@sjcrh/proteinpaint-server 2.84.0 → 2.85.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.84.0",
+  "version": "2.85.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -28,7 +28,6 @@
     "dedup": "./dedupjs.sh",
     "//todo": "refactor or deprecate the scripts below",
     "pretest": "tsc && ./test/pretest.js",
-    "prepare": "ts-patch install",
     "pretest:type": "npm run checkers",
     "pretest:integration": "tsc",
     "test:integration": "echo 'TODO: server integration tests'",
@@ -43,7 +42,6 @@
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
-    "@sjcrh/proteinpaint-types": "2.84.0",
     "@types/node": "^20.11.24",
     "@types/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^5.60.0",
@@ -63,9 +61,10 @@
     "typia": "^4.1.14"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.46.0",
+    "@sjcrh/augen": "2.85.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.83.0",
+    "@sjcrh/proteinpaint-shared": "2.85.0",
+    "@sjcrh/proteinpaint-types": "2.85.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/_template_.js

@@ -1,28 +1,31 @@
+import { snpPayload } from "#types";
 const api = {
   // route endpoint
   // - no need for trailing slash
-  // - should be a noun (method is based on HTTP GET, POST, etc)
+  // - should be a noun
   // - don't add 'Data' as response is assumed to be data
-  endpoint: "...",
+  // - don't prefix with `get`, such as `/getmyroute`, the method is already indicated via HTTP GET
+  endpoint: "/myroute",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...snpPayload,
+      // this would "spread"/copy-over payload key-values from snpPayload, such as {request: {typeId}, examples: []}
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...snpPayload,
+      // repeat for post method, since PP routes are mostly read-only and POST can handle bigger payloads
       init
     }
+    // !!! DO NOT USE expressjs 'all' method shortcut !!!
+    // it will initialize 20+ methods includng HEAD which can break expected HTTP response
   }
 };
 function init({ genomes }) {
   return async function(req, res) {
-    console.log(genomes, req, res);
+    const q = req.query;
+    console.log(genomes[q.genome]);
+    res.send({});
   };
 }
 export {

package/routes/brainImaging.js

@@ -1,28 +1,19 @@
 import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
+import { brainImagingPayload } from "#types";
 import { spawn } from "child_process";
 import { getData } from "../src/termdb.matrix.js";
 const api = {
   endpoint: "brainImaging",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "GetBrainImagingRequest"
-      },
-      response: {
-        typeId: "GetBrainImagingResponse"
-      }
+      ...brainImagingPayload,
+      init
     },
     post: {
-      init,
-      request: {
-        typeId: "GetBrainImagingRequest"
-      },
-      response: {
-        typeId: "GetBrainImagingResponse"
-      }
+      ...brainImagingPayload,
+      init
     }
   }
 };

package/routes/brainImagingSamples.js

@@ -8,10 +8,10 @@ const api = {
     get: {
       init,
       request: {
-        typeId: "GetBrainImagingSamplesRequest"
+        typeId: "BrainImagingSamplesRequest"
       },
       response: {
-        typeId: "GetBrainImagingSamplesResponse"
+        typeId: "BrainImagingSamplesResponse"
       }
     }
   }
@@ -62,7 +62,7 @@ async function getBrainImageSamples(query, genomes) {
     throw "no reference or sample files";
   }
 }
-async function validate_query_NIdata(ds, genome) {
+async function validate_query_NIdata(ds) {
   const q = ds.queries.NIdata;
   if (!q || !serverconfig.features?.showBrainImaging)
     return;

