@sjcrh/proteinpaint-server 2.84.0 → 2.85.1

package/routes/genesetOverrepresentation.js

@@ -1,29 +1,24 @@
+import { genesetOverrepresentationPayload } from "#types";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";
 const api = {
   endpoint: "genesetOverrepresentation",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "genesetOverrepresentationRequest"
-      },
-      response: {
-        typeId: "genesetOverrepresentationResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      }
+    get: {
+      ...genesetOverrepresentationPayload,
+      init
+    },
+    post: {
+      ...genesetOverrepresentationPayload,
+      init
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
     try {
-      const results = await run_genesetOverrepresentation_analysis(
-        req.query,
-        genomes
-      );
+      const results = await run_genesetOverrepresentation_analysis(req.query, genomes);
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });

package/routes/healthcheck.js

@@ -1,43 +1,37 @@
 import { getStat } from "#src/health.ts";
+import { healthcheckPayload } from "#types";
 const api = {
   endpoint: "healthcheck",
   methods: {
     get: {
-      init({ genomes }) {
-        return async (req, res) => {
-          try {
-            const health = await getStat(genomes);
-            const q = req.query;
-            if (q.dslabel) {
-              for (const gn in genomes) {
-                const ds = genomes[gn]?.datasets?.[q.dslabel];
-                if (!ds?.getHealth)
-                  continue;
-                if (!health.byDataset)
-                  health.byDataset = {};
-                if (!health.byDataset[q.dslabel])
-                  health.byDataset[q.dslabel] = {};
-                health.byDataset[q.dslabel][gn] = ds.getHealth(ds);
-              }
-            }
-            res.send(health);
-          } catch (e) {
-            res.send({ status: "error", error: e.message || e });
-          }
-        };
-      },
-      request: {
-        typeId: null
-        //valid: default to type checker
-      },
-      response: {
-        typeId: "HealthCheckResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      }
+      ...healthcheckPayload,
+      init
     }
   }
 };
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const q = req.query;
+      const health = await getStat(genomes);
+      if (q.dslabel) {
+        for (const gn in genomes) {
+          const ds = genomes[gn]?.datasets?.[q.dslabel];
+          if (!ds?.getHealth)
+            continue;
+          if (!health.byDataset)
+            health.byDataset = {};
+          if (!health.byDataset[q.dslabel])
+            health.byDataset[q.dslabel] = {};
+          health.byDataset[q.dslabel][gn] = ds.getHealth(ds);
+        }
+      }
+      res.send(health);
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
 export {
   api
 };

package/routes/hicdata.js

@@ -1,3 +1,4 @@
+import { hicdataPayload } from "#types";
 import { fileurl } from "#src/utils.js";
 import { spawn } from "child_process";
 import readline from "readline";
@@ -6,34 +7,11 @@ const api = {
   endpoint: "hicdata",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "HicdataRequest"
-      },
-      response: {
-        typeId: "HicdataResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              embedder: "localhost",
-              url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
-              matrixType: "observed",
-              nmeth: "NONE",
-              pos1: "3",
-              pos2: "2",
-              resolution: 1e6
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...hicdataPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...hicdataPayload,
       init
     }
   }
@@ -41,7 +19,8 @@ const api = {
 function init() {
   return async (req, res) => {
     try {
-      const payload = await handle_hicdata(req.query);
+      const q = req.query;
+      const payload = await handle_hicdata(q);
       res.send(payload);
     } catch (e) {
       res.send({ error: e?.message || e });
@@ -52,7 +31,7 @@ function init() {
 }
 function handle_hicdata(q) {
   return new Promise((resolve, reject) => {
-    const [e, file, isurl] = fileurl({ query: q });
+    const [e, file] = fileurl({ query: q });
     if (e)
       reject({ error: "illegal file name" });
     const matrixType = q.matrixType == "log(oe)" ? "oe" : q.matrixType ? q.matrixType : "observed";

package/routes/hicgenome.js

@@ -1,3 +1,4 @@
+import { hicGenomePayload } from "#types";
 import { fileurl } from "#src/utils.js";
 import { spawn } from "child_process";
 import readline from "readline";
@@ -6,43 +7,21 @@ const api = {
   endpoint: "hicgenome",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "HicGenomeRequest"
-      },
-      response: {
-        typeId: "HicGenomeResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              chrlst: ["chr1", "chr2"],
-              embedder: "localhost",
-              url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
-              matrixType: "observed",
-              nmeth: "NONE",
-              nochr: true,
-              resolution: 25e5
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...hicGenomePayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...hicGenomePayload,
       init
     }
   }
 };
 function init() {
   return async (req, res) => {
+    const query = req.query;
     const data = [];
     const erroutput = [];
-    const [e, file, isurl] = fileurl({ query: req.query });
+    const [e, file] = fileurl({ query });
     if (e)
       res.send({ error: "illegal file name" });
     const matrixType = req.query.matrixType == "log(oe)" ? "oe" : req.query.matrixType ? req.query.matrixType : "observed";

