@sjcrh/proteinpaint-server 2.189.0 → 2.190.0

package/routes/_template_.js

@@ -1,33 +0,0 @@
-import { snpPayload } from "#types/checkers";
-const api = {
-  // route endpoint
-  // - no need for trailing slash
-  // - should be a noun
-  // - don't add 'Data' as response is assumed to be data
-  // - don't prefix with `get`, such as `/getmyroute`, the method is already indicated via HTTP GET
-  endpoint: "/myroute",
-  methods: {
-    get: {
-      ...snpPayload,
-      // this would "spread"/copy-over payload key-values from snpPayload, such as {request: {typeId}, examples: []}
-      init
-    },
-    post: {
-      ...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) {
-    const q = req.query;
-    console.log(genomes[q.genome]);
-    res.send({});
-  };
-}
-export {
-  api
-};

package/routes/aiProjectTrainModel.js

@@ -1,68 +0,0 @@
-import { aiProjectTrainModelPayload } from "#types/checkers";
-import { TileServerSessionsHandler } from "#src/wsisessions/TileServerSessionsHandler.ts";
-import SessionManager from "#src/wsisessions/SessionManager.ts";
-import { getDbConnection } from "#src/aiHistoDBConnection.js";
-import { getImages } from "#routes/aiProjectAdmin.js";
-const api = {
-  endpoint: "aiProjectTrainModel",
-  methods: {
-    get: {
-      ...aiProjectTrainModelPayload,
-      init
-    },
-    post: {
-      ...aiProjectTrainModelPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async function(req, res) {
-    try {
-      const query = req.query;
-      const g = genomes[query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[query.dslabel];
-      if (!ds) throw "invalid dataset name";
-      if (typeof ds.queries.WSImages.retrainModel == "function") {
-        const connection = getDbConnection(ds);
-        const project = {
-          id: query.projectId
-        };
-        const wsimages = getImages(connection, project);
-        await ds.queries.WSImages.retrainModel(query.projectId, wsimages);
-        try {
-          const handler = new TileServerSessionsHandler();
-          const sessionMgr = SessionManager.getInstance();
-          const keySessions = await sessionMgr.getAllKeyValues();
-          const sessions = keySessions.map((kv) => kv?.sessionData).filter(Boolean);
-          if (sessions && sessions.length) {
-            await handler.resetSessions(sessions);
-            await Promise.all(keySessions.map((kv) => sessionMgr.deleteSession(kv.key)));
-          }
-        } catch (err) {
-          console.warn("TileServerSessionsHandler error:", err);
-        }
-      } else {
-        res.status(500).send({
-          status: "error",
-          error: "No retraining script defined"
-        });
-        return;
-      }
-      res.status(200).send({
-        status: "ok",
-        message: `Retraining model completed`
-      });
-    } catch (e) {
-      console.warn(e);
-      res.status(500).send({
-        status: "error",
-        error: e.message || e
-      });
-    }
-  };
-}
-export {
-  api
-};

package/routes/alphaGenome.js

@@ -1,41 +0,0 @@
-import { alphaGenomePayload } from "#types/checkers";
-import { run_python } from "@sjcrh/proteinpaint-python";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "alphaGenome",
-  methods: {
-    get: {
-      ...alphaGenomePayload,
-      init
-    },
-    post: {
-      ...alphaGenomePayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      const query = req.query;
-      const params = {
-        API_KEY: serverconfig.alphaGenome.API_KEY,
-        chromosome: query.chromosome,
-        position: query.position,
-        reference: query.reference,
-        alternate: query.alternate,
-        interval: query.interval
-      };
-      if (query.ontologyTerms) params["ontologyTerms"] = query.ontologyTerms;
-      if (query.outputType) params["outputType"] = Number(query.outputType);
-      const url = await run_python("alphaGenome.py", JSON.stringify(params));
-      res.send({ plotImage: url });
-    } catch (e) {
-      console.log(e);
-      res.status(404).send({ error: e });
-    }
-  };
-}
-export {
-  api
-};

package/routes/alphaGenomeTypes.js

@@ -1,36 +0,0 @@
-import { alphaGenomeTypesPayload } from "#types/checkers";
-import { run_python } from "@sjcrh/proteinpaint-python";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "AlphaGenomeTypes",
-  methods: {
-    get: {
-      ...alphaGenomeTypesPayload,
-      init
-    },
-    post: {
-      ...alphaGenomeTypesPayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      const params = { API_KEY: serverconfig.alphaGenome.API_KEY };
-      const result = await run_python("AlphaGenomeTypes.py", JSON.stringify(params));
-      const { ontologyTerms, outputTypes, intervals } = JSON.parse(result);
-      res.send({
-        ontologyTerms: ontologyTerms.sort((a, b) => a.label.localeCompare(b.label)),
-        outputTypes,
-        intervals
-      });
-    } catch (e) {
-      console.log(e);
-      res.status(404).send({ error: e });
-    }
-  };
-}
-export {
-  api
-};

