Delete files in db model methods.

web/app/corpora/tasks.py

-from datetime import datetime
 from .. import db
 from ..decorators import background
 from ..models import Corpus, CorpusFile
-import xml.etree.ElementTree as ET
-import os
-import shutil
 
 
 @background
@@ -13,68 +9,26 @@ def build_corpus(corpus_id, *args, **kwargs):
     with app.app_context():
         corpus = Corpus.query.get(corpus_id)
         if corpus is None:
-            return
-        corpus.status = 'File processing'
-        db.session.commit()
-        corpus_dir = os.path.join(app.config['NOPAQUE_STORAGE'],
-                                  str(corpus.user_id), 'corpora',
-                                  str(corpus.id))
-        output_dir = os.path.join(corpus_dir, 'merged')
-        shutil.rmtree(output_dir, ignore_errors=True)
-        os.mkdir(output_dir)
-        master_element_tree = ET.ElementTree(
-            ET.fromstring('<corpus>\n</corpus>'))
-        for corpus_file in corpus.files:
-            file = os.path.join(corpus_dir, corpus_file.filename)
-            element_tree = ET.parse(file)
-            text_node = element_tree.find('text')
-            text_node.set('address', corpus_file.address or "NULL")
-            text_node.set('author', corpus_file.author)
-            text_node.set('booktitle', corpus_file.booktitle or "NULL")
-            text_node.set('chapter', corpus_file.chapter or "NULL")
-            text_node.set('editor', corpus_file.editor or "NULL")
-            text_node.set('institution', corpus_file.institution or "NULL")
-            text_node.set('journal', corpus_file.journal or "NULL")
-            text_node.set('pages', corpus_file.pages or "NULL")
-            text_node.set('publisher', corpus_file.publisher or "NULL")
-            text_node.set('publishing_year', str(corpus_file.publishing_year))
-            text_node.set('school', corpus_file.school or "NULL")
-            text_node.set('title', corpus_file.title)
-            element_tree.write(file)
-            master_element_tree.getroot().insert(1, text_node)
-        output_file = os.path.join(output_dir, 'corpus.vrt')
-        master_element_tree.write(output_file, xml_declaration=True,
-                                  encoding='utf-8')
-        corpus.status = 'submitted'
-        corpus.last_edited_date = datetime.utcnow()
+            raise Exception('Corpus {} not found'.format(corpus_id))
+        corpus.build()
         db.session.commit()
 
 
 @background
 def delete_corpus(corpus_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         corpus = Corpus.query.get(corpus_id)
         if corpus is None:
-            return
-        path = os.path.join(app.config['NOPAQUE_STORAGE'], str(corpus.user_id),
-                            'corpora', str(corpus.id))
-        shutil.rmtree(path, ignore_errors=True)
+            raise Exception('Corpus {} not found'.format(corpus_id))
         corpus.delete()
+        db.session.commit()
 
 
 @background
 def delete_corpus_file(corpus_file_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         corpus_file = CorpusFile.query.get(corpus_file_id)
         if corpus_file is None:
-            return
-        path = os.path.join(app.config['NOPAQUE_STORAGE'], corpus_file.dir,
-                            corpus_file.filename)
-        try:
-            os.remove(path)
-        except Exception:
-            pass
-        else:
-            corpus_file.delete()
+            raise Exception('Corpus file {} not found'.format(corpus_file_id))
+        corpus_file.delete()
+        db.session.commit()

web/app/decorators.py

@@ -2,7 +2,6 @@ from . import socketio
 from flask import abort, current_app, request
 from flask_login import current_user
 from functools import wraps
-from threading import Thread
 
 
 def admin_required(f):
@@ -27,8 +26,7 @@ def background(f):
     @wraps(f)
     def wrapped(*args, **kwargs):
         kwargs['app'] = current_app._get_current_object()
-        thread = Thread(target=f, args=args, kwargs=kwargs)
-        thread.start()
+        thread = socketio.start_background_task(f, *args, **kwargs)
         return thread
     return wrapped
 

web/app/jobs/tasks.py

+from .. import db
 from ..decorators import background
 from ..models import Job
 
 
 @background
 def delete_job(job_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         job = Job.query.get(job_id)
         if job is None:
-            raise Exception('Could not find job with id {}'.format(job_id))
+            raise Exception('Job {} not found'.format(job_id))
         job.delete()
+        db.session.commit()
 
 
 @background
 def restart_job(job_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         job = Job.query.get(job_id)
         if job is None:
-            raise Exception('Could not find job with id {}'.format(job_id))
+            raise Exception('Job {} not found'.format(job_id))
         job.restart()
+        db.session.commit()

web/app/jobs/views.py

@@ -60,10 +60,6 @@ def restart(job_id):
     else:
         tasks.restart_job(job_id)
         flash('Job has been restarted!', 'job')
-    job_inputs = [dict(filename=input.filename,
-                       id=input.id,
-                       job_id=job.id)
-                  for input in job.inputs]
     return redirect(url_for('jobs.job', job_id=job_id))
 
