test restructuring and cleaning

pepdbagent/db_utils.py

@@ -1,32 +1,26 @@
 import datetime
 import logging
-from typing import Optional, List
+from typing import List, Optional
 
 from sqlalchemy import (
+    TIMESTAMP,
     BigInteger,
     FetchedValue,
+    ForeignKey,
     Result,
     Select,
     String,
+    UniqueConstraint,
     event,
     select,
-    TIMESTAMP,
-    ForeignKey,
-    UniqueConstraint,
 )
 from sqlalchemy.dialects.postgresql import JSON
 from sqlalchemy.engine import URL, create_engine
 from sqlalchemy.exc import ProgrammingError
 from sqlalchemy.ext.compiler import compiles
-from sqlalchemy.orm import (
-    DeclarativeBase,
-    Mapped,
-    Session,
-    mapped_column,
-    relationship,
-)
+from sqlalchemy.orm import DeclarativeBase, Mapped, Session, mapped_column, relationship
 
-from pepdbagent.const import POSTGRES_DIALECT, PKG_NAME
+from pepdbagent.const import PKG_NAME, POSTGRES_DIALECT
 from pepdbagent.exceptions import SchemaError
 
 _LOGGER = logging.getLogger(PKG_NAME)

pepdbagent/models.py

@@ -1,7 +1,8 @@
 # file with pydantic models
-from typing import List, Optional, Union, Dict
-from pydantic import BaseModel, Field, ConfigDict, field_validator
-from peppy.const import CONFIG_KEY, SUBSAMPLE_RAW_LIST_KEY, SAMPLE_RAW_DICT_KEY
+from typing import Dict, List, Optional, Union
+
+from peppy.const import CONFIG_KEY, SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 from pepdbagent.const import DEFAULT_TAG
 

pepdbagent/modules/annotation.py

@@ -3,16 +3,16 @@
 from typing import List, Literal, Optional, Union
 
 from sqlalchemy import and_, func, or_, select
-from sqlalchemy.sql.selectable import Select
 from sqlalchemy.orm import Session
+from sqlalchemy.sql.selectable import Select
 
 from pepdbagent.const import (
     DEFAULT_LIMIT,
     DEFAULT_OFFSET,
     DEFAULT_TAG,
+    LAST_UPDATE_DATE_KEY,
     PKG_NAME,
     SUBMISSION_DATE_KEY,
-    LAST_UPDATE_DATE_KEY,
 )
 from pepdbagent.db_utils import BaseEngine, Projects
 from pepdbagent.exceptions import FilterError, ProjectNotFoundError, RegistryPathError

pepdbagent/modules/namespace.py

@@ -1,20 +1,20 @@
 import logging
-from typing import List, Union, Tuple
 from collections import Counter
 from datetime import datetime, timedelta
+from typing import List, Tuple, Union
 
 from sqlalchemy import distinct, func, or_, select, text
-from sqlalchemy.sql.selectable import Select
 from sqlalchemy.orm import Session
+from sqlalchemy.sql.selectable import Select
 
-from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_OFFSET, PKG_NAME, DEFAULT_LIMIT_INFO
+from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_LIMIT_INFO, DEFAULT_OFFSET, PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects
 from pepdbagent.exceptions import NamespaceNotFoundError
-from pepdbagent.db_utils import Projects, BaseEngine
 from pepdbagent.models import (
+    ListOfNamespaceInfo,
     Namespace,
-    NamespaceList,
     NamespaceInfo,
-    ListOfNamespaceInfo,
+    NamespaceList,
     NamespaceStats,
 )
 from pepdbagent.utils import tuple_converter

pepdbagent/modules/project.py

@@ -1,43 +1,33 @@
 import datetime
 import json
 import logging
-from typing import Union, List, NoReturn, Dict
+from typing import Dict, List, NoReturn, Union
 
-import peppy
-from sqlalchemy import and_, delete, select
-from sqlalchemy.exc import IntegrityError, NoResultFound
-from sqlalchemy.orm import Session
-from sqlalchemy import Select
-from sqlalchemy.orm.attributes import flag_modified
 import numpy as np
-
+import peppy
 from peppy.const import (
-    SAMPLE_RAW_DICT_KEY,
-    SUBSAMPLE_RAW_LIST_KEY,
     CONFIG_KEY,
-    SAMPLE_TABLE_INDEX_KEY,
     SAMPLE_NAME_ATTR,
+    SAMPLE_RAW_DICT_KEY,
+    SAMPLE_TABLE_INDEX_KEY,
+    SUBSAMPLE_RAW_LIST_KEY,
 )
+from sqlalchemy import Select, and_, delete, select
+from sqlalchemy.exc import IntegrityError, NoResultFound
+from sqlalchemy.orm import Session
+from sqlalchemy.orm.attributes import flag_modified
 
