OpenConceptLab/ocl_issues#22 | Retired concepts and/or mappings are n…

…ow excluded from exports

core/collections/views.py

@@ -33,7 +33,7 @@
 from core.collections.utils import is_version_specified
 from core.common.constants import (
     HEAD, RELEASED_PARAM, PROCESSING_PARAM, OK_MESSAGE,
-    ACCESS_TYPE_NONE)
+    ACCESS_TYPE_NONE, INCLUDE_RETIRED_PARAM)
 from core.common.mixins import (
     ConceptDictionaryCreateMixin, ListWithHeadersMixin, ConceptDictionaryUpdateMixin,
     ConceptContainerExportMixin,
@@ -578,7 +578,8 @@ class CollectionVersionExportView(ConceptContainerExportMixin, CollectionVersion
     def handle_export_version(self):
         version = self.get_object()
         try:
-            export_collection.delay(version.id)
+            include_retired = parse_boolean_query_param(self.request, INCLUDE_RETIRED_PARAM, "True")
+            export_collection.delay(version.id, include_retired)
             return status.HTTP_202_ACCEPTED
         except AlreadyQueued:
             return status.HTTP_409_CONFLICT

core/common/mixins.py

@@ -15,12 +15,12 @@
 from rest_framework.mixins import ListModelMixin, CreateModelMixin
 from rest_framework.response import Response
 
-from core.common.constants import HEAD, ACCESS_TYPE_EDIT, ACCESS_TYPE_VIEW, ACCESS_TYPE_NONE, INCLUDE_FACETS, \
+from core.common.constants import HEAD, ACCESS_TYPE_EDIT, ACCESS_TYPE_VIEW, ACCESS_TYPE_NONE, INCLUDE_FACETS, INCLUDE_RETIRED_PARAM, \
     LIST_DEFAULT_LIMIT, HTTP_COMPRESS_HEADER, CSV_DEFAULT_LIMIT, FACETS_ONLY, NOT_FOUND, \
     MUST_SPECIFY_EXTRA_PARAM_IN_BODY
 from core.common.permissions import HasPrivateAccess, HasOwnership, CanViewConceptDictionary
 from core.common.services import S3
-from .utils import write_csv_to_s3, get_csv_from_s3, get_query_params_from_url_string, compact_dict_by_values
+from .utils import write_csv_to_s3, get_csv_from_s3, get_query_params_from_url_string, compact_dict_by_values, parse_boolean_query_param
 
 logger = logging.getLogger('oclapi')
 
@@ -542,16 +542,8 @@ def get_object(self):
         return instance
 
     def get(self, request, *args, **kwargs):  # pylint: disable=unused-argument
-        version = self.get_object()
-        logger.debug(
-            'Export requested for %s version %s - Requesting AWS-S3 key', self.entity.lower(), version.version
-        )
-        if version.is_head and not request.user.is_staff:
-            return Response(status=status.HTTP_405_METHOD_NOT_ALLOWED)
-
-        if version.has_export():
-            export_url = version.get_export_url()
 
+        def export_response():
             no_redirect = request.query_params.get('noRedirect', False) in ['true', 'True', True]
             if no_redirect:
                 return Response(dict(url=export_url), status=status.HTTP_200_OK)
@@ -567,6 +559,24 @@ def get(self, request, *args, **kwargs):  # pylint: disable=unused-argument
             response['Last-Updated-Timezone'] = settings.TIME_ZONE_PLACE
             return response
 
+        version = self.get_object()
+        include_retired = parse_boolean_query_param(request, INCLUDE_RETIRED_PARAM, "True")
+        logger.debug(
+            'Export requested for %s version %s - Requesting AWS-S3 key', self.entity.lower(), version.version
+        )
+
+        if version.is_head and not request.user.is_staff:
+            return Response(status=status.HTTP_405_METHOD_NOT_ALLOWED)
+
+        if include_retired:
+            if version.has_export():
+                export_url = version.get_export_url()
+                return export_response()
+        else:
+            if version.has_unretired_export():
+                export_url = version.get_unretired_export_url()
+                return export_response()
+
         if version.is_exporting:
             return Response(status=status.HTTP_208_ALREADY_REPORTED)
 

core/common/models.py

@@ -722,6 +722,11 @@ def is_exporting(self):
     def export_path(self):
         last_update = self.last_child_update.strftime('%Y%m%d%H%M%S')
         return self.generic_export_path(suffix=f"{last_update}.zip")
+
+    @cached_property
+    def exclude_retired_export_path(self):
+        last_update = self.last_child_update.strftime('%Y%m%d%H%M%S')
+        return self.generic_export_path(suffix=f"{last_update}_unretired.zip")
 
     def generic_export_path(self, suffix='*'):
         path = f"{self.parent_resource}/{self.mnemonic}_{self.version}."
@@ -733,9 +738,15 @@ def generic_export_path(self, suffix='*'):
     def get_export_url(self):
         return S3.url_for(self.export_path)
 
