gps-global-types 1.0.27 → 1.0.30

package/dist/cluster.types.d.ts

@@ -0,0 +1,11 @@
+export declare const ClusterFields: {
+    threshold: NumberConstructor;
+    scheme: StringConstructor;
+    clusterNickName: StringConstructor;
+    isActive: BooleanConstructor;
+    dateCreated: DateConstructor;
+    lastModified: DateConstructor;
+    minimumPatientCount: NumberConstructor;
+    distances: MapConstructor;
+};
+//# sourceMappingURL=cluster.types.d.ts.map

package/dist/cluster.types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cluster.types.d.ts","sourceRoot":"","sources":["cluster.types.tsx"],"names":[],"mappings":"AAAA,eAAO,MAAM,aAAa;;;;;;;;;CAWzB,CAAA"}

package/{cluster.types.tsx → dist/cluster.types.tsx}

@@ -9,4 +9,6 @@ export const ClusterFields = {
     'minimumPatientCount': Number,
     // 'isolates': [clusterIsoSchema], //array of ClusterIsolates
     'distances': Map,
-}
+}
+
+// module.exports = {ClusterFields}

package/dist/global.types.d.ts

@@ -0,0 +1,15 @@
+export type StringDictionary = {
+    [key: string]: string;
+};
+export type RegexMatchedString<Pattern extends string> = `${string & {
+    __brand: Pattern;
+}}`;
+export type armordAccessionNumber = string;
+export type ObjectId = RegexMatchedString<'[a-zA-Z0-9]{12}'>;
+export type armordMrsnId = string;
+export type mrsnId = string;
+export type armordPatientId = RegexMatchedString<'M\d+'>;
+export type Hex = RegexMatchedString<'#\d{6}'>;
+export type Rgb = RegexMatchedString<'rgb\([1-256],[1-256],[1-256]\)'>;
+export type Color = Hex | Rgb | string;
+//# sourceMappingURL=global.types.d.ts.map

package/dist/global.types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"global.types.d.ts","sourceRoot":"","sources":["global.types.tsx"],"names":[],"mappings":"AAAA,MAAM,MAAM,gBAAgB,GAAG;IAC7B,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CACvB,CAAC;AAEF,MAAM,MAAM,kBAAkB,CAAC,OAAO,SAAS,MAAM,IACnD,GAAG,MAAM,GAAG;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,EAAE,CAAC;AAIrC,MAAM,MAAM,qBAAqB,GAAG,MAAM,CAAA;AAC1C,MAAM,MAAM,QAAQ,GAAG,kBAAkB,CAAC,iBAAiB,CAAC,CAAA;AAC5D,MAAM,MAAM,YAAY,GAAG,MAAM,CAAA;AACjC,MAAM,MAAM,MAAM,GAAG,MAAM,CAAA;AAC3B,MAAM,MAAM,eAAe,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAA;AACxD,MAAM,MAAM,GAAG,GAAG,kBAAkB,CAAC,QAAQ,CAAC,CAAA;AAC9C,MAAM,MAAM,GAAG,GAAG,kBAAkB,CAAC,gCAAgC,CAAC,CAAA;AACtE,MAAM,MAAM,KAAK,GAAG,GAAG,GAAG,GAAG,GAAG,MAAM,CAAA"}