-from pepdbagent.const import (
-    DEFAULT_TAG,
-    DESCRIPTION_KEY,
-    NAME_KEY,
-    PKG_NAME,
-    PEPHUB_SAMPLE_ID_KEY,
-)
-
-from pepdbagent.db_utils import Projects, Samples, Subsamples, BaseEngine
+from pepdbagent.const import DEFAULT_TAG, DESCRIPTION_KEY, NAME_KEY, PEPHUB_SAMPLE_ID_KEY, PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects, Samples, Subsamples
 from pepdbagent.exceptions import (
+    PEPDatabaseAgentError,
+    ProjectDuplicatedSampleGUIDsError,
     ProjectNotFoundError,
     ProjectUniqueNameError,
-    PEPDatabaseAgentError,
     SampleTableUpdateError,
-    ProjectDuplicatedSampleGUIDsError,
 )
-from pepdbagent.models import UpdateItems, UpdateModel, ProjectDict
-from pepdbagent.utils import create_digest, registry_path_converter, order_samples, generate_guid
-
+from pepdbagent.models import ProjectDict, UpdateItems, UpdateModel
+from pepdbagent.utils import create_digest, generate_guid, order_samples, registry_path_converter
 
 _LOGGER = logging.getLogger(PKG_NAME)
 

pepdbagent/modules/sample.py

@@ -1,20 +1,16 @@
+import datetime
 import logging
 from typing import Union
-import datetime
 
 import peppy
 from peppy.const import SAMPLE_TABLE_INDEX_KEY
-from sqlalchemy import select, and_
+from sqlalchemy import and_, select
 from sqlalchemy.orm import Session
 from sqlalchemy.orm.attributes import flag_modified
 
-from pepdbagent.const import (
-    DEFAULT_TAG,
-    PKG_NAME,
-)
-from pepdbagent.exceptions import SampleNotFoundError, SampleAlreadyExistsError
-
-from pepdbagent.db_utils import BaseEngine, Samples, Projects
+from pepdbagent.const import DEFAULT_TAG, PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects, Samples
+from pepdbagent.exceptions import SampleAlreadyExistsError, SampleNotFoundError
 from pepdbagent.utils import generate_guid, order_samples
 
 _LOGGER = logging.getLogger(PKG_NAME)

pepdbagent/modules/user.py

@@ -2,17 +2,13 @@
 from typing import Union
 
 from sqlalchemy import and_, delete, select
-from sqlalchemy.orm import Session
 from sqlalchemy.exc import IntegrityError
+from sqlalchemy.orm import Session
 
-from pepdbagent.const import (
-    PKG_NAME,
-)
-
-from pepdbagent.db_utils import BaseEngine, User, Stars, Projects
+from pepdbagent.const import PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects, Stars, User
+from pepdbagent.exceptions import ProjectAlreadyInFavorites, ProjectNotInFavorites
 from pepdbagent.models import AnnotationList, AnnotationModel
-from pepdbagent.exceptions import ProjectNotInFavorites, ProjectAlreadyInFavorites
-
 
 _LOGGER = logging.getLogger(PKG_NAME)
 

pepdbagent/modules/view.py

@@ -1,29 +1,24 @@
 # View of the PEP. In other words, it is a part of the PEP, or subset of the samples in the PEP.
 
 import logging
-from typing import Union, List
+from typing import List, Union
 
 import peppy
-from sqlalchemy import select, and_, delete
-from sqlalchemy.orm import Session
+from sqlalchemy import and_, delete, select
 from sqlalchemy.exc import IntegrityError
+from sqlalchemy.orm import Session
 
-
-from pepdbagent.const import (
-    DEFAULT_TAG,
-    PKG_NAME,
-)
+from pepdbagent.const import DEFAULT_TAG, PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects, Samples, Views, ViewSampleAssociation
 from pepdbagent.exceptions import (
-    ViewNotFoundError,
-    SampleAlreadyInView,
     ProjectNotFoundError,
+    SampleAlreadyInView,
     SampleNotFoundError,
-    ViewAlreadyExistsError,
     SampleNotInViewError,
+    ViewAlreadyExistsError,
+    ViewNotFoundError,
 )
-
-from pepdbagent.db_utils import BaseEngine, Samples, Projects, Views, ViewSampleAssociation
-from pepdbagent.models import ViewAnnotation, CreateViewDictModel, ProjectViews
+from pepdbagent.models import CreateViewDictModel, ProjectViews, ViewAnnotation
 
 _LOGGER = logging.getLogger(PKG_NAME)
 

pepdbagent/pepdbagent.py

@@ -3,8 +3,8 @@
 from pepdbagent.modules.annotation import PEPDatabaseAnnotation
 from pepdbagent.modules.namespace import PEPDatabaseNamespace
 from pepdbagent.modules.project import PEPDatabaseProject
-from pepdbagent.modules.user import PEPDatabaseUser
 from pepdbagent.modules.sample import PEPDatabaseSample
+from pepdbagent.modules.user import PEPDatabaseUser
 from pepdbagent.modules.view import PEPDatabaseView
 
 

pepdbagent/utils.py

@@ -1,9 +1,9 @@
 import datetime
 import json
+import uuid
 from collections.abc import Iterable
 from hashlib import md5
-from typing import Tuple, Union, List
-import uuid
+from typing import List, Tuple, Union
 
 import ubiquerg
 from peppy.const import SAMPLE_RAW_DICT_KEY

tests/conftest.py

@@ -1,9 +1,8 @@
-import peppy
-import pytest
 import os
 
-from sqlalchemy import create_engine
-from sqlalchemy import text
+import peppy
+import pytest
+from sqlalchemy import create_engine, text
 
 from pepdbagent import PEPDatabaseAgent