FIX #72

.gitignore

@@ -11,6 +11,9 @@ tramp
 # emacs projectiles files
 .projectile
 
+# directory configuration
+.dir-locals.el
+
 # backup
 *.bak
 *.gho

server/src/scimodom/api/queries.py

@@ -1,11 +1,7 @@
-import os
 import json
-
-import scimodom.utils.specifications as specs
-
-# import scimodom.database.queries as queries
-
+import os
 from pathlib import Path
+
 from flask import request
 from flask_cors import cross_origin
 from sqlalchemy import select, func, and_, or_, not_, literal_column
@@ -28,7 +24,10 @@
     Selection,
     GenomicAnnotation,
 )
-
+from scimodom.services.importer import BEDImporter
+from scimodom.utils.models import records_factory
+from scimodom.utils.operations import get_op
+import scimodom.utils.specifications as specs
 
 prop_comparators = {
     "startsWith": "istartswith",
@@ -380,10 +379,6 @@ def get_dataset():
 def get_comparison(step):
     """Retrieve ..."""
 
-    from scimodom.services.importer import BEDImporter
-    from scimodom.utils.operations import get_op
-    from scimodom.utils.models import records_factory
-
     # API call in compare, then pass as params to SPA components
     # but sending all datasets may be too large?
     # final call after dataset selection + query
@@ -501,7 +496,7 @@ def upload_file():
 
     # TODO: define app.config['UPLOAD_PATH'] = UPLOAD_FOLDER
     # ALLOWED_EXTENSIONS are dealt with PrimeVue FileUpload
-
+    # PEP8 import
     from werkzeug.utils import secure_filename
 
     upload = os.getenv("UPLOAD_PATH")

server/src/scimodom/app.py

@@ -1,13 +1,16 @@
+from logging.config import dictConfig
+
+from flask_cors import CORS
+from sqlalchemy.orm import scoped_session
+
+from scimodom.api import api
 from scimodom.app_singleton import create_app_singleton
+from scimodom.database.database import make_session, init
+from scimodom.frontend import frontend
 
 
 def create_app():
     """Function factory to create Flask app."""
-    from logging.config import dictConfig
-    from flask_cors import CORS
-
-    from sqlalchemy.orm import scoped_session
-    from scimodom.database.database import make_session, init
 
     app = create_app_singleton()
     CORS(app)
@@ -20,9 +23,6 @@ def create_app():
     app.session = scoped_session(session)
     init(engine, lambda: app.session)
 
-    from scimodom.frontend import frontend
-    from scimodom.api import api
-
     app.register_blueprint(api, url_prefix="/api/v0")
     app.register_blueprint(frontend, url_prefix="/")
 

server/src/scimodom/config.py

@@ -1,10 +1,9 @@
-import os
 import logging
-
-from typing import ClassVar
+import os
 from pathlib import Path
-from dotenv import load_dotenv
+from typing import ClassVar
 
+from dotenv import load_dotenv
 
 DEFAULT_FRONTEND_PATH = (
     Path(__file__).parent.parent.parent.parent.joinpath("client").joinpath("dist")

server/src/scimodom/database/database.py

@@ -1,5 +1,6 @@
 import os
 from typing import Callable, Optional
+
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker, DeclarativeBase, Session
 from sqlalchemy.engine import Engine

server/src/scimodom/database/maintenance/add_all.py

@@ -10,22 +10,20 @@
 to the DB in the short-term.
 """
 
-import os
-import json
-import logging
-
-import scimodom.utils.utils as utils
-
-from pathlib import Path
 from argparse import ArgumentParser, SUPPRESS
-from concurrent.futures import ProcessPoolExecutor
 from collections import defaultdict
+from concurrent.futures import ProcessPoolExecutor
 from functools import partial
+import json
+import logging
+import os
+from pathlib import Path
 from subprocess import Popen, PIPE
 
 from scimodom.config import Config
 from scimodom.database.database import make_session
 from scimodom.services.project import ProjectService
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)
 

server/src/scimodom/database/maintenance/add_dataset.py

@@ -5,19 +5,14 @@
 project.
 """
 
+from argparse import ArgumentParser, SUPPRESS
 import logging
-
-import scimodom.utils.utils as utils
-import scimodom.database.queries as queries
-
 from pathlib import Path
+
 from sqlalchemy import select
-from argparse import ArgumentParser, SUPPRESS
 
 from scimodom.config import Config
 from scimodom.database.database import make_session
-from scimodom.services.dataset import DataService
-from scimodom.services.annotation import AnnotationService
 from scimodom.database.models import (
     Project,
     Taxa,
@@ -28,6 +23,10 @@
     Organism,
     Selection,
 )
+import scimodom.database.queries as queries
+from scimodom.services.annotation import AnnotationService
+from scimodom.services.dataset import DataService
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)
 

server/src/scimodom/database/maintenance/add_project.py

@@ -6,17 +6,15 @@
 and upsert all DB tables.
 """
 
+from argparse import ArgumentParser, SUPPRESS
 import json
 import logging
 
-import scimodom.utils.utils as utils
-
-from argparse import ArgumentParser, SUPPRESS
-
 from scimodom.config import Config
 from scimodom.database.database import make_session
 from scimodom.services.project import ProjectService
 from scimodom.services.setup import SetupService
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)
 

server/src/scimodom/database/maintenance/upsert.py

@@ -4,15 +4,14 @@
 This script allows to upsert selected or all DB tables.
 """
 
