Skip to content

Improvement on MorphoCut server #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
saeedehsp wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Improvement on MorphoCut server #6

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0938366
feat:add login page
saeedehsp May 7, 2023
612d845
feat: login and project improvement
saeedehsp May 8, 2023
a8b0556
fix: fix some bugs in login and logout
saeedehsp May 16, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
92 changes: 57 additions & 35 deletions morphocut_server/api.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
from flask.blueprints import Blueprint
from flask.helpers import send_from_directory
from flask_cors import CORS
from flask_login import logout_user
from flask_login import logout_user, login_user
from flask_user import (UserManager, UserMixin, current_user, login_required,
roles_required)
from rq import Queue
Expand All @@ -39,6 +39,7 @@
from morphocut_server.frontend import frontend
from morphocut_server.worker import redis_conn
from morphocut_server.pipeline import *
from flask_jwt_extended import jwt_required, get_jwt_identity

api = Blueprint("api", __name__)

Expand All @@ -49,14 +50,14 @@


@api.route("/users", methods=['GET', 'POST'])
@login_required
@roles_required('admin')
# @login_required
# @roles_required('admin')
def get_current_users_route():
"""Get the users currently registered.

Returns
-------
repsonse : str
response : str
The jsonified response object.

"""
Expand All @@ -65,6 +66,9 @@ def get_current_users_route():
user = request.get_json()
morphocut.add_user_to_database(
user['email'], user['password'], user['admin'])

response_object = {'status': 'success', 'message': 'User added successfully'}
return jsonify(response_object)
else:
response_object = {'status': 'success'}
users = models.User.query.all()
Expand All @@ -80,8 +84,7 @@ def get_current_users_route():
'users': user_list
}

return jsonify(response_object)

return jsonify(response_object)

@api.route("/users/current", methods=['GET'])
def get_current_user_route():
Expand Down Expand Up @@ -171,8 +174,8 @@ def get_user_jobs_route(id):
# Projects Routes
# ===============================================================================


@api.route('/projects', methods=['GET', 'POST'])
@login_required
def get_projects_route():
"""Get the projects from the database.

Expand All @@ -190,6 +193,10 @@ def get_projects_route():
response_object['message'] = 'Project added!'
else:
response_object['projects'] = get_projects()

if not current_user.is_authenticated:
return jsonify({'status': 'error', 'message': 'User not authenticated'}), 401

return jsonify(response_object)


Expand Down Expand Up @@ -358,14 +365,14 @@ def remove_project(project_id):
response_object = {'status': 'success'}
with database.engine.begin() as connection:

stmt = select([models.projects.c.path]).where(
stmt = select(models.projects.c.path).where(
models.projects.c.project_id == project_id)
project = connection.execute(stmt).first()

if project:
app = flask.current_app
project_path = os.path.join(
app.root_path, app.config['DATA_DIRECTORY'], project['path'])
app.root_path, app.config['DATA_DIRECTORY'], project._asdict()['path'])
if 'morphocut' in project_path and app.config['DATA_DIRECTORY'] in project_path:
print('removing project with id {}'.format(project_id))
if os.path.exists(project_path):
Expand Down Expand Up @@ -519,8 +526,8 @@ def get_running_task_dicts(tasks):
for task in tasks:
print(json.loads(task.meta))
job = Job.fetch(task.id, connection=redis_conn)
project = connection.execute(select([sqlalchemy.text(
'*')]).select_from(models.projects).where(models.projects.c.project_id == task.project_id)).first()
project = connection.execute(select(sqlalchemy.text(
'*')).select_from(models.projects).where(models.projects.c.project_id == task.project_id)).first()
task_dict = dict(id=task.id, name=task.name, description=task.description,
complete=task.complete, result=task.result, progress=task.get_progress(), project_id=task.project_id)
task_dict['meta'] = json.loads(
Expand All @@ -532,7 +539,7 @@ def get_running_task_dicts(tasks):
# task_dict['meta']['scheduled_at'])
# print('scheduled_at: {}'.format(task_dict['started_at']))
if project:
task_dict['project_name'] = project['name']
task_dict['project_name'] = project[1]
running_task_dicts.append(task_dict)
return running_task_dicts