package/dist/isolate.types.d.ts

@@ -0,0 +1,130 @@
+export declare const KlebFields: {
+    Yersiniabactin: StringConstructor;
+    Colibactin: StringConstructor;
+    Aerobactin: StringConstructor;
+    Salmochelin: StringConstructor;
+    RmpADC: StringConstructor;
+    rmpA2: StringConstructor;
+    K_locus: StringConstructor;
+    O_locus: StringConstructor;
+    O_type: StringConstructor;
+    SHV_mutations: StringConstructor;
+    Omp_mutations: StringConstructor;
+    Col_mutations: StringConstructor;
+    Flq_mutations: StringConstructor;
+};
+export declare const IsolateFields: {
+    _id: StringConstructor;
+    mrsnId: StringConstructor;
+    qcCallFinal: StringConstructor;
+    rawOrganismId: StringConstructor;
+    genus: StringConstructor;
+    species: StringConstructor;
+    wgsId: StringConstructor;
+    topHits: StringConstructor;
+    wgsIdMethod: StringConstructor;
+    dbBuild: StringConstructor;
+    isContaminated: BooleanConstructor;
+    projects: ArrayConstructor;
+    libraryPlate: StringConstructor;
+    sequencingRun: StringConstructor;
+    numberOfContigsRaw: NumberConstructor;
+    numberOfContigsFilteredForLength: NumberConstructor;
+    totalLengthOfContigsFilteredForLength: NumberConstructor;
+    numberOfContigsFilteredForLowCoverage: NumberConstructor;
+    totalLengthOfContigsFilteredForLowCoverage: StringConstructor;
+    numberOfGoodContigs: NumberConstructor;
+    averageReadDepthOfGoodContigs: NumberConstructor;
+    totalLengthOfGoodContigs: NumberConstructor;
+    medianInsertSize: StringConstructor;
+    assembler: StringConstructor;
+    qcCallAssembly: StringConstructor;
+    scheme: StringConstructor;
+    mlst: StringConstructor;
+    gene1: StringConstructor;
+    gene2: StringConstructor;
+    gene3: StringConstructor;
+    gene4: StringConstructor;
+    gene5: StringConstructor;
+    gene6: StringConstructor;
+    gene7: StringConstructor;
+    gene8: StringConstructor;
+    qcCallMlst: StringConstructor;
+    uploadProcessed: StringConstructor;
+    uploadUser: StringConstructor;
+    sequencingRunDate: DateConstructor;
+    qcCallId: StringConstructor;
+    manuallyEnteredWgsId: BooleanConstructor;
+    accessionNumber: StringConstructor;
+    deprecatedSequencedIsolatesCollectionId: StringConstructor;
+    amr: ArrayConstructor;
+    armordAccessionNumber: StringConstructor;
+    armordBed: StringConstructor;
+    armordCultureDate: DateConstructor;
+    armordCultureSite: StringConstructor;
+    armordFacility: StringConstructor;
+    armordFacilityCode: StringConstructor;
