Merge pull request #595 from jbernal0019/master

Implement PACS query API endpoint

Author: jbernal0019

chris_backend/core/api.py

@@ -31,6 +31,7 @@
     path('v1/users/<int:pk>/groups/',
          user_views.UserGroupList.as_view(), name='user-group-list'),
 
+
     path('v1/groups/',
          user_views.GroupList.as_view(),
          name='group-list'),
@@ -373,6 +374,22 @@
          pacsfile_views.PACSDetail.as_view(),
          name='pacs-detail'),
 
+    path('v1/pacs/<int:pk>/queries/',
+         pacsfile_views.PACSQueryList.as_view(),
+         name='pacsquery-list'),
+
+    path('v1/pacs/queries/',
+         pacsfile_views.AllPACSQueryList.as_view(),
+         name='allpacsquery-list'),
+
+    path('v1/pacs/queries/search/',
+         pacsfile_views.AllPACSQueryListQuerySearch.as_view(),
+         name='allpacsquery-list-query-search'),
+
+    path('v1/pacs/queries/<int:pk>/',
+         pacsfile_views.PACSQueryDetail.as_view(),
+         name='pacsquery-detail'),
+
     path('v1/pacs/<int:pk>/series/',
          pacsfile_views.PACSSpecificSeriesList.as_view(),
          name='pacs-specific-series-list'),
@@ -523,4 +540,4 @@
 # Login and logout views for Djangos' browsable API
 urlpatterns += [
     path('v1/auth/', include('rest_framework.urls',  namespace='rest_framework')),
-]
+]

chris_backend/feeds/views.py

@@ -329,6 +329,7 @@ def list(self, request, *args, **kwargs):
                                                 request=request),
                  'userfiles': reverse('userfile-list', request=request),
                  'pacs': reverse('pacs-list', request=request),
+                 'pacsqueries': reverse('allpacsquery-list', request=request),
                  'pacsfiles': reverse('pacsfile-list', request=request),
                  'pacsseries': reverse('pacsseries-list', request=request),
                  'filebrowser': reverse('chrisfolder-list', request=request)}

chris_backend/pacsfiles/migrations/0003_pacsquery.py

@@ -0,0 +1,33 @@
+# Generated by Django 4.2.5 on 2024-11-05 21:13
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('pacsfiles', '0002_pacs_active'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PACSQuery',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('creation_date', models.DateTimeField(auto_now_add=True)),
+                ('title', models.CharField(db_index=True, max_length=300)),
+                ('query', models.JSONField()),
+                ('description', models.CharField(blank=True, max_length=700)),
+                ('result', models.TextField(blank=True)),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+                ('pacs', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='query_list', to='pacsfiles.pacs')),
+            ],
+            options={
+                'ordering': ('pacs', 'owner', '-creation_date'),
+                'unique_together': {('pacs', 'owner', 'title')},
+            },
+        ),
+    ]

chris_backend/pacsfiles/models.py

@@ -43,6 +43,43 @@ class Meta:
         fields = ['id', 'identifier', 'active']
 
