@sjcrh/proteinpaint-server 2.86.0 → 2.87.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.86.0",
+  "version": "2.87.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -8,7 +8,7 @@
   "bin": "start.js",
   "imports": {
     "#types": "@sjcrh/proteinpaint-types",
-    "#types/*": "@sjcrh/proteinpaint-types/*",
+    "#types/checkers": "@sjcrh/proteinpaint-types/checkers",
     "#shared/*": "@sjcrh/proteinpaint-shared/*",
     "#src/*": "./src/*",
     "#routes/*": "./routes/*"
@@ -55,17 +55,13 @@
     "ts-node": "^10.9.1",
     "ts-patch": "^3.0.2",
     "tsx": "^4.7.1",
-    "typedoc": "^0.26.11",
-    "typedoc-plugin-missing-exports": "^3.0.0",
-    "typedoc-plugin-replace-text": "^4.0.0",
-    "typescript": "^5.6.3",
-    "typia": "^4.1.14"
+    "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.86.0",
+    "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.86.0",
-    "@sjcrh/proteinpaint-types": "2.86.0",
+    "@sjcrh/proteinpaint-shared": "2.87.0",
+    "@sjcrh/proteinpaint-types": "2.87.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/_template_.js

@@ -1,4 +1,4 @@
-import { snpPayload } from "#types";
+import { snpPayload } from "#types/checkers";
 const api = {
   // route endpoint
   // - no need for trailing slash

package/routes/brainImaging.js

@@ -1,6 +1,6 @@
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-import { brainImagingPayload } from "#types";
+import { brainImagingPayload } from "#types/checkers";
 import { spawn } from "child_process";
 import { getData } from "../src/termdb.matrix.js";
 import { isNumericTerm } from "@sjcrh/proteinpaint-shared/terms.js";
@@ -134,14 +134,7 @@ async function getBrainImage(query, genomes, plane, index) {
 }
 async function generateBrainImage(refFile, plane, index, maxLength, filesJson) {
   return new Promise((resolve, reject) => {
-    const cmd = [
-      `${serverconfig.binpath}/../python/src/plotBrainImaging.py`,
-      refFile,
-      plane,
-      index,
-      maxLength,
-      filesJson
-    ];
+    const cmd = [`${serverconfig.binpath}/utils/plotBrainImaging.py`, refFile, plane, index, maxLength, filesJson];
     const ps = spawn(serverconfig.python, cmd);
     const imgData = [];
     ps.stdout.on("data", (data) => {

package/routes/burden.js

@@ -1,4 +1,4 @@
-import { burdenPayload } from "#types";
+import { burdenPayload } from "#types/checkers";
 import run_R from "#src/run_R.js";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";

package/routes/dataset.js

@@ -1,7 +1,7 @@
 import * as mds2_init from "#src/mds2.init.js";
 import * as mds3_init from "#src/mds3.init.js";
 import * as common from "#shared/common.js";
-import { datasetPayload } from "#types";
+import { datasetPayload } from "#types/checkers";
 const api = {
   endpoint: "getDataset",
   // should rename to simply 'dataset', method is based on HTTP method

package/routes/dsdata.js

@@ -2,7 +2,7 @@ import path from "path";
 import { spawn } from "child_process";
 import serverconfig from "#src/serverconfig.js";
 import * as common from "#shared/common.js";
-import { dsDataPayload } from "#types";
+import { dsDataPayload } from "#types/checkers";
 const api = {
   // route endpoint
   // - no need for trailing slash

package/routes/dzimages.js

@@ -1,7 +1,7 @@
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { illegalpath } from "#src/utils.js";
-import { dzImagesPayload } from "#types";
+import { dzImagesPayload } from "#types/checkers";
 const api = {
   endpoint: `dzimages/:sampleId`,
   methods: {

package/routes/gdc.maf.js

@@ -1,4 +1,4 @@
-import { gdcMafPayload } from "#types";
+import { gdcMafPayload } from "#types/checkers";
 import path from "path";
 import got from "got";
 import serverconfig from "#src/serverconfig.js";
@@ -72,7 +72,7 @@ async function listMafFiles(q, ds) {
   let re;
   try {
     re = JSON.parse(response.body);
-  } catch (e) {
+  } catch (_) {
     throw "invalid JSON from " + api.endpoint;
   }
   if (!Number.isInteger(re.data?.pagination?.total))

