fix bug

Author: ChrOertlin

cg/services/deliver_files/file_fetcher/analysis_service.py

@@ -42,7 +42,10 @@ def get_files_to_deliver(self, case_id: str, sample_id: str | None = None) -> De
         """Return a list of analysis files to be delivered for a case."""
         LOG.debug(f"[FETCH SERVICE] Fetching analysis files for case: {case_id}")
         case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
-        analysis_case_files: list[CaseFile] = self._get_analysis_case_delivery_files(case)
+        analysis_case_files: list[CaseFile] = self._get_analysis_case_delivery_files(
+            case=case, sample_id=sample_id
+        )
+
         analysis_sample_files: list[SampleFile] = self._get_analysis_sample_delivery_files(
             case=case, sample_id=sample_id
         )
@@ -73,9 +76,11 @@ def _validate_delivery_has_content(delivery_files: DeliveryFiles) -> DeliveryFil
     @handle_missing_bundle_errors
     def _get_sample_files_from_case_bundle(
         self, workflow: Workflow, sample_id: str, case_id: str
-    ) -> list[SampleFile]:
+    ) -> list[SampleFile] | None:
         """Return a list of files from a case bundle with a sample id as tag."""
         sample_tags: list[set[str]] = self.tags_fetcher.fetch_tags(workflow).sample_tags
+        if not sample_tags:
+            return []
         sample_tags_with_sample_id: list[set[str]] = [tag | {sample_id} for tag in sample_tags]
         sample_files: list[File] = self.hk_api.get_files_from_latest_version_containing_tags(
             bundle_name=case_id, tags=sample_tags_with_sample_id
@@ -105,13 +110,17 @@ def _get_analysis_sample_delivery_files(
         return delivery_files
 
     @handle_missing_bundle_errors
-    def _get_analysis_case_delivery_files(self, case: Case) -> list[CaseFile]:
+    def _get_analysis_case_delivery_files(
+        self, case: Case, sample_id: str | None
+    ) -> list[CaseFile] | None:
         """
         Return a complete list of analysis case files to be delivered and ignore analysis sample
         files.
         """
         case_tags: list[set[str]] = self.tags_fetcher.fetch_tags(case.data_analysis).case_tags
-        sample_id_tags: list[str] = case.sample_ids
+        if not case_tags:
+            return []
+        sample_id_tags: list[str] = [sample_id] if sample_id else case.sample_ids
         case_files: list[File] = self.hk_api.get_files_from_latest_version_containing_tags(
             bundle_name=case.internal_id, tags=case_tags, excluded_tags=sample_id_tags
         )

cg/services/deliver_files/tag_fetcher/fohm_upload_service.py

@@ -16,12 +16,15 @@ def fetch_tags(self, workflow: Workflow) -> DeliveryFileTags:
         if workflow is RAW_DATA, return tags for fastq to fetch fastq files from the sample bundle.
         Required since some of the sample specific files are stored on the case bundle, but also fastq files.
         Not separating these would cause fetching of case bundle fastq files if present.
+
+        args:
+            workflow: Workflow: The workflow to fetch tags
         """
         self._validate_workflow(workflow=workflow)
         return (
             DeliveryFileTags(
                 case_tags=None,
-                sample_tags=[{"consensus-sample", "vcf-report"}],
+                sample_tags=[{"consensus-sample"}, {"vcf-report"}],
             )
             if workflow == Workflow.MUTANT
             else DeliveryFileTags(
@@ -35,6 +38,8 @@ def _validate_workflow(workflow: Workflow):
         """
         Validate the workflow.
         NOTE: workflow raw data here is required to fit the implementation of the raw data delivery file fetcher.
+        args:
+            workflow: Workflow: The workflow to validate.
         """
         if workflow not in [Workflow.MUTANT, Workflow.RAW_DATA]:
             raise ValueError(f"Workflow {workflow} is not supported for FOHM upload file delivery.")