Expand Down Expand Up @@ -561,10 +568,10 @@ def get_finished_task_dicts(tasks):
task_dict['meta'] = json.loads(
task.meta) if task.meta is not None else {}
finished_task_dicts.append(task_dict)
project = connection.execute(select([sqlalchemy.text(
'*')]).select_from(models.projects).where(models.projects.c.project_id == task.project_id)).first()
project = connection.execute(select(sqlalchemy.text(
'*')).select_from(models.projects).where(models.projects.c.project_id == task.project_id)).first()
if project:
task_dict['project_name'] = project['name']
task_dict['project_name'] = project[1]
except Exception as err:
print('exception in api.get_finished_task_dicts')
print(err)
Expand All @@ -590,12 +597,12 @@ def process_project(project_id, params):
app = flask.current_app
with database.engine.begin() as connection:
result = connection.execute(select(
[models.projects.c.path])
models.projects.c.path)
.select_from(models.projects)
.where(models.projects.c.project_id == project_id))
r = result.fetchone()
if (r is not None):
rel_project_path = r['path']
rel_project_path = r._asdict()['path']
abs_project_path = os.path.join(
app.root_path, app.config['DATA_DIRECTORY'], rel_project_path)
export_filename = 'ecotaxa_segmentation_{:%Y_%m_%d}_{}.zip'.format(
Expand Down Expand Up @@ -641,6 +648,7 @@ def process_and_zip(import_path, export_path, params=None):
return export_path


@login_required
def get_projects():
"""Get the projects belonging to the current user.

Expand All @@ -650,16 +658,28 @@ def get_projects():
The projects belonging to the current user.

"""
print("Access token received")
print("get_projects called, current_user ID:", current_user.get_id()) # Add this line

if current_user.get_id() is None:
return
with database.engine.begin() as connection:
result = connection.execute(select(
[models.projects.c.project_id, models.projects.c.name, models.projects.c.path, models.projects.c.creation_date, models.projects.c.user_id, func.count(models.objects.c.object_id).label('object_count')])
result = connection.execute(
select(
models.projects.c.project_id,
models.projects.c.name,
models.projects.c.path,
models.projects.c.creation_date,
models.projects.c.user_id,
func.count(models.objects.c.object_id).label('object_count')
)
.select_from(models.projects.outerjoin(models.objects))
.where(and_(models.projects.c.active == True, models.projects.c.user_id == current_user.id))
.group_by(models.projects.c.project_id)
.order_by(models.projects.c.project_id))
projects = [dict(row) for row in result]
.order_by(models.projects.c.project_id)
)
projects = [row._asdict() for row in result]
print("Fetched projects:", projects) # Add this line
for project in projects:
user = models.User.query.filter_by(
id=project['user_id']).first()
Expand All @@ -684,26 +704,28 @@ def get_project_files(id):
"""
with database.engine.begin() as connection:
result = connection.execute(select(
[models.objects.c.filename, models.objects.c.object_id, models.objects.c.modification_date, models.objects.c.creation_date])
models.objects.c.filename, models.objects.c.object_id, models.objects.c.modification_date, models.objects.c.creation_date)
.select_from(models.objects)
.where(models.objects.c.project_id == id))
print(f'Query result for project_id {id}: {result}')
project = connection.execute(select(
[models.projects.c.path])
models.projects.c.path)
.select_from(models.projects)
.where(models.projects.c.project_id == id))
r = project.fetchone()
project = ''
if (r is not None):
project_path = r['path']
return [dict(filename=row['filename'],
object_id=row['object_id'],
modification_date=row['modification_date'],
creation_date=row['creation_date'],
project_path = r._asdict()['path']
objects = [dict(filename=row._asdict()['filename'],
object_id=row._asdict()['object_id'],
modification_date=row._asdict()['modification_date'],
creation_date=row._asdict()['creation_date'],
filepath=url_for(
'data', path=os.path.join(project_path, row['filename']))
)

for row in result]
'data', path=os.path.join(project_path, row._asdict()['filename']))
)
for row in result]
print(f'Objects for project_id {id}: {objects}')
return objects


def get_project(id):
Expand All @@ -722,12 +744,12 @@ def get_project(id):
"""
with database.engine.begin() as connection:
result = connection.execute(select(
[sqlalchemy.text('*')])
sqlalchemy.text('*'))
.select_from(models.projects)
.where(models.projects.c.project_id == id))
row = result.fetchone()
if (row is not None):
return dict(row)
return row._asdict()
return


Expand All @@ -748,7 +770,6 @@ def add_project(project):
try_insert_or_update(models.projects.insert(), # pylint: disable=no-value-for-parameter
[dict(
name=project['name'], path=project['name'], active=True, user_id=current_user.id)])
return


def add_object(_object):
Expand All @@ -769,6 +790,7 @@ def add_object(_object):
models.objects.insert(), # pylint: disable=no-value-for-parameter
[dict(
project_id=_object['project_id'], filename=_object['filename'])])
print(f'Object added: {_object}')


def try_insert_or_update(insert_function, data):
Expand Down
Loading