Update imports of Housekeeper store (#2889)(patch)

In Clinical-Genomics/housekeeper#191 the location of the Housekeeepr Store was changed


### Fixed

- The imports to Housekeeper store point to the correct location

cg/apps/housekeeper/hk.py

@@ -7,9 +7,9 @@
 
 from housekeeper.include import checksum as hk_checksum
 from housekeeper.include import include_version
-from housekeeper.store import Store, models
 from housekeeper.store.database import create_all_tables, drop_all_tables, initialize_database
-from housekeeper.store.models import Archive, Bundle, File, Version
+from housekeeper.store.models import Archive, Bundle, File, Tag, Version
+from housekeeper.store.store import Store
 from sqlalchemy.orm import Query
 
 from cg.constants import SequencingFileTag
@@ -256,7 +256,7 @@ def last_version(self, bundle: str) -> Version:
             self._store._get_query(table=Version)
             .join(Version.bundle)
             .filter(Bundle.name == bundle)
-            .order_by(models.Version.created_at.desc())
+            .order_by(Version.created_at.desc())
             .first()
         )
 
@@ -299,13 +299,13 @@ def new_tag(self, name: str, category: str = None):
         """Create a new tag."""
         return self._store.new_tag(name, category)
 
-    def add_tag(self, name: str, category: str = None) -> models.Tag:
+    def add_tag(self, name: str, category: str = None) -> Tag:
         """Add a tag to the database."""
         tag_obj = self._store.new_tag(name, category)
         self.add_commit(tag_obj)
         return tag_obj
 
-    def get_tag(self, name: str) -> models.Tag:
+    def get_tag(self, name: str) -> Tag:
         """Fetch a tag."""
         return self._store.get_tag(name)
 

cg/meta/upload/gt.py

@@ -1,9 +1,10 @@
 import logging
 from pathlib import Path
 
+from housekeeper.store.models import File, Version
+
 from cg.apps.gt import GenotypeAPI
 from cg.apps.housekeeper.hk import HousekeeperAPI
-from cg.apps.housekeeper.hk import models as housekeeper_models
 from cg.constants.constants import FileFormat, Pipeline, PrepCategory
 from cg.constants.housekeeper_tags import HkMipAnalysisTag
 from cg.constants.subject import Sex
@@ -55,7 +56,7 @@ def data(self, analysis_obj: Analysis) -> dict:
             raise ValueError(f"Pipeline {analysis_obj.pipeline} does not support Genotype upload")
         return data
 
-    def _get_samples_sex_mip(self, case_obj: Case, hk_version: housekeeper_models.Version) -> dict:
+    def _get_samples_sex_mip(self, case_obj: Case, hk_version: Version) -> dict:
         qc_metrics_file = self.get_qcmetrics_file(hk_version)
         analysis_sexes = self.analysis_sex(qc_metrics_file)
         samples_sex = {}
@@ -87,7 +88,7 @@ def analysis_sex(self, qc_metrics_file: Path) -> dict:
             for sample_id_metric in qc_metrics.sample_id_metrics
         }
 
-    def get_bcf_file(self, hk_version_obj: housekeeper_models.Version) -> housekeeper_models.File:
+    def get_bcf_file(self, hk_version_obj: Version) -> File:
         """Fetch a bcf file and return the file object"""
         genotype_files: list = self._get_genotype_files(version_id=hk_version_obj.id)
         for genotype_file in genotype_files:
@@ -96,7 +97,7 @@ def get_bcf_file(self, hk_version_obj: housekeeper_models.Version) -> housekeepe
                 return genotype_file
         raise FileNotFoundError(f"No vcf or bcf file found for bundle {hk_version_obj.bundle_id}")
 
-    def get_qcmetrics_file(self, hk_version_obj: housekeeper_models.Version) -> Path:
+    def get_qcmetrics_file(self, hk_version_obj: Version) -> Path:
         """Fetch a qc_metrics file and return the path"""
         hk_qcmetrics = self.hk.files(
             version=hk_version_obj.id, tags=HkMipAnalysisTag.QC_METRICS
@@ -117,7 +118,7 @@ def upload(self, data: dict, replace: bool = False):
         self.gt.upload(str(data["bcf"]), data["samples_sex"], force=replace)
 
     @staticmethod
-    def _is_variant_file(genotype_file: housekeeper_models.File):
+    def _is_variant_file(genotype_file: File):
         return genotype_file.full_path.endswith("vcf.gz") or genotype_file.full_path.endswith("bcf")
 
     def _get_genotype_files(self, version_id: int) -> list: