Restructure code and use APScheduler for daemon functionality

app/__init__.py

@@ -1,4 +1,5 @@
 from config import Config
+from docker import DockerClient
 from flask import Flask
 from flask_apscheduler import APScheduler
 from flask_assets import Environment
@@ -11,18 +12,19 @@ from flask_sqlalchemy import SQLAlchemy
 from flask_hashids import Hashids
 
 
-assets: Environment = Environment()
+assets = Environment()
-db: SQLAlchemy = SQLAlchemy()
+db = SQLAlchemy()
-hashids: Hashids = Hashids()
+docker_client = DockerClient()
-login: LoginManager = LoginManager()
+hashids = Hashids()
+login = LoginManager()
 login.login_view = 'auth.login'
 login.login_message = 'Please log in to access this page.'
-mail: Mail = Mail()
+mail = Mail()
-migrate: Migrate = Migrate()
+migrate = Migrate()
-paranoid: Paranoid = Paranoid()
+paranoid = Paranoid()
 paranoid.redirect_view = '/'
-scheduler: APScheduler = APScheduler()  # TODO: Use this!
+scheduler = APScheduler()
-socketio: SocketIO = SocketIO()
+socketio = SocketIO()
 
 
 def create_app(config: Config = Config) -> Flask:
@@ -30,6 +32,11 @@ def create_app(config: Config = Config) -> Flask:
     app: Flask = Flask(__name__)
     app.config.from_object(config)
     config.init_app(app)
+    docker_client.login(
+        username=app.config['NOPAQUE_DOCKER_REGISTRY_USERNAME'],
+        password=app.config['NOPAQUE_DOCKER_REGISTRY_PASSWORD'],
+        registry=app.config['NOPAQUE_DOCKER_REGISTRY']
+    )
 
     assets.init_app(app)
     db.init_app(app)
@@ -38,10 +45,11 @@ def create_app(config: Config = Config) -> Flask:
     mail.init_app(app)
     migrate.init_app(app, db)
     paranoid.init_app(app)
+    scheduler.init_app(app)
     socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])  # noqa
 
-    from app import socketio_event_listeners
+    from . import tasks
-    from app import sqlalchemy_event_listeners
+    tasks.register(app, scheduler)
 
     from .admin import bp as admin_blueprint
     app.register_blueprint(admin_blueprint, url_prefix='/admin')

app/cli.py

@@ -1,7 +1,6 @@
+from app.models import Role, User, TesseractOCRModel, TranskribusHTRModel
 from flask import current_app
 from flask_migrate import upgrade
-from . import db
-from .models import Corpus, Role, User, TesseractOCRModel, TranskribusHTRModel
 import click
 import os
 
@@ -41,22 +40,6 @@ def register(app):
         current_app.logger.info('Insert/Update default TranskribusHTRModels')
         TranskribusHTRModel.insert_defaults()
 
-    @app.cli.group()
-    def daemon():
-        ''' Daemon commands. '''
-        pass
-
-    @daemon.command('run')
-    def run_daemon():
-        ''' Run daemon '''
-        corpus: Corpus
-        for corpus in Corpus.query.filter(Corpus.num_analysis_sessions > 0):
-            corpus.num_analysis_sessions = 0
-        db.session.commit()
-        from app.daemon import Daemon
-        daemon: Daemon = Daemon()
-        daemon.run()
-
     @app.cli.group()
     def converter():
         ''' Converter commands. '''

app/daemon/__init__.py

@@ -1,23 +1,9 @@
 from app import db
-from flask import current_app
+from .corpus_utils import check_corpora
-from time import sleep
+from .job_utils import check_jobs
-from .corpus_utils import CheckCorporaMixin
-from .job_utils import CheckJobsMixin
-import docker
 
 
-class Daemon(CheckCorporaMixin, CheckJobsMixin):
+def daemon():
-    def __init__(self):
+    check_corpora()
-        self.docker = docker.from_env()
+    check_jobs()
-        self.docker.login(
-            username=current_app.config['NOPAQUE_DOCKER_REGISTRY_USERNAME'],
-            password=current_app.config['NOPAQUE_DOCKER_REGISTRY_PASSWORD'],
-            registry=current_app.config['NOPAQUE_DOCKER_REGISTRY']
-        )
-
-    def run(self):
-        while True:
-            self.check_corpora()
-            self.check_jobs()
     db.session.commit()
-            sleep(1.5)

app/daemon/corpus_utils.py

@@ -1,3 +1,4 @@
+from app import docker_client
 from app.models import Corpus, CorpusStatus
 from flask import current_app
 import docker
@@ -5,25 +6,24 @@ import os
 import shutil
 
 
-class CheckCorporaMixin:
+def check_corpora():
-    def check_corpora(self):
     corpora = Corpus.query.all()
-        for corpus in (x for x in corpora if x.status == CorpusStatus.SUBMITTED):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.SUBMITTED]:
-            self.create_build_corpus_service(corpus)
+        _create_build_corpus_service(corpus)
-        for corpus in (x for x in corpora if x.status == CorpusStatus.QUEUED or x.status == CorpusStatus.BUILDING):  # noqa
+    for corpus in [x for x in corpora if x.status in [CorpusStatus.QUEUED, CorpusStatus.BUILDING]]:
-            self.checkout_build_corpus_service(corpus)
+        _checkout_build_corpus_service(corpus)
-        for corpus in (x for x in corpora if x.status == CorpusStatus.BUILT and x.num_analysis_sessions > 0):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.BUILT and x.num_analysis_sessions > 0]:
         corpus.status = CorpusStatus.STARTING_ANALYSIS_SESSION
-        for corpus in (x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION and x.num_analysis_sessions == 0):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION and x.num_analysis_sessions == 0]:
         corpus.status = CorpusStatus.CANCELING_ANALYSIS_SESSION
-        for corpus in (x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION]:
-            self.checkout_analysing_corpus_container(corpus)
+        _checkout_analysing_corpus_container(corpus)
-        for corpus in (x for x in corpora if x.status == CorpusStatus.STARTING_ANALYSIS_SESSION):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.STARTING_ANALYSIS_SESSION]:
-            self.create_cqpserver_container(corpus)
+        _create_cqpserver_container(corpus)
-        for corpus in (x for x in corpora if x.status == CorpusStatus.CANCELING_ANALYSIS_SESSION):  # noqa
+    for corpus in [x for x in corpora if x.status == CorpusStatus.CANCELING_ANALYSIS_SESSION]:
-            self.remove_cqpserver_container(corpus)
+        _remove_cqpserver_container(corpus)
 
-    def create_build_corpus_service(self, corpus):
+def _create_build_corpus_service(corpus):
     ''' # Docker service settings # '''
     ''' ## Command ## '''
     command = ['bash', '-c']
@@ -37,7 +37,7 @@ class CheckCorporaMixin:
         f' -R /usr/local/share/cwb/registry/nopaque_{corpus.id}'
         ' -P pos -P lemma -P simple_pos'
         ' -S ent:0+type -S s:0'
-            ' -S text:0+address+author+booktitle+chapter+editor+institution+journal+pages+publisher+publishing_year+school+title'  # noqa
+        ' -S text:0+address+author+booktitle+chapter+editor+institution+journal+pages+publisher+publishing_year+school+title'
         ' -xsB -9'
         ' && '
         f'cwb-make -V NOPAQUE_{corpus.id}'
@@ -80,7 +80,7 @@ class CheckCorporaMixin:
     ''' ## Restart policy ## '''
     restart_policy = docker.types.RestartPolicy()
     try:
-            self.docker.services.create(
+        docker_client.services.create(
             image,
             command=command,
             constraints=constraints,
@@ -98,10 +98,10 @@ class CheckCorporaMixin:
         return
     corpus.status = CorpusStatus.QUEUED
 
-    def checkout_build_corpus_service(self, corpus):
+def _checkout_build_corpus_service(corpus):
     service_name = f'build-corpus_{corpus.id}'
     try:
-            service = self.docker.services.get(service_name)
+        service = docker_client.services.get(service_name)
     except docker.errors.NotFound as e:
         current_app.logger.error(
             f'Get service "{service_name}" failed '
@@ -118,12 +118,12 @@ class CheckCorporaMixin:
     if not service_tasks:
         return
     task_state = service_tasks[0].get('Status').get('State')
-        if corpus.status == CorpusStatus.QUEUED and task_state != 'pending':  # noqa
+    if corpus.status == CorpusStatus.QUEUED and task_state != 'pending':
         corpus.status = CorpusStatus.BUILDING
         return
-        elif corpus.status == CorpusStatus.BUILDING and task_state == 'complete':  # noqa
+    elif corpus.status == CorpusStatus.BUILDING and task_state == 'complete':
         corpus.status = CorpusStatus.BUILT
-        elif corpus.status == CorpusStatus.BUILDING and task_state == 'failed':  # noqa
+    elif corpus.status == CorpusStatus.BUILDING and task_state == 'failed':
         corpus.status = CorpusStatus.FAILED
     else:
         return
@@ -135,7 +135,7 @@ class CheckCorporaMixin:
             f'due to "docker.errors.APIError": {e}'
         )
 
-    def create_cqpserver_container(self, corpus):
+def _create_cqpserver_container(corpus):
     ''' # Docker container settings # '''
     ''' ## Command ## '''
     command = []
@@ -166,12 +166,12 @@ class CheckCorporaMixin:
     ''' ### Corpus registry volume ### '''
     registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry')
     registry_volume_target = '/usr/local/share/cwb/registry'
-        registry_volume = f'{registry_volume_source}:{registry_volume_target}:rw'  # noqa
+    registry_volume = f'{registry_volume_source}:{registry_volume_target}:rw'
     volumes.append(registry_volume)
     # Check if a cqpserver container already exists. If this is the case,
     # remove it and create a new one
     try:
-            container = self.docker.containers.get(name)
+        container = docker_client.containers.get(name)
     except docker.errors.NotFound:
         pass
     except docker.errors.APIError as e:
@@ -190,7 +190,7 @@ class CheckCorporaMixin:
             )
             return
     try:
-            self.docker.containers.run(
+        docker_client.containers.run(
             image,
             command=command,
             detach=detach,
@@ -215,10 +215,10 @@ class CheckCorporaMixin:
         return
     corpus.status = CorpusStatus.RUNNING_ANALYSIS_SESSION
 
-    def checkout_analysing_corpus_container(self, corpus):
+def _checkout_analysing_corpus_container(corpus):
     container_name = f'cqpserver_{corpus.id}'
     try:
-            self.docker.containers.get(container_name)
+        docker_client.containers.get(container_name)
     except docker.errors.NotFound as e:
         current_app.logger.error(
             f'Get container "{container_name}" failed '
@@ -232,10 +232,10 @@ class CheckCorporaMixin:
             f'due to "docker.errors.APIError": {e}'
         )
 
-    def remove_cqpserver_container(self, corpus):
+def _remove_cqpserver_container(corpus):
     container_name = f'cqpserver_{corpus.id}'
     try:
-            container = self.docker.containers.get(container_name)
+        container = docker_client.containers.get(container_name)
     except docker.errors.NotFound:
         corpus.status = CorpusStatus.BUILT
         return

app/daemon/job_utils.py

@@ -1,4 +1,4 @@
-from app import db
+from app import db, docker_client
 from app.models import (
     Job,
     JobResult,
@@ -15,39 +15,38 @@ import os
 import shutil
 
 
-class CheckJobsMixin:
+def check_jobs():
-    def check_jobs(self):
     jobs = Job.query.all()
-        for job in (x for x in jobs if x.status == JobStatus.SUBMITTED):
+    for job in [x for x in jobs if x.status == JobStatus.SUBMITTED]:
-            self.create_job_service(job)
+        _create_job_service(job)
-        for job in (x for x in jobs if x.status in [JobStatus.QUEUED, JobStatus.RUNNING]):  # noqa
+    for job in [x for x in jobs if x.status in [JobStatus.QUEUED, JobStatus.RUNNING]]:
-            self.checkout_job_service(job)
+        _checkout_job_service(job)
-        for job in (x for x in jobs if x.status == JobStatus.CANCELING):
+    for job in [x for x in jobs if x.status == JobStatus.CANCELING]:
-            self.remove_job_service(job)
+        _remove_job_service(job)
 
-    def create_job_service(self, job):
+def _create_job_service(job):
     ''' # Docker service settings # '''
     ''' ## Service specific settings ## '''
     if job.service == 'file-setup-pipeline':
         mem_mb = 512
         n_cores = 2
         executable = 'file-setup-pipeline'
-            image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}file-setup-pipeline:v{job.service_version}'  # noqa
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}file-setup-pipeline:v{job.service_version}'
     elif job.service == 'tesseract-ocr-pipeline':
         mem_mb = 1024
         n_cores = 4
         executable = 'tesseract-ocr-pipeline'
-            image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}tesseract-ocr-pipeline:v{job.service_version}'  # noqa
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}tesseract-ocr-pipeline:v{job.service_version}'
     elif job.service == 'transkribus-htr-pipeline':
         mem_mb = 1024
         n_cores = 4
         executable = 'transkribus-htr-pipeline'
-            image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}transkribus-htr-pipeline:v{job.service_version}'  # noqa
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}transkribus-htr-pipeline:v{job.service_version}'
     elif job.service == 'spacy-nlp-pipeline':
         mem_mb = 1024
         n_cores = 1
         executable = 'spacy-nlp-pipeline'
-            image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}spacy-nlp-pipeline:v{job.service_version}'  # noqa
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}spacy-nlp-pipeline:v{job.service_version}'
     ''' ## Command ## '''
     command = f'{executable} -i /input -o /output'
     command += ' --log-dir /logs'
@@ -55,7 +54,7 @@ class CheckJobsMixin:
     command += f' --n-cores {n_cores}'
     if job.service == 'spacy-nlp-pipeline':
         command += f' -m {job.service_args["model"]}'
-            if 'encoding_detection' in job.service_args and job.service_args['encoding_detection']:  # noqa
+        if 'encoding_detection' in job.service_args and job.service_args['encoding_detection']:
             command += ' --check-encoding'
     elif job.service == 'tesseract-ocr-pipeline':
         command += f' -m {job.service_args["model"]}'
@@ -86,7 +85,7 @@ class CheckJobsMixin:
         input_mount_target_base += f'/{secure_filename(job.title)}'
     for job_input in job.inputs:
         input_mount_source = job_input.path
-            input_mount_target = f'{input_mount_target_base}/{job_input.filename}'  # noqa
+        input_mount_target = f'{input_mount_target_base}/{job_input.filename}'
         input_mount = f'{input_mount_source}:{input_mount_target}:ro'
         mounts.append(input_mount)
     if job.service == 'tesseract-ocr-pipeline':
@@ -109,7 +108,7 @@ class CheckJobsMixin:
     ''' ### Pipeline data mount ### '''
     pyflow_data_mount_source = os.path.join(job.path, 'pipeline_data')
     pyflow_data_mount_target = '/logs/pyflow.data'
-        pyflow_data_mount = f'{pyflow_data_mount_source}:{pyflow_data_mount_target}:rw'  # noqa
+    pyflow_data_mount = f'{pyflow_data_mount_source}:{pyflow_data_mount_target}:rw'
     # Make sure that their is no data in the output directory
     shutil.rmtree(pyflow_data_mount_source, ignore_errors=True)
     os.makedirs(pyflow_data_mount_source)
@@ -124,7 +123,7 @@ class CheckJobsMixin:
     ''' ## Restart policy ## '''
     restart_policy = docker.types.RestartPolicy()
     try:
-            self.docker.services.create(
+        docker_client.services.create(
             image,
             command=command,
             constraints=constraints,
@@ -143,10 +142,10 @@ class CheckJobsMixin:
         return
     job.status = JobStatus.QUEUED
 