package/routes/burden.js

@@ -1,3 +1,4 @@
+import { burdenPayload } from "#types";
 import run_R from "#src/run_R.js";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
@@ -5,68 +6,35 @@ const api = {
   endpoint: "burden",
   methods: {
     get: {
-      init({ genomes }) {
-        return async (req, res) => {
-          try {
-            const genome = genomes[req.query.genome];
-            if (!genome)
-              throw `invalid q.genome=${req.query.genome}`;
-            const q = req.query;
-            const ds = genome.datasets[q.dslabel];
-            if (!ds)
-              throw `invalid q.genome=${req.query.dslabel}`;
-            if (!ds.cohort.cumburden?.files)
-              throw `missing ds.cohort.cumburden.files`;
-            const estimates = await getBurdenEstimates(req, ds);
-            const { keys, rows } = formatPayload(estimates);
-            res.send({ status: "ok", keys, rows });
-          } catch (e) {
-            res.send({ status: "error", error: e.message || e });
-          }
-        };
-      },
-      request: {
-        typeId: "BurdenRequest"
-      },
-      response: {
-        typeId: "BurdenResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38",
-              // TODO: !!! use hg38-test and TermdbTest !!!
-              dslabel: "SJLife",
-              diaggrp: 5,
-              sex: 1,
-              white: 1,
-              agedx: 1,
-              bleo: 0,
-              etop: 0,
-              cisp: 0,
-              carbo: 0,
-              steriod: 0,
-              vcr: 0,
-              hdmtx: 0,
-              itmt: 0,
-              ced: 0,
-              dox: 0,
-              heart: 0,
-              brain: 0,
-              abd: 0,
-              pelvis: 0,
-              chest: 0
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      init,
+      ...burdenPayload
+    },
+    post: {
+      init,
+      ...burdenPayload
     }
   }
 };
+function init({ genomes }) {
+  return async function handler(req, res) {
+    try {
+      const genome = genomes[req.query.genome];
+      if (!genome)
+        throw `invalid q.genome=${req.query.genome}`;
+      const q = req.query;
+      const ds = genome.datasets[q.dslabel];
+      if (!ds)
+        throw `invalid q.genome=${req.query.dslabel}`;
+      if (!ds.cohort.cumburden?.files)
+        throw `missing ds.cohort.cumburden.files`;
+      const estimates = await getBurdenEstimates(req, ds);
+      const { keys, rows } = formatPayload(estimates);
+      res.send({ status: "ok", keys, rows });
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
 async function getBurdenEstimates(q, ds) {
   for (const k in q.query) {
     q.query[k] = Number(q.query[k]);

package/routes/dataset.js

@@ -1,49 +1,41 @@
 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";
 const api = {
   endpoint: "getDataset",
   // should rename to simply 'dataset', method is based on HTTP method
   methods: {
     get: {
       init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...datasetPayload
     },
     post: {
-      alternativeFor: "get",
-      init
+      init,
+      ...datasetPayload
     }
   }
 };
 function init({ genomes }) {
   return function(req, res) {
     try {
-      const genome = genomes[req.query.genome];
+      const q = req.query;
+      const genome = genomes[q.genome];
       if (!genome)
         throw "unknown genome";
       if (!genome.datasets)
         throw "genomeobj.datasets{} missing";
       let ds;
       for (const k in genome.datasets) {
-        if (k.toLowerCase() == req.query.dsname.toLowerCase()) {
+        if (k.toLowerCase() == q.dsname.toLowerCase()) {
           ds = genome.datasets[k];
           break;
         }
       }
       if (!ds)
         throw "invalid dsname";
-      if (ds.isMds3) {
-        return res.send({ ds: mds3_init.client_copy(ds) });
-      }
-      if (ds.isMds) {
-        return res.send({ ds: mds_clientcopy(ds) });
-      }
-      return res.send({ ds: copy_legacyDataset(ds) });
+      const copy = ds.isMds3 ? mds3_init.client_copy(ds) : ds.isMds ? mds_clientcopy(ds) : copy_legacyDataset(ds);
+      return res.send({ ds: copy });
     } catch (e) {
       res.send({ error: e.message || e });
     }

