@sjcrh/proteinpaint-server 2.189.0 → 2.190.0

package/routes/hicstat.js

@@ -1,35 +0,0 @@
-import { fileurl, file_is_readable } from "#src/utils.js";
-import { do_hicstat } from "#src/hicstat.ts";
-import { hicstatPayload } from "#types/checkers";
-const api = {
-  endpoint: "hicstat",
-  methods: {
-    get: {
-      ...hicstatPayload,
-      init
-    },
-    post: {
-      ...hicstatPayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      const [e, file, isurl] = fileurl(req);
-      if (e) throw "illegal file name";
-      if (!isurl) {
-        await file_is_readable(file);
-      }
-      const out = await do_hicstat(file, isurl);
-      res.send({ out });
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-export {
-  api
-};

package/routes/img.js

@@ -1,46 +0,0 @@
-import { imgPayload } from "#types/checkers";
-import path from "path";
-import fs from "fs";
-import * as utils from "../src/utils.js";
-import { imageSize } from "image-size";
-const api = {
-  endpoint: "img",
-  methods: {
-    get: {
-      ...imgPayload,
-      init
-    },
-    post: {
-      ...imgPayload,
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      sendImage(req, res);
-    } catch (e) {
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-async function sendImage(req, res) {
-  const [e, file] = utils.fileurl(req, true);
-  try {
-    if (e) throw "invalid image file";
-    const data = await fs.promises.readFile(file);
-    const ext = path.extname(file).substring(1);
-    const { width, height } = imageSize(file);
-    const image = {
-      src: `data:image/${ext};base64,${Buffer.from(data).toString("base64")}`,
-      size: `${width}x${height}`
-    };
-    res.send({ ...image });
-  } catch (e2) {
-    res.send({ error: e2.message || e2 });
-  }
-}
-export {
-  api
-};

package/routes/isoformlst.js

@@ -1,48 +0,0 @@
-import { isoformlstPayload } from "#types/checkers";
-const api = {
-  // route endpoint
-  // - no need for trailing slash
-  // - should be a noun (method is based on HTTP GET, POST, etc)
-  // - don't add 'Data' as response is assumed to be data
-  endpoint: "isoformlst",
-  methods: {
-    get: {
-      ...isoformlstPayload,
-      init
-    },
-    post: {
-      ...isoformlstPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return function handle_isoformlst(req, res) {
-    try {
-      const q = req.query;
-      const g = genomes[q.genome];
-      if (!g) throw "invalid genome";
-      if (!Array.isArray(q.lst)) throw ".lst missing";
-      const lst = [];
-      for (const isoform of q.lst) {
-        if (g.genomicNameRegexp.test(isoform)) continue;
-        const tmp = g.genedb.getjsonbyisoform.all(isoform);
-        lst.push(
-          tmp.map((i) => {
-            const j = JSON.parse(i.genemodel);
-            if (i.isdefault) j.isdefault = true;
-            return j;
-          })
-        );
-      }
-      res.send({ lst });
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-      else console.trace(e);
-    }
-  };
-}
-export {
-  api
-};

package/routes/ntseq.js

@@ -1,36 +0,0 @@
-import { ntseqPayload } from "#types/checkers";
-import { get_fasta } from "#src/utils.js";
-const api = {
-  endpoint: "ntseq",
-  methods: {
-    get: {
-      ...ntseqPayload,
-      init
-    },
-    post: {
-      ...ntseqPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async function handle_ntseq(req, res) {
-    try {
-      const q = req.query;
-      if (!q.coord) throw "coord missing";
-      const g = genomes[q.genome];
-      if (!g) throw "invalid genome";
-      if (!g.genomefile) throw "no sequence file available";
-      const seq = await get_fasta(g, q.coord);
-      res.send({
-        seq: seq.split("\n").slice(1).join("")
-      });
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-    }
-  };
-}
-export {
-  api
-};

