@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/chunk-74QJDBIP.js

@@ -1,480 +0,0 @@
-import {
-  renderTable
-} from "./chunk-XZZLEHWC.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst
-} from "./chunk-QEHUEG4X.js";
-import {
-  TermTypes
-} from "./chunk-2UWHV2SB.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/hierCluster.interactivity.js
-var hierCluster_interactivity_exports = {};
-__export(hierCluster_interactivity_exports, {
-  addSelectedRowsOptions: () => addSelectedRowsOptions,
-  addSelectedSamplesOptions: () => addSelectedSamplesOptions,
-  getAllChildrenClusterIds: () => getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
-  setClusteringBtn: () => setClusteringBtn,
-  showTable4selectedRows: () => showTable4selectedRows,
-  showTable4selectedSamples: () => showTable4selectedSamples,
-  triggerZoomBranch: () => triggerZoomBranch
-});
-function getAllChildrenClusterIds(clickedClusterId, left) {
-  const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
-  const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
-  let allChildren = [...children];
-  for (const child of children) {
-    allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
-  }
-  return allChildren;
-}
-function addSelectedSamplesOptions(clickedSampleNames, event) {
-  const l = this.settings.matrix.controlLabels;
-  const ss = this.opts.allow2selectSamples;
-  const optionArr = [
-    {
-      label: "Zoom in",
-      callback: () => {
-        this.triggerZoomBranch(this, clickedSampleNames);
-      }
-    },
-    {
-      label: `List ${clickedSampleNames.length} ${l.samples}`,
-      callback: () => this.showTable4selectedSamples(clickedSampleNames)
-    }
-  ];
-  if (ss) {
-    optionArr.push({
-      label: ss.buttonText || `Select ${l.samples}`,
-      callback: async () => {
-        const samples = clickedSampleNames.map((c) => this.data.samples[c]);
-        ss.callback({
-          samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
-          source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
-        });
-      }
-    });
-  } else {
-    if (this.state.nav && this.state.nav.header_mode !== "hidden") {
-      const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
-      for (const s of samples) {
-        if (!s.sampleId) s.sampleId = s.sample;
-      }
-      optionArr.push({
-        label: "Add to a group",
-        callback: async () => {
-          const group = {
-            name: "Group",
-            items: samples
-          };
-          this.addGroup(group);
-        }
-      });
-    }
-  }
-  this.mouseout();
-  this.dom.tip.hide();
-  this.dom.dendroClickMenu.d.selectAll("*").remove();
-  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
-    this.dom.dendroClickMenu.d.selectAll("*").remove();
-    event2.target.__data__.callback();
-  });
-  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
-}
-function addSelectedRowsOptions(clickedRowNames, event) {
-  const rowType = this.config.dataType == "geneExpression" ? "genes" : this.config.dataType == "metaboliteIntensity" ? "metabolites" : this.config.dataType == "proteomeAbundance" ? "proteins" : "items";
-  const optionArr = [
-    {
-      label: `List ${clickedRowNames.length} ${rowType}`,
-      callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
-    }
-  ];
-  if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
-    const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
-    const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
-    optionArr.push({
-      label: `Gene set overrepresentation analysis`,
-      disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
-      callback: () => {
-        if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
-        this.dom.dendroClickMenu.d.selectAll("*").remove();
-        const lst = [];
-        for (const x of clickedRowNames) {
-          const j = this.terms?.find?.((t) => t.tw.$id == x);
-          if (j) {
-            const n = j.tw?.term?.gene;
-            if (n) lst.push(n);
-          }
-        }
-        const config = {
-          chartType: "geneORA",
-          geneORAparams: {
-            sample_genes: lst.join(","),
-            genome: this.app.vocabApi.opts.state.vocab.genome
-          }
-        };
-        this.app.dispatch({
-          type: "plot_create",
-          config
-        });
-      }
-    });
-  }
-  this.mouseout();
-  this.dom.tip.hide();
-  this.dom.dendroClickMenu.d.selectAll("*").remove();
-  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
-    (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
-  ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
-    if (event2.target.__data__?.callback) event2.target.__data__.callback();