+    def get_unretired_export_url(self):
+        return S3.url_for(self.exclude_retired_export_path)
+
     def has_export(self):
         return S3.exists(self.export_path)
 
+    def has_unretired_export(self):
+        return S3.exists(self.exclude_retired_export_path)
+
 
 class CelerySignalProcessor(RealTimeSignalProcessor):
     def handle_save(self, sender, instance, **kwargs):

core/common/tasks.py

@@ -60,7 +60,7 @@ def delete_source(source_id):
 
 
 @app.task(base=QueueOnce, bind=True)
-def export_source(self, version_id):
+def export_source(self, version_id, include_retired=True):
     from core.sources.models import Source
     logger.info('Finding source version...')
 
@@ -75,14 +75,14 @@ def export_source(self, version_id):
     version.add_processing(self.request.id)
     try:
         logger.info('Found source version %s.  Beginning export...', version.version)
-        write_export_file(version, 'source', 'core.sources.serializers.SourceVersionExportSerializer', logger)
+        write_export_file(version, include_retired, 'source', 'core.sources.serializers.SourceVersionExportSerializer', logger)
         logger.info('Export complete!')
     finally:
         version.remove_processing(self.request.id)
 
 
 @app.task(base=QueueOnce, bind=True)
-def export_collection(self, version_id):
+def export_collection(self, version_id, include_retired=True):
     from core.collections.models import Collection
     logger.info('Finding collection version...')
 
@@ -98,7 +98,7 @@ def export_collection(self, version_id):
     try:
         logger.info('Found collection version %s.  Beginning export...', version.version)
         write_export_file(
-            version, 'collection', 'core.collections.serializers.CollectionVersionExportSerializer', logger
+            version, include_retired, 'collection', 'core.collections.serializers.CollectionVersionExportSerializer', logger
         )
         logger.info('Export complete!')
     finally:

core/common/utils.py

@@ -191,7 +191,7 @@ def get_class(kls):
 
 
 def write_export_file(
-        version, resource_type, resource_serializer_type, logger
+        version, include_retired, resource_type, resource_serializer_type, logger
 ):  # pylint: disable=too-many-statements,too-many-locals,too-many-branches
     from core.concepts.models import Concept
     from core.mappings.models import Mapping
@@ -207,6 +207,12 @@ def write_export_file(
     logger.info('Done serializing attributes.')
 
     batch_size = 100
+    concepts_qs = version.concepts
+    mappings_qs = version.mappings
+    if not include_retired:
+        concepts_qs = concepts_qs.filter(retired=False)
+        mappings_qs = mappings_qs.filter(retired=False)
+
     is_collection = resource_type == 'collection'
 
     if is_collection:
@@ -328,7 +334,7 @@ def write_export_file(
     logger.info(file_path)
     logger.info('Done compressing.  Uploading...')
 
-    s3_key = version.export_path
+    s3_key = version.export_path if include_retired else version.exclude_retired_export_path
     S3.upload_file(
         key=s3_key, file_path=file_path, binary=True, metadata=dict(ContentType='application/zip'),
         headers={'content-type': 'application/zip'}

core/integration_tests/tests_collections.py

@@ -857,29 +857,29 @@ def test_post_303(self, s3_exists_mock):
     def test_post_202(self, s3_exists_mock, export_collection_mock):
         s3_exists_mock.return_value = False
         response = self.client.post(
-            self.collection_v1.uri + 'export/',
+            self.collection_v1.uri + 'export/?includeRetired=False',
             HTTP_AUTHORIZATION='Token ' + self.token,
             format='json'
         )
 
         self.assertEqual(response.status_code, 202)
         s3_exists_mock.assert_called_once_with(f"username/coll_v1.{self.v1_updated_at}.zip")
-        export_collection_mock.delay.assert_called_once_with(self.collection_v1.id)
+        export_collection_mock.delay.assert_called_once_with(self.collection_v1.id, False)
 
