
let i = 1;
|
|
312
|
-
const values = Object.values(this.components.plots);
|
|
313
|
-
for (const plot of values) {
|
|
314
|
-
const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
|
|
315
|
-
const chartImages = chart.getChartImages ? chart.getChartImages() : null;
|
|
316
|
-
if (!chartImages) {
|
|
317
|
-
console.log(`The ${chart.type} does not support downloading images yet`);
|
|
318
|
-
continue;
|
|
319
|
-
}
|
|
320
|
-
for (const chartImage of chartImages) {
|
|
321
|
-
if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
|
|
322
|
-
chartImagesAll.push(chartImage);
|
|
323
|
-
}
|
|
324
|
-
i++;
|
|
325
|
-
}
|
|
326
|
-
if (chartImagesAll.length > 0) {
|
|
327
|
-
const filters = [];
|
|
328
|
-
const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
|
|
329
|
-
if (globalFilterImg) filters.push(globalFilterImg);
|
|
330
|
-
downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
|
|
331
|
-
} else alert("No chart images available for download");
|
|
332
|
-
}
|
|
333
|
-
};
|
|
334
|
-
var appInit = AppApi.getInitFxn(MassApp);
|
|
335
|
-
|
|
336
|
-
export {
|
|
337
|
-
appInit
|
|
338
|
-
};
|
|
339
|
-
//# sourceMappingURL=chunk-G6WVVRDA.js.map
|