Restructure files

config_parser.py → config/config_parser.py

@@ -23,7 +23,7 @@ def get_conn_str():
     """
     Get database related configurations
     """
-    config = os.environ.get('DB_CONFIG', 'database.ini')
+    config = os.environ.get('DB_CONFIG', '../database.ini')
     db_info = parse_config(config)
     hostname = db_info.get("host")
     database = db_info.get("database")
@@ -34,17 +34,17 @@ def get_conn_str():
     return conn_str
 
 
-def security_API_key():
-    config = os.environ.get('DB_CONFIG', 'database.ini')
-    security_info = parse_info(config, 'security')
-    apikey = security_info.get("apikey")
-    return apikey
+# def security_API_key():
+#     config = os.environ.get('DB_CONFIG', '../database.ini')
+#     security_info = parse_config(config, 'security')
+#     apikey = security_info.get("apikey")
+#     return apikey
 
 
 def get_api_configs():
     """
     Get API related configurations
     """
-    config = os.environ.get('DB_CONFIG', 'database.ini')
+    config = os.environ.get('DB_CONFIG', '../database.ini')
     api_configs = parse_config(config, "api")
     return api_configs

index.py → config/index.py

@@ -1,4 +1,4 @@
-from app.config.database import SessionLocal
+from config.database import SessionLocal
 
 
 # Helper function to get database session

logging.ini

@@ -21,7 +21,7 @@ args=(sys.stdout,)
 class=handlers.TimedRotatingFileHandler
 level=DEBUG
 formatter=fileFormatter
-args=('logs/xi_mzidentml_converter.log', 'midnight', 1, 30, 'utf-8')
+args=('../logs/xi_mzidentml_converter.log', 'midnight', 1, 30, 'utf-8')
 
 [formatter_consoleFormatter]
 format=%(asctime)s - %(name)s - %(levelname)s - %(message)s

app/models/analysiscollection.py → models/analysiscollection.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, ForeignKeyConstraint, Integer
-from app.models.base import Base
+from models.base import Base
 
 
 class AnalysisCollection(Base):

app/models/dbsequence.py → models/dbsequence.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, Integer
-from app.models.base import Base
+from models.base import Base
 
 
 class DBSequence(Base):

app/models/enzyme.py → models/enzyme.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
-from sqlalchemy import ForeignKey, Text, Integer, BOOLEAN, ForeignKeyConstraint, Integer
-from app.models.base import Base
+from sqlalchemy import ForeignKey, Text, BOOLEAN, ForeignKeyConstraint, Integer
+from models.base import Base
 
 
 class Enzyme(Base):

app/models/modifiedpeptide.py → models/modifiedpeptide.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, Integer, JSON, FLOAT
-from app.models.base import Base
+from models.base import Base
 from typing import Optional, Any
 
 class ModifiedPeptide(Base):

app/models/peptideevidence.py → models/peptideevidence.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, Integer, BOOLEAN, ForeignKeyConstraint
-from app.models.base import Base
+from models.base import Base
 
 
 class PeptideEvidence(Base):

app/models/projectdetail.py → models/projectdetail.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy import ForeignKey, Text, Integer
-from app.models.base import Base
+from sqlalchemy import Text, Integer
+from models.base import Base
 
 
 class ProjectDetail(Base):

app/models/projectsubdetail.py → models/projectsubdetail.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy import ForeignKey, Text, Integer, Boolean
-from app.models.base import Base
+from models.base import Base
 
 
 class ProjectSubDetail(Base):

app/models/searchmodification.py → models/searchmodification.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, BOOLEAN, BIGINT, FLOAT, JSON, ForeignKeyConstraint, Integer
-from app.models.base import Base
+from models.base import Base
 from typing import Any
 
 

app/models/spectrum.py → models/spectrum.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, LargeBinary, SMALLINT, FLOAT, Integer
-from app.models.base import Base
+from models.base import Base
 
 
 class Spectrum(Base):

app/models/spectrumidentification.py → models/spectrumidentification.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, FLOAT, JSON, BOOLEAN, Integer, ForeignKeyConstraint
-from app.models.base import Base
+from models.base import Base
 from typing import Optional, Any
 
 

app/models/spectrumidentificationprotocol.py → models/spectrumidentificationprotocol.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column
 from sqlalchemy import ForeignKey, Text, JSON, Integer, Float
-from app.models.base import Base
+from models.base import Base
 from typing import Optional, Any
 
 

app/models/upload.py → models/upload.py

@@ -1,6 +1,6 @@
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy import ForeignKey, Text, JSON, BOOLEAN, TIMESTAMP, func, Integer
-from app.models.base import Base
+from sqlalchemy.orm import Mapped, mapped_column
+from sqlalchemy import Text, JSON, BOOLEAN, TIMESTAMP, func, Integer
+from models.base import Base
 from typing import Optional, Any
 import datetime
 

parser/api_writer.py

@@ -1,7 +1,7 @@
 import traceback
 import requests
 
-from config_parser import get_api_configs
+from config.config_parser import get_api_configs
 from parser.writer import Writer
 
 

create_db_schema.py → parser/database/create_db_schema.py

@@ -3,8 +3,7 @@
 from sqlalchemy import create_engine
 from sqlalchemy_utils import database_exists, drop_database, create_database
 
-from app.models.base import Base
-from app.models import *
+from models.base import Base
 
 
 def create_db(connection_str):
@@ -27,7 +26,7 @@ def create_schema(connection_str):
 
 if __name__ == "__main__":
     try:
-        from config_parser import get_conn_str
+        from config.config_parser import get_conn_str
     except ModuleNotFoundError:
         raise ModuleNotFoundError(
             'Database credentials missing! '

parser/database_writer.py

@@ -1,6 +1,6 @@
 from sqlalchemy import create_engine, MetaData
 from sqlalchemy import Table
-from create_db_schema import create_schema
+from parser.database.create_db_schema import create_schema
 from sqlalchemy_utils import database_exists
 
 

parser/process_dataset.py

@@ -13,10 +13,9 @@
 from urllib.parse import urlparse
 
 from parser.MzIdParser import MzIdParser
-from parser.writer import Writer
 import logging.config
-from parser.api_writer import Writer, APIWriter
-from config_parser import get_conn_str
+from parser.api_writer import APIWriter
+from config.config_parser import get_conn_str
 from parser.database_writer import DatabaseWriter
 
 logging.config.fileConfig("../logging.ini")

setup.py

@@ -24,7 +24,7 @@ def get_version(rel_path):
 
 setup(
     name="xi-mzidentml-converter",
-    version=get_version("app/__init__.py"),
+    version="0.1.12",
     description="xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a relational database (PostgreSQL or SQLite) using sqlalchemy.",
     long_description_content_type="text/markdown",
     long_description=long_description,

tests/db_pytest_fixtures.py

@@ -1,4 +1,4 @@
-from create_db_schema import create_schema, create_db, drop_db
+from parser.database.create_db_schema import create_schema, create_db, drop_db
 import pytest
 from sqlalchemy import create_engine