tests/fixture_plugins/delivery_fixtures/bundle_fixtures.py

@@ -109,8 +109,12 @@ def hk_delivery_case_bundle_fohm_upload(
     sample_id: str,
     another_sample_id: str,
     delivery_report_file: Path,
-    delivery_cram_file: Path,
-    delivery_another_cram_file: Path,
+    delivery_case_fastq_file: Path,
+    delivery_another_case_fastq_file: Path,
+    delivery_consensus_sample_file: Path,
+    delivery_another_consensus_sample_file: Path,
+    delivery_vcf_report_file: Path,
+    delivery_another_vcf_report_file: Path,
 ) -> dict:
     case_hk_bundle: dict[str, Any] = deepcopy(case_hk_bundle_no_files)
     case_hk_bundle["name"] = case_id
@@ -122,12 +126,32 @@ def hk_delivery_case_bundle_fohm_upload(
         },
         {
             "archive": False,
-            "path": delivery_cram_file.as_posix(),
+            "path": delivery_case_fastq_file.as_posix(),
+            "tags": ["fastq", sample_id],
+        },
+        {
+            "archive": False,
+            "path": delivery_another_case_fastq_file.as_posix(),
+            "tags": ["fastq", another_sample_id],
+        },
+        {
+            "archive": False,
+            "path": delivery_consensus_sample_file.as_posix(),
             "tags": ["consensus-sample", sample_id],
         },
         {
             "archive": False,
-            "path": delivery_another_cram_file.as_posix(),
+            "path": delivery_another_consensus_sample_file.as_posix(),
+            "tags": ["consensus-sample", another_sample_id],
+        },
+        {
+            "archive": False,
+            "path": delivery_vcf_report_file.as_posix(),
+            "tags": ["vcf-report", sample_id],
+        },
+        {
+            "archive": False,
+            "path": delivery_another_vcf_report_file.as_posix(),
             "tags": ["vcf-report", another_sample_id],
         },
     ]

tests/fixture_plugins/delivery_fixtures/context_fixtures.py

@@ -21,16 +21,33 @@ def delivery_housekeeper_api(
     hk_delivery_case_bundle: dict[str, Any],
 ) -> HousekeeperAPI:
     """Delivery API Housekeeper context."""
+    hk_api: HousekeeperAPI = real_housekeeper_api
+    helpers.ensure_hk_bundle(store=hk_api, bundle_data=hk_delivery_sample_bundle, include=True)
     helpers.ensure_hk_bundle(
-        store=real_housekeeper_api, bundle_data=hk_delivery_sample_bundle, include=True
+        store=hk_api, bundle_data=hk_delivery_another_sample_bundle, include=True
     )
+    helpers.ensure_hk_bundle(store=hk_api, bundle_data=hk_delivery_case_bundle, include=True)
+    return hk_api
+
+
+@pytest.fixture
+def delivery_fohm_upload_housekeeper_api(
+    real_housekeeper_api: HousekeeperAPI,
+    helpers: StoreHelpers,
+    hk_delivery_case_bundle_fohm_upload: dict[str, Any],
+    hk_delivery_sample_bundle: dict[str, Any],
+    hk_delivery_another_sample_bundle: dict[str, Any],
+) -> HousekeeperAPI:
+    """Delivery API Housekeeper context."""
+    hk_api: HousekeeperAPI = real_housekeeper_api
+    helpers.ensure_hk_bundle(store=hk_api, bundle_data=hk_delivery_sample_bundle, include=True)
     helpers.ensure_hk_bundle(
-        store=real_housekeeper_api, bundle_data=hk_delivery_another_sample_bundle, include=True
+        store=hk_api, bundle_data=hk_delivery_another_sample_bundle, include=True
     )
     helpers.ensure_hk_bundle(
-        store=real_housekeeper_api, bundle_data=hk_delivery_case_bundle, include=True
+        store=hk_api, bundle_data=hk_delivery_case_bundle_fohm_upload, include=True
     )
-    return real_housekeeper_api
+    return hk_api
 
 
 @pytest.fixture
@@ -144,6 +161,68 @@ def delivery_store_microsalt(
     return status_db
 
 
+@pytest.fixture
+def delivery_store_mutant(
+    cg_context: CGConfig,
+    helpers: StoreHelpers,
+    case_id: str,
+    no_sample_case_id: str,
+    case_name: str,
+    sample_id: str,
+    another_sample_id: str,
+    sample_id_not_enough_reads: str,
+    total_sequenced_reads_pass: int,
+    total_sequenced_reads_not_pass: int,
+    sample_name: str,
+    another_sample_name: str,
+    microbial_application_tag: str,
+) -> Store:
+    """Delivery API StatusDB context for Mutant."""
+    status_db: Store = cg_context.status_db
+
+    # Error case without samples
+    helpers.add_case(store=status_db, internal_id=no_sample_case_id, name=no_sample_case_id)
+
+    # Mutant case with fastq-analysis as data delivery
+    case: Case = helpers.add_case(
+        store=status_db,
+        internal_id=case_id,
+        name=case_name,
+        data_analysis=Workflow.MUTANT,
+        data_delivery=DataDelivery.FASTQ_ANALYSIS,
+    )
+    order: Order = helpers.add_order(store=status_db, customer_id=case.customer.id, ticket_id=1)
+    case.orders.append(order)
+    # Mutant samples
+    sample: Sample = helpers.add_sample(
+        store=status_db,
+        application_tag=microbial_application_tag,
+        internal_id=sample_id,
+        name=sample_name,
+        reads=total_sequenced_reads_pass,
+    )
+
+    another_sample: Sample = helpers.add_sample(
+        store=status_db,
+        application_tag=microbial_application_tag,
+        internal_id=another_sample_id,
+        name=another_sample_name,
+        reads=total_sequenced_reads_pass,
+    )
+
+    sample_not_enough_reads: Sample = helpers.add_sample(
+        store=status_db,
+        application_tag=microbial_application_tag,
+        internal_id=sample_id_not_enough_reads,
+        reads=total_sequenced_reads_not_pass,
+    )
+
+    for sample_mutant in [sample, another_sample, sample_not_enough_reads]:
+        helpers.add_relationship(store=status_db, case=case, sample=sample_mutant)
+
+    return status_db
+
+
 @pytest.fixture
 def delivery_context_balsamic(
     cg_context: CGConfig,

