@sjcrh/proteinpaint-server 2.187.0 → 2.188.1

package/dataset/termdb.test.js

@@ -244,6 +244,8 @@ function termdb_test_default() {
         plots: [
           {
             name: "TermdbTest TSNE",
+            description: "Transcriptome t-SNE plot based on termdb data which is a 2D or 3D visualization of 									gene expression data where each point represents a single cell (or sample) and the distance between 									points reflects how similar their gene expression profiles are.",
+            descriptionShort: "transcriptome t-SNE plot",
             dimension: 2,
             file: "files/hg38/TermdbTest/tsne.txt",
             colorTW: { id: "diaggrp" },
@@ -400,9 +402,7 @@ function termdb_test_default() {
           unit: "M-value"
         }
       },
-      topVariablyExpressedGenes: {
-        src: "native"
-      },
+      topVariablyExpressedGenes: {},
       rnaseqGeneCount: {
         storage_type: "HDF5",
         file: "files/hg38/TermdbTest/rnaseq/TermdbTest.geneCounts.new.h5"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.187.0",
+  "version": "2.188.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,11 +62,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.181.1",
-    "@sjcrh/proteinpaint-python": "2.187.0",
-    "@sjcrh/proteinpaint-r": "2.181.0",
-    "@sjcrh/proteinpaint-rust": "2.186.0",
-    "@sjcrh/proteinpaint-shared": "2.187.0",
-    "@sjcrh/proteinpaint-types": "2.187.0",
+    "@sjcrh/proteinpaint-python": "2.188.0",
+    "@sjcrh/proteinpaint-r": "2.188.0",
+    "@sjcrh/proteinpaint-rust": "2.188.0",
+    "@sjcrh/proteinpaint-shared": "2.188.1",
+    "@sjcrh/proteinpaint-types": "2.188.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/aiProjectAdmin.js

@@ -146,7 +146,9 @@ function editProject(connection, project) {
 function deleteProject(connection, projectId) {
   if (!projectId) throw new Error("Invalid project ID [aiProjectAdmin route deleteProject()]");
   const stmts = [
+    { sql: "DELETE FROM project_flagged_annotations WHERE project_id = ?", params: [[projectId]] },
     { sql: "DELETE FROM project_annotations WHERE project_id = ?", params: [[projectId]] },
+    { sql: "DELETE FROM project_flagged_predictions WHERE project_id = ?", params: [[projectId]] },
     { sql: "DELETE FROM project_classes WHERE project_id = ?", params: [[projectId]] },
     { sql: "DELETE FROM project_images WHERE project_id = ?", params: [[projectId]] },
     { sql: "DELETE FROM project_users WHERE project_id = ?", params: [[projectId]] },

