formatted backend files

backend/src/core/annotation.py

@@ -86,7 +86,10 @@ def queue_annotation_tasks(self, analysis: Analysis, annotation_task_queue: Anno
                 annotation_task_queue.put(annotation_unit_queued)
 
     @staticmethod
-    def process_tasks(annotation_queue: AnnotationQueue, analysis_name: str, genomic_unit_collection: GenomicUnitCollection, analysis_collection: AnalysisCollection):  # pylint: disable=too-many-branches
+    def process_tasks(
+        annotation_queue: AnnotationQueue, analysis_name: str, genomic_unit_collection: GenomicUnitCollection,
+        analysis_collection: AnalysisCollection
+    ):  # pylint: disable=too-many-branches
         """Processes items that have been added to the queue"""
         logger.info("%s Processing annotation tasks queue ...", annotation_log_label())
 
@@ -108,8 +111,12 @@ def process_tasks(annotation_queue: AnnotationQueue, analysis_name: str, genomic
                         missing_dependencies = annotation_unit.get_missing_dependencies()
                         for missing_dataset_name in missing_dependencies:
                             # missing_dataset_name
-                            dependency_dataset = analysis_collection.get_manifest_dataset_config(analysis_name, missing_dataset_name)
-                            dependency_annotation_unit = AnnotationUnit(annotation_unit.genomic_unit, dependency_dataset)
+                            dependency_dataset = analysis_collection.get_manifest_dataset_config(
+                                analysis_name, missing_dataset_name
+                            )
+                            dependency_annotation_unit = AnnotationUnit(
+                                annotation_unit.genomic_unit, dependency_dataset
+                            )
                             annotation_value = genomic_unit_collection.find_genomic_unit_annotation_value(
                                 dependency_annotation_unit
                             )

backend/src/core/annotation_task.py

@@ -122,9 +122,7 @@ def extract_version(self, incomming_version_json):
         try:
             jq_results = self.__json_extract__(jq_query, incomming_version_json)
         except ValueError as value_error:
-            logger.info((
-                'Failed to extract ',  value_error
-            ))
+            logger.info(('Failed to extract ', value_error))
         jq_result = next(jq_results, None)
 
         return jq_result
@@ -255,19 +253,15 @@ def get_annotation_version_from_rosalution(self):
         """Gets version for rosalution type and returns the version data"""
         version_from_rosalution = "rosalution-temp-manifest-00"
 
-        version = {
-            "rosalution": "rosalution-temp-manifest-00"
-        }
+        version = {"rosalution": "rosalution-temp-manifest-00"}
         return version
 
     def get_annotation_version_from_date(self):
         """Gets version for date type and returns the version data"""
         version_from_date = "rosalution-temp-manifest-00"
         # getting version from date
 
-        version = {
-            "date": "rosalution-temp-manifest-00"
-        }
+        version = {"date": "rosalution-temp-manifest-00"}
         return version_from_date
 
 

backend/src/core/dataset_manifest.py

@@ -1,9 +1,5 @@
-
-
 class DatasetManifest:
-  """a helper to streamline getting the config for a dataset"""
-
-  def __init__(self, manifest):
-    self.manifest = manifest
+    """a helper to streamline getting the config for a dataset"""
 
-
+    def __init__(self, manifest):
+        self.manifest = manifest

backend/src/models/analysis.py

@@ -90,8 +90,7 @@ class Analysis(BaseAnalysis):
     sections: List[Section] = []
     discussions: List = []
     supporting_evidence_files: List = []
-    manifest: List = [
-    ]
+    manifest: List = []
 
     def units_to_annotate(self):
         """Returns the types of genomic units within the analysis"""

backend/src/repository/analysis_collection.py

@@ -136,34 +136,28 @@ def add_dataset_to_manifest(self, analysis_name: str, annotation_unit: Annotatio
         """Adds this dataset and its version to this Analysis."""
 
         dataset = {
-            annotation_unit.get_dataset_name(): {
-                annotation_unit.get_dataset_source(),
-                annotation_unit.get_version()
-            }
+            annotation_unit.get_dataset_name(): {annotation_unit.get_dataset_source(),
+                                                 annotation_unit.get_version()}
         }
-   
+
         updated_document = self.collection.find_one_and_update({"name": analysis_name},
                                                                {"$push": {"manifest": dataset}},
                                                                return_document=ReturnDocument.AFTER)
 
         return updated_document['manifest']
-    
+
     def get_manifest_dataset_config(self, analysis_name: str, dataset_name: str):
         dataset_attribute = f"manifest.{dataset_name}"
-        result = self.collection.find_one({
-            "name": analysis_name,
-            dataset_attribute : {'$exists': True }
-        })
+        result = self.collection.find_one({"name": analysis_name, dataset_attribute: {'$exists': True}})
 
         if not result:
             return None
-        
+
         return {
-            "data_set": dataset_name,
-            "data_source": result[dataset_name]['data_source'],
+            "data_set": dataset_name, "data_source": result[dataset_name]['data_source'],
             "version": result[dataset_name]['version']
         }
-    
+
     def get_dataset_manifest(self, analysis_name):
         analysis = self.find_by_name(analysis_name)
         if analysis is None:

backend/src/repository/genomic_unit_collection.py

@@ -75,7 +75,7 @@ def annotation_exist(self, annotation_unit: AnnotationUnit):
         data_set_name = annotation_unit.get_dataset_name()
         dataset_version = annotation_unit.get_version()
         dataset_source = annotation_unit.get_dataset_source()
- 
+
         find_query = self.__find_genomic_unit_query__(annotation_unit)
 
