@sjcrh/proteinpaint-server 2.174.1 → 2.175.0

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 });
     }
   };