-import sys
+from argparse import ArgumentParser, SUPPRESS
 import logging
+import sys
 
-import scimodom.utils.utils as utils
-
-from argparse import ArgumentParser, SUPPRESS
 from scimodom.config import Config
 from scimodom.database.database import make_session
 from scimodom.services.setup import SetupService
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)
 

server/src/scimodom/database/models.py

@@ -1,12 +1,11 @@
-from scimodom.database.database import Base
-
 from datetime import datetime
-
 from typing import List, Optional
 
 from sqlalchemy import String, Text, DateTime, ForeignKey, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+from scimodom.database.database import Base
+
 
 class Modomics(Base):
     """Modified residues"""

server/src/scimodom/database/queries.py

@@ -1,8 +1,8 @@
 # template queries
-
 from sqlalchemy import select
-from scimodom.database.models import AssemblyVersion, AnnotationVersion
 
+from scimodom.database.models import AssemblyVersion, AnnotationVersion
+import scimodom.utils.utils as utils
 
 # -- special queries
 
@@ -20,7 +20,6 @@ def get_annotation_version():
 
 def query_column_where(model, column, filters=dict()):
     # query one column w/ or w/o filters
-    import scimodom.utils.utils as utils
 
     try:
         query = select(getattr(model, column))

server/src/scimodom/frontend.py

@@ -4,17 +4,18 @@
 #
 #
 from flask import Blueprint
+
 from scimodom.config import Config
 
 frontend = Blueprint("frontend", __name__, static_folder=Config.FRONTEND_PATH)
 
 
-@frontend.route('/')
+@frontend.route("/")
 def index():
-    return frontend.send_static_file('index.html')
+    return frontend.send_static_file("index.html")
 
 
-@frontend.route('/<path:filename>')
+@frontend.route("/<path:filename>")
 def assets(filename):
     print(filename)
     return frontend.send_static_file(filename)

server/src/scimodom/services/annotation.py

@@ -1,23 +1,29 @@
 #! /usr/bin/env python3
 
-import os
+import gzip
 import logging
-
-import scimodom.database.queries as queries
-
+import os
 from pathlib import Path
+from posixpath import join as urljoin
 from typing import ClassVar
+import zlib
+
+import requests  # type: ignore
 from sqlalchemy import select, insert
 from sqlalchemy.orm import Session
 
 from scimodom.config import Config
+import scimodom.database.queries as queries
 from scimodom.database.models import (
     Data,
     Dataset,
     Annotation,
     AnnotationVersion,
     GenomicAnnotation,
 )
+from scimodom.utils.models import records_factory
+from scimodom.utils.operations import get_genomic_annotation
+import scimodom.utils.specifications as specs
 
 # T = TypeVar('T', bound='Parent')
 
@@ -248,15 +254,6 @@ def create_annotation(
         :param fmt: Annotation file format
         :type fmt: str
         """
-        import gzip
-        import zlib
-        import requests  # type: ignore
-
-        import scimodom.utils.specifications as specs
-
-        from sqlalchemy import insert
-
-        from posixpath import join as urljoin
 
         # from scimodom.utils.operations import get_genomic_annotation
 
@@ -390,8 +387,6 @@ def annotate_data(self):
         See scimodom.utils.operations.get_genomic_annotation
 
         """
-        from scimodom.utils.operations import get_genomic_annotation
-        from scimodom.utils.models import records_factory
 
         query = select(
             Data.chrom,

server/src/scimodom/services/dataset.py

@@ -1,16 +1,12 @@
 #! /usr/bin/env python3
 
 import logging
-
-import scimodom.utils.utils as utils
-import scimodom.utils.specifications as specs
-import scimodom.database.queries as queries
-
 from pathlib import Path
 from typing import TextIO, ClassVar, Any
+
 from sqlalchemy import select, func
 from sqlalchemy.orm import Session
-from scimodom.services.importer import EUFImporter
+
 from scimodom.database.models import (
     Data,
     Dataset,
@@ -22,6 +18,10 @@
     Organism,
     Assembly,
 )
+import scimodom.database.queries as queries
+from scimodom.services.importer import EUFImporter
+import scimodom.utils.specifications as specs
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)
 

server/src/scimodom/services/importer.py

@@ -1,21 +1,20 @@
 #! /usr/bin/env python3
 
-import re
-import logging
 import itertools
-
-import scimodom.utils.utils as utils
-import scimodom.database.queries as queries
-import scimodom.utils.specifications as specs
-
+import logging
 from pathlib import Path
+import re
 from typing import TextIO, Iterable, ClassVar, Any
+
 from sqlalchemy import insert, select
 from sqlalchemy.orm import Session
 
-from scimodom.services.annotation import AnnotationService
-from scimodom.database.models import Data, Dataset
 from scimodom.database.database import Base
+from scimodom.database.models import Data, Dataset
+import scimodom.database.queries as queries
+from scimodom.services.annotation import AnnotationService
+import scimodom.utils.specifications as specs
+import scimodom.utils.utils as utils
 
 logger = logging.getLogger(__name__)