gps-global-types 1.0.0

package/mst.types.tsx

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+
+export interface mstGlobalTypes {
+    //form values
+    charge: number, //= -100, // repulsion
+    radius: number, //= 15, // user adjustment of node radius
+    cluster: number, //= 0, // less than highlight threshold for links
+    distance: number //= 
+    linkLabelSize: number, //= 12, // fontSize of link labels
+    center: [number, number,]//[800,500],// where on the page does the tree spawn (x,y )
+    fuzzyThreshold: number, //= 0, // nodes outside of requested list that are x alleles away from the original mst
+    neighbor: number, //= 1, // how many isolate neighbors to return (minimum) 
+    slim?: boolean, //false //are the node labels collapsed or expanded?
+    
+    //interactive nodes
+    //  checkedNodes:mrsnId[], ????
+    //  highlightedNodes:mrsnId[] ????
+}
+
+export const colorFields= ['armordPatientId','mlst','sampleType','armordFacility','armordCountry','custom color'] as const; //no :string[] ! removes 'const'
+export const dateFields= ['armordCultureDate','month','quarter','year'] as const;
+export const labelFields= ['armordMrsnIdLBL','mrsnIdLBL','armordAccessionNumberLBL','armordPatientIdLBL','custom label'] as const;
+
+export type colorKey = typeof colorFields[number];
+export type dateKey = typeof dateFields[number];
+export type labelKey = typeof labelFields[number];
+
+type RegexMatchedString<Pattern extends string> =
+    `${string & { __brand: Pattern }}`;
+//TYPES OF STRINGS
+type armordAccessionNumber = string // who KNOWS the format of these 
+type ObjectId = RegexMatchedString<'[a-zA-Z0-9]{12}'> //12 byte string meant to index mongo docs
+type armordMrsnId = string  //  6 o/*  */r 7 digit number typically, but the bi-db is a cesspool
+type mrsnId = string  // ###### ('MRSN' + 6 or 7 digit number) typically, but the bi-db is a cesspool
+type armordPatientId = RegexMatchedString<'M\d+'>  // M###### ('M'+6 digit number), but the bi-db is a cesspool
+type Hex = RegexMatchedString<'#\d{6}'>  // 6 digit String hexadecimal w/ '#' prepended
+type Rgb = RegexMatchedString<'rgb\([1-256],[1-256],[1-256]\)'>  // format rgb(\d[1-256],\d[1-256],\d[1-256])
+type Color = Hex|Rgb|String
+
+
+
+
+
+
+interface ColorType {
+    color:Color, //unique hex of parameter
+    value:number //count of how many times value will be represented in the pie
+}
+type LabelType = RegexMatchedString<'(\w&)*'> // if many, seperated by '&' qhich are interpreted as newlines in front-end. var names ends with 'LBL'.
+type DateType = string | Date  // must be able to be interpreted as date type by Date js object
+
+
+interface ExtraNodeTypeFields {
+id:ObjectId,//unique identifier referenced by Graph.links and d3 Force. String but it's a string of a mongo id
+beforeAndAfter?:ColorType[] //[=[{color:'#fff',value:1}]] so it doesnt break on recalculation
+dateArr:DateType[], // array of armordCultureDates used for beforeAndAfter coloring
+hover?:String, // [=""] //unique fieldfields \/ \/ list seperated by ', ' (only tier1 alleles for now)
+mrsnIds: String[] // for selection logic between table and node=
+}
+
+type NodeType = ExtraNodeTypeFields | Record<colorKey|dateKey, ColorType[]> | Record<labelKey, LabelType[]>;
+
+interface EdgeType {
+    source:string, //node _id edge to
+    target:string, //node _id edge from
+    value:number   //distance between source and target
+}
+
+type CustomDictEntry  = Record<colorKey|dateKey,Color> | Record<labelKey,string>;
+type CustomDict = Record<ObjectId,CustomDictEntry>
+
+
+
+export interface MSTGraph {
+nodes :NodeType[] // core parameter of d3tree.js . keeps all isolates collection data
+links :EdgeType[] // core parameter of d3tree.js
+latest :{armordCultureDate:Date, armordMrsnId:mrsnId[]} // 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
+legend :MSTLegend // saves legend configs across all color fields
+}interface FlashTable {
+  "_id": ObjectId,
+  "MRSN ID¹": mrsnId,
+  "Cx Date": Date|string,
+  "Cx Source": string,
+  "Wards": string,
+  "Prev Report #²": string,
+  "Accession #": armordAccessionNumber,
+  "Last Name": "...",
+  "DOD ID": "..."
+}
+
+interface FlashData { //todo: add 'tier1s' here
+    dateCreated:Date,
+    first:boolean, //first node added to thec cluster
+    isolateCount:number, 
+    lastModified:Date,
+    mostRecent:{
+        _id:ObjectId[],
+        armordCultureDate:Date|string,
+        isos:Record<string,any>[], //todo
+    }
+    mostCloselyRelated:{
+        _id:ObjectId,
+        armordCultureDate:Date|string,
+        distance:number
+    },
+    patientCount:number,
+    st:string,
+    table:FlashTable[],
+    wardCount:string,
+    wgsId:string
+}
+
+
+interface MSTResult {
+    flash:FlashData,
+    graph:MSTGraph,
+    tabular:{
+        isolate:Record<string,any>[],
+        amr:Record<string,any>[]
+    }
+}
+
+interface LegendBullet { //or custom upload data
+    color:Color,
+    label:string
+}
+
+type MSTLegend = Record<colorKey,LegendBullet[]>|Record<dateKey,'date'> | {'beforeAndAfter':[{color:'#666666', label:'Before '} ,{color:'#4a64aa', label:'After '}]}
+
+
+
+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
+ */
+//IDK WHY THESE EXIST
+/**
+ * @typedef MstFields
+ * @property {String[]} clusterNickName
+ * @property {String[]} scheme
+ * @property {Date} lastModified
+ * @property {Date} dateModified
+ *
+ * 
+ * 
+ * 
+ * 
+ * 
+* @typedef {{...SplashReq,...MstFields}} MSTreeReq
+     *
+*/
+    // module.exports = { MSTGraph, MSTLegend, NodeType,EdgeType,Hex, ColorField,LabelField}
+    // exports.unused = {};