package/routes/dzimages.js

@@ -1,55 +0,0 @@
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
-import { illegalpath } from "#src/utils.js";
-import { dzImagesPayload } from "#types/checkers";
-const api = {
-  endpoint: `dzimages/:sampleId`,
-  methods: {
-    get: {
-      ...dzImagesPayload,
-      init
-    },
-    post: {
-      ...dzImagesPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const q = req.query;
-      const g = genomes[q.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[q.dslabel];
-      if (!ds) throw "invalid dataset name";
-      const sampleId = q.sampleId;
-      if (!sampleId) throw "invalid sampleId";
-      if (illegalpath(req.query.file)) throw `illegalpath filepath`;
-      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 ${allowedExtensions.join(", ")}`;
-      }
-      const imagePath = path.join(
-        `${serverconfig.tpmasterdir}/${ds.queries.DZImages.imageBySampleFolder}`,
-        `${sampleId}/${req.query.file}`
-      );
-      res.sendFile(imagePath, (err) => {
-        if (err) {
-          res.status(404).send("Image not found");
-        }
-      });
-    } catch (e) {
-      console.log(e);
-      res.send({
-        status: "error",
-        error: e.error || e
-      });
-    }
-  };
-}
-export {
-  api
-};

package/routes/gene2canonicalisoform.js

@@ -1,37 +0,0 @@
-const api = {
-  endpoint: "gene2canonicalisoform",
-  // should rename to simply 'canonicalIsoform' or 'isoform', gene and type: 'canonical' can be part of payload
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return function(req, res) {
-    try {
-      if (!req.query.gene) throw ".gene missing";
-      const genome = genomes[req.query.genome];
-      if (!genome) throw "unknown genome";
-      if (!genome.genedb.get_gene2canonicalisoform) throw "gene2canonicalisoform not supported on this genome";
-      const data = genome.genedb.get_gene2canonicalisoform.get(req.query.gene);
-      res.send(data);
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-    }
-  };
-}
-export {
-  api
-};

package/routes/genelookup.js

@@ -1,32 +0,0 @@
-import { getResult } from "#src/gene.js";
-import { geneLookupPayload } from "#types/checkers";
-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[q.genome];
-      if (!g) throw "invalid genome name";
-      const result = getResult(g, q);
-      res.send(result);
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-    }
-  };
-}
-export {
-  api
-};

package/routes/genesetOverrepresentation.js

@@ -1,49 +0,0 @@
-import { genesetOverrepresentationPayload } from "#types/checkers";
-import { run_rust } from "@sjcrh/proteinpaint-rust";
-import serverconfig from "#src/serverconfig.js";
-import path from "path";
-const api = {
-  endpoint: "genesetOverrepresentation",
-  methods: {
-    get: {
-      ...genesetOverrepresentationPayload,
-      init
-    },
-    post: {
-      ...genesetOverrepresentationPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const results = await run_genesetOverrepresentation_analysis(req.query, genomes);
-      res.send(results);
-    } catch (e) {
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-async function run_genesetOverrepresentation_analysis(q, genomes) {
-  if (!genomes[q.genome].termdbs) throw "termdb database is not available for " + q.genome;
-  const gene_overrepresentation_input_type = {
-    sample_genes: q.sample_genes,
-    msigdb: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
-    gene_set_group: q.geneSetGroup,
-    filter_non_coding_genes: q.filter_non_coding_genes,
-    genedb: path.join(serverconfig.tpmasterdir, genomes[q.genome].genedb.dbfile)
-  };
-  if (q.background_genes) {
-    gene_overrepresentation_input_type.background_genes = q.background_genes;
-  }
-  const time1 = (/* @__PURE__ */ new Date()).valueOf();
-  const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input_type));
-  const time2 = (/* @__PURE__ */ new Date()).valueOf();
-  console.log("Time taken to run rust gene over representation pipeline:", time2 - time1, "ms");
-  const result = JSON.parse(rust_output);
-  return result;
-}
-export {
-  api
-};

