Add species and admitting parsing

Author: igoroctaviano

src/components/Patient.tsx

@@ -2,6 +2,7 @@
 import type * as dmv from 'dicom-microscopy-viewer'
 import React from 'react'
 import {
+  formatAdmittingDiagnoses,
   formatPatientSpeciesCodeSequence,
   parseDate,
   parseName,
@@ -20,10 +21,11 @@ interface PatientProps {
  */
 class Patient extends React.Component<PatientProps, Record<string, never>> {
   render(): React.ReactNode {
+    const meta = this.props.metadata as unknown as Record<string, unknown>
     const species = formatPatientSpeciesCodeSequence(
-      (this.props.metadata as unknown as Record<string, unknown>)
-        .PatientSpeciesCodeSequence,
+      meta.PatientSpeciesCodeSequence,
     )
+    const admittingDiagnosis = formatAdmittingDiagnoses(meta)
     const attributes = [
       {
         name: 'ID',
@@ -44,9 +46,11 @@ class Patient extends React.Component<PatientProps, Record<string, never>> {
       },
       {
         name: 'Age',
-        value: (this.props.metadata as unknown as Record<string, unknown>)
-          .PatientAge as string | undefined,
+        value: meta.PatientAge as string | undefined,
       },
+      ...(admittingDiagnosis !== undefined
+        ? [{ name: 'Admitting diagnosis', value: admittingDiagnosis }]
+        : []),
     ]
     return <Description attributes={attributes} />
   }

src/components/SpecimenItem.tsx

@@ -4,10 +4,6 @@ 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'
 
@@ -17,35 +13,6 @@ 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.
@@ -193,16 +160,6 @@ class SpecimenItem extends React.Component<
       },
     )
 
-    const admittingDiagnoses = formatAdmittingDiagnoses(
-      this.props.metadata as unknown as Record<string, unknown>,
-    )
-    if (admittingDiagnoses !== undefined) {
-      attributes.push({
-        name: 'Admitting Diagnoses',
-        value: admittingDiagnoses,
-      })
-    }
-
     const uid = specimenDescription.SpecimenUID
     const identifier = specimenDescription.SpecimenIdentifier
 

src/utils/values.ts

@@ -86,6 +86,67 @@ function dedupeStringsPreserveOrder(strings: string[]): string[] {
   return out
 }
 
+/**
+ * (0008,1080) LO + (0008,1084) SQ (standard keywords use plural "Diagnoses").
+ * Also accepts singular / legacy keys (e.g. dcmjs) for interoperability.
+ */
+function formatAdmittingDiagnoses(
+  metadata: Record<string, unknown>,
+): string | undefined {
+  let desc = ''
+  for (const key of [
+    'AdmittingDiagnosesDescription',
+    'AdmittingDiagnosisDescription',
+  ] as const) {
+    const v = metadata[key]
+    if (typeof v === 'string' && v.trim() !== '') {
+      desc = v.trim()
+      break
+    }
+  }
+
+  const codeSeqKeys = [
+    'AdmittingDiagnosesCodeSequence',
+    'AdmittingDiagnosisCodeSequence',
+    'AdmittingDiagnosisCodeSeq',
+  ] as const
+  let seq: unknown[] = []
+  for (const key of codeSeqKeys) {
+    const v = metadata[key]
+    if (Array.isArray(v) && v.length > 0) {
+      seq = v
+      break
+    }
+  }
+  if (seq.length === 0) {
+    for (const key of codeSeqKeys) {
+      const v = metadata[key]
+      if (Array.isArray(v)) {
+        seq = v
+        break
+      }
+    }
+  }
+
+  const codeParts: string[] = []
+  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
+}
+
 /** (00102202) PatientSpeciesCodeSequence — meanings only; undefined if absent or empty. */
 function formatPatientSpeciesCodeSequence(
   sequence: unknown,
@@ -105,6 +166,7 @@ function formatPatientSpeciesCodeSequence(
 export {
   codedConceptDisplayText,
   dedupeStringsPreserveOrder,
+  formatAdmittingDiagnoses,
   formatPatientSpeciesCodeSequence,
   parseDate,
   parseDateTime,