@sjcrh/proteinpaint-client 2.195.0 → 2.196.0

package/dist/chunk-2XBWB6P2.js

@@ -1,37 +0,0 @@
-import {
-  addGeneSearchbox,
-  getGEunit
-} from "./chunk-LYULXXGR.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  TermTypes
-} from "./chunk-UAALI7MC.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol)
-    });
-  }
-  async selectGene(gene) {
-    const unit = getGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    if (!gene) throw new Error("No gene selected");
-    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-2XBWB6P2.js.map

package/dist/chunk-34VSTY2U.js

@@ -1,234 +0,0 @@
-import {
-  DownloadMenu,
-  ListSamples,
-  filterJoin,
-  getFilterItemByTag,
-  renderTable
-} from "./chunk-LYULXXGR.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-UAALI7MC.js";
-import {
-  niceNumLabels
-} from "./chunk-BKPDYW5T.js";
-
-// plots/violin.interactivity.js
-function setInteractivity(self) {
-  self.getChartImages = function() {
-    const charts = [];
-    for (const [key, chart] of Object.entries(self.data.charts)) {
-      const title = self.getChartTitle(chart.chartId);
-      const name = `${self.config.term.term.name}  ${title}`;
-      const chartDiv = chart.chartDiv;
-      charts.push({ name, svg: chartDiv.select("svg") });
-    }
-    return charts;
-  };
-  self.download = function(event) {
-    if (!self.state) return;
-    const name2svg = self.getChartImages();
-    const dm = new DownloadMenu(name2svg, self.config.term.term.name);
-    dm.show(event.clientX, event.clientY, event.target);
-  };
-  self.displayLabelClickMenu = function(t1, t2, plot, event) {
-    if (!t2) return;
-    if (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) return;
-    const label = t1.q.mode === "continuous" ? "term2" : "term";
-    const options = [];
-    if (this.app.getState().nav.header_mode !== "only_buttons")
-      options.push({
-        label: `Add filter: ${plot.label.split(",")[0]}`,
-        testid: "sjpp-violinLabOpt-addf",
-        callback: getAddFilterCallback(self, plot)
-      });
-    options.push({
-      label: `Hide: ${plot.label}`,
-      testid: "sjpp-violinLabOpt-hide",
-      callback: () => {
-        const term = self.config[label];
-        const isHidden = true;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            [label]: {
-              isAtomic: true,
-              term: term.term,
-              q: getUpdatedQfromClick(plot, term, isHidden)
-            }
-          }
-        });
-      }
-    });
-    if (self.state.displaySampleIds && self.state.hasVerifiedToken) {
-      options.push({
-        label: `List samples`,
-        testid: "sjpp-violinLabOpt-list",
-        callback: async () => {
-          const [start, end] = [self.data.min, self.data.max];
-          await self.callListSamples(event, plot, start, end);
-        }
-      });
-      if (self.opts.allow2selectSamples) {
-        const ss = self.opts.allow2selectSamples;
-        options.push({
-          label: ss.buttonText,
-          callback: async () => {
-            const [start, end] = [self.data.min, self.data.max];
-            await self.selectSamples(plot, start, end, ss);
-          }
-        });
-      }
-    }
-    self.displayMenu(event, options);
-  };
-  self.displayBrushMenu = function(t1, t2, self2, plot, event, scale, isH) {
-    const selection = event.selection;
-    const [start, end] = isH ? [scale.invert(selection[0]), scale.invert(selection[1])] : [scale.invert(selection[1]), scale.invert(selection[0])];
-    const options = [];
-    if (this.app.getState().nav.header_mode === "with_tabs")
-      options.push({
-        label: `Add filter`,
-        testid: "sjpp-violinBrushOpt-addf",
-        callback: getAddFilterCallback(self2, plot, start, end)
-      });
-    if (self2.state.displaySampleIds && self2.state.hasVerifiedToken) {
-      options.push({
-        label: `List samples`,
-        testid: "sjpp-violinBrushOpt-list",
-        callback: async () => self2.callListSamples(event.sourceEvent, plot, start, end)
-      });
-      if (self2.opts.allow2selectSamples) {
-        const ss = self2.opts.allow2selectSamples;
-        options.push({
-          label: ss.buttonText,
-          callback: async () => {
-            await self2.selectSamples(plot, start, end, ss);
-          }
-        });
-      }
-    }
-    self2.displayMenu(event.sourceEvent, options, start, end);
-  };
