gps-global-types 1.0.11 → 1.0.13

package/cluster.types.tsx

@@ -0,0 +1,12 @@
+export const ClusterFields = {
+    '_id': ObjectId,
+    'threshold': Number,
+    'scheme': String,
+    'clusterNickName': String,
+    'isActive': Boolean,
+    'dateCreated': Date,
+    'lastModified': Date,
+    'minimumPatientCount': Number,
+    // 'isolates': [clusterIsoSchema], //array of ClusterIsolates
+    'distances': Map,
+}

package/index.tsx

@@ -1,4 +1,5 @@
 export * from './global.types.js'
 export * from './link.types.js'
 export * from './mst.types.js'
-export * from './pie.types.js'
+export * from './pie.types.js'
+export * from './isolate.types.js'

package/isolate.types.tsx

@@ -0,0 +1,134 @@
+export const KlebFields = {
+    'Yersiniabactin': String,
+    'Colibactin': String,
+    'Aerobactin': String,
+    'Salmochelin': String,
+    'RmpADC': String,
+    'rmpA2': String,
+    'K_locus': String,
+    'O_locus': String,
+    'O_type': String,
+    "SHV_mutations": String,
+    "Omp_mutations": String,
+    "Col_mutations": String,
+    "Flq_mutations": String,
+
+}
+
+
+export const IsolateFields = {
+     "_id":String,
+    "mrsnId": String,
+    "qcCallFinal": String,
+    "rawOrganismId": String,
+    "genus": String,
+    "species": String,
+    "wgsId": String,
+    "topHits": String,
+    "wgsIdMethod": String,
+    "dbBuild": String,
+    "isContaminated": Boolean,
+    "projects": Array,
+    "libraryPlate": String,
+    "sequencingRun": String,
+    "numberOfContigsRaw": Number,
+    "numberOfContigsFilteredForLength": Number,
+    "totalLengthOfContigsFilteredForLength": Number,
+    "numberOfContigsFilteredForLowCoverage": Number,
+    "totalLengthOfContigsFilteredForLowCoverage": String,
+    "numberOfGoodContigs": Number,
+    "averageReadDepthOfGoodContigs": Number,
+    "totalLengthOfGoodContigs": Number,
+    "medianInsertSize": String,
+    "assembler": String,
+    "qcCallAssembly": String,
+    "scheme": String,
+    "mlst": String,
+    "gene1": String,
+    "gene2": String,
+    "gene3": String,
+    "gene4": String,
+    "gene5": String,
+    "gene6": String,
+    "gene7": String,
+    "gene8": String,
+    "qcCallMlst": String,
+    "uploadProcessed": String,
+    "uploadUser": String,
+    "sequencingRunDate": Date,
+    "qcCallId": String,
+    "manuallyEnteredWgsId": Boolean,
+    "accessionNumber": String,
+    "deprecatedSequencedIsolatesCollectionId": String,
+    "amr": Array,
+    "armordAccessionNumber": String,
+    "armordBed": String,
+    "armordCultureDate": Date,
+    "armordCultureSite": String,
+    "armordFacility": String,
+    "armordFacilityCode": String,
+    "armordFile": String,
+    "armordIsolateNumber": String,
+    "armordIsolateType": String,
+    "armordMrsnId": String,
+    "armordPatientId": String,
+    "armordRawOrganismId": String,
+    "armordUnit": String,
+    "submittedOrganismId": String, 
+    "isManuallyEntered": Boolean,
+    "sampleType": String,
+    "qcPoc": String,
+    "qcReviewer": String,
+    "facilityCode": String,
+    "facilityName": String,
+    "collectionDate": String,
+    "index1": String,
+    "index2": String,
+    "r1FileNameRaw": String,
+    "r1FileNameRenamed": String,
+    "r1ReadCount": Number,
+    "r1ReadsWithWarningsCount": Number,
+    "r2FileNameRaw": String,
+    "r2FileNameRenamed": String,
+    "r2ReadCount": Number,
+    "r2ReadsWithWarningsCount": Number,
+    "qcCallFastQc": String,
+    "inputReads": Number,
+    "inputBases": Number,
+    "qtrimmedReadsCount": Number,
+    "qtrimmedReadsPercent": Number,
+    "qtrimmedBasesCount": Number,
+    "qtrimmedBasesPercent": Number,
+    "ktrimmedReadsCount": Number,
+    "ktrimmedReadsPercent": Number,
+    "ktrimmedBasesCount": Number,
+    "ktrimmedBasesPercent": Number,
+    "totalRemovedReadsCount": Number,
+    "totalRemovedReadsPercent": Number,
+    "totalRemovedBasesCount": Number,
+    "totalRemovedBasesPercent": Number,
+    "resultReadsCount": Number,
+    "resultReadsPercent": Number,
+    "resultBasesCount": Number,
+    "resultBasesPercent": Number,
+    "qcCallTrim": String,
+    "assemblyFile": String,
+    "assemblerVersion": String,
+    "assemblerStatus": Boolean,
+    "schemeSelection": String,
+    "source": String,
+    "mlstUtility": String,
+    "mlstUtilityVersion": String,
+    "mlstDatabaseVersion": Date,
+    "isRepresentative": Boolean,
+    "username": String,
+    "uploadDate": Date,
+    // $addFields with the intent of unpacking objects (amr + projects) 
+    "tier": Number,
+    "allele": String,
+    "alleles": Array,
+    "projectCode": Array,
+    "mrsnSuperFamily": String,
+    "expectedPhenotype": String,
+    // "kleborate": [KlebSchema]
+}