 
+class PACSQuery(models.Model):
+    creation_date = models.DateTimeField(auto_now_add=True)
+    title = models.CharField(max_length=300, db_index=True)
+    query = models.JSONField()
+    description = models.CharField(max_length=700, blank=True)
+    result = models.TextField(blank=True)
+    pacs = models.ForeignKey(PACS, on_delete=models.CASCADE, related_name='query_list')
+    owner = models.ForeignKey('auth.User', on_delete=models.CASCADE)
+
+    class Meta:
+        ordering = ('pacs', 'owner', '-creation_date',)
+        unique_together = ('pacs', 'owner', 'title',)
+
+    def __str__(self):
+        return self.query
+
+
+class PACSQueryFilter(FilterSet):
+    min_creation_date = django_filters.IsoDateTimeFilter(field_name='creation_date',
+                                                         lookup_expr='gte')
+    max_creation_date = django_filters.IsoDateTimeFilter(field_name='creation_date',
+                                                         lookup_expr='lte')
+    title_exact = django_filters.CharFilter(field_name='title', lookup_expr='exact')
+    title = django_filters.CharFilter(field_name='title', lookup_expr='icontains')
+    description = django_filters.CharFilter(field_name='description',
+                                            lookup_expr='icontains')
+    pacs_identifier = django_filters.CharFilter(field_name='pacs__identifier',
+                                                lookup_expr='exact')
+    owner_username = django_filters.CharFilter(field_name='owner__username',
+                                                lookup_expr='exact')
+
+    class Meta:
+        model = PACSQuery
+        fields = ['id', 'min_creation_date', 'max_creation_date', 'title_exact',
+                  'title', 'description', 'pacs_identifier', 'owner_username']
+
+
 class PACSSeries(models.Model):
     creation_date = models.DateTimeField(auto_now_add=True)
     PatientID = models.CharField(max_length=100, db_index=True)

chris_backend/pacsfiles/permissions.py

@@ -16,3 +16,34 @@ def has_permission(self, request, view):
 
         return (request.method in permissions.SAFE_METHODS and user.groups.filter(
                 name='pacs_users').exists())
+
+
+class IsChrisOrIsPACSUserOrReadOnly(permissions.BasePermission):
+    """
+    Custom permission to only allow superuser 'chris' and other users in the pacs_users
+    group to create objects. Read only is allowed to all other users.
+    """
+
+    def has_permission(self, request, view):
+        user = request.user
+
+        if request.method in permissions.SAFE_METHODS:
+            return True
+
+        return user.username == 'chris' or user.groups.filter(name='pacs_users').exists()
+
+
+class IsChrisOrOwnerOrIsPACSUserReadOnly(permissions.BasePermission):
+    """
+    Custom permission to only allow superuser 'chris' to create it.
+    Read only is allowed to other users in the pacs_users group.
+    """
+
+    def has_object_permission(self, request, view, obj):
+        user = request.user
+
+        if user.username == 'chris' or user == obj.owner:
+            return True
+
+        return (request.method in permissions.SAFE_METHODS and user.groups.filter(
+                name='pacs_users').exists())

chris_backend/pacsfiles/serializers.py

@@ -3,15 +3,18 @@
 import os
 import time
 
+from django.db.utils import IntegrityError
 from django.contrib.auth.models import Group
 from django.conf import settings
 from rest_framework import serializers
 
 from core.models import ChrisFolder
 from core.storage import connect_storage
 from core.serializers import ChrisFileSerializer
+from core.utils import json_zip2str
 
-from .models import PACS, PACSSeries, PACSFile
+from .models import PACS, PACSQuery, PACSSeries, PACSFile
+from .services import PfdcmClient
 
 
 logger = logging.getLogger(__name__)
@@ -21,13 +24,76 @@ class PACSSerializer(serializers.HyperlinkedModelSerializer):
     folder_path = serializers.ReadOnlyField(source='folder.path')
     folder = serializers.HyperlinkedRelatedField(view_name='chrisfolder-detail',
                                                  read_only=True)
-    pacs_series_list = serializers.HyperlinkedIdentityField(
-        view_name='pacs-specific-series-list')
+    query_list = serializers.HyperlinkedIdentityField(view_name='pacsquery-list')
+    series_list = serializers.HyperlinkedIdentityField(view_name='pacs-specific-series-list')
 