-  self.displayMenu = function(event, options, start, end) {
-    const tip = self.dom.clicktip.clear().show(event.clientX, event.clientY);
-    const isBrush = start != null && end != null;
-    if (isBrush) {
-      const [niceStart, niceEnd] = self.config.term.term.type == "integer" ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end]);
-      tip.d.append("div").style("margin", "10px").text(`From ${niceStart} to ${niceEnd}`);
-    }
-    tip.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", (d) => d.testid).text((d) => d.label).on("click", async (event2, d) => {
-      if (event2.target._clicked) return;
-      event2.target._clicked = true;
-      event2.target.textContent = "Loading...";
-      await d.callback();
-      tip.hide();
-    });
-  };
-  self.selectSamples = async function(plot, start, end, ss) {
-    const ls = self.getSampleList(plot, start, end);
-    const data = await ls.getData();
-    const table = ls.setTableData(data);
-    const samples = table[2];
-    ss.callback({
-      samples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),
-      source: ss.defaultSelectionLabel || `Selected from violin`
-    });
-  };
-  self.getSampleList = function(plot, start, end) {
-    const { term, term2, term0 } = self.config;
-    const bins = self.data.bins;
-    const rangeStart = start !== void 0 ? start : null;
-    const rangeStop = end !== void 0 ? end : null;
-    const ls = new ListSamples({
-      app: self.app,
-      termfilter: self.state.termfilter,
-      term,
-      term2,
-      term0,
-      plot,
-      bins,
-      start: rangeStart,
-      end: rangeStop
-    });
-    return ls;
-  };
-  self.callListSamples = async function(event, plot, start, end) {
-    const ls = self.getSampleList(plot, start, end);
-    const data = await ls.getData();
-    const [rows, columns] = ls.setTableData(data);
-    const tip = self.dom.sampletabletip;
-    tip.clear().show(event.clientX, event.clientY, false);
-    renderTable({
-      rows,
-      columns,
-      div: tip.d,
-      showLines: true,
-      maxHeight: "40vh",
-      resize: true,
-      dataTestId: "sjpp-listsampletable"
-    });
-  };
-  self.labelHideLegendClicking = function(t2, plot) {
-    self.dom.legendDiv.selectAll(".sjpp-htmlLegend").on("click", (event) => {
-      event.stopPropagation();
-      const d = event.target.__data__;
-      const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && self.config.term?.q.mode === "continuous" ? "term2" : "term";
-      const term = self.config[termNum];
-      if (t2) {
-        for (const key of Object.keys(term?.q?.hiddenValues)) {
-          if (d.text === key) {
-            delete term.q.hiddenValues[key];
-          }
-        }
-        const isHidden = false;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            [termNum]: {
-              isAtomic: true,
-              term: term.term,
-              q: getUpdatedQfromClick(plot, term, isHidden)
-            }
-          }
-        });
-      }
-    }).on("mouseover", (event) => {
-      const q = event.target.__data__;
-      if (q === void 0) return;
-      if (q.isHidden === true && q.isClickable === true) {
-        self.dom.hovertip.clear().show(event.clientX, event.clientY).d.append("span").text("Click to unhide plot");
-      }
-    }).on("mouseout", function() {
-      self.dom.hovertip.hide();
-    });
-  };
-}
-function getAddFilterCallback(self, plot, rangeStart, rangeStop) {
-  const ls = self.getSampleList(plot, rangeStart, rangeStop);
-  return () => {
-    const filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, "filterUiRoot");
-    const filter = filterJoin([filterUiRoot, ls.tvslst]);
-    filter.tag = "filterUiRoot";
-    self.app.dispatch({
-      type: "filter_replace",
-      filter
-    });
-  };
-}
-function getUpdatedQfromClick(plot, term, isHidden = false) {
-  const label = plot.label;
-  const valueId = term?.term?.values ? term?.term?.values?.[label]?.label : label;
-  const id = !valueId ? label : valueId;
-  const q = term.q;
-  if (!q.hiddenValues) q.hiddenValues = {};
-  if (isHidden) q.hiddenValues[id] = 1;
-  else delete q.hiddenValues[id];
-  return q;
-}
-
-export {
-  setInteractivity
-};
-//# sourceMappingURL=chunk-34VSTY2U.js.map

package/dist/chunk-34VSTY2U.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/violin.interactivity.js"],