         if annotation_unit.is_transcript_dataset():
@@ -111,7 +111,7 @@ def find_genomic_unit_annotation_value(self, annotation_unit: AnnotationUnit):
 
         if result is None:
             return None
-        
+
         if dataset_name == "HPO_NCBI_GENE_ID" and annotation_unit.get_genomic_unit() == "DLG4":
             logger.info("\n\n\n")
             logger.info(f"{result}")

backend/src/routers/analysis_router.py

@@ -67,7 +67,10 @@ async def create_file(
     analysis = Analysis(**new_analysis)
     annotation_service = AnnotationService(repositories["annotation_config"])
     annotation_service.queue_annotation_tasks(analysis, annotation_task_queue)
-    background_tasks.add_task(AnnotationService.process_tasks, annotation_task_queue, analysis.name, repositories['genomic_unit'], repositories["analysis"])
+    background_tasks.add_task(
+        AnnotationService.process_tasks, annotation_task_queue, analysis.name, repositories['genomic_unit'],
+        repositories["analysis"]
+    )
 
     return new_analysis
 

backend/src/routers/annotation_router.py

@@ -95,8 +95,9 @@ def get_annotations_by_hgvs_variant(variant: str, analysis_name: str, repositori
             if dataset_config is None:
                 continue
             "annotation[dataset][0]['value']"
-            found_dataset = next((by_version for by_version in annotation[dataset] if by_version in dataset_manifest), None)
-            annotations[dataset] = 
+            found_dataset = next((by_version for by_version in annotation[dataset] if by_version in dataset_manifest),
+                                 None)
+            # annotations[dataset] =
 
     transcript_annotation_list = []
     for transcript_annotation in queried_genomic_unit['transcripts']:

backend/tests/unit/conftest.py

@@ -115,29 +115,28 @@ def fixture_annotation_config_collection(annotation_config_collection_json):
     mock_collection.find_one = Mock(return_value=read_test_fixture("annotations-config.json"))
     return AnnotationConfigCollection(mock_collection)
 
+
 @pytest.fixture(name='get_dataset_manifest_config')
 def get_dataset_manifest_config(analysis_collection_json):
     """Fixture factory method to create an dataset from the genomic unit information and name of the datset."""
 
     def _create_dataset_manifest(analysis_name, dataset_name):
         """Method to create the dataset manifest config"""
 
-        analysis_json = next((item for item in analysis_collection_json if item['name'] == analysis_name),
-                        None)
+        analysis_json = next((item for item in analysis_collection_json if item['name'] == analysis_name), None)
         analysis = Analysis(**analysis_json)
-        dataset_manifest = next((item for item in analysis.manifest if dataset_name in item),
-                None)
-
+        dataset_manifest = next((item for item in analysis.manifest if dataset_name in item), None)
+
         dataset_config = {
-            "data_set": dataset_name,
-            "data_source": dataset_manifest[dataset_name]['data_source'],
+            "data_set": dataset_name, "data_source": dataset_manifest[dataset_name]['data_source'],
             "version": dataset_manifest[dataset_name]['version']
         }
-        
+
         return dataset_config
 
     return _create_dataset_manifest
 
+
 @pytest.fixture(name='get_annotation_unit')
 def get_standard_annotation_unit(annotation_config_collection_json):
     """Fixture factory method to create an AnnotationUnit from the genomic unit information and name of the datset."""

backend/tests/unit/core/test_annotate.py

@@ -107,10 +107,14 @@ def fixture_extract_and_annotate_cpam0002(cpam0002_annotation_queue, get_dataset
         mock_genomic_unit_collection.find_genomic_unit_annotation_value.side_effect = (
             skip_depends.skip_hgncid_get_value_first_time_mock
         )
-        mock_analysis_collection.get_manifest_dataset_config.return_value = get_dataset_manifest_config("CPAM0002",'HGNC_ID')
+        mock_analysis_collection.get_manifest_dataset_config.return_value = get_dataset_manifest_config(
+            "CPAM0002", 'HGNC_ID'
+        )
         mock_genomic_unit_collection.annotation_exist.return_value = False
 
-        AnnotationService.process_tasks(cpam0002_annotation_queue, "CPAM0002", mock_genomic_unit_collection,mock_analysis_collection)
+        AnnotationService.process_tasks(
+            cpam0002_annotation_queue, "CPAM0002", mock_genomic_unit_collection, mock_analysis_collection
+        )
         yield {
             'extract': extract_task_annotate, 'version': version_task_annotate, 'http': http_task_annotate,
             'none': none_task_annotate, 'forge': forge_task_annotate,
@@ -162,11 +166,13 @@ def fixture_extract_and_annotate_cpam0046(cpam0046_annotation_queue, get_dataset
         mock_genomic_unit_collection.find_genomic_unit_annotation_value.side_effect = (
             skip_depends.skip_hgncid_get_value_first_time_mock
         )
-        dependency_dataset =  get_dataset_manifest_config("CPAM0046", 'HGNC_ID')
+        dependency_dataset = get_dataset_manifest_config("CPAM0046", 'HGNC_ID')
         mock_analysis_collection.get_manifest_dataset_config.return_value = dependency_dataset
         mock_genomic_unit_collection.annotation_exist.return_value = False
 
-        AnnotationService.process_tasks(cpam0046_annotation_queue, "CPAM0046", mock_genomic_unit_collection, mock_analysis_collection)
+        AnnotationService.process_tasks(
+            cpam0046_annotation_queue, "CPAM0046", mock_genomic_unit_collection, mock_analysis_collection
+        )
         yield {
             'extract': extract_task_annotate, 'version': version_task_annotate, 'http': http_task_annotate,
             'none': none_task_annotate, 'forge': forge_task_annotate,