package/routes/aiProjectSelectedWSImages.js

@@ -1,4 +1,5 @@
 import { aiProjectSelectedWSImagesResponsePayload } from "#types/checkers";
+import { createSelectionID, SelectionPrefixes, FlagStatus } from "#shared";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
 const api = {
   endpoint: "aiProjectSelectedWSImages",
@@ -54,16 +55,23 @@ function init({ genomes }) {
                 return `${zc[0]},${zc[1]}`;
               }).filter(Boolean)
             );
-            let flaggedPredictions = /* @__PURE__ */ new Set();
+            let flaggedPredictions = /* @__PURE__ */ new Map();
             if (typeof ds.queries.WSImages.getFlaggedPredictions === "function") {
-              flaggedPredictions = await ds.queries.WSImages.getFlaggedPredictions(projectId);
+              flaggedPredictions = await ds.queries.WSImages.getFlaggedPredictions(projectId, wsimageFilename);
             }
             wsimage.predictions = (predictions || []).map((p) => {
               const label = classMap.get(p.class) ?? p.class;
-              return { ...p, class: label };
+              const flagged_counterpart = flaggedPredictions.get(JSON.stringify(p.zoomCoordinates));
+              return {
+                ...p,
+                class: label,
+                timestamp: flagged_counterpart?.timestamp ?? (/* @__PURE__ */ new Date()).toISOString(),
+                flag: flagged_counterpart?.flag ?? FlagStatus.Normal,
+                id: createSelectionID(SelectionPrefixes.Prediction, p.zoomCoordinates)
+              };
             }).filter((p) => {
               const key = `${p.zoomCoordinates[0]},${p.zoomCoordinates[1]}`;
-              return !annotationKeys.has(key) && !flaggedPredictions.has(key);
+              return !annotationKeys.has(key) && p.flag !== FlagStatus.Deleted;
             });
           }
           wsimages.push(wsimage);
@@ -91,23 +99,43 @@ async function validate_query_getWSIClassesQuery(ds) {
 function validateWSIAnnotationsQuery(ds, connection) {
   if (!ds.queries?.WSImages?.db) return;
   const GET_ANNOTATIONS_SQL = `
-        SELECT
-            pa.id,
-            pa.project_id,
-            pa.user_id,
-            pa.coordinates,
-            pa.timestamp,
-            pa.status,
-            pc.label AS label
-        FROM project_annotations pa
-                 INNER JOIN project_images pi
-                            ON pi.id = pa.image_id
-                 LEFT JOIN project_classes pc
-                           ON pc.id = pa.class_id
-        WHERE pa.project_id = ?
-          AND pi.image_path = ?
-          AND pa.status = 1
-        ORDER BY pa.timestamp DESC, pa.id DESC
+		SELECT *
+		FROM (
+			SELECT
+				pa.id,
+				pa.project_id,
+				pa.user_id,
+				pa.coordinates,
+				pa.timestamp,
+				pa.flagged,
+				pc.label AS label
+			FROM project_flagged_annotations pa
+					 INNER JOIN project_images pi
+								ON pi.id = pa.image_id
+					 LEFT JOIN project_classes pc
+							   ON pc.id = pa.class_id
+			WHERE pa.project_id = ?
+			  AND pi.image_path = ?
+
+			UNION ALL
+
+			SELECT
+				pa.id,
+				pa.project_id,
+				pa.user_id,
+				pa.coordinates,
+				pa.timestamp,
+				${FlagStatus.Normal} AS flagged,
+				pc.label AS label
+			FROM project_annotations pa
+					 INNER JOIN project_images pi
+								ON pi.id = pa.image_id
+					 LEFT JOIN project_classes pc
+							   ON pc.id = pa.class_id
+			WHERE pa.project_id = ?
+			  AND pi.image_path = ?
+		)
+		ORDER BY timestamp DESC, id DESC
     `;
   const GET_PROJECT_IMAGES_SQL = `
         SELECT DISTINCT pi.image_path AS image_path
@@ -116,16 +144,22 @@ function validateWSIAnnotationsQuery(ds, connection) {
         ORDER BY pi.id
     `;
   const GET_FLAGGED_PREDICTIONS_SQL = `
-        SELECT coordinates
-        FROM project_flagged_predictions
-        WHERE project_id = ?
+        SELECT
+            pa.coordinates,
+            pa.flag_type,
+            pa.timestamp
+        FROM project_flagged_predictions pa
+                 INNER JOIN project_images pi
+                            ON pi.id = pa.image_id
+        WHERE pa.project_id = ?
+          AND pa.image_id = ?
     `;
   if (!ds.queries) ds.queries = {};
   if (!ds.queries.WSImages) ds.queries.WSImages = {};
   ds.queries.WSImages.getWSIAnnotations = async (projectId, filename) => {
     try {
       const stmt = connection.prepare(GET_ANNOTATIONS_SQL);
-      const rows = stmt.all(projectId, filename);
+      const rows = stmt.all(projectId, filename, projectId, filename);
       return rows.map((r) => {
         let coords = [NaN, NaN];
         try {
@@ -141,7 +175,9 @@ function validateWSIAnnotationsQuery(ds, connection) {
           zoomCoordinates: coords,
           class: r.label ?? "",
           status: r.status,
-          timestamp: r.timestamp
+          flag: r.flagged === void 0 ? FlagStatus.Normal : r.flagged,
+          timestamp: r.timestamp,
+          id: createSelectionID(SelectionPrefixes.Annotation, coords)
         };
       });
     } catch (error) {
@@ -159,28 +195,32 @@ function validateWSIAnnotationsQuery(ds, connection) {
       return [];
     }
   };
-  ds.queries.WSImages.getFlaggedPredictions = async (projectId) => {
+  ds.queries.WSImages.getFlaggedPredictions = async (projectId, filename) => {
+    const predictionMap = /* @__PURE__ */ new Map();
+    const getImageIdSql = `
+				SELECT id
+				FROM project_images
+				WHERE project_id = ?
+				  AND image_path = ?
+				LIMIT 1
+			`;
+    const getImageStmt = connection.prepare(getImageIdSql);
+    const imageRow = getImageStmt.get(projectId, filename);
+    if (!imageRow?.id) {
+      return predictionMap;
+    }
+    const imageId = Math.floor(imageRow.id);
     try {
       const stmt = connection.prepare(GET_FLAGGED_PREDICTIONS_SQL);
-      const rows = stmt.all(projectId) || [];
-      const keys = /* @__PURE__ */ new Set();
-      for (const r of rows) {
-        try {
-          const parsed = typeof r.coordinates === "string" ? JSON.parse(r.coordinates) : r.coordinates;
-          if (Array.isArray(parsed) && parsed.length >= 2) {
-            const x = Number(parsed[0]);
-            const y = Number(parsed[1]);
-            if (!Number.isNaN(x) && !Number.isNaN(y)) {
-              keys.add(`${x},${y}`);
-            }
-          }
-        } catch {
-        }
+      const rows = stmt.all(projectId, imageId) || [];
+      for (const p of rows) {
+        if (p.coordinates && typeof p.coordinates === "string" && typeof p.flag_type === "number")
+          predictionMap.set(p.coordinates, { flag: p.flag_type, timestamp: p.timestamp });
       }
-      return keys;
+      return predictionMap;
     } catch (error) {
       console.error("Error loading flagged predictions:", error);
-      return /* @__PURE__ */ new Set();
+      return predictionMap;
     }
   };
 }

