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Python lint #133

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Python lint #133

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68c68c1
add flask-testing dependency
xinaesthete Feb 7, 2025
4866a3f
use ResponseReturnValue type where appropriate
xinaesthete Feb 7, 2025
a815dd9
allow test to work from different working directory
xinaesthete Feb 7, 2025
f354444
fix some basic str type checking
xinaesthete Feb 7, 2025
dfde36a
update module reference to dbservice
xinaesthete Feb 7, 2025
e35ea81
update dbmodels to use DeclarativeBase and mapped_column
xinaesthete Feb 7, 2025
68e9100
add 'Mapped' type annotations to db models
xinaesthete Feb 7, 2025
4d306e1
change dbservice to not use kwargs, pacify type check
xinaesthete Feb 7, 2025
42d982b
change relationship and ForeignKey in line with modern usage
xinaesthete Feb 7, 2025
841579a
pacify type-check that doesn't understand model constructor args
xinaesthete Feb 7, 2025
4957046
wip changes to test_projects so they don't interfere with running test
xinaesthete Feb 7, 2025
08761f8
add server_debug.py helper
xinaesthete Feb 10, 2025
0d93688
some comments and a type annotation
xinaesthete Feb 13, 2025
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216 changes: 111 additions & 105 deletions python/mdvtools/dbutils/dbmodels.py
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Original file line number Diff line number Diff line change
@@ -1,47 +1,53 @@
from flask_sqlalchemy import SQLAlchemy

Check failure on line 1 in python/mdvtools/dbutils/dbmodels.py

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GitHub Actions / pyright (3.12, 1.1.343) 

Import "flask_sqlalchemy" could not be resolved (reportMissingImports)
from datetime import datetime
from sqlalchemy import String, Integer, DateTime, Boolean, Text, JSON, ForeignKey

Check failure on line 3 in python/mdvtools/dbutils/dbmodels.py

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Import "sqlalchemy" could not be resolved (reportMissingImports)
from sqlalchemy.orm import Mapped, mapped_column, DeclarativeBase, relationship

Check failure on line 4 in python/mdvtools/dbutils/dbmodels.py

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GitHub Actions / pyright (3.12, 1.1.343) 

Import "sqlalchemy.orm" could not be resolved (reportMissingImports)
from typing import Any
# https://flask-sqlalchemy.readthedocs.io/en/stable/models/
class Base(DeclarativeBase):
pass

db = SQLAlchemy()
db = SQLAlchemy(model_class=Base)

class User(db.Model):
__tablename__ = 'users'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
email = db.Column(db.String(255), unique=True, nullable=False, default='')
confirmed_at = db.Column(db.DateTime, nullable=True)
password = db.Column(db.String(255), nullable=False, default='')
is_active = db.Column(db.Boolean, nullable=False, default=False)
first_name = db.Column(db.String(50), nullable=False, default='')
last_name = db.Column(db.String(50), nullable=False, default='')
administrator = db.Column(db.Boolean, nullable=False, default=False)
institution = db.Column(db.Text, nullable=True)
projects = db.relationship('UserProject', backref='user', lazy=True)
jobs = db.relationship('Job', backref='user', lazy=True)
permissions = db.relationship('Permission', backref='user', lazy=True)
preferences = db.relationship('UserPreference', backref='user', lazy=True)
#shared_objects = db.relationship('SharedObject', foreign_keys='SharedObject.shared_with', backref='shared_with_user', lazy=True)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
email: Mapped[str] = mapped_column(String(255), unique=True, nullable=False, default='')
confirmed_at: Mapped[datetime] = mapped_column(DateTime, nullable=True)
password: Mapped[str] = mapped_column(String(255), nullable=False, default='')
is_active: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
first_name: Mapped[str] = mapped_column(String(50), nullable=False, default='')
last_name: Mapped[str] = mapped_column(String(50), nullable=False, default='')
administrator: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
institution: Mapped[str] = mapped_column(Text, nullable=True)
projects = relationship('UserProject', backref='user', lazy=True)
jobs = relationship('Job', backref='user', lazy=True)
permissions = relationship('Permission', backref='user', lazy=True)
preferences = relationship('UserPreference', backref='user', lazy=True)
#shared_objects = relationship('SharedObject', foreign_keys='SharedObject.shared_with', backref='shared_with_user', lazy=True)

