@sjcrh/proteinpaint-server 2.190.2 → 2.191.1

package/routes/termdb.config.js

@@ -1,347 +0,0 @@
-import serverconfig from "#src/serverconfig.js";
-import { authApi } from "#src/auth.js";
-import { get_ds_tdb } from "#src/termdb.js";
-import {
-  TermTypeGroups,
-  SINGLECELL_CELLTYPE,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION,
-  DNA_METHYLATION,
-  SSGSEA
-} from "#shared/terms.js";
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const genome = genomes[q.genome];
-      if (!genome) throw "invalid genome";
-      const [ds] = get_ds_tdb(genome, q);
-      return make(q, req, res, ds, genome);
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-      else console.log(e);
-    }
-  };
-}
-function make(q, req, res, ds, genome) {
-  const tdb = ds.cohort.termdb;
-  const c = {
-    selectCohort: getSelectCohort(ds, req),
-    supportedChartTypes: tdb.q?.getSupportedChartTypes(req),
-    renamedChartTypes: ds.cohort.renamedChartTypes,
-    allowedTermTypes: getDsAllowedTermTypes(ds),
-    massSessionDuration: serverconfig.features.massSessionDuration || 30,
-    dataDownloadCatch: tdb.dataDownloadCatch,
-    matrix: tdb.matrix,
-    hierCluster: tdb.hierCluster,
-    numericDictTermCluster: tdb.numericDictTermCluster,
-    mclass: tdb.mclass,
-    alwaysRefillCategoricalTermValues: tdb.alwaysRefillCategoricalTermValues,
-    isGeneSetTermdb: tdb.isGeneSetTermdb,
-    lollipop: tdb.lollipop,
-    urlTemplates: tdb.urlTemplates,
-    title: "title" in ds.cohort ? ds.cohort.title : { text: ds.label },
-    massNav: ds.cohort.massNav,
-    tracks: tdb.tracks,
-    sampleTypes: ds.cohort.termdb.sampleTypes,
-    hasSampleAncestry: ds.cohort.termdb.hasSampleAncestry,
-    defaultChartType: ds.cohort.defaultChartType,
-    invalidTokenErrorHandling: tdb.invalidTokenErrorHandling,
-    colorMap: tdb.colorMap,
-    defaultTw4correlationPlot: tdb.defaultTw4correlationPlot,
-    authFilter: req.query.filter
-  };
-  if (tdb.plotConfigByCohort) c.plotConfigByCohort = structuredClone(tdb.plotConfigByCohort);
-  if (tdb.multipleTestingCorrection) c.multipleTestingCorrection = tdb.multipleTestingCorrection;
-  if (tdb.helpPages) c.helpPages = tdb.helpPages;
-  if (tdb.minTimeSinceDx) c.minTimeSinceDx = tdb.minTimeSinceDx;
-  if (tdb.timeUnit) c.timeUnit = tdb.timeUnit;
-  if (tdb.cohortStartTimeMsg) c.cohortStartTimeMsg = tdb.cohortStartTimeMsg;
-  if (tdb.hasAncestry) c.hasAncestry = tdb.hasAncestry;
-  if (tdb.logscaleBase2) c.logscaleBase2 = tdb.logscaleBase2;
-  if (tdb.useCasesExcluded) c.useCasesExcluded = tdb.useCasesExcluded;
-  if (tdb.excludedTermtypeByTarget) c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
-  if (tdb.survival) c.survival = tdb.survival;
-  if (tdb.regression) c.regression = tdb.regression;
-  if (tdb.uiLabels) c.uiLabels = tdb.uiLabels;
-  if (tdb.termCollections) c.termCollections = tdb.termCollections;
-  if (ds.assayAvailability) c.assayAvailability = ds.assayAvailability;
-  if (ds.cohort.correlationVolcano) c.correlationVolcano = ds.cohort.correlationVolcano;
-  if (ds.cohort.boxplots) c.boxplots = ds.cohort.boxplots;
-  if (tdb.maxGeneVariantGeneSetSize) c.maxGeneVariantGeneSetSize = tdb.maxGeneVariantGeneSetSize;
