Merge branch 'master' into fix-enum-spelling

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 19.0.1
+current_version = 19.0.2
 commit = True
 tag = True
 tag_name = {new_version}

setup.py

@@ -52,7 +52,7 @@ def parse_reqs(req_path="./requirements.txt"):
 
 setup(
     name=NAME,
-    version="19.0.1",
+    version="19.0.2",
     description=DESCRIPTION,
     long_description=LONG_DESCRIPTION,
     long_description_content_type="text/markdown",

tests/mocks/store_mock.py

@@ -1,4 +1,4 @@
-from trailblazer.store.api import Store
+from trailblazer.store.core import Store
 
 
 class MockStore(Store):

tests/store/utils/store_helper.py

@@ -1,8 +1,8 @@
 """Utility functions to simply add test data in a Trailblazer store."""
-from datetime import datetime, date
+from datetime import date, datetime
 
-from trailblazer.store.api import Store
-from trailblazer.store.models import Info, User, Job
+from trailblazer.store.core import Store
+from trailblazer.store.models import Info, Job, User
 
 
 class StoreHelpers:

trailblazer/cli/core.py

@@ -14,7 +14,7 @@
 from trailblazer.environ import environ_email
 from trailblazer.io.controller import ReadFile
 from trailblazer.models import Config
-from trailblazer.store.api import Store
+from trailblazer.store.core import Store
 from trailblazer.store.models import Analysis, User
 
 LOG = logging.getLogger(__name__)

trailblazer/server/ext.py

@@ -1,10 +1,10 @@
 from flask_alchy import Alchy
 
-from trailblazer.store.api import BaseHandler
+from trailblazer.store.core import CoreHandler
 from trailblazer.store.models import Model
 
 
-class TrailblazerAlchy(Alchy, BaseHandler):
+class TrailblazerAlchy(Alchy, CoreHandler):
     pass
 
 

trailblazer/store/base.py

@@ -12,12 +12,15 @@
 
 
 @dataclass
-class BaseHandler_2:
+class BaseHandler:
     """All models in one base class."""
 
     def __init__(self):
         pass
 
+    def setup(self):
+        self.create_all()
+
     def get_query(self, table: Type[Model]) -> Query:
         """Return a query for the given table."""
         return self.query(table)

trailblazer/store/core.py

@@ -1,7 +1,10 @@
+import alchy
+
 from trailblazer.store.crud.create import CreateHandler
 from trailblazer.store.crud.delete import DeleteHandler
 from trailblazer.store.crud.read import ReadHandler
 from trailblazer.store.crud.update import UpdateHandler
+from trailblazer.store.models import Model
 
 
 class CoreHandler(
@@ -14,3 +17,8 @@ class CoreHandler(
 
     def __init__(self):
         pass
+
+
+class Store(alchy.Manager, CoreHandler):
+    def __init__(self, uri: str):
+        super(Store, self).__init__(config=dict(SQLALCHEMY_DATABASE_URI=uri), Model=Model)

trailblazer/store/crud/create.py

@@ -1,11 +1,11 @@
 from datetime import datetime
 
 from trailblazer.constants import TrailblazerStatus
-from trailblazer.store.base import BaseHandler_2
+from trailblazer.store.base import BaseHandler
 from trailblazer.store.models import Analysis, User
 
 
-class CreateHandler(BaseHandler_2):
+class CreateHandler(BaseHandler):
     """Class for creating items in the database."""
 
     def add_pending_analysis(

trailblazer/store/crud/delete.py

@@ -3,13 +3,13 @@
 
 from trailblazer.constants import TrailblazerStatus
 from trailblazer.exc import MissingAnalysis, TrailblazerError
-from trailblazer.store.base import BaseHandler_2
+from trailblazer.store.base import BaseHandler
 from trailblazer.store.models import Analysis
 
 LOG = logging.getLogger(__name__)
 
 
-class DeleteHandler(BaseHandler_2):
+class DeleteHandler(BaseHandler):
     """Class for deleting items in the database."""
 
     def delete_analysis_jobs(self, analysis: Analysis) -> None:

trailblazer/store/crud/read.py

@@ -5,7 +5,7 @@
 from sqlalchemy.orm import Query
 
 from trailblazer.constants import TrailblazerStatus
-from trailblazer.store.base import BaseHandler_2
+from trailblazer.store.base import BaseHandler
 from trailblazer.store.filters.analyses_filters import (
     AnalysisFilter,
     apply_analysis_filter,
@@ -15,7 +15,7 @@
 from trailblazer.store.models import Analysis, Job, User
 
 
-class ReadHandler(BaseHandler_2):
+class ReadHandler(BaseHandler):
     """Class for reading items in the database."""
 
     def get_nr_jobs_with_status_per_category(

trailblazer/store/crud/update.py

@@ -14,13 +14,13 @@
 from trailblazer.apps.tower.api import TowerAPI, get_tower_api
 from trailblazer.constants import SlurmJobStatus, TrailblazerStatus, WorkflowManager
 from trailblazer.exc import MissingAnalysis, TrailblazerError
-from trailblazer.store.base import BaseHandler_2
+from trailblazer.store.base import BaseHandler
 from trailblazer.store.models import Analysis, Job, User
 
 LOG = logging.getLogger(__name__)
 
 
-class UpdateHandler(BaseHandler_2):
+class UpdateHandler(BaseHandler):
     """Class for updating items in the database."""
 
     def update_analysis_jobs(self, analysis: Analysis, jobs: List[dict]) -> None: