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Emeka000Emeka000
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Merge pull request #76 from fathima200/issue-26
Feat: Implemented Pathology and Diagnostic Services
2 parents bbe939c + 55d7eb6 commit 155f8e2

9 files changed

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‎src/pathology/entities/pathology-case.entity.ts‎

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import { Entity, PrimaryGeneratedColumn, Column, ManyToOne, OneToMany, CreateDateColumn, UpdateDateColumn } from 'typeorm';
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import { Patient } from '../../patients/entities/patient.entity';
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import { Doctor } from '../../doctors/entities/doctor.entity';
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import { PathologyReport } from './pathology-report.entity';
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import { PathologyImage } from './pathology-image.entity';
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import { QualityAssurance } from './quality-assurance.entity';
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export enum CaseStatus {
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RECEIVED = 'received',
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IN_PROGRESS = 'in_progress',
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REVIEWED = 'reviewed',
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COMPLETED = 'completed',
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ARCHIVED = 'archived'
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}
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export enum CaseType {
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HISTOLOGY = 'histology',
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CYTOLOGY = 'cytology',
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MOLECULAR = 'molecular',
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GENETIC = 'genetic',
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IMMUNOHISTOCHEMISTRY = 'immunohistochemistry',
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FLOW_CYTOMETRY = 'flow_cytometry'
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}
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export enum Priority {
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LOW = 'low',
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NORMAL = 'normal',
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HIGH = 'high',
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URGENT = 'urgent',
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STAT = 'stat'
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}
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@Entity('pathology_cases')
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export class PathologyCase {
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@PrimaryGeneratedColumn('uuid')
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id: string;
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@Column({ unique: true })
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caseNumber: string;
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@Column({
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type: 'enum',
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enum: CaseType
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})
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caseType: CaseType;
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@Column({
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type: 'enum',
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enum: CaseStatus,
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default: CaseStatus.RECEIVED
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})
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status: CaseStatus;
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@Column({
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type: 'enum',
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enum: Priority,
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default: Priority.NORMAL
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})
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priority: Priority;
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@Column('text')
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clinicalHistory: string;
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@Column('text')
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specimenDescription: string;
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@Column()
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collectionDate: Date;
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@Column()
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receivedDate: Date;
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@Column({ nullable: true })
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expectedCompletionDate: Date;
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@Column({ nullable: true })
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completedDate: Date;
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@Column('simple-json', { nullable: true })
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specimenDetails: {
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site: string;
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procedure: string;
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fixative: string;
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containerType: string;
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quantity: number;
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grossDescription: string;
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};
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@Column('simple-json', { nullable: true })
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clinicalData: {
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symptoms: string[];
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previousDiagnosis: string;
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medications: string[];
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relevantHistory: string;
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};
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@ManyToOne(() => Patient, patient => patient.pathologyCases)
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patient: Patient;
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@ManyToOne(() => Doctor, doctor => doctor.requestedPathologyCases)
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requestingDoctor: Doctor;
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@ManyToOne(() => Doctor, doctor => doctor.reviewedPathologyCases)
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pathologist: Doctor;
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@OneToMany(() => PathologyReport, (report: PathologyReport) => report.pathologyCase)
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reports: PathologyReport[];
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@OneToMany(() => PathologyImage, (image: PathologyImage) => image.pathologyCase)
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images: PathologyImage[];
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@OneToMany(() => QualityAssurance, (qa: QualityAssurance) => qa.pathologyCase)
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qualityAssurances: QualityAssurance[];
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@CreateDateColumn()
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createdAt: Date;
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@UpdateDateColumn()
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updatedAt: Date;
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}

