Cleanup Scanning Page

bfd9000_web/archive/constants.py

@@ -1,6 +1,6 @@
 """Shared code systems and identifier system URLs."""
 
-SYSTEM_RECORD_TYPE = 'http://snomed.info/sct'
+SYSTEM_RECORD_TYPE = 'https://orthodontics.case.edu/fhir/identifier-system/record-type'
 SYSTEM_ORIENTATION = 'http://snomed.info/sct'
 SYSTEM_MODALITY = 'http://dicom.nema.org/resources/ontology/DCM'
 SYSTEM_PROCEDURE = 'http://snomed.info/sct'
@@ -10,6 +10,32 @@
 SYSTEM_IDENTIFIER_LANCASTER_SUBJECT = 'https://cleftclinic.org/fhir/identifier-system/lancaster-subject-id'
 SYSTEM_IDENTIFIER_IMAGE_TYPE = 'https://orthodontics.case.edu/fhir/identifier-system/image-type'
 
+RECORD_TYPE_MODALITY_MAP = {
+    # Map CWRU record type codes to DICOM modality codes.
+    # Used when creating records if modality is not supplied.
+    # Update this if new record types are added or modality rules change.
+    'L': 'RG',
+    'F': 'RG',
+    'P': 'RG',
+    'FA': 'RG',
+    'H': 'RG',
+    'CS': 'RG',
+    'E': 'RG',
+    'K': 'RG',
+    'RE': 'DOCD',
+    'RF': 'DOCD',
+    'SM': 'OSS',
+    'SU': 'OSS',
+    'SL': 'OSS',
+    'FM': 'OSS',
+}
+
+VALUESET_EXPAND_URLS = {
+    # FHIR $expand endpoints used by import_valuesets.
+    # Update when valueset locations move or new valuesets are added.
+    'record_types': 'http://terminology.open-ortho.org/fhir/cwru-ortho-record-types/$expand',
+}
+
 BFD9000_ROOT_UID = "1.3.6.1.4.1.61741.11.8"
 STUDYINSTANCEUID_ROOT = f"{BFD9000_ROOT_UID}.2"
 SERIESINSTANCEUID_ROOT = f"{BFD9000_ROOT_UID}.3"

bfd9000_web/archive/management/commands/import_valuesets.py

@@ -0,0 +1,34 @@
+from __future__ import annotations
+
+from typing import Any
+from django.core.management.base import BaseCommand, CommandError
+from archive.management.importers.valuesets import import_valueset
+from archive.constants import VALUESET_EXPAND_URLS
+
+class Command(BaseCommand):
+    help = "Import FHIR ValueSet expansions. Use --all or provide --slug and --expand-url."
+
+    def add_arguments(self, parser) -> None:
+        parser.add_argument('--slug', type=str, help='Internal ValueSet slug')
+        parser.add_argument('--expand-url', type=str, help='FHIR $expand URL')
+        parser.add_argument('--all', action='store_true', help='Import all valuesets from constants mapping')
+
+    def handle(self, *args: Any, **options: Any) -> None:
+        if options.get('all'):
+            if not VALUESET_EXPAND_URLS:
+                raise CommandError('No valuesets configured in VALUESET_EXPAND_URLS.')
+            for slug, expand_url in VALUESET_EXPAND_URLS.items():
+                count = import_valueset(expand_url=expand_url, slug=slug)
+                self.stdout.write(self.style.SUCCESS(
+                    f"Imported {count} codings into ValueSet '{slug}'."
+                ))
+            return
+
+        slug = options.get('slug')
+        expand_url = options.get('expand_url')
+        if not slug or not expand_url:
+            raise CommandError('Use --all or provide both --slug and --expand-url.')
+        count = import_valueset(expand_url=expand_url, slug=slug)
+        self.stdout.write(self.style.SUCCESS(
+            f"Imported {count} codings into ValueSet '{slug}'."
+        ))

bfd9000_web/archive/management/commands/initialize.py

@@ -9,6 +9,8 @@
 from django.contrib.auth import get_user_model
 from django.core.management import BaseCommand, CommandError, call_command
 
