@sjcrh/proteinpaint-server 2.27.2 → 2.29.0

package/cards/hic.json

@@ -1,5 +1,5 @@
 {
-    "ribbonMessage": "Versions 7, 8 and 9 Hi-C files are accepted.",
+    "ribbonMessage": "Versions 7, 8 and 9 Hi-C files are accepted.<br> See the new example for displaying a hic data across two chromosomes.",
     "ppcalls": [
         {
             "label": "Hi-C",
@@ -12,19 +12,61 @@
                 "genome": "hg19",
                 "position": "chr7:13749862-20841903",
                 "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "hicstraw",
-                    "file": "proteinpaint_demo/hg19/hic/hic_demo.hic",
-                    "name": "Hi-C Demo",
-                    "percentile_max": 95,
-                    "mincutoff": 1,
-                    "pyramidup": 1,
-                    "enzyme": "MboI",
-					"normalizationmethod":"VC"
-                }]
+                "tracks": [
+                    {
+                        "type": "hicstraw",
+                        "file": "proteinpaint_demo/hg19/hic/hic_demo.hic",
+                        "name": "Hi-C Demo",
+                        "percentile_max": 95,
+                        "mincutoff": 1,
+                        "pyramidup": 1,
+                        "enzyme": "MboI",
+                        "normalizationmethod": "VC"
+                    }
+                ]
             },
             "testSpec": {
-                "expected": {"image": 1 }
+                "expected": {
+                    "image": 1
+                }
+            }
+        },
+        {
+            "label": "Two chromosome view",
+            "runargs": {
+                "parseurl": true,
+                "block": true,
+                "nobox": true,
+                "noheader": true,
+                "genome": "hg19",
+                "position": "chr8:128688997-128888997",
+                "nativetracks": "RefGene",
+                "width": 300,
+                "subpanels": [
+                    {
+                        "chr": "chr4",
+                        "start": 174408608,
+                        "stop": 175268609,
+                        "width": 600,
+                        "leftborder": "rgba(200,0,0,.1)"
+                    }
+                ],
+                "tracks": [
+                    {
+                        "type": "hicstraw",
+                        "file": "files/hg19/nbl-hic/hic_NB69.inter.hic",
+                        "name": "SJNBL046418_C1/NB69 Hi-C",
+                        "percentile_max": 95,
+                        "mincutoff": 1,
+                        "pyramidup": 1,
+                        "enzyme": "MboI"
+                    }
+                ]
+            },
+            "testSpec": {
+                "expected": {
+                    "image": 1
+                }
             }
         }
     ],
@@ -34,4 +76,4 @@
             "link": "https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit"
         }
     ]
-}
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.27.2",
+  "version": "2.29.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "server.js",
   "bin": "start.js",
@@ -74,7 +74,7 @@
     "micromatch": "^4.0.5",
     "minimatch": "^3.1.2",
     "node-fetch": "^2.6.1",
-    "partjson": "^0.58.1",
+    "partjson": "^0.58.2",
     "tiny-async-pool": "^1.2.0",
     "typedoc-plugin-missing-exports": "^2.0.1"
   },

package/routes/termdb.categories.ts

@@ -0,0 +1,212 @@
+// import { getcategoriesRequest, getcategoriesResponse } from '#shared/types/routes/termdb.categories'
+import { getOrderedLabels } from '#src/termdb.barchart.js'
+import { getData } from '#src/termdb.matrix.js'
+
+export const api: any = {
+	endpoint: 'termdb/categories',
+	methods: {
+		get: {
+			init,
+			request: {
+				typeId: 'getcategoriesRequest'
+			},
+			response: {
+				typeId: 'getcategoriesResponse'
+			},
+			examples: [
+				{
+					request: {
+						body: {
+							genome: 'hg38-test',
+							dslabel: 'TermdbTest',
+							embedder: 'localhost',
+							getcategories: 1,
+							tid: 'diaggrp',
+							filter: {
+								type: 'tvslst',
+								in: true,
+								join: '',
+								lst: [
+									{
+										tag: 'cohortFilter',
+										type: 'tvs',
+										tvs: {
+											term: {
+												name: 'Cohort',
+												type: 'categorical',
+												values: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },
+												id: 'subcohort',
+												isleaf: false,
+												groupsetting: { disabled: true }
+											},
+											values: [{ key: 'ABC', label: 'ABC' }]
+										}
+									}
+								]
+							}
+						}
+					},
+					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]
+			const ds = g.datasets[req.query.dslabel]
+			const tdb = ds.cohort.termdb
+
+			if (!g) throw 'invalid genome name'
+			if (!ds) throw 'invalid dataset name'
+			if (!tdb) throw 'invalid termdb object'
+			await trigger_getcategories(q, res, tdb, ds, g) // 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_getcategories(q, res, tdb, ds, genome) {
+	// thin wrapper of get_summary
+	// works for all types of terms
+	if (!q.tid) throw '.tid missing'
+	const term =
+		q.type == 'geneVariant' ? { name: q.tid, type: 'geneVariant', isleaf: true } : tdb.q.termjsonByOneid(q.tid)
+	const arg = {
+		filter: q.filter,
+		terms:
+			q.type == 'geneVariant'
+				? [{ term: term, q: { isAtomic: true } }]
+				: [{ id: q.tid, term, q: q.term1_q || getDefaultQ(term, q) }],
+		currentGeneNames: q.currentGeneNames
+	}
+
+	const data = await getData(arg, ds, genome)
+	if (data.error) throw data.error
+
+	const lst = []
+	if (q.type == 'geneVariant') {
+		const samples = data.samples
+		const dtClassMap = new Map()
+		if (ds.assayAvailability?.byDt) {
+			for (const [dtType, dtValue] of Object.entries(ds.assayAvailability.byDt)) {
+				if (dtValue.byOrigin) {
+					dtClassMap.set(parseInt(dtType), { byOrigin: { germline: {}, somatic: {} } })
+				}
+			}
+		}
+		const sampleCountedFor = new Set() // if the sample is conunted for the
+		for (const [sampleId, sampleData] of Object.entries(samples)) {
+			const values = sampleData[q.tid].values
+			sampleCountedFor.clear()
+			/* values here is an array of result entires, one or more entries for each dt. e.g.
+			[
+				{ dt: 1, class: 'Blank', _SAMPLEID_: 1, origin: 'germline' },
+				{ dt: 1, class: 'WT', _SAMPLEID_: 1, origin: 'somatic' },
+				{ dt: 2, class: 'Blank', _SAMPLEID_: 1 },
+				{ dt: 4, class: 'WT', _SAMPLEID_: 1 }
+			]
+			*/
+			for (const value of values) {
+				if (!dtClassMap.has(value.dt)) {
+					dtClassMap.set(value.dt, {})
+				}
+				const dtClasses = dtClassMap.get(value.dt)
+				if (dtClasses.byOrigin) {
+					if (!dtClasses.byOrigin[value.origin][value.class]) {
+						dtClasses.byOrigin[value.origin][value.class] = 1
+						sampleCountedFor.add(`${value.dt} ${value.origin} ${value.class}`)
+					}
+					if (!sampleCountedFor.has(`${value.dt} ${value.origin} ${value.class}`)) {
+						sampleCountedFor.add(`${value.dt} ${value.origin} ${value.class}`)
+						dtClasses.byOrigin[value.origin][value.class] += 1
+					}
+				} else {
+					if (!dtClasses[value.class]) {
+						sampleCountedFor.add(`${value.dt} ${value.class}`)
+						dtClasses[value.class] = 1
+					}
+					if (!sampleCountedFor.has(`${value.dt} ${value.class}`)) {
+						sampleCountedFor.add(`${value.dt} ${value.class}`)
+						dtClasses[value.class] += 1
+					}
+				}
+			}
+		}
+		for (const [dt, classes] of dtClassMap) {
+			lst.push({
+				dt,
+				classes
+			})
+		}
+	} else {
+		const key2count = new Map()
+		// k: category key
+		// v: number of samples
+		for (const sid in data.samples) {
+			const v = data.samples[sid][q.tid]
+			if (!v) continue
+			if (!('key' in v)) continue
+			key2count.set(v.key, 1 + (key2count.get(v.key) || 0))
+		}
+		for (const [key, count] of key2count) {
+			lst.push({
+				samplecount: count,
+				key,
+				label:
+					data.refs?.byTermId?.[q.tid]?.events?.find(e => e.event === key).label || term?.values?.[key]?.label || key
+			})
+		}
+	}
+
+	const orderedLabels = getOrderedLabels(
+		term,
+		data.refs?.byTermId?.[q.tid]?.bins || [],
+		data.refs?.byTermId?.[q.tid]?.events,
+		q.term1_q
+	)
+	if (orderedLabels.length) {
+		lst.sort((a, b) => orderedLabels.indexOf(a.label) - orderedLabels.indexOf(b.label))
+	}
+	res.send({
+		lst,
+		orderedLabels
+	})
+}
+
+function getDefaultQ(term, q) {
+	if (term.type == 'categorical') return {}
+	if (term.type == 'survival') return {}
+	if (term.type == 'integer' || term.type == 'float') return term.bins.default
+	if (term.type == 'condition') {
+		return {
+			mode: q.mode,
+			breaks: q.breaks,
+			bar_by_grade: q.bar_by_grade,
+			/*Leave this here until bug with term1_q not passing to getCategories is figured out.
+			Commented out b/c tvs condition tests fail.*/
+			//bar_by_children: term.subconditions || q.bar_by_children,
+			bar_by_children: q.bar_by_children,
+			value_by_max_grade: q.value_by_max_grade,
+			value_by_most_recent: q.value_by_most_recent,
+			//value_by_computable_grade: term.subconditions || q.value_by_computable_grade
+			value_by_computable_grade: q.value_by_computable_grade
+		}
+	}
+	if (term.type == 'geneVariant') return {}
+	throw 'unknown term type'
+}

package/routes/termdb.violin.ts

@@ -1,5 +1,5 @@
-import { trigger_getViolinPlotData } from '#src/termdb.violin.js'
 // import { getViolinRequest, getViolinResponse } from '#shared/types/routes/termdb.violin'
+import { trigger_getViolinPlotData } from '#src/termdb.violin.js'
 
 export const api: any = {
 	endpoint: 'termdb/violin',