-  });
-  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
-}
-function triggerZoomBranch(self, clickedSampleNames) {
-  if (self.zoomArea) {
-    self.zoomArea.remove();
-    delete self.zoomArea;
-  }
-  const c = {
-    startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
-    endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
-  };
-  const s = self.settings.matrix;
-  const d = self.dimensions;
-  const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
-  const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
-  const centerCell = self.sampleOrder[zoomIndex];
-  const colw = self.computedSettings.colw || self.settings.matrix.colw;
-  const maxZoomLevel = s.colwMax / colw;
-  const minZoomLevel = s.colwMin / colw;
-  const tentativeZoomLevel = Math.max(
-    1,
-    s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
-  );
-  const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
-  self.app.dispatch({
-    type: "plot_edit",
-    id: self.id,
-    config: {
-      settings: {
-        matrix: {
-          zoomLevel,
-          zoomCenterPct: 0.5,
-          //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
-          zoomIndex,
-          zoomGrpIndex: centerCell.grpIndex
-        }
-      }
-    }
-  });
-  self.resetInteractions();
-}
-function showTable4selectedSamples(clickedSampleNames) {
-  const templates = this.state.termdbConfig.urlTemplates;
-  const rows = templates?.sample ? clickedSampleNames.map((c) => [
-    { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
-  ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
-  const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
-  renderTable({
-    rows,
-    columns,
-    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
-    showLines: true,
-    maxHeight: "35vh",
-    resize: true
-  });
-}
-function showTable4selectedRows(clickedRowNames, rowType) {
-  const templates = this.state.termdbConfig.urlTemplates;
-  const rows = [];
-  if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
-    for (const i of clickedRowNames) {
-      const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
-      if (!genesymbol) continue;
-      const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
-      if (gencode) {
-        rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
-      } else {
-        rows.push([{ value: genesymbol }]);
-      }
-    }
-  } else {
-    for (const i of clickedRowNames) {
-      const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
-      if (!tw) continue;
-      const n = tw.term?.gene || tw.term?.name;
-      if (!n) continue;
-      rows.push([{ value: n }]);
-    }
-  }
-  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
-  const buttonDiv = div.append("div").style("padding", "5px");
-  const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
-    const geneNames = rows.map((row) => row[0].value).join("\n");
-    navigator.clipboard.writeText(geneNames).then(() => {
-    }, console.warn);
-    copyButton.html(`Copy ${rowType}&nbsp;&check;`);
-  });
-  renderTable({
-    rows,
-    columns: [{ label: rowType }],
-    div: div.append("div"),
-    showLines: true,
-    maxHeight: "35vh",
-    resize: true
-  });
-}
-function getClusterFromTopDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
-    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
-    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function getClusterFromLeftDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
-    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
-    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function setClusteringBtn(holder, callback) {
-  const cl = this.config.settings.matrix.controlLabels;
-  const dataType = this.config.dataType;
-  const clusterRowLabel = dataType == "geneExpression" ? "Genes" : dataType == "metaboliteIntensity" ? "Metabolites" : dataType == "proteomeAbundance" ? "Proteins" : "Rows";
-  const cluteringButtonLabel = dataType == "geneExpression" ? "Gene Expression Clustering" : dataType == "metaboliteIntensity" ? "Metabolite Intensity Clustering" : dataType == "proteomeAbundance" ? "Protein Abundance Clustering" : "Clustering";
-  holder.append("button").datum({
-    label: cluteringButtonLabel,
-    getCount: () => this.hcTermGroup?.lst.length || 0,
-    showCount: dataType == TermTypes.METABOLITE_INTENSITY || dataType == TermTypes.PROTEOME_ABUNDANCE ? "append" : "hide",
-    rows: [
-      {
-        label: `Cluster ${cl.Samples}`,
-        title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "clusterSamples",
-        boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.yDendrogramHeight = 0;
