Merge branch 'access-pipeline' of gitlab.ub.uni-bielefeld.de:sfb1288inf/nopaque into access-pipeline

.dockerignore

@@ -5,9 +5,9 @@
 !app
 !migrations
 !tests
+!.flaskenv
 !boot.sh
 !config.py
 !docker-nopaque-entrypoint.sh
+!nopaque.py
 !requirements.txt
-!requirements.freezed.txt
-!wsgi.py

.env.tpl

@@ -1,20 +1,32 @@
 ##############################################################################
-# Environment variables used by Docker Compose config files.                 #
+# Variables for use in Docker Compose YAML files                             #
 ##############################################################################
 # HINT: Use this bash command `id -u`
 # NOTE: 0 (= root user) is not allowed
 HOST_UID=
 
 # HINT: Use this bash command `id -g`
-# NOTE: 0 (= root group) is not allowed
 HOST_GID=
 
 # HINT: Use this bash command `getent group docker | cut -d: -f3`
 HOST_DOCKER_GID=
 
 # DEFAULT: nopaque
-NOPAQUE_DOCKER_NETWORK_NAME=nopaque
+# DOCKER_DEFAULT_NETWORK_NAME=
+
+# DEFAULT: ./volumes/db/data
+# NOTE: Use `.` as <project-basedir>
+# DOCKER_DB_SERVICE_DATA_VOLUME_SOURCE_PATH=
+
+# DEFAULT: ./volumes/mq/data
+# NOTE: Use `.` as <project-basedir>
+# DOCKER_MQ_SERVICE_DATA_VOLUME_SOURCE_PATH=
 
 # NOTE: This must be a network share and it must be available on all
-#       Docker Swarm nodes, mounted to the same path.
-HOST_NOPAQUE_DATA_PATH=/mnt/nopaque
+#       Docker Swarm nodes, mounted to the same path with the same
+#       user and group ownership.
+DOCKER_NOPAQUE_SERVICE_DATA_VOLUME_SOURCE_PATH=
+
+# DEFAULT: ./volumes/nopaque/logs
+# NOTE: Use `.` as <project-basedir>
+# DOCKER_NOPAQUE_SERVICE_LOGS_VOLUME_SOURCE_PATH=.

.flaskenv

@@ -0,0 +1 @@
+FLASK_APP=nopaque.py

.gitignore

@@ -2,6 +2,8 @@
 app/static/gen/
 volumes/
 docker-compose.override.yml
+logs/
+!logs/dummy
 *.env
 
 *.pjentsch-testing

.vscode/settings.json

@@ -1,10 +1,19 @@
 {
     "editor.rulers": [79],
-    "editor.tabSize": 4,
     "files.insertFinalNewline": true,
-    "files.trimFinalNewlines": true,
-    "files.trimTrailingWhitespace": true,
+    "[css]": {
+        "editor.tabSize": 2
+    },
+    "[html]": {
+        "editor.tabSize": 2
+    },
     "[javascript]": {
-        "editor.tabSize": 2,
+        "editor.tabSize": 2
+    },
+    "[jinja-html]": {
+        "editor.tabSize": 2
+    },
+    "[scss]": {
+        "editor.tabSize": 2
     }
 }

Dockerfile

@@ -35,17 +35,20 @@ ENV PATH="${NOPAQUE_PYTHON3_VENV_PATH}/bin:${PATH}"
 
 
 # Install Python dependencies
-COPY --chown=nopaque:nopaque requirements.freezed.txt requirements.freezed.txt
-RUN python3 -m pip install --requirement requirements.freezed.txt \
- && rm requirements.freezed.txt
+COPY --chown=nopaque:nopaque requirements.txt requirements.txt
+RUN python3 -m pip install --requirement requirements.txt \
+ && rm requirements.txt
 
 
 # Install the application
 COPY docker-nopaque-entrypoint.sh /usr/local/bin/
+
 COPY --chown=nopaque:nopaque app app
 COPY --chown=nopaque:nopaque migrations migrations
 COPY --chown=nopaque:nopaque tests tests
-COPY --chown=nopaque:nopaque boot.sh config.py wsgi.py ./
+COPY --chown=nopaque:nopaque .flaskenv boot.sh config.py nopaque.py requirements.txt ./
+
+RUN mkdir logs
 
 
 EXPOSE 5000

README.md

@@ -35,7 +35,7 @@ username@hostname:~$ sudo mount --types cifs --options gid=${USER},password=nopa
 # Clone the nopaque repository
 username@hostname:~$ git clone https://gitlab.ub.uni-bielefeld.de/sfb1288inf/nopaque.git
 # Create data directories
-username@hostname:~$ mkdir volumes/{db,mq}
+username@hostname:~$ mkdir data/{db,logs,mq}
 username@hostname:~$ cp db.env.tpl db.env
 username@hostname:~$ cp .env.tpl .env
 # Fill out the variables within these files.

app/__init__.py

@@ -2,9 +2,9 @@ from apifairy import APIFairy
 from config import Config
 from docker import DockerClient
 from flask import Flask
-from flask.logging import default_handler
 from flask_apscheduler import APScheduler
 from flask_assets import Environment
+from flask_breadcrumbs import Breadcrumbs, default_breadcrumb_root
 from flask_login import LoginManager
 from flask_mail import Mail
 from flask_marshmallow import Marshmallow
@@ -13,142 +13,98 @@ from flask_paranoid import Paranoid
 from flask_socketio import SocketIO
 from flask_sqlalchemy import SQLAlchemy
 from flask_hashids import Hashids
-from logging import Formatter, StreamHandler
-from werkzeug.middleware.proxy_fix import ProxyFix
 
 
-docker_client = DockerClient.from_env()
-
 apifairy = APIFairy()
 assets = Environment()
+breadcrumbs = Breadcrumbs()
 db = SQLAlchemy()
+docker_client = DockerClient()
 hashids = Hashids()
 login = LoginManager()
+login.login_view = 'auth.login'
+login.login_message = 'Please log in to access this page.'
 ma = Marshmallow()
 mail = Mail()
 migrate = Migrate(compare_type=True)
 paranoid = Paranoid()
+paranoid.redirect_view = '/'
 scheduler = APScheduler()
 socketio = SocketIO()
 
 
 def create_app(config: Config = Config) -> Flask:
-    ''' Creates an initialized Flask object. '''
-
+    ''' Creates an initialized Flask (WSGI Application) object. '''
     app = Flask(__name__)
     app.config.from_object(config)
-
-    # region Logging
-    log_formatter = Formatter(
-        fmt=app.config['NOPAQUE_LOG_FORMAT'],
-        datefmt=app.config['NOPAQUE_LOG_DATE_FORMAT']
-    )
-
-    log_handler = StreamHandler()
-    log_handler.setFormatter(log_formatter)
-    log_handler.setLevel(app.config['NOPAQUE_LOG_LEVEL'])
-
-    app.logger.setLevel('DEBUG')
-    app.logger.removeHandler(default_handler)
-    app.logger.addHandler(log_handler)
-    # endregion Logging
-
-    # region Middlewares
-    if app.config['NOPAQUE_PROXY_FIX_ENABLED']:
-        app.wsgi_app = ProxyFix(
-            app.wsgi_app,
-            x_for=app.config['NOPAQUE_PROXY_FIX_X_FOR'],
-            x_host=app.config['NOPAQUE_PROXY_FIX_X_HOST'],
-            x_port=app.config['NOPAQUE_PROXY_FIX_X_PORT'],
-            x_prefix=app.config['NOPAQUE_PROXY_FIX_X_PREFIX'],
-            x_proto=app.config['NOPAQUE_PROXY_FIX_X_PROTO']
-        )
-    # endregion Middlewares
-
-    # region Extensions
+    config.init_app(app)
     docker_client.login(
         app.config['NOPAQUE_DOCKER_REGISTRY_USERNAME'],
         password=app.config['NOPAQUE_DOCKER_REGISTRY_PASSWORD'],
         registry=app.config['NOPAQUE_DOCKER_REGISTRY']
     )
 