-  "sourcesContent": ["import { filterJoin, getFilterItemByTag } from '#filter'\nimport { DownloadMenu, niceNumLabels, ListSamples, renderTable } from '#dom'\nimport { SINGLECELL_GENE_EXPRESSION } from '#shared/terms.js'\n\nexport function setInteractivity(self) {\n\tself.getChartImages = function () {\n\t\tconst charts = []\n\n\t\tfor (const [key, chart] of Object.entries(self.data.charts)) {\n\t\t\tconst title = self.getChartTitle(chart.chartId)\n\t\t\tconst name = `${self.config.term.term.name}  ${title}`\n\t\t\tconst chartDiv = chart.chartDiv\n\t\t\tcharts.push({ name, svg: chartDiv.select('svg') })\n\t\t}\n\t\treturn charts\n\t}\n\n\tself.download = function (event) {\n\t\tif (!self.state) return\n\t\tconst name2svg = self.getChartImages()\n\t\tconst dm = new DownloadMenu(name2svg, self.config.term.term.name)\n\t\tdm.show(event.clientX, event.clientY, event.target)\n\t}\n\n\tself.displayLabelClickMenu = function (t1, t2, plot, event) {\n\t\tif (!t2) return // when no term 2 do not show options on the sole violin label\n\t\tif (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) return // is sc gene exp data, none of the options below work, thus disable\n\n\t\tconst label = t1.q.mode === 'continuous' ? 'term2' : 'term'\n\t\tconst options = []\n\t\tif (this.app.getState().nav.header_mode !== 'only_buttons')\n\t\t\toptions.push({\n\t\t\t\tlabel: `Add filter: ${plot.label.split(',')[0]}`,\n\t\t\t\ttestid: 'sjpp-violinLabOpt-addf',\n\t\t\t\tcallback: getAddFilterCallback(self, plot)\n\t\t\t})\n\n\t\toptions.push({\n\t\t\tlabel: `Hide: ${plot.label}`,\n\t\t\ttestid: 'sjpp-violinLabOpt-hide',\n\t\t\tcallback: () => {\n\t\t\t\tconst term = self.config[label]\n\n\t\t\t\tconst isHidden = true\n\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\t[label]: {\n\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tq: getUpdatedQfromClick(plot, term, isHidden)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\tif (self.state.displaySampleIds && self.state.hasVerifiedToken) {\n\t\t\toptions.push({\n\t\t\t\tlabel: `List samples`,\n\t\t\t\ttestid: 'sjpp-violinLabOpt-list',\n\t\t\t\tcallback: async () => {\n\t\t\t\t\t/** self.data.max * 2 appears to be a workaround for a\n\t\t\t\t\t * previous bug in the list samples logic. Since that logic\n\t\t\t\t\t * has been refined, this appears to be no longer necessary.\n\t\t\t\t\t * Commenting out for now, but leaving in place in case.*/\n\t\t\t\t\t// const [start, end] = [self.data.min, self.data.max * 2]\n\t\t\t\t\tconst [start, end] = [self.data.min, self.data.max]\n\t\t\t\t\tawait self.callListSamples(event, plot, start, end)\n\t\t\t\t}\n\t\t\t})\n\n\t\t\tif (self.opts.allow2selectSamples) {\n\t\t\t\tconst ss = self.opts.allow2selectSamples\n\t\t\t\toptions.push({\n\t\t\t\t\tlabel: ss.buttonText,\n\t\t\t\t\tcallback: async () => {\n\t\t\t\t\t\tconst [start, end] = [self.data.min, self.data.max]\n\t\t\t\t\t\tawait self.selectSamples(plot, start, end, ss)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tself.displayMenu(event, options)\n\t}\n\n\tself.displayBrushMenu = function (t1, t2, self, plot, event, scale, isH) {\n\t\tconst selection = event.selection\n\t\tconst [start, end] = isH\n\t\t\t? [scale.invert(selection[0]), scale.invert(selection[1])]\n\t\t\t: [scale.invert(selection[1]), scale.invert(selection[0])]\n\n\t\tconst options = []\n\n\t\tif (this.app.getState().nav.header_mode === 'with_tabs')\n\t\t\toptions.push({\n\t\t\t\tlabel: `Add filter`,\n\t\t\t\ttestid: 'sjpp-violinBrushOpt-addf',\n\t\t\t\tcallback: getAddFilterCallback(self, plot, start, end)\n\t\t\t})\n\n\t\tif (self.state.displaySampleIds && self.state.hasVerifiedToken) {\n\t\t\toptions.push({\n\t\t\t\tlabel: `List samples`,\n\t\t\t\ttestid: 'sjpp-violinBrushOpt-list',\n\t\t\t\tcallback: async () => self.callListSamples(event.sourceEvent, plot, start, end)\n\t\t\t})\n\n\t\t\tif (self.opts.allow2selectSamples) {\n\t\t\t\tconst ss = self.opts.allow2selectSamples\n\t\t\t\toptions.push({\n\t\t\t\t\tlabel: ss.buttonText,\n\t\t\t\t\tcallback: async () => {\n\t\t\t\t\t\tawait self.selectSamples(plot, start, end, ss)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tself.displayMenu(event.sourceEvent, options, start, end)\n\t}\n\n\tself.displayMenu = function (event, options, start, end) {\n\t\tconst tip = self.dom.clicktip.clear().show(event.clientX, event.clientY)\n\n\t\tconst isBrush = start != null && end != null\n\n\t\tif (isBrush) {\n\t\t\tconst [niceStart, niceEnd] =\n\t\t\t\tself.config.term.term.type == 'integer' ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end])\n\n\t\t\ttip.d.append('div').style('margin', '10px').text(`From ${niceStart} to ${niceEnd}`)\n\t\t}\n\t\t//show menu options for label clicking and brush selection\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.selectAll('div')\n\t\t\t.data(options)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.attr('data-testid', d => d.testid)\n\t\t\t.text(d => d.label)\n\t\t\t.on('click', async (event, d) => {\n\t\t\t\tif (event.target._clicked) return\n\t\t\t\tevent.target._clicked = true\n\t\t\t\tevent.target.textContent = 'Loading...'