Change delete execution

app/admin/views.py

@@ -2,7 +2,7 @@ from app import db
 from app.decorators import admin_required
 from app.models import Role, User
 from app.tables import AdminUserItem, AdminUserTable
-from app.utils import background_delete_user
+from app.background_functions import delete_user_
 from flask import current_app, flash, redirect, render_template, url_for
 from flask_login import login_required
 from . import admin
@@ -50,10 +50,9 @@ def admin_user_page(user_id):
 @login_required
 @admin_required
 def admin_delete_user(user_id):
-    delete_thread = threading.Thread(
+    delete_thread = threading.Thread(target=delete_user_,
-        target=background_delete_user,
+                                     args=(current_app._get_current_object(),
-        args=(current_app._get_current_object(), user_id)
+                                           user_id))
-    )
     delete_thread.start()
     flash('User {} has been deleted!'.format(user_id))
     return redirect(url_for('admin.for_admins_only'))

app/background_functions.py

@@ -0,0 +1,25 @@
+from .models import Corpus, Job, User
+
+
+def delete_corpus_(app, corpus_id):
+    with app.app_context():
+        corpus = Corpus.query.filter_by(id=corpus_id).first()
+        if corpus is None:
+            raise Exception('Corpus {} not found!'.format(corpus_id))
+        corpus.delete()
+
+
+def delete_job_(app, job_id):
+    with app.app_context():
+        job = Job.query.filter_by(id=job_id).first()
+        if job is None:
+            raise Exception('Job {} not found!'.format(job_id))
+        job.delete()
+
+
+def delete_user_(app, user_id):
+    with app.app_context():
+        user = User.query.filter_by(id=user_id).first()
+        if user is None:
+            raise Exception('User {} not found!'.format(user_id))
+        user.delete()

app/corpora/views.py

@@ -5,7 +5,7 @@ from flask import (abort, current_app, flash, redirect, request,
 from flask_login import current_user, login_required
 from werkzeug.utils import secure_filename
 from . import corpora
-from .background_tasks import (delete_corpus_, delete_corpus_file_,
+from .background_functions import (delete_corpus_, delete_corpus_file_,
                                edit_corpus_file_)
 from .forms import (AddCorpusFileForm, AddCorpusForm, EditCorpusFileForm,
                     QueryDownloadForm, QueryForm)
@@ -28,11 +28,11 @@ def add_corpus():
         try:
             os.makedirs(dir)
         except OSError:
-            flash('OSError!')
+            flash('[ERROR]: Could not add corpus!')
-            db.session.remove(corpus)
+            corpus.delete()
-            db.session.commit()
+        else:
-        flash('Corpus added!')
+            flash('Corpus added!')
-        return redirect(url_for('corpora.corpus', corpus_id=corpus.id))
+            return redirect(url_for('corpora.corpus', corpus_id=corpus.id))
     return render_template('corpora/add_corpus.html.j2',
                            add_corpus_form=add_corpus_form,
                            title='Add corpus')

app/jobs/views.py

@@ -1,5 +1,5 @@
 from app.models import Job, JobInput, JobResult
-from app.utils import background_delete_job
+from app.background_functions import delete_job_
 from flask import (abort, current_app, flash, redirect, render_template,
                    send_from_directory, url_for)
 from flask_login import current_user, login_required
@@ -23,7 +23,7 @@ def delete_job(job_id):
     job = Job.query.get_or_404(job_id)
     if not (job.creator == current_user or current_user.is_administrator()):
         abort(403)
-    delete_thread = threading.Thread(target=background_delete_job,
+    delete_thread = threading.Thread(target=delete_job_,
                                      args=(current_app._get_current_object(),
                                            job_id))
     delete_thread.start()

app/models.py

@@ -3,8 +3,7 @@ from flask import current_app
 from flask_login import UserMixin, AnonymousUserMixin
 from itsdangerous import BadSignature, TimedJSONWebSignatureSerializer
 from werkzeug.security import generate_password_hash, check_password_hash
-from . import db
+from . import db, logger, login_manager
-from . import login_manager
 import os
 import shutil
 import xml.etree.ElementTree as ET
@@ -83,12 +82,9 @@ class Role(db.Model):
         to them. Order of the roles dictionary determines the ID of each role.
         User hast the ID 1 and Administrator has the ID 2.
         """
-        roles = {
+        roles = {'User': [Permission.CREATE_JOB],
-                    'User': [Permission.CREATE_JOB],
+                 'Administrator': [Permission.ADMIN, Permission.CREATE_JOB,
-                    'Administrator': [Permission.ADMIN,
+                                   Permission.DELETE_JOB]}
-                                      Permission.CREATE_JOB,
-                                      Permission.DELETE_JOB]
-        }
         default_role = 'User'
         for r in roles:
             role = Role.query.filter_by(name=r).first()
@@ -208,17 +204,21 @@ class User(UserMixin, db.Model):
         """
         return self.can(Permission.ADMIN)
 