+    armordFile: StringConstructor;
+    armordIsolateNumber: StringConstructor;
+    armordIsolateType: StringConstructor;
+    armordMrsnId: StringConstructor;
+    armordPatientId: StringConstructor;
+    armordRawOrganismId: StringConstructor;
+    armordUnit: StringConstructor;
+    submittedOrganismId: StringConstructor;
+    isManuallyEntered: BooleanConstructor;
+    sampleType: StringConstructor;
+    qcPoc: StringConstructor;
+    qcReviewer: StringConstructor;
+    facilityCode: StringConstructor;
+    facilityName: StringConstructor;
+    collectionDate: StringConstructor;
+    index1: StringConstructor;
+    index2: StringConstructor;
+    r1FileNameRaw: StringConstructor;
+    r1FileNameRenamed: StringConstructor;
+    r1ReadCount: NumberConstructor;
+    r1ReadsWithWarningsCount: NumberConstructor;
+    r2FileNameRaw: StringConstructor;
+    r2FileNameRenamed: StringConstructor;
+    r2ReadCount: NumberConstructor;
+    r2ReadsWithWarningsCount: NumberConstructor;
+    qcCallFastQc: StringConstructor;
+    inputReads: NumberConstructor;
+    inputBases: NumberConstructor;
+    qtrimmedReadsCount: NumberConstructor;
+    qtrimmedReadsPercent: NumberConstructor;
+    qtrimmedBasesCount: NumberConstructor;
+    qtrimmedBasesPercent: NumberConstructor;
+    ktrimmedReadsCount: NumberConstructor;
+    ktrimmedReadsPercent: NumberConstructor;
+    ktrimmedBasesCount: NumberConstructor;
+    ktrimmedBasesPercent: NumberConstructor;
+    totalRemovedReadsCount: NumberConstructor;
+    totalRemovedReadsPercent: NumberConstructor;
+    totalRemovedBasesCount: NumberConstructor;
+    totalRemovedBasesPercent: NumberConstructor;
+    resultReadsCount: NumberConstructor;
+    resultReadsPercent: NumberConstructor;
+    resultBasesCount: NumberConstructor;
+    resultBasesPercent: NumberConstructor;
+    qcCallTrim: StringConstructor;
+    assemblyFile: StringConstructor;
+    assemblerVersion: StringConstructor;
+    assemblerStatus: BooleanConstructor;
+    schemeSelection: StringConstructor;
+    source: StringConstructor;
+    mlstUtility: StringConstructor;
+    mlstUtilityVersion: StringConstructor;
+    mlstDatabaseVersion: DateConstructor;
+    isRepresentative: BooleanConstructor;
+    username: StringConstructor;
+    uploadDate: DateConstructor;
+    tier: NumberConstructor;
+    allele: StringConstructor;
+    alleles: ArrayConstructor;
+    projectCode: ArrayConstructor;
+    mrsnSuperFamily: StringConstructor;
+    expectedPhenotype: StringConstructor;
+};
+//# sourceMappingURL=isolate.types.d.ts.map

