@sjcrh/proteinpaint-client 2.190.2 → 2.191.0

package/dist/WsiSamplesPlot-Z5C3NPF7.js

@@ -1,165 +0,0 @@
-import {
-  renderTable
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import {
-  dofetch3
-} from "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/wsisamples/defaults.ts
-function wsiSamplesDefaults(overrides = {}) {
-  const defaults = {
-    selectedSampleIndex: -1
-  };
-  return copyMerge(defaults, overrides);
-}
-
-// plots/wsisamples/WsiSamplesPlot.ts
-var WSISamplesPlot = class _WSISamplesPlot {
-  static {
-    this.type = "WSISamplesPlot";
-  }
-  constructor(opts) {
-    this.type = _WSISamplesPlot.type;
-    this.opts = opts;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      dslabel: appState.vocab.dslabel,
-      genome: appState.vocab.genome
-    };
-  }
-  async init() {
-    const state = this.app.getState();
-    const plotConfig = state.plots.find((p) => p.id === this.id);
-    const settings = plotConfig.settings;
-    const selectedRows = [];
-    const selectedSampleIndex = settings.selectedSampleIndex;
-    if (selectedSampleIndex != -1) selectedRows.push(selectedSampleIndex);
-    const holder = this.opts.holder;
-    const contentDiv = holder.append("div").attr("class", "wsi-samples-content");
-    const columns = [
-      {
-        label: "Sample"
-      }
-    ];
-    const rows = [];
-    const wsiImages = plotConfig.wsimages;
-    wsiImages.forEach((wsiImage) => {
-      const row = [];
-      const tableCell = {
-        value: wsiImage.sampleId
-      };
-      row.push(tableCell);
-      rows.push(row);
-    });
-    renderTable({
-      rows,
-      columns,
-      resize: true,
-      singleMode: true,
-      div: contentDiv,
-      maxHeight: "50vh",
-      selectedRows,
-      noButtonCallback: (index) => {
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config: {
-            settings: {
-              selectedSampleIndex: index
-            }
-          }
-        });
-      },
-      striped: true,
-      header: { style: { "text-transform": "capitalize" } }
-    });
-  }
-  async main() {
-    const state = this.app.getState();
-    const plotConfig = state.plots.find((p) => p.id === this.id);
-    const settings = plotConfig.settings;
-    const selectedSampleIndex = settings.selectedSampleIndex;
-    const contentDiv = this.opts.holder.select(".wsi-samples-content");
-    const wsiImages = plotConfig.wsimages;
-    if (selectedSampleIndex != -1) {
-      const existingViewer = contentDiv.select(".wsi-viewer");
-      if (!existingViewer.empty()) {
-        existingViewer.remove();
-      }
-      const viewerDiv = contentDiv.append("div").attr("class", "wsi-viewer").style("width", "100%");
-      const wsiViewer = await import("./plot.wsi-UKTLZSYW.js");
-      wsiViewer.default(
-        this.app.opts.state.vocab.dslabel,
-        viewerDiv,
-        this.app.opts.genome,
-        wsiImages[selectedSampleIndex].sampleId
-      );
-    }
-  }
-};
-var wsiSamplesPlot = getCompInit(WSISamplesPlot);
-var componentInit = wsiSamplesPlot;
-async function getPlotConfig(opts, app) {
-  return {
-    chartType: "WSISamplesPlot",
-    subfolder: "wsisamples",
-    extension: "ts",
-    wsimages: await getWSISamples(app),
-    settings: wsiSamplesDefaults(opts.overrides),
-    hidePlotFilter: true
-  };
-}
-async function getWSISamples(app) {
-  const data = await dofetch3("wsisamples", {
-    body: {
-      genome: app.opts.state.vocab.genome,
-      dslabel: app.opts.state.vocab.dslabel
-    }
-  });
-  return data.samples;
-}
-export {
-  componentInit,
-  WSISamplesPlot as default,
-  getPlotConfig,
-  wsiSamplesPlot
-};
-//# sourceMappingURL=WsiSamplesPlot-Z5C3NPF7.js.map

package/dist/adSandbox-KQKENDNQ.js

@@ -1,38 +0,0 @@
-import {
-  openSandbox
-} from "./chunk-IOQV2VX3.js";
-import "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  openSandbox
-};
-//# sourceMappingURL=adSandbox-KQKENDNQ.js.map