-    def checkout_job_service(self, job):
+def _checkout_job_service(job):
     service_name = f'job_{job.id}'
     try:
-            service = self.docker.services.get(service_name)
+        service = docker_client.services.get(service_name)
     except docker.errors.NotFound as e:
         current_app.logger.error(
             f'Get service "{service_name}" failed '
@@ -167,7 +166,7 @@ class CheckJobsMixin:
     if job.status == JobStatus.QUEUED and task_state != 'pending':
         job.status = JobStatus.RUNNING
         return
-        elif job.status == JobStatus.RUNNING and task_state == 'complete':  # noqa
+    elif job.status == JobStatus.RUNNING and task_state == 'complete':
         job.status = JobStatus.COMPLETED
         results_dir = os.path.join(job.path, 'results')
         with open(os.path.join(results_dir, 'outputs.json')) as f:
@@ -201,10 +200,10 @@ class CheckJobsMixin:
             f'due to "docker.errors.APIError": {e}'
         )
 
-    def remove_job_service(self, job):
+def _remove_job_service(job):
     service_name = f'job_{job.id}'
     try:
-            service = self.docker.services.get(service_name)
+        service = docker_client.services.get(service_name)
     except docker.errors.NotFound:
         job.status = JobStatus.CANCELED
         return

app/decorators.py

@@ -1,8 +1,8 @@
+from app.models import Permission
 from flask import abort, current_app
 from flask_login import current_user
 from functools import wraps
 from threading import Thread
-from .models import Permission
 
 
 def permission_required(permission):

app/email.py

@@ -1,27 +1,27 @@
-from flask import current_app, render_template
+from app import mail
+from flask import current_app, Flask, render_template
 from flask_mail import Message
-from typing import Any, Text
+from threading import Thread
-from . import mail
+from typing import Any
-from .decorators import background
 
 
-def create_message(
+def create_message(recipient: str, subject: str, template: str, **kwargs: Any) -> Message:
-    recipient: str,
-    subject: str,
-    template: str,
-    **kwargs: Any
-) -> Message:
     subject_prefix: str = current_app.config['NOPAQUE_MAIL_SUBJECT_PREFIX']
     msg: Message = Message(
-        f'{subject_prefix} {subject}',
+        body=render_template(f'{template}.txt.j2', **kwargs),
-        recipients=[recipient]
+        html=render_template(f'{template}.html.j2', **kwargs),
+        recipients=[recipient],
+        subject=f'{subject_prefix} {subject}'
     )
-    msg.body = render_template(f'{template}.txt.j2', **kwargs)
-    msg.html = render_template(f'{template}.html.j2', **kwargs)
     return msg
 
 
-@background
+def _send(app: Flask, msg):
-def send(msg: Message, *args, **kwargs):
+    with app.app_context():
-    with kwargs['app'].app_context():
         mail.send(msg)
+
+
+def send(msg: Message, *args, **kwargs):
+    thread = Thread(target=_send, args=[current_app._get_current_object(), msg])
+    thread.start()
+    return thread

app/jobs/routes.py

@@ -58,6 +58,23 @@ def download_job_input(job_id, job_input_id):
     )
 
 
+@bp.route('/<hashid:job_id>/log')
+@login_required
+@admin_required
+def job_log(job_id):
+    job = Job.query.get_or_404(job_id)
+    if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
+        flash(
+            f'Can\'t restart job "{job.title}": Status is not "Completed/Failed"',  # noqa
+            category='error'
+        )
+    return send_from_directory(
+        attachment_filename=f'job_{job.hashid}_log.txt',
+        directory=os.path.join(job.path, 'pipeline_data'),
+        filename=os.path.join('logs', 'pyflow_log.txt')
+    )
+
+
 @bp.route('/<hashid:job_id>/restart')
 @login_required
 @admin_required

app/main/__init__.py

@@ -2,4 +2,4 @@ from flask import Blueprint
 
 
 bp = Blueprint('main', __name__)
-from . import routes
+from . import events, routes

app/main/events.py

@@ -1,8 +1,8 @@
 from app import hashids, socketio
-from app.decorators import socketio_login_required
+from app.models import User
-from app.models import TesseractOCRModel, TranskribusHTRModel, User
 from flask_login import current_user
 from flask_socketio import join_room
+from app.decorators import socketio_login_required
 
