fixes

Author: ChrOertlin

cg/apps/downsample/downsample.py

@@ -4,12 +4,14 @@
 from typing import List
 
 from cg.apps.downsample.utils import case_exists_in_statusdb, sample_exists_in_statusdb
+from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.constants import SequencingFileTag
 from cg.exc import DownsampleFailedError
 from cg.meta.meta import MetaAPI
 from cg.meta.workflow.downsample.downsample import DownsampleWorkflow
 from cg.models.cg_config import CGConfig
 from cg.models.downsample.downsample_data import DownsampleData
+from cg.store import Store
 from cg.store.models import Family, Sample
 from cg.utils.calculations import multiply_by_million
 from cg.utils.files import get_files_matching_pattern
@@ -28,7 +30,9 @@ def __init__(
     ):
         """Initialize the API."""
         super().__init__(config)
-        self.config = config
+        self.config: CGConfig = config
+        self.status_db: Store = config.status_db
+        self.hk_api: HousekeeperAPI = config.housekeeper_api
         self.sample_id: str = sample_id
         self.number_of_reads: float = number_of_reads
         self.case_id: str = case_id
@@ -77,7 +81,7 @@ def add_downsampled_case_to_statusdb(self) -> Family:
         if case_exists_in_statusdb(status_db=self.status_db, case_id=downsampled_case.internal_id):
             raise ValueError(f"Case {downsampled_case.internal_id} already exists in StatusDB.")
         if not self.dry_run:
-            self.status_db.session.add_commit(downsampled_case)
+            self.status_db.session.commit(downsampled_case)
             LOG.info(f"New down sampled case created: {downsampled_case.internal_id}")
             return downsampled_case
         return downsampled_case

tests/apps/downsample/test_downsample.py

@@ -0,0 +1,18 @@
+"""Tests for the DownsampleAPI."""
+from cg.apps.downsample.downsample import DownSampleAPI
+from cg.apps.housekeeper.hk import HousekeeperAPI
+from cg.models.downsample.downsample_data import DownsampleData
+from cg.store import Store
+
+
+def test_add_downsampled_sample_entry_to_statusdb(downsample_api: DownSampleAPI) -> None:
+    """Test to add the downsampled sample entry to StatusDB."""
+    # GIVEN a DownsampleAPI
+
+    # WHEN adding a downsampled case to statusDB
+    downsample_api.add_downsampled_case_to_statusdb()
+
+    # THEN a downsampled case is added to the store
+    assert downsample_api.status_db.get_case_by_name(
+        downsample_api.downsample_data.downsampled_case.name
+    )

tests/conftest.py

@@ -18,6 +18,7 @@
     FlowCellSampleBcl2Fastq,
     FlowCellSampleBCLConvert,
 )
+from cg.apps.downsample.downsample import DownSampleAPI
 from cg.apps.gens import GensAPI
 from cg.apps.gt import GenotypeAPI
 from cg.apps.hermes.hermes_api import HermesApi
@@ -3259,3 +3260,113 @@ def flow_cell_encryption_api(
     )
     flow_cell_encryption_api.slurm_api.set_dry_run(dry_run=True)
     return flow_cell_encryption_api
+
+
+# Downsample
+@pytest.fixture()
+def store_with_case_and_sample_with_reads(
+    store: Store,
+    helpers: StoreHelpers,
+    downsample_case_internal_id: str,
+    downsample_sample_internal_id_1: str,
+    downsample_sample_internal_id_2: str,
+) -> Store:
+    """Return a store with a case and a sample with reads."""
+    case: Family = helpers.add_case(store=store, internal_id=downsample_case_internal_id)
+
+    for sample_internal_id in [downsample_sample_internal_id_1, downsample_sample_internal_id_2]:
+        helpers.add_sample(
+            store=store,
+            internal_id=sample_internal_id,
+            customer_id=case.customer_id,
+            reads=100_000_000,
+        )
+        sample: Sample = store.get_sample_by_internal_id(internal_id=sample_internal_id)
+        helpers.add_relationship(store=store, case=case, sample=sample)
+
+    return store
+
+
+@pytest.fixture()
+def downsample_case_internal_id() -> str:
+    """Return a case internal id."""
+    return "supersonicturtle"
+
+
+@pytest.fixture()
+def downsample_sample_internal_id_1() -> str:
+    """Return a sample internal id."""
+    return "ACC12345675213"
+
+
+@pytest.fixture()
+def downsample_sample_internal_id_2() -> str:
+    """Return a sample internal id."""
+    return "ACC12345684213"
+
+
+@pytest.fixture()
+def number_of_reads_in_millions() -> int:
+    """Return a number of reads in millions."""
+    return 50
+
+
+@pytest.fixture()
+def downsample_hk_api(
+    real_housekeeper_api: HousekeeperAPI,
+    fastq_file: Path,
+    downsample_sample_internal_id_1: str,
+    downsample_sample_internal_id_2: str,
+    timestamp_yesterday: str,
+    helpers: StoreHelpers,
+    tmp_path_factory,
+) -> HousekeeperAPI:
+    """Return a Housekeeper API with a real database."""
+    for sample_internal_id in [downsample_sample_internal_id_1, downsample_sample_internal_id_2]:
+        tmp_fastq_file = tmp_path_factory.mktemp(f"{sample_internal_id}.fastq.gz")
+        downsample_bundle: dict = {
+            "name": sample_internal_id,
+            "created": timestamp_yesterday,
+            "expires": timestamp_yesterday,
+            "files": [
+                {
+                    "path": tmp_fastq_file.as_posix(),
+                    "archive": False,
+                    "tags": [SequencingFileTag.FASTQ, sample_internal_id],
+                }
+            ],
+        }
+        helpers.ensure_hk_bundle(store=real_housekeeper_api, bundle_data=downsample_bundle)
+    return real_housekeeper_api
+
+
+@pytest.fixture()
+def downsample_context(
+    cg_context: CGConfig,
+    store_with_case_and_sample_with_reads: Store,
+    downsample_hk_api: HousekeeperAPI,
+) -> CGConfig:
+    """Return cg context with added Store and Housekeeper API."""
+    cg_context.status_db_ = store_with_case_and_sample_with_reads
+    cg_context.housekeeper_api_ = downsample_hk_api
+    return cg_context
+
+
+@pytest.fixture()
+def downsample_api(
+    downsample_context: CGConfig,
+    store_with_case_and_sample_with_reads: Store,
+    downsample_hk_api: HousekeeperAPI,
+    downsample_sample_internal_id_1: str,
+    downsample_case_internal_id: str,
+    number_of_reads_in_millions: int,
+    tmp_path_factory,
+) -> DownSampleAPI:
+    """Return a DownsampleAPI."""
+    downsample_api = DownSampleAPI(
+        config=downsample_context,
+        sample_id=downsample_sample_internal_id_1,
+        number_of_reads=number_of_reads_in_millions,
+        case_id=downsample_case_internal_id,
+    )
+    return downsample_api

