@sjcrh/proteinpaint-server 2.44.0 → 2.46.0

package/dataset/termdb.test.js

@@ -0,0 +1,257 @@
+import serverconfig from "@sjcrh/proteinpaint-server/src/serverconfig.js";
+import * as path from "path";
+import { existsSync, unlinkSync, symlinkSync, access, constants } from "fs";
+copyDataFilesFromRepo2Tp();
+var termdb_test_default = {
+  isMds3: true,
+  cohort: {
+    db: {
+      file: "files/hg38/TermdbTest/db"
+    },
+    allowedChartTypes: [
+      "summary",
+      "survival",
+      "matrix",
+      "sampleScatter",
+      "cuminc",
+      "dataDownload",
+      "sampleView",
+      "regression"
+    ],
+    termdb: {
+      displaySampleIds: true,
+      // allow to display sample-level data
+      timeUnit: "years",
+      minTimeSinceDx: 5,
+      // enrollment in sjlife requires 5 years since cancer diagnosis
+      ageEndOffset: 274e-5,
+      // number of years to offset ending age of patients
+      // for cox outcome with timeScale='age'
+      // 1 day (i.e. 1/365 or 0.00274) needs to be added
+      // to age_end to prevent age_end = age_start (which
+      // would cause regression analysis to fail in R)
+      cohortStartTimeMsg: "5 years post cancer diagnosis",
+      selectCohort: {
+        // wrap term.id into a term json object so as to use it in tvs;
+        // the term is not required to exist in termdb
+        // term.id is specific to this dataset, should not use literally in client/server code but always through a variable
+        term: {
+          id: "subcohort",
+          type: "categorical"
+        },
+        prompt: "Select a cohort and test the plots.",
+        values: [
+          // <ul><li> for items, with a radio button for each.
+          {
+            keys: ["ABC"],
+            label: "ABC Cohort (ABC)",
+            shortLabel: "ABC",
+            isdefault: true
+          },
+          {
+            keys: ["XYZ"],
+            label: "XYZ cohort (XYZ)",
+            shortLabel: "XYZ"
+          },
+          {
+            keys: ["ABC", "XYZ"],
+            label: "Combined ABC+XYZ*",
+            shortLabel: "ABC+XYZ"
+            // show note under label in smaller text size
+          }
+        ],
+        asterisk: "*fineprint on an item"
+      },
+      dataDownloadCatch: {
+        helpLink: "https://university.stjude.cloud/docs/visualization-community/data-download/",
+        missingAccess: {
+          message: "You are missing approval to one or more of the required datasets. Please go to <a target=_blank href='MISSING-ACCESS-LINK'>Genomics Platform Data Browser</a> to request access. For more information, please see this <a target=_blank href='https://university.stjude.cloud/docs/visualization-community/data-download/'>tutorial.</a>",
+          links: {
+            sjlife: "https://platform.stjude.cloud/data/cohorts?selected_tags=SJC-DS-1002",
+            ccss: "https://platform.stjude.cloud/data/cohorts?selected_tags=SJC-DS-1005",
+            "sjlife,ccss": "https://platform.stjude.cloud/data/cohorts?selected_tags=SJC-DS-1002,SJC-DS-1005",
+            fake: "https://platform.stjude.cloud/data/cohorts?selected_tags=SJC-DS-1002"
+          }
+        },
+        jwt: {
+          "Invalid token": "https://university.stjude.cloud/docs/visualization-community/data-download/"
+        }
+      },
+      matrix: {
+        settings: {
+          ignoreCnvValues: true
+        }
+      },
+      termid2totalsize2: {}
+    },
+    scatterplots: {
+      plots: [
+        {
+          name: "TermdbTest TSNE",
+          dimension: 2,
+          file: "files/hg38/TermdbTest/tnse.txt",
+          colorTW: { id: "diaggrp" }
+        }
+      ]
+    },
+    matrixplots: {
+      plots: [
+        {
+          name: "Matrix plot",
+          file: "files/hg38/TermdbTest/TermdbTest_matrix.json"
+        }
+      ]
+    }
+  },
+  customTwQByType: {
+    // dataset-specific termsetting configs on certain term types
+    geneVariant: {
+      default: { cnvGainCutoff: 0.1, cnvLossCutoff: -0.1, cnvMaxLength: 0 },
+      byGene: {
+        // key is term.name, thus possible to use non-gene names e.g. C19MC
+        MYCN: { cnvGainCutoff: 0.5, cnvLossCutoff: -0.1, cnvMaxLength: 0 }
+      }
+    }
+  },
+  variant2samples: {
+    variantkey: "ssm_id",
+    // required, tells client to return ssm_id for identifying variants
+    // list of term ids as sample details
+    twLst: [
