@sjcrh/proteinpaint-client 2.212.0 → 2.213.0

package/dist/chunk-2KM4PRQM.js

@@ -1,117 +0,0 @@
-import {
-  copyMerge,
-  getInitFxn
-} from "./chunk-WINIL2KN.js";
-
-// termdb/termInfo.js
-var defaultState = { isVisible: false, term: null };
-var TdbTermInfo = class {
-  /*
-  		Will display background information about a term, 
-  		such as rubric, publication source, description, etc
-  
-  		opts{}
-  			.content_holder: required d3-wrapped DOM element
-  				****TODO: Create menu on the fly if content_holder is not supplied****
-  			
-  			.icon_holder: optional, creates information icon for terms
-  			
-  			.vocabApi: 
-  				- for termInfoInit(), required as opts.vocabApi
-  				- for termInfoComp(), required as part of opts.app
-  				- a vocabulary API that has a getTermInfo() method
-  			
-  			.state{} optional, see defaultState value above
-  				.isVisible: boolean, optional
-  				.term: {id, ...} optional (may be supplied with either getState() or main({state}))
-  	*/
-  constructor(opts) {
-    this.vocabApi = opts.vocabApi || opts.app && opts.app.vocabApi;
-    this.state = Object.assign({}, defaultState, opts.state ? opts.state : {});
-    this.api = this;
-    setInteractivity(this);
-    setRenderers(this);
-    this.initUI(opts);
-  }
-  /*
-  	state: replace 1 or more state values by attribute key
-  */
-  async main(state = {}) {
-    copyMerge(this.state, state);
-    this.dom.content_holder.style("display", this.state.isVisible ? "block" : "none");
-    this.dom.icon_holder.style("background-color", this.state.isVisible ? "darkgray" : "transparent").style("color", this.state.isVisible ? "white" : "#797a7a");
-    if (!this.state.isVisible) return;
-    const data = await this.vocabApi.getTermInfo(this.state.term.id);
-    this.render(data);
-  }
-};
-var termInfoInit = getInitFxn(TdbTermInfo);
-function setRenderers(self) {
-  self.initUI = function(opts) {
-    self.dom = {
-      content_holder: opts.content_holder.style("margin-left", "25px").attr("class", "term_info_div").style("display", self.state.isVisible ? "block" : "none").style("white-space", "normal").style("padding-bottom", "20px"),
-      //Term information/description
-      details: opts.content_holder.append("div"),
-      tbody: opts.content_holder.append("table").append("tbody"),
-      //Information icon button div. Term description appears in content_holder
-      icon_holder: opts.icon_holder.style("margin", "1px 0px 1px 5px").style("padding", "2px 5px").style("font-family", "Times New Roman").style("font-size", "14px").style("font-weight", "bold").style("cursor", "pointer").style("background-color", "transparent").style("color", "#797a7a").style("align-items", "center").style("justify-content", "center").style("border", "none").style("border-radius", "3px").attr("aria-label", "Term Information").html("ⓘ").on("mouseenter", () => {
-        if (self.state.isVisible == true) return;
-        self.dom.icon_holder.style("color", "blue");
-      }).on("mouseleave", () => {
-        if (self.state.isVisible == true) return;
-        self.dom.icon_holder.style("color", "#797a7a");
-      }).on("click", self.toggleDescription)
-    };
-  };
-  self.render = function(data) {
-    if (!data?.terminfo) {
-      self.dom.details.append("div").style("margin-top", "10px").text("No definition found.");
-      return;
-    }
-    self.dom.tbody.selectAll("*").remove();
-    if (data.terminfo.src) {
-      for (let s of data.terminfo.src) {
-        const source_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0");
-        source_td.append("div").style("font-weight", "bold").text("Source");
-        source_td.append("div").style("margin-left", "20px").text(s.pub);
-        source_td.append("div").style("margin-left", "20px").html(s.title + ":&nbsp;<i>" + s.section + "</i>");
-      }
-    }
-    if (data.terminfo.rubric) {
-      const grade_td = self.dom.tbody.append("tr").append("td").style("padding", "5px 0").append("div").style("font-weight", "bold").text("Grading Rubric").append("ol").style("margin", "0px");
-      for (let grade of data.terminfo.rubric) {
-        grade_td.append("li").style("font-weight", "normal").text(grade);
-      }
-    }
-    self.dom.details.selectAll("*").remove();
-    if (data.terminfo.description) {
-      const header = self.dom.details.append("div").style("padding-top", "20px").style("padding-bottom", "10px").style("font-weight", "bold").text("Description");
-      for (const d of data.terminfo.description) {
-        self.renderDetail(d, self.dom.details.append("div").style("padding-bottom", "3px"));
-      }
-    }
-  };
-  self.renderDetail = function(d, div) {
-    if (Array.isArray(d.value)) {
-      div.append("span").html("<i>" + d.label + "</i>");
-      const section = div.append("div").style("padding-left", "20px");
-      for (const v of d.value) {
-        v.label = "- " + v.label;
-        self.renderDetail(v, section.append("div"));
-      }
-    } else {
-      div.html("<i>" + d.label + ":</i>&nbsp;" + d.value);
-    }
-  };
-}
-function setInteractivity(self) {
-  self.toggleDescription = function() {
-    self.state.isVisible = !self.state.isVisible;
-    self.main({ isVisible: self.state.isVisible });
-  };
-}
-
-export {
-  termInfoInit
-};
-//# sourceMappingURL=chunk-2KM4PRQM.js.map