+from archive.constants import VALUESET_EXPAND_URLS
+
 
 class Command(BaseCommand):
     """Run migrate, create superuser, and import seed subject datasets."""
@@ -75,6 +77,17 @@ def handle(self, *args, **options) -> None:
             self.stdout.write(self.style.NOTICE("Running migrate..."))
             call_command("migrate", verbosity=verbosity)
 
+            self.stdout.write(self.style.NOTICE("Importing all valuesets..."))
+            try:
+                call_command(
+                    "import_valuesets",
+                    "--all",
+                    verbosity=verbosity,
+                )
+            except Exception as exc:
+                import warnings
+                self.stdout.write(self.style.WARNING(f"WARNING: import_valuesets --all failed: {exc}"))
+
         if not options["skip_superuser"]:
             self._run_createsuperuser(options, verbosity)
 

bfd9000_web/archive/management/importers/valuesets.py

@@ -0,0 +1,110 @@
+from __future__ import annotations
+
+import json
+from typing import Any, Dict, List
+from urllib.request import urlopen
+
+from archive.models import Coding, ValueSet, ValueSetConcept
+
+def import_valueset(expand_url: str, slug: str) -> int:
+    """
+    Import a FHIR ValueSet via $expand, upsert ValueSet and Coding rows,
+    and sync ValueSetConcept join links. Returns count of codings.
+    """
+    payload = _fetch_valueset(expand_url)
+    valueset = _upsert_valueset(payload, slug)
+    codings = _upsert_codings(valueset, payload)
+    _sync_valueset_links(valueset, codings)
+    return len(codings)
+
+def _fetch_valueset(url: str) -> Dict[str, Any]:
+    with urlopen(url) as response:
+        raw = response.read().decode("utf-8")
+    data: Dict[str, Any] = json.loads(raw)
+    return data
+
+def _upsert_valueset(payload: Dict[str, Any], slug: str) -> ValueSet:
+    compose = payload.get("compose") or {}
+    include = list(compose.get("include") or [])
+    code_system_url = None
+    if include:
+        code_system_url = include[0].get("system")
+    expansion = payload.get("expansion") or {}
+    contains = list(expansion.get("contains") or [])
+    if contains and not code_system_url:
+        code_system_url = contains[0].get("system")
+
+    valueset, created = ValueSet.objects.get_or_create(
+        slug=slug,
+        defaults={
+            "url": payload.get("url", ""),
+            "name": payload.get("name", slug),
+            "title": payload.get("title", ""),
+            "description": payload.get("description", ""),
+            "version": payload.get("version", ""),
+            "status": payload.get("status", ""),
+            "publisher": payload.get("publisher", ""),
+            "code_system_url": code_system_url or "",
+        },
+    )
+
+    if not created:
+        updates: Dict[str, str] = {
+            "url": payload.get("url", ""),
+            "name": payload.get("name", slug),
+            "title": payload.get("title", ""),
+            "description": payload.get("description", ""),
+            "version": payload.get("version", ""),
+            "status": payload.get("status", ""),
+            "publisher": payload.get("publisher", ""),
+            "code_system_url": code_system_url or "",
+        }
+        changed_fields: List[str] = []
+        for field, value in updates.items():
+            if getattr(valueset, field) != value:
+                setattr(valueset, field, value)
+                changed_fields.append(field)
+        if changed_fields:
+            valueset.save(update_fields=changed_fields)
+
+    return valueset
+
+def _upsert_codings(valueset: ValueSet, payload: Dict[str, Any]) -> List[Coding]:
+    expansion = payload.get("expansion") or {}
+    contains = expansion.get("contains") or []
+    codings: List[Coding] = []
+
+    for concept in contains:
+        system = str(concept.get("system") or "").strip()
+        code = str(concept.get("code") or "").strip()
+        display = str(concept.get("display") or "").strip()
+        definition = str(concept.get("definition") or "").strip()
+
+        if not system or not code:
+            continue
+
+        coding, _ = Coding.objects.get_or_create(
+            system=system,
+            version="",
+            code=code,
+            defaults={"display": display, "meaning": definition},
+        )
+        updates: List[str] = []
+        if display and coding.display != display:
+            coding.display = display
+            updates.append("display")
+        if definition and coding.meaning != definition:
+            coding.meaning = definition
+            updates.append("meaning")
+        if updates:
+            coding.save(update_fields=updates)
+        codings.append(coding)
+
+    return codings
+
+def _sync_valueset_links(valueset: ValueSet, codings: List[Coding]) -> None:
+    for coding in codings:
+        ValueSetConcept.objects.get_or_create(valueset=valueset, coding=coding)
+
+    coding_ids = [coding.id for coding in codings]
+    ValueSetConcept.objects.filter(valueset=valueset).exclude(coding_id__in=coding_ids).delete()