\n\t\t\t\tawait d.callback()\n\t\t\t\ttip.hide()\n\t\t\t})\n\t}\n\n\tself.selectSamples = async function (plot, start, end, ss) {\n\t\tconst ls = self.getSampleList(plot, start, end)\n\t\tconst data = await ls.getData()\n\t\tconst table = ls.setTableData(data)\n\t\tconst samples = table[2]\n\t\tss.callback({\n\t\t\tsamples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),\n\t\t\tsource: ss.defaultSelectionLabel || `Selected from violin`\n\t\t})\n\t}\n\n\t//get sample list for menu option callbacks\n\tself.getSampleList = function (plot, start, end) {\n\t\tconst { term, term2, term0 } = self.config\n\t\tconst bins = self.data.bins\n\t\tconst rangeStart = start !== undefined ? start : null\n\t\tconst rangeStop = end !== undefined ? end : null\n\n\t\tconst ls = new ListSamples({\n\t\t\tapp: self.app,\n\t\t\ttermfilter: self.state.termfilter,\n\t\t\tterm,\n\t\t\tterm2,\n\t\t\tterm0,\n\t\t\tplot,\n\t\t\tbins,\n\t\t\tstart: rangeStart,\n\t\t\tend: rangeStop\n\t\t})\n\t\treturn ls\n\t}\n\n\tself.callListSamples = async function (event, plot, start, end) {\n\t\tconst ls = self.getSampleList(plot, start, end)\n\t\tconst data = await ls.getData()\n\t\tconst [rows, columns] = ls.setTableData(data)\n\n\t\tconst tip = self.dom.sampletabletip\n\t\ttip.clear().show(event.clientX, event.clientY, false)\n\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: tip.d,\n\t\t\tshowLines: true,\n\t\t\tmaxHeight: '40vh',\n\t\t\tresize: true,\n\t\t\tdataTestId: 'sjpp-listsampletable'\n\t\t})\n\t}\n\n\tself.labelHideLegendClicking = function (t2, plot) {\n\t\t// whoever wrote this tangled mess needs to be fired\n\t\tself.dom.legendDiv\n\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t.on('click', event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tconst d = event.target.__data__\n\t\t\t\tconst termNum =\n\t\t\t\t\tt2?.term.type === 'condition' ||\n\t\t\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && self.config.term?.q.mode === 'continuous')\n\t\t\t\t\t\t? 'term2'\n\t\t\t\t\t\t: 'term'\n\t\t\t\tconst term = self.config[termNum]\n\t\t\t\tif (t2) {\n\t\t\t\t\tfor (const key of Object.keys(term?.q?.hiddenValues)) {\n\t\t\t\t\t\tif (d.text === key) {\n\t\t\t\t\t\t\tdelete term.q.hiddenValues[key]\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tconst isHidden = false\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t[termNum]: {\n\t\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\t\tq: getUpdatedQfromClick(plot, term, isHidden)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseover', event => {\n\t\t\t\tconst q = event.target.__data__\n\t\t\t\tif (q === undefined) return\n\t\t\t\tif (q.isHidden === true && q.isClickable === true) {\n\t\t\t\t\tself.dom.hovertip.clear().show(event.clientX, event.clientY).d.append('span').text('Click to unhide plot')\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseout', function () {\n\t\t\t\tself.dom.hovertip.hide()\n\t\t\t})\n\t}\n}\n\nfunction getAddFilterCallback(self, plot, rangeStart, rangeStop) {\n\tconst ls = self.getSampleList(plot, rangeStart, rangeStop)\n\n\treturn () => {\n\t\tconst filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, 'filterUiRoot')\n\t\tconst filter = filterJoin([filterUiRoot, ls.tvslst])\n\t\tfilter.tag = 'filterUiRoot'\n\t\tself.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter\n\t\t})\n\t}\n}\n\nfunction getUpdatedQfromClick(plot, term, isHidden = false) {\n\tconst label = plot.label\n\tconst valueId = term?.term?.values ? term?.term?.values?.[label]?.label : label\n\tconst id = !valueId ? label : valueId\n\tconst q = term.q\n\tif (!q.hiddenValues) q.hiddenValues = {}\n\tif (isHidden) q.hiddenValues[id] = 1\n\telse delete q.hiddenValues[id]\n\treturn q\n}\n"],
-  "mappings": 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