package/dist/chunk-33FULV5M.js

@@ -1,302 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  makeNumericAxisConfig,
-  rgb2hex
-} from "./chunk-VHDYIOWU.js";
-import {
-  dofetch3
-} from "./chunk-RMUK3TLD.js";
-import {
-  axisLeft
-} from "./chunk-Z2ZITHT4.js";
-import {
-  format,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// src/block.tk.bigwig.js
-function bigwigfromtemplate(tk, template) {
-  tk.scale = {};
-  if (template.scale) {
-    for (const k in template.scale) {
-      tk.scale[k] = template.scale[k];
-    }
-  } else {
-    tk.scale.auto = 1;
-  }
-  if (tk.normalize) {
-  } else {
-    tk.normalize = {
-      dividefactor: 1,
-      disable: 1
-    };
-  }
-  tk.barheight = template.height || 50;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  if (!tk.ncolor) tk.ncolor = "#BD005E";
-  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
-  if (!tk.pcolor) tk.pcolor = "#005EBD";
-  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
-}
-function bigwigmaketk(tk, block) {
-  tk.img = tk.glider.append("image");
-  tk.tklabel.attr("y", tk.barheight / 2);
-  tk.leftaxis = tk.gleft.append("g");
-  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
-    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
-  });
-}
-async function bigwigload(tk, block) {
-  block.tkcloakon(tk);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
-  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  tk.img.attr("width", block.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    let data;
-    if (tk.imgData) {
-      data = tk.imgData;
-    } else {
-      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    }
-    if (data.error) throw data.error;
-    if (!data.src) throw "data.src missing";
-    tk.tklabel.transition().attr("y", tk.barheight / 2);
-    tk.img.attr("xlink:href", data.src);
-    if (data.minv != void 0) {
-      tk.scale.min = data.minv;
-    }
-    if (data.maxv != void 0) {
-      tk.scale.max = data.maxv;
-    }
-    tk.leftaxis.selectAll("*").remove();
-    if (data.nodata) {
-      throw "No data in view range";
-    }
-    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
-    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
-    if (tk.integer4axis) {
-      axis.tickFormat(format("d"));
-    }
-    axisstyle({
-      axis: tk.leftaxis.call(axis),
-      color: "black",
-      showline: true
-    });
-  } catch (err) {
-    tk.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff(tk, { error: errtext });
-    block.block_setheight();
-    for (const panel of tk.subpanels) {
-      bigwigloadsubpanel(tk, block, panel);
-    }
-  }
-}
-async function bigwigloadsubpanel(tk, block, panel) {
-  block.tkcloakon_subpanel(panel);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) {
-    par.dotplotfactor = tk.dotplotfactor;
-  }
-  par.width = panel.width;
-  par.rglst = [
-    {
-      chr: panel.chr,
-      start: panel.start,
-      stop: panel.stop,
-      width: panel.width
-    }
-  ];
-  delete par.percentile;
-  delete par.autoscale;
-  panel.img.attr("width", panel.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    if (tk.imgData) throw "subpanel not supported by imgData yet";
-    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    if (data.error) throw data.error;
-    panel.img.attr("xlink:href", data.src);
-  } catch (err) {
-    panel.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff_subpanel(panel, { error: errtext });
-  }
-}
-function bigwigconfigpanel(tk, block, holder, loader) {
-  const config = {
-    pcolor: {},
-    ncolor: {},
-    pcolor2: {},
-    ncolor2: {},
-    // .row
-    // .lab
-    dotplot: {},
-    // .row
-    dividefactor: {}
-  };
-  {
-    const row = holder.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Height  ");
-    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
-      if (event.code != "Enter") return;
-      const s = event.target.value;
-      if (s == "") return;
-      const v = Number.parseInt(s);
-      if (Number.isNaN(v) || v <= 1) {
-        alert("track height must be positive integer");
-        return;
-      }
-      tk.barheight = v;
-      loader(bwSetting.height);
-    });
-  }
-  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
-  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
-    tk.pcolor = event.target.value;
-    loader(bwSetting.pcolor);
-  });
-  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
-  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
-    tk.ncolor = event.target.value;
-    loader(bwSetting.ncolor);
-  });
-  if (!tk.scale.auto) {
-    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
-    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
-      tk.pcolor2 = event.target.value;
-      loader(bwSetting.pcolor2);
-    });
-    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
-    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
-      tk.ncolor2 = event.target.value;
-      loader(bwSetting.ncolor2);
-    });
-  }
-  {
-    const setting = {};
-    if (tk.scale.auto) {
-      setting.auto = 1;
-    } else if (tk.scale.percentile) {
-      setting.percentile = tk.scale.percentile;
-    } else {
-      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
-    }
-    makeNumericAxisConfig({
-      holder: holder.append("div").style("margin-bottom", "15px"),
-      setting,
-      callback: (s) => {
-        if (s.auto) {
-          tk.scale.auto = 1;
-          loader(bwSetting.autoscale);
-          return;
-        }
-        if (s.fixed) {
-          delete tk.scale.auto;
-          delete tk.scale.percentile;
-          tk.scale.max = s.fixed.max;
-          tk.scale.min = s.fixed.min;
-          loader(bwSetting.fixedscale);
-          return;
-        }
-        delete tk.scale.auto;
-        tk.scale.percentile = s.percentile;
-        loader(bwSetting.percentilescale);
-      }
-    });
-  }
-  {
-    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
-    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
-    const s = config.dotplot.row.append("select").on("change", (event) => {
-      const i = event.target.selectedIndex;
-      if (i == 0) {
-        delete tk.dotplotfactor;
-      } else {
-        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
-      }
-      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
-    });
-    let o = s.append("option").text("no");
-    if (!tk.dotplotfactor) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("5");
-    if (tk.dotplotfactor == 5) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("10");
-    if (tk.dotplotfactor == 10) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("15");
-    if (tk.dotplotfactor == 15) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("20");
-    if (tk.dotplotfactor == 20) {
-      o.property("selected", 1);
-    }
-  }
-  config.dividefactor.row = holder.append("div");
-  {
-    const id = Math.random().toString();
-    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
-    if (!tk.normalize.disable) {
-      input.property("checked", 1);
-    }
-    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
-    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
-    folder.append("span").html("Divide raw value by&nbsp;");
-    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      const v = event.target.value;
-      if (v <= 0) {
-        return;
-      }
-      tk.normalize.dividefactor = v;
-      loader(bwSetting.usedividefactor);
-    });
-    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
-    input.on("change", (event) => {
-      if (event.target.checked) {
-        appear(folder);
-        delete tk.normalize.disable;
-        factorinput.property("value", tk.normalize.dividefactor);
-        loader(bwSetting.usedividefactor);
-        return;
-      }
-      disappear(folder);
-      tk.normalize.disable = 1;
-      loader(bwSetting.nodividefactor);
-    });
-  }
-  return config;
-}
-
-export {
-  bigwigfromtemplate,
-  bigwigmaketk,
-  bigwigload,
-  bigwigloadsubpanel,
-  bigwigconfigpanel
-};
-//# sourceMappingURL=chunk-33FULV5M.js.map