+      { id: "sex", q: {} },
+      { id: "diaggrp", q: {} },
+      { id: "agedx", q: {} }
+    ],
+    // small list of terms for sunburst rings
+    sunburst_twLst: [{ id: "sex", q: {} }]
+  },
+  queries: {
+    // temporary fix for genomeBrowser app to show gene model
+    defaultBlock2GeneMode: true,
+    snvindel: {
+      forTrack: true,
+      byrange: {
+        bcffile: "files/hg38/TermdbTest/TermdbTest.bcf.gz"
+      },
+      skewerRim: {
+        type: "format",
+        formatKey: "origin",
+        rim1value: "germline",
+        noRimValue: "somatic"
+      }
+    },
+    svfusion: {
+      byrange: {
+        file: "files/hg38/TermdbTest/TermdbTest_Fusion.gz"
+      }
+    },
+    cnv: {
+      byrange: {
+        src: "native",
+        file: "files/hg38/TermdbTest/TermdbTest_CNV_gene.gz"
+      }
+    },
+    /*
+    on the fly cnv calls from gene body probe signals are no longer used
+    probe2cnv:{
+    	file: 'files/hg19/pnet/PNET.probesignals.gz'
+    }
+    */
+    singleSampleMutation: {
+      src: "native",
+      sample_id_key: "sample_id",
+      folder: "files/hg38/TermdbTest/mutationpersample/"
+    },
+    singleSampleGenomeQuantification: {
+      // to show genome-wide quantification plot for a sample
+      MethylationArray: {
+        description: "Genome-wide copy number variation based on tumor/normal methylation array, averaged at genomic bins.",
+        min: -1.2,
+        max: 1.2,
+        sample_id_key: "sample_id",
+        folder: "files/hg38/TermdbTest/methylationArrayNormalSubtracted_bins/",
+        // binned data, not probe-level
+        positiveColor: "#a35069",
+        negativeColor: "#5051a3",
+        singleSampleGbtk: "methylationProbeSignal"
+      }
+    },
+    singleSampleGbtk: {
+      methylationProbeSignal: {
+        description: "Probe signals from methylation array.",
+        min: -1.2,
+        max: 1.2,
+        sample_id_key: "sample_id",
+        folder: "files/hg38/TermdbTest/methylationArrayNormalSubtracted/"
+        // probe-level data, only for locus view as genome browser track
+        // each file is 1.gz and 1.gz.tbi, bedgraph format
+      }
+    },
+    geneExpression: {
+      src: "native",
+      file: "files/hg38/TermdbTest/TermdbTest.fpkm.matrix.gz"
+    },
+    topVariablyExpressedGenes: { src: "native" }
+  },
+  assayAvailability: {
+    // use "genetic_race" as fake sources of assay availability
+    byDt: {
+      // snvindel, differentiating sample origin
+      1: {
+        byOrigin: {
+          germline: {
+            term_id: "genetic_race",
+            label: "Germline",
+            // human readable label of this origin
+            yes: { value: ["European Ancestry", "Asian Ancestry"] },
+            no: { value: ["Multi-Ancestry-Admixed", "African Ancestry"] }
+          },
+          somatic: {
+            term_id: "genetic_race",
+            label: "Somatic",
+            yes: { value: ["European Ancestry", "African Ancestry"] },
+            no: { value: ["Multi-Ancestry-Admixed", "Asian Ancestry"] }
+          }
+        }
+      },
+      // fusion
+      2: {
+        //mutations are detected from RNAseq
+        term_id: "genetic_race",
+        yes: { value: ["European Ancestry", "African Ancestry"] },
+        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+      },
+      // cnv
+      4: {
+        // mutations are detected from Methylation
+        term_id: "genetic_race",
+        yes: { value: ["European Ancestry", "African Ancestry"] },
+        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+      }
+    }
+  }
+};
+function copyDataFilesFromRepo2Tp() {
+  if (existsSync("/home/root/pp"))
+    return;
+  const targetDir = path.join(serverconfig.binpath, "test/tp/files/hg38/TermdbTest");
+  const datadir = path.join(serverconfig.tpmasterdir, "files/hg38/TermdbTest");
+  if (datadir == `${serverconfig.binpath}/test/tp`) {
+    access(datadir, constants.R_OK | constants.W_OK, (err) => {
+      if (!err) {
+        try {
+          if (!existsSync(datadir))
+            unlinkSync(datadir);
+          symlinkSync(targetDir, datadir);
+        } catch (error) {
+          console.warn("Error while coping data files from Repo to Tp: " + error);
+        }
+      } else {
+        console.warn(`user doesn't have sufficient permissions for `);
+      }
+    });
+  }
+}
+export {
+  termdb_test_default as default
+};