package/routes/gdc.mafBuild.js

@@ -2,7 +2,7 @@ import got from "got";
 import path from "path";
 import { run_rust_stream } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
-import { gdcMafPayload } from "#types";
+import { gdcMafPayload } from "#types/checkers";
 import { maxTotalSizeCompressed } from "./gdc.maf.ts";
 const api = {
   endpoint: "gdc/mafBuild",
@@ -80,7 +80,7 @@ async function getFileLstUnderSizeLimit(lst, host, headers) {
   let re;
   try {
     re = JSON.parse(response.body);
-  } catch (e) {
+  } catch (_) {
     throw "invalid json from getFileLstUnderSizeLimit";
   }
   if (!Array.isArray(re.data?.hits))

package/routes/gdc.topMutatedGenes.js

@@ -1,4 +1,4 @@
-import { gdcTopMutatedGenePayload } from "#types";
+import { gdcTopMutatedGenePayload } from "#types/checkers";
 import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
 import ky from "ky";
 const api = {

package/routes/genelookup.js

@@ -1,5 +1,5 @@
 import { getResult } from "#src/gene.js";
-import { geneLookupPayload } from "#types";
+import { geneLookupPayload } from "#types/checkers";
 const api = {
   endpoint: "genelookup",
   methods: {

package/routes/genesetEnrichment.js

@@ -1,4 +1,4 @@
-import { genesetEnrichmentPayload } from "#types";
+import { genesetEnrichmentPayload } from "#types/checkers";
 import fs from "fs";
 import path from "path";
 import { spawn } from "child_process";
@@ -55,7 +55,9 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     geneset_group: q.geneSetGroup,
     cachedir: serverconfig.cachedir,
     geneset_name: q.geneset_name,
-    pickle_file: q.pickle_file
+    pickle_file: q.pickle_file,
+    genedb: path.join(serverconfig.tpmasterdir, genomes[q.genome].genedb.dbfile),
+    filter_non_coding_genes: q.filter_non_coding_genes
   };
   const gsea_output = await run_gsea(
     `${serverconfig.binpath}/utils/gsea.py`,
@@ -88,7 +90,7 @@ async function run_genesetEnrichment_analysis(q, genomes) {
 async function run_gsea(path2, data) {
   try {
     await fs.promises.stat(path2);
-  } catch (e) {
+  } catch (_) {
     throw `${path2} does not exist`;
   }
   return new Promise((resolve, reject) => {

package/routes/genesetOverrepresentation.js

@@ -1,4 +1,4 @@
-import { genesetOverrepresentationPayload } from "#types";
+import { genesetOverrepresentationPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";

package/routes/healthcheck.js

@@ -1,5 +1,5 @@
 import { getStat } from "#src/health.ts";
-import { healthcheckPayload } from "#types";
+import { healthcheckPayload } from "#types/checkers";
 const api = {
   endpoint: "healthcheck",
   methods: {

package/routes/hicdata.js

@@ -1,4 +1,4 @@
-import { hicdataPayload } from "#types";
+import { hicdataPayload } from "#types/checkers";
 import { fileurl } from "#src/utils.js";
 import { spawn } from "child_process";
 import readline from "readline";

package/routes/hicgenome.js

@@ -1,4 +1,4 @@
-import { hicGenomePayload } from "#types";
+import { hicGenomePayload } from "#types/checkers";
 import { fileurl } from "#src/utils.js";
 import { spawn } from "child_process";
 import readline from "readline";

package/routes/hicstat.js

@@ -1,6 +1,6 @@
 import { fileurl, file_is_readable } from "#src/utils.js";
 import { do_hicstat } from "#src/hicstat.ts";
-import { hicstatPayload } from "#types";
+import { hicstatPayload } from "#types/checkers";
 const api = {
   endpoint: "hicstat",
   methods: {

