@sjcrh/proteinpaint-server 2.29.2 → 2.29.4

package/cards/bam.json

@@ -259,5 +259,6 @@
 			"name": "BAM track supporting information",
 			"link": "https://proteinpaint.stjude.org/bam"
 		}
-	]
+	],
+	"citation_id": 1004
 }

package/cards/citations.json

@@ -25,6 +25,15 @@
             "pmid": "32466770",
             "pmidURL": "https://pubmed.ncbi.nlm.nih.gov/32466770/",
             "doi": "https://doi.org/10.1186/s13059-020-02043-x"
+        },
+        {
+            "id": 1004,
+            "title": "ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping",
+            "year": "2023",
+            "journal": "Bioinformatics",
+            "pmid": "37140547",
+            "pmidURL": "https://ncbi.nlm.nih.gov/pmc/articles/PMC10182850/",
+            "doi": "https://doi.org/10.1093/bioinformatics/btad300"
         }
     ]
 }

package/cards/gdcbam.json

@@ -18,5 +18,6 @@
             "name": "Launch App from Link",
             "link": "https://proteinpaint.stjude.org/?gdcbamslice=1"
         }
-    ]
+    ],
+    "citation_id": 1004
 }

package/cards/index.json

@@ -3,9 +3,6 @@
         {
             "gridarea": "col1",
             "sections": [
-                {
-                    "id": "nestedCards"
-                },
                 {
                     "id": "tracks",
                     "name": "Tracks"
@@ -22,6 +19,9 @@
                 {
                     "id": "apps",
                     "name": "Launch Apps"
+                },
+                {
+                    "id": "nestedCards"
                 }
             ]
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.29.2",
+  "version": "2.29.4",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",

package/routes/termdb.categories.ts

@@ -22,6 +22,13 @@ export const api: any = {
 							embedder: 'localhost',
 							getcategories: 1,
 							tid: 'diaggrp',
+							term1_q: {
+								isAtomic: true,
+								hiddenValues: {},
+								type: 'values',
+								groupsetting: { disabled: true },
+								mode: 'discrete'
+							},
 							filter: {
 								type: 'tvslst',
 								in: true,

package/routes/termdb.termbyid.ts

@@ -0,0 +1,64 @@
+// import { gettermbyidRequest, gettermbyidResponse } from '#shared/types/routes/termdb.termbyid'
+import { copy_term } from '#src/termdb.js'
+
+export const api: any = {
+	endpoint: 'termdb/termbyid',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'gettermbyidRequest'
+			},
+			response: {
+				typeId: 'gettermbyidResponse'
+			},
+			examples: [
+				{
+					request: {
+						body: {
+							genome: 'hg38-test',
+							dslabel: 'TermdbTest',
+							embedder: 'localhost',
+							gettermbyid: 'subcohort'
+						}
+					},
+					response: {
+						header: { status: 200 }
+					}
+				}
+			]
+		},
+		post: {
+			alternativeFor: 'get',
+			init
+		}
+	}
+}
+
+function init({ genomes }) {
+	return async (req: any, res: any): Promise<void> => {
+		const q = req.query // as getcategoriesRequest
+		try {
+			const g = genomes[req.query.genome]
+			if (!g) throw 'invalid genome name'
+			const ds = g.datasets[req.query.dslabel]
+			if (!ds) throw 'invalid dataset name'
+			const tdb = ds.cohort.termdb
+			if (!tdb) throw 'invalid termdb object'
+
+			await trigger_gettermbyid(q, res, tdb) // as getcategoriesResponse
+		} catch (e) {
+			// eslint-disable-next-line @typescript-eslint/ban-ts-comment
+			// @ts-ignore
+			res.send({ error: e?.message || e })
+			if (e instanceof Error && e.stack) console.log(e)
+		}
+	}
+}
+
+async function trigger_gettermbyid(q, res, tdb) {
+	const t = tdb.q.termjsonByOneid(q.gettermbyid)
+	res.send({
+		term: t ? copy_term(t) : undefined
+	})
+}