tweaks

pnrobinson · pnrobinson · commit a6a7dbe03a51 · 2026-02-20T19:25:46.000+01:00
diff --git a/src/app/individual_edit/individual_edit.component.html b/src/app/individual_edit/individual_edit.component.html
@@ -31,7 +31,7 @@ <h2 mat-dialog-title>Edit Individual</h2>
           >
           <!-- dropdown list -->
           <mat-autocomplete #auto="matAutocomplete" autoActiveFirstOption>
-            @for (term of ageInputService.onsetTerms; track term) {
+            @for (term of ageInputService.ALLOWED_AGE_LABELS; track term) {
               <mat-option [value]="term">
                 {{ term }}
               </mat-option>
@@ -52,7 +52,7 @@ <h2 mat-dialog-title>Edit Individual</h2>
           >
           <!-- dropdown list -->
           <mat-autocomplete #auto="matAutocomplete" autoActiveFirstOption>
-            @for (term of ageInputService.onsetTerms; track term) {
+            @for (term of ageInputService.ALLOWED_AGE_LABELS; track term) {
               <mat-option [value]="term">
                 {{ term }}
               </mat-option>
diff --git a/src/app/multihpo/multihpo.component.html b/src/app/multihpo/multihpo.component.html
@@ -1,3 +1,4 @@
+ <h2 mat-dialog-title style="margin-bottom: 0;">{{title}}</h2>
 <mat-dialog-content class="mat-typography">
   <div class="review-table-container">
     <table class="custom-curation-table">
diff --git a/src/app/multihpo/multihpo.component.ts b/src/app/multihpo/multihpo.component.ts
@@ -67,7 +67,7 @@ export class MultiHpoComponent {
     const processed = (this.data.concepts ?? [])
       .filter(c => {
         const text = c.originalText.toLowerCase().trim();
-        return !NOT_APPLICABLE.has(text) && /[a-zA-Z]/.test(text);
+        return !NOT_APPLICABLE.has(text) && text.length > 0;
       })
       .map(c => ({
         ...c,
diff --git a/src/app/services/age_service.ts b/src/app/services/age_service.ts
@@ -2,18 +2,44 @@ import { computed, Injectable, signal } from '@angular/core';
 import { AbstractControl, ValidationErrors, ValidatorFn } from '@angular/forms';
 
 
+// regexes for human strings such as 4y2m and 4yrs 2nth
+const RE_YEAR = /(\d+(?:\.\d+)?)\s*y/i;
+const RE_MONTH = /(\d+(?:\.\d+)?)\s*m/i;
+const RE_WEEK = /(\d+(?:\.\d+)?)\s*w/i;
+const RE_DAY = /(\d+)\s*d/i;
+// Matches ISO 8601 durations like "P1Y6M3D" or "P0D"
+const ISO8601_RE = /^P(?:\d+Y)?(?:\d+M)?(?:\d+D)?$/i;
+const GESTATIONAL_AGE_RE = /^G(\d+)w(?:([0-6])d)?$/i;
+
+
 @Injectable({
     providedIn: 'root'
 })
 export class AgeInputService {
-    readonly onsetTerms = ['na', 'Antenatal onset',
+    readonly ALLOWED_AGE_LABELS = new Set(['na', 'Antenatal onset',
         'Embryonal onset', 'Fetal onset',
         'Late first trimester onset' , 'Second trimester onset' ,'Third trimester onset', 
         'Congenital onset',
         'Pediatric onset',
         'Neonatal onset', 'Infantile onset',  'Childhood onset',  'Juvenile onset' ,
         'Adult onset','Young adult onset',  'Early young adult onset' , 'Intermediate young adult onset' , 'Late young adult onset',
-        'Middle age onset', 'Late onset' ];
+        'Middle age onset', 'Late onset' ]);
+
+    readonly AGE_TERM_MAP: Record<string, string> = {
+        antenatal: "Antenatal onset",
+        neonate: "Neonatal onset",
+        neonatal: "Neonatal onset",
+        birth: "Congenital onset",
+        congenital: "Congenital onset",
+        childhood: "Childhood onset",
+        adult: "Adult onset",
+        unk: "na",
+        na: "na",
+    };
+
+  
+
+     
 
