Merge pull request #589 from jbernal0019/master

Implement PACS list API endpoint based on a new PFDCM microservice

chris_backend/config/settings/local.py

@@ -164,6 +164,10 @@
 # NATS settings
 NATS_ADDRESS = 'nats://nats:4222'
 
+# PFDCM settings
+PFDCM_ADDRESS = 'http://pfdcm:4005'
+
+
 # Celery settings
 
 #CELERY_BROKER_URL = 'amqp://guest:guest@localhost'

chris_backend/config/settings/production.py

@@ -133,6 +133,11 @@ def get_secret(setting, secret_type=env):
 NATS_ADDRESS = get_secret('NATS_ADDRESS')
 
 
+# PFDCM SETTINGS
+# ------------------------------------------------------------------------------
+PFDCM_ADDRESS = get_secret('PFDCM_ADDRESS')
+
+
 # CELERY SETTINGS
 # ------------------------------------------------------------------------------
 CELERY_BROKER_URL = get_secret('CELERY_BROKER_URL')

chris_backend/core/api.py

@@ -361,6 +361,22 @@
         name='userfile-resource'),
 
 
+    path('v1/pacs/',
+         pacsfile_views.PACSList.as_view(),
+         name='pacs-list'),
+
+    path('v1/pacs/search/',
+         pacsfile_views.PACSListQuerySearch.as_view(),
+         name='pacs-list-query-search'),
+
+    path('v1/pacs/<int:pk>/',
+         pacsfile_views.PACSDetail.as_view(),
+         name='pacs-detail'),
+
+    path('v1/pacs/<int:pk>/series/',
+         pacsfile_views.PACSSpecificSeriesList.as_view(),
+         name='pacs-specific-series-list'),
+
     path('v1/pacs/series/',
          pacsfile_views.PACSSeriesList.as_view(),
          name='pacsseries-list'),

chris_backend/core/serializers.py

@@ -1,6 +1,11 @@
+
 from rest_framework import serializers
 
-from .models import ChrisInstance, FileDownloadToken
+from drf_spectacular.utils import OpenApiTypes, extend_schema_field
+
+from collectionjson.fields import ItemLinkField
+from .models import ChrisInstance, FileDownloadToken, ChrisFile, ChrisLinkFile
+from .utils import get_file_resource_link
 
 
 class ChrisInstanceSerializer(serializers.HyperlinkedModelSerializer):
@@ -18,3 +23,45 @@ class FileDownloadTokenSerializer(serializers.HyperlinkedModelSerializer):
     class Meta:
         model = FileDownloadToken
         fields = ('url', 'id', 'creation_date', 'token', 'owner_username', 'owner')
+
+
+class _ChrisFileSerializerMetaclass(serializers.SerializerMetaclass):
+    """
+    A metaclass to require that the Meta inner class' model attribute is ChrisFile.
+    """
+    def __new__(cls, name, bases, dct):
+        if set(bases) == {serializers.HyperlinkedModelSerializer}:
+            # skip validation of ChrisFileSerializer, which is a
+            # direct subclass of HyperlinkedModelSerializer
+            return super().__new__(cls, name, bases, dct)
+        if (Meta := dct.get('Meta', None)) is None:
+            raise TypeError(f'{name} must have an inner class called Meta')
+        if not issubclass(getattr(Meta, 'model', None), (ChrisFile, ChrisLinkFile)):
+            raise TypeError(f'{name}.Meta.model must be ChrisFile or ChrisLinkFile')
+        return super().__new__(cls, name, bases, dct)
+
+
+class ChrisFileSerializer(serializers.HyperlinkedModelSerializer, metaclass=_ChrisFileSerializerMetaclass):
+    """
+    A superclass for serializers of ``ChrisFile`` or similar.
+    """
+
+    fname = serializers.FileField(use_url=False, required=False)
+    fsize = serializers.SerializerMethodField()
+    file_resource = ItemLinkField('get_file_link')
+    owner_username = serializers.ReadOnlyField(source='owner.username')
+    parent_folder = serializers.HyperlinkedRelatedField(view_name='chrisfolder-detail', read_only=True)
+    owner = serializers.HyperlinkedRelatedField(view_name='user-detail', read_only=True)
+
+    def get_fsize(self, obj) -> int:
+        """
+        Get the size of the file in bytes.
+        """
+        return obj.fname.size
+
+    @extend_schema_field(OpenApiTypes.URI)
+    def get_file_link(self, obj):
+        """
+        Custom method to get the hyperlink to the actual file resource.
+        """
+        return get_file_resource_link(self, obj)

chris_backend/core/tests/test_file_serializer.py → chris_backend/core/tests/test_serializers.py