class Project(db.Model):
__tablename__ = 'projects'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
name = db.Column(db.String(255), nullable=False, default='unnamed_project')
path = db.Column(db.String(1024), nullable=False, unique=True)
created_timestamp = db.Column(db.DateTime, nullable=False, default=datetime.now)
is_deleted = db.Column(db.Boolean, nullable=False, default=False)
deleted_timestamp = db.Column(db.DateTime, nullable=True)
update_timestamp = db.Column(db.DateTime, nullable=False, default=datetime.now)
accessed_timestamp = db.Column(db.DateTime, nullable=False, default=datetime.now)
owner = db.Column(db.Integer)
type = db.Column(db.Text)
data = db.Column(db.JSON)
is_public = db.Column(db.Boolean, nullable=False, default=False)
date_made_public = db.Column(db.DateTime)
status = db.Column(db.Text)
genome = db.Column(db.String, db.ForeignKey('genomes.name'))
parent = db.Column(db.Integer)
description = db.Column(db.Text)
access_level = db.Column(db.String(50), nullable=False, default='editable') # Default access level
users = db.relationship('UserProject', backref='project', lazy=True)
files = db.relationship('File', backref='project', lazy=True)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
name: Mapped[str] = mapped_column(String(255), nullable=False, default='unnamed_project')
path: Mapped[str] = mapped_column(String(1024), nullable=False, unique=True)
created_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
is_deleted: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
deleted_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=True)
update_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
accessed_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
owner: Mapped[int] = mapped_column(Integer)
type: Mapped[str] = mapped_column(Text)
data: Mapped[Any] = mapped_column(JSON)
is_public: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
date_made_public: Mapped[datetime] = mapped_column(DateTime)
status: Mapped[str] = mapped_column(Text)
genome: Mapped[str] = mapped_column(String, ForeignKey('genomes.name'))
parent: Mapped[str] = mapped_column(Integer)
description: Mapped[str] = mapped_column(Text)
access_level: Mapped[str] = mapped_column(String(50), nullable=False, default='editable') # Default access level
users = relationship('UserProject', backref='project', lazy=True)
files = relationship('File', backref='project', lazy=True)
Comment on lines +31 to +50
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⚠️ Potential issue

Project model typed columns.

Be mindful of line 46:

parent: Mapped[str] = mapped_column(Integer)

The type annotation (str) conflicts with the column type (Integer). This may cause runtime confusion.

-    parent: Mapped[str] = mapped_column(Integer)
+    parent: Mapped[int] = mapped_column(Integer)


__table_args__ = (
db.Index('idx_projects_genome', 'genome'),
Expand All @@ -51,100 +57,100 @@

class File(db.Model):
__tablename__ = 'files'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
name = db.Column(db.String(255), nullable=False)
file_path = db.Column(db.String(255), nullable=False, unique=True)
upload_timestamp = db.Column(db.DateTime, nullable=False, default=datetime.now)
update_timestamp = db.Column(db.DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
project_id = db.Column(db.Integer, db.ForeignKey('projects.id'), nullable=False)
#project = db.relationship('Project', backref=db.backref('files', lazy=True))
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
name: Mapped[str] = mapped_column(String(255), nullable=False)
file_path: Mapped[str] = mapped_column(String(255), nullable=False, unique=True)
upload_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
update_timestamp: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
project_id: Mapped[int] = mapped_column(Integer, ForeignKey('projects.id'), nullable=False)
#project = relationship('Project', backref=db.backref('files', lazy=True))