-    def delete_user(self):
+    def delete(self):
         """
-        Delete user from database. Also delete all associated jobs and corpora
+        Delete the user and its corpora and jobs from database and filesystem.
-        files.
         """
-        delete_path = os.path.join('/mnt/opaque/', str(self.id))
+        for job in self.jobs:
-        while os.path.exists(delete_path):
+            job.delete()
-            try:
+        for corpus in self.corpora:
-                shutil.rmtree(delete_path, ignore_errors=True)
+            corpus.delete()
-            except OSError:
+        path = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
-                pass
+                            str(self.id))
+        try:
+            shutil.rmtree(path)
+        except Exception as e:
+            logger.warning(e)
+            pass
         db.session.delete(self)
         db.session.commit()
 
@@ -246,9 +246,7 @@ class JobInput(db.Model):
     dir = db.Column(db.String(255))
     job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
     # Relationships
-    results = db.relationship('JobResult',
+    results = db.relationship('JobResult', backref='job_input', lazy='dynamic',
-                              backref='job_input',
-                              lazy='dynamic',
                               cascade='save-update, merge, delete')
 
     def __repr__(self):
@@ -314,24 +312,44 @@ class Job(db.Model):
     title = db.Column(db.String(32))
     user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
     # Relationships
-    inputs = db.relationship('JobInput',
+    inputs = db.relationship('JobInput', backref='job', lazy='dynamic',
-                             backref='job',
-                             lazy='dynamic',
                              cascade='save-update, merge, delete')
-    results = db.relationship('JobResult',
+    results = db.relationship('JobResult', backref='job', lazy='dynamic',
-                              backref='job',
-                              lazy='dynamic',
                               cascade='save-update, merge, delete')
 
-    def __init__(self, **kwargs):
-        super(Job, self).__init__(**kwargs)
-
     def __repr__(self):
         """
         String representation of the Job. For human readability.
         """
         return '<Job %r>' % self.title
 
+    def delete(self):
+        """
+        Delete the job and its inputs and outputs from database and filesystem.
+        """
+        self.status = 'stopping'
+        db.session.commit()
+        while self.status != 'deleted':
+            ''' TODO: wait a second '''
+            db.session.refresh(self)
+        path = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
+                            str(self.user_id), 'jobs', str(self.id))
+        '''
+        ' TODO: Remove this workaround by executing the following command
+        '       before service removal.
+        '
+        '       docker service update --mount-rm <service>
+        '''
+        while os.path.exists(path):
+            try:
+                shutil.rmtree(path)
+            except Exception as e:
+                ''' TODO: Proper exception handling '''
+                logger.warning(e)
+                pass
+        db.session.delete(self)
+        db.session.commit()
+
     def to_dict(self):
         return {'id': self.id,
                 'creation_date': self.creation_date.timestamp(),
@@ -349,34 +367,6 @@ class Job(db.Model):
                 'title': self.title,
                 'user_id': self.user_id}
 
-    def flag_for_stop(self):
-        """
-        Flag running or failed job (anything that is not completed) with
-        stopping. Opaque daemon will end services flaged with 'stopping'.
-        """
-        self.status = 'stopping'
-        db.session.commit()
-
-    def delete_job(self):
-        """
-        Delete job with given job id from database. Also delete associated job
-        files. Contianers are still running for a few seconds after
-        the associated service has been removed. This is the reason for the
-        while loop. The loop checks if the file path to all the job files still
-        exists and removes it again and again till the container did shutdown
-        for good.
-        See: https://docs.docker.com/engine/swarm/swarm-tutorial/delete-service/
-        """
-        delete_path = os.path.join('/mnt/opaque/', str(self.user_id), 'jobs',
-                                   str(self.id))
-        while os.path.exists(delete_path):
-            try:
-                shutil.rmtree(delete_path, ignore_errors=True)
-            except OSError:
-                pass
-        db.session.delete(self)
-        db.session.commit()
-
 
 class CorpusFile(db.Model):
     """
@@ -394,20 +384,20 @@ class CorpusFile(db.Model):
 
     def delete(self):
         path = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
-                            self.dir,
+                            self.dir, self.filename)
-                            self.filename)
         try:
             os.remove(path)
-        except:
+        except Exception as e:
-            return
+            ''' TODO: Proper exception handling '''
+            logger.warning(e)
+            pass
         self.corpus.status = 'unprepared'
         db.session.delete(self)
         db.session.commit()
 
