@sjcrh/proteinpaint-server 2.172.0 → 2.174.0

package/routes/termdb.cluster.js

@@ -69,7 +69,7 @@ async function getResult(q, ds) {
     ({ term2sample2value, byTermId, bySampleId } = await getNumericDictTermAnnotation(q, ds));
   } else {
     ;
-    ({ term2sample2value, byTermId, bySampleId, skippedSexChrGenes } = await ds.queries[q.dataType].get(_q));
+    ({ term2sample2value, byTermId, bySampleId, skippedSexChrGenes } = await ds.queries[q.dataType].get(_q, ds));
   }
   const noValueTerms = [];
   for (const [term, obj] of term2sample2value) {
@@ -206,6 +206,7 @@ async function validate_query_geneExpression(ds, genome) {
   const q = ds.queries.geneExpression;
   if (!q) return;
   q.geneExpression2bins = {};
+  if (typeof q.get == "function") return;
   if (q.src == "gdcapi") {
     gdc_validate_query_geneExpression(ds, genome);
     return;

package/routes/termdb.runChart.js

@@ -1,4 +1,5 @@
 import { runChartPayload } from "#types/checkers";
+import { getNumberFromDate } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/runChart",
   methods: {
@@ -13,23 +14,9 @@ const api = {
   }
 };
 async function getRunChart(q, ds) {
-  const terms = [];
-  let xTermId;
-  let yTermId;
-  if (q.term && q.term2) {
-    const tws = [
-      { term: q.term, q: { mode: "continuous" }, $id: q.term.id },
-      { term: q.term2, q: { mode: "continuous" }, $id: q.term2.id }
-    ];
-    terms.push(...tws);
-    xTermId = q.term.id;
-    yTermId = q.term2.id;
-  } else {
-    throw new Error("term and term2 must be provided");
-  }
-  if (!xTermId || !yTermId) {
-    throw new Error("Unable to determine term IDs for x and y axes");
-  }
+  const terms = [q.term, q.term2];
+  const xTermId = q.term["$id"];
+  const yTermId = q.term2["$id"];
   const { getData } = await import("../src/termdb.matrix.js");
   const data = await getData(
     {
@@ -81,16 +68,20 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
         month = Math.floor(frac * 12) + 1;
       }
     } else {
-      month = 1;
+      year = null;
     }
     if (year == null || month == null || Number.isNaN(year) || Number.isNaN(month)) {
-      throw new Error(
-        `Invalid date value for sample ${sampleId}: xTermId=${xTermId}, xRaw=${xRaw}, parsed year=${year}, month=${month}`
+      skippedSamples++;
+      console.log(
+        `Skipping sample ${sampleId}: Invalid date value - xTermId=${xTermId}, xRaw=${xRaw}, parsed year=${year}, month=${month}`
       );
+      continue;
     }
-    const bucketKey = `${year}-${String(month).padStart(2, "0")}`;
-    const x = Number(`${year}.${String(month).padStart(2, "0")}`);
-    const date = new Date(year, month - 1, 1);
+    const yearNum = year;
+    const monthNum = month;
+    const bucketKey = `${yearNum}-${String(monthNum).padStart(2, "0")}`;
+    const x = Number(`${yearNum}.${String(monthNum).padStart(2, "0")}`);
+    const date = new Date(yearNum, monthNum - 1, 1);
     const xName = date.toLocaleString("en-US", { month: "long", year: "numeric" });
     if (!buckets[bucketKey]) {
       buckets[bucketKey] = {
@@ -101,7 +92,7 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
         success: 0,
         total: 0,
         countSum: 0,
-        sortKey: year * 100 + month,
+        sortKey: yearNum * 100 + monthNum,
         yValues: []
       };
     }
@@ -162,18 +153,33 @@ function buildRunChartFromData(aggregation, xTermId, yTermId, data) {
   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;
+    const x = getNumberFromDate(new Date(yearNum, monthNum - 1, 15));
+    return Math.round(x * 100) / 100;
+  }
   const points = Object.values(buckets).sort((a, b) => a.sortKey - b.sortKey).map((b) => {
+    const x = xFromBucket(b);
     if (aggregation === "proportion") {
       const total = b.total || 0;
       const succ = b.success || 0;
       const y = total ? Math.round(succ / total * 1e3) / 1e3 : 0;
-      return { x: b.x, xName: b.xName, y, sampleCount: total };
+      return { x, xName: b.xName, y, sampleCount: total };
     } else if (aggregation === "count") {
       const y = Math.round((b.countSum || 0) * 100) / 100;
-      return { x: b.x, xName: b.xName, y, sampleCount: b.count };
+      return { x, xName: b.xName, y, sampleCount: b.count };
     } else {
-      const avg = b.count ? Math.round(b.ySum / b.count * 100) / 100 : 0;
-      return { x: b.x, xName: b.xName, y: avg, sampleCount: b.count };
+      let y;
+      if (aggregation === "median" && (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 = Math.round(y * 100) / 100;
+      return { x, xName: b.xName, y, sampleCount: b.count };
     }
   });
   const yValues = points.map((p) => p.y).filter((v) => typeof v === "number" && !Number.isNaN(v));