package/dist/alphaGenome-PN2SEPCK.js

@@ -1,175 +0,0 @@
-import {
-  PlotBase,
-  controlsInit
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import {
-  dofetch3
-} from "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/alphaGenome.js
-var AlphaGenome = class _AlphaGenome extends PlotBase {
-  static type = "alphaGenome";
-  constructor(opts) {
-    super(opts);
-    this.type = _AlphaGenome.type;
-    this.dom = {
-      holder: opts.holder,
-      controlsDiv: opts.holder.append("div").style("display", "inline-block"),
-      plotDiv: opts.holder.append("div").style("display", "inline-block")
-    };
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config
-    };
-  }
-  async init(appState) {
-    const body = {
-      dslabel: this.app.vocabApi.vocab.dslabel
-    };
-    this.opts.header.text("Alpha Genome Variant Predictor");
-    const { ontologyTerms, outputTypes, intervals } = await dofetch3("AlphaGenomeTypes", { body });
-    this.setControls({ ontologyTerms, outputTypes, intervals });
-  }
-  async setControls({ ontologyTerms, outputTypes, intervals }) {
-    const inputs = [
-      {
-        label: "Chromosome",
-        type: "text",
-        chartType: this.type,
-        settingsKey: "chromosome",
-        title: "Genomic chromosome of the variant"
-      },
-      {
-        label: "Position",
-        type: "number",
-        chartType: this.type,
-        settingsKey: "position",
-        title: "Genomic position of the variant"
-      },
-      {
-        label: "Reference Bases",
-        type: "text",
-        chartType: this.type,
-        settingsKey: "reference",
-        title: "Reference base of the variant"
-      },
-      {
-        label: "Alternate Bases",
-        type: "text",
-        chartType: this.type,
-        settingsKey: "alternate",
-        title: "Alternate base of the variant"
-      },
-      {
-        label: "Ontology term",
-        type: "dropdown",
-        options: ontologyTerms,
-        title: "Ontology term",
-        chartType: this.type,
-        settingsKey: "ontologyTerm"
-      },
-      {
-        label: "Output type",
-        type: "dropdown",
-        options: outputTypes,
-        title: "Output type",
-        chartType: this.type,
-        settingsKey: "outputType"
-      },
-      {
-        label: "Interval",
-        type: "dropdown",
-        options: intervals,
-        title: "Interval",
-        chartType: this.type,
-        settingsKey: "interval"
-      }
-    ];
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsDiv,
-        inputs
-      })
-    };
-  }
-  async main() {
-    const settings = this.state.config.settings[this.type];
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      chromosome: settings.chromosome,
-      position: settings.position,
-      reference: settings.reference,
-      alternate: settings.alternate,
-      ontologyTerms: [settings.ontologyTerm],
-      outputType: settings.outputType,
-      interval: Number(settings.interval)
-    };
-    const data = await dofetch3("alphaGenome", { body });
-    if (data.error) throw data.error;
-    this.dom.plotDiv.selectAll("*").remove();
-    this.dom.plotDiv.append("img").attr("width", "1250px").attr("src", data.plotImage);
-  }
-};
-function getPlotConfig(opts, app) {
-  const alphaGenome = app.vocabApi.termdbConfig.alphaGenome = app.vocabApi.termdbConfig.queries.alphaGenome;
-  const config = {
-    hidePlotFilter: true,
-    settings: {
-      alphaGenome: {
-        controls: { isOpen: false },
-        ...alphaGenome.default,
-        interval: 16384
-      }
-    }
-  };
-  copyMerge(config, opts);
-  return config;
-}
-var alphaGenomeInit = getCompInit(AlphaGenome);
-var componentInit = alphaGenomeInit;
-export {
-  alphaGenomeInit,
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=alphaGenome-PN2SEPCK.js.map