-  if (tdb.maxAnnoTermsPerClientRequest) c.maxAnnoTermsPerClientRequest = tdb.maxAnnoTermsPerClientRequest;
-  addRestrictAncestries(c, tdb);
-  addMatrixplots(c, ds);
-  addNonDictionaryQueries(c, ds, genome);
-  c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
-  const info = authApi.getNonsensitiveInfo(req);
-  c.clientAuthResult = info?.clientAuthResult || {};
-  if (tdb.displaySampleIds) c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
-  c.authFilter = req.query.filter;
-  addScatterplots(c, ds, info);
-  tdb.pruneTermdbConfig?.(c, q, ds);
-  res.send({ termdbConfig: c });
-}
-function addRestrictAncestries(c, tdb) {
-  if (!tdb.restrictAncestries) return;
-  c.restrictAncestries = tdb.restrictAncestries.map((i) => {
-    return { name: i.name, tvs: i.tvs, PCcount: i.PCcount };
-  });
-}
-function addScatterplots(c, ds, info) {
-  if (!ds.cohort.scatterplots) return;
-  if (ds.cohort.scatterplots.get) {
-    c.scatterplots = ds.cohort.scatterplots.get(info?.clientAuthResult);
-    return;
-  }
-  c.scatterplots = ds.cohort.scatterplots.plots.map((p) => {
-    return {
-      name: p.name,
-      dimensions: p.dimensions,
-      colorTW: p.colorTW,
-      shapeTW: p.shapeTW,
-      colorColumn: p.colorColumn,
-      sampleType: p.sampleType,
-      coordsColumns: p.coordsColumns,
-      settings: { sampleScatter: p.settings },
-      //the client settings are under sampleScatter so we add it here to avoid adding it in the dataset
-      sampleCategory: p.sampleCategory
-    };
-  });
-}
-function addMatrixplots(c, ds) {
-  if (!ds.cohort.matrixplots) return;
-  c.matrixplots = ds.cohort.matrixplots.plots.map((p) => {
-    return { name: p.name };
-  });
-}
-function addNonDictionaryQueries(c, ds, genome) {
-  const q = ds.queries;
-  if (!q) return;
-  c.queries = {
-    defaultCoord: q.defaultCoord || genome.defaultcoord,
-    gbRestrictMode: q.gbRestrictMode
-  };
-  const q2 = c.queries;
-  if (q.snvindel) {
-    q2.snvindel = {
-      allowSNPs: q.snvindel.allowSNPs,
-      // details{} lists default method for computing variants, can be modified and is part of state
-      // some of the stuff here are to provide user-selectable choices
-      // e.g. computing methods, info fields, populations.
-      details: q.snvindel.details,
-      populations: q.snvindel.populations,
-      mafFilter: q.snvindel.mafFilter
-    };
-    if (q.snvindel.byisoform?.processTwsInOneQuery) q2.snvindel.byisoform = { processTwsInOneQuery: true };
-  }
-  if (q.svfusion) {
-    q2.svfusion = { dtLst: q.svfusion.dtLst };
-  }
-  if (q.cnv) {
-    q2.cnv = {};
-    for (const k of [
-      "cnvMaxLength",
-      "cnvGainCutoff",
-      "cnvLossCutoff",
-      "cnvCutoffsByGene",
-      "absoluteValueRenderMax",
-      "gainColor",
-      "lossColor",
-      "requiresHardcodeCnvOnlyFlag"
-    ]) {
-      if (k in q.cnv) q2.cnv[k] = q.cnv[k];
-    }
-  }
-  if (q.geneCnv) {
-  }
-  if (q.topMutatedGenes) q2.topMutatedGenes = q.topMutatedGenes;
-  if (q.topVariablyExpressedGenes) q2.topVariablyExpressedGenes = q.topVariablyExpressedGenes;
-  if (q.singleSampleMutation) {
-    q2.singleSampleMutation = {
-      sample_id_key: q.singleSampleMutation.sample_id_key,
-      discoPlot: q.singleSampleMutation.discoPlot
-    };
-  }
-  if (q.singleSampleGenomeQuantification) {
