@sjcrh/proteinpaint-server 2.174.1 → 2.176.0

package/routes/termdb.cluster.js

@@ -62,6 +62,7 @@ async function getResult(q, ds) {
   if (q.dataType == TermTypes.GENE_EXPRESSION) {
     _q = JSON.parse(JSON.stringify(q));
     _q.forClusteringAnalysis = true;
+    _q.__abortSignal = q.__abortSignal;
   }
   let term2sample2value, byTermId, bySampleId, skippedSexChrGenes;
   if (q.dataType == NUMERIC_DICTIONARY_TERM) {

package/routes/termdb.config.js

@@ -80,7 +80,6 @@ function make(q, req, res, ds, genome) {
   if (ds.cohort.boxplots) c.boxplots = ds.cohort.boxplots;
   if (tdb.maxGeneVariantGeneSetSize) c.maxGeneVariantGeneSetSize = tdb.maxGeneVariantGeneSetSize;
   addRestrictAncestries(c, tdb);
-  addScatterplots(c, ds);
   addMatrixplots(c, ds);
   addMutationSignatureplots(c, ds);
   addNonDictionaryQueries(c, ds, genome);
@@ -89,6 +88,7 @@ function make(q, req, res, ds, genome) {
   c.clientAuthResult = info?.clientAuthResult || {};
   if (tdb.displaySampleIds) c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
   c.authFilter = req.query.filter;
+  addScatterplots(c, ds, info);
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {
@@ -97,8 +97,12 @@ function addRestrictAncestries(c, tdb) {
     return { name: i.name, tvs: i.tvs, PCcount: i.PCcount };
   });
 }
-function addScatterplots(c, ds) {
+function addScatterplots(c, ds, info) {
   if (!ds.cohort.scatterplots) return;
+  if (ds.cohort.scatterplots.get) {
+    c.scatterplots = ds.cohort.scatterplots.get(info?.clientAuthResult);
+    return;
+  }
   c.scatterplots = ds.cohort.scatterplots.plots.map((p) => {
     return {
       name: p.name,

package/routes/termdb.descrstats.js

@@ -37,14 +37,20 @@ function init({ genomes }) {
 }
 async function trigger_getDescrStats(q, ds) {
   const data = await getData(
-    { filter: q.filter, filter0: q.filter0, terms: [q.tw], __protected__: q.__protected__ },
+    {
+      filter: q.filter,
+      filter0: q.filter0,
+      terms: [q.tw],
+      __protected__: q.__protected__,
+      __abortSignal: q.__abortSignal
+    },
     ds
   );
   if (data.error) throw data.error;
   const values = [];
   for (const key in data.samples) {
     const sample = data.samples[key];
-    const v = sample[q.tw.$id];
+    const v = sample[q.tw.$id || ""];
     if (!v && v !== 0) {
       continue;
     }