 
 @socketio.on('users.user.get')

app/models.py

@@ -1,8 +1,8 @@
-from app import db, login
+from app import db, login, mail, socketio
 from app.converters.vrt import normalize_vrt_file
-from app.sqlalchemy_type_decorators import ContainerColumn, IntEnumColumn
+from app.email import create_message
 from datetime import datetime, timedelta
-from enum import IntEnum
+from enum import Enum, IntEnum
 from flask import current_app, url_for
 from flask_hashids import HashidMixin
 from flask_login import UserMixin
@@ -20,9 +20,57 @@ import yaml
 
 
 TRANSKRIBUS_HTR_MODELS = \
-    json.loads(requests.get('https://transkribus.eu/TrpServer/rest/models/text').content)['trpModelMetadata']  # noqa
+    json.loads(requests.get('https://transkribus.eu/TrpServer/rest/models/text', params={'docType': 'handwritten'}).content)['trpModelMetadata']  # noqa
 
 
+##############################################################################
+# enums                                                                      #
+##############################################################################
+# region enums
+class CorpusStatus(IntEnum):
+    UNPREPARED = 1
+    SUBMITTED = 2
+    QUEUED = 3
+    BUILDING = 4
+    BUILT = 5
+    FAILED = 6
+    STARTING_ANALYSIS_SESSION = 7
+    RUNNING_ANALYSIS_SESSION = 8
+    CANCELING_ANALYSIS_SESSION = 9
+
+
+class JobStatus(IntEnum):
+    INITIALIZING = 1
+    SUBMITTED = 2
+    QUEUED = 3
+    RUNNING = 4
+    CANCELING = 5
+    CANCELED = 6
+    COMPLETED = 7
+    FAILED = 8
+
+
+class Permission(IntEnum):
+    '''
+    Defines User permissions as integers by the power of 2. User permission
+    can be evaluated using the bitwise operator &.
+    '''
+    ADMINISTRATE = 1
+    CONTRIBUTE = 2
+    USE_API = 4
+
+
+class UserSettingJobStatusMailNotificationLevel(IntEnum):
+    NONE = 1
+    END = 2
+    ALL = 3
+# endregion enums
+
+
+##############################################################################
+# mixins                                                                     #
+##############################################################################
+# region mixins
 class FileMixin:
     '''
     Mixin for db.Model classes. All file related models should use this.
@@ -39,18 +87,59 @@ class FileMixin:
             'last_edited_date': self.last_edited_date.isoformat() + 'Z',
             'mimetype': self.mimetype
         }
+# endregion mixins
 
 
-class Permission(IntEnum):
+##############################################################################
-    '''
+# type_decorators                                                            #
-    Defines User permissions as integers by the power of 2. User permission
+##############################################################################
-    can be evaluated using the bitwise operator &.
+# region type_decorators
-    '''
+class IntEnumColumn(db.TypeDecorator):
-    ADMINISTRATE = 1
+    impl = db.Integer
-    CONTRIBUTE = 2
+
-    USE_API = 4
+    def __init__(self, enum_type, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.enum_type = enum_type
+
+    def process_bind_param(self, value, dialect):
+        if isinstance(value, self.enum_type) and isinstance(value.value, int):
+            return value.value
+        elif isinstance(value, int):
+            return self.enum_type(value).value
+        else:
+            return TypeError()
+
+    def process_result_value(self, value, dialect):
+        return self.enum_type(value)
 
 
+class ContainerColumn(db.TypeDecorator):
+    impl = db.String
+
+    def __init__(self, container_type, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.container_type = container_type
+
+    def process_bind_param(self, value, dialect):
+        if isinstance(value, self.container_type):
+            return json.dumps(value)
+        elif (
+            isinstance(value, str)
+            and isinstance(json.loads(value), self.container_type)
+        ):
+            return value
+        else:
+            return TypeError()
+
+    def process_result_value(self, value, dialect):
+        return json.loads(value)
+# endregion type_decorators
+
+
+##############################################################################
+# Models                                                                     #
+##############################################################################
+# region models
 class Role(HashidMixin, db.Model):
     __tablename__ = 'roles'
     # Primary key
@@ -123,12 +212,6 @@ class Role(HashidMixin, db.Model):
         db.session.commit()
 