package/dist/isolate.types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"isolate.types.d.ts","sourceRoot":"","sources":["isolate.types.tsx"],"names":[],"mappings":"AAAA,eAAO,MAAM,UAAU;;;;;;;;;;;;;;CAetB,CAAA;AAGD,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmHzB,CAAA"}

package/dist/link.types.d.ts

@@ -0,0 +1,8 @@
+import { SimulationLinkDatum } from 'd3';
+import { NodeType } from './pie.types.tsx';
+export interface EdgeType extends SimulationLinkDatum<NodeType> {
+    source: NodeType;
+    target: NodeType;
+    value: number;
+}
+//# sourceMappingURL=link.types.d.ts.map

package/dist/link.types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"link.types.d.ts","sourceRoot":"","sources":["link.types.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAuB,mBAAmB,EAAuB,MAAM,IAAI,CAAC;AAEnF,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAE3C,MAAM,WAAW,QAAS,SAAQ,mBAAmB,CAAC,QAAQ,CAAC;IAC3D,MAAM,EAAE,QAAQ,CAAA;IAChB,MAAM,EAAE,QAAQ,CAAA;IAChB,KAAK,EAAE,MAAM,CAAA;CAChB"}

package/dist/mst.types.d.ts

@@ -0,0 +1,105 @@
+import { ClusterFields } from "./cluster.types.tsx";
+import { Color, ObjectId } from "./global.types.tsx";
+import { IsolateFields } from "./isolate.types.tsx";
+import { EdgeType } from "./link.types.tsx";
+export interface mstGlobalTypes {
+    charge: number;
+    radius: number;
+    cluster: number;
+    distance: number;
+    linkLabelSize: number;
+    center: [number, number];
+    fuzzyThreshold: number;
+    neighbor: number;
+    slim?: boolean;
+    checkedNodes: ObjectId[];
+    highlightedNodes: ObjectId[];
+    graph?: MSTGraph;
+}
+export declare const colorFields: readonly ["armordPatientId", "mlst", "sampleType", "armordFacility", "country", "custom color"];
+export declare const dateFields: readonly ["armordCultureDate", "month", "quarter", "year"];
+export declare const labelFields: readonly ["armordMrsnIdLBL", "mrsnIdLBL", "armordAccessionNumberLBL", "armordPatientIdLBL", "custom label"];
+export type colorKey = typeof colorFields[number];
+export type dateKey = typeof dateFields[number];
+export type labelKey = typeof labelFields[number];
+type CustomDictEntry = Partial<Record<colorKey & dateKey, Color>> | Partial<Record<labelKey, string>>;
+export type CustomDict = Record<ObjectId, CustomDictEntry>;
+export interface LatestNodes {
+    armordCultureDate: Date | string;
+    isos: any[];
+    _id: ObjectId[];
+}
+export interface MSTGraph {
+    name?: string;
+    colorCalendar: Partial<Record<dateKey, Record<string, Color>>>;
+    snapshotData?: SnapshotType;
+    nodes: any;
+    links: EdgeType[];
+    latest: LatestNodes;
+    custom: CustomDict;
+    legend: MSTLegend;
+    missing: Record<string, any>[];
+}
+export interface LegendBullet {
+    color: Color;
+    label: string;
+}
+export type MSTLegend = Partial<Record<colorKey | 'beforeAndAfter' | 'custom color', LegendBullet[]>> & Partial<Record<dateKey, 'date'>>;
+export interface SnapshotType {
+    _id: ObjectId;
+    form: mstGlobalTypes;
+    legend: LegendBullet[];
+    nodes: Record<ObjectId, LegendBullet>;
+    scheme: string;
+    transforms: Record<ObjectId, {
+        x: number;
+        y: number;
+    }>;
+}
+/** /mst route RESULT
+
+/**
+ * @typedef D3treeProps
+ * @property {MSTGraph} data except it only requires links,nodes,legend, and custom
+ * @property {ForceObject} form
+ * @property {String|null} _id cluster _id
+ * @property {function(Snapshot)} setSnapshot
+ * @property {function(MSTGraph)} setData trigger parent data state which affects variables in parent
+ * @property {function([[import('../../typedefs/MSTree').mrsnId[],Boolean ]])} setSelected connects nodes to table rows on click
+ */
+/**force
+ * @typedef d3Data
+ * @property {EdgeType[]} links
+ * @property {NodeType[]} pies
+ */
+/**string
+ * @typedef ItolProps
+ * @property {string} scheme
+ * @property {ObjectId[]} isolates targets centered for analysis
+ * @property {int} neighbors min # of nearest samples to include (beyond targets)
+ * @property {int} threshold max allelic distance from the targets to include
+ */
+/**
+ * @typedef MstFields
+ * @property {String[]} clusterNickName
+ * @property {String[]} scheme
+ * @property {Date} lastModified
+ * @property {Date} dateModified
+ *
+ *
+ *
+ *
+ *
+ *
+* @typedef {{...SplashReq,...MstFields}} MSTreeReq
+     *
+*/
+export type QueryFields = keyof typeof IsolateFields | 'cluster' | `cluster.${keyof typeof ClusterFields}` | keyof typeof ClusterFields;
+export interface getAClusterBody {
+    query?: Partial<Record<QueryFields, Object>>;
+    fuzzy?: number;
+    neighbors?: number;
+    snapshotData?: SnapshotType;
+}
+export {};
+//# sourceMappingURL=mst.types.d.ts.map

package/dist/mst.types.d.ts.map

@@ -0,0 +1 @@
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package/dist/pie.types.d.ts