-            this.config.settings.hierCluster.clusterSamples = false;
-          } else {
-            this.config.divideBy = null;
-            this.config.settings.hierCluster.yDendrogramHeight = 200;
-            this.config.settings.hierCluster.clusterSamples = true;
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Cluster ${clusterRowLabel}`,
-        title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "clusterRows",
-        boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.clusterRows = false;
-            this.config.settings.hierCluster.sortClusterRows = "asListed";
-          } else {
-            this.config.settings.hierCluster.clusterRows = true;
-            this.config.settings.hierCluster.sortClusterRows = void 0;
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Sort ${clusterRowLabel}`,
-        title: `Set how to order the ${clusterRowLabel} as rows`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "sortClusterRows",
-        options: [
-          { label: `By input ${clusterRowLabel} order`, value: "asListed" },
-          { label: `By ${clusterRowLabel} name`, value: "byName" }
-        ],
-        styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
-        }
-      },
-      {
-        label: "Z-score Transformation",
-        title: `Option to do Z-score transformation`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "zScoreTransformation",
-        boxLabel: `Perform Z-score Transformation`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.zScoreTransformation = false;
-            this.config.settings.hierCluster.colorScale = "whiteRed";
-          } else {
-            this.config.settings.hierCluster.zScoreTransformation = true;
-            this.config.settings.hierCluster.colorScale = "blueWhiteRed";
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Clustering Method`,
-        title: `Sets which clustering method to use`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "clusterMethod",
-        options: clusterMethodLst
-      },
-      {
-        label: `Distance Method`,
-        title: `Sets which distance method to use for clustering`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "distanceMethod",
-        options: distanceMethodLst
-      },
-      {
-        label: `Column Dendrogram Height`,
-        title: `The maximum height to render the column dendrogram`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "yDendrogramHeight",
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
-        }
-      },
-      {
-        label: `Row Dendrogram Width`,
-        title: `The maximum width to render the row dendrogram`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "xDendrogramHeight",
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
-        }
-      },
-      {
-        label: `Z-score Cap`,
-        title: `Cap the Z-score scale to not exceed this absolute value`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "zScoreCap"
-      },
-      {
-        label: `Color Scheme`,
-        title: `Sets which color scheme to use`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "colorScale",
-        options: [
-          {
-            label: "Blue-White-Red",
-            value: "blueWhiteRed",
-            title: `color scheme Blue-White-Red`
-          },
-          {
-            label: "Green-Black-Red",
-            value: "greenBlackRed",
-            title: `color scheme Green-Black-Red`
-          },
-          {
-            label: "Blue-Yellow-Red",
-            value: "blueYellowRed",
-            title: `color scheme Blue-Yellow-Red`
-          },
-          {
-            label: "Green-White-Red",
-            value: "greenWhiteRed",
-            title: `color scheme Green-White-Red`
-          },
-          {
-            label: "Blue-Black-Yellow",
-            value: "blueBlackYellow",
-            title: `color scheme Blue-Black-Yellow`
-          }
-        ]
-      }
-    ],
-    customInputs: updateClusteringControls
-  }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
-}
-function updateClusteringControls(self, app, parent, table) {
-  if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
-    const zScoreCapControl = select_default(
-      table.selectAll("td").filter(function() {
-        return select_default(this).text() == "Z-score Cap";
-      }).node().closest("tr")
-    );
-    zScoreCapControl.style("display", "none");
-    const colorSchemeControl = select_default(
-      table.selectAll("td").filter(function() {
-        return select_default(this).text() == "Color Scheme";
-      }).node().closest("tr")
-    );
-    colorSchemeControl.style("display", "none");
-  }