package/routes/brainImaging.js

@@ -3,7 +3,7 @@ import serverconfig from "#src/serverconfig.js";
 import { brainImagingPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { isNumericTerm } from "#shared";
-import { getColors } from "#shared/common.js";
+import { getColors } from "#shared";
 import { run_python } from "@sjcrh/proteinpaint-python";
 const api = {
   endpoint: "brainImaging",

package/routes/deleteWSITileSelection.js

@@ -1,4 +1,5 @@
 import { deleteWSITileSelectionPayload } from "#types/checkers";
+import { checkSelectionType, SelectionPrefixes, FlagStatus } from "#shared";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
 const api = {
   endpoint: `deleteWSITileSelection`,
@@ -48,7 +49,8 @@ async function validate_query_deleteWSIAnnotation(ds) {
 }
 function validateQuery(ds, connection) {
   ds.queries.WSImages.deleteAnnotation = async (query) => {
-    if (query.tileSelectionType === 0) {
+    const zoomCoordinates = JSON.stringify(query.tileSelection.zoomCoordinates);
+    if (checkSelectionType(query.tileSelection, SelectionPrefixes.Prediction) && query.tileSelection.flag !== FlagStatus.Normal) {
       try {
         const projectId = query.projectId;
         if (projectId == null) {
@@ -57,21 +59,41 @@ function validateQuery(ds, connection) {
             error: "Missing required field: projectId"
           };
         }
-        const predictionId = query.predictionClassId;
-        const zoomCoordinates = JSON.stringify(query.tileSelection.zoomCoordinates);
-        const flagType = 0;
+        const predictionId = query.classID;
+        const flagType = query.tileSelection.flag;
         if (predictionId == null) {
           return {
             status: "error",
             error: "Missing prediction id in tileSelection (expected predictionId, prediction.id, or id)."
           };
         }
-        const insertSql = `
-                    INSERT INTO project_flagged_predictions (project_id, prediction_class_id, coordinates, flag_type)
-                    VALUES (?, ?, ?, ?)
-                `;
-        const insertStmt = connection.prepare(insertSql);
-        insertStmt.run(projectId, predictionId, zoomCoordinates, flagType);
+        const getImageIdSql = `
+				SELECT id FROM project_images 
+				WHERE project_id = ? AND image_path = ? LIMIT 1
+`;
+        const imageRow = connection.prepare(getImageIdSql).get(projectId, query.wsimage);
+        const imageId = imageRow?.id;
+        if (!imageId) {
+          return { status: "error", error: "Image not found" };
+        }
+        connection.prepare(
+          `
+					DELETE FROM project_flagged_predictions 
+					WHERE project_id = ?  AND coordinates = ? 
+					AND image_id = (
+                        SELECT id FROM project_images
+                        WHERE project_id = ?
+                          AND image_path = ?
+                      )
+				`
+        ).run(projectId, zoomCoordinates, projectId, query.wsimage);
+        connection.prepare(
+          `
+				INSERT INTO project_flagged_predictions 
+				(project_id, prediction_class_id, coordinates, flag_type, timestamp, image_id)
+				VALUES (?, ?, ?, ?, ?, ?)
+			    `
+        ).run(projectId, predictionId, zoomCoordinates, flagType, (/* @__PURE__ */ new Date()).toISOString(), imageId);
         return { status: "ok" };
       } catch (error) {
         console.error("Error inserting flagged prediction:", error);
@@ -82,7 +104,20 @@ function validateQuery(ds, connection) {
       }
     } else
       try {
-        const deleteSql = `
+        connection.prepare(
+          `
+                    DELETE FROM project_flagged_annotations
+                    WHERE project_id = ?
+                      AND coordinates = ?
+                      AND image_id = (
+                        SELECT id FROM project_images
+                        WHERE project_id = ?
+                          AND image_path = ?
+                      )
+                `
+        ).run(query.projectId, zoomCoordinates, query.projectId, query.wsimage);
+        connection.prepare(
+          `
                     DELETE FROM project_annotations
                     WHERE project_id = ?
                       AND coordinates = ?
@@ -91,10 +126,8 @@ function validateQuery(ds, connection) {
                         WHERE project_id = ?
                           AND image_path = ?
                       )
-                `;
-        const coords = JSON.stringify(query.tileSelection?.zoomCoordinates);
-        const stmt = connection.prepare(deleteSql);
-        stmt.run(query.projectId, coords, query.projectId, query.wsimage);
+                `
+        ).run(query.projectId, zoomCoordinates, query.projectId, query.wsimage);
         return { status: "ok" };
       } catch (error) {
         console.error("Error deleting annotation:", error);

