style: 🎨 fix code style issues with Black

alembic/versions/0defbfc71c59_add_identifier_to_version.py

@@ -5,6 +5,7 @@
 Create Date: 2024-01-05 13:25:15.547450
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op

alembic/versions/29e42ce4be3f_adding_license_text.py

@@ -5,6 +5,7 @@
 Create Date: 2023-12-21 13:34:26.478808
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op

alembic/versions/31703d707dfb_contributor_name_change.py

@@ -5,22 +5,25 @@
 Create Date: 2024-02-20 08:25:11.511833
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op
 import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision: str = '31703d707dfb'
-down_revision: Union[str, None] = '0defbfc71c59'
+revision: str = "31703d707dfb"
+down_revision: Union[str, None] = "0defbfc71c59"
 branch_labels: Union[str, Sequence[str], None] = None
 depends_on: Union[str, Sequence[str], None] = None
 
 
 def upgrade() -> None:
     op.drop_column("dataset_contributor", "name")
-    op.add_column("dataset_contributor", sa.Column("family_name", sa.String, nullable=True))
+    op.add_column(
+        "dataset_contributor", sa.Column("family_name", sa.String, nullable=True)
+    )
     op.add_column("dataset_contributor", sa.Column("given_name", sa.String))
     op.execute("UPDATE dataset_contributor SET given_name = 'name'")
     with op.batch_alter_table("dataset_contributor") as batch_op:

alembic/versions/72ac2b020c7c_delete_dataset_readme_table.py

@@ -5,6 +5,7 @@
 Create Date: 2023-11-08 15:47:00.205940
 
 """
+
 from typing import Sequence, Union
 
 import alembic

apis/__init__.py

@@ -1,4 +1,5 @@
 """Initialize the api system for the backend"""
+
 from flask_restx import Api, Resource
 
 from apis.dataset_metadata_namespace import api as dataset_metadata_namespace

apis/authentication.py

@@ -1,6 +1,7 @@
 """This module is used to authenticate users to the system and
 handle few authentication errors. Also, it sets token for logged user
 along with expiration date"""
+
 import datetime
 import importlib
 import os

apis/dataset_metadata/dataset_alternate_identifier.py

@@ -1,4 +1,5 @@
 """API endpoints for dataset alternate identifier"""
+
 from typing import Any, Union
 
 from flask import Response, request

apis/dataset_metadata/dataset_consent.py

@@ -1,4 +1,5 @@
 """API for dataset consent metadata"""
+
 from flask import request
 from flask_restx import Resource, fields
 from jsonschema import ValidationError, validate

apis/dataset_metadata/dataset_contributor.py

@@ -1,4 +1,5 @@
 """API for dataset contributor metadata"""
+
 from typing import Any, Union
 
 from flask import Response, request
@@ -57,10 +58,7 @@ def post(self, study_id: int, dataset_id: int):
                         "type": "string",
                         "minLength": 1,
                     },
-                    "family_name": {
-                        "type":
-                            ["string", "null"]
-                    },
+                    "family_name": {"type": ["string", "null"]},
                     "name_identifier": {
                         "type": "string",
                         "minLength": 1,
@@ -201,10 +199,7 @@ def post(self, study_id: int, dataset_id: int):
                         "type": "string",
                         "minLength": 1,
                     },
-                    "family_name": {
-                        "type":
-                            ["string", "null"]
-                    },
+                    "family_name": {"type": ["string", "null"]},
                     "name_identifier": {
                         "type": "string",
                         "minLength": 1,

apis/dataset_metadata/dataset_date.py

@@ -1,4 +1,5 @@
 """APIs for dataset date metadata"""
+
 from typing import Any, Union
 
 from flask import Response, request

apis/dataset_metadata/dataset_funder.py

@@ -1,4 +1,5 @@
 """API endpoints for dataset funder"""
+
 from typing import Any, Union
 
 from flask import Response, request

apis/dataset_metadata/dataset_other.py

@@ -1,4 +1,5 @@
 """API endpoints for other dataset metadata"""
+
 from flask import request
 from flask_restx import Resource, fields
 from jsonschema import ValidationError, validate

apis/dataset_metadata/dataset_record_keys.py

@@ -1,4 +1,5 @@
 """API endpoints for dataset record keys"""
+
 from flask import request
 from flask_restx import Resource, fields
 from jsonschema import ValidationError, validate

apis/dataset_metadata/dataset_related_item.py

@@ -1,4 +1,5 @@
 """API for dataset related item"""
+
 from typing import Any, Union
 
 from flask import Response, request

apis/dataset_metadata/dataset_title.py

@@ -1,4 +1,5 @@
 """API for dataset title metadata"""
+
 from typing import Any, Union
 
 from flask import Response, request

apis/file.py

@@ -1,4 +1,5 @@
 """APIs for study files"""
+
 import importlib
 import os
 import uuid

apis/study_metadata/study_arm.py

@@ -1,4 +1,5 @@
 """API routes for study arm metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_available_ipd.py

@@ -1,4 +1,5 @@
 """API routes for study available ipd metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_contact.py

@@ -1,4 +1,5 @@
 """API routes for study contact metadata"""
+
 import typing
 
 from email_validator import EmailNotValidError, validate_email

apis/study_metadata/study_description.py

@@ -1,4 +1,5 @@
 """API routes for study description metadata"""
+
 from flask import request
 from flask_restx import Resource, fields
 from jsonschema import ValidationError, validate

apis/study_metadata/study_design.py

@@ -1,4 +1,5 @@
 """API routes for study design metadata"""
+
 import typing
 
 from flask import request

apis/study_metadata/study_eligibility.py

@@ -1,4 +1,5 @@
 """API routes for study eligibility metadata"""
+
 from flask import request
 from flask_restx import Resource, fields
 from jsonschema import ValidationError, validate

apis/study_metadata/study_identification.py

@@ -1,4 +1,5 @@
 """API routes for study identification metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_intervention.py