-    from .models import AnonymousUser, User
-
     apifairy.init_app(app)
     assets.init_app(app)
+    breadcrumbs.init_app(app)
     db.init_app(app)
     hashids.init_app(app)
     login.init_app(app)
-    login.anonymous_user = AnonymousUser
-    login.login_view = 'auth.login'
-    login.user_loader(lambda user_id: User.query.get(int(user_id)))
     ma.init_app(app)
     mail.init_app(app)
     migrate.init_app(app, db)
     paranoid.init_app(app)
-    paranoid.redirect_view = '/'
     scheduler.init_app(app)
-    socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])
-    # endregion Extensions
+    socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])  # noqa
 
-    # region Blueprints
-    from .blueprints.admin import bp as admin_blueprint
-    app.register_blueprint(admin_blueprint, url_prefix='/admin')
-
-    from .blueprints.api import bp as api_blueprint
-    app.register_blueprint(api_blueprint, url_prefix='/api')
-
-    from .blueprints.auth import bp as auth_blueprint
-    app.register_blueprint(auth_blueprint)
-
-    from .blueprints.contributions import bp as contributions_blueprint
-    app.register_blueprint(contributions_blueprint, url_prefix='/contributions')
-
-    from .blueprints.corpora import bp as corpora_blueprint
-    app.register_blueprint(corpora_blueprint, cli_group='corpus', url_prefix='/corpora')
-
-    from .blueprints.errors import bp as errors_bp
-    app.register_blueprint(errors_bp)
-
-    from .blueprints.jobs import bp as jobs_blueprint
-    app.register_blueprint(jobs_blueprint, url_prefix='/jobs')
-
-    from .blueprints.main import bp as main_blueprint
-    app.register_blueprint(main_blueprint, cli_group=None)
-
-    from .blueprints.services import bp as services_blueprint
-    app.register_blueprint(services_blueprint, url_prefix='/services')
-
-    from .blueprints.settings import bp as settings_blueprint
-    app.register_blueprint(settings_blueprint, url_prefix='/settings')
-
-    from .blueprints.users import bp as users_blueprint
-    app.register_blueprint(users_blueprint, cli_group='user', url_prefix='/users')
-
-    from .blueprints.workshops import bp as workshops_blueprint
-    app.register_blueprint(workshops_blueprint, url_prefix='/workshops')
-    # endregion Blueprints
-
-    # region SocketIO Namespaces
-    from .namespaces.cqi_over_sio import CQiOverSocketIONamespace
-    socketio.on_namespace(CQiOverSocketIONamespace('/cqi_over_sio'))
-
-    from .namespaces.users import UsersNamespace
-    socketio.on_namespace(UsersNamespace('/users'))
-    # endregion SocketIO Namespaces
-
-    # region Database event Listeners
     from .models.event_listeners import register_event_listeners
     register_event_listeners()
-    # endregion Database event Listeners
 
-    # region Add scheduler jobs
-    if app.config['NOPAQUE_IS_PRIMARY_INSTANCE']:
-        from .jobs import handle_corpora
-        scheduler.add_job('handle_corpora', handle_corpora, seconds=3, trigger='interval')
+    from .admin import bp as admin_blueprint
+    default_breadcrumb_root(admin_blueprint, '.admin')
+    app.register_blueprint(admin_blueprint, url_prefix='/admin')
 