package/routes/termdb.runChart.js

@@ -14,9 +14,9 @@ const api = {
   }
 };
 async function getRunChart(q, ds) {
-  const terms = [q.term, q.term2];
-  const xTermId = q.term["$id"];
-  const yTermId = q.term2["$id"];
+  const terms = [q.xtw, q.ytw];
+  const xTermId = q.xtw["$id"] ?? q.xtw.term?.id;
+  const yTermId = q.ytw["$id"] ?? q.ytw.term?.id;
   const { getData } = await import("../src/termdb.matrix.js");
   const data = await getData(
     {
@@ -28,20 +28,47 @@ async function getRunChart(q, ds) {
     true
   );
   if (data.error) throw new Error(data.error);
-  return buildRunChartFromData(q.aggregation, xTermId, yTermId, data);
+  const shouldPartition = q.xtw?.q?.mode === "discrete";
+  return buildRunChartFromData(q.aggregation, xTermId, yTermId, data, shouldPartition, xTermId);
 }
-function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
+function buildRunChartFromData(aggregation, xTermId, yTermId, data, shouldPartition, partitionTermId) {
+  const allSamples = data.samples || {};
+  if (shouldPartition && partitionTermId) {
+    const period2Samples = {};
+    for (const sampleId in allSamples) {
+      const sample = allSamples[sampleId];
+      const partitionTerm = sample?.[partitionTermId];
+      if (partitionTerm?.key == null) {
+        continue;
+      }
+      const periodKey = partitionTerm.key;
+      if (!period2Samples[periodKey]) period2Samples[periodKey] = {};
+      period2Samples[periodKey][sampleId] = sample;
+    }
+    const periodKeys = Object.keys(period2Samples).sort();
+    const series = periodKeys.map((seriesId) => {
+      const subset = { samples: period2Samples[seriesId] };
+      const one2 = buildOneSeries(aggregation, xTermId, yTermId, subset);
+      return { seriesId, ...one2 };
+    });
+    return { status: "ok", series };
+  }
+  const one = buildOneSeries(aggregation, xTermId, yTermId, data);
+  return { status: "ok", series: [{ ...one }] };
+}
+function buildOneSeries(aggregation, xTermId, yTermId, data) {
+  const supportedAggregations = ["proportion", "count", "median"];
+  if (!supportedAggregations.includes(aggregation)) {
+    throw new Error(
+      `Unsupported aggregation method: ${aggregation}. Supported values are: ${supportedAggregations.join(", ")}`
+    );
+  }
   const buckets = {};
-  let skippedSamples = 0;
   for (const sampleId in data.samples || {}) {
     const sample = data.samples[sampleId];
     const xRaw = sample?.[xTermId]?.value ?? sample?.[xTermId]?.key;
     const yRaw = sample?.[yTermId]?.value ?? sample?.[yTermId]?.key;
-    if (xRaw == null || yRaw == null) {
-      skippedSamples++;
-      console.log(
-        `Skipping sample ${sampleId}: Missing x or y value - xTermId=${xTermId} (value: ${xRaw}), yTermId=${yTermId} (value: ${yRaw})`
-      );
+    if (xRaw == null) {
       continue;
     }
     if (typeof xRaw !== "number") {
@@ -68,13 +95,9 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
         month = Math.floor(frac * 12) + 1;
       }
     } else {
-      year = null;
+      month = 1;
     }
     if (year == null || month == null || Number.isNaN(year) || Number.isNaN(month)) {
-      skippedSamples++;
-      console.log(
-        `Skipping sample ${sampleId}: Invalid date value - xTermId=${xTermId}, xRaw=${xRaw}, parsed year=${year}, month=${month}`
-      );
       continue;
     }
     const yearNum = year;
@@ -87,8 +110,8 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
       buckets[bucketKey] = {
         x,
         xName,
-        ySum: 0,
         count: 0,
+        missingCount: 0,
         success: 0,
         total: 0,
         countSum: 0,
@@ -96,6 +119,10 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
         yValues: []
       };
     }
+    if (yRaw == null) {
+      buckets[bucketKey].missingCount = (buckets[bucketKey].missingCount || 0) + 1;
+      continue;
+    }
     if (aggregation === "proportion") {
       if (typeof yRaw === "boolean") {
         buckets[bucketKey].success += yRaw ? 1 : 0;
@@ -142,17 +169,13 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
       const yn = Number(yRaw);
       if (!Number.isFinite(yn)) {
         throw new Error(
-          `Non-finite y value for mean aggregation in sample ${sampleId}: yTermId=${yTermId}, yRaw=${yRaw}`
+          `Non-finite y value for ${aggregation} aggregation in sample ${sampleId}: yTermId=${yTermId}, yRaw=${yRaw}`
         );
       }
-      buckets[bucketKey].ySum += yn;
       buckets[bucketKey].count += 1;
       buckets[bucketKey].yValues.push(yn);
     }
   }
-  if (skippedSamples > 0) {
-    console.log(`buildRunChartFromData: Skipped ${skippedSamples} sample(s) due to missing x or y values`);
-  }
   function xFromBucket(b) {
     const yearNum = Math.floor(b.sortKey / 100);
     const monthNum = b.sortKey % 100;
@@ -171,15 +194,16 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
       return { x, xName: b.xName, y, sampleCount: b.count };
     } else {
       let y;
-      if (aggregation === "median" && (b.yValues?.length ?? 0) > 0) {
+      if ((b.yValues?.length ?? 0) > 0) {
         const sorted = [...b.yValues].sort((a, b2) => a - b2);
         const mid = Math.floor(sorted.length / 2);
         y = sorted.length % 2 === 1 ? sorted[mid] : (sorted[mid - 1] + sorted[mid]) / 2;
       } else {
-        y = b.count ? b.ySum / b.count : 0;
+        y = 0;
       }
       y = Math.round(y * 100) / 100;
-      return { x, xName: b.xName, y, sampleCount: b.count };
+      const sampleCount = b.count > 0 ? b.count : b.missingCount || 0;
+      return { x, xName: b.xName, y, sampleCount };
     }
   });
   const yValues = points.map((p) => p.y).filter((v) => typeof v === "number" && !Number.isNaN(v));
@@ -188,15 +212,7 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
     const mid = Math.floor(sorted.length / 2);
     return sorted.length % 2 === 0 ? (sorted[mid - 1] + sorted[mid]) / 2 : sorted[mid];
   })() : 0;
-  return {
-    status: "ok",
-    series: [
-      {
-        median,
-        points
-      }
-    ]
-  };
+  return { median, points };
 }
 function init({ genomes }) {
   return async (req, res) => {
@@ -209,7 +225,6 @@ function init({ genomes }) {
       const result = await getRunChart(q, ds);
       res.send(result);
     } catch (e) {
-      console.log(e.stack);
       res.send({ error: e.message || e });
     }
   };

package/routes/termdb.sampleScatter.js

@@ -40,14 +40,14 @@ function init({ genomes }) {
       if (q.scaleDotTW) terms.push(q.scaleDotTW);
       if (q.coordTWs) for (const tw of q.coordTWs) terms.push(tw);
       const data = await getData(
-        { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ },
+        { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__, __abortSignal: q.__abortSignal },
         ds,
         true
         // FIXME 3rd arg hardcoded to true
       );
       if (data.error) throw new Error(data.error);
       let result;
-      if (q.coordTWs.length > 0) {
+      if (q.coordTWs && q.coordTWs.length > 0) {
         const tmp = await getSampleCoordinatesByTerms(req, q, ds, data);
         cohortSamples = tmp[0];
       } else {
@@ -465,6 +465,8 @@ async function loadFile(p, ds) {
 }
 async function mayInitiateScatterplots(ds) {
   if (!ds.cohort.scatterplots) return;
+  if (typeof ds.cohort.scatterplots.get == "function") {
+  }
   if (!Array.isArray(ds.cohort.scatterplots.plots)) throw new Error("cohort.scatterplots.plots is not array");
   for (const p of ds.cohort.scatterplots.plots) {
     if (!p.name) throw new Error(".name missing from one of scatterplots.plots[]");

package/routes/termdb.violin.js

@@ -52,7 +52,8 @@ async function getViolin(q, ds) {
       filter: q.filter,
       filter0: q.filter0,
       currentGeneNames: q.currentGeneNames,
-      __protected__: q.__protected__
+      __protected__: q.__protected__,
+      __abortSignal: q.__abortSignal
     },
     ds
   );