@sjcrh/proteinpaint-server 2.83.0 → 2.85.0

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) {

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);