@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/oncomatrix-YJCPKS72.js

@@ -1,290 +0,0 @@
-import {
-  appInit
-} from "./chunk-SQGAWR2L.js";
-import "./chunk-V7UVHM57.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  fillTermWrapper,
-  vocabInit
-} from "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// gdc/oncomatrix.js
-var gdcGenome = "hg38";
-var gdcDslabel = "GDC";
-async function init(arg, holder, genomes) {
-  const toolGenome = arg.genome || gdcGenome;
-  const toolDslabel = arg.dslabel || gdcDslabel;
-  const genome = genomes[toolGenome];
-  try {
-    if (!genome) throw toolGenome + " missing";
-    const settings = arg.settings || {};
-    if (typeof settings != "object") throw "arg.settings{} not object";
-    if (!settings.matrix) settings.matrix = {};
-    if (typeof settings.matrix != "object") throw "arg.settings.matrix{} not object";
-    if (!settings.matrix.geneFilter) settings.matrix.geneFilter = "CGC";
-    if (!Number.isInteger(settings.matrix.maxGenes)) settings.matrix.maxGenes = 50;
-    if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
-    const vocabApi = await vocabInit({
-      state: { vocab: { genome: toolGenome, dslabel: toolDslabel } }
-    });
-    vocabApi.getTermdbConfig();
-    const plotAppApi = await appInit({
-      holder: select_default(arg.holder).select(".sja_root_holder"),
-      genome,
-      state: copyMerge(
-        {
-          genome: toolGenome,
-          dslabel: toolDslabel,
-          termfilter: { filter0: arg.filter0 },
-          plots: [
-            // initialize with a geneset component, in case the genes lst is empty.
-            // This will be replaced with the actual matrix/hierCluster app once
-            // a valid geneset is selected.
-            {
-              chartType: "geneset",
-              toolName: "OncoMatrix",
-              settings: {
-                maxGenes: settings.matrix.maxGenes,
-                geneFilter: settings.matrix.geneFilter
-              }
-            }
-          ]
-        },
-        arg.state || {}
-      ),
-      app: arg.opts?.app || {},
-      geneset: {
-        mode: "geneVariant",
-        // consistent mode value as GeneSetEdit
-        genome,
-        genes: arg.genes,
-        reactsTo(action) {
-          if (action.type.startsWith("plot_")) return action.id === this.id;
-          if (action.type.startsWith("filter")) return true;
-          if (action.type == "app_refresh") return true;
-        },
-        showWaitMessage(div) {
-          div.style("margin", "20px");
-          div.append("div").text("Loading the top mutated genes in the current cohort...");
-        },
-        async callback(_genesetCompApi, twlst) {
-          if (!_genesetCompApi) return;
-          genesetCompApi = _genesetCompApi;
-          if (!matrixApi) {
-            const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
-            if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-          }
-          const termgroups = [
-            ...arg.termgroups || [],
-            {
-              //name: 'Gene Expression',
-              lst: twlst
-            }
-          ];
-          if (matrixApi) {
-            plotAppApi.dispatch({
-              type: "plot_edit",
-              id: matrixApi.id,
-              config: { termgroups }
-            });
-          } else {
-            plotAppApi.dispatch({
-              type: "plot_create",
-              config: {
-                chartType: "matrix",
-                // avoid making a dictionary request when there is no gene data;
-                // if there is gene data, then the arg.termgroups can be submitted and rehydrated on app/store.init()
-                termgroups,
-                divideBy: arg.divideBy || void 0,
-                // moved default settings to gdc.hg38.js termdb[chartType].settings
-                // but can still override in the runpp() argument
-                settings
-              }
-            });
-          }
-        }
-      },
-      recover: {
-        undoHtml: "Undo",
-        redoHtml: "Redo",
-        resetHtml: "Restore",
-        hide(state) {
-          return state.plots[0]?.chartType != "matrix";
-        },
-        adjustTrackedState: (state) => {
-          const s = structuredClone(state);
-          delete s.termfilter.filter0;
-          if (s.plots) {
-            for (const plot of s.plots) {
-              if (!plot.termgroups) continue;