     def insert_metadata(self):
         file = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
-                            self.dir,
+                            self.dir, self.filename)
-                            self.filename)
         element_tree = ET.parse(file)
         text_node = element_tree.find('text')
         text_node.set('author', self.author)
@@ -433,9 +423,7 @@ class Corpus(db.Model):
     analysis_container_ip = db.Column(db.String(16))
     analysis_container_name = db.Column(db.String(32))
     # Relationships
-    files = db.relationship('CorpusFile',
+    files = db.relationship('CorpusFile', backref='corpus', lazy='dynamic',
-                            backref='corpus',
-                            lazy='dynamic',
                             cascade='save-update, merge, delete')
 
     def __repr__(self):
@@ -456,13 +444,20 @@ class Corpus(db.Model):
         for corpus_file in self.files:
             corpus_file.delete()
         path = os.path.join(current_app.config['OPAQUE_STORAGE_DIRECTORY'],
-                            str(self.user_id),
+                            str(self.user_id), 'corpora', str(self.id))
-                            'corpora',
+        '''
-                            str(self.id))
+        ' TODO: Remove this workaround by executing the following command
-        try:
+        '       before service removal.
-            shutil.rmtree(path)
+        '
-        except:
+        '       docker service update --mount-rm <service>
-            return
+        '''
+        while os.path.exists(path):
+            try:
+                shutil.rmtree(path)
+            except Exception as e:
+                ''' TODO: Proper exception handling '''
+                logger.warning(e)
+                pass
         db.session.delete(self)
         db.session.commit()
 

app/profile/views.py

@@ -1,5 +1,5 @@
 from app import db, logger
-from app.utils import background_delete_user
+from app.background_functions import delete_user_
 from flask import abort, current_app, flash, redirect, render_template, url_for
 from flask_login import current_user, login_required, logout_user
 from . import profile
@@ -94,10 +94,9 @@ def delete_self():
     """
     View to delete yourslef and all associated data.
     """
-    delete_thread = threading.Thread(
+    delete_thread = threading.Thread(target=delete_user_,
-        target=background_delete_user,
+                                     args=(current_app._get_current_object(),
-        args=(current_app._get_current_object(), current_user.id)
+                                           current_user.id))
-    )
     delete_thread.start()
     logout_user()
     flash('Your account has been deleted!')

app/services/views.py

@@ -46,9 +46,8 @@ def service(service):
         try:
             os.makedirs(absolut_dir)
         except OSError:
-            flash('[OSError] Could not add job!')
+            flash('[ERROR]: Could not add job!')
-            db.session.delete(job)
+            job.delete()
-            db.session.commit()
         else:
             for file in add_job_form.files.data:
                 filename = secure_filename(file.filename)

app/utils.py

@@ -1,54 +0,0 @@
-from . import db, logger
-from .models import Job, User, Corpus, CorpusFile
-
-
-'''
-' A list of background process functions. Functions should be called using the
-  Thread class from the module threading.
-'''
-
-
-def background_delete_user(app, current_user_id):
-    with app.app_context():
-        logger.warning('Called by delete_thread.')
-        logger.warning('User id is: {}.'.format(current_user_id))
-        jobs = Job.query.filter_by(user_id=current_user_id).all()
-        corpora = Corpus.query.filter_by(user_id=current_user_id).all()
-        logger.warning('Jobs to delete are: {}'.format(jobs))
-        user = User.query.get_or_404(current_user_id)
-        for job in jobs:
-            job.flag_for_stop()
-            logger.warning('Job status: {}'.format(job.status))
-            deleted = False
-            while deleted is False:
-                logger.warning('Refreshing')
-                db.session.refresh(job)
-                logger.warning('Refreshed')
-                if job.status == 'deleted':
-                    logger.warning('Job status is deleted.')
-                    job.delete_job()
-                    deleted = True
-            logger.warning('Job deletion loop has ended.')
-        for corpus in corpora:
-            corpus.delete_corpus()
-            logger.warning('Corpus deletion loop has ended.')
-        user.delete_user()
-
-
-def background_delete_job(app, job_id):
-    with app.app_context():
-        logger.warning('Called by delete_thread.')
-        logger.warning('Job id is: {}.'.format(job_id))
-        job = Job.query.filter_by(id=job_id).first()
-        logger.warning('Job object is: {}'.format(job))
-        logger.warning('Job status: {}'.format(job.status))
-        job.flag_for_stop()
-        logger.warning('Job status: {}'.format(job.status))
-        deleted = False
-        while deleted is False:
-            db.session.refresh(job)
-            if job.status == 'deleted':
-                logger.warning('Job status is deleted.')
-                job.delete_job()
-                deleted = True
-        logger.warning('Loop has ended.')