package/dist/alphaGenome-PN2SEPCK.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/alphaGenome.js"],
-  "sourcesContent": ["import { PlotBase } from './PlotBase'\nimport { getCompInit, copyMerge } from '#rx'\nimport { dofetch3 } from '#common/dofetch'\nimport { controlsInit } from './controls'\nimport { interval } from 'd3'\n\nclass AlphaGenome extends PlotBase {\n\tstatic type = 'alphaGenome'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = AlphaGenome.type\n\t\tthis.dom = {\n\t\t\tholder: opts.holder,\n\t\t\tcontrolsDiv: opts.holder.append('div').style('display', 'inline-block'),\n\t\t\tplotDiv: opts.holder.append('div').style('display', 'inline-block')\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tconst body = {\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel\n\t\t}\n\t\tthis.opts.header.text('Alpha Genome Variant Predictor')\n\t\tconst { ontologyTerms, outputTypes, intervals } = await dofetch3('AlphaGenomeTypes', { body })\n\n\t\tthis.setControls({ ontologyTerms, outputTypes, intervals })\n\t}\n\n\tasync setControls({ ontologyTerms, outputTypes, intervals }) {\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Chromosome',\n\t\t\t\ttype: 'text',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'chromosome',\n\t\t\t\ttitle: 'Genomic chromosome of the variant'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Position',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'position',\n\t\t\t\ttitle: 'Genomic position of the variant'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Reference Bases',\n\t\t\t\ttype: 'text',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'reference',\n\t\t\t\ttitle: 'Reference base of the variant'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Alternate Bases',\n\t\t\t\ttype: 'text',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'alternate',\n\t\t\t\ttitle: 'Alternate base of the variant'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Ontology term',\n\t\t\t\ttype: 'dropdown',\n\t\t\t\toptions: ontologyTerms,\n\t\t\t\ttitle: 'Ontology term',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'ontologyTerm'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Output type',\n\t\t\t\ttype: 'dropdown',\n\t\t\t\toptions: outputTypes,\n\t\t\t\ttitle: 'Output type',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'outputType'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Interval',\n\t\t\t\ttype: 'dropdown',\n\t\t\t\toptions: intervals,\n\t\t\t\ttitle: 'Interval',\n\t\t\t\tchartType: this.type,\n\t\t\t\tsettingsKey: 'interval'\n\t\t\t}\n\t\t]\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv,\n\t\t\t\tinputs\n\t\t\t})\n\t\t}\n\t}\n\n\tasync main() {\n\t\tconst settings = this.state.config.settings[this.type]\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tchromosome: settings.chromosome,\n\t\t\tposition: settings.position,\n\t\t\treference: settings.reference,\n\t\t\talternate: settings.alternate,\n\t\t\tontologyTerms: [settings.ontologyTerm],\n\t\t\toutputType: settings.outputType,\n\t\t\tinterval: Number(settings.interval)\n\t\t}\n\t\tconst data = await dofetch3('alphaGenome', { body })\n\t\tif (data.error) throw data.error\n\t\tthis.dom.plotDiv.selectAll('*').remove()\n\t\tthis.dom.plotDiv.append('img').attr('width', '1250px').attr('src', data.plotImage)\n\t}\n}\n\nexport function getPlotConfig(opts, app) {\n\tconst alphaGenome = (app.vocabApi.termdbConfig.alphaGenome = app.vocabApi.termdbConfig.queries.alphaGenome)\n\tconst config = {\n\t\thidePlotFilter: true,\n\t\tsettings: {\n\t\t\talphaGenome: {\n\t\t\t\tcontrols: { isOpen: false },\n\t\t\t\t...alphaGenome.default,\n\t\t\t\tinterval: 16384\n\t\t\t}\n\t\t}\n\t}\n\tcopyMerge(config, opts)\n\n\treturn config\n}\n\nexport const alphaGenomeInit = getCompInit(AlphaGenome)\nexport const componentInit = alphaGenomeInit\n"],
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-  "names": []
-}

package/dist/app-4OEY56FN.js

@@ -1,49 +0,0 @@
-import {
-  appInit
-} from "./chunk-G6WVVRDA.js";
-import "./chunk-OSWTQVAX.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-S6OIEQXG.js";
-import "./chunk-XUFWJJM5.js";
-import "./chunk-WKMZ4ZQ3.js";
-import "./chunk-NPTHYZY4.js";
-import "./chunk-DNM2DKYE.js";
-import "./chunk-RRWP2LM4.js";
-import "./chunk-OHELNDGK.js";
-import "./chunk-NWAUBRGM.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  appInit
-};
-//# sourceMappingURL=app-4OEY56FN.js.map

package/dist/app-TGMYXJ4E.js

@@ -1,37 +0,0 @@
-import {
-  appInit
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  appInit
-};
-//# sourceMappingURL=app-TGMYXJ4E.js.map