package/package.json

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+{
+  "name": "gps-global-types",
+  "version": "1.0.0",
+  "description": "types shared between front-end and back-end",
+  "main": "index.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "author": "lizz",
+  "type":"module",
+  "license": "ISC"
+}

package/pie.types.tsx

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+import { BaseType, Selection, SimulationNodeDatum } from "d3"
+import { Ref, RefObject } from "react"
+import { EdgeType, svgSelection } from "../../Link/link.types"
+import { ObjectId, Color, RegexMatchedString } from "@/assets/types/global.types"
+import { colorKey, dateKey, labelKey } from "../../mst.types"
+
+export interface ColorField {//TYPES OF GRAPH FIELDS ColorField datefields become colorFields but require additional processing  
+    color: string, //  unique hex or rgb  of parameter 
+    value: number, //  count of how many times value will be represented in the pie
+    latest?: string // most recent node designation; diff coloring logic for 'latest' nodes
+}
+
+export type LabelField = string //if n>1, seperated by '&' which are interpreted as newlines in front-end. var names ends with 'LBL'.
+export interface ColorType {
+    color: Color, //unique hex of parameter
+    value: number //count of how many times value will be represented in the pie
+}
+type LabelType = RegexMatchedString<'(\w&)*'> // if many, seperated by '&' qhich are interpreted as newlines in front-end. var names ends with 'LBL'.
+type DateType = string | Date  // must be able to be interpreted as date type by Date js object
+
+
+interface ExtraNodeTypeFields extends d3.SimulationNodeDatum {
+    id: ObjectId,//unique identifier referenced by Graph.links and d3 Force. String but it's a string of a mongo id
+    beforeAndAfter?: ColorType[], //[=[{color:'#fff',value:1}]] so it doesnt break on recalculation
+    dateArr: DateType[], // array of armordCultureDates used for beforeAndAfter coloring
+    hover?: string, // [=""] //unique fieldfields \/ \/ list seperated by ', ' (only tier1 alleles for now)
+    nodeids: ObjectId[] // for selection logic between table and node=
+    x?: number,
+    y?: number,
+    fx?: number | null,
+    fy?: number | null,
+}
+
+export type NodeType = ExtraNodeTypeFields & {
+    [K in colorKey | dateKey]: ColorType[];
+} & {
+    [K in labelKey]: LabelType[];
+}; //d3.Selection<SVGGElement, NodeType, d3.BaseType, unknown>
+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, //todo acceptable strings!
+}
+export interface SelectionObj {
+    mrsnIds: string[],
+    active: boolean
+}
+export interface InitializeDragProps {
+    sticky: boolean,
+    sim: RefObject<d3.Simulation<d3.SimulationNodeDatum, any>>,
+    setSelected: React.Dispatch<React.SetStateAction<SelectionObj>>,
+    height: number,
+    width: number// todo can this be a global const somewhere instead?
+}
+export interface NodeColorProps {
+    colorField: keyof NodeType,
+    svg: ParentSelection,
+    formRadius: number
+}
+
+export interface newLabelProps {
+    labelField: keyof NodeType,
+    svg: ParentSelection,
+    slim: boolean
+}