     readonly isoPattern = /^P(?:\d+Y)?(?:\d+M)?(?:\d+D)?$/;
     readonly gestationalAgePattern = /^G\d{1,2}w(?:[0-6]d)?$/;
@@ -24,14 +50,14 @@ export class AgeInputService {
     readonly selectedTerms = this._selectedTerms.asReadonly();
     /** for autocomplete lists */
     readonly allAvailableTerms = computed(() => {
-        return Array.from(new Set([...this.onsetTerms, ...this._selectedTerms()]));
+        return Array.from(new Set([...this.ALLOWED_AGE_LABELS, ...this._selectedTerms()]));
     });
     /**
      * Returns true if the input is a valid ISO8601 age string, a gestational age string, or a known HPO term ("na" is also an allowed entry)
      */
     validateAgeInput(input: string): boolean {
         return input == "na" ||
-        this.onsetTerms.includes(input) || 
+        this.ALLOWED_AGE_LABELS.has(input) || 
         this.isoPattern.test(input) || 
         this.gestationalAgePattern.test(input);
     }
@@ -67,4 +93,50 @@ export class AgeInputService {
         this._selectedTerms.set(["na"]);
     }
 
+    mapAgeStringToSymbolic(input: string): string | null {
+        const lower = input.toLowerCase();
+        if (this.AGE_TERM_MAP[lower]) return this.AGE_TERM_MAP[lower];
+        if (this.ALLOWED_AGE_LABELS.has(input)) return input;
+        return null;
+    }
+
+    mapYmdToIso(input: string): string | undefined {
+        const yMatch = RE_YEAR.exec(input);
+        const mMatch = RE_MONTH.exec(input);
+        const wMatch = RE_WEEK.exec(input);
+        const dMatch = RE_DAY.exec(input);
+
+        const yVal = yMatch ? parseFloat(yMatch[1]) : 0;
+        const mVal = mMatch ? parseFloat(mMatch[1]) : 0;
+        const wVal = wMatch ? parseFloat(wMatch[1]) : 0;
+        const dVal = dMatch ? parseFloat(dMatch[1]) : 0;
+
+        console.log(`input=${input} y=${yVal} m=${mVal} w=${wVal} d=${dVal}`);
+
+        if (yVal === 0 && mVal === 0 && wVal === 0 && dVal === 0) return undefined;
+
+        const years = Math.floor(yVal);
+        const monthsFromY = Math.round((yVal - years) * 12);
+        const totalMonths = Math.floor(mVal) + monthsFromY;
+
+        const daysFromW = Math.round(wVal * 7);
+        const totalDays = Math.floor(dVal) + daysFromW;
+
+        let res = "P";
+        if (years > 0) res += `${years}Y`;
+        if (totalMonths > 0) res += `${totalMonths}M`;
+        if (totalDays > 0) res += `${totalDays}D`;
+
+        return res === "P" ? undefined : res;
+    }
+
+    mapEtlAgeString(input: string | null | undefined): string | undefined {
+        if (! input) return undefined;
+        const symbolic = this.mapAgeStringToSymbolic(input);
+        if (symbolic) return symbolic;
+        if (GESTATIONAL_AGE_RE.test(input)) return input;
+        if (ISO8601_RE.test(input)) return input;
+        return this.mapYmdToIso(input);
+    }
+
 }
diff --git a/src/app/services/etl_session_service.ts b/src/app/services/etl_session_service.ts
@@ -5,22 +5,6 @@ import { DiseaseData } from "../models/cohort_dto";
 import { PmidDto } from "../models/pmid_dto";
 