 
-class UserSettingJobStatusMailNotificationLevel(IntEnum):
-    NONE = 1
-    END = 2
-    ALL = 3
-
-
 class User(HashidMixin, UserMixin, db.Model):
     __tablename__ = 'users'
     # Primary key
@@ -449,7 +532,6 @@ class TranskribusHTRModel(HashidMixin, db.Model):
             'user_id': self.user.hashid,
             'shared': self.shared,
             'transkribus_model_id': self.transkribus_model_id,
-            'transkribus_name': self.transkribus_name
         }
         if backrefs:
             dict_tesseract_ocr_model['user'] = \
@@ -466,20 +548,14 @@ class TranskribusHTRModel(HashidMixin, db.Model):
         #     and 'creator' in m and m['creator'] == 'Transkribus Team'
         #     and 'docType' in m and m['docType'] == 'handwritten'
         # ]
-        models = [
+        for m in TRANSKRIBUS_HTR_MODELS:
-            m for m in TRANSKRIBUS_HTR_MODELS
-            if m['modelId'] in [35909, 33744, 33597, 29820, 37789, 13685, 37855, 26124, 37738, 30919, 34763]
-        ]
-        for m in models:
             model = TranskribusHTRModel.query.filter_by(transkribus_model_id=m['modelId']).first()  # noqa
             if model is not None:
                 model.shared = True
                 model.transkribus_model_id = m['modelId']
-                model.transkribus_name = m['name']
                 continue
             model = TranskribusHTRModel(
                 shared=True,
-                transkribus_name=m['name'],
                 transkribus_model_id=m['modelId'],
                 user=user,
             )
@@ -605,17 +681,6 @@ class JobResult(FileMixin, HashidMixin, db.Model):
         return self.job.user_id
 
 
-class JobStatus(IntEnum):
-    INITIALIZING = 1
-    SUBMITTED = 2
-    QUEUED = 3
-    RUNNING = 4
-    CANCELING = 5
-    CANCELED = 6
-    COMPLETED = 7
-    FAILED = 8
-
-
 class Job(HashidMixin, db.Model):
     '''
     Class to define Jobs.
@@ -828,18 +893,6 @@ class CorpusFile(FileMixin, HashidMixin, db.Model):
         return dict_corpus_file
 
 
-class CorpusStatus(IntEnum):
-    UNPREPARED = 1
-    SUBMITTED = 2
-    QUEUED = 3
-    BUILDING = 4
-    BUILT = 5
-    FAILED = 6
-    STARTING_ANALYSIS_SESSION = 7
-    RUNNING_ANALYSIS_SESSION = 8
-    CANCELING_ANALYSIS_SESSION = 9
-
-
 class Corpus(HashidMixin, db.Model):
     '''
     Class to define a corpus.
@@ -964,8 +1017,95 @@ class Corpus(HashidMixin, db.Model):
                 for x in self.files
             }
         return dict_corpus
+# endregion models
 
 
+##############################################################################
+# event_handlers                                                             #
+##############################################################################
+# region event_handlers
+@db.event.listens_for(Corpus, 'after_delete')
+@db.event.listens_for(CorpusFile, 'after_delete')
+@db.event.listens_for(Job, 'after_delete')
+@db.event.listens_for(JobInput, 'after_delete')
+@db.event.listens_for(JobResult, 'after_delete')
+def ressource_after_delete(mapper, connection, ressource):
+    jsonpatch = [{'op': 'remove', 'path': ressource.jsonpatch_path}]
+    room = f'users.{ressource.user_hashid}'
+    socketio.emit('users.patch', jsonpatch, room=room)
+
+
+@db.event.listens_for(Corpus, 'after_insert')
+@db.event.listens_for(CorpusFile, 'after_insert')
+@db.event.listens_for(Job, 'after_insert')
+@db.event.listens_for(JobInput, 'after_insert')
+@db.event.listens_for(JobResult, 'after_insert')
+def ressource_after_insert_handler(mapper, connection, ressource):
+    value = ressource.to_dict(backrefs=False, relationships=False)
+    for attr in mapper.relationships:
+        value[attr.key] = {}
+    jsonpatch = [
+        {'op': 'add', 'path': ressource.jsonpatch_path, 'value': value}
+    ]
+    room = f'users.{ressource.user_hashid}'
+    socketio.emit('users.patch', jsonpatch, room=room)
+
+
+@db.event.listens_for(Corpus, 'after_update')
+@db.event.listens_for(CorpusFile, 'after_update')
+@db.event.listens_for(Job, 'after_update')
+@db.event.listens_for(JobInput, 'after_update')
+@db.event.listens_for(JobResult, 'after_update')
+def ressource_after_update_handler(mapper, connection, ressource):
+    jsonpatch = []
+    for attr in db.inspect(ressource).attrs:
+        if attr.key in mapper.relationships:
+            continue
+        if not attr.load_history().has_changes():
+            continue
+        if isinstance(attr.value, datetime):
+            value = attr.value.isoformat() + 'Z'
+        elif isinstance(attr.value, Enum):
+            value = attr.value.name
+        else:
+            value = attr.value
+        jsonpatch.append(
+            {
+                'op': 'replace',
+                'path': f'{ressource.jsonpatch_path}/{attr.key}',
+                'value': value
+            }
+        )
+    if jsonpatch:
+        room = f'users.{ressource.user_hashid}'
+        socketio.emit('users.patch', jsonpatch, room=room)
+
+
+@db.event.listens_for(Job, 'after_update')
+def job_after_update_handler(mapper, connection, job):
+    for attr in db.inspect(job).attrs:
+        if attr.key != 'status':
+            continue
+        if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.NONE:
+            return
+        if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.END:
+            if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
+                return
+        msg = create_message(
+            job.user.email,
+            f'Status update for your Job "{job.title}"',
+            'tasks/email/notification',
+            job=job
+        )
+        mail.send(msg)
+# endregion event_handlers
+
+
+##############################################################################
+# misc                                                                       #
+##############################################################################
+# region misc
 @login.user_loader
 def load_user(user_id):
     return User.query.get(int(user_id))
+# endregion misc