package/routes/isoformlst.js

@@ -1,4 +1,4 @@
-import { isoformlstPayload } from "#types";
+import { isoformlstPayload } from "#types/checkers";
 const api = {
   // route endpoint
   // - no need for trailing slash

package/routes/ntseq.js

@@ -1,4 +1,4 @@
-import { ntseqPayload } from "#types";
+import { ntseqPayload } from "#types/checkers";
 import { get_fasta } from "#src/utils.js";
 const api = {
   endpoint: "ntseq",

package/routes/pdomain.js

@@ -1,4 +1,4 @@
-import { pdomainPayload } from "#types";
+import { pdomainPayload } from "#types/checkers";
 const api = {
   // route endpoint
   // - no need for trailing slash

package/routes/sampledzimages.js

@@ -1,7 +1,7 @@
 import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-import { dzImagesPayload } from "#types";
+import { dzImagesPayload } from "#types/checkers";
 const api = {
   endpoint: "sampledzimages",
   methods: {

package/routes/samplewsimages.js

@@ -1,4 +1,4 @@
-import { sampleWSImagesPayload } from "#types";
+import { sampleWSImagesPayload } from "#types/checkers";
 const api = {
   endpoint: "samplewsimages",
   methods: {

package/routes/snp.js

@@ -1,4 +1,4 @@
-import { snpPayload } from "#types";
+import { snpPayload } from "#types/checkers";
 import * as utils from "#src/utils.js";
 const api = {
   // route endpoint

package/routes/termdb.DE.js

@@ -1,5 +1,5 @@
 import path from "path";
-import { diffExpPayload } from "#types";
+import { diffExpPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { get_ds_tdb } from "../src/termdb.js";
 import run_R from "../src/run_R.js";

package/routes/termdb.boxplot.js

@@ -1,4 +1,4 @@
-import { boxplotPayload } from "#types";
+import { boxplotPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortKey2values } from "../src/termdb.violin.js";
@@ -71,7 +71,7 @@ function init({ genomes }) {
         }
       }
       const plots = [];
-      let absMin = null, absMax = null, maxLabelLgth = null;
+      let absMin = null, absMax = null;
       for (const [key, values] of sortKey2values(data, key2values, overlayTerm)) {
         const sortedValues = values.sort((a, b) => a - b);
         if (absMin === null || sortedValues[0] < absMin)
@@ -87,26 +87,23 @@ function init({ genomes }) {
           throw "boxplot_getvalue failed [termdb.boxplot init()]";
         const descrStats = setDescrStats(boxplot, sortedValues);
         const _plot = {
-          // values,
           boxplot,
           descrStats
         };
         if (overlayTerm) {
           const _key = overlayTerm?.term?.values?.[key]?.label || key;
           const plotLabel = `${_key}, n=${values.length}`;
-          if (maxLabelLgth === null || plotLabel.length > maxLabelLgth)
-            maxLabelLgth = plotLabel.length;
+          const overlayBins = numericBins(overlayTerm, data);
           const plot = Object.assign(_plot, {
             color: overlayTerm?.term?.values?.[key]?.color || null,
             key: _key,
+            overlayBins: overlayBins.has(key) ? overlayBins.get(key) : null,
             seriesId: key
           });
           plot.boxplot.label = plotLabel;
           plots.push(plot);
         } else {
           const plotLabel = `${sampleType}, n=${values.length}`;
-          if (maxLabelLgth === null || plotLabel.length > maxLabelLgth)
-            maxLabelLgth = plotLabel.length;
           const plot = Object.assign(_plot, {
             key: sampleType
           });
@@ -114,16 +111,15 @@ function init({ genomes }) {
           plots.push(plot);
         }
       }
-      if (absMin == null || absMax == null || maxLabelLgth == null)
-        throw "absMin, absMax, or maxLabelLgth is null [termdb.boxplot init()]";
+      if (absMin == null || absMax == null)
+        throw "absMin or absMax is null [termdb.boxplot init()]";
       if (q.tw.term?.values)
-        setUncomputablePlots(q.tw, plots);
+        setHiddenPlots(q.tw, plots);
       if (overlayTerm && overlayTerm.term?.values)
-        setUncomputablePlots(overlayTerm, plots);
+        setHiddenPlots(overlayTerm, plots);
       const returnData = {
         absMin,
         absMax,
-        maxLabelLgth,
         plots,
         uncomputableValues: setUncomputableValues(uncomputableValues)
       };
@@ -135,11 +131,18 @@ function init({ genomes }) {
     }
   };
 }
-function setUncomputablePlots(term, plots) {
-  for (const v of Object.values(term.term.values)) {
+function setHiddenPlots(term, plots) {
+  for (const v of Object.values(term.term?.values)) {
     const plot = plots.find((p) => p.key === v.label);
     if (plot)
-      plot.uncomputable = v.uncomputable;
+      plot.isHidden = v?.uncomputable;
+  }
+  if (term.q?.hiddenValues) {
+    for (const key of Object.keys(term.q.hiddenValues)) {
+      const plot = plots.find((p) => p.key === key);
+      if (plot)
+        plot.isHidden = true;
+    }
   }
   return plots;
 }
@@ -171,6 +174,10 @@ function setUncomputableValues(values) {
   } else
     return null;
 }
+function numericBins(overlayTerm, data) {
+  const overlayBins = data.refs.byTermId[overlayTerm?.term?.id]?.bins ?? [];
+  return new Map(overlayBins.map((bin) => [bin.label, bin]));
+}
 export {
   api
 };

