@sjcrh/proteinpaint-server 2.209.0 → 2.210.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dataset/termdb.test.js +2 -1
- package/package.json +5 -5
- package/routes/termdb.diffMeth.js +9 -1
- package/src/app.js +624 -518
- package/src/serverconfig.js +7 -0
package/dataset/termdb.test.js
CHANGED
|
@@ -3,9 +3,10 @@ const mafFields = [
|
|
|
3
3
|
id: "tumor_DNA",
|
|
4
4
|
name: "Tumor DNA",
|
|
5
5
|
parent_id: null,
|
|
6
|
-
|
|
6
|
+
mafFormatKey: "tumor_DNA_WGS",
|
|
7
7
|
isleaf: true,
|
|
8
8
|
type: "float",
|
|
9
|
+
mafFilterMode: "maf",
|
|
9
10
|
default: true,
|
|
10
11
|
// indicates default maf term (e.g. will be used by default for making maf filters in predefined groupset)
|
|
11
12
|
min: 0,
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@sjcrh/proteinpaint-server",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.210.1",
|
|
4
4
|
"type": "module",
|
|
5
5
|
"description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
|
|
6
6
|
"main": "src/app.js",
|
|
@@ -56,12 +56,12 @@
|
|
|
56
56
|
"typescript": "^5.6.3"
|
|
57
57
|
},
|
|
58
58
|
"dependencies": {
|
|
59
|
-
"@sjcrh/augen": "2.
|
|
59
|
+
"@sjcrh/augen": "2.210.1",
|
|
60
60
|
"@sjcrh/proteinpaint-python": "2.209.0",
|
|
61
61
|
"@sjcrh/proteinpaint-r": "2.207.1",
|
|
62
62
|
"@sjcrh/proteinpaint-rust": "2.209.0",
|
|
63
|
-
"@sjcrh/proteinpaint-shared": "2.
|
|
64
|
-
"@sjcrh/proteinpaint-types": "2.
|
|
63
|
+
"@sjcrh/proteinpaint-shared": "2.210.1",
|
|
64
|
+
"@sjcrh/proteinpaint-types": "2.210.1",
|
|
65
65
|
"@types/express": "^5.0.0",
|
|
66
66
|
"@types/express-session": "^1.18.1",
|
|
67
67
|
"better-sqlite3": "^12.4.1",
|
|
@@ -121,5 +121,5 @@
|
|
|
121
121
|
]
|
|
122
122
|
]
|
|
123
123
|
},
|
|
124
|
-
"_buildTime": "2026-09-
|
|
124
|
+
"_buildTime": "2026-09-21T21:01:24Z"
|
|
125
125
|
}
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import { DMR_SCAN_ELEMENT_TYPE } from "#types";
|
|
2
2
|
import { runDmrBatch } from "#src/routes/termdb.dmrBatch.ts";
|
|
3
|
-
import { dmrScanToRows, summarizeProfile, coarsenProfile } from "#src/utils/dmrScanRows.ts";
|
|
3
|
+
import { dmrScanToRows, summarizeProfile, coarsenProfile, dmrBedjLines } from "#src/utils/dmrScanRows.ts";
|
|
4
|
+
import { writeBedjFile } from "#src/utils/bedjCache.ts";
|
|
4
5
|
import { resolveGroupNames, matchedSamplelst, eligibleMethylationSamples } from "#src/utils/methylationMatrix.ts";
|
|
5
6
|
import { mayLog } from "#src/helpers.ts";
|
|
6
7
|
import { run_R } from "@sjcrh/proteinpaint-r";
|
|
@@ -179,6 +180,13 @@ async function getDmrScanAsDm(req, genomes) {
|
|
|
179
180
|
});
|
|
180
181
|
scan.matchedSamplelst = await matchedSamplelst(req.samplelst, eligible, ds);
|
|
181
182
|
scan.cacheId = cacheId;
|
|
183
|
+
try {
|
|
184
|
+
scan.bedjFile = await writeBedjFile(`dmr-${cacheId}-${scan.minCpgs}.gz`, {
|
|
185
|
+
text: dmrBedjLines(payload, scan.minCpgs)
|
|
186
|
+
});
|
|
187
|
+
} catch (e) {
|
|
188
|
+
console.error("DMR scan: bedj cache write failed, browser track unavailable:", e?.message || e);
|
|
189
|
+
}
|
|
182
190
|
return {
|
|
183
191
|
result: { promoterRows: rows, sample_size1: group1.length, sample_size2: group2.length, scan },
|
|
184
192
|
cacheId
|