package/routes/pdomain.js

@@ -1,53 +0,0 @@
-import { pdomainPayload } from "#types/checkers";
-const api = {
-  // route endpoint
-  // - no need for trailing slash
-  // - should be a noun (method is based on HTTP GET, POST, etc)
-  // - don't add 'Data' as response is assumed to be data
-  endpoint: "pdomain",
-  methods: {
-    get: {
-      ...pdomainPayload,
-      init
-    },
-    post: {
-      ...pdomainPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return function handle_pdomain(req, res) {
-    try {
-      const q = req.query;
-      const gn = q.genome;
-      if (!gn) throw "no genome";
-      const g = genomes[gn];
-      if (!g) throw "invalid genome " + gn;
-      if (!g.proteindomain) {
-        return res.send({ lst: [] });
-      }
-      if (!Array.isArray(q.isoforms)) throw "isoforms[] missing";
-      const lst = [];
-      for (const isoform of q.isoforms) {
-        if (g.genomicNameRegexp.test(isoform)) continue;
-        const tmp = g.proteindomain.getbyisoform.all(isoform);
-        lst.push({
-          name: isoform,
-          pdomains: tmp.map((i) => {
-            const j = JSON.parse(i.data);
-            j.refseq = isoform;
-            return j;
-          })
-        });
-      }
-      res.send({ lst });
-    } catch (e) {
-      res.send({ error: e.message || e });
-      if (e.stack) console.log(e.stack);
-    }
-  };
-}
-export {
-  api
-};

package/routes/profile.barchart2.js

@@ -1,114 +0,0 @@
-import { ProfileScoresPayload } from "#types/checkers";
-import { getData } from "../src/termdb.matrix.js";
-const api = {
-  endpoint: "termdb/profileBarchart2Scores",
-  methods: {
-    get: {
-      ...ProfileScoresPayload,
-      init
-    },
-    post: {
-      ...ProfileScoresPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScores(req.query, ds);
-      res.send(result);
-    } catch (e) {
-      console.log(e);
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-function derivePrefix(query) {
-  const firstScoreId = query.scoreTerms?.[0]?.score?.term?.id;
-  if (firstScoreId?.startsWith("F")) return "F";
-  if (firstScoreId?.startsWith("A")) return "A";
-  for (const entry of query.filter?.lst || []) {
-    const id = entry.tvs?.term?.id;
-    if (id?.startsWith("F")) return "F";
-    if (id?.startsWith("A")) return "A";
-  }
-  throw "cannot determine cohort prefix from scoreTerms or filter term IDs";
-}
-async function getScores(query, ds) {
-  const { activeCohort, clientAuthResult } = query.__protected__;
-  const prefix = derivePrefix(query);
-  const facilityTermId = `${prefix}UNIT`;
-  const facilityTW = { term: { id: facilityTermId }, q: {} };
-  const terms = [facilityTW];
-  for (const t of query.scoreTerms) {
-    terms.push(t.score);
-    if (t.maxScore?.term) terms.push(t.maxScore);
-  }
-  if (!query.filterByUserSites) {
-    query.__protected__.ignoredTermIds.push(facilityTermId);
-  }
-  const cohortAuth = clientAuthResult[activeCohort];
-  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
-  const userSites = cohortAuth?.sites;
-  const raw = await getData(
-    {
-      terms,
-      filter: query.filter,
-      __protected__: query.__protected__
-    },
-    ds
-  );
-  if (raw.error) throw raw.error;
-  const sampleList = Object.values(raw.samples);
-  let sites = sampleList.map((s) => {
-    const val = s[facilityTW.$id].value;
-    let label = facilityTW.term.values?.[val]?.label || val;
-    if (label.length > 50) label = label.slice(0, 47) + "...";
-    return { value: val, label };
-  });
-  if (userSites && query.filterByUserSites) {
-    sites = sites.filter((s) => userSites.includes(s.value));
-  }
-  sites.sort((a, b) => a.label.localeCompare(b.label));
-  const samples = Object.values(raw.samples);
-  const eligibleSamples = userSites && query.filterByUserSites ? samples.filter((s) => userSites.includes(s[facilityTW.$id].value)) : samples;
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    const score = computeMedianPercentage(d, eligibleSamples);
-    if (score !== null) term2Score[d.score.term.id] = score;
-  }
-  return {
-    term2Score,
-    // Public users see only aggregated scores — do not expose site IDs or names
-    sites: isPublic ? [] : sites,
-    n: eligibleSamples.length
-  };
-}
-function computeMedianPercentage(d, samples) {
-  const percentages = [];
-  for (const s of samples) {
-    const scoreValue = s[d.score.$id]?.value;
-    if (scoreValue == null) continue;
-    let maxScoreValue = null;
-    if (typeof d.maxScore === "number") {
-      maxScoreValue = d.maxScore;
-    } else {
-      maxScoreValue = s[d.maxScore.$id]?.value;
-    }
-    if (maxScoreValue == null || maxScoreValue === 0) continue;
-    const percentage = scoreValue / maxScoreValue * 100;
-    percentages.push(percentage);
-  }
-  if (percentages.length === 0) return null;
-  percentages.sort((a, b) => a - b);
-  const mid = Math.floor(percentages.length / 2);
-  const median = percentages.length % 2 !== 0 ? percentages[mid] : (percentages[mid - 1] + percentages[mid]) / 2;
-  return Math.round(median);
-}
-export {
-  api
-};

package/routes/profile.forms2.js

@@ -1,107 +0,0 @@
-import { ProfileForms2ScoresPayload } from "#types/checkers";
-import { getData } from "../src/termdb.matrix.js";
-const api = {
-  endpoint: "termdb/profileForms2Scores",
-  methods: {
-    get: {
-      ...ProfileForms2ScoresPayload,
-      init
-    },
-    post: {
-      ...ProfileForms2ScoresPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScores(req.query, ds);
-      res.send(result);
-    } catch (e) {
-      console.log(e);
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-async function getScores(query, ds) {
-  const { activeCohort, clientAuthResult } = query.__protected__;
-  const facilityTermId = ds.cohort.termdb.plotConfigByCohort?.[activeCohort]?.profileForms2?.facilityTW?.id;
-  if (!facilityTermId) throw `profileForms2.facilityTW.id missing for cohort '${activeCohort}'`;
-  const facilityTW = { term: { id: facilityTermId }, q: {} };
-  const terms = [facilityTW, ...query.scoreTerms];
-  if (query.scScoreTerms) terms.push(...query.scScoreTerms);
-  if (!query.filterByUserSites) query.__protected__.ignoredTermIds.push(facilityTermId);
-  const cohortAuth = clientAuthResult[activeCohort];
-  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
-  const userSites = cohortAuth?.sites;
-  const raw = await getData(
-    {
-      terms,
-      filter: query.filter,
-      __protected__: query.__protected__
-    },
-    ds
-  );
-  if (raw.error) throw raw.error;
-  const samples = Object.values(raw.samples);
-  let sites = samples.map((s) => {
-    const val = s[facilityTW.$id].value;
-    let label = facilityTW.term.values?.[val]?.label || val;
-    if (label.length > 50) label = label.slice(0, 47) + "...";
-    return { value: val, label };
-  });
-  if (userSites && query.filterByUserSites) sites = sites.filter((s) => userSites.includes(s.value));
-  sites.sort((a, b) => a.label.localeCompare(b.label));
-  const eligibleSamples = userSites && query.filterByUserSites ? samples.filter((s) => userSites.includes(s[facilityTW.$id].value)) : samples;
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    term2Score[d.term.id] = getPercentsDict((sample) => getDict(d.$id, sample), eligibleSamples);
-  }
-  if (query.scScoreTerms) {
-    for (const d of query.scScoreTerms) {
-      term2Score[d.term.id] = getSCPercentsDict(d, eligibleSamples);
-    }
-  }
-  return {
-    term2Score,
-    sites: isPublic ? [] : sites,
-    // public never sees site IDs
-    n: eligibleSamples.length
-  };
-}
-function getDict(key, sample) {
-  if (!sample[key]) return null;
-  const termData = sample[key].value;
-  return JSON.parse(termData);
-}
-function getPercentsDict(getDictFunc, samples) {
-  const percentageDict = {};
-  for (const sample of samples) {
-    const percents = getDictFunc(sample);
-    if (!percents) continue;
-    for (const key in percents) {
-      const value = percents[key];
-      if (!percentageDict[key]) percentageDict[key] = 0;
-      percentageDict[key] += value;
-    }
-  }
-  return percentageDict;
-}
-function getSCPercentsDict(tw, samples) {
-  if (!tw) throw "tw not defined";
-  const percentageDict = {};
-  for (const sample of samples) {
-    const key = sample[tw.$id]?.value;
-    if (key == null) continue;
-    if (!percentageDict[key]) percentageDict[key] = 0;
-    percentageDict[key] += 1;
-  }
-  return percentageDict;
-}
-export {
-  api
-};

package/routes/profile.polar2.js

@@ -1,101 +0,0 @@
-import { ProfileScoresPayload } from "#types/checkers";
-import { getData } from "../src/termdb.matrix.js";
-const api = {
-  endpoint: "termdb/profilePolar2Scores",
-  methods: {
-    get: {
-      ...ProfileScoresPayload,
-      init
-    },
-    post: {
-      ...ProfileScoresPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScores(req.query, ds);
-      res.send(result);
-    } catch (e) {
-      console.log(e);
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-function derivePrefix(query) {
-  const firstScoreId = query.scoreTerms?.[0]?.score?.term?.id;
-  if (firstScoreId?.startsWith("F")) return "F";
-  if (firstScoreId?.startsWith("A")) return "A";
-  for (const entry of query.filter?.lst || []) {
-    const id = entry.tvs?.term?.id;
-    if (id?.startsWith("F")) return "F";
-    if (id?.startsWith("A")) return "A";
-  }
-  throw "cannot determine cohort prefix from scoreTerms or filter term IDs";
-}
-async function getScores(query, ds) {
-  const { activeCohort, clientAuthResult } = query.__protected__;
-  const prefix = derivePrefix(query);
-  const facilityTermId = `${prefix}UNIT`;
-  const facilityTW = { term: { id: facilityTermId }, q: {} };
-  const terms = [facilityTW];
-  for (const t of query.scoreTerms) {
-    terms.push(t.score);
-    if (t.maxScore?.term) terms.push(t.maxScore);
-  }
-  if (!query.filterByUserSites) {
-    query.__protected__.ignoredTermIds.push(facilityTermId);
-  }
-  const cohortAuth = clientAuthResult[activeCohort];
-  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
-  const userSites = cohortAuth?.sites;
-  const raw = await getData(
-    {
-      terms,
-      filter: query.filter,
-      __protected__: query.__protected__
-    },
-    ds
-  );
-  if (raw.error) throw raw.error;
-  const sampleList = Object.values(raw.samples);
-  let sites = sampleList.map((s) => {
-    const val = s[facilityTW.$id].value;
-    let label = facilityTW.term.values?.[val]?.label || val;
-    if (label.length > 50) label = label.slice(0, 47) + "...";
-    return { value: val, label };
-  });
-  if (userSites && query.filterByUserSites) {
-    sites = sites.filter((s) => userSites.includes(s.value));
-  }
-  sites.sort((a, b) => a.label.localeCompare(b.label));
-  const samples = Object.values(raw.samples);
-  const eligibleSamples = userSites && query.filterByUserSites ? samples.filter((s) => userSites.includes(s[facilityTW.$id].value)) : samples;
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    const score = computeMedianPercentage(d, eligibleSamples);
-    if (score !== null) term2Score[d.score.term.id] = score;
-  }
-  return {
-    term2Score,
-    // Public users see only aggregated scores — do not expose site IDs or names
-    sites: isPublic ? [] : sites,
-    n: eligibleSamples.length
-  };
-}
-function computeMedianPercentage(d, samples) {
-  const percentages = samples.filter((s) => s[d.score.$id]?.value != null).map((s) => s[d.score.$id].value / (s[d.maxScore.$id]?.value || d.maxScore) * 100);
-  if (percentages.length === 0) return null;
-  percentages.sort((a, b) => a - b);
-  const mid = Math.floor(percentages.length / 2);
-  const median = percentages.length % 2 !== 0 ? percentages[mid] : (percentages[mid - 1] + percentages[mid]) / 2;
-  return Math.round(median);
-}
-export {
-  api
-};

package/routes/profile.radar2.js

@@ -1,112 +0,0 @@
-import { ProfileScoresPayload } from "#types/checkers";
-import { getData } from "../src/termdb.matrix.js";
-const api = {
-  endpoint: "termdb/profileRadar2Scores",
-  methods: {
-    get: {
-      ...ProfileScoresPayload,
-      init
-    },
-    post: {
-      ...ProfileScoresPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScores(req.query, ds);
-      res.send(result);
-    } catch (e) {
-      console.log(e);
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-function derivePrefix(query) {
-  const firstScoreId = query.scoreTerms?.[0]?.score?.term?.id;
-  if (firstScoreId?.startsWith("F")) return "F";
-  if (firstScoreId?.startsWith("A")) return "A";
-  for (const entry of query.filter?.lst || []) {
-    const id = entry.tvs?.term?.id;
-    if (id?.startsWith("F")) return "F";
-    if (id?.startsWith("A")) return "A";
-  }
-  throw "cannot determine cohort prefix from scoreTerms or filter term IDs";
-}
-async function getScores(query, ds) {
-  const { activeCohort, clientAuthResult } = query.__protected__;
-  const prefix = derivePrefix(query);
-  const facilityTermId = `${prefix}UNIT`;
-  const facilityTW = { term: { id: facilityTermId }, q: {} };
-  const terms = [facilityTW];
-  for (const t of query.scoreTerms) {
-    terms.push(t.score);
-    if (t.maxScore?.term) terms.push(t.maxScore);
-  }
-  if (!query.filterByUserSites) {
-    query.__protected__.ignoredTermIds.push(facilityTermId);
-  }
-  const cohortAuth = clientAuthResult[activeCohort];
-  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
-  const userSites = cohortAuth?.sites;
-  const raw = await getData(
-    {
-      terms,
-      filter: query.filter,
-      __protected__: query.__protected__
-    },
-    ds
-  );
-  if (raw.error) throw raw.error;
-  const sampleList = Object.values(raw.samples);
-  let sites = sampleList.map((s) => {
-    const val = s[facilityTW.$id].value;
-    let label = facilityTW.term.values?.[val]?.label || val;
-    if (label.length > 50) label = label.slice(0, 47) + "...";
-    return { value: val, label };
-  });
-  if (userSites && query.filterByUserSites) {
-    sites = sites.filter((s) => userSites.includes(s.value));
-  }
-  sites.sort((a, b) => a.label.localeCompare(b.label));
-  const samples = Object.values(raw.samples);
-  const eligibleSamples = userSites && query.filterByUserSites ? samples.filter((s) => userSites.includes(s[facilityTW.$id].value)) : samples;
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    const score = computeMedianPercentage(d, eligibleSamples);
-    if (score !== null) term2Score[d.score.term.id] = score;
-  }
-  return {
-    term2Score,
-    sites: isPublic ? [] : sites,
-    n: eligibleSamples.length
-  };
-}
-function computeMedianPercentage(d, samples) {
-  const percentages = [];
-  for (const s of samples) {
-    const scoreValue = s[d.score.$id]?.value;
-    if (scoreValue == null) continue;
-    let maxScoreValue = null;
-    if (typeof d.maxScore === "number") {
-      maxScoreValue = d.maxScore;
-    } else {
-      maxScoreValue = s[d.maxScore.$id]?.value;
-    }
-    if (maxScoreValue == null || maxScoreValue === 0) continue;
-    percentages.push(scoreValue / maxScoreValue * 100);
-  }
-  if (percentages.length === 0) return null;
-  percentages.sort((a, b) => a - b);
-  const mid = Math.floor(percentages.length / 2);
-  const median = percentages.length % 2 !== 0 ? percentages[mid] : (percentages[mid - 1] + percentages[mid]) / 2;
-  return Math.round(median);
-}
-export {
-  api
-};