package/dist/chunk-3AXQF6GL.js

@@ -1,103 +0,0 @@
-import {
-  SearchHandler,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-VHDYIOWU.js";
-
-// plots/summarizeMutationDiagnosis.ts
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
-    if (!t) throw "defaultTw4correlationPlot missing";
-    dictTw = structuredClone(t);
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-  }
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "0px 10px 10px 10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Mutation Variable");
-    const searchDiv = td2.append("div");
-    const geneSearchInst = new SearchHandler();
-    geneSearchInst.init({
-      holder: searchDiv,
-      app: chartsInstance.app,
-      // required to supply "opts.app.vocabApi" for the search ui
-      genomeObj: chartsInstance.app.opts.genome,
-      msg: "Hit ENTER to launch plot.",
-      /* the geneTw below is used as it comes, so a grouping the user built for this gene
-      elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
-      keepsQ: true,
-      callback: async (geneTw) => {
-        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
-        launchPlot({
-          tw1: dictTw,
-          tw2: geneTw,
-          chartsInstance,
-          holder
-        });
-      }
-    });
-    searchDiv.style("padding", "0px 0px 5px 0px");
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Compare Mutations Against");
-    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
-    const pill = await termsettingInit({
-      menuOptions: "{edit,replace}",
-      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
-      target="filter" works for gdc since in gdc ds it is overriding filter to dict
-      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
-      maybe this is okay for non-gdc ds as the default dictTw is meaningful
-      */
-      usecase: { target: "filter" },
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        waitDiv.text("LOADING ...");
-        try {
-          await pill.main(tw);
-          dictTw = tw;
-          waitDiv.text("Click to edit/replace the variable before searching gene.");
-        } catch (e) {
-          waitDiv.text("Error: " + (e.message || e));
-        }
-      }
-    });
-    try {
-      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-      await pill.main(dictTw);
-      waitDiv.text("Click to edit/replace the variable before searching gene.");
-    } catch (e) {
-      waitDiv.text("Error: " + (e.message || e));
-    }
-  }
-}
-function launchPlot({ tw1, tw2, chartsInstance, holder }) {
-  const chart = {
-    config: {
-      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
-      // TODO define sandbox header with gene+term name
-      term: tw1,
-      term2: tw2
-    }
-  };
-  chartsInstance.plotCreate(chart);
-  holder.selectAll("*").remove();
-  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
-  setTimeout(() => {
-    holder.style("display", "none");
-  }, 1e3);
-}
-
-export {
-  makeChartBtnMenu,
-  launchPlot
-};
-//# sourceMappingURL=chunk-3AXQF6GL.js.map

package/dist/chunk-3JHCCJ4I.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox,
-  getSCGEunit,
-  getSampleAssayInfo
-} from "./chunk-VHDYIOWU.js";
-import {
-  Menu
-} from "./chunk-7XZA2XR2.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-57Z4VYLM.js";
-
-// termdb/handlers/singleCellGeneExpression.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const sample = opts.usecase?.specialCase?.config?.sample;
-    const { genes: geneList } = await getSampleAssayInfo(this.app.vocabApi, sample);
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      geneList,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol, sample)
-    });
-  }
-  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
-   * with sample info not included.*/
-  async selectGene(gene, sample) {
-    if (!gene) throw new Error("No gene selected");
-    const unit = getSCGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.genomeObj == null) throw new Error("genomeObj is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.usecase?.specialCase?.config?.sample) {
-      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-3JHCCJ4I.js.map