-        from .jobs import handle_jobs
-        scheduler.add_job('handle_jobs', handle_jobs, seconds=3, trigger='interval')
-    # endregion Add scheduler jobs
+    from .api import bp as api_blueprint
+    app.register_blueprint(api_blueprint, url_prefix='/api')
+
+    from .auth import bp as auth_blueprint
+    default_breadcrumb_root(auth_blueprint, '.')
+    app.register_blueprint(auth_blueprint)
+
+    from .contributions import bp as contributions_blueprint
+    default_breadcrumb_root(contributions_blueprint, '.contributions')
+    app.register_blueprint(contributions_blueprint, url_prefix='/contributions')
+
+    from .corpora import bp as corpora_blueprint
+    from .corpora.cqi_over_sio import CQiNamespace
+    default_breadcrumb_root(corpora_blueprint, '.corpora')
+    app.register_blueprint(corpora_blueprint, cli_group='corpus', url_prefix='/corpora')
+    socketio.on_namespace(CQiNamespace('/cqi_over_sio'))
+
+    from .errors import bp as errors_bp
+    app.register_blueprint(errors_bp)
+
+    from .jobs import bp as jobs_blueprint
+    default_breadcrumb_root(jobs_blueprint, '.jobs')
+    app.register_blueprint(jobs_blueprint, url_prefix='/jobs')
+
+    from .main import bp as main_blueprint
+    default_breadcrumb_root(main_blueprint, '.')
+    app.register_blueprint(main_blueprint, cli_group=None)
+
+    from .services import bp as services_blueprint
+    default_breadcrumb_root(services_blueprint, '.services')
+    app.register_blueprint(services_blueprint, url_prefix='/services')
+
+    from .settings import bp as settings_blueprint
+    default_breadcrumb_root(settings_blueprint, '.settings')
+    app.register_blueprint(settings_blueprint, url_prefix='/settings')
+
+    from .users import bp as users_blueprint
+    default_breadcrumb_root(users_blueprint, '.users')
+    app.register_blueprint(users_blueprint, cli_group='user', url_prefix='/users')
+
+    from .workshops import bp as workshops_blueprint
+    app.register_blueprint(workshops_blueprint, url_prefix='/workshops')
 
     return app

app/admin/json_routes.py

@@ -1,6 +1,6 @@
 from flask import abort, request
-from app.decorators import content_negotiation
 from app import db
+from app.decorators import content_negotiation
 from app.models import User
 from . import bp
 

app/admin/routes.py

@@ -1,7 +1,8 @@
 from flask import abort, flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from app import db, hashids
 from app.models import Avatar, Corpus, Role, User
-from app.blueprints.users.settings.forms import (
+from app.users.settings.forms import (
     UpdateAvatarForm,
     UpdatePasswordForm,
     UpdateNotificationsForm,
@@ -10,9 +11,14 @@ from app.blueprints.users.settings.forms import (
 )
 from . import bp
 from .forms import UpdateUserForm
+from app.users.utils import (
+    user_endpoint_arguments_constructor as user_eac,
+    user_dynamic_list_constructor as user_dlc
+)
 
 
 @bp.route('')
+@register_breadcrumb(bp, '.', '<i class="material-icons left">admin_panel_settings</i>Administration')
 def admin():
     return render_template(
         'admin/admin.html.j2',
@@ -21,6 +27,7 @@ def admin():
 
 
 @bp.route('/corpora')
+@register_breadcrumb(bp, '.corpora', 'Corpora')
 def corpora():
     corpora = Corpus.query.all()
     return render_template(
@@ -31,6 +38,7 @@ def corpora():
 
 
 @bp.route('/users')
+@register_breadcrumb(bp, '.users', '<i class="material-icons left">group</i>Users')
 def users():
     users = User.query.all()
     return render_template(
@@ -41,6 +49,7 @@ def users():
 
 
 @bp.route('/users/<hashid:user_id>')
+@register_breadcrumb(bp, '.users.entity', '', dynamic_list_constructor=user_dlc)
 def user(user_id):
     user = User.query.get_or_404(user_id)
     corpora = Corpus.query.filter(Corpus.user == user).all()
@@ -53,6 +62,7 @@ def user(user_id):
 