@@ -1,4 +1,5 @@
 """API routes for study intervention metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_ipdsharing.py

@@ -1,4 +1,5 @@
 """API routes for study ipdsharing metadata"""
+
 import typing
 
 from flask import request

apis/study_metadata/study_link.py

@@ -1,4 +1,5 @@
 """API routes for study link metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_location.py

@@ -1,4 +1,5 @@
 """API routes for study location metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_other.py

@@ -1,4 +1,5 @@
 """API routes for study other metadata"""
+
 import typing
 
 from flask import request

apis/study_metadata/study_overall_official.py

@@ -1,4 +1,5 @@
 """API routes for study overall official metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_reference.py

@@ -1,4 +1,5 @@
 """API routes for study reference metadata"""
+
 import typing
 
 from flask import Response, request

apis/study_metadata/study_sponsors_collaborators.py

@@ -1,4 +1,5 @@
 """API routes for study sponsors and collaborators metadata"""
+
 import typing
 
 from flask import request

apis/study_metadata/study_status.py

@@ -1,4 +1,5 @@
 """API routes for study status metadata"""
+
 import typing
 
 from flask import request

apis/utils.py

@@ -1,4 +1,5 @@
 """Utils Endpoints"""
+
 from flask import request
 from flask_restx import Namespace, Resource
 

apis/utils_namespace.py

@@ -1,4 +1,5 @@
 """Namespace for utils operations"""
+
 from flask_restx import Namespace
 
 api = Namespace("Utils", description="utils operations", path="/")

app.py

@@ -1,4 +1,5 @@
 """Entry point for the application."""
+
 import datetime
 import importlib
 import logging

config.py

@@ -1,4 +1,5 @@
 """Configuration for the application."""
+
 from os import environ
 from pathlib import Path
 from dotenv import dotenv_values

core/__init__.py

@@ -1,4 +1,3 @@
 """Core package for the application."""
 
-
 from . import utils  # noqa: F401

core/utils.py

@@ -1,4 +1,5 @@
 """Utils for core"""
+
 import requests
 
 

model/dataset_metadata/dataset_related_item.py

@@ -63,33 +63,51 @@ def to_dict(self):
             ],
             "creators": [c.to_dict() for c in creators],
             "contributors": [c.to_dict() for c in contributors],
-            "publication_year": self.dataset_related_item_other.publication_year
-            if self.dataset_related_item_other
-            else None,
-            "volume": self.dataset_related_item_other.volume
-            if self.dataset_related_item_other
-            else None,
-            "issue": self.dataset_related_item_other.issue
-            if self.dataset_related_item_other
-            else None,
-            "number_value": self.dataset_related_item_other.number_value
-            if self.dataset_related_item_other
-            else None,
-            "number_type": self.dataset_related_item_other.number_type
-            if self.dataset_related_item_other
-            else None,
-            "first_page": self.dataset_related_item_other.first_page
-            if self.dataset_related_item_other
-            else None,
-            "last_page": self.dataset_related_item_other.last_page
-            if self.dataset_related_item_other
-            else None,
-            "publisher": self.dataset_related_item_other.publisher
-            if self.dataset_related_item_other
-            else None,
-            "edition": self.dataset_related_item_other.edition
-            if self.dataset_related_item_other
-            else None,
+            "publication_year": (
+                self.dataset_related_item_other.publication_year
+                if self.dataset_related_item_other
+                else None
+            ),
+            "volume": (
+                self.dataset_related_item_other.volume
+                if self.dataset_related_item_other
+                else None
+            ),
+            "issue": (
+                self.dataset_related_item_other.issue
+                if self.dataset_related_item_other
+                else None
+            ),
+            "number_value": (
+                self.dataset_related_item_other.number_value
+                if self.dataset_related_item_other
+                else None
+            ),
+            "number_type": (
+                self.dataset_related_item_other.number_type
+                if self.dataset_related_item_other
+                else None
+            ),
+            "first_page": (
+                self.dataset_related_item_other.first_page
+                if self.dataset_related_item_other
+                else None
+            ),
+            "last_page": (
+                self.dataset_related_item_other.last_page
+                if self.dataset_related_item_other
+                else None
+            ),
+            "publisher": (
+                self.dataset_related_item_other.publisher
+                if self.dataset_related_item_other
+                else None
+            ),
+            "edition": (
+                self.dataset_related_item_other.edition
+                if self.dataset_related_item_other
+                else None
+            ),
             "identifiers": [
                 i.to_dict()
                 for i in self.dataset_related_item_identifier  # type: ignore

model/study.py

@@ -165,9 +165,9 @@ def to_dict(self):
             "created_at": self.created_at,
             "updated_on": self.updated_on,
             "size": self.study_other.size if self.study_other else None,
-            "description": self.study_description.brief_summary
-            if self.study_description
-            else None,
+            "description": (
+                self.study_description.brief_summary if self.study_description else None
+            ),
             "owner": owner.to_dict()["id"] if owner else None,
             "role": contributor_permission.to_dict()["role"],
         }

model/study_contributor.py

@@ -30,9 +30,9 @@ def __init__(self, study: Study, user: User, permission):
     def to_dict(self):
         return {
             "id": self.user_id,
-            "name": self.user.user_details.first_name
-            if self.user.user_details
-            else None,
+            "name": (
+                self.user.user_details.first_name if self.user.user_details else None
+            ),
             "email_address": self.user.email_address,
             "orcid": self.user.user_details.orcid if self.user.user_details else None,
             "role": self.permission,