 
-const AGE_TERM_MAP: Record<string, string> = {
-  antenatal: "Antenal onset",
-  neonate: "Neonatal onset",
-  neonatal: "Neonatal onset",
-  "neonatal onset": "Neonatal onset",
-  newborn: "Neonatal onset",
-  "newborn onset": "Neonatal onset",
-  birth: "Congenital onset",
-  congenital: "Congenital onset",
-  child: "Childhood onset",
-  childhood: "Childhood onset",
-  adult: "Adult onset",
-  adulthood: "Adult onset",
-  unk: "na",
-  na: "na"
-};
 
 
 // 4. ETL Session Service
@@ -160,76 +144,7 @@ export class EtlSessionService {
     return undefined
   }
   
-  /* Try to parse a variety of age strings to Iso8601. 
-    If another kind of valid age string is found, keep it (.e., Gestational or ISO) */
-  parseAgeToIso8601(ageStr: string | null | undefined): string | undefined {
-    if (!ageStr?.trim()) return undefined;
-    if (this.ageService.validateAgeInput(ageStr)) return ageStr;
-    const lower = ageStr.trim().toLowerCase();
-    if (AGE_TERM_MAP[lower]) return AGE_TERM_MAP[lower];
-    
-    const yearMatch = /(\d+(?:\.\d+)?)\s*(y(?:ear)?s?|yr?s?|yo)\b/.exec(lower);
-    const monthMatch = /(\d+(?:\.\d+)?)\s*(m(?:onth)?s?|mo?s?)\b/.exec(lower);
-    const dayMatch = /(\d+)\s*(d(?:ay)?s?)\b/.exec(lower);
-
-    if (!yearMatch && !monthMatch && !dayMatch) return undefined;
-    const rawYears: number = yearMatch ? parseFloat(yearMatch[1]) : 0;
-    const rawMonths: number = monthMatch ? parseFloat(monthMatch[1]) : 0;
-    const days: number = dayMatch ? parseInt(dayMatch[1], 10) : 0;
-
-    const years = Math.floor(rawYears);
-    const monthsFromYears = Math.round((rawYears - years) * 12);
-    const totalMonths = Math.floor(rawMonths) + monthsFromYears;
-    // Build ISO8601 string
-    const parts = [
-      years > 0 ? `${years}Y` : '',
-      totalMonths > 0 ? `${totalMonths}M` : '',
-      days > 0 ? `${days}D` : ''
-    ].join('');
-    return parts ? `P${parts}` : undefined;
-  }
-
-  /**
-   * Converts a decimal number representing years into ISO 8601 duration format.
-   * Examples: 
-   * - "4" -> "P4Y"
-   * - "4.5" -> "P4Y6M" 
-   * - "2.25" -> "P2Y3M"
-   * - "0.75" -> "P9M"
-   * @param input - String containing a decimal number
-   * @returns ISO 8601 duration string or empty string if invalid
-   */
-  parseDecimalYearsToIso8601(input: string | null | undefined): string {
-    if (input == null || input == undefined) {
-      return '';
-    }
-    const trimmed = input.trim();
-    // May be integer or decimal
-    const numberMatch = /^\d+(?:\.\d+)?$/.exec(trimmed);
-    if (!numberMatch) {
-      return '';
-    }
-    const totalYears = parseFloat(trimmed);
-    if (isNaN(totalYears) || totalYears < 0) {
-      return '';
-    }
-    const wholeYears = Math.floor(totalYears);
-    const fractionalYears = totalYears - wholeYears;
-    const months = Math.round(fractionalYears * 12);
-    let result = 'P';
-    if (wholeYears > 0) {
-      result += `${wholeYears}Y`;
-    }
-    if (months > 0) {
-      result += `${months}M`;
-    }
-    // Handle edge case where input is 0
-    return result === 'P' ? '' : result;
-  }
-
-
-
-
+  
   