‎src/pathology/entities/pathology-image.entity.ts‎

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import { Entity, PrimaryGeneratedColumn, Column, ManyToOne, CreateDateColumn, UpdateDateColumn } from 'typeorm';
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import { PathologyCase } from './pathology-case.entity';
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import { Doctor } from '../../doctors/entities/doctor.entity';
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export enum ImageType {
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MICROSCOPIC = 'microscopic',
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MACROSCOPIC = 'macroscopic',
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GROSS = 'gross',
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FLUORESCENCE = 'fluorescence',
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ELECTRON_MICROSCOPY = 'electron_microscopy',
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WHOLE_SLIDE = 'whole_slide',
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IMMUNOFLUORESCENCE = 'immunofluorescence'
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}
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export enum ImageFormat {
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JPEG = 'jpeg',
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PNG = 'png',
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TIFF = 'tiff',
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SVS = 'svs',
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NDPI = 'ndpi',
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CZI = 'czi',
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DICOM = 'dicom'
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}
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export enum StainType {
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H_AND_E = 'h_and_e',
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PAS = 'pas',
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MASSON_TRICHROME = 'masson_trichrome',
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RETICULIN = 'reticulin',
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CONGO_RED = 'congo_red',
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GRAM = 'gram',
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AFB = 'afb',
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IMMUNOHISTOCHEMICAL = 'immunohistochemical',
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SPECIAL_STAIN = 'special_stain'
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}
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@Entity('pathology_images')
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export class PathologyImage {
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@PrimaryGeneratedColumn('uuid')
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id: string;
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@Column()
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filename: string;
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@Column()
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originalFilename: string;
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@Column()
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filePath: string;
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@Column()
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fileSize: number;
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@Column({
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type: 'enum',
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enum: ImageFormat
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})
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format: ImageFormat;
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@Column({
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type: 'enum',
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enum: ImageType
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})
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imageType: ImageType;
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@Column({
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type: 'enum',
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enum: StainType,
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nullable: true
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})
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stainType: StainType;
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@Column('decimal', { precision: 10, scale: 2, nullable: true })
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magnification: number;
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@Column({ nullable: true })
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slideNumber: string;
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@Column({ nullable: true })
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blockNumber: string;
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@Column('simple-json', { nullable: true })
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metadata: {
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width: number;
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height: number;
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resolution: string;
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colorDepth: number;
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compressionType: string;
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acquisitionDate: Date;
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scannerModel: string;
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objective: string;
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};
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@Column('simple-json', { nullable: true })
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annotations: Array<{
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id: string;
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type: string;
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coordinates: number[];
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description: string;
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createdBy: string;
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createdAt: Date;
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}>;
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@Column('text', { nullable: true })
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description: string;
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@Column({ default: false })
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isKeyImage: boolean;
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@Column({ default: false })
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isArchived: boolean;
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@Column({ nullable: true })
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thumbnailPath: string;
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@Column('simple-json', { nullable: true })
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qualityMetrics: {
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focusScore: number;
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brightnessLevel: number;
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contrastLevel: number;
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colorBalance: string;
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artifactPresence: boolean;
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};
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@ManyToOne(() => PathologyCase, pathologyCase => pathologyCase.images)
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pathologyCase: PathologyCase;
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@ManyToOne(() => Doctor, doctor => doctor.capturedImages)
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capturedBy: Doctor;
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@CreateDateColumn()
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createdAt: Date;
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@UpdateDateColumn()
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updatedAt: Date;
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}

‎src/pathology/entities/pathology-report.entity.ts‎

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import { Entity, PrimaryGeneratedColumn, Column, ManyToOne, CreateDateColumn, UpdateDateColumn } from 'typeorm';
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import { PathologyCase } from './pathology-case.entity';
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import { Doctor } from '../../doctors/entities/doctor.entity';
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export enum ReportStatus {
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DRAFT = 'draft',
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PRELIMINARY = 'preliminary',
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FINAL = 'final',
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AMENDED = 'amended',
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CORRECTED = 'corrected'
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}
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export enum DiagnosisType {
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BENIGN = 'benign',
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MALIGNANT = 'malignant',
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SUSPICIOUS = 'suspicious',
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INFLAMMATORY = 'inflammatory',
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REACTIVE = 'reactive',
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NORMAL = 'normal',
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INADEQUATE = 'inadequate'
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}
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@Entity('pathology_reports')
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export class PathologyReport {
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@PrimaryGeneratedColumn('uuid')
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id: string;
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@Column({ unique: true })
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reportNumber: string;
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@Column({
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type: 'enum',
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enum: ReportStatus,
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default: ReportStatus.DRAFT
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})
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status: ReportStatus;
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@Column('text')
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macroscopicDescription: string;
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@Column('text')
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microscopicDescription: string;
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@Column('text')
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diagnosis: string;
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@Column({
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type: 'enum',
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enum: DiagnosisType
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})
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diagnosisType: DiagnosisType;
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@Column('text', { nullable: true })
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comments: string;
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@Column('text', { nullable: true })
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recommendations: string;
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@Column('simple-json', { nullable: true })
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immunohistochemistry: {
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markers: Array<{
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name: string;
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result: string;
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intensity: string;
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distribution: string;
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}>;
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interpretation: string;
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};
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@Column('simple-json', { nullable: true })
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molecularFindings: {
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mutations: Array<{
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gene: string;
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variant: string;
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significance: string;
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}>;
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biomarkers: Array<{
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name: string;
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status: string;
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value: string;
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}>;
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};
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@Column('simple-json', { nullable: true })
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stagingInformation: {
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tnmStaging: {
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t: string;
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n: string;
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m: string;
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stage: string;
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};
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gradingSystem: string;
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grade: string;
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};
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@Column('simple-json', { nullable: true })
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specialStains: Array<{
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stainName: string;
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result: string;
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interpretation: string;
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}>;
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@Column()
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reportDate: Date;
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@Column({ nullable: true })
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verifiedDate: Date;
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@Column({ default: false })
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isVerified: boolean;
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@Column('text', { nullable: true })
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templateUsed: string;
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@Column('simple-json', { nullable: true })
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additionalTesting: {
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flowCytometry: string;
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cytogenetics: string;
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molecularTesting: string;
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otherTests: string[];
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};
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@ManyToOne(() => PathologyCase, pathologyCase => pathologyCase.reports)
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pathologyCase: PathologyCase;
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@ManyToOne(() => Doctor, doctor => doctor.authoredReports)
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author: Doctor;
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@ManyToOne(() => Doctor, doctor => doctor.verifiedReports)
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verifiedBy: Doctor;
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@CreateDateColumn()
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createdAt: Date;
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@UpdateDateColumn()
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updatedAt: Date;
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}

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