 
 @bp.route('/users/<hashid:user_id>/settings', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.users.entity.settings', '<i class="material-icons left">settings</i>Settings')
 def user_settings(user_id):
     user = User.query.get_or_404(user_id)
     update_account_information_form = UpdateAccountInformationForm(user)

app/api/jobs.py

@@ -5,8 +5,8 @@ from flask import abort, Blueprint
 from werkzeug.exceptions import InternalServerError
 from app import db, hashids
 from app.models import Job, JobInput, JobStatus, TesseractOCRPipelineModel
-from .auth import auth_error_responses, token_auth
 from .schemas import EmptySchema, JobSchema, SpaCyNLPPipelineJobSchema, TesseractOCRPipelineJobSchema, TesseractOCRPipelineModelSchema
+from .auth import auth_error_responses, token_auth
 
 
 bp = Blueprint('jobs', __name__)
@@ -77,7 +77,7 @@ def delete_job(job_id):
     job = Job.query.get(job_id)
     if job is None:
         abort(404)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     try:
         job.delete()
@@ -97,6 +97,6 @@ def get_job(job_id):
     job = Job.query.get(job_id)
     if job is None:
         abort(404)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     return job

app/api/schemas.py

@@ -10,7 +10,7 @@ from app.models import (
     User,
     UserSettingJobStatusMailNotificationLevel
 )
-from app.blueprints.services import SERVICES
+from app.services import SERVICES
 
 
 

app/api/users.py

@@ -3,11 +3,11 @@ from apifairy import authenticate, body, response
 from apifairy.decorators import other_responses
 from flask import abort, Blueprint
 from werkzeug.exceptions import InternalServerError
-from app.email import create_message, send
 from app import db
+from app.email import create_message, send
 from app.models import User
-from .auth import auth_error_responses, token_auth
 from .schemas import EmptySchema, UserSchema
+from .auth import auth_error_responses, token_auth
 
 
 bp = Blueprint('users', __name__)
@@ -60,7 +60,7 @@ def delete_user(user_id):
     user = User.query.get(user_id)
     if user is None:
         abort(404)
-    if not (user == current_user or current_user.is_administrator):
+    if not (user == current_user or current_user.is_administrator()):
         abort(403)
     user.delete()
     db.session.commit()
@@ -78,7 +78,7 @@ def get_user(user_id):
     user = User.query.get(user_id)
     if user is None:
         abort(404)
-    if not (user == current_user or current_user.is_administrator):
+    if not (user == current_user or current_user.is_administrator()):
         abort(403)
     return user
 
@@ -94,6 +94,6 @@ def get_user_by_username(username):
     user = User.query.filter(User.username == username).first()
     if user is None:
         abort(404)
-    if not (user == current_user or current_user.is_administrator):
+    if not (user == current_user or current_user.is_administrator()):
         abort(403)
     return user

app/auth/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, request, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user, login_user, login_required, logout_user
 from app import db
 from app.email import create_message, send
@@ -18,21 +19,18 @@ def before_request():
     Checks if a user is unconfirmed when visiting specific sites. Redirects to
     unconfirmed view if user is unconfirmed.
     """
-    if not current_user.is_authenticated:
-        return
-
-    current_user.ping()
-    db.session.commit()
-    if (not current_user.confirmed
-            and request.endpoint
-            and request.blueprint != 'auth'
-            and request.endpoint != 'static'):
-        return redirect(url_for('auth.unconfirmed'))
-    if not current_user.terms_of_use_accepted:
-        return redirect(url_for('main.terms_of_use'))
+    if current_user.is_authenticated:
+        current_user.ping()
+        db.session.commit()
+        if (not current_user.confirmed
+                and request.endpoint
+                and request.blueprint != 'auth'
+                and request.endpoint != 'static'):
+            return redirect(url_for('auth.unconfirmed'))
 
 
 @bp.route('/register', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.register', 'Register')
 def register():
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))
@@ -69,6 +67,7 @@ def register():
 
 
 @bp.route('/login', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.login', 'Login')
 def login():
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))
@@ -99,6 +98,7 @@ def logout():
 
 
 @bp.route('/unconfirmed')
+@register_breadcrumb(bp, '.unconfirmed', 'Unconfirmed')
 @login_required
 def unconfirmed():
     if current_user.confirmed:
@@ -141,6 +141,7 @@ def confirm(token):
 