package/routes/genomes.js

@@ -1,150 +0,0 @@
-import fs from "fs";
-import serverconfig from "#src/serverconfig.js";
-import { authApi } from "#src/auth.js";
-import { versionInfo } from "#src/health.ts";
-const api = {
-  endpoint: "genomes",
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async function handle_genomes(req, res) {
-    try {
-      await fs.promises.stat(serverconfig.tpmasterdir);
-    } catch (e) {
-      let message = "Error with TP directory (" + e.code + ")";
-      const m = serverconfig.maintenance || {};
-      if ("start" in m && "stop" in m && m.tpMessage) {
-        const start = +new Date(m.start);
-        const stop = +new Date(m.stop);
-        const currTime = +/* @__PURE__ */ new Date();
-        if (start <= currTime && currTime <= stop) {
-          message = m.tpMessage;
-        }
-      }
-      res.send({ error: message });
-      return;
-    }
-    const hash = {};
-    if (req.query && req.query.genome) {
-      hash[req.query.genome] = clientcopy_genome(req.query.genome, genomes);
-    } else {
-      for (const genomename in genomes) {
-        hash[genomename] = clientcopy_genome(genomename, genomes);
-      }
-    }
-    let hasblat = false;
-    for (const n in genomes) {
-      if (genomes[n].blat) hasblat = true;
-    }
-    res.send({
-      genomes: hash,
-      debugmode: serverconfig.debugmode,
-      headermessage: serverconfig.headermessage,
-      base_zindex: serverconfig.base_zindex,
-      pkgver: versionInfo.pkgver,
-      codedate: versionInfo.codedate,
-      // still useful to know the package build/publish date in the response payload, even if it's not displayed
-      launchdate: versionInfo.launchdate,
-      hasblat,
-      features: serverconfig.features,
-      dsAuth: authApi.getDsAuth(req),
-      commonOverrides: serverconfig.commonOverrides,
-      targetPortal: serverconfig.targetPortal,
-      //sending target portal to the client
-      cardsPath: serverconfig.cards?.path
-    });
-  };
-}
-function clientcopy_genome(genomename, genomes) {
-  const g = genomes[genomename];
-  const g2 = {
-    species: g.species,
-    name: genomename,
-    hasSNP: g.snp ? true : false,
-    hasIdeogram: g.genedb.hasIdeogram,
-    fimo_motif: g.fimo_motif ? true : false,
-    blat: g.blat ? true : false,
-    geneset: g.geneset,
-    defaultcoord: g.defaultcoord,
-    isdefault: g.isdefault,
-    majorchr: g.majorchr,
-    majorchrorder: g.majorchrorder,
-    minorchr: g.minorchr,
-    tracks: g.tracks,
-    hicenzymefragment: g.hicenzymefragment,
-    datasets: {},
-    hideOnClient: g.hideOnClient
-  };
-  if (g.termdbs) {
-    g2.termdbs = {};
-    for (const k in g.termdbs) {
-      g2.termdbs[k] = {
-        label: g.termdbs[k].label,
-        analysisGenesetGroups: g.termdbs[k].analysisGenesetGroups,
-        geneORAparam: g.termdbs[k].geneORAparam
-      };
-    }
-  }
-  for (const dsname in g.datasets) {
-    const ds = g.datasets[dsname];
-    if (ds.isMds3) {
-      g2.datasets[ds.label] = {
-        isMds3: true,
-        noHandleOnClient: ds.noHandleOnClient,
-        label: ds.label
-      };
-      continue;
-    }
-    if (ds.isMds) {
-      g2.datasets[ds.label] = {
-        isMds: true,
-        mdsIsUninitiated: true,
-        noHandleOnClient: ds.noHandleOnClient,
-        label: ds.label
-      };
-      continue;
-    }
-    g2.datasets[ds.label] = {
-      isofficial: true,
-      legacyDsIsUninitiated: true,
-      // so client only gets copy_legacyDataset once
-      noHandleOnClient: ds.noHandleOnClient,
-      label: ds.label
-    };
-  }
-  if (g.hicdomain) {
-    g2.hicdomain = { groups: {} };
-    for (const s1 in g.hicdomain.groups) {
-      const tt = g.hicdomain.groups[s1];
-      g2.hicdomain.groups[s1] = {
-        name: tt.name,
-        reference: tt.reference,
-        sets: {}
-      };
-      for (const s2 in tt.sets) {
-        g2.hicdomain.groups[s1].sets[s2] = {
-          name: tt.sets[s2].name,
-          longname: tt.sets[s2].longname
-        };
-      }
-    }
-  }
-  return g2;
-}
-export {
-  api
-};

package/routes/healthcheck.js

@@ -1,35 +0,0 @@
-import { getStat } from "#src/health.ts";
-import { healthcheckPayload } from "#types/checkers";
-const api = {
-  endpoint: "healthcheck",
-  methods: {
-    get: {
-      ...healthcheckPayload,
-      init
-    }
-  }
-};
-function init(arg) {
-  const genomes = arg.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