package/routes/hicstat.js

@@ -1,33 +1,15 @@
 import { fileurl, file_is_readable } from "#src/utils.js";
 import { do_hicstat } from "#src/hicstat.ts";
+import { hicstatPayload } from "#types";
 const api = {
   endpoint: "hicstat",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "HicstatRequest"
-      },
-      response: {
-        typeId: "HicstatResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg19",
-              file: "proteinpaint_demo/hg19/hic/hic_demo.hic",
-              embedder: "localhost"
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...hicstatPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...hicstatPayload,
       init
     }
   }

package/routes/isoformlst.js

@@ -1,3 +1,4 @@
+import { isoformlstPayload } from "#types";
 const api = {
   // route endpoint
   // - no need for trailing slash
@@ -6,16 +7,11 @@ const api = {
   endpoint: "isoformlst",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...isoformlstPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...isoformlstPayload,
       init
     }
   }
@@ -23,13 +19,14 @@ const api = {
 function init({ genomes }) {
   return function handle_isoformlst(req, res) {
     try {
-      const g = genomes[req.query.genome];
+      const q = req.query;
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome";
-      if (!Array.isArray(req.query.lst))
+      if (!Array.isArray(q.lst))
         throw ".lst missing";
       const lst = [];
-      for (const isoform of req.query.lst) {
+      for (const isoform of q.lst) {
         if (g.genomicNameRegexp.test(isoform))
           continue;
         const tmp = g.genedb.getjsonbyisoform.all(isoform);

package/routes/ntseq.js

@@ -1,18 +1,14 @@
+import { ntseqPayload } from "#types";
 import { get_fasta } from "#src/utils.js";
 const api = {
   endpoint: "ntseq",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...ntseqPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...ntseqPayload,
       init
     }
   }
@@ -20,14 +16,15 @@ const api = {
 function init({ genomes }) {
   return async function handle_ntseq(req, res) {
     try {
-      if (!req.query.coord)
+      const q = req.query;
+      if (!q.coord)
         throw "coord missing";
-      const g = genomes[req.query.genome];
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome";
       if (!g.genomefile)
         throw "no sequence file available";
-      const seq = await get_fasta(g, req.query.coord);
+      const seq = await get_fasta(g, q.coord);
       res.send({
         seq: seq.split("\n").slice(1).join("")
       });

package/routes/pdomain.js

@@ -1,3 +1,4 @@
+import { pdomainPayload } from "#types";
 const api = {
   // route endpoint
   // - no need for trailing slash
@@ -6,16 +7,11 @@ const api = {
   endpoint: "pdomain",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...pdomainPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...pdomainPayload,
       init
     }
   }
@@ -23,7 +19,8 @@ const api = {
 function init({ genomes }) {
   return function handle_pdomain(req, res) {
     try {
-      const gn = req.query.genome;
+      const q = req.query;
+      const gn = q.genome;
       if (!gn)
         throw "no genome";
       const g = genomes[gn];
@@ -32,10 +29,10 @@ function init({ genomes }) {
       if (!g.proteindomain) {
         return res.send({ lst: [] });
       }
-      if (!Array.isArray(req.query.isoforms))
+      if (!Array.isArray(q.isoforms))
         throw "isoforms[] missing";
       const lst = [];
-      for (const isoform of req.query.isoforms) {
+      for (const isoform of q.isoforms) {
         if (g.genomicNameRegexp.test(isoform))
           continue;
         const tmp = g.proteindomain.getbyisoform.all(isoform);

package/routes/sampledzimages.js

@@ -1,40 +1,40 @@
 import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
+import { dzImagesPayload } from "#types";
 const api = {
   endpoint: "sampledzimages",
   methods: {
     get: {
       init,
-      request: {
-        typeId: "GetSampleDZImagesRequest"
-      },
-      response: {
-        typeId: "GetSampleDZImagesResponse"
-      }
+      ...dzImagesPayload
     },
     post: {
-      alternativeFor: "get",
-      init
+      init,
+      ...dzImagesPayload
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
+    const q = req.query;
     try {
-      const g = genomes[req.query.genome];
+      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.query.sample_id;
+      const sampleId = q.sample_id || "";
       const sampleDZImagesPath = path.join(
         `${serverconfig.tpmasterdir}/${ds.queries.DZImages.imageBySampleFolder}`,
         sampleId
       );
       const sampleDZImages = getDZImages(sampleDZImagesPath);
-      res.send({ sampleDZImages });
+      res.send(
+        { sampleDZImages }
+        /*satisfies DZImagesResponse*/
+      );
     } catch (e) {
       console.log(e);
       res.status(404).send("Sample images not found");