 
 @bp.route('/reset-password-request', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.reset_password_request', 'Password Reset')
 def reset_password_request():
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))
@@ -170,6 +171,7 @@ def reset_password_request():
 
 
 @bp.route('/reset-password/<token>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.reset_password', 'Password Reset')
 def reset_password(token):
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))

app/blueprints/jobs/__init__.py

@@ -1,18 +0,0 @@
-from flask import Blueprint
-from flask_login import login_required
-
-
-bp = Blueprint('jobs', __name__)
-
-
-@bp.before_request
-@login_required
-def before_request():
-    '''
-    Ensures that the routes in this package can only be visited by users that
-    are logged in.
-    '''
-    pass
-
-
-from . import routes, json_routes

app/contributions/routes.py

@@ -1,7 +1,9 @@
 from flask import redirect, url_for
+from flask_breadcrumbs import register_breadcrumb
 from . import bp
 
 
 @bp.route('')
+@register_breadcrumb(bp, '.', '<i class="material-icons left">new_label</i>My Contributions')
 def contributions():
     return redirect(url_for('main.dashboard', _anchor='contributions'))

app/contributions/spacy_nlp_pipeline_models/forms.py

@@ -1,7 +1,7 @@
 from flask_wtf.file import FileField, FileRequired
 from wtforms import StringField, ValidationError
 from wtforms.validators import InputRequired, Length
-from app.blueprints.services import SERVICES
+from app.services import SERVICES
 from ..forms import ContributionBaseForm, UpdateContributionBaseForm
 
 

app/contributions/spacy_nlp_pipeline_models/json_routes.py

@@ -4,7 +4,7 @@ from threading import Thread
 from app import db
 from app.decorators import content_negotiation, permission_required
 from app.models import SpaCyNLPPipelineModel
-from . import bp
+from .. import bp
 
 
 @bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['DELETE'])
@@ -17,7 +17,7 @@ def delete_spacy_model(spacy_nlp_pipeline_model_id):
             db.session.commit()
     
     snpm = SpaCyNLPPipelineModel.query.get_or_404(spacy_nlp_pipeline_model_id)
-    if not (snpm.user == current_user or current_user.is_administrator):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_spacy_model,
@@ -39,7 +39,7 @@ def update_spacy_nlp_pipeline_model_is_public(spacy_nlp_pipeline_model_id):
     if not isinstance(is_public, bool):
         abort(400)
     snpm = SpaCyNLPPipelineModel.query.get_or_404(spacy_nlp_pipeline_model_id)
-    if not (snpm.user == current_user or current_user.is_administrator):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     snpm.is_public = is_public
     db.session.commit()

app/contributions/spacy_nlp_pipeline_models/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 from app import db
 from app.models import SpaCyNLPPipelineModel
@@ -7,9 +8,13 @@ from .forms import (
     CreateSpaCyNLPPipelineModelForm,
     UpdateSpaCyNLPPipelineModelForm
 )
+from .utils import (
+    spacy_nlp_pipeline_model_dlc as spacy_nlp_pipeline_model_dlc
+)
 
 
 @bp.route('/spacy-nlp-pipeline-models')
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models', 'SpaCy NLP Pipeline Models')
 def spacy_nlp_pipeline_models():
     return render_template(
         'contributions/spacy_nlp_pipeline_models/spacy_nlp_pipeline_models.html.j2',
@@ -18,6 +23,7 @@ def spacy_nlp_pipeline_models():
 
 
 @bp.route('/spacy-nlp-pipeline-models/create', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models.create', 'Create')
 def create_spacy_nlp_pipeline_model():
     form = CreateSpaCyNLPPipelineModelForm()
     if form.is_submitted():
@@ -51,9 +57,10 @@ def create_spacy_nlp_pipeline_model():
 
