@sjcrh/proteinpaint-server 2.189.0 → 2.190.0

package/routes/termdb.percentile.js

@@ -1,66 +0,0 @@
-import { percentilePayload } from "#types/checkers";
-import { isNumericTerm } from "#shared/terms.js";
-import { getData } from "#src/termdb.matrix.js";
-import computePercentile from "#shared/compute.percentile.js";
-const api = {
-  endpoint: "termdb/getpercentile",
-  methods: {
-    get: {
-      ...percentilePayload,
-      init
-    },
-    post: {
-      ...percentilePayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
-      if (!ds) throw "invalid dataset name";
-      await trigger_getpercentile(q, res, ds);
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-async function trigger_getpercentile(q, res, ds) {
-  const term = q.term;
-  if (!term) throw "term is missing";
-  if (!isNumericTerm(term)) throw "not numeric term";
-  const tw = { $id: "_", term, q: { mode: "continuous" } };
-  const data = await getData({ filter: q.filter, filter0: q.filter0, terms: [tw], __protected__: q.__protected__ }, ds);
-  if (data.error) throw data.error;
-  const values = [];
-  for (const key in data.samples) {
-    const sample = data.samples[key];
-    const v = sample[tw.$id];
-    if (!v?.value) {
-      continue;
-    }
-    const value = v.value;
-    if (term.values && term.values[value] && term.values[value].uncomputable) {
-      continue;
-    }
-    if (term.skip0forPercentile && value == 0) {
-      continue;
-    }
-    values.push(Number(value));
-  }
-  const percentile_lst = q.getpercentile;
-  const perc_values = [];
-  for (const percentile of percentile_lst) {
-    const perc_value = computePercentile(values, percentile);
-    perc_values.push(perc_value);
-  }
-  res.send({ values: perc_values });
-}
-export {
-  api
-};

package/routes/termdb.profileFormScores.js

@@ -1,92 +0,0 @@
-import { ProfileFormScoresPayload } from "#types/checkers";
-import { getScoresData } from "./termdb.profileScores.ts";
-const api = {
-  endpoint: "termdb/profileFormScores",
-  methods: {
-    get: {
-      ...ProfileFormScoresPayload,
-      init
-    },
-    post: {
-      ...ProfileFormScoresPayload,
-      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 getScoresDict(req.query, ds);
-      res.send(result);
-    } catch (e) {
-      console.log(e);
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-async function getScoresDict(query, ds) {
-  const terms = [...query.scoreTerms, query.facilityTW];
-  if (query.scScoreTerms) terms.push(...query.scScoreTerms);
-  const data = await getScoresData(query, ds, terms);
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    const getDictFunc = (sample) => getDict(d.$id, sample);
-    const percents = getPercentsDict(getDictFunc, data.samples);
-    term2Score[d.term.id] = percents;
-  }
-  if (query.scScoreTerms)
-    for (const d of query.scScoreTerms) {
-      const percents = getSCPercentsDict(d, data.samples);
-      term2Score[d.term.id] = percents;
-    }
-  const { clientAuthResult, activeCohort } = query.__protected__;
-  const isPublic = !clientAuthResult[activeCohort]?.role || clientAuthResult[activeCohort].role === "public";
-  let hospital;
-  if (!isPublic && data.sampleData) {
-    const facilityValue = data.sampleData[query.facilityTW.$id];
-    const termValue = query.facilityTW.term.values[facilityValue?.value];
-    hospital = termValue?.label || termValue?.key;
-  }
-  return {
-    term2Score,
-    // Do not expose individual site IDs, names, or hospital to public-role users
-    sites: isPublic ? [] : data.sites,
-    hospital,
-    n: data.sampleData ? 1 : data.samples.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 twData = sample[tw.$id];
-    const key = twData?.value;
-    if (!percentageDict[key]) percentageDict[key] = 0;
-    percentageDict[key] += 1;
-  }
-  return percentageDict;
-}
-export {
-  api
-};