bfd9000_web/archive/migrations/0002_seed_codings.py

@@ -8,14 +8,6 @@
 
 
 VALUESETS = [
-    {
-        "slug": "record_types",
-        "url": "https://orthodontics.case.edu/fhir/ValueSet/record-types",
-        "name": "RecordTypes",
-        "title": "Record types",
-        "status": "active",
-        "publisher": "Case Western Reserve University",
-    },
     {
         "slug": "orientations",
         "url": "https://orthodontics.case.edu/fhir/ValueSet/orientations",
@@ -88,13 +80,6 @@
 
 
 CODINGS = {
-    "record_types": [
-        (SCT, "201456002", "Cephalogram", ""),
-        (SCT, "268425006", "Pelvis X-ray", ""),
-        (SCT, "39714003", "Skeletal X-ray of wrist and hand", ""),
-        (SCT, "1597004", "Skeletal X-ray of ankle and foot", ""),
-        (SCT, "302189007", "Dental model", ""),
-    ],
     "orientations": [
         (SCT, "399198007", "Right lateral projection", ""),
         (SCT, "399173006", "Left lateral projection", ""),
@@ -221,7 +206,6 @@ def unseed_valuesets_and_codings(apps, schema_editor):
     ValueSet = apps.get_model("archive", "ValueSet")
     ValueSet.objects.filter(
         slug__in=[
-            "record_types",
             "orientations",
             "modalities",
             "body_sites",

bfd9000_web/archive/serializers.py

@@ -40,19 +40,12 @@
     SYSTEM_RECORD_TYPE,
     SYSTEM_IDENTIFIER_BOLTON_SUBJECT,
     SYSTEM_IDENTIFIER_IMAGE_TYPE,
+    RECORD_TYPE_MODALITY_MAP,
 )
 from .media_utils import generate_thumbnail_jpeg_bytes
 
 
-RECORD_TYPE_CODES = (
-    '201456002',
-    '268425006',
-    '39714003',
-    '1597004',
-    '302189007',
-)
-
-LATERAL_IMAGE_TYPE_CODE = 'L'
+LATERAL_RECORD_TYPE_CODE = 'L'
 
 
 def _encode_patient_orientation(value: Optional[list[str]]) -> str:
@@ -403,13 +396,15 @@ class RecordUploadSerializer(serializers.ModelSerializer):
     # Use SlugRelatedField for idiomatic lookup by 'code'
     record_type = serializers.SlugRelatedField(
         slug_field='code',
-        queryset=Coding.objects.filter(system=SYSTEM_RECORD_TYPE, code__in=RECORD_TYPE_CODES),
-        write_only=True
+        queryset=Coding.objects.filter(system=SYSTEM_RECORD_TYPE),
+        write_only=True,
     )
     modality = serializers.SlugRelatedField(
         slug_field='code',
         queryset=Coding.objects.filter(system=SYSTEM_MODALITY),
-        write_only=True
+        required=False,
+        allow_null=True,
+        write_only=True,
     )
 
     acquisition_date = serializers.DateField(required=False, write_only=True)
@@ -486,6 +481,22 @@ def validate_image_transform_ops(self, value: Any) -> Any:
 