package/routes/genesetEnrichment.js

@@ -8,6 +8,7 @@ import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
 import { formatElapsedTime } from "#shared";
 import { readCacheFileOrRecompute, stableStringify } from "#src/diffAnalysis.ts";
+import { get_ds_tdb } from "#src/termdb.js";
 const api = {
   endpoint: "genesetEnrichment",
   methods: {
@@ -100,6 +101,28 @@ async function resolveGseaGenesAndFoldChange({
     }
     throw new Error(`unexpected result kind: ${result.kind}`);
   }
+  if (q.dapParams) {
+    const genome = genomes[q.genome];
+    if (!genome) throw new Error("invalid genome");
+    const [ds] = get_ds_tdb(genome, q);
+    const { organism, assay, cohort } = q.dapParams;
+    const cohortConfig = ds.queries?.proteome?.organisms?.[organism]?.assays?.[assay]?.cohorts?.[cohort];
+    if (!cohortConfig?.DAPfile) throw new Error("DAP file not configured for this cohort");
+    const filePath = path.join(serverconfig.tpmasterdir, cohortConfig.DAPfile);
+    const content = await fs.promises.readFile(filePath, "utf8");
+    const lines = content.trim().split("\n");
+    const genes = [];
+    const fold_change = [];
+    for (let i = 1; i < lines.length; i++) {
+      const parts = lines[i].split("	");
+      if (parts.length < 4) continue;
+      const fc = Number(parts[2]);
+      if (!Number.isFinite(fc)) continue;
+      genes.push(parts[1]);
+      fold_change.push(fc);
+    }
+    return { genes, fold_change };
+  }
   if (!q.genes || !q.fold_change) throw new Error("requires genes and fold_change when cacheId is absent");
   return { genes: q.genes, fold_change: q.fold_change };
 }