 
 @bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models.entity', '', dynamic_list_constructor=spacy_nlp_pipeline_model_dlc)
 def spacy_nlp_pipeline_model(spacy_nlp_pipeline_model_id):
     snpm = SpaCyNLPPipelineModel.query.get_or_404(spacy_nlp_pipeline_model_id)
-    if not (snpm.user == current_user or current_user.is_administrator):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     form = UpdateSpaCyNLPPipelineModelForm(data=snpm.to_json_serializeable())
     if form.validate_on_submit():

app/contributions/spacy_nlp_pipeline_models/utils.py

@@ -0,0 +1,13 @@
+from flask import request, url_for
+from app.models import SpaCyNLPPipelineModel
+
+
+def spacy_nlp_pipeline_model_dlc():
+    snpm_id = request.view_args['spacy_nlp_pipeline_model_id']
+    snpm = SpaCyNLPPipelineModel.query.get_or_404(snpm_id)
+    return [
+        {
+            'text': f'{snpm.title} {snpm.version}',
+            'url': url_for('.spacy_nlp_pipeline_model', spacy_nlp_pipeline_model_id=snpm_id)
+        }
+    ]

app/contributions/tesseract_ocr_pipeline_models/forms.py

@@ -1,6 +1,6 @@
 from flask_wtf.file import FileField, FileRequired
 from wtforms import ValidationError
-from app.blueprints.services import SERVICES
+from app.services import SERVICES
 from ..forms import ContributionBaseForm, UpdateContributionBaseForm
 
 
@@ -9,7 +9,7 @@ class CreateTesseractOCRPipelineModelForm(ContributionBaseForm):
         'File',
         validators=[FileRequired()]
     )
-
+    
     def validate_tesseract_model_file(self, field):
         if not field.data.filename.lower().endswith('.traineddata'):
             raise ValidationError('traineddata files only!')

app/contributions/tesseract_ocr_pipeline_models/json_routes.py

@@ -17,7 +17,7 @@ def delete_tesseract_model(tesseract_ocr_pipeline_model_id):
             db.session.commit()
 
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_tesseract_ocr_pipeline_model,
@@ -39,7 +39,7 @@ def update_tesseract_ocr_pipeline_model_is_public(tesseract_ocr_pipeline_model_i
     if not isinstance(is_public, bool):
         abort(400)
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     topm.is_public = is_public
     db.session.commit()

app/contributions/tesseract_ocr_pipeline_models/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 from app import db
 from app.models import TesseractOCRPipelineModel
@@ -7,9 +8,13 @@ from .forms import (
     CreateTesseractOCRPipelineModelForm,
     UpdateTesseractOCRPipelineModelForm
 )
+from .utils import (
+    tesseract_ocr_pipeline_model_dlc as tesseract_ocr_pipeline_model_dlc
+)
 
 
 @bp.route('/tesseract-ocr-pipeline-models')
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline_models', 'Tesseract OCR Pipeline Models')
 def tesseract_ocr_pipeline_models():
     return render_template(
         'contributions/tesseract_ocr_pipeline_models/tesseract_ocr_pipeline_models.html.j2',
@@ -18,6 +23,7 @@ def tesseract_ocr_pipeline_models():
 
 
 @bp.route('/tesseract-ocr-pipeline-models/create', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline_models.create', 'Create')
 def create_tesseract_ocr_pipeline_model():
     form = CreateTesseractOCRPipelineModelForm()
     if form.is_submitted():
@@ -50,9 +56,10 @@ def create_tesseract_ocr_pipeline_model():
 
 
 @bp.route('/tesseract-ocr-pipeline-models/<hashid:tesseract_ocr_pipeline_model_id>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline_models.entity', '', dynamic_list_constructor=tesseract_ocr_pipeline_model_dlc)
 def tesseract_ocr_pipeline_model(tesseract_ocr_pipeline_model_id):
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     form = UpdateTesseractOCRPipelineModelForm(data=topm.to_json_serializeable())
     if form.validate_on_submit():

app/contributions/tesseract_ocr_pipeline_models/utils.py

@@ -0,0 +1,13 @@
+from flask import request, url_for
+from app.models import TesseractOCRPipelineModel
+
+
+def tesseract_ocr_pipeline_model_dlc():
+    topm_id = request.view_args['tesseract_ocr_pipeline_model_id']
+    topm = TesseractOCRPipelineModel.query.get_or_404(topm_id)
+    return [
+        {
+            'text': f'{topm.title} {topm.version}',
+            'url': url_for('.tesseract_ocr_pipeline_model', tesseract_ocr_pipeline_model_id=topm_id)
+        }
+    ]