package/routes/termdb.profileScores.js

@@ -1,113 +0,0 @@
-import { ProfileScoresPayload } from "#types/checkers";
-import { getData } from "../src/termdb.matrix.js";
-const api = {
-  endpoint: "termdb/profileScores",
-  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 });
-    }
-  };
-}
-async function getScoresData(query, ds, terms) {
-  if (!query.filterByUserSites) query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
-  const { clientAuthResult, activeCohort } = query.__protected__;
-  const userSites = clientAuthResult[activeCohort].sites;
-  const data = await getData(
-    {
-      terms,
-      filter: query.filter,
-      __protected__: query.__protected__
-    },
-    ds
-  );
-  if (data.error) throw data.error;
-  const lst = Object.values(data.samples);
-  let sites = lst.map((s) => {
-    let label = query.facilityTW.term.values[s[query.facilityTW.$id].value]?.label || s[query.facilityTW.$id].value;
-    if (label.length > 50) label = label.slice(0, 47) + "...";
-    return {
-      value: s[query.facilityTW.$id].value,
-      label
-    };
-  });
-  if (userSites) {
-    sites = sites.filter((s) => userSites.includes(s.value));
-  }
-  sites.sort((a, b) => {
-    return a.label.localeCompare(b.label);
-  });
-  const samples = Object.values(data.samples);
-  let sampleData, site;
-  if ("facilitySite" in query) {
-    const facilitySite = query.facilitySite || sites[0].value;
-    const index = lst.findIndex((s) => s[query.facilityTW.$id].value == facilitySite);
-    sampleData = lst[index];
-    site = sites.find((s) => s.value == facilitySite);
-  } else if (sites.length == 1) {
-    sampleData = data.samples[sites[0].value];
-    site = sites[0];
-  }
-  return { samples, sampleData, sites, site };
-}
-async function getScores(query, ds) {
-  const terms = [query.facilityTW];
-  for (const term of query.scoreTerms) {
-    terms.push(term.score);
-    if (term.maxScore?.term) {
-      terms.push(term.maxScore);
-    }
-  }
-  const data = await getScoresData(query, ds, terms);
-  const term2Score = {};
-  for (const d of query.scoreTerms) {
-    term2Score[d.score.term.id] = getPercentage(d, data.samples, data.sampleData);
-  }
-  const { clientAuthResult, activeCohort } = query.__protected__;
-  const isPublic = !clientAuthResult[activeCohort]?.role || clientAuthResult[activeCohort].role === "public";
-  return {
-    term2Score,
-    // Do not expose individual site IDs or names to public-role users
-    sites: isPublic ? [] : data.sites,
-    site: isPublic ? void 0 : data.site,
-    n: data.sampleData ? 1 : data.samples.length
-  };
-}
-function getPercentage(d, samples, sampleData) {
-  if (!d) return null;
-  const isAggregate = sampleData == null;
-  if (isAggregate) {
-    const scores = samples.filter((sample) => sample[d.score.$id]?.value).map((sample) => sample[d.score.$id].value / (sample[d.maxScore.$id]?.value || d.maxScore) * 100);
-    scores.sort((s1, s2) => s1 - s2);
-    const middle = Math.floor(scores.length / 2);
-    const score = scores.length % 2 !== 0 ? scores[middle] : (scores[middle - 1] + scores[middle]) / 2;
-    return Math.round(score);
-  } else {
-    const score = sampleData[d.score.$id]?.value;
-    const maxScore = d.maxScore.term ? sampleData[d.maxScore.$id]?.value : d.maxScore;
-    const percentage = score / maxScore * 100;
-    return Math.round(percentage);
-  }
-}
-export {
-  api,
-  getScoresData
-};

package/routes/termdb.rootterm.js

@@ -1,39 +0,0 @@
-import { rootTermPayload } from "#types/checkers";
-import { get_ds_tdb } from "#src/termdb.js";
-const api = {
-  endpoint: "termdb/rootterm",
-  methods: {
-    get: {
-      ...rootTermPayload,
-      init
-    },
-    post: {
-      ...rootTermPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const [ds, tdb] = get_ds_tdb(g, q);
-      if (!ds) throw "invalid dataset name";
-      if (!tdb) throw "invalid termdb object";
-      await trigger_rootterm(req, q, res, tdb);
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-async function trigger_rootterm(req, q, res, tdb) {
-  const cohortValues = q.cohortValues ? q.cohortValues : "";
-  const treeFilter = q.treeFilter ? q.treeFilter : "";
-  res.send({ lst: await tdb.q.getRootTerms(req, cohortValues, treeFilter) });
-}
-export {
-  api
-};