@@ -0,0 +1,69 @@
+import { BaseType, Selection, SimulationNodeDatum } from "d3";
+import { ObjectId, Color, RegexMatchedString, mrsnId } from "./global.types.tsx";
+import { colorKey, dateKey, labelKey } from "./mst.types.tsx";
+export interface ColorField {
+    color: string;
+    value: number;
+    latest?: string;
+}
+export type LabelField = string;
+export interface ColorType {
+    color: Color;
+    value: number;
+    latest?: 'latest';
+}
+export type LabelType = RegexMatchedString<'(\w&)*'>;
+type DateType = string | Date;
+export interface ExtraNodeTypeFields extends SimulationNodeDatum {
+    id: ObjectId;
+    beforeAndAfter?: ColorType[];
+    dateArr: DateType[];
+    hover?: string;
+    nodeids: ObjectId[];
+    mrsnIds: mrsnId[];
+    x?: number;
+    y?: number;
+    fx?: number | null;
+    fy?: number | null;
+}
+export type NodeType = ExtraNodeTypeFields & {
+    [K in colorKey | dateKey]: ColorType[];
+} & {
+    [K in labelKey]: LabelType[];
+};
+export type ParentSelection = Selection<SVGGElement, NodeType, BaseType, unknown>;
+export type PieSelection = Selection<SVGCircleElement, NodeType, BaseType, NodeType[]>;
+export type PieTextSelection = Selection<SVGTextElement, NodeType, SVGGElement, NodeType>;
+export interface PieType {
+    g: ParentSelection;
+    data: NodeType[];
+    labelField: keyof NodeType;
+}
+export interface SelectionObj {
+    mrsnIds: string[];
+    active: boolean;
+}
+export interface NodeColorProps {
+    colorField: keyof NodeType;
+    svg: ParentSelection;
+    formRadius: number;
+}
+export interface newLabelProps {
+    labelField: keyof NodeType;
+    svg: ParentSelection;
+    slim: boolean;
+}
+type ColorCountTemp = Record<Color, number>;
+type ExcludeB4A<T> = Omit<T, 'beforeAndAfter'>;
+export type PreNodeInterface = ExcludeB4A<ExtraNodeTypeFields> & {
+    [K in colorKey | dateKey]: ColorCountTemp;
+} & {
+    [K in labelKey]: LabelType;
+} & {
+    populate: (field: colorKey | dateKey, value: Color) => void;
+} & {
+    tier1: Set<string>;
+    beforeAndAfter: any;
+};
+export {};
+//# sourceMappingURL=pie.types.d.ts.map

package/dist/pie.types.d.ts.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,13 +1,17 @@
 {
   "name": "gps-global-types",
-  "version": "1.0.27",
+  "version": "1.0.30",
   "description": "types shared between front-end and back-end",
-  "main": "index.js",
+  "main": "dist/index.js",
+  "files": [
+    "dist"
+  ],
   "scripts": {
-    "test": "echo \"Error: no test specified\" && exit 1"
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "build": "tsc",
+    "prepublishOnly": "npm run build"
   },
   "author": "lizz",
-  "type": "module",
   "license": "ISC",
   "dependencies": {
     "d3": "^7.9.0",

package/tsconfig.json

@@ -1,41 +0,0 @@
-{
-  // Visit https://aka.ms/tsconfig to read more about this file
-  "compilerOptions": {
-    // File Layout
-    // "rootDir": "./src",
-    // "outDir": "./dist",
-    // Environment Settings
-    // See also https://aka.ms/tsconfig/module
-    "module": "nodenext",
-    "target": "esnext",
-    "types": [],
-    // For nodejs:
-    // "lib": ["esnext"],
-    // "types": ["node"],
-    // and npm install -D @types/node
-    // Other Outputs
-    "sourceMap": true,
-    "declaration": true,
-    "declarationMap": true,
-    "emitDeclarationOnly": true,
-    "allowImportingTsExtensions": true,
-    // Stricter Typechecking Options
-    "noUncheckedIndexedAccess": true,
-    "exactOptionalPropertyTypes": true,
-    // Style Options
-    // "noImplicitReturns": true,
-    // "noImplicitOverride": true,
-    // "noUnusedLocals": true,
-    // "noUnusedParameters": true,
-    // "noFallthroughCasesInSwitch": true,
-    // "noPropertyAccessFromIndexSignature": true,
-    // Recommended Options
-    "strict": true,
-    "jsx": "react-jsx",
-    "verbatimModuleSyntax": false,
-    "isolatedModules": true,
-    "noUncheckedSideEffectImports": true,
-    "moduleDetection": "force",
-    "skipLibCheck": true,
-  }
-}