@@ -1,74 +0,0 @@
-import { hicdataPayload } from "#types/checkers";
-import { fileurl } from "#src/utils.js";
-import { spawn } from "child_process";
-import readline from "readline";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "hicdata",
-  methods: {
-    get: {
-      ...hicdataPayload,
-      init
-    },
-    post: {
-      ...hicdataPayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      const q = req.query;
-      const payload = await handle_hicdata(q);
-      res.send(payload);
-    } catch (e) {
-      res.send({ error: e?.message || e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-function handle_hicdata(q) {
-  return new Promise((resolve, reject) => {
-    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";
-    const par = [matrixType, q.nmeth || "NONE", file, q.pos1, q.pos2, q.isfrag ? "FRAG" : "BP", q.resolution];
-    const ps = spawn(serverconfig.hicstraw, par);
-    const rl = readline.createInterface({ input: ps.stdout });
-    const items = [];
-    const erroutput = [];
-    let linenot3fields = 0;
-    let fieldnotnumerical = 0;
-    rl.on("line", (line) => {
-      const l = line.split("	");
-      if (l.length != 3) {
-        linenot3fields++;
-        return;
-      }
-      const n1 = Number.parseInt(l[0]);
-      const n2 = Number.parseInt(l[1]);
-      const v = q.matrixType == "log(oe)" ? Math.log(Number.parseFloat(l[2])) : Number.parseFloat(l[2]);
-      if (Number.isNaN(n1) || Number.isNaN(n2) || Number.isNaN(v)) {
-        fieldnotnumerical++;
-        return;
-      }
-      if (q.mincutoff != void 0 && v <= q.mincutoff) {
-        return;
-      }
-      items.push([n1, n2, v]);
-    });
-    ps.stderr.on("data", (i) => erroutput.push(i));
-    ps.on("close", () => {
-      const err = erroutput.join("");
-      if (err) reject({ error: err });
-      if (linenot3fields) reject({ error: linenot3fields + " lines have other than 3 fields" });
-      if (fieldnotnumerical)
-        reject({ error: fieldnotnumerical + " lines have non-numerical values in any of the 3 fields" });
-      resolve({ items });
-    });
-  });
-}
-export {
-  api
-};

package/routes/hicgenome.js

@@ -1,75 +0,0 @@
-import { hicGenomePayload } from "#types/checkers";
-import { fileurl } from "#src/utils.js";
-import { spawn } from "child_process";
-import readline from "readline";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "hicgenome",
-  methods: {
-    get: {
-      ...hicGenomePayload,
-      init
-    },
-    post: {
-      ...hicGenomePayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    const query = req.query;
-    const data = [];
-    const erroutput = [];
-    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";
-    const promises = req.query.chrlst.map((lead, i) => {
-      return req.query.chrlst.slice(0, i + 1).map((follow, j) => {
-        if (j <= i) {
-          return new Promise((resolve, reject) => {
-            const pos1 = req.query.nochr ? lead.replace("chr", "") : lead;
-            const pos2 = req.query.nochr ? follow.replace("chr", "") : follow;
-            const par = [matrixType, req.query.nmeth || "NONE", file, pos1, pos2, "BP", req.query.resolution];
-            const ps = spawn(serverconfig.hicstraw, par);
-            const rl = readline.createInterface({ input: ps.stdout });
-            const items = [];
-            let linenot3fields = 0;
-            let fieldnotnumerical = 0;
-            rl.on("line", (line) => {
-              const l = line.split("	");
-              if (l.length != 3) {
-                linenot3fields++;
-                return;
-              }
-              const n1 = Number.parseInt(l[0]);
-              const n2 = Number.parseInt(l[1]);
-              const v = req.query.matrixType == "log(oe)" ? Math.log(Number.parseFloat(l[2])) : Number.parseFloat(l[2]);
-              if (Number.isNaN(n1) || Number.isNaN(n2) || Number.isNaN(v)) {
-                fieldnotnumerical++;
-                return;
-              }
-              items.push([n1, n2, v]);
-            });
-            data.push({ items, lead, follow });
-            ps.stderr.on("data", (i2) => erroutput.push(`${lead} - ${follow}: `, i2));
-            ps.on("close", () => {
-              if (erroutput.length) reject({ error: erroutput.join("") });
-              if (linenot3fields) reject({ error: `${linenot3fields} lines have other than 3 fields` });
-              if (fieldnotnumerical)
-                reject(`${fieldnotnumerical} lines have non-numerical values in any of the 3 fields`);
-              resolve();
-            });
-          });
-        }
-      });
-    }).flat();
-    Promise.allSettled(promises).then(() => res.send({ data, error: erroutput.join("") })).catch((e2) => {
-      res.send({ error: e2?.message || e2 });
-      if (e2 instanceof Error && e2.stack) console.log(e2);
-    });
-  };
-}
-export {
-  api
-};