package/routes/samplewsimages.js

@@ -1,17 +1,13 @@
+import { sampleWSImagesPayload } from "#types";
 const api = {
   endpoint: "samplewsimages",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "GetSampleWSImagesRequest"
-      },
-      response: {
-        typeId: "GetSampleWSImagesResponse"
-      }
+      ...sampleWSImagesPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...sampleWSImagesPayload,
       init
     }
   }
@@ -35,8 +31,8 @@ function init({ genomes }) {
     }
   };
 }
-function validate_query_getSampleWSImages(ds, genome) {
-  const q = ds.queries.WSImages;
+function validate_query_getSampleWSImages(ds) {
+  const q = ds.queries?.WSImages;
   if (!q)
     return;
   nativeValidateQuery(ds);

package/routes/snp.js

@@ -1,3 +1,4 @@
+import { snpPayload } from "#types";
 import * as utils from "#src/utils.js";
 const api = {
   // route endpoint
@@ -7,16 +8,11 @@ const api = {
   endpoint: "snp",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...snpPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...snpPayload,
       init
     }
   }
@@ -24,10 +20,12 @@ const api = {
 function init({ genomes }) {
   return async function handle_snp(req, res) {
     try {
-      const n = req.query.genome;
+      const q = req.query;
+      const n = q.genome;
       if (!n)
         throw "no genome";
-      res.send({ results: await searchSNP(req.query, genomes[n]) });
+      const results = await searchSNP(q, genomes[n]);
+      res.send({ results });
     } catch (e) {
       if (e.stack)
         console.log(e.stack);

package/routes/termdb.DE.js

@@ -1,4 +1,5 @@
 import path from "path";
+import { diffExpPayload } from "#types";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { get_ds_tdb } from "../src/termdb.js";
 import run_R from "../src/run_R.js";
@@ -6,16 +7,13 @@ import serverconfig from "../src/serverconfig.js";
 const api = {
   endpoint: "DEanalysis",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "DERequest"
-      },
-      response: {
-        typeId: "DEResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      }
+    get: {
+      ...diffExpPayload,
+      init
+    },
+    post: {
+      ...diffExpPayload,
+      init
     }
   }
 };

package/routes/termdb.boxplot.js

@@ -1,18 +1,17 @@
+import { boxplotPayload } from "#types";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortKey2values } from "../src/termdb.violin.js";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "BoxplotRequest"
-      },
-      response: {
-        typeId: "BoxplotResponse"
-      },
-      examples: []
+    get: {
+      ...boxplotPayload,
+      init
+    },
+    post: {
+      ...boxplotPayload,
+      init
     }
   }
 };

package/routes/termdb.categories.js

@@ -1,56 +1,15 @@
+import { termdbCategoriesPayload } from "#types";
 import { getOrderedLabels } from "#src/termdb.barchart.js";
 import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/categories",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "getcategoriesRequest"
-      },
-      response: {
-        typeId: "getcategoriesResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              term: { id: "diaggrp" },
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                lst: [
-                  {
-                    tag: "cohortFilter",
-                    type: "tvs",
-                    tvs: {
-                      term: {
-                        name: "Cohort",
-                        type: "categorical",
-                        values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
-                        id: "subcohort",
-                        isleaf: false,
-                        groupsetting: { disabled: true }
-                      },
-                      values: [{ key: "ABC", label: "ABC" }]
-                    }
-                  }
-                ]
-              }
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...termdbCategoriesPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...termdbCategoriesPayload,
       init
     }
   }

package/routes/termdb.cluster.js

@@ -1,5 +1,6 @@
 import path from "path";
 import run_R from "#src/run_R.js";
+import { termdbClusterPayload } from "#types";
 import * as utils from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
@@ -11,14 +12,13 @@ import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbClusterRequest"
-      },
-      response: {
-        typeId: "TermdbClusterResponse"
-      }
+    get: {
+      ...termdbClusterPayload,
+      init
+    },
+    post: {
+      ...termdbClusterPayload,
+      init
     }
   }
 };
@@ -135,7 +135,7 @@ async function doClustering(data, q, numCases = 1e3) {
     for (const s of inputData.col_names) {
       row.push(o[s] || 0);
     }
-    inputData.matrix.push(getZscore(row));
+    inputData.matrix.push(q.zScoreTransformation ? getZscore(row) : row);
   }
   if (inputData.matrix.length == 0)
     throw "Clustering matrix is empty";