   private generateId(): string {
     return Date.now().toString(36) + Math.random().toString(36).substr(2);
diff --git a/src/app/tableeditor/tableeditor.component.ts b/src/app/tableeditor/tableeditor.component.ts
@@ -36,6 +36,7 @@ import { TransformType, TransformCategory, StringTransformFn, columnTypeColors,
 import { CellReviewComponent } from '../cellreview/cellreview.component';
 import { HelpButtonComponent } from "../util/helpbutton/help-button.component";
 import { AppStatusService } from '../services/app_status_service';
+import { AgeInputService } from '../services/age_service';
 
 export const RAW: EtlCellStatus = 'raw' as EtlCellStatus;
 export const TRANSFORMED: EtlCellStatus = 'transformed' as EtlCellStatus;
@@ -69,6 +70,7 @@ export class TableEditorComponent implements OnInit {
   Object = Object;
 
   private configService = inject(ConfigService);
+  private ageService = inject(AgeInputService);
   private dialog = inject(MatDialog);
   public etl_service = inject(EtlSessionService);
   private notificationService = inject(NotificationService);
@@ -149,7 +151,7 @@ export class TableEditorComponent implements OnInit {
 
   /* Functions that perform a fixed operation on cells and DO expect the column type to change */
   readonly ELEMENTWISE_MAP: Partial<Record<TransformType, StringTransformFn>> = {
-    [TransformType.ONSET_AGE]: (val) => this.etl_service.parseAgeToIso8601(val),
+    [TransformType.ONSET_AGE]: (val) => this.ageService.mapEtlAgeString(val),
     [TransformType.SEX_COLUMN]: (val) => this.etl_service.parseSexColumn(val),
     [TransformType.SEX_COLUMN_TYPE]: (val) => this.etl_service.parseSexColumn(val),
     [TransformType.INDIVIDUAL_ID_COLUMN_TYPE]: (val) => sanitizeString(val),
@@ -1307,11 +1309,9 @@ export class TableEditorComponent implements OnInit {
           break;
         case TransformType.ONSET_AGE:
         case TransformType.LAST_ENCOUNTER_AGE:
-          transformed = this.etl_service.parseAgeToIso8601(original);
-          break;
         case TransformType.ONSET_AGE_ASSUME_YEARS:
         case TransformType.LAST_ECOUNTER_AGE_ASSUME_YEARS:
-          transformed = this.etl_service.parseDecimalYearsToIso8601(original);
+          transformed = this.ageService.mapEtlAgeString(original) ?? `Could not convert ${original}`;
           break;
         case TransformType.SEX_COLUMN:
           transformed = this.etl_service.parseSexColumn(original);
@@ -1537,18 +1537,14 @@ export class TableEditorComponent implements OnInit {
       case TransformType.TO_LOWERCASE:
         output = input.toLowerCase();
         break;
-      case TransformType.ONSET_AGE:
-        output = this.etl_service.parseAgeToIso8601(input);
-        break;
-      case TransformType.LAST_ENCOUNTER_AGE:
-        output = this.etl_service.parseAgeToIso8601(input);
-        break;
       case TransformType.SEX_COLUMN:
         output = this.etl_service.parseSexColumn(input);
         break;
+      case TransformType.ONSET_AGE:
+      case TransformType.LAST_ENCOUNTER_AGE:
       case TransformType.ONSET_AGE_ASSUME_YEARS:
       case TransformType.LAST_ECOUNTER_AGE_ASSUME_YEARS:
-        output = this.etl_service.parseDecimalYearsToIso8601(input);
+        output = this.ageService.mapEtlAgeString(input);
         break;
     }
     if (output) {

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+ <h2 mat-dialog-title style="margin-bottom: 0;">{{title}}</h2>`
`1`	`2`	`<mat-dialog-content class="mat-typography">`
`2`	`3`	`<div class="review-table-container">`
`3`	`4`	`<table class="custom-curation-table">`