-    q2.singleSampleGenomeQuantification = {};
-    for (const k in q.singleSampleGenomeQuantification) {
-      q2.singleSampleGenomeQuantification[k] = JSON.parse(JSON.stringify(q.singleSampleGenomeQuantification[k]));
-      delete q2.singleSampleGenomeQuantification[k].folder;
-    }
-  }
-  if (q.geneExpression) {
-    q2.geneExpression = { unit: q.geneExpression.unit };
-  }
-  if (q.isoformExpression) {
-    q2.isoformExpression = { unit: q.isoformExpression.unit };
-  }
-  if (q.proteome) {
-    q2.proteome = {};
-    if (q.proteome.organisms) {
-      q2.proteome.organisms = {};
-      for (const organism in q.proteome.organisms) {
-        q2.proteome.organisms[organism] = {};
-        const orgSrc = q.proteome.organisms[organism];
-        if (orgSrc.overlayTerm) {
-          q2.proteome.organisms[organism].overlayTerm = JSON.parse(JSON.stringify(orgSrc.overlayTerm));
-        }
-        if (orgSrc.genomeName) {
-          q2.proteome.organisms[organism].genomeName = orgSrc.genomeName;
-        }
-        if (orgSrc.assays) {
-          q2.proteome.organisms[organism].assays = {};
-          for (const assay in orgSrc.assays) {
-            q2.proteome.organisms[organism].assays[assay] = {};
-            if (orgSrc.assays[assay].cohorts) {
-              q2.proteome.organisms[organism].assays[assay].cohorts = {};
-              for (const cohort in orgSrc.assays[assay].cohorts) {
-                q2.proteome.organisms[organism].assays[assay].cohorts[cohort] = {};
-                const src = orgSrc.assays[assay].cohorts[cohort];
-                if ("controlFilter" in src) {
-                  q2.proteome.organisms[organism].assays[assay].cohorts[cohort].controlFilter = JSON.parse(
-                    JSON.stringify(src.controlFilter)
-                  );
-                }
-                if ("caseFilter" in src) {
-                  q2.proteome.organisms[organism].assays[assay].cohorts[cohort].caseFilter = JSON.parse(
-                    JSON.stringify(src.caseFilter)
-                  );
-                }
-                if (src.DAPfile) {
-                  q2.proteome.organisms[organism].assays[assay].cohorts[cohort].DAPfile = true;
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-  if (q.geneRanking) {
-    q2.geneRanking = {
-      rankings: Object.fromEntries(Object.keys(q.geneRanking.rankings).map((k) => [k, true])),
-      modalities: q.geneRanking.modalities,
-      description: q.geneRanking.description,
-      appName: q.geneRanking.appName
-    };
-  }
-  if (q.dnaMethylation) {
-    q2.dnaMethylation = { unit: q.dnaMethylation.unit };
-    if (q.dnaMethylation.promoter) {
-      q2.dnaMethylation.promoter = { unit: q.dnaMethylation.promoter.unit };
-    }
-  }
-  if (q.ld) {
-    q2.ld = structuredClone(q.ld);
-  }
-  if (q.trackLst) {
-    q2.trackLst = q.trackLst;
-  }
-  if (q.chat) {
-    q2.chat = {};
-  }
-  if (q.alphaGenome) q2.alphaGenome = q.alphaGenome;
-  if (q.NIdata && serverconfig.features.showBrainImaging) {
-    q2.NIdata = {};
-    for (const k in q.NIdata) {
-      q2.NIdata[k] = JSON.parse(JSON.stringify(q.NIdata[k]));
-    }
-  }
-  if (q.DZImages && serverconfig.features.showDZImages) {
-    q2.DZImages = {
-      type: q.DZImages.type