     class Meta:
         model = PACS
         fields = ('url', 'id', 'identifier', 'active', 'folder_path', 'folder',
-                  'pacs_series_list')
+                  'query_list', 'series_list')
+
+
+class PACSQuerySerializer(serializers.HyperlinkedModelSerializer):
+    query = serializers.JSONField(binary=True, required=False)
+    result = serializers.ReadOnlyField()
+    pacs_identifier = serializers.ReadOnlyField(source='pacs.identifier')
+    owner_username = serializers.ReadOnlyField(source='owner.username')
+
+    class Meta:
+        model = PACSQuery
+        fields = ('url', 'id', 'creation_date', 'title', 'query', 'description',
+                  'result', 'pacs_identifier', 'owner_username')
+
+    def create(self, validated_data):
+        """
+        Overriden to rise a serializer error when attempting to create a PACSQuery
+        object that results in a DB conflict. Then a query is made to the PFDCM service.
+        """
+        title = validated_data['title']
+        query = validated_data['query']
+        pacs_name = validated_data['pacs'].identifier
+
+        try:
+            pacs_query  = super(PACSQuerySerializer, self).create(validated_data)
+        except IntegrityError:
+            error_msg = (f'You have already registered a PACS query with title={title} '
+                         f'for pacs {pacs_name}')
+            raise serializers.ValidationError([error_msg])
+
+        pfdcm_cl = PfdcmClient()
+        result = pfdcm_cl.query(pacs_name, query)
+
+        if result:
+            pacs_query.result = json_zip2str(result)
+            pacs_query.save()
+        return pacs_query
+
+    def update(self, instance, validated_data):
+        """
+        Overriden to rise a serializer error when attempting to update a PACSQuery
+        object that results in a DB conflict.
+        """
+        pacs = instance.pacs
+        title = validated_data.get('title')
+
+        if title is None:
+            title = instance.title
+        try:
+            return super(PACSQuerySerializer, self).update(instance, validated_data)
+        except IntegrityError:
+            error_msg = (f'You have already registered a PACS query with title={title} '
+                         f'for pacs {pacs.identifier}')
+            raise serializers.ValidationError([error_msg])
+
+    def validate(self, data):
+        """
+        Overriden to validate that the query field is in data when creating a new query.
+        """
+        if not self.instance:  # on create
+            if 'query' not in data:
+                raise serializers.ValidationError(
+                    {'query': ["This field is required."]})
+        return data
 
 
 class PACSSeriesSerializer(serializers.HyperlinkedModelSerializer):

chris_backend/pacsfiles/services.py

@@ -63,7 +63,12 @@ def query(self, pacs_name, query, timeout=30):
                     raise
                 time.sleep(0.4)
             else:
-                return resp.json()
+                result = resp.json()
+                if result.get('status'):
+                    pypx = result.get('pypx')
+                    if pypx and 'data' in pypx:
+                        return pypx['data']
+                return []
 
     def retrieve(self, pacs_name, query, timeout=30):
         """

chris_backend/pacsfiles/tests/test_serializers.py

@@ -7,27 +7,114 @@
 from unittest import mock
 from rest_framework import serializers
 
-from pacsfiles.serializers import PACSSeriesSerializer
+from core.models import ChrisFolder
+from core.utils import json_zip2str
+from pacsfiles.models import PACS, PACSQuery
+from pacsfiles.serializers import PACSQuerySerializer, PACSSeriesSerializer
 
 
 CHRIS_SUPERUSER_PASSWORD = settings.CHRIS_SUPERUSER_PASSWORD
 
 
-class PACSSeriesSerializerTests(TestCase):
-
+class SerializerTests(TestCase):
     def setUp(self):
         # avoid cluttered console output (for instance logging all the http requests)
         logging.disable(logging.WARNING)
 
-        # create superuser chris (owner of root folders)
+        # superuser chris (owner of root folders)
         self.chris_username = 'chris'
-        self.chris_password = CHRIS_SUPERUSER_PASSWORD
+        chris_user = User.objects.get(username=self.chris_username)
+
+        # create normal user
+        self.username = 'foo'
+        self.password = 'bar'
+        User.objects.create_user(username=self.username, password=self.password)
+
+        # create a PACS
+        self.pacs_name = 'myPACS'
+        folder_path = f'SERVICES/PACS/{self.pacs_name}'
+        (pacs_folder, tf) = ChrisFolder.objects.get_or_create(path=folder_path,
+                                                              owner=chris_user)
+        PACS.objects.get_or_create(folder=pacs_folder, identifier=self.pacs_name)
 
     def tearDown(self):
         # re-enable logging
         logging.disable(logging.NOTSET)
 