package/routes/termdb.sampleImages.js

@@ -1,63 +0,0 @@
-import { termdbSampleImagesPayload } from "#types/checkers";
-import path from "path";
-import fs from "fs";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "termdb/getSampleImages",
-  methods: {
-    get: {
-      ...termdbSampleImagesPayload,
-      init
-    },
-    post: {
-      ...termdbSampleImagesPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const q = req.query;
-      const sampleId = q.sampleId;
-      const genome = genomes[q.genome];
-      if (!genome) throw "invalid genome";
-      const ds = genome.datasets?.[q.dslabel];
-      if (!ds) throw "invalid dslabel";
-      const images = await ds.queries.images.getSampleImages({ sampleId });
-      res.send({ images });
-    } catch (e) {
-      res.send({ status: "error", error: e.message || e });
-    }
-  };
-}
-function validate_query_getSampleImages(ds) {
-  const q = ds.queries.images;
-  if (!q) return;
-  nativeValidateQuery(ds);
-}
-function nativeValidateQuery(ds) {
-  ds.queries.images.getSampleImages = async (q) => {
-    const folder = ds.queries.images.folder;
-    const images = await getSampleImages(ds, folder, q.sampleId);
-    return images;
-  };
-}
-async function getSampleImages(ds, folder, sampleId) {
-  const sql = `SELECT * FROM images WHERE sample = ${sampleId}`;
-  const rows = ds.cohort.db.connection.prepare(sql).all();
-  const images = [];
-  for (const row of rows) {
-    const file = path.join(serverconfig.tpmasterdir, folder, row.fileName);
-    if (!fs.existsSync(file)) throw new Error(`File ${row.fileName} does not exist`);
-    const data = await fs.promises.readFile(file);
-    images.push({
-      src: "data:image/jpeg;base64," + Buffer.from(data).toString("base64")
-    });
-  }
-  return images;
-}
-export {
-  api,
-  validate_query_getSampleImages
-};

package/routes/termdb.singleSampleMutation.js

@@ -1,75 +0,0 @@
-import path from "path";
-import { read_file, file_is_readable, fileurl, illegalpath } from "#src/utils.js";
-import { termdbSingleSampleMutationPayload } from "#types/checkers";
-import { gdcValidate_query_singleSampleMutation } from "#src/mds3.gdc.js";
-const api = {
-  endpoint: "termdb/singleSampleMutation",
-  methods: {
-    get: {
-      ...termdbSingleSampleMutationPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    let result;
-    try {
-      const g = genomes[q.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[q.dslabel];
-      if (!ds) throw "invalid dataset name";
-      if (!ds.queries?.singleSampleMutation) throw "not supported on this dataset";
-      result = await ds.queries.singleSampleMutation.get(q);
-    } catch (e) {
-      if (e.stack) console.log(e.stack);
-      result = {
-        status: e.status || 400,
-        error: e.message || e
-      };
-    }
-    res.send(result);
-  };
-}
-async function validate_query_singleSampleMutation(ds, genome) {
-  const _q = ds.queries.singleSampleMutation;
-  if (!_q) return;
-  if (typeof _q.get == "function") {
-  } else if (_q.src == "gdcapi") {
-    gdcValidate_query_singleSampleMutation(ds, genome);
-  } else if (_q.src == "native") {
-    _q.get = async (q) => {
-      let sample;
-      {
-        const vt = typeof q.sample;
-        if (vt == "string") {
-          if (q.sample == "") throw "sample is blank string";
-          sample = q.sample;
-        } else if (vt == "number") {
-          sample = q.sample.toString();
-        } else {
-          throw "sample value is not string or number";
-        }
-      }
-      if (illegalpath(sample)) throw "invalid sample name";
-      const tmp = fileurl({
-        query: {
-          file: path.join(_q.folder, sample)
-        }
-      });
-      if (tmp[0]) throw tmp[0];
-      const file = tmp[1];
-      if (!file) throw "no file returned";
-      await file_is_readable(file);
-      const data = await read_file(file);
-      return { mlst: JSON.parse(data) };
-    };
-  } else {
-    throw "unknown singleSampleMutation.src";
-  }
-}
-export {
-  api,
-  validate_query_singleSampleMutation
-};

