fest(sql): Refactor read handler (#2831)

### Changed

- Refactor read handler to CRUD

Author: henrikstranneheim

cg/cli/workflow/mutant/base.py

@@ -23,7 +23,7 @@
 @click.group(invoke_without_command=True)
 @click.pass_context
 def mutant(context: click.Context) -> None:
-    """Covid analysis workflow"""
+    """Mutant analysis workflow"""
     AnalysisAPI.get_help(context)
     context.obj.meta_apis["analysis_api"] = MutantAnalysisAPI(
         config=context.obj,

cg/store/api/core.py

@@ -1,10 +1,10 @@
 import logging
 
 from cg.store.api.find_basic_data import FindBasicDataHandler
-from cg.store.api.find_business_data import FindBusinessDataHandler
 from cg.store.api.status import StatusHandler
 from cg.store.crud.create import CreateHandler
 from cg.store.crud.delete import DeleteDataHandler
+from cg.store.crud.read import ReadHandler
 from cg.store.crud.update import UpdateHandler
 from cg.store.database import get_session
 
@@ -15,7 +15,7 @@ class CoreHandler(
     CreateHandler,
     DeleteDataHandler,
     FindBasicDataHandler,
-    FindBusinessDataHandler,
+    ReadHandler,
     StatusHandler,
     UpdateHandler,
 ):
@@ -24,7 +24,7 @@ class CoreHandler(
     def __init__(self, session):
         DeleteDataHandler(session)
         FindBasicDataHandler(session)
-        FindBusinessDataHandler(session)
+        ReadHandler(session)
         StatusHandler(session)
         UpdateHandler(session)
 

cg/store/api/find_business_data.py renamed to cg/store/crud/read.py

@@ -1,4 +1,4 @@
-"""Handler to find business data objects."""
+"""Handler to read data objects."""
 import datetime as dt
 import logging
 from typing import Callable, Iterator
@@ -54,8 +54,8 @@
 LOG = logging.getLogger(__name__)
 
 
-class FindBusinessDataHandler(BaseHandler):
-    """Contains methods to find business data model instances."""
+class ReadHandler(BaseHandler):
+    """Class for reading items in the database."""
 
     def __init__(self, session: Session):
         super().__init__(session=session)

tests/cli/workflow/conftest.py

@@ -8,7 +8,7 @@
 from cg.constants import DataDelivery, FlowCellStatus, Pipeline
 from cg.models.cg_config import CGConfig
 from cg.store import Store
-from cg.store.api.find_business_data import FindBusinessDataHandler
+from cg.store.crud.read import ReadHandler
 from cg.store.models import Case
 from tests.store_helpers import StoreHelpers
 
@@ -239,5 +239,5 @@ def mock_analysis_flow_cell(mocker) -> None:
     on disk."""
     flow_cell = Mock()
     flow_cell.status = FlowCellStatus.ON_DISK
-    mocker.patch.object(FindBusinessDataHandler, "get_flow_cells_by_case")
-    FindBusinessDataHandler.get_flow_cells_by_case.return_value = [flow_cell]
+    mocker.patch.object(ReadHandler, "get_flow_cells_by_case")
+    ReadHandler.get_flow_cells_by_case.return_value = [flow_cell]

tests/cli/workflow/mip/conftest.py

@@ -13,8 +13,8 @@
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
 from cg.meta.workflow.prepare_fastq import PrepareFastqAPI
 from cg.models.cg_config import CGConfig
-from cg.store.api.find_business_data import FindBusinessDataHandler
 from cg.store.api.status import StatusHandler
+from cg.store.crud.read import ReadHandler
 from cg.store.models import Case
 from tests.store_helpers import StoreHelpers
 
@@ -197,5 +197,5 @@ def setup_mocks(
         return_value=["a str"],
     )
 
-    mocker.patch.object(FindBusinessDataHandler, "are_all_flow_cells_on_disk")
-    FindBusinessDataHandler.are_all_flow_cells_on_disk.return_value = True
+    mocker.patch.object(ReadHandler, "are_all_flow_cells_on_disk")
+    ReadHandler.are_all_flow_cells_on_disk.return_value = True