class UserProject(db.Model):
__tablename__ = 'user_projects'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
user_id = db.Column(db.Integer, db.ForeignKey('users.id'), nullable=False)
project_id = db.Column(db.Integer, db.ForeignKey('projects.id'), nullable=False)
can_read = db.Column(db.Boolean, nullable=False, default=False)
can_write = db.Column(db.Boolean, nullable=False, default=False)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
user_id: Mapped[int] = mapped_column(Integer, ForeignKey('users.id'), nullable=False)
project_id: Mapped[int] = mapped_column(Integer, ForeignKey('projects.id'), nullable=False)
can_read: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
can_write: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)

class Genome(db.Model):
__tablename__ = 'genomes'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
name = db.Column(db.String(50), nullable=False, unique=True)
label = db.Column(db.Text)
data = db.Column(db.JSON)
database = db.Column(db.Text)
date_added = db.Column(db.DateTime, nullable=False, default=datetime.now)
connections = db.Column(db.Integer)
icon = db.Column(db.Text)
is_public = db.Column(db.Boolean, nullable=False, default=True)
chrom_sizes = db.Column(db.JSON)
small_icon = db.Column(db.Text)
projects = db.relationship('Project', backref='genomes', lazy=True)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
name: Mapped[str] = mapped_column(String(50), nullable=False, unique=True)
label: Mapped[str] = mapped_column(Text)
data: Mapped[Any] = mapped_column(JSON)
database: Mapped[str] = mapped_column(Text)
date_added: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
connections: Mapped[int] = mapped_column(Integer)
icon: Mapped[str] = mapped_column(Text)
is_public: Mapped[bool] = mapped_column(Boolean, nullable=False, default=True)
chrom_sizes: Mapped[Any] = mapped_column(JSON)
small_icon: Mapped[str] = mapped_column(Text)
projects = relationship('Project', backref='genomes', lazy=True)

class Job(db.Model):
__tablename__ = 'jobs'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
inputs = db.Column(db.JSON)
user_id = db.Column(db.Integer, db.ForeignKey('users.id'), nullable=True)
outputs = db.Column(db.JSON)
sent_on = db.Column(db.DateTime, nullable=False, default=datetime.now)
status = db.Column(db.String(200))
class_name = db.Column(db.String(200))
genome = db.Column(db.String(100))
finished_on = db.Column(db.DateTime)
is_deleted = db.Column(db.Boolean, nullable=False, default=False)
type = db.Column(db.String(200))
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
inputs: Mapped[Any] = mapped_column(JSON)
user_id: Mapped[int] = mapped_column(Integer, ForeignKey('users.id'), nullable=True)
outputs: Mapped[Any] = mapped_column(JSON)
sent_on: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
status: Mapped[str] = mapped_column(String(200))
class_name: Mapped[str] = mapped_column(String(200))
genome: Mapped[str] = mapped_column(String(100))
finished_on: Mapped[datetime] = mapped_column(DateTime)
is_deleted: Mapped[bool] = mapped_column(Boolean, nullable=False, default=False)
type: Mapped[str] = mapped_column(String(200))

class Permission(db.Model):
__tablename__ = 'permissions'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
user_id = db.Column(db.Integer, db.ForeignKey('users.id'), nullable=True)
permission = db.Column(db.String(200), nullable=False)
value = db.Column(db.String(200), nullable=False)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
user_id: Mapped[int] = mapped_column(Integer, ForeignKey('users.id'), nullable=True)
permission: Mapped[str] = mapped_column(String(200), nullable=False)
value: Mapped[str] = mapped_column(String(200), nullable=False)

class SharedObject(db.Model):
__tablename__ = 'shared_objects'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
owner = db.Column(db.Integer)
shared_with = db.Column(db.Integer)
object_id = db.Column(db.Integer)
date_shared = db.Column(db.DateTime, nullable=False, default=datetime.now)
level = db.Column(db.Text, nullable=False, default='view')
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
owner: Mapped[int] = mapped_column(Integer)
shared_with: Mapped[int] = mapped_column(Integer)
object_id: Mapped[int] = mapped_column(Integer)
date_shared: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
level: Mapped[str] = mapped_column(Text, nullable=False, default='view')