 

web/app/models.py

@@ -5,6 +5,7 @@ from itsdangerous import BadSignature, TimedJSONWebSignatureSerializer
 from time import sleep
 from werkzeug.security import generate_password_hash, check_password_hash
 from werkzeug.utils import secure_filename
+import xml.etree.ElementTree as ET
 from . import db, login_manager
 import os
 import shutil
@@ -246,9 +247,10 @@ class User(UserMixin, db.Model):
         '''
         Delete the user and its corpora and jobs from database and filesystem.
         '''
-
+        user_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
+                                str(self.id))
+        shutil.rmtree(user_dir, ignore_errors=True)
         db.session.delete(self)
-        db.session.commit()
 
 
 class AnonymousUser(AnonymousUserMixin):
@@ -383,7 +385,6 @@ class Job(db.Model):
                                str(self.id))
         shutil.rmtree(job_dir, ignore_errors=True)
         db.session.delete(self)
-        db.session.commit()
 
     def restart(self):
         '''
@@ -400,7 +401,6 @@ class Job(db.Model):
         shutil.rmtree(os.path.join(job_dir, 'pyflow.data'), ignore_errors=True)
         self.end_date = None
         self.status = 'submitted'
-        db.session.commit()
 
     def to_dict(self):
         return {'id': self.id,
@@ -504,9 +504,17 @@ class CorpusFile(db.Model):
     title = db.Column(db.String(255))
 
     def delete(self):
-        self.corpus.status = 'unprepared'
+        corpus_file = os.path.join(current_app.config['NOPAQUE_STORAGE'],
+                                   str(self.corpus.user_id),
+                                   'corpora',
+                                   str(self.corpus_id),
+                                   self.filename)
+        try:
+            os.remove(corpus_file)
+        except OSError:
+            pass
         db.session.delete(self)
-        db.session.commit()
+        self.corpus.status = 'unprepared'
 
     def to_dict(self):
         return {'id': self.id,
@@ -557,9 +565,49 @@ class Corpus(db.Model):
                 'title': self.title,
                 'files': {file.id: file.to_dict() for file in self.files}}
 
+    def build(self):
+        corpus_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
+                                  str(self.user_id),
+                                  'corpora',
+                                  str(self.id))
+        output_dir = os.path.join(corpus_dir, 'merged')
+        shutil.rmtree(output_dir, ignore_errors=True)
+        os.mkdir(output_dir)
+        master_element_tree = ET.ElementTree(
+            ET.fromstring('<corpus>\n</corpus>')
+        )
+        for corpus_file in self.files:
+            corpus_file_path = os.path.join(corpus_dir, corpus_file.filename)
+            element_tree = ET.parse(corpus_file_path)
+            text_node = element_tree.find('text')
+            text_node.set('address', corpus_file.address or "NULL")
+            text_node.set('author', corpus_file.author)
+            text_node.set('booktitle', corpus_file.booktitle or "NULL")
+            text_node.set('chapter', corpus_file.chapter or "NULL")
+            text_node.set('editor', corpus_file.editor or "NULL")
+            text_node.set('institution', corpus_file.institution or "NULL")
+            text_node.set('journal', corpus_file.journal or "NULL")
+            text_node.set('pages', corpus_file.pages or "NULL")
+            text_node.set('publisher', corpus_file.publisher or "NULL")
+            text_node.set('publishing_year', str(corpus_file.publishing_year))
+            text_node.set('school', corpus_file.school or "NULL")
+            text_node.set('title', corpus_file.title)
+            element_tree.write(corpus_file_path)
+            master_element_tree.getroot().insert(1, text_node)
+        output_file = os.path.join(output_dir, 'corpus.vrt')
+        master_element_tree.write(output_file,
+                                  xml_declaration=True,
+                                  encoding='utf-8')
+        self.last_edited_date = datetime.utcnow()
+        self.status = 'submitted'
+
     def delete(self):
+        corpus_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
+                                  str(self.user_id),
+                                  'corpora',
+                                  str(self.id))
+        shutil.rmtree(corpus_dir, ignore_errors=True)
         db.session.delete(self)
-        db.session.commit()
 
     def __repr__(self):
         '''
@@ -582,8 +630,10 @@ class Result(db.Model):
                            cascade='save-update, merge, delete')
 
     def delete(self):
+        result_file_path = os.path.join(current_app.config['NOPAQUE_STORAGE'],
+                                        self.file[0].dir)
+        shutil.rmtree(result_file_path)
         db.session.delete(self)
-        db.session.commit()
 
     def __repr__(self):
         '''

web/app/profile/tasks.py

+from .. import db
 from ..decorators import background
 from ..models import User
-import os
-import shutil
 
 
 @background
 def delete_user(user_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         user = User.query.get(user_id)
         if user is None:
-            raise Exception('User {} not found!'.format(user_id))
-        path = os.path.join(app.config['NOPAQUE_STORAGE'], str(user.id))
-        shutil.rmtree(path, ignore_errors=True)
+            raise Exception('User {} not found'.format(user_id))
         user.delete()
+        db.session.commit()

web/app/results/tasks.py

+from .. import db
 from ..decorators import background
 from ..models import Result
-import os
-import shutil
 
 
 @background
 def delete_result(result_id, *args, **kwargs):
-    app = kwargs['app']
-    with app.app_context():
+    with kwargs['app'].app_context():
         result = Result.query.get(result_id)
         if result is None:
-            return
-        result_file_path = os.path.join(app.config['NOPAQUE_STORAGE'],
-                                        result.file[0].dir)
-        shutil.rmtree(result_file_path)
+            raise Exception('Result {} not found'.format(result_id))
         result.delete()  # cascades down and also deletes ResultFile
+        db.session.commit()

web/config.py

@@ -33,8 +33,7 @@ class Config:
     os.makedirs('logs', exist_ok=True)
     logging.basicConfig(filename='logs/nopaque.log',
                         format='[%(asctime)s] %(levelname)s in '
-                               '%(name)s/%(filename)s:%(lineno)d - '
-                               '%(message)s',
+                               '%(pathname)s:%(lineno)d - %(message)s',
                         datefmt='%Y-%m-%d %H:%M:%S', filemode='w')
 
     ''' ### Security enhancements ### '''