@sjcrh/proteinpaint-server 2.48.1 → 2.50.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.48.1",
+  "version": "2.50.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.44.0",
+    "@sjcrh/proteinpaint-rust": "2.49.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",
@@ -97,7 +97,7 @@
     "start.js",
     "src/app.js",
     "src/serverconfig.js",
-    "src/lines2R.js",
+    "src/run_R.js",
     "src/mds3.gdc.filter.js",
     "src/checkReadingFrame.js",
     "src/bedj.parseBed.js",

package/routes/burden.js

@@ -1,7 +1,6 @@
-import lines2R from "#src/lines2R.js";
+import run_R from "#src/run_R.js";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-import { write_file } from "#src/utils.js";
 const api = {
   endpoint: "burden",
   methods: {
@@ -69,23 +68,21 @@ const api = {
   }
 };
 async function getBurdenEstimates(q, ds) {
-  const infile = path.join(serverconfig.cachedir, Math.random().toString() + ".json");
   for (const k in q.query) {
     q.query[k] = Number(q.query[k]);
   }
   const data = Object.assign({}, defaults, q.query);
-  await write_file(infile, JSON.stringify(data));
   const { fit, surv, sample } = ds.cohort.cumburden.files;
   if (!fit || !surv || !sample)
     throw `missing one or more of ds.cohort.burden.files.{fit, surv, sample}`;
   const args = [
-    infile,
     `${serverconfig.tpmasterdir}/${fit}`,
     `${serverconfig.tpmasterdir}/${surv}`,
     `${serverconfig.tpmasterdir}/${sample}`
   ];
-  const Routput = await lines2R(path.join(serverconfig.binpath, "utils/burden.R"), [], args);
-  const estimates = JSON.parse(Routput[0]);
+  const estimates = JSON.parse(
+    await run_R(path.join(serverconfig.binpath, "utils", "burden.R"), JSON.stringify(data), args)
+  );
   return estimates;
 }
 function formatPayload(estimates) {

package/routes/gdc.maf.js

@@ -67,7 +67,6 @@ async function listMafFiles(q, ds) {
   const { host, headers } = ds.getHostHeaders(q);
   const data = {
     filters,
-    case_filters,
     size: maxFileNumber,
     fields: [
       "id",
@@ -80,6 +79,8 @@ async function listMafFiles(q, ds) {
       // may add diagnosis and primary site
     ].join(",")
   };
+  if (case_filters.content.length)
+    data.case_filters = case_filters;
   const response = await got.post(path.join(host.rest, "files"), { headers, body: JSON.stringify(data) });
   let re;
   try {

package/routes/gdc.topMutatedGenes.js

@@ -1,6 +1,5 @@
 import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
 import got from "got";
-import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "gdc/topMutatedGenes",
   methods: {
@@ -33,195 +32,6 @@ function init({ genomes }) {
     }
   };
 }
-const queryV1 = {
-  query: `
-query GenesTable_relayQuery(
-  $genesTable_filters: FiltersArgument
-  $genesTable_size: Int
-  $genesTable_offset: Int
-  $score: String
-  $ssmCase: FiltersArgument
-  $geneCaseFilter: FiltersArgument
-  $ssmTested: FiltersArgument
-  $cnvTested: FiltersArgument
-  $cnvGainFilters: FiltersArgument
-  $cnvLossFilters: FiltersArgument
-) {
-  genesTableViewer: viewer {
-    explore {
-      cases {
-        hits(first: 0, filters: $ssmTested) {
-          total
-        }
-      }
-      filteredCases: cases {
-        hits(first: 0, filters: $geneCaseFilter) {
-          total
-        }
-      }
-      cnvCases: cases {
-        hits(first: 0, filters: $cnvTested) {
-          total
-        }
-      }
-      genes {
-        hits(first: $genesTable_size, offset: $genesTable_offset, filters: $genesTable_filters, score: $score) {
-          total
-          edges {
-            node {
-              id
-              numCases: score
-              symbol
-              name
-              cytoband
-              biotype
-              gene_id
-              is_cancer_gene_census
-              ssm_case: case {
-                hits(first: 0, filters: $ssmCase) {
-                  total
-                }
-              }
-              cnv_case: case {
-                hits(first: 0, filters: $cnvTested) {
-                  total
-                }
-              }
-              case_cnv_gain: case {
-                hits(first: 0, filters: $cnvGainFilters) {
-                  total
-                }
-              }
-              case_cnv_loss: case {
-                hits(first: 0, filters: $cnvLossFilters) {
-                  total
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-}
-`,
-  getVariables: (q) => {
-    const variables = {
-      genesTable_filters: { op: "and", content: [] },
-      genesTable_size: q.maxGenes || 50,
-      genesTable_offset: 0,
-      score: "case.project.project_id",
-      ssmCase: {
-        op: "and",
-        content: [
-          {
-            op: "in",
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            }
-          },
-          {
-            op: "NOT",
-            content: {
-              field: "genes.case.ssm.observation.observation_id",
-              value: "MISSING"
-            }
-          }
-        ]
-      },
-      geneCaseFilter: {
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            },
-            op: "in"
-          }
-        ],
-        op: "and"
-      },
-      ssmTested: {
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            },
-            op: "in"
-          }
-        ],
-        op: "and"
-      },
-      cnvTested: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          }
-        ]
-      },
-      cnvGainFilters: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          },
-          {
-            content: {
-              field: "cnvs.cnv_change",
-              value: ["Gain"]
-            },
-            op: "in"
-          }
-        ]
-      },
-      cnvLossFilters: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          },
-          {
-            content: {
-              field: "cnvs.cnv_change",
-              value: ["Loss"]
-            },
-            op: "in"
-          }
-        ]
-      }
-    };
-    if (q.filter0) {
-      variables.genesTable_filters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvTested.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvGainFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-    }
-    if (q.geneFilter == "CGC") {
-      variables.genesTable_filters.content.push(geneCGC());
-      variables.geneCaseFilter.content.push(geneCGC());
-      variables.cnvTested.content.push(geneCGC());
-      variables.cnvGainFilters.content.push(geneCGC());
-      variables.cnvLossFilters.content.push(geneCGC());
-    }
-    return variables;
-  }
-};
 const queryV2 = {
   query: `
           query GenesTable(
@@ -419,15 +229,9 @@ const queryV2 = {
   }
 };
 async function getGenesGraphql(q, ds) {
-  let query, variables;
   const { host, headers } = ds.getHostHeaders(q);
-  if (serverconfig.features?.geneExpHost) {
-    query = queryV1.query;
-    variables = queryV1.getVariables(q);
-  } else {
-    query = queryV2.query;
-    variables = queryV2.getVariables(q);
-  }
+  const query = queryV2.query;
+  const variables = queryV2.getVariables(q);
   const response = await got.post(host.graphql, {
     headers,
     body: JSON.stringify({ query, variables })