-  if (parent.chartType == "hierCluster" && (parent.config.dataType == TermTypes.METABOLITE_INTENSITY || parent.config.dataType == TermTypes.PROTEOME_ABUNDANCE)) {
-    const geneInputTr = table.insert("tr", () => table.select("tr").node());
-    geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
-    const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
-    const editGrpDiv = td1.append("div").append("label");
-    const clusteringBtn = self.btns.node();
-    editGrpDiv.append("button").html("Edit Set").on("click", () => {
-      app.tip.clear();
-      const backDiv = app.tip.d.append("div").style("padding", "5px");
-      backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
-        if (event.key == "Enter") event.target.click();
-      });
-      const setEdiUiHolder = app.tip.d.append("div");
-      parent.showDictTermSelection(setEdiUiHolder);
-    });
-  }
-}
-
-export {
-  getAllChildrenClusterIds,
-  addSelectedSamplesOptions,
-  addSelectedRowsOptions,
-  triggerZoomBranch,
-  showTable4selectedSamples,
-  showTable4selectedRows,
-  getClusterFromTopDendrogram,
-  getClusterFromLeftDendrogram,
-  setClusteringBtn,
-  hierCluster_interactivity_exports
-};
-//# sourceMappingURL=chunk-74QJDBIP.js.map

package/dist/chunk-75EBDB7G.js

@@ -1,21 +0,0 @@
-// ../shared/types/src/routes/termdb.violinBox.ts
-function isErrorResponse(response) {
-  return "error" in response && "status" in response;
-}
-function isBoxPlotResponse(response) {
-  return !isErrorResponse(response) && "charts" in response && "descrStats" in response;
-}
-
-// ../shared/types/src/routes/samplewsimages.ts
-var WSImage = class {
-  constructor(filename) {
-    this.filename = filename;
-  }
-};
-
-export {
-  WSImage,
-  isErrorResponse,
-  isBoxPlotResponse
-};
-//# sourceMappingURL=chunk-75EBDB7G.js.map

package/dist/chunk-75EBDB7G.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/types/src/routes/termdb.violinBox.ts", "../../shared/types/src/routes/samplewsimages.ts"],
-  "sourcesContent": ["import type { RoutePayload } from './routeApi.js'\nimport type { TermWrapper } from '../terms/tw.ts'\nimport type { Filter } from '../filter.ts'\nimport type { ErrorResponse } from './errorResponse.ts'\nimport type { DescrStats } from './termdb.descrstats.ts'\n\n/** Common properties shared by both violin and box plots */\ntype CommonProps = {\n\t/** numeric tw to fetch numeric data. tw.q.mode must be continuous */\n\ttw: TermWrapper\n\tdslabel: string\n\tgenome: string\n\t/** overlay tw for multiple violins/boxplots */\n\toverlayTw?: TermWrapper\n\t/** tw to divide to multiple charts */\n\tdivideTw?: TermWrapper\n\t/** mass filter */\n\tfilter?: Filter\n\t/** read-only invisible filter */\n\tfilter0?: any\n\t/** TODO: Needs description FIXME delete */\n\tcurrentGeneNames?: string[]\n\t/** if true, use log scale; if false or undefined, use linear scale */\n\tisLogScale?: boolean\n}\n\n/** Request type for violin plots with required violin-specific parameters */\nexport type ViolinRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'violin'\n\t/** A number representing the dimension perpendicular to the violin spread */\n\taxisHeight?: number\n\t/** A string representing the type of symbol used on the plot */\n\tdatasymbol?: string\n\t/** A number representing the device's pixel ratio */\n\tdevicePixelRatio: number\n\t/** If true, uses KDE method to build plot */\n\tisKDE?: boolean\n\t/** A string with two possible values: 'horizontal' or 'vertical' */\n\torientation: string\n\t/** A number representing the radius of the data symbols */\n\tradius: number\n\t/** A number representing the right margin */\n\trightMargin?: number\n\t/** Term may be scaled from regression analysis */\n\tscale?: any\n\t/** A number representing the width of the stroke */\n\tstrokeWidth?: number\n\t/** A number representing the width of the SVG box */\n\tsvgw: number\n\t/** Number of bins to build the plot. Default is 20. */\n\tticks?: number\n}\n\n/** Request type for box plots with required box-specific parameters */\nexport type BoxRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'box'\n\t/** sort plots by median value */\n\torderByMedian?: boolean\n\t/** Remove outliers from the plot */\n\tremoveOutliers?: boolean\n\t/** If true, show association tests table */\n\tshowAssocTests?: boolean\n}\n\n/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */\nexport type ViolinBoxRequest = ViolinRequest | BoxRequest\n\nexport type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse\n\n/** Type guard to check if response is an ErrorResponse */\nexport function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {\n\treturn 'error' in response && 'status' in response\n}\n\n/** Type guard to check