package/routes/termdb.singlecellDEgenes.js

@@ -1,55 +0,0 @@
-import { termdbSingleCellDEgenesPayload } from "#types/checkers";
-import { gdc_validate_query_singleCell_DEgenes } from "#src/mds3.gdc.js";
-const api = {
-  endpoint: "termdb/singlecellDEgenes",
-  methods: {
-    get: {
-      ...termdbSingleCellDEgenesPayload,
-      init
-    },
-    post: {
-      ...termdbSingleCellDEgenesPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    let result;
-    try {
-      const g = genomes[q.genome];
-      if (!g) throw new Error("invalid genome name");
-      const ds = g.datasets[q.dslabel];
-      if (!ds) throw new Error("invalid dataset name");
-      if (!ds.queries?.singleCell?.DEgenes || !ds.queries.singleCell.DEgenes.get)
-        throw new Error("DE genes not supported on this dataset.");
-      result = await ds.queries.singleCell.DEgenes.get(q);
-      const isEmpty = !result || !result.data || (Array.isArray(result.data) ? result.data.length === 0 : !result.data.totalRows);
-      if (isEmpty) {
-        result = {
-          status: 404,
-          error: !result ? "No data found." : "No differentially expressed genes found."
-        };
-      }
-    } catch (e) {
-      if (e.stack) console.log(e.stack);
-      result = {
-        status: e.status || 400,
-        error: e.message || e
-      };
-    }
-    res.send(result);
-  };
-}
-async function validate_query_singleCell_DEgenes(ds) {
-  if (ds.queries.singleCell.DEgenes.src == "gdcapi") {
-    gdc_validate_query_singleCell_DEgenes(ds);
-  } else {
-    throw new Error("unknown singleCell.DEgenes.src");
-  }
-}
-export {
-  api,
-  validate_query_singleCell_DEgenes
-};

package/routes/termdb.singlecellData.js

@@ -1,39 +0,0 @@
-import { termdbSingleCellDataPayload } from "#types/checkers";
-const api = {
-  endpoint: "termdb/singlecellData",
-  methods: {
-    get: {
-      ...termdbSingleCellDataPayload,
-      init
-    },
-    post: {
-      ...termdbSingleCellDataPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    let result;
-    try {
-      const g = genomes[q.genome];
-      if (!g) throw new Error("invalid genome name");
-      const ds = g.datasets[q.dslabel];
-      if (!ds) throw new Error("invalid dataset name");
-      if (!ds.queries?.singleCell) throw new Error("no single cell data on this dataset");
-      if (!ds.queries.singleCell.data?.get) throw new Error("dataset has no single cell data get() function");
-      result = await ds.queries.singleCell.data.get(q);
-    } catch (e) {
-      if (e.stack) console.log(e);
-      result = {
-        status: e.status || 400,
-        error: e.message || e
-      };
-    }
-    res.send(result);
-  };
-}
-export {
-  api
-};

package/routes/termdb.termchildren.js

@@ -1,42 +0,0 @@
-import { termChildrenPayload } from "#types/checkers";
-import { copy_term, get_ds_tdb } from "#src/termdb.js";
-const api = {
-  endpoint: "termdb/termchildren",
-  methods: {
-    get: {
-      ...termChildrenPayload,
-      init
-    },
-    post: {
-      ...termChildrenPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const [ds, tdb] = await get_ds_tdb(g, q);
-      if (!ds) throw "invalid dataset name";
-      if (!tdb) throw "invalid termdb object";
-      const result = await trigger_children(req, q, tdb);
-      res.send(result);
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-async function trigger_children(req, q, tdb) {
-  if (!q.tid) throw "no parent term id";
-  const cohortValues = q.cohortValues ? q.cohortValues : "";
-  const treeFilter = q.treeFilter ? q.treeFilter : "";
-  const terms = await tdb.q.getTermChildren(req, q.tid, cohortValues, treeFilter);
-  return { lst: terms.map(copy_term) };
-}
-export {
-  api
-};

package/routes/termdb.termsbyids.js

@@ -1,50 +0,0 @@
-import { termsByIdsPayload } from "#types/checkers";
-import { copy_term } from "#src/termdb.js";
-const api = {
-  endpoint: "termdb/termsbyids",
-  methods: {
-    get: {
-      ...termsByIdsPayload,
-      init
-    },
-    post: {
-      ...termsByIdsPayload,
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const g = genomes[req.query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
-      if (!ds) throw "invalid dataset name";
-      const tdb = ds.cohort.termdb;
-      if (!tdb) throw "invalid termdb object";
-      const results = await trigger_gettermsbyid(q, tdb);
-      res.send(results);
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack) console.log(e);
-    }
-  };
-}
-async function trigger_gettermsbyid(q, tdb) {
-  const terms = {};
-  for (const id of q.ids) {
-    const term = tdb.q.termjsonByOneid(id);
-    if (term) {
-      if (term.type == "categorical" && !term.values) {
-        term.values = {};
-        term.samplecount = {};
-      }
-    }
-    terms[id] = term ? copy_term(term) : void 0;
-  }
-  return { terms };
-}
-export {
-  api
-};