@sjcrh/proteinpaint-server 2.126.2 → 2.127.1-0

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Files changed (5) hide show
  1. package/package.json +1 -1
  2. package/routes/gdcGRIN2list.js +6 -3
  3. package/routes/gdcGRIN2run.js +36 -46
  4. package/src/app.js +71 -67
  5. package/src/serverconfig.js +1 -0
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": "2.126.2",
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+ "version": "2.127.1-0",
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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",
package/routes/gdcGRIN2list.js CHANGED
@@ -1,19 +1,20 @@
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- import { gdcMafPayload } from "#types/checkers";
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+ import { gdcGRIN2listPayload } from "#types/checkers";
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  import ky from "ky";
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  import { joinUrl } from "#shared/joinUrl.js";
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  import serverconfig from "#src/serverconfig.js";
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  const maxFileNumber = 1e3;
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  const allowedWorkflowType = "Aliquot Ensemble Somatic Variant Merging and Masking";
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+ const maxFileSizeAllowed = 1e6;
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  const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 4e8;
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  const api = {
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  endpoint: "gdc/GRIN2list",
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  methods: {
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  get: {
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- ...gdcMafPayload,
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+ ...gdcGRIN2listPayload,
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  init
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  },
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  post: {
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- ...gdcMafPayload,
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+ ...gdcGRIN2listPayload,
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  init
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  }
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  }
@@ -84,6 +85,8 @@ async function listMafFiles(q, ds) {
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  const c = h.cases?.[0];
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  if (!c)
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  throw "h.cases[0] missing";
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+ if (h.file_size >= maxFileSizeAllowed)
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+ continue;
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  const file = {
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  id: h.id,
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  project_id: c.project.project_id,
package/routes/gdcGRIN2run.js CHANGED
@@ -31,53 +31,43 @@ function init({ genomes }) {
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  if (!caseFiles) {
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  throw "Missing or invalid cases data";
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  }
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+ console.log("[GRIN2] Calling Rust for file processing...");
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+ const rustInput = JSON.stringify(caseFiles);
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+ console.log("[GRIN2] Executing Rust function...");
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+ const rustResult = await run_rust("gdcGRIN2", rustInput);
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+ console.log("[GRIN2] Rust execution completed");
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+ if (!rustResult) {
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+ throw new Error("Failed to process MAF files: No result from Rust");
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+ }
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+ let parsedRustResult;
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+ try {
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+ parsedRustResult = typeof rustResult === "string" ? JSON.parse(rustResult) : rustResult;
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+ console.log(`[GRIN2] Parsed Rust result: ${JSON.stringify(parsedRustResult).substring(0, 200)}...`);
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+ } catch (parseError) {
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+ console.error("[GRIN2] Error parsing Rust result:", parseError);
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+ }
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+ const genedbfile = path.join(serverconfig.tpmasterdir, g.genedb.dbfile);
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+ const imagefile = path.join(serverconfig.cachedir, `grin2_${Date.now()}_${Math.floor(Math.random() * 1e9)}.png`);
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+ const rInput = JSON.stringify({
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+ genedb: genedbfile,
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+ chromosomelist: g.majorchr,
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+ imagefile,
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+ lesion: rustResult
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+ // The mutation string from Rust
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+ });
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+ console.log(`R input: ${rInput}`);
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+ console.log("[GRIN2] Executing R script...");
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+ const rResult = await run_R("gdcGRIN2.R", rInput, []);
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+ console.log(`[GRIN2] R execution completed, result: ${rResult}`);
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+ let resultData;
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  try {
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- console.log("[GRIN2] Calling Rust for file processing...");
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- const rustInput = JSON.stringify(caseFiles);
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- console.log("[GRIN2] Executing Rust function...");
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- const rustResult = await run_rust("gdcGRIN2", rustInput);
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- console.log("[GRIN2] Rust execution completed");
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- console.log(`[GRIN2] Rust result type: ${typeof rustResult}`);
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- if (!rustResult) {
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- throw new Error("Failed to process MAF files: No result from Rust");
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- }
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- let parsedRustResult;
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- try {
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- parsedRustResult = typeof rustResult === "string" ? JSON.parse(rustResult) : rustResult;
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- console.log(`[GRIN2] Parsed Rust result: ${JSON.stringify(parsedRustResult).substring(0, 200)}...`);
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- } catch (parseError) {
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- console.error("[GRIN2] Error parsing Rust result:", parseError);
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- }
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- const genedbfile = path.join(serverconfig.tpmasterdir, g.genedb.dbfile);
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- const imagefile = path.join(serverconfig.cachedir, `grin2_${Date.now()}_${Math.floor(Math.random() * 1e9)}.png`);
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- const rInput = JSON.stringify({
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- genedb: genedbfile,
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- chromosomelist: g.majorchr,
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- imagefile,
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- lesion: rustResult
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- // The mutation string from Rust
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- });
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- console.log(`R input: ${rInput}`);
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- const parsedInput = JSON.parse(rInput);
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- console.log("Parsed lesion data type:", typeof parsedInput.lesion);
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- console.log(
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- "Parsed lesion data length:",
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- typeof parsedInput.lesion === "string" ? parsedInput.lesion.length : "not a string"
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- );
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- console.log("[GRIN2] Executing R script...");
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- const rResult = await run_R("gdcGRIN2.R", rInput, []);
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- console.log(`[GRIN2] R execution completed, result: ${rResult}`);
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- let resultData;
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- try {
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- resultData = JSON.parse(rResult);
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- console.log("[GRIN2] Finished R analysis");
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- const pngImg = resultData.png[0];
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- return res.json({ pngImg });
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- } catch (parseError) {
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- console.error("[GRIN2] Error parsing R result:", parseError);
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- console.log("[GRIN2] Raw R result:", rResult);
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- }
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- } finally {
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+ resultData = JSON.parse(rResult);
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+ console.log("[GRIN2] Finished R analysis");
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+ const pngImg = resultData.png[0];
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+ return res.json({ pngImg });
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+ } catch (parseError) {
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+ console.error("[GRIN2] Error parsing R result:", parseError);
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+ console.log("[GRIN2] Raw R result:", rResult);
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  }
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  } catch (e) {
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  console.error("[GRIN2] Error running analysis:", e);