Add species and admitting parsing

Author: igoroctaviano

src/components/Patient.tsx

@@ -1,7 +1,12 @@
 // skipcq: JS-C1003
 import type * as dmv from 'dicom-microscopy-viewer'
 import React from 'react'
-import { parseDate, parseName, parseSex } from '../utils/values'
+import {
+  formatPatientSpeciesCodeSequence,
+  parseDate,
+  parseName,
+  parseSex,
+} from '../utils/values'
 import Description from './Description'
 
 interface PatientProps {
@@ -15,6 +20,10 @@ interface PatientProps {
  */
 class Patient extends React.Component<PatientProps, Record<string, never>> {
   render(): React.ReactNode {
+    const species = formatPatientSpeciesCodeSequence(
+      (this.props.metadata as unknown as Record<string, unknown>)
+        .PatientSpeciesCodeSequence,
+    )
     const attributes = [
       {
         name: 'ID',
@@ -24,6 +33,7 @@ class Patient extends React.Component<PatientProps, Record<string, never>> {
         name: 'Name',
         value: parseName(this.props.metadata.PatientName),
       },
+      ...(species !== undefined ? [{ name: 'Species', value: species }] : []),
       {
         name: 'Sex',
         value: parseSex(this.props.metadata.PatientSex),

src/components/SpecimenItem.tsx

@@ -4,6 +4,10 @@ import * as dcmjs from 'dcmjs'
 import type * as dmv from 'dicom-microscopy-viewer'
 import React from 'react'
 import { SpecimenPreparationStepItems } from '../data/specimens'
+import {
+  codedConceptDisplayText,
+  dedupeStringsPreserveOrder,
+} from '../utils/values'
 import type { Attribute } from './Description'
 import Item from './Item'
 
@@ -13,6 +17,35 @@ interface SpecimenItemProps {
   showstain: boolean
 }
 
+/** (0008,1080) LO and (0008,1084) SQ — separate DICOM attributes; combine for display. */
+function formatAdmittingDiagnoses(
+  metadata: Record<string, unknown>,
+): string | undefined {
+  const descRaw = metadata.AdmittingDiagnosesDescription
+  const desc = typeof descRaw === 'string' ? descRaw.trim() : ''
+
+  const seq = metadata.AdmittingDiagnosesCodeSequence
+  const codeParts: string[] = []
+  if (Array.isArray(seq)) {
+    for (const item of seq) {
+      const part = codedConceptDisplayText(item)
+      if (part !== '') codeParts.push(part)
+    }
+  }
+  const uniqueCodes = dedupeStringsPreserveOrder(codeParts)
+  const codesJoined = uniqueCodes.join(', ')
+
+  if (desc !== '' && codesJoined !== '') {
+    if (desc.toLowerCase() === codesJoined.toLowerCase()) {
+      return desc
+    }
+    return `${desc}; ${codesJoined}`
+  }
+  if (desc !== '') return desc
+  if (codesJoined !== '') return codesJoined
+  return undefined
+}
+
 /**
  * React component representing a DICOM Specimen Information Entity and
  * displays specimen-related attributes of a DICOM Slide Microscopy image.
@@ -160,14 +193,13 @@ class SpecimenItem extends React.Component<
       },
     )
 
-    if (
-      (this.props.metadata as unknown as Record<string, unknown>)
-        .AdmittingDiagnosesDescription !== undefined
-    ) {
+    const admittingDiagnoses = formatAdmittingDiagnoses(
+      this.props.metadata as unknown as Record<string, unknown>,
+    )
+    if (admittingDiagnoses !== undefined) {
       attributes.push({
         name: 'Admitting Diagnoses',
-        value: (this.props.metadata as unknown as Record<string, unknown>)
-          .AdmittingDiagnosesDescription as string,
+        value: admittingDiagnoses,
       })
     }
 

src/utils/values.ts

@@ -56,4 +56,59 @@ function parseSex(value: string | null | undefined): string {
   return ''
 }
 
-export { parseDate, parseDateTime, parseName, parseSex, parseTime }
+/**
+ * Human-readable text for a DICOM coded concept: prefer CodeMeaning.
+ * Does not show SNOMED CT numeric codes (SCT) when meaning is absent.
+ */
+function codedConceptDisplayText(item: unknown): string {
+  if (item == null || typeof item !== 'object') return ''
+  const o = item as {
+    CodeValue?: string
+    CodeMeaning?: string
+    CodingSchemeDesignator?: string
+  }
+  const cm = (o.CodeMeaning ?? '').trim()
+  if (cm !== '') return cm
+  const scheme = (o.CodingSchemeDesignator ?? '').toUpperCase()
+  if (scheme === 'SCT') return ''
+  return (o.CodeValue ?? '').trim()
+}
+
+function dedupeStringsPreserveOrder(strings: string[]): string[] {
+  const seen = new Set<string>()
+  const out: string[] = []
+  for (const s of strings) {
+    const key = s.toLowerCase()
+    if (seen.has(key)) continue
+    seen.add(key)
+    out.push(s)
+  }
+  return out
+}
+
+/** (00102202) PatientSpeciesCodeSequence — meanings only; undefined if absent or empty. */
+function formatPatientSpeciesCodeSequence(
+  sequence: unknown,
+): string | undefined {
+  if (!Array.isArray(sequence) || sequence.length === 0) {
+    return undefined
+  }
+  const parts: string[] = []
+  for (const item of sequence) {
+    const part = codedConceptDisplayText(item)
+    if (part !== '') parts.push(part)
+  }
+  const unique = dedupeStringsPreserveOrder(parts)
+  return unique.length > 0 ? unique.join(', ') : undefined
+}
+
+export {
+  codedConceptDisplayText,
+  dedupeStringsPreserveOrder,
+  formatPatientSpeciesCodeSequence,
+  parseDate,
+  parseDateTime,
+  parseName,
+  parseSex,
+  parseTime,
+}