@sjcrh/proteinpaint-server 2.211.0 → 2.212.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.211.0",
+  "version": "2.212.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -19,6 +19,7 @@
     "start": "tsx watch ./start.js",
     "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx --conditions=sjpp/dev serverTests.js && rm -rf ./cache",
     "test": "tsc && npm run test:unit",
+    "test:request": "code=0; for f in src/test/*.request.integration.spec.ts; do tsx --conditions=sjpp/dev $f || code=1; done; exit $code",
     "precombined:coverage": "tsx emitImports.js unit > serverTests.js",
     "combined:coverage": "coverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
     "postcombined:coverage": "rm -rf ./cache",
@@ -58,10 +59,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.210.1",
     "@sjcrh/proteinpaint-python": "2.209.0",
-    "@sjcrh/proteinpaint-r": "2.207.1",
+    "@sjcrh/proteinpaint-r": "2.212.0",
     "@sjcrh/proteinpaint-rust": "2.209.0",
-    "@sjcrh/proteinpaint-shared": "2.210.1",
-    "@sjcrh/proteinpaint-types": "2.211.0",
+    "@sjcrh/proteinpaint-shared": "2.211.1-0",
+    "@sjcrh/proteinpaint-types": "2.212.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",
@@ -121,5 +122,5 @@
       ]
     ]
   },
-  "_buildTime": "2026-09-24T02:12:34Z"
+  "_buildTime": "2026-09-26T07:30:19Z"
 }

package/routes/termdb.proteome.js

@@ -3,6 +3,7 @@ import { get_ds_tdb } from "#src/termdb.js";
 import * as utils from "#src/utils.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import serverconfig from "#src/serverconfig.js";
+import { sql } from "#src/sql.ts";
 import { readGeneRows, baseUniProtAcc } from "../src/routes/termdb.bubbleHeatmap.ts";
 const missingDapWarned = /* @__PURE__ */ new Set();
 function init({ genomes }) {
@@ -180,7 +181,7 @@ async function validate_query_proteome(ds) {
       }
     }
   }
-  const geneIndexHint = q.db.prepare("SELECT 1 FROM sqlite_master WHERE type = ? AND name = ?").get("index", "proteome_abundance_gene") ? " INDEXED BY proteome_abundance_gene" : "";
+  const geneIndexHint = q.db.prepare("SELECT 1 FROM sqlite_master WHERE type = ? AND name = ?").get("index", "proteome_abundance_gene") ? sql` INDEXED BY proteome_abundance_gene` : sql``;
   q.find = async (arg) => {
     const proteins = arg?.proteins;
     if (!Array.isArray(proteins) || proteins.length == 0) throw "queries.proteome.find arg.proteins[] missing";
@@ -215,16 +216,15 @@ async function validate_query_proteome(ds) {
       const upperToken = `${token}\uFFFF`;
       const rawRows = [];
       if (filters?.length) {
-        const { conditions, params } = buildFilterClause(filters);
-        const sql = `SELECT DISTINCT gene, identifier FROM proteome_abundance${geneIndexHint} WHERE gene >= ? COLLATE NOCASE AND gene < ? COLLATE NOCASE AND ${conditions.join(
-          " AND "
+        const query = sql`SELECT DISTINCT gene, identifier FROM proteome_abundance${geneIndexHint} WHERE gene >= ${token} COLLATE NOCASE AND gene < ${upperToken} COLLATE NOCASE AND ${buildFilterClause(
+          filters
         )} LIMIT ${MAX_FIND_RESULTS}`;
-        rawRows.push(...q.db.prepare(sql).all(token, upperToken, ...params));
+        rawRows.push(...q.db.prepare(query).all());
       } else {
         rawRows.push(
           ...q.db.prepare(
-            `SELECT DISTINCT gene, identifier FROM proteome_abundance WHERE gene >= ? COLLATE NOCASE AND gene < ? COLLATE NOCASE LIMIT ${MAX_FIND_RESULTS}`
-          ).all(token, upperToken)
+            sql`SELECT DISTINCT gene, identifier FROM proteome_abundance WHERE gene >= ${token} COLLATE NOCASE AND gene < ${upperToken} COLLATE NOCASE LIMIT ${MAX_FIND_RESULTS}`
+          ).all()
         );
       }
       for (const row of rawRows) {
@@ -256,14 +256,10 @@ function resolveColumnName(idx) {
   return name;
 }
 function buildFilterClause(filters) {
-  const conditions = [];
-  const params = [];
-  for (const f of filters) {
-    const colName = resolveColumnName(f.columnIdx);
-    conditions.push(`${colName} = ?`);
-    params.push(f.columnValue);
-  }
-  return { conditions, params };
+  return sql.join(
+    filters.map((f) => sql`${sql.id(resolveColumnName(f.columnIdx))} = ${f.columnValue}`),
+    sql` AND `
+  );
 }
 function listCohortSamples(db, filters) {
   if (!filters?.length) throw "listCohortSamples: filters must not be empty";
@@ -272,26 +268,22 @@ function listCohortSamples(db, filters) {
   const key = JSON.stringify(filters);
   const hit = perDb.get(key);
   if (hit) return hit;
-  const { conditions, params } = buildFilterClause(filters);
-  const samples = db.prepare(`SELECT DISTINCT sample FROM proteome_abundance WHERE ${conditions.join(" AND ")}`).all(...params).map((r) => String(r.sample));
+  const samples = db.prepare(sql`SELECT DISTINCT sample FROM proteome_abundance WHERE ${buildFilterClause(filters)}`).all().map((r) => String(r.sample));
   perDb.set(key, samples);
   return samples;
 }
 const cohortSampleCache = /* @__PURE__ */ new WeakMap();
 function listIdentifierAnnotations(db, gene, filters) {
-  const { conditions, params } = buildFilterClause(filters);
   const rows = db.prepare(
-    `SELECT identifier, modsite, isoform FROM proteome_abundance WHERE gene = ? COLLATE NOCASE${conditions.length ? " AND " + conditions.join(" AND ") : ""} GROUP BY identifier`
-  ).all(gene, ...params);
+    sql`SELECT identifier, modsite, isoform FROM proteome_abundance WHERE gene = ${gene} COLLATE NOCASE${filters.length ? sql` AND ${buildFilterClause(filters)}` : sql``} GROUP BY identifier`
+  ).all();
   return new Map(rows.map((r) => [r.identifier, { modsite: r.modsite, isoform: r.isoform }]));
 }
 function queryDbRows(db, identifier, filters) {
-  const { conditions, params } = buildFilterClause(filters);
-  const allConditions = [`identifier = ? COLLATE NOCASE`, ...conditions];
-  const sql = `SELECT organism, disease, identifier, protein_accession, isoform, modsite, gene, sample, value, brain_region
+  const query = sql`SELECT organism, disease, identifier, protein_accession, isoform, modsite, gene, sample, value, brain_region
 		FROM proteome_abundance
-		WHERE ${allConditions.join(" AND ")}`;
-  return db.prepare(sql).all(identifier, ...params);
+		WHERE identifier = ${identifier} COLLATE NOCASE${filters.length ? sql` AND ${buildFilterClause(filters)}` : sql``}`;
+  return db.prepare(query).all();
 }
 async function getProteomeValuesFromCohort(ds, param, q) {
   const db = ds.queries.proteome.db;