app/services/routes.py

@@ -144,7 +144,6 @@ def tesseract_ocr_pipeline():
         x for x in TesseractOCRModel.query.filter().all()
         if version in x.compatible_service_versions and (x.shared == True or x.user == current_user)
     ]
-    current_app.logger.warning(tesseract_ocr_models)
     return render_template(
         'services/tesseract_ocr_pipeline.html.j2',
         form=form,

app/sqlalchemy_event_listeners.py

@@ -1,87 +0,0 @@
-from app import db, mail, socketio
-from app.email import create_message
-from app.models import (
-    Corpus,
-    CorpusFile,
-    Job,
-    JobInput,
-    JobResult,
-    JobStatus,
-    UserSettingJobStatusMailNotificationLevel
-)
-from datetime import datetime
-from enum import Enum
-
-
-@db.event.listens_for(Corpus, 'after_delete')
-@db.event.listens_for(CorpusFile, 'after_delete')
-@db.event.listens_for(Job, 'after_delete')
-@db.event.listens_for(JobInput, 'after_delete')
-@db.event.listens_for(JobResult, 'after_delete')
-def ressource_after_delete(mapper, connection, ressource):
-    jsonpatch = [{'op': 'remove', 'path': ressource.jsonpatch_path}]
-    room = f'users.{ressource.user_hashid}'
-    socketio.emit('users.patch', jsonpatch, room=room)
-
-
-@db.event.listens_for(Corpus, 'after_insert')
-@db.event.listens_for(CorpusFile, 'after_insert')
-@db.event.listens_for(Job, 'after_insert')
-@db.event.listens_for(JobInput, 'after_insert')
-@db.event.listens_for(JobResult, 'after_insert')
-def ressource_after_insert_handler(mapper, connection, ressource):
-    value = ressource.to_dict(backrefs=False, relationships=False)
-    for attr in mapper.relationships:
-        value[attr.key] = {}
-    jsonpatch = [
-        {'op': 'add', 'path': ressource.jsonpatch_path, 'value': value}
-    ]
-    room = f'users.{ressource.user_hashid}'
-    socketio.emit('users.patch', jsonpatch, room=room)
-
-
-@db.event.listens_for(Corpus, 'after_update')
-@db.event.listens_for(CorpusFile, 'after_update')
-@db.event.listens_for(Job, 'after_update')
-@db.event.listens_for(JobInput, 'after_update')
-@db.event.listens_for(JobResult, 'after_update')
-def ressource_after_update_handler(mapper, connection, ressource):
-    jsonpatch = []
-    for attr in db.inspect(ressource).attrs:
-        if attr.key in mapper.relationships:
-            continue
-        if not attr.load_history().has_changes():
-            continue
-        if isinstance(attr.value, datetime):
-            value = attr.value.isoformat() + 'Z'
-        elif isinstance(attr.value, Enum):
-            value = attr.value.name
-        else:
-            value = attr.value
-        jsonpatch.append(
-            {
-                'op': 'replace',
-                'path': f'{ressource.jsonpatch_path}/{attr.key}',
-                'value': value
-            }
-        )
-        if isinstance(ressource, Job) and attr.key == 'status':
-            _job_status_email_handler(ressource)
-    if jsonpatch:
-        room = f'users.{ressource.user_hashid}'
-        socketio.emit('users.patch', jsonpatch, room=room)
-
-
-def _job_status_email_handler(job):
-    if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.NONE:  # noqa
-        return
-    if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.END:  # noqa
-        if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
-            return
-    msg = create_message(
-        job.user.email,
-        f'Status update for your Job "{job.title}"',
-        'tasks/email/notification',
-        job=job
-    )
-    mail.send(msg)

app/sqlalchemy_type_decorators.py

@@ -1,43 +0,0 @@
-from app import db
-import json
-
-
-class IntEnumColumn(db.TypeDecorator):
-    impl = db.Integer
-
-    def __init__(self, enum_type, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.enum_type = enum_type
-
-    def process_bind_param(self, value, dialect):
-        if isinstance(value, self.enum_type) and isinstance(value.value, int):
-            return value.value
-        elif isinstance(value, int):
-            return self.enum_type(value).value
-        else:
-            return TypeError()
-
-    def process_result_value(self, value, dialect):
-        return self.enum_type(value)
-
-
-class ContainerColumn(db.TypeDecorator):
-    impl = db.String
-
-    def __init__(self, container_type, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.container_type = container_type
-
-    def process_bind_param(self, value, dialect):
-        if isinstance(value, self.container_type):
-            return json.dumps(value)
-        elif (
-            isinstance(value, str)
-            and isinstance(json.loads(value), self.container_type)
-        ):
-            return value
-        else:
-            return TypeError()
-
-    def process_result_value(self, value, dialect):
-        return json.loads(value)