         return normalized
 
+    def _infer_modality(self, record_type: Coding) -> Coding:
+        record_type_code = str(getattr(record_type, 'code', '') or '')
+        modality_code = RECORD_TYPE_MODALITY_MAP.get(record_type_code)
+
+        if not modality_code:
+            raise serializers.ValidationError({
+                'modality': f"Unable to infer modality for record type {record_type_code or 'unknown'}."
+            })
+
+        modality = Coding.objects.filter(system=SYSTEM_MODALITY, code=modality_code).first()
+        if modality is None:
+            raise serializers.ValidationError({
+                'modality': f"Modality code {modality_code} not found in system {SYSTEM_MODALITY}."
+            })
+        return modality
+
     def to_representation(self, instance: Record) -> Dict[str, Any]:
         """Use standard RecordSerializer for response."""
         return cast(Dict[str, Any], RecordSerializer(instance, context=self.context).data)
@@ -543,7 +554,7 @@ def create(self, validated_data: Dict[str, Any]) -> Record:
 
         # These are now Coding objects, not strings!
         rt_coding = validated_data.pop('record_type')
-        mod_coding = validated_data.pop('modality')
+        mod_coding = validated_data.pop('modality', None)
 
         acquisition_date = validated_data.pop('acquisition_date', None)
         image_type = validated_data.pop('image_type', None)
@@ -564,7 +575,7 @@ def create(self, validated_data: Dict[str, Any]) -> Record:
         if request and getattr(request, 'user', None) and request.user.is_authenticated:
             scan_operator = request.user
 
-        if patient_orientation is None and image_type and getattr(image_type, 'code', None) == LATERAL_IMAGE_TYPE_CODE:
+        if patient_orientation is None and getattr(rt_coding, 'code', None) == LATERAL_RECORD_TYPE_CODE:
             patient_orientation = ['A', 'F']
 
         with transaction.atomic():
@@ -586,6 +597,9 @@ def create(self, validated_data: Dict[str, Any]) -> Record:
                 study.collection = collection
                 study.save(update_fields=['collection'])
 
+            if mod_coding is None:
+                mod_coding = self._infer_modality(rt_coding)
+
             # Get or create Series within the study
             series, _ = Series.objects.get_or_create(
                 imaging_study=study,

bfd9000_web/archive/templates/archive/record_detail.html

@@ -114,10 +114,6 @@ <h2 class="card-title text-lg">Series & Acquisition</h2>
                                     <th>Modality</th>
                                     <td id="modality">-</td>
                                 </tr>
-                                <tr>
-                                    <th>Image Type</th>
-                                    <td id="image-type">-</td>
-                                </tr>
                                 <tr>
                                     <th>Patient Orientation</th>
                                     <td id="patient-orientation">-</td>
@@ -182,7 +178,6 @@ <h2 class="card-title text-lg">Series & Acquisition</h2>
 
         // Series & acquisition details come from record payload
         document.getElementById('modality').textContent = record.series_modality?.display || '-';
-        document.getElementById('image-type').textContent = record.image_type?.display || '-';
         document.getElementById('patient-orientation').textContent = Array.isArray(record.patient_orientation)
             ? record.patient_orientation.join('\\')
             : '-';

bfd9000_web/archive/templates/archive/records.html

@@ -28,7 +28,7 @@
                     <th>Subject</th>
                     <th>Age</th>
                     <th>File Size</th>
-                    <th>Image Type</th>
+                    <th>Modality</th>
                 </tr>
             </thead>
             <tbody id="record_table_body">
@@ -189,17 +189,22 @@
                 const fileSize = document.createElement("td");
                 fileSize.textContent = formatFileSize(record.file_size);
 
-                // Image type column (plain text)
-                const imageType = document.createElement("td");
-                imageType.textContent = record.image_type?.display || "-";
+                // Modality column (code with full term tooltip)
+                const modality = document.createElement("td");
+                const modalityCode = record.series_modality?.code || "-";
+                const modalityDisplay = record.series_modality?.display;
+                modality.textContent = modalityCode;
+                if (modalityDisplay) {
+                    modality.title = modalityDisplay;
+                }
 
                 row.replaceChildren(
                     recordId,
                     encounter,
                     subject,
                     age,
                     fileSize,
-                    imageType
+                    modality
                 );
                 return row;
             });