package/routes/saveWSIAnnotation.js

@@ -1,4 +1,5 @@
 import { saveWSIAnnotationPayload } from "#types/checkers";
+import { FlagStatus, SelectionPrefixes, checkSelectionType } from "#shared";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
 const routePath = "saveWSIAnnotation";
 const api = {
@@ -47,12 +48,21 @@ async function validate_query_saveWSIAnnotation(ds) {
 function validateQuery(ds, connection) {
   ds.queries.WSImages.saveWSIAnnotation = async (annotation) => {
     try {
+      const tileSelection = annotation.tileSelection;
       const timestamp = (/* @__PURE__ */ new Date()).toISOString();
       const projectId = annotation.projectId;
       const wsimageFilename = annotation.wsimage;
-      const coords = JSON.stringify(annotation.coordinates ?? []);
-      const status = 1;
+      const coords = JSON.stringify(tileSelection.zoomCoordinates ?? []);
+      const flag = tileSelection.flag;
       const classId = annotation.classId;
+      const isAnnotation = checkSelectionType(tileSelection, SelectionPrefixes.Annotation);
+      const isPrediction = checkSelectionType(tileSelection, SelectionPrefixes.Prediction);
+      if (!isAnnotation && !isPrediction) {
+        return {
+          status: "error",
+          error: `Invalid tileSelection id "${tileSelection.id}". Must start with "${SelectionPrefixes.Annotation}" or "${SelectionPrefixes.Prediction}".`
+        };
+      }
       if (projectId == null || wsimageFilename == null) {
         return {
           status: "error",
@@ -75,41 +85,72 @@ function validateQuery(ds, connection) {
         };
       }
       const imageId = imageRow.id;
-      const duplicateCheckSql = `
-				SELECT id
-				FROM project_annotations
-				WHERE project_id = ?
-				  AND image_id = ?
-				  AND coordinates = ?
-				LIMIT 1
-			`;
-      const duplicateCheckStmt = connection.prepare(duplicateCheckSql);
-      const duplicateRow = duplicateCheckStmt.get(projectId, imageId, coords);
-      if (duplicateRow) {
-        const deleteDuplicateSql = `
-					DELETE FROM project_annotations
-					WHERE id = ?
-				`;
-        const deleteDuplicateStmt = connection.prepare(deleteDuplicateSql);
-        deleteDuplicateStmt.run(duplicateRow.id);
-        console.log(
-          `Deleted duplicate annotation with id=${duplicateRow.id} for project_id=${projectId}, image_id=${imageId}.`
-        );
-      }
-      const insertSql = `
-				INSERT INTO project_annotations (
-					project_id, user_id, coordinates, timestamp, status, class_id, image_id
-				) VALUES (?, ?, ?, ?, ?, ?, ?)
-			`;
-      const insertStmt = connection.prepare(insertSql);
-      const userRow = connection.prepare(
-        `SELECT id
+      connection.prepare(
+        `DELETE FROM project_flagged_annotations
+					 WHERE project_id = ?
+					   AND image_id = ?
+					   AND coordinates = ?`
+      ).run(projectId, imageId, coords);
+      connection.prepare(
+        `DELETE FROM project_flagged_predictions
+					 WHERE project_id = ?
+					   AND image_id = ?
+					   AND coordinates = ?`
+      ).run(projectId, imageId, coords);
+      connection.prepare(
+        `DELETE FROM project_annotations
+					 WHERE project_id = ?
+					   AND image_id = ?
+					   AND coordinates = ?`
+      ).run(projectId, imageId, coords);
+      if (isAnnotation) {
+        const userRow = connection.prepare(
+          `SELECT id
 						  FROM project_users
 						  ORDER BY id
 						  LIMIT 1`
-      ).get();
-      const userId = userRow?.id;
-      insertStmt.run(projectId, userId, coords, timestamp, status, classId, imageId);
+        ).get();
+        const userId = userRow?.id;
+        if (userId === void 0) {
+          return {
+            status: "error",
+            error: "No users found in project_users table."
+          };
+        }
+        if (tileSelection.flag === FlagStatus.Normal) {
+          connection.prepare(
+            `
+						INSERT INTO project_annotations (
+							project_id, user_id, coordinates, timestamp,class_id, image_id
+						) VALUES (?, ?, ?, ?, ?, ?)
+					`
+          ).run(projectId, userId, coords, timestamp, classId, imageId);
+        } else {
+          connection.prepare(
+            `
+				INSERT INTO project_flagged_annotations (
+					project_id, user_id, coordinates, timestamp, flagged,class_id, image_id
+				) VALUES (?, ?, ?, ?, ?, ?, ?)
+				`
+          ).run(projectId, userId, coords, timestamp, flag, classId, imageId);
+        }
+      } else if (isPrediction) {
+        if (tileSelection.flag !== FlagStatus.Normal) {
+          const insertSql = `
+                    INSERT INTO project_flagged_predictions (project_id, prediction_class_id, coordinates, flag_type,image_id,timestamp)
+                    VALUES (?, ?, ?, ?,?,?)
+                `;
+          const insertStmt = connection.prepare(insertSql);
+          insertStmt.run(
+            annotation.projectId,
+            annotation.classId,
+            JSON.stringify(tileSelection.zoomCoordinates),
+            tileSelection.flag,
+            imageId,
+            timestamp
+          );
+        }
+      }
       return { status: "ok" };
     } catch (error) {
       console.error("Error saving annotation:", error);