tests/fixture_plugins/delivery_fixtures/delivery_files_models_fixtures.py

@@ -102,6 +102,66 @@ def expected_bam_delivery_files_single_sample(
     return expected_bam_delivery_files
 
 
+@pytest.fixture
+def expected_fohm_delivery_files(
+    delivery_fohm_upload_housekeeper_api: HousekeeperAPI,
+    case_id: str,
+    case_name: str,
+    sample_id: str,
+    sample_name: str,
+    another_sample_id: str,
+    another_sample_name: str,
+    delivery_store_mutant: Store,
+) -> DeliveryFiles:
+    """Return the expected fastq delivery files."""
+    sample_info: list[tuple[str, str]] = [
+        (sample_id, sample_name),
+        (another_sample_id, another_sample_name),
+    ]
+    sample_files: list[SampleFile] = [
+        SampleFile(
+            case_id=case_id,
+            sample_id=sample[0],
+            sample_name=sample[1],
+            file_path=delivery_fohm_upload_housekeeper_api.get_files_from_latest_version(
+                bundle_name=sample[0], tags=[SequencingFileTag.FASTQ]
+            )[0].full_path,
+        )
+        for sample in sample_info
+    ]
+    case_sample_info: list[tuple[str, str, str]] = [
+        (sample_id, sample_name, "consensus-sample"),
+        (sample_id, sample_name, "vcf-report"),
+        (another_sample_id, another_sample_name, "consensus-sample"),
+        (another_sample_id, another_sample_name, "vcf-report"),
+    ]
+    case_sample_files: list[SampleFile] = [
+        SampleFile(
+            case_id=case_id,
+            sample_id=sample[0],
+            sample_name=sample[1],
+            file_path=delivery_fohm_upload_housekeeper_api.get_files_from_latest_version_containing_tags(
+                bundle_name=case_id, tags=[{sample[2], sample[0]}]
+            )[
+                0
+            ].full_path,
+        )
+        for sample in case_sample_info
+    ]
+
+    case: Case = delivery_store_mutant.get_case_by_internal_id(case_id)
+    delivery_meta_data = DeliveryMetaData(
+        case_id=case.internal_id,
+        customer_internal_id=case.customer.internal_id,
+        ticket_id=case.latest_ticket,
+    )
+    return DeliveryFiles(
+        delivery_data=delivery_meta_data,
+        case_files=[],
+        sample_files=case_sample_files + sample_files,
+    )
+
+
 @pytest.fixture
 def expected_analysis_delivery_files(
     delivery_housekeeper_api: HousekeeperAPI,

tests/fixture_plugins/delivery_fixtures/delivery_services_fixtures.py

@@ -73,20 +73,6 @@ def bam_data_delivery_service(
     )
 
 
-@pytest.fixture
-def fohm_data_delivery_service(
-    delivery_housekeeper_api: HousekeeperAPI,
-    delivery_store_microsalt: Store,
-) -> RawDataAndAnalysisDeliveryFileFetcher:
-    """Fixture to get an instance of FetchFastqDeliveryFilesService."""
-    tag_service = FOHMUploadTagsFetcher()
-    return RawDataAndAnalysisDeliveryFileFetcher(
-        hk_api=delivery_housekeeper_api,
-        status_db=delivery_store_microsalt,
-        tags_fetcher=tag_service,
-    )
-
-
 @pytest.fixture
 def bam_data_delivery_service_no_housekeeper_bundle(
     real_housekeeper_api: HousekeeperAPI,
@@ -101,6 +87,20 @@ def bam_data_delivery_service_no_housekeeper_bundle(
     )
 
 
+@pytest.fixture
+def fohm_data_delivery_service(
+    delivery_fohm_upload_housekeeper_api: HousekeeperAPI,
+    delivery_store_mutant: Store,
+) -> RawDataAndAnalysisDeliveryFileFetcher:
+    """Fixture to get an instance of FetchFastqDeliveryFilesService."""
+    tag_service = FOHMUploadTagsFetcher()
+    return RawDataAndAnalysisDeliveryFileFetcher(
+        hk_api=delivery_fohm_upload_housekeeper_api,
+        status_db=delivery_store_mutant,
+        tags_fetcher=tag_service,
+    )
+
+
 @pytest.fixture
 def analysis_delivery_service(
     delivery_housekeeper_api: HousekeeperAPI,