app/converters/sandpaper.py

@@ -1,10 +1,11 @@
-from datetime import datetime
 from flask import current_app
-from pathlib import Path
-import json
-import shutil
 from app import db
 from app.models import User, Corpus, CorpusFile
+from datetime import datetime
+from pathlib import Path
+from typing import Dict, List
+import json
+import shutil
 
 
 class SandpaperConverter:
@@ -14,7 +15,7 @@ class SandpaperConverter:
 
     def run(self):
         with self.json_db_file.open('r') as f:
-            json_db: list[dict] = json.load(f)
+            json_db: List[Dict] = json.load(f)
 
         for json_user in json_db:
             if not json_user['confirmed']:
@@ -25,7 +26,7 @@ class SandpaperConverter:
             db.session.commit()
 
 
-    def convert_user(self, json_user: dict, user_dir: Path):
+    def convert_user(self, json_user: Dict, user_dir: Path):
         current_app.logger.info(f'Create User {json_user["username"]}...')
         try:
             user = User.create(
@@ -47,7 +48,7 @@ class SandpaperConverter:
         current_app.logger.info('Done')
 
 
-    def convert_corpus(self, json_corpus: dict, user: User, corpus_dir: Path):
+    def convert_corpus(self, json_corpus: Dict, user: User, corpus_dir: Path):
         current_app.logger.info(f'Create Corpus {json_corpus["title"]}...')
         try:
             corpus = Corpus.create(
@@ -63,7 +64,7 @@ class SandpaperConverter:
         current_app.logger.info('Done')
 
 
-    def convert_corpus_file(self, json_corpus_file: dict, corpus: Corpus, corpus_dir: Path):
+    def convert_corpus_file(self, json_corpus_file: Dict, corpus: Corpus, corpus_dir: Path):
         current_app.logger.info(f'Create CorpusFile {json_corpus_file["title"]}...')
         corpus_file = CorpusFile(
             corpus=corpus,

app/converters/vrt.py

@@ -1,25 +1,69 @@
 from flask import current_app
-from pathlib import Path
 
 
-def normalize_vrt_file(input_file: Path, output_file: Path):
+def normalize_vrt_file(input_file, output_file):
+    def check_pos_attribute_order(vrt_lines):
+        # The following orders are possible:
+        # since 26.02.2019: 'word,lemma,simple_pos,pos,ner'
+        # since 26.03.2021: 'word,pos,lemma,simple_pos,ner'
+        # since 27.01.2022: 'word,pos,lemma,simple_pos'
+        # This Function tries to find out which order we have by looking at the
+        # number of attributes and the position of the simple_pos attribute
+        SIMPLE_POS_LABELS = [
+            'ADJ', 'ADP', 'ADV', 'AUX', 'CONJ',
+            'DET', 'INTJ', 'NOUN', 'NUM', 'PART',
+            'PRON', 'PROPN', 'PUNCT', 'SCONJ', 'SYM',
+            'VERB', 'X'
+        ]
+        for line in vrt_lines:
+            if line.startswith('<'):
+                continue
+            pos_attrs = line.rstrip('\n').split('\t')
+            num_pos_attrs = len(pos_attrs)
+            if num_pos_attrs == 4:
+                if pos_attrs[3] in SIMPLE_POS_LABELS:
+                    return ['word', 'pos', 'lemma', 'simple_pos']
+                continue
+            elif num_pos_attrs == 5:
+                if pos_attrs[2] in SIMPLE_POS_LABELS:
+                    return ['word', 'lemma', 'simple_pos', 'pos', 'ner']
+                elif pos_attrs[3] in SIMPLE_POS_LABELS:
+                    return ['word', 'pos', 'lemma', 'simple_pos', 'ner']
+                continue
+        return None
+
+
+    def check_has_