package/routes/dsdata.js

@@ -2,6 +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";
 const api = {
   // route endpoint
   // - no need for trailing slash
@@ -10,16 +11,11 @@ const api = {
   endpoint: "dsdata",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...dsDataPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...dsDataPayload,
       init
     }
   }
@@ -27,19 +23,20 @@ const api = {
 function init({ genomes }) {
   return async function handle_dsdata(req, res) {
     try {
-      if (!genomes[req.query.genome])
+      const q = req.query;
+      if (!genomes[q.genome])
         throw "invalid genome";
-      if (!req.query.dsname)
+      if (!q.dsname)
         throw ".dsname missing";
-      const ds = genomes[req.query.genome].datasets[req.query.dsname];
+      const ds = genomes[q.genome].datasets[q.dsname];
       if (!ds)
         throw "invalid dsname";
       const data = [];
       for (const query of ds.queries) {
-        if (req.query.expressiononly && !query.isgeneexpression) {
+        if (q.expressiononly && !query.isgeneexpression) {
           continue;
         }
-        if (req.query.noexpression && query.isgeneexpression) {
+        if (q.noexpression && query.isgeneexpression) {
           continue;
         }
         if (query.dsblocktracklst) {
@@ -110,7 +107,7 @@ function handle_dsdata_vcf(query, req) {
     const out = [], out2 = [];
     ps.stdout.on("data", (i) => out.push(i));
     ps.stderr.on("data", (i) => out2.push(i));
-    ps.on("close", (code) => {
+    ps.on("close", () => {
       const e = out2.join("").trim();
       if (e != "")
         reject("error querying vcf file");

package/routes/dzimages.js

@@ -1,47 +1,42 @@
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { illegalpath } from "#src/utils.js";
-const routePath = "dzimages";
+import { dzImagesPayload } from "#types";
 const api = {
-  endpoint: `${routePath}/:sampleId`,
+  endpoint: `dzimages/:sampleId`,
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...dzImagesPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...dzImagesPayload,
       init
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
-    let imagePath;
     try {
-      const g = genomes[req.query.genome];
+      const q = req.query;
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
+      const ds = g.datasets[q.dslabel];
       if (!ds)
         throw "invalid dataset name";
-      const sampleId = req.params.sampleId;
+      const sampleId = q.sampleId;
       if (!sampleId)
         throw "invalid sampleId";
       if (illegalpath(req.query.file))
         throw `illegalpath filepath`;
-      const filename = path.basename(req.query.file);
+      const filename = path.basename(q.file);
       const allowedExtensions = [".dzi", ".jpeg", ".png"];
       const extension = path.extname(filename);
       if (!allowedExtensions.includes(extension)) {
         throw `Invalid file extension. Allowed extensions are ${allowedExtensions.join(", ")}`;
       }
-      imagePath = path.join(
+      const imagePath = path.join(
         `${serverconfig.tpmasterdir}/${ds.queries.DZImages.imageBySampleFolder}`,
         `${sampleId}/${req.query.file}`
       );

package/routes/gdc.maf.js

@@ -1,3 +1,4 @@
+import { gdcMafPayload } from "#types";
 import path from "path";
 import got from "got";
 import serverconfig from "#src/serverconfig.js";
@@ -7,29 +8,13 @@ const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 4e8;
 const api = {
   endpoint: "gdc/maf",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "GdcMafRequest"
-      },
-      response: {
-        typeId: "GdcMafResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              experimentalStrategy: "WXS",
-              embedder: "localhost"
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+    get: {
+      ...gdcMafPayload,
+      init
+    },
+    post: {
+      ...gdcMafPayload,
+      init
     }
   }
 };

