@sjcrh/proteinpaint-server 2.129.6 → 2.131.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.129.6",
+  "version": "2.131.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,10 +62,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-r": "2.129.6",
-    "@sjcrh/proteinpaint-rust": "2.129.6",
+    "@sjcrh/proteinpaint-r": "2.130.0",
+    "@sjcrh/proteinpaint-rust": "2.130.0",
     "@sjcrh/proteinpaint-shared": "2.129.6",
-    "@sjcrh/proteinpaint-types": "2.129.6",
+    "@sjcrh/proteinpaint-types": "2.131.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.list.js

@@ -177,35 +177,37 @@ async function mayListCnvFiles(q, result, ds) {
     console.log("No cnvOptions provided, returning empty cnvFiles");
     return;
   }
-  const fields = [
-    "cases.samples.tissue_type",
-    "cases.project.project_id",
-    "cases.submitter_id",
-    "cases.case_id",
-    "data_type",
-    "file_id",
-    "file_size",
-    "data_format",
-    "experimental_strategy",
-    "analysis.workflow_type"
-  ];
+  const case_filters = { op: "and", content: [] };
+  if (q.filter0) {
+    case_filters.content.push(q.filter0);
+  }
+  const body = {
+    size: cnvMaxFileNumber,
+    fields: [
+      "cases.samples.tissue_type",
+      "cases.project.project_id",
+      "cases.submitter_id",
+      "cases.case_id",
+      "data_type",
+      "file_id",
+      "file_size",
+      "data_format",
+      "experimental_strategy",
+      "analysis.workflow_type"
+    ].join(","),
+    filters: {
+      op: "in",
+      content: {
+        field: "data_type",
+        value: ["Copy Number Segment", "Masked Copy Number Segment", "Allele-specific Copy Number Segment"]
+      }
+    }
+  };
+  if (case_filters.content.length)
+    body.case_filters = case_filters;
   const { host, headers } = ds.getHostHeaders(q);
   try {
-    const re = await ky.post(joinUrl(host.rest, "files"), {
-      timeout: false,
-      headers,
-      json: {
-        size: cnvMaxFileNumber,
-        fields: fields.join(","),
-        filters: {
-          op: "in",
-          content: {
-            field: "data_type",
-            value: ["Masked Copy Number Segment", "Allele-specific Copy Number Segment"]
-          }
-        }
-      }
-    }).json();
+    const re = await ky.post(joinUrl(host.rest, "files"), { timeout: false, headers, json: body }).json();
     console.log("API Response:", {
       hits: re.data?.hits?.length || 0,
       firstHit: re.data?.hits?.[0]
@@ -215,37 +217,27 @@ async function mayListCnvFiles(q, result, ds) {
     }
     const cnvFiles = [];
     for (const h of re.data.hits) {
-      console.log("Processing file:", {
-        file_id: h.file_id,
-        data_format: h.data_format,
-        data_type: h.data_type,
-        cases_length: h.cases?.length
-      });
-      if (h.data_format === "TXT") {
-        if (h.data_type === "Masked Copy Number Segment" || h.data_type === "Allele-specific Copy Number Segment") {
-          const c = h.cases?.[0];
-          if (!c) {
-            console.warn(`Skipping file ${h.file_id} - missing case data`);
-            continue;
-          }
-          console.log("Case structure:", {
-            case_id: c.case_id,
-            submitter_id: c.submitter_id,
-            project: c.project,
-            samples: c.samples?.length
-          });
-          const file = {
-            id: h.file_id || h.id,
-            // Handle both field names
-            project_id: c.project?.project_id || "unknown",
-            // Safe access with fallback
-            file_size: h.file_size,
-            case_submitter_id: c.submitter_id,
-            case_uuid: c.case_id,
-            sample_types: c.samples?.map((s) => s.tissue_type).filter(Boolean) || []
-          };
-          cnvFiles.push(file);
-        }
+      if (h.data_format != "TXT") {
+        continue;
+      }
+      if (!h.analysis?.workflow_type)
+        throw "h.analysis.workflow_type missing";
+      const c = h.cases?.[0];
+      if (!c)
+        throw "h.cases[0] missing";
+      if (h.data_type == "Allele-specific Copy Number Segment") {
+      } else if (h.data_type == "Masked Copy Number Segment" || h.data_type == "Copy Number Segment" && h.analysis.workflow_type != "DNACopy") {
+        const file = {
+          id: h.file_id || h.id,
+          // Handle both field names
+          project_id: c.project?.project_id || "unknown",
+          // Safe access with fallback
+          file_size: h.file_size,
+          case_submitter_id: c.submitter_id,
+          case_uuid: c.case_id,
+          sample_types: c.samples?.map((s) => s.tissue_type).filter(Boolean) || []
+        };
+        cnvFiles.push(file);
       }
     }
     result.cnvFiles = { files: cnvFiles };

package/routes/gdc.grin2.run.js

@@ -50,7 +50,12 @@ function parseJsonlOutput(rustOutput) {
     summary: {
       total_files: finalSummary.total_files,
       successful_files: finalSummary.successful_files,
-      failed_files: finalSummary.failed_files
+      failed_files: finalSummary.failed_files,
+      errors: finalSummary.errors || [],
+      filtered_records: finalSummary.filtered_records || 0,
+      filtered_maf_records: finalSummary.filtered_maf_records || 0,
+      filtered_cnv_records: finalSummary.filtered_cnv_records || 0,
+      filtered_records_by_case: finalSummary.filtered_records_by_case || {}
     }
   };
 }
@@ -149,8 +154,15 @@ function init({ genomes }) {
         console.log("[GRIN2] Finished R analysis");
         const pngImg = resultData.png[0];
         const topGeneTable = resultData.topGeneTable || null;
+        const analysisStats = parsedRustResult.summary || {};
         console.log("[GRIN2] Total GRIN2 processing time:", formatElapsedTime(Date.now() - downloadStartTime));
-        return res.json({ pngImg, topGeneTable, rustResult: parsedRustResult, status: "success" });
+        return res.json({
+          pngImg,
+          topGeneTable,
+          rustResult: parsedRustResult,
+          analysisStats,
+          status: "success"
+        });
       } catch (parseError) {
         console.error("[GRIN2] Error parsing R result:", parseError);
       }

package/routes/termdb.singleSampleMutation.js

@@ -1,7 +1,5 @@
-import fs from "fs";
 import path from "path";
-import { read_file } from "#src/utils.js";
-import serverconfig from "#src/serverconfig.js";
+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 = {
@@ -46,16 +44,32 @@ async function validate_query_singleSampleMutation(ds, genome) {
     gdcValidate_query_singleSampleMutation(ds, genome);
   } else if (_q.src == "native") {
     _q.get = async (q) => {
-      const file = path.join(serverconfig.tpmasterdir, _q.folder, q.sample);
-      try {
-        await fs.promises.stat(file);
-      } catch (e) {
-        if (e.code == "EACCES")
-          throw "cannot read file, permission denied";
-        if (e.code == "ENOENT")
-          throw "no data for this sample";
-        throw "failed to load data";
+      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) };
     };