app/static/js/RessourceDisplays/JobDisplay.js

@@ -69,6 +69,14 @@ class JobDisplay extends RessourceDisplay {
         element.classList.remove('hide');
       }
     }
+    elements = this.displayElement.querySelectorAll('.job-log-trigger');
+    for (element of elements) {
+      if (['COMPLETED', 'FAILED'].includes(status)) {
+        element.classList.remove('hide');
+      } else {
+        element.classList.add('hide');
+      }
+    }
     elements = this.displayElement.querySelectorAll('.job-restart-trigger');
     for (element of elements) {
       if (['COMPLETED', 'FAILED'].includes(status)) {

app/tasks.py

@@ -0,0 +1,9 @@
+from app.daemon import daemon
+
+
+def register(app, scheduler):
+    if app.config['NOPAQUE_IS_PRIMARY_INSTANCE']:
+        @scheduler.task('interval', id='daemon', seconds=3)
+        def daemon_task():
+            with app.app_context():
+                daemon()

app/templates/jobs/job.html.j2

@@ -79,6 +79,7 @@
         </div>
         <div class="card-action right-align">
           {% if current_user.is_administrator()  %}
+          <a class="btn hide modal-trigger job-log-trigger waves-effect waves-light" data-target="job-log-modal"><i class="material-icons left">repeat</i>Log</a>
           <a class="btn hide modal-trigger restart-job-trigger waves-effect waves-light" data-target="restart-job-modal"><i class="material-icons left">repeat</i>Restart</a>
           {% endif %}
           <!-- <a href="#" class="btn disabled waves-effect waves-light"><i class="material-icons left">settings</i>Export Parameters</a> -->
@@ -143,6 +144,16 @@
 
 {% block modals %}
 {{ super() }}
+<div id="job-log-modal" class="modal">
+  <div class="modal-content">
+    <h4>Job logs</h4>
+    <iframe src="{{ url_for('jobs.job_log', job_id=job.id) }}" style="border: 0; width: 100%; height: 450px;"></iframe>
+  </div>
+  <div class="modal-footer">
+    <a href="#!" class="btn modal-close waves-effect waves-light">Close</a>
+  </div>
+</div>
+
 <div id="delete-job-modal" class="modal">
   <div class="modal-content">
     <h4>Confirm deletion</h4>

boot.sh

@@ -1,28 +1,37 @@
 #!/bin/bash
+
 source venv/bin/activate
+
+display_help() {
+    local script_name=$(basename "${0}")
+    echo ""
+    echo "Usage: ${script_name} [COMMAND]"
+    echo ""
+    echo "Run wrapper for a nopaque instance"
+    echo ""
+    echo "Commands:"
+    echo "  flask    A general utility script for Flask applications."
+    echo ""
+    echo "Run '${script_name} COMMAND --help' for more information on a command."
+}
+
 if [[ "${#}" -eq 0 ]]; then
     if [[ "${NOPAQUE_IS_PRIMARY_INSTANCE:-True}" == "True" ]]; then
         while true; do
-            echo "INFO  Run deployment tasks..."
             flask deploy
             if [[ "${?}" == "0" ]]; then
                 break
             fi
-            echo "WARNING  ...Failed, retrying in 5 secs..."
+            echo "Deploy command failed, retrying in 5 secs..."
             sleep 5
         done
-        echo "INFO  Start nopaque daemon..."
-        flask daemon run &
     fi
-    echo "INFO  Start nopaque..."
     python nopaque.py
 elif [[ "${1}" == "flask" ]]; then
-    exec ${@:1}
+    flask "${@:2}"
+elif [[ "${1}" == "--help" || "${1}" == "-h" ]]; then
+    display_help
 else
-    echo "${0} [COMMAND]"
+    display_help
-    echo ""
+    exit 1
-    echo "nopaque startup script"
-    echo ""
-    echo "Commands:"
-    echo "  flask"
 fi

nopaque.py

@@ -3,7 +3,7 @@
 import eventlet
 eventlet.monkey_patch()
 
-from app import db, cli, create_app, socketio  # noqa
+from app import cli, create_app, db, scheduler, socketio  # noqa
 from app.models import (
     Corpus,
     CorpusFile,
@@ -49,6 +49,12 @@ def make_shell_context() -> Dict[str, Any]:
 
 
 def main():
+    with app.app_context():
+        if app.config['NOPAQUE_IS_PRIMARY_INSTANCE']:
+            for corpus in Corpus.query.filter(Corpus.num_analysis_sessions > 0).all():
+                corpus.num_analysis_sessions = 0
+            db.session.commit()
+        scheduler.start()
     socketio.run(app, host='0.0.0.0')