package/routes/gdc.mafBuild.js

@@ -2,32 +2,32 @@ 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 { maxTotalSizeCompressed } from "./gdc.maf.ts";
 const api = {
   endpoint: "gdc/mafBuild",
   methods: {
-    all: {
+    get: {
       init,
-      request: {
-        typeId: "GdcMafBuildRequest"
-      },
-      response: {
-        typeId: null
-        // 'GdcMafBuildResponse'
-      }
+      ...gdcMafPayload
+    },
+    post: {
+      init,
+      ...gdcMafPayload
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
     try {
+      const q = req.query;
       const g = genomes.hg38;
       if (!g)
         throw "hg38 missing";
       const ds = g.datasets.GDC;
       if (!ds)
         throw "hg38 GDC missing";
-      await buildMaf(req.query, res, ds);
+      await buildMaf(q, res, ds);
     } catch (e) {
       if (e.stack)
         console.log(e.stack);

package/routes/gdc.topMutatedGenes.js

@@ -1,16 +1,16 @@
+import { gdcTopMutatedGenePayload } from "#types";
 import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
 import ky from "ky";
 const api = {
   endpoint: "gdc/topMutatedGenes",
   methods: {
-    all: {
+    get: {
       init,
-      request: {
-        typeId: "GdcTopMutatedGeneRequest"
-      },
-      response: {
-        typeId: "GdcTopMutatedGeneResponse"
-      }
+      ...gdcTopMutatedGenePayload
+    },
+    post: {
+      init,
+      ...gdcTopMutatedGenePayload
     }
   }
 };

package/routes/genelookup.js

@@ -1,12 +1,26 @@
 import { getResult } from "#src/gene.js";
+import { geneLookupPayload } from "#types";
+const api = {
+  endpoint: "genelookup",
+  methods: {
+    get: {
+      init,
+      ...geneLookupPayload
+    },
+    post: {
+      init,
+      ...geneLookupPayload
+    }
+  }
+};
 function init({ genomes }) {
   return (req, res) => {
     try {
       const q = req.query;
-      const g = genomes[req.query.genome];
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome name";
-      const result = getResult(g, req.query);
+      const result = getResult(g, q);
       res.send(result);
     } catch (e) {
       res.send({ error: e.message || e });
@@ -15,38 +29,6 @@ function init({ genomes }) {
     }
   };
 }
-const api = {
-  endpoint: "genelookup",
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "GeneLookupRequest"
-        //valid: default to type checker
-      },
-      response: {
-        typeId: "GeneLookupResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      },
-      examples: [
-        {
-          request: {
-            body: { input: "kr", genome: "hg38-test" }
-          },
-          response: {
-            header: { status: 200 },
-            body: { hits: ["KRAS"] }
-          }
-        }
-      ]
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
 export {
   api
 };

package/routes/genesetEnrichment.js

@@ -1,3 +1,4 @@
+import { genesetEnrichmentPayload } from "#types";
 import fs from "fs";
 import path from "path";
 import { spawn } from "child_process";
@@ -6,26 +7,27 @@ import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "genesetEnrichment",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "genesetEnrichmentRequest"
-      },
-      response: {
-        typeId: "genesetEnrichmentResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      }
+    get: {
+      ...genesetEnrichmentPayload,
+      init
+    },
+    post: {
+      ...genesetEnrichmentPayload,
+      init
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
     try {
-      const results = await run_genesetEnrichment_analysis(req.query, genomes);
-      if (!req.query.geneset_name) {
-        res.send(results);
-      } else {
+      const q = req.query;
+      const results = await run_genesetEnrichment_analysis(q, genomes);
+      if (!q.geneset_name) {
+        if (typeof results != "string")
+          res.send(results);
+        else
+          throw `invalid results type when !req.query.geneset_name`;
+      } else if (typeof results == "string") {
         res.sendFile(results, (err) => {
           fs.unlink(results, (del_err) => {
             if (del_err) {
@@ -79,6 +81,8 @@ async function run_genesetEnrichment_analysis(q, genomes) {
   } else if (image_found) {
     const imagePath = path.join(serverconfig.cachedir, result.image_file);
     return imagePath;
+  } else {
+    throw ``;
   }
 }
 async function run_gsea(path2, data) {