@sjcrh/proteinpaint-server 2.99.1-1 → 2.99.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.99.1-1",
+  "version": "2.99.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.99.0",
-    "@sjcrh/proteinpaint-shared": "2.99.0",
-    "@sjcrh/proteinpaint-types": "2.99.1-1",
+    "@sjcrh/proteinpaint-shared": "2.99.1",
+    "@sjcrh/proteinpaint-types": "2.99.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/clearwsisession.js

@@ -1,4 +1,4 @@
-import { clearWSImagesSessionsPayload } from "@sjcrh/proteinpaint-types/routes/clearwsisessions.js";
+import { clearWSImagesSessionsPayload } from "#types/checkers";
 import SessionManager from "#src/wsisessions/SessionManager.js";
 import ky from "ky";
 import serverconfig from "#src/serverconfig.js";

package/routes/termdb.singlecellSamples.js

@@ -1,12 +1,13 @@
 import fs from "fs";
 import path from "path";
 import { read_file, file_is_readable } from "#src/utils.js";
-import { joinUrl, mayLog } from "#src/helpers.ts";
+import { mayLog } from "#src/helpers.ts";
+import { joinUrl } from "#shared/joinUrl.js";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { termdbSingleCellSamplesPayload } from "#types/checkers";
 import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
-import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
+import { gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 import ky from "ky";
 const api = {
   endpoint: "termdb/singlecellSamples",
@@ -50,12 +51,8 @@ async function validate_query_singleCell(ds, genome) {
   const q = ds.queries.singleCell;
   if (!q)
     return;
-  if (q.samples.src == "gdcapi") {
-    gdc_validate_query_singleCell_samples(ds, genome);
-  } else if (q.samples.src == "native") {
+  if (typeof q.samples.get != "function") {
     validateSamplesNative(q.samples, q.data, ds);
-  } else {
-    throw "unknown singleCell.samples.src";
   }
   if (q.data.src == "gdcapi") {
     gdc_validate_query_singleCell_data(ds, genome);

package/routes/termdb.topVariablyExpressedGenes.js

@@ -4,7 +4,7 @@ import serverconfig from "#src/serverconfig.js";
 import { get_samples } from "#src/termdb.sql.js";
 import { makeFilter } from "#src/mds3.gdc.js";
 import { cachedFetch } from "#src/utils.js";
-import { joinUrl } from "#src/helpers.ts";
+import { joinUrl } from "#shared/joinUrl.js";
 const api = {
   endpoint: "termdb/topVariablyExpressedGenes",
   methods: {