package/routes/termdb.categories.js

@@ -1,4 +1,4 @@
-import { termdbCategoriesPayload } from "#types";
+import { termdbCategoriesPayload } from "#types/checkers";
 import { getOrderedLabels } from "#src/termdb.barchart.js";
 import { getData } from "#src/termdb.matrix.js";
 const api = {

package/routes/termdb.cluster.js

@@ -1,6 +1,6 @@
 import path from "path";
 import run_R from "#src/run_R.js";
-import { termdbClusterPayload } from "#types";
+import { termdbClusterPayload } from "#types/checkers";
 import * as utils from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";

package/routes/termdb.cohort.summary.js

@@ -1,4 +1,4 @@
-import { termdbCohortSummaryPayload } from "#types";
+import { termdbCohortSummaryPayload } from "#types/checkers";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
 const api = {

package/routes/termdb.cohorts.js

@@ -1,4 +1,4 @@
-import { termdbCohortsPayload } from "#types";
+import { termdbCohortsPayload } from "#types/checkers";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
 const api = {

package/routes/termdb.descrstats.js

@@ -1,4 +1,4 @@
-import { descrStatsPayload } from "#types";
+import { descrStatsPayload } from "#types/checkers";
 import Summarystats from "#shared/descriptive.stats.js";
 import { getData } from "#src/termdb.matrix.js";
 const api = {

package/routes/termdb.numericcategories.js

@@ -1,4 +1,4 @@
-import { numericCategoriesPayload } from "#types";
+import { numericCategoriesPayload } from "#types/checkers";
 import * as termdbsql from "#src/termdb.sql.js";
 const api = {
   endpoint: "termdb/numericcategories",

package/routes/termdb.percentile.js

@@ -1,4 +1,4 @@
-import { percentilePayload } from "#types";
+import { percentilePayload } from "#types/checkers";
 import * as termdbsql from "#src/termdb.sql.js";
 import computePercentile from "#shared/compute.percentile.js";
 const api = {

package/routes/termdb.rootterm.js

@@ -1,4 +1,4 @@
-import { rootTermPayload } from "#types";
+import { rootTermPayload } from "#types/checkers";
 import { get_ds_tdb } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/rootterm",

package/routes/termdb.sampleImages.js

@@ -1,4 +1,4 @@
-import { termdbSampleImagesPayload } from "#types";
+import { termdbSampleImagesPayload } from "#types/checkers";
 import path from "path";
 import fs from "fs";
 import serverconfig from "#src/serverconfig.js";

package/routes/termdb.singleSampleMutation.js

@@ -2,7 +2,7 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
-import { termdbSingleSampleMutationPayload } from "#types";
+import { termdbSingleSampleMutationPayload } from "#types/checkers";
 import { gdcValidate_query_singleSampleMutation } from "#src/mds3.gdc.js";
 const api = {
   endpoint: "termdb/singleSampleMutation",