package/routes/termdb.cluster.js

@@ -1,6 +1,5 @@
 import path from "path";
-import fs from "fs";
-import lines2R from "#src/lines2R.js";
+import run_R from "#src/run_R.js";
 import * as utils from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
@@ -90,10 +89,9 @@ async function doClustering(data, q) {
     }
     inputData.matrix.push(getZscore(row));
   }
-  const Rinputfile = path.join(serverconfig.cachedir, Math.random().toString() + ".json");
-  await utils.write_file(Rinputfile, JSON.stringify(inputData));
-  const Routput = JSON.parse(await lines2R(path.join(serverconfig.binpath, "utils/hclust.R"), [], [Rinputfile]));
-  await fs.promises.unlink(Rinputfile);
+  const Routput = JSON.parse(
+    await run_R(path.join(serverconfig.binpath, "utils", "hclust.R"), JSON.stringify(inputData))
+  );
   const row_names_index = Routput.RowOrder.map((row) => inputData.row_names.indexOf(row.name));
   const col_names_index = Routput.ColOrder.map((col) => inputData.col_names.indexOf(col.name));
   const output_matrix = [];

package/routes/termdb.config.js

@@ -103,6 +103,8 @@ function addScatterplots(c, ds) {
       colorTW: p.colorTW,
       shapeTW: p.shapeTW,
       colorColumn: p.colorColumn,
+      sampleType: p.sampleType,
+      coordsColumns: p.coordsColumns,
       settings: p.settings
     };
   });

package/routes/termdb.singlecellSamples.js

@@ -66,32 +66,19 @@ async function validate_query_singleCell(ds, genome) {
   }
 }
 async function getSamplesNative(S, ds) {
-  const isSamples = ds.cohort.termdb.q.getAllValues4term(S.isSampleTerm);
-  if (isSamples.size == 0)
-    throw "no samples found that are identified by isSampleTerm";
-  const samples = [];
-  for (const sampleid of isSamples.keys()) {
-    if (isSamples.get(sampleid) == "1")
-      samples.push({
-        sample: ds.cohort.termdb.q.id2sampleName(sampleid),
-        // string name for display
-        sampleid
-        // temporarily kept to assign term value to each sample
-      });
-  }
+  const samples = {};
   if (S.sampleColumns) {
     for (const term of S.sampleColumns) {
       const s2v = ds.cohort.termdb.q.getAllValues4term(term.termid);
-      for (const s of samples) {
-        if (s2v.has(s.sampleid))
-          s[term.termid] = s2v.get(s.sampleid);
+      for (const [s, v] of s2v.entries()) {
+        if (!samples[s])
+          samples[s] = { sample: ds.cohort.termdb.q.id2sampleName(s) };
+        samples[s][term.termid] = v;
       }
     }
   }
-  for (const s of samples)
-    delete s.sampleid;
   S.get = () => {
-    return { samples };
+    return { samples: Object.values(samples) };
   };
 }
 function getDataNative(D, ds) {

package/routes/termdb.topVariablyExpressedGenes.js

@@ -1,4 +1,4 @@
-import { gdcGetCasesWithExressionDataFromCohort } from "../src/mds3.gdc.js";
+import { gdcGetCasesWithExpressionDataFromCohort } from "../src/mds3.gdc.js";
 import path from "path";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import got from "got";
@@ -47,12 +47,12 @@ function validate_query_TopVariablyExpressedGenes(ds, genome) {
   if (q.src == "gdcapi") {
     gdcValidateQuery(ds, genome);
   } else if (q.src == "native") {
-    nativeValidateQuery(ds, genome);
+    nativeValidateQuery(ds);
   } else {
     throw "unknown topVariablyExpressedGenes.src";
   }
 }
-function nativeValidateQuery(ds, genome) {
+function nativeValidateQuery(ds) {
   const gE = ds.queries.geneExpression;
   if (!gE)
     throw "topVariablyExpressedGenes query given but geneExpression missing";
@@ -111,7 +111,7 @@ function gdcValidateQuery(ds, genome) {
     }
     if (!ds.__gdc.doneCaching)
       throw "The server has not finished caching the case IDs: try again in ~2 minutes";
-    const caseLst = await gdcGetCasesWithExressionDataFromCohort(q, ds);
+    const caseLst = await gdcGetCasesWithExpressionDataFromCohort(q, ds);
     if (caseLst.length == 0) {
       return [];
     }