class UserPreference(db.Model):
__tablename__ = 'user_preferences'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
preference = db.Column(db.Text, nullable=False)
data = db.Column(db.JSON)
user_id = db.Column(db.Integer, db.ForeignKey('users.id'), nullable=True)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
preference: Mapped[str] = mapped_column(Text, nullable=False)
data: Mapped[Any] = mapped_column(JSON)
user_id: Mapped[int] = mapped_column(Integer, ForeignKey('users.id'), nullable=True)

class ViewSet(db.Model):
__tablename__ = 'view_sets'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
table_name = db.Column(db.String(100))
name = db.Column(db.String(200))
description = db.Column(db.Text)
date_added = db.Column(db.DateTime, nullable=False, default=datetime.now)
date_modified = db.Column(db.DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
owner = db.Column(db.Integer, default=0)
is_public = db.Column(db.Boolean, default=False)
fields = db.Column(db.JSON)
data = db.Column(db.JSON)
date_made_public = db.Column(db.DateTime)
status = db.Column(db.Text)
is_deleted = db.Column(db.Boolean, default=False)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
table_name: Mapped[str] = mapped_column(String(100))
name: Mapped[str] = mapped_column(String(200))
description: Mapped[str] = mapped_column(Text)
date_added: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
date_modified: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
owner: Mapped[int] = mapped_column(Integer, default=0)
is_public: Mapped[bool] = mapped_column(Boolean, default=False)
fields: Mapped[Any] = mapped_column(JSON)
data: Mapped[Any] = mapped_column(JSON)
date_made_public: Mapped[datetime] = mapped_column(DateTime)
status: Mapped[str] = mapped_column(Text)
is_deleted: Mapped[bool] = mapped_column(Boolean, default=False)

class GeneSet(db.Model):
__tablename__ = 'gene_sets'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
name = db.Column(db.String(100), nullable=False)
table_name = db.Column(db.String(150))
data = db.Column(db.JSON)
date_added = db.Column(db.DateTime, nullable=False, default=datetime.now)
date_modified = db.Column(db.DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
is_deleted = db.Column(db.Boolean, default=False)
description = db.Column(db.Text)
id: Mapped[int] = mapped_column(Integer, primary_key=True, autoincrement=True)
name: Mapped[str] = mapped_column(String(100), nullable=False)
table_name: Mapped[str] = mapped_column(String(150))
data: Mapped[Any] = mapped_column(JSON)
date_added: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now)
date_modified: Mapped[datetime] = mapped_column(DateTime, nullable=False, default=datetime.now, onupdate=datetime.now)
is_deleted: Mapped[bool] = mapped_column(Boolean, default=False)
description: Mapped[str] = mapped_column(Text)

# Indexes
db.Index('idx_genes_name', GeneSet.name)
Expand Down
22 changes: 12 additions & 10 deletions python/mdvtools/dbutils/dbservice.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# project_service.py
# dbservice.py

from mdvtools.dbutils.dbmodels import db, Project, File
from datetime import datetime
Expand Down Expand Up @@ -34,9 +34,12 @@ def get_next_project_id():

@staticmethod
# Routes -> /create_project
def add_new_project(path, name='unnamed_project'):
def add_new_project(path, name='unnamed project'):
try:
new_project = Project(name=name, path=path)
# can't see simple way to make type check happy with kwargs here
new_project = Project()
new_project.name = name
new_project.path = path
db.session.add(new_project)
db.session.commit()
return new_project
Expand Down Expand Up @@ -169,13 +172,12 @@ def add_or_update_file_in_project(file_name, file_path, project_id):
print(f"Updated file name in DB: {existing_file}")
else:
# Add new file to the database
new_file = File(
name=file_name,
file_path=file_path,
project_id=project_id,
upload_timestamp=datetime.now(),
update_timestamp=datetime.now()
)
new_file = File()
new_file.name = file_name
new_file.file_path = file_path
new_file.project_id = project_id
new_file.upload_timestamp = datetime.now()
new_file.update_timestamp = datetime.now()
db.session.add(new_file)
print(f"Added new file to DB: {new_file}")

Expand Down
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