@@ -1,6 +1,7 @@
+
 from django.test import TestCase
 
-from core.file_serializer import ChrisFileSerializer
+from core.serializers import ChrisFileSerializer
 
 
 class ChrisFileSerializerTests(TestCase):

chris_backend/feeds/views.py

@@ -328,6 +328,7 @@ def list(self, request, *args, **kwargs):
                  'pipelinesourcefiles': reverse('pipelinesourcefile-list',
                                                 request=request),
                  'userfiles': reverse('userfile-list', request=request),
+                 'pacs': reverse('pacs-list', request=request),
                  'pacsfiles': reverse('pacsfile-list', request=request),
                  'pacsseries': reverse('pacsseries-list', request=request),
                  'filebrowser': reverse('chrisfolder-list', request=request)}

chris_backend/filebrowser/serializers.py

@@ -11,7 +11,7 @@
 from core.models import (ChrisFolder, ChrisFile, ChrisLinkFile, FolderGroupPermission,
                          FolderUserPermission, FileGroupPermission, FileUserPermission,
                          LinkFileGroupPermission, LinkFileUserPermission)
-from core.file_serializer import ChrisFileSerializer
+from core.serializers import ChrisFileSerializer
 
 
 class FileBrowserFolderSerializer(serializers.HyperlinkedModelSerializer):

chris_backend/pacsfiles/migrations/0002_pacs_active.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.5 on 2024-10-22 18:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('pacsfiles', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='pacs',
+            name='active',
+            field=models.BooleanField(blank=True, default=True),
+        ),
+    ]

chris_backend/pacsfiles/models.py

@@ -19,6 +19,7 @@
 
 class PACS(models.Model):
     identifier = models.CharField(max_length=20, unique=True)
+    active = models.BooleanField(blank=True, default=True)
     # pacs top folder
     folder = models.OneToOneField(ChrisFolder, on_delete=models.CASCADE,
                                   related_name='pacs')
@@ -35,6 +36,13 @@ def auto_delete_pacs_folder_with_pacs(sender, instance, **kwargs):
         pass
 
 
+class PACSFilter(FilterSet):
+
+    class Meta:
+        model = PACS
+        fields = ['id', 'identifier', 'active']
+
+
 class PACSSeries(models.Model):
     creation_date = models.DateTimeField(auto_now_add=True)
     PatientID = models.CharField(max_length=100, db_index=True)

chris_backend/pacsfiles/serializers.py

@@ -9,7 +9,7 @@
 
 from core.models import ChrisFolder
 from core.storage import connect_storage
-from core.file_serializer import ChrisFileSerializer
+from core.serializers import ChrisFileSerializer
 
 from .models import PACS, PACSSeries, PACSFile
 
@@ -18,16 +18,21 @@
 
 
 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')
 
     class Meta:
         model = PACS
-        fields = ('url', 'id', 'identifier', 'folder')
+        fields = ('url', 'id', 'identifier', 'active', 'folder_path', 'folder',
+                  'pacs_series_list')
 
 
 class PACSSeriesSerializer(serializers.HyperlinkedModelSerializer):
     path = serializers.CharField(max_length=1024, write_only=True)
+    folder_path = serializers.ReadOnlyField(source='folder.path')
     ndicom = serializers.IntegerField(write_only=True)
     pacs_name = serializers.CharField(max_length=20, write_only=True)
     pacs_identifier = serializers.ReadOnlyField(source='pacs.identifier')
@@ -36,11 +41,12 @@ class PACSSeriesSerializer(serializers.HyperlinkedModelSerializer):
 