-    };
-  }
-  if (q.WSImages && serverconfig.features.showWSImages) {
-    q2.WSImages = {
-      type: q.WSImages.type
-    };
-  }
-  if (q.singleSampleGbtk) {
-    q2.singleSampleGbtk = {};
-    for (const k in q.singleSampleGbtk) {
-      q2.singleSampleGbtk[k] = JSON.parse(JSON.stringify(q.singleSampleGbtk[k]));
-      delete q2.singleSampleGbtk[k].folder;
-    }
-  }
-  if (q.rnaseqGeneCount) {
-    q2.rnaseqGeneCount = true;
-  }
-  if (q.singleCell) {
-    q2.singleCell = {
-      samples: {
-        sampleColumns: q.singleCell.samples.sampleColumns,
-        experimentColumns: q.singleCell.samples.experimentColumns,
-        extraSampleTabLabel: q.singleCell.samples.extraSampleTabLabel
-      },
-      images: q.singleCell.images,
-      data: {
-        sameLegend: q.singleCell.data.sameLegend,
-        refName: q.singleCell.data.refName,
-        settings: q.singleCell.data.settings,
-        plots: q.singleCell.data.plots.map((p) => {
-          return { name: p.name, colorColumns: p.colorColumns, selected: p.selected };
-        })
-      }
-    };
-    if (q.singleCell.geneExpression) {
-      q2.singleCell.geneExpression = {
-        unit: q.singleCell.geneExpression?.unit
-      };
-    }
-    if (q.singleCell.DEgenes) {
-      q2.singleCell.DEgenes = { termId: q.singleCell.DEgenes.termId };
-    }
-    if (q.singleCell?.terms?.length) {
-      if (!c.termType2terms) c.termType2terms = {};
-      c.termType2terms[TermTypeGroups.SINGLECELL_CELLTYPE] = q.singleCell.terms;
-    }
-  }
-  if (q.images) {
-    q2.images = {};
-  }
-}
-function getDsAllowedTermTypes(ds) {
-  const typeSet = /* @__PURE__ */ new Set();
-  for (const r of ds.cohort.termdb.termtypeByCohort) {
-    if (r.termType) typeSet.add(r.termType);
-  }
-  if (ds.cohort.termdb.allowedTermTypes) {
-    for (const t of ds.cohort.termdb.allowedTermTypes) typeSet.add(t);
-  }
-  if (ds.queries?.geneExpression) typeSet.add(GENE_EXPRESSION);
-  if (ds.queries?.isoformExpression) typeSet.add(ISOFORM_EXPRESSION);
-  if (ds.queries?.metaboliteIntensity) typeSet.add(METABOLITE_INTENSITY);
-  if (ds.queries?.proteome) typeSet.add(PROTEOME_ABUNDANCE);
-  if (ds.queries?.ssGSEA) typeSet.add(SSGSEA);
-  if (ds.queries?.dnaMethylation) typeSet.add(DNA_METHYLATION);
-  if (ds.queries?.singleCell) {
-    typeSet.add(SINGLECELL_CELLTYPE);
-    if (ds.queries.singleCell?.geneExpression) typeSet.add(SINGLECELL_GENE_EXPRESSION);
-  }
-  if (ds.cohort.termdb.termCollections?.length) typeSet.add("termCollection");
-  return [...typeSet];
-}
-function getSelectCohort(ds, req) {
-  if (!ds.cohort.termdb.selectCohort) return;
-  const copy = Object.assign({}, ds.cohort.termdb.selectCohort);
-  if (ds.cohort.termdb.selectCohort.descriptionByUser) {
-    copy.description = ds.cohort.termdb.selectCohort.descriptionByUser(authApi.getNonsensitiveInfo(req));
-    delete copy.descriptionByUser;
-  } else if (ds.cohort.termdb.selectCohort.descriptionByCohortBasedOnUserRole) {
-    copy.descriptionByCohort = ds.cohort.termdb.selectCohort.descriptionByCohortBasedOnUserRole(
-      authApi.getNonsensitiveInfo(req)
-    );
-    delete copy.descriptionByCohortBasedOnUserRole;
-  }
-  return copy;
-}
-export {
-  getDsAllowedTermTypes,
-  init
-};