package/mst.types.tsx

@@ -1,4 +1,6 @@
+import type { ClusterFields } from "./cluster.types.js";
 import type { armordAccessionNumber, Color, mrsnId, ObjectId, RegexMatchedString } from "./global.types.js";
+import type { IsolateFields } from "./isolate.types.js";
 import type { EdgeType } from "./link.types.js";
 import type { NodeType } from "./pie.types.js";
 
@@ -40,7 +42,7 @@ export interface LatestNodes { armordCultureDate: Date | string, isos: any[], _i
 export interface MSTGraph {
     name?:string,
     snapshotData?:SnapshotType
-    nodes: NodeType[] // core parameter of d3tree.js . keeps all isolates collection data
+    nodes: any //todo:temp//NodeType[] // core parameter of d3tree.js . keeps all isolates collection data
     links: EdgeType[] // core parameter of d3tree.js
     latest: LatestNodes // earliest node for easy toggling
     custom: CustomDict // . I KNOW THIS IS DUMB but from user's pov it results in seamless color transitions across pages
@@ -95,7 +97,7 @@ export interface LegendBullet { //or custom upload data
     label: string
 }
 
-export type MSTLegend = Record<colorKey&'beforeAndAfter'&'custom color', LegendBullet[]> & Record<dateKey, 'date'>;
+export type MSTLegend = Partial<Record<colorKey|'beforeAndAfter'|'custom color', LegendBullet[]>> & Partial<Record<dateKey, 'date'>>;
 // & { 'beforeAndAfter': [{ color: '#666666', label: 'Before ' }, { color: '#4a64aa', label: 'After ' }] }
 
 
@@ -150,3 +152,14 @@ export interface SnapshotType {
 // module.exports = { MSTGraph, MSTLegend, NodeType,EdgeType,Hex, ColorField,LabelField}
 // exports.unused = {};
 
+
+export interface clusterProps {
+    //theres 4 ways of calling this function
+    //1. through a BAQ involving iso and/or cluster fields
+    isolatesQuery?:Partial<Record<keyof typeof IsolateFields, Object>>,
+    clusterQuery?:Partial<Record<keyof typeof ClusterFields, Object>>, //2. selecting a cluster on /clusters (sending cluster _id)
+    fuzzy?:number, //3. by recalculating a previous query
+    neighbors?:number, // (fuzzy and neighbors are only available on recalc)
+    snapshotData?:SnapshotType //4. uploading a snapshot. (should i extrapolate ),
+
+  }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gps-global-types",
-  "version": "1.0.11",
+  "version": "1.0.13",
   "description": "types shared between front-end and back-end",
   "main": "index.js",
   "scripts": {