if response is a BoxPlotResponse */\nexport function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {\n\treturn !isErrorResponse(response) && 'charts' in response && 'descrStats' in response\n}\n\n/** Type guard to check if response is a ViolinResponse */\nexport function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {\n\treturn !isErrorResponse(response) && 'min' in response && 'max' in response\n}\n\n/** Violin response types */\ninterface BinsEntries {\n\tx0: number\n\tx1: number\n\tdensity: number\n}\n\ninterface ValuesEntries {\n\tid: string\n\tlabel: string\n\tvalue: number\n}\n\ninterface PValueEntries {\n\tvalue?: string\n\thtml?: string\n}\n\ntype ViolinDensity = {\n\tbins: BinsEntries[]\n\tdensityMax: number\n\tdensityMin: number\n}\n\nexport type ViolinPlotEntry = {\n\tcolor: string\n\tchartId: string\n\tdensity: ViolinDensity\n\tlabel: string\n\tplotValueCount: number\n\tseriesId: string\n\tsrc: string\n\tsummaryStats: ValuesEntries[]\n}\n\nexport type ViolinResponse = {\n\tbins: { [index: string]: any }\n\tcharts: {\n\t\t[index: string]: {\n\t\t\tchartId: string\n\t\t\tplots: ViolinPlotEntry[]\n\t\t\tpvalues?: PValueEntries[][]\n\t\t}\n\t}\n\tmin: number\n\tmax: number\n\tuncomputableValues: { [index: string]: number }[] | null\n\tdescrStats?: DescrStats\n}\n\n/** Boxplot response types */\nexport type BoxPlotData = {\n\tw1: number | undefined\n\tw2: number | undefined\n\tp05: number\n\tp25: number\n\tp50: number\n\tp75: number\n\tp95: number\n\tiqr: number\n\tout: { value: number }[]\n}\n\nexport type BoxPlotEntry = {\n\tboxplot: BoxPlotData & { label: string }\n\tcolor?: string\n\tdescrStats: DescrStats\n\tisHidden?: boolean\n\tkey: string\n\tseriesId?: string\n}\n\nexport type BoxPlotChartEntry = {\n\tchartId: string\n\tplots: BoxPlotEntry[]\n\tsampleCount: number\n\twilcoxon?: [{ value: string }, { value: string }, { html: string }][]\n}\n\nexport type BoxPlotResponse = {\n\tabsMin?: number\n\tabsMax?: number\n\tbins?: {\n\t\t[index: string]: any\n\t}\n\tcharts: {\n\t\t[chartId: string]: BoxPlotChartEntry\n\t}\n\tdescrStats: DescrStats\n\tuncomputableValues: { label: string; value: number }[] | null\n}\n\nexport const violinBoxPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'ViolinBoxRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'ViolinBoxResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'aaclassic_5', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tdevicePixelRatio: 2,\n\t\t\t\t\tsvgw: 200,\n\t\t\t\t\torientation: 'horizontal',\n\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\tradius: 5,\n\t\t\t\t\tisLogScale: false\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'box',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'agedx', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\toverlayTw: {\n\t\t\t\t\t\tterm: { id: 'sex', type: 'categorical' }\n\t\t\t\t\t},\n\t\t\t\t\torderByMedian: true\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { RoutePayload } from './routeApi.ts'\nimport type { WSIClass } from '../dataset.ts'\nimport type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'\n\nexport type SampleWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tsample_id: string\n\twsimage: string\n}\n\nexport type SampleWSImagesResponse = {\n\tsampleWSImages: WSImage[]\n}\n\nexport class WSImage {\n\tid?: number\n\tfilename: string\n\tmetadata?: string\n\tpredictionLayers?: Array<string>\n\tannotations?: Array<Annotation>\n\tpredictions?: Array<Prediction>\n\tclasses?: Array<WSIClass>\n\t/** ds defined uncertainity labels and colors */\n\tuncertainty?: any\n\t/** Color to highlight active patches */\n\tactivePatchColor?: string\n\t/** Tile size in pixels needed for AI scripts */\n\ttileSize?: number\n\n\tconstructor(filename: string) {\n\t\tthis.filename = filename\n\t}\n}\n\nexport const sampleWSImagesPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'SampleWSImagesRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'SampleWSImagesResponse'\n\t}\n\t// examples: []\n}\n"],
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-  "names": []
-}

package/dist/chunk-7FXPMQRW.js

@@ -1,34 +0,0 @@
-import {
-  appInit
-} from "./chunk-XZZLEHWC.js";
-import {
-  TermTypes
-} from "./chunk-2UWHV2SB.js";
-
-// termdb/handlers/ssGSEA.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
-    if (!genesetDbName) throw "genesetDbName missing";
-    await appInit({
-      holder: opts.holder,
-      state: {
-        dslabel: genesetDbName,
-        genome: opts.genomeObj.name,
-        nav: { header_mode: "search_only" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
-        }
-      }
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-7FXPMQRW.js.map