package/routes/termdb.singlecellDEgenes.js

@@ -1,4 +1,4 @@
-import { termdbSingleCellDEgenesPayload } from "#types";
+import { termdbSingleCellDEgenesPayload } from "#types/checkers";
 import { gdc_validate_query_singleCell_DEgenes } from "#src/mds3.gdc.js";
 const api = {
   endpoint: "termdb/singlecellDEgenes",

package/routes/termdb.singlecellData.js

@@ -1,4 +1,4 @@
-import { termdbSingleCellDataPayload } from "#types";
+import { termdbSingleCellDataPayload } from "#types/checkers";
 const api = {
   endpoint: "termdb/singlecellData",
   methods: {

package/routes/termdb.singlecellSamples.js

@@ -4,7 +4,7 @@ import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
-import { termdbSingleCellSamplesPayload } from "#types";
+import { termdbSingleCellSamplesPayload } from "#types/checkers";
 import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
 import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 import ky from "ky";
@@ -179,7 +179,7 @@ function validateGeneExpressionNative(G) {
       const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".rds");
       try {
         await fs.promises.stat(rdsfile);
-      } catch (e) {
+      } catch (_) {
         return {};
       }
       let out;
@@ -187,7 +187,7 @@ function validateGeneExpressionNative(G) {
         out = JSON.parse(
           await run_R(path.join(serverconfig.binpath, "utils", "getGeneFromMatrix.R"), null, [rdsfile, q.gene])
         );
-      } catch (e) {
+      } catch (_) {
         return {};
       }
       console.log("out:", out);
@@ -198,7 +198,7 @@ function validateGeneExpressionNative(G) {
       const rdsfile = path.join(serverconfig.tpmasterdir, G.folder, (q.sample.eID || q.sample.sID) + ".h5");
       try {
         await fs.promises.stat(rdsfile);
-      } catch (e) {
+      } catch (_) {
         return {};
       }
       const read_hdf5_input_type = { gene: q.gene, hdf5_file: rdsfile };
@@ -215,7 +215,7 @@ function validateGeneExpressionNative(G) {
             console.log(line);
           }
         }
-      } catch (e) {
+      } catch (_) {
         return {};
       }
       return out;

package/routes/termdb.termchildren.js

@@ -1,4 +1,4 @@
-import { termChildrenPayload } from "#types";
+import { termChildrenPayload } from "#types/checkers";
 import { copy_term, get_ds_tdb } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/termchildren",

package/routes/termdb.termsbyids.js

@@ -1,4 +1,4 @@
-import { termsByIdsPayload } from "#types";
+import { termsByIdsPayload } from "#types/checkers";
 import { copy_term } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/termsbyids",

package/routes/termdb.topTermsByType.js

@@ -1,4 +1,4 @@
-import { termdbTopTermsByTypePayload } from "#types";
+import { termdbTopTermsByTypePayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { get_samples } from "#src/termdb.sql.js";
 import { TermTypes } from "#shared/terms.js";

package/routes/termdb.topVariablyExpressedGenes.js

@@ -1,4 +1,4 @@
-import { termdbTopVariablyExpressedGenesPayload } from "#types";
+import { termdbTopVariablyExpressedGenesPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { get_samples } from "#src/termdb.sql.js";

package/routes/termdb.violin.js

@@ -1,4 +1,4 @@
-import { violinPayload } from "#types";
+import { violinPayload } from "#types/checkers";
 import { trigger_getViolinPlotData } from "#src/termdb.violin.js";
 const api = {
   endpoint: "termdb/violin",

package/routes/tileserver.js

@@ -1,4 +1,4 @@
-import { tilePayload } from "#types";
+import { tilePayload } from "#types/checkers";
 import ky from "ky";
 import serverconfig from "#src/serverconfig.js";
 const api = {

package/routes/wsimages.js

@@ -4,7 +4,7 @@ import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { CookieJar } from "tough-cookie";
 import { promisify } from "util";
-import { wsImagesPayload } from "#types";
+import { wsImagesPayload } from "#types/checkers";
 const routePath = "wsimages";
 const api = {
   endpoint: `${routePath}`,