 
+class PACSQuerySerializerTests(SerializerTests):
+
+    def test_create_success(self):
+        """
+        Test whether overriden 'create' method successfully creates a new PACS query.
+        """
+        user = User.objects.get(username=self.username)
+        pacs = PACS.objects.get(identifier=self.pacs_name)
+        query = {'SeriesInstanceUID': '2.3.15.2.1057'}
+        data = {'title': 'query1', 'query': query, 'owner': user, 'pacs': pacs}
+
+        with mock.patch('pacsfiles.serializers.PfdcmClient.query') as pfdcm_query_mock:
+            result = {'mock': 'mock'}
+            pfdcm_query_mock.return_value = result
+            pacs_query_serializer = PACSQuerySerializer(data=data)
+            pacs_query = pacs_query_serializer.create(data)
+            pfdcm_query_mock.assert_called_with(self.pacs_name, query)
+            self.assertEqual(pacs_query.result, json_zip2str(result))
+
+
+    def test_create_failure_pacs_user_title_combination_already_exists(self):
+        """
+        Test whether overriden 'create' method raises a ValidationError when a user has
+        already registered a PACS query with the same title and pacs.
+        """
+        user = User.objects.get(username=self.username)
+        pacs = PACS.objects.get(identifier=self.pacs_name)
+        query = {'SeriesInstanceUID': '1.3.12.2.1107'}
+
+        PACSQuery.objects.get_or_create(title='query2', query=query, owner=user, pacs=pacs)
+
+        data = {'title': 'query2', 'query': query, 'owner': user, 'pacs': pacs}
+        pacs_query_serializer = PACSQuerySerializer(data=data)
+        with self.assertRaises(serializers.ValidationError):
+            pacs_query_serializer.create(data)
+
+    def test_update_success(self):
+        """
+        Test whether overriden 'update' method successfully updates an existing PACS query.
+        """
+        user = User.objects.get(username=self.username)
+        pacs = PACS.objects.get(identifier=self.pacs_name)
+        query = {'SeriesInstanceUID': '2.3.15.2.1057'}
+
+        pacs_query, _ = PACSQuery.objects.get_or_create(title='query2', query=query,
+                                                        owner=user, pacs=pacs)
+
+        data = {'title': 'query4'}
+        pacs_query_serializer = PACSQuerySerializer(pacs_query, data)
+        pacs_query = pacs_query_serializer.update(pacs_query, data)
+        self.assertEqual(pacs_query.title, 'query4')
+
+    def test_update_failure_pacs_user_title_combination_already_exists(self):
+        """
+        Test whether overriden 'update' method raises a ValidationError when a user has
+        already registered a PACS query with the same title and pacs.
+        """
+        user = User.objects.get(username=self.username)
+        pacs = PACS.objects.get(identifier=self.pacs_name)
+        query = {'SeriesInstanceUID': '1.3.12.2.1107'}
+
+        pacs_query, _ = PACSQuery.objects.get_or_create(title='query2', query=query,
+                                                        owner=user, pacs=pacs)
+        PACSQuery.objects.get_or_create(title='query3', query=query, owner=user, pacs=pacs)
+
+        data = {'title': 'query3'}
+        pacs_query_serializer = PACSQuerySerializer(pacs_query, data)
+        with self.assertRaises(serializers.ValidationError):
+            pacs_query_serializer.update(pacs_query, data)
+
+
+class PACSSeriesSerializerTests(SerializerTests):
+
     def test_validate_ndicom_failure_not_positive(self):
         """
         Test whether overriden validate_ndicom method validates submitted ndicom must