tests/models/downsample/conftest.py

@@ -9,80 +9,3 @@
 from cg.store import Store
 from cg.store.models import Family, Sample
 from tests.store_helpers import StoreHelpers
-
-
-@pytest.fixture()
-def store_with_case_and_sample_with_reads(
-    store: Store,
-    helpers: StoreHelpers,
-    downsample_case_internal_id: str,
-    downsample_sample_internal_id_1: str,
-    downsample_sample_internal_id_2: str,
-) -> Store:
-    """Return a store with a case and a sample with reads."""
-    case: Family = helpers.add_case(store=store, internal_id=downsample_case_internal_id)
-
-    for sample_internal_id in [downsample_sample_internal_id_1, downsample_sample_internal_id_2]:
-        helpers.add_sample(
-            store=store,
-            internal_id=sample_internal_id,
-            customer_id=case.customer_id,
-            reads=100_000_000,
-        )
-        sample: Sample = store.get_sample_by_internal_id(internal_id=sample_internal_id)
-        helpers.add_relationship(store=store, case=case, sample=sample)
-
-    return store
-
-
-@pytest.fixture()
-def downsample_case_internal_id() -> str:
-    """Return a case internal id."""
-    return "supersonicturtle"
-
-
-@pytest.fixture()
-def downsample_sample_internal_id_1() -> str:
-    """Return a sample internal id."""
-    return "ACC12345675213"
-
-
-@pytest.fixture()
-def downsample_sample_internal_id_2() -> str:
-    """Return a sample internal id."""
-    return "ACC12345684213"
-
-
-@pytest.fixture()
-def number_of_reads_in_millions() -> int:
-    """Return a number of reads in millions."""
-    return 50
-
-
-@pytest.fixture()
-def downsample_hk_api(
-    real_housekeeper_api: HousekeeperAPI,
-    fastq_file: Path,
-    downsample_sample_internal_id_1: str,
-    downsample_sample_internal_id_2: str,
-    timestamp_yesterday: str,
-    helpers: StoreHelpers,
-    tmp_path_factory,
-) -> HousekeeperAPI:
-    """Return a Housekeeper API with a real database."""
-    for sample_internal_id in [downsample_sample_internal_id_1, downsample_sample_internal_id_2]:
-        tmp_fastq_file = tmp_path_factory.mktemp(f"{sample_internal_id}.fastq.gz")
-        downsample_bundle: Dict = {
-            "name": sample_internal_id,
-            "created": timestamp_yesterday,
-            "expires": timestamp_yesterday,
-            "files": [
-                {
-                    "path": tmp_fastq_file.as_posix(),
-                    "archive": False,
-                    "tags": [SequencingFileTag.FASTQ, sample_internal_id],
-                }
-            ],
-        }
-        helpers.ensure_hk_bundle(store=real_housekeeper_api, bundle_data=downsample_bundle)
-    return real_housekeeper_api