-              for (const grp of plot.termgroups) {
-                if (!grp.lst) continue;
-                for (const tw of grp.lst) {
-                  if (!tw?.term) continue;
-                  delete tw.term.category2samplecount;
-                  delete tw.term.values;
-                }
-              }
-            }
-          }
-          return s;
-        }
-      },
-      matrix: copyMerge(
-        {
-          reactsTo(action) {
-            if (action.type.startsWith("plot_")) return action.id === this.id;
-            if (action.type.startsWith("filter")) return true;
-            if (action.type == "app_refresh") return true;
-          },
-          // these will display the inputs together in the Genes menu,
-          // instead of being rendered outside of the matrix holder
-          customInputs: {
-            genes: [
-              {
-                label: `Maximum # Genes`,
-                title: "Limit the number of displayed genes",
-                type: "number",
-                chartType: "matrix",
-                settingsKey: "maxGenes",
-                callback: async (value) => {
-                  for (const key in arg.opts?.app?.callbacks) {
-                    if (key.startsWith("preDispatch")) {
-                      arg.opts?.app?.callbacks[key]();
-                      break;
-                    }
-                  }
-                  const genes = await getGenes(
-                    arg,
-                    { maxGenes: value, geneFilter: settings.matrix.geneFilter },
-                    vocabApi
-                  );
-                  api.update({
-                    termgroups: [{ lst: genes }],
-                    settings: {
-                      matrix: { maxGenes: value }
-                    }
-                  });
-                }
-              }
-            ]
-          },
-          callbacks: {
-            "firstRender.gdcMatrix": async (matrixApi2) => {
-              matrixApi2.on("firstRender.gdcMatrix", null);
-              if (!genesetCompApi) return;
-              plotAppApi.dispatch({
-                type: "plot_delete",
-                id: genesetCompApi.id
-              });
-              genesetCompApi = void 0;
-            }
-          }
-        },
-        arg.opts?.matrix || {}
-      )
-    });
-    let matrixApi, genesetCompApi;
-    const api = {
-      getState: () => plotAppApi.getState(),
-      destroy: () => plotAppApi.destroy(),
-      update: async (arg2) => {
-        if (!matrixApi) {
-          const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
-          if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-        }
-        if (arg2.genes) {
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: matrixApi.id,
-            config: {
-              termgroups: [
-                {
-                  lst: await Promise.all(
-                    arg2.genes.map(async (g) => {
-                      return await fillTermWrapper(
-                        {
-                          term: { gene: g.gene, type: "geneVariant", name: g.gene }
-                        },
-                        vocabApi
-                      );
-                    })
-                  )
-                }
-              ]
-            }
-          });
-        } else if ("filter0" in arg2) {
-          plotAppApi.dispatch({
-            type: "filter_replace",
-            filter0: arg2.filter0
-          });
-        } else if (matrixApi) {
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: matrixApi.id,
-            config: arg2
-          });
-        }
-      },
-      triggerAbort: (_) => plotAppApi.triggerAbort(_)
-    };
-    return api;
-  } catch (e) {
-    throw e;
-  }
-}
-async function getGenes(arg, settings, vocabApi) {
-  const body = {
-    genome: gdcGenome,
-    dslabel: arg.dslabel || gdcDslabel,
-    maxGenes: settings.maxGenes,
-    geneFilter: settings.geneFilter
-  };
-  if (arg.filter0) body.filter0 = arg.filter0;
-  const data = await dofetch3("termdb/topMutatedGenes", { body });
-  if (data.error) throw data.error;
-  if (!data.genes) return;
-  return await Promise.all(
-    // do tempfix of "data.genes.slice(0,3).map" for faster testing
-    data.genes.map(async (i) => {
-      return fillTermWrapper({ term: { gene: i.gene, type: "geneVariant" } }, vocabApi);
-    })
-  );
-}
-export {
-  init
-};
-//# sourceMappingURL=oncomatrix-YJCPKS72.js.map