@sjcrh/proteinpaint-server 2.170.6 → 2.170.9

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Files changed (10) hide show
  1. package/package.json +3 -3
  2. package/routes/termdb.boxplot.js +4 -1
  3. package/routes/termdb.categories.js +2 -1
  4. package/routes/termdb.cluster.js +1 -0
  5. package/routes/termdb.descrstats.js +8 -2
  6. package/routes/termdb.sampleScatter.js +2 -2
  7. package/routes/termdb.violin.js +2 -1
  8. package/routes/types.js +0 -0
  9. package/src/app.js +258 -110
  10. package/src/mds3.gdc.filter.js +1 -1
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@sjcrh/proteinpaint-server",
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- "version": "2.170.6",
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+ "version": "2.170.9",
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  "type": "module",
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  "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
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  "main": "src/app.js",
@@ -65,8 +65,8 @@
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  "@sjcrh/proteinpaint-python": "2.169.0",
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  "@sjcrh/proteinpaint-r": "2.152.1-0",
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  "@sjcrh/proteinpaint-rust": "2.170.0",
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- "@sjcrh/proteinpaint-shared": "2.170.6",
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- "@sjcrh/proteinpaint-types": "2.170.6",
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+ "@sjcrh/proteinpaint-shared": "2.170.9",
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+ "@sjcrh/proteinpaint-types": "2.170.9-57f94bf9a.0",
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  "@types/express": "^5.0.0",
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  "@types/express-session": "^1.18.1",
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  "better-sqlite3": "^12.4.1",
package/routes/termdb.boxplot.js CHANGED
@@ -30,7 +30,10 @@ function init({ genomes }) {
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  if (q.overlayTw) terms.push(q.overlayTw);
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  if (q.divideTw) terms.push(q.divideTw);
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  try {
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- const data = await getData({ filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ }, ds);
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+ const data = await getData(
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+ { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__, __abortSignal: q.__abortSignal },
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+ ds
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+ );
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  if (data.error) throw new Error(data.error);
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  const { absMin, absMax, bins, charts, uncomputableValues, descrStats, outlierMin, outlierMax } = await processData(data, q);
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  const returnData = {
package/routes/termdb.categories.js CHANGED
@@ -42,7 +42,8 @@ async function trigger_getcategories(q, res, tdb, ds) {
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  // optional, from mds3 mayAddGetCategoryArgs()
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  rglst: q.rglst,
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  // optional, from mds3 mayAddGetCategoryArgs()
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- __protected__: q.__protected__
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+ __protected__: q.__protected__,
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+ __abortSignal: q.__abortSignal
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  };
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  const data = await getData(arg, ds);
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  if (data.error) throw data.error;
package/routes/termdb.cluster.js CHANGED
@@ -62,6 +62,7 @@ async function getResult(q, ds) {
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  if (q.dataType == TermTypes.GENE_EXPRESSION) {
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  _q = JSON.parse(JSON.stringify(q));
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  _q.forClusteringAnalysis = true;
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+ _q.__abortSignal = q.__abortSignal;
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  }
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  let term2sample2value, byTermId, bySampleId, skippedSexChrGenes;
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  if (q.dataType == NUMERIC_DICTIONARY_TERM) {
package/routes/termdb.descrstats.js CHANGED
@@ -37,14 +37,20 @@ function init({ genomes }) {
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  }
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  async function trigger_getDescrStats(q, ds) {
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  const data = await getData(
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- { filter: q.filter, filter0: q.filter0, terms: [q.tw], __protected__: q.__protected__ },
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+ {
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+ filter: q.filter,
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+ filter0: q.filter0,
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+ terms: [q.tw],
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+ __protected__: q.__protected__,
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+ __abortSignal: q.__abortSignal
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+ },
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  ds
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  );
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  if (data.error) throw data.error;
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  const values = [];
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  for (const key in data.samples) {
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  const sample = data.samples[key];
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- const v = sample[q.tw.$id];
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+ const v = sample[q.tw.$id || ""];
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  if (!v && v !== 0) {
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  continue;
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  }
package/routes/termdb.sampleScatter.js CHANGED
@@ -40,14 +40,14 @@ function init({ genomes }) {
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  if (q.scaleDotTW) terms.push(q.scaleDotTW);
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  if (q.coordTWs) for (const tw of q.coordTWs) terms.push(tw);
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  const data = await getData(
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- { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ },
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+ { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__, __abortSignal: q.__abortSignal },
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  ds,
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  true
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  // FIXME 3rd arg hardcoded to true
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  );
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  if (data.error) throw new Error(data.error);
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  let result;
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- if (q.coordTWs.length > 0) {
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+ if (q.coordTWs && q.coordTWs.length > 0) {
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  const tmp = await getSampleCoordinatesByTerms(req, q, ds, data);
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  cohortSamples = tmp[0];
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  } else {
package/routes/termdb.violin.js CHANGED
@@ -52,7 +52,8 @@ async function getViolin(q, ds) {
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  filter: q.filter,
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  filter0: q.filter0,
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  currentGeneNames: q.currentGeneNames,
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- __protected__: q.__protected__
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+ __protected__: q.__protected__,
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+ __abortSignal: q.__abortSignal
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  },
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  ds
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  );
package/routes/types.js ADDED
File without changes