     @patch('core.collections.views.export_collection')
     @patch('core.common.services.S3.exists')
     def test_post_409(self, s3_exists_mock, export_collection_mock):
         s3_exists_mock.return_value = False
         export_collection_mock.delay.side_effect = AlreadyQueued('already-queued')
         response = self.client.post(
-            self.collection_v1.uri + 'export/',
+            self.collection_v1.uri + 'export/?includeRetired=False',
             HTTP_AUTHORIZATION='Token ' + self.token,
             format='json'
         )
 
         self.assertEqual(response.status_code, 409)
         s3_exists_mock.assert_called_once_with(f"username/coll_v1.{self.v1_updated_at}.zip")
-        export_collection_mock.delay.assert_called_once_with(self.collection_v1.id)
+        export_collection_mock.delay.assert_called_once_with(self.collection_v1.id, False)
 
 
 class CollectionVersionListViewTest(OCLAPITestCase):
@@ -999,6 +999,62 @@ def test_export_collection(self, s3_mock):  # pylint: disable=too-many-locals
         import shutil
         shutil.rmtree(latest_temp_dir)
 
+    @patch('core.common.utils.S3')
+    def test_unretired_export_collection(self, s3_mock):  # pylint: disable=too-many-locals
+        s3_mock.url_for = Mock(return_value='https://s3-url')
+        s3_mock.upload_file = Mock()
+        source = OrganizationSourceFactory()
+        concept1 = ConceptFactory(parent=source)
+        concept2 = ConceptFactory(parent=source)
+        mapping = MappingFactory(from_concept=concept2, to_concept=concept1, parent=source)
+        collection = OrganizationCollectionFactory()
+        collection.add_references([concept1.uri, concept2.uri, mapping.uri])
+        collection.refresh_from_db()
+
+        export_collection(collection.id, include_retired=False)  # pylint: disable=no-value-for-parameter
+
+        latest_temp_dir = get_latest_dir_in_path('/tmp/')
+        zipped_file = zipfile.ZipFile(latest_temp_dir + '/export.zip')
+        exported_data = json.loads(zipped_file.read('export.json').decode('utf-8'))
+
+        self.assertEqual(
+            exported_data,
+            {**CollectionVersionExportSerializer(collection).data, 'concepts': ANY, 'mappings': ANY, 'references': ANY}
+        )
+
+        exported_concepts = exported_data['concepts']
+        expected_concepts = ConceptVersionExportSerializer(
+            [concept2.get_latest_version(), concept1.get_latest_version()], many=True
+        ).data
+
+        self.assertEqual(len(exported_concepts), 2)
+        self.assertIn(expected_concepts[0], exported_concepts)
+        self.assertIn(expected_concepts[1], exported_concepts)
+
+        exported_mappings = exported_data['mappings']
+        expected_mappings = MappingDetailSerializer([mapping.get_latest_version()], many=True).data
+
+        self.assertEqual(len(exported_mappings), 1)
+        self.assertEqual(expected_mappings, exported_mappings)
+
+        exported_references = exported_data['references']
+        expected_references = CollectionReferenceSerializer(collection.references.all(), many=True).data
+
+        self.assertEqual(len(exported_references), 3)
+        self.assertIn(exported_references[0], expected_references)
+        self.assertIn(exported_references[1], expected_references)
+        self.assertIn(exported_references[2], expected_references)
+
+        s3_upload_key = collection.exclude_retired_export_path
+        s3_mock.upload_file.assert_called_once_with(
+            key=s3_upload_key, file_path=latest_temp_dir + '/export.zip', binary=True,
+            metadata={'ContentType': 'application/zip'}, headers={'content-type': 'application/zip'}
+        )
+        s3_mock.url_for.assert_called_once_with(s3_upload_key)
+
+        import shutil
+        shutil.rmtree(latest_temp_dir)
+
 
 class CollectionConceptsViewTest(OCLAPITestCase):
     def setUp(self):

core/integration_tests/tests_sources.py

@@ -704,29 +704,29 @@ def test_post_303(self, s3_exists_mock):
     def test_post_202(self, s3_exists_mock, export_source_mock):
         s3_exists_mock.return_value = False
         response = self.client.post(
-            self.source_v1.uri + 'export/',
+            self.source_v1.uri + 'export/?includeRetired=False',
             HTTP_AUTHORIZATION='Token ' + self.token,
             format='json'
         )
 
         self.assertEqual(response.status_code, 202)
         s3_exists_mock.assert_called_once_with(f"username/source1_v1.{self.v1_updated_at}.zip")
-        export_source_mock.delay.assert_called_once_with(self.source_v1.id)
+        export_source_mock.delay.assert_called_once_with(self.source_v1.id, False)
 