     class Meta:
         model = PACSSeries
-        fields = ('url', 'id', 'creation_date', 'path', 'ndicom', 'PatientID',
-                  'PatientName', 'PatientBirthDate', 'PatientAge', 'PatientSex',
-                  'StudyDate', 'AccessionNumber', 'Modality', 'ProtocolName',
-                  'StudyInstanceUID', 'StudyDescription', 'SeriesInstanceUID',
-                  'SeriesDescription', 'pacs_name', 'pacs_identifier', 'folder')
+        fields = ('url', 'id', 'creation_date', 'path', 'folder_path', 'ndicom',
+                  'PatientID', 'PatientName', 'PatientBirthDate', 'PatientAge',
+                  'PatientSex', 'StudyDate', 'AccessionNumber', 'Modality',
+                  'ProtocolName', 'StudyInstanceUID', 'StudyDescription',
+                  'SeriesInstanceUID', 'SeriesDescription', 'pacs_name',
+                  'pacs_identifier', 'folder')
 
     def create(self, validated_data):
         """

chris_backend/pacsfiles/services.py

@@ -0,0 +1,91 @@
+
+import logging
+import time
+
+from django.conf import settings
+
+from requests import get, post, exceptions
+
+
+logger = logging.getLogger(__name__)
+
+
+class PfdcmClient(object):
+    """
+    A pfcdm API client.
+    """
+
+    def __init__(self):
+        self._pfdcm_address = settings.PFDCM_ADDRESS.rstrip('/')
+        self.content_type = 'application/json'
+
+        # urls of the high level API resources
+        self.pacs_list_url = self._pfdcm_address + '/api/v1/PACSservice/list/'
+        self.pacs_query_url = self._pfdcm_address + '/api/v1/PACS/sync/pypx/'
+        self.pacs_retrieve_url = self._pfdcm_address + '/api/v1/PACS/thread/pypx/'
+
+    def get_pacs_list(self, timeout=30):
+        """
+        Get a list of PACS names.
+        """
+        headers = {'Content-Type': self.content_type, 'Accept': self.content_type}
+
+        for i in range(5):
+            try:
+                resp = get(self.pacs_list_url, timeout=timeout, headers=headers)
+            except (exceptions.Timeout, exceptions.RequestException) as e:
+                logger.error(f'Error while retrieving data from pfdcm url '
+                             f'-->{self.pacs_list_url}<--, detail: {str(e)}')
+                if i == 4:
+                    raise
+                time.sleep(0.4)
+            else:
+                return resp.json()
+
+    def query(self, pacs_name, query, timeout=30):
+        """
+        Send a PACS query dictionary to pfdcm.
+        """
+        headers = {'Content-Type': self.content_type, 'Accept': self.content_type}
+        data = {
+            'PACSservice' : {'value': pacs_name},
+            'listenerService' : {'value': 'default'},
+            'PACSdirective' : query
+        }
+        for i in range(5):
+            try:
+                resp = post(self.pacs_query_url, json=data, timeout=timeout,
+                            headers=headers)
+            except (exceptions.Timeout, exceptions.RequestException) as e:
+                logger.error(f'Error while querying pfdcm url '
+                             f'-->{self.pacs_query_url}<--, detail: {str(e)}')
+                if i == 4:
+                    raise
+                time.sleep(0.4)
+            else:
+                return resp.json()
+
+    def retrieve(self, pacs_name, query, timeout=30):
+        """
+        Send a PACS query dictionary to pfdcm to initiate a PACS retrieve.
+        """
+        headers = {'Content-Type': self.content_type, 'Accept': self.content_type}
+        data = {
+            'PACSservice' : {'value': pacs_name},
+            'listenerService' : {'value': 'default'},
+            'PACSdirective' : query,
+            'withFeedBack': True,
+            'then': 'retrieve'
+        }
+        for i in range(5):
+            try:
+                resp = post(self.pacs_retrieve_url, json=data, timeout=timeout,
+                            headers=headers)
+            except (exceptions.Timeout, exceptions.RequestException) as e:
+                logger.error(f'Error while querying pfdcm url '
+                             f'-->{self.pacs_retrieve_url}<--, detail: {str(e)}')
+                if i == 4:
+                    raise
+                time.sleep(0.4)
+            else:
+                return resp.json()