     @patch('core.sources.views.export_source')
     @patch('core.common.services.S3.exists')
     def test_post_409(self, s3_exists_mock, export_source_mock):
         s3_exists_mock.return_value = False
         export_source_mock.delay.side_effect = AlreadyQueued('already-queued')
         response = self.client.post(
-            self.source_v1.uri + 'export/',
+            self.source_v1.uri + 'export/?includeRetired=False',
             HTTP_AUTHORIZATION='Token ' + self.token,
             format='json'
         )
 
         self.assertEqual(response.status_code, 409)
         s3_exists_mock.assert_called_once_with(f"username/source1_v1.{self.v1_updated_at}.zip")
-        export_source_mock.delay.assert_called_once_with(self.source_v1.id)
+        export_source_mock.delay.assert_called_once_with(self.source_v1.id, False)
 
 
 class ExportSourceTaskTest(OCLAPITestCase):
@@ -777,6 +777,53 @@ def test_export_source(self, s3_mock):  # pylint: disable=too-many-locals
         import shutil
         shutil.rmtree(latest_temp_dir)
 
+    @patch('core.common.utils.S3')
+    def test_unretired_export_source(self, s3_mock):  # pylint: disable=too-many-locals
+        s3_mock.url_for = Mock(return_value='https://s3-url')
+        s3_mock.upload_file = Mock()
+        source = OrganizationSourceFactory()
+        concept1 = ConceptFactory(parent=source)
+        concept2 = ConceptFactory(parent=source)
+        mapping = MappingFactory(from_concept=concept2, to_concept=concept1, parent=source)
+
+        source_v1 = OrganizationSourceFactory(mnemonic=source.mnemonic, organization=source.organization, version='v1')
+        concept1.sources.add(source_v1)
+        concept2.sources.add(source_v1)
+        mapping.sources.add(source_v1)
+
+        export_source(source_v1.id, include_retired=False)  # pylint: disable=no-value-for-parameter
+
+        latest_temp_dir = get_latest_dir_in_path('/tmp/')
+        zipped_file = zipfile.ZipFile(latest_temp_dir + '/export.zip')
+        exported_data = json.loads(zipped_file.read('export.json').decode('utf-8'))
+
+        self.assertEqual(
+            exported_data, {**SourceVersionExportSerializer(source_v1).data, 'concepts': ANY, 'mappings': ANY}
+        )
+
+        exported_concepts = exported_data['concepts']
+        expected_concepts = ConceptVersionExportSerializer([concept2, concept1], many=True).data
+
+        self.assertEqual(len(exported_concepts), 2)
+        self.assertIn(expected_concepts[0], exported_concepts)
+        self.assertIn(expected_concepts[1], exported_concepts)
+
+        exported_mappings = exported_data['mappings']
+        expected_mappings = MappingDetailSerializer([mapping], many=True).data
+
+        self.assertEqual(len(exported_mappings), 1)
+        self.assertEqual(expected_mappings, exported_mappings)
+
+        s3_upload_key = source_v1.exclude_retired_export_path
+        s3_mock.upload_file.assert_called_once_with(
+            key=s3_upload_key, file_path=latest_temp_dir + '/export.zip', binary=True,
+            metadata={'ContentType': 'application/zip'}, headers={'content-type': 'application/zip'}
+        )
+        s3_mock.url_for.assert_called_once_with(s3_upload_key)
+
+        import shutil
+        shutil.rmtree(latest_temp_dir)
+
 
 class SourceLogoViewTest(OCLAPITestCase):
     def setUp(self):

core/sources/views.py

@@ -14,7 +14,7 @@
 from rest_framework.response import Response
 
 from core.client_configs.views import ResourceClientConfigsView
-from core.common.constants import HEAD, RELEASED_PARAM, PROCESSING_PARAM, ACCESS_TYPE_NONE
+from core.common.constants import HEAD, RELEASED_PARAM, PROCESSING_PARAM, ACCESS_TYPE_NONE, INCLUDE_RETIRED_PARAM
 from core.common.mixins import ListWithHeadersMixin, ConceptDictionaryCreateMixin, ConceptDictionaryUpdateMixin, \
     ConceptContainerExportMixin, ConceptContainerProcessingMixin, ConceptContainerExtraRetrieveUpdateDestroyView
 from core.common.permissions import CanViewConceptDictionary, CanEditConceptDictionary, HasAccessToVersionedObject, \
@@ -392,7 +392,8 @@ class SourceVersionExportView(ConceptContainerExportMixin, SourceVersionBaseView
     def handle_export_version(self):
         version = self.get_object()
         try:
-            export_source.delay(version.id)
+            include_retired = parse_boolean_query_param(self.request, INCLUDE_RETIRED_PARAM, "True")
+            export_source.delay(version.id, include_retired)
             return status.HTTP_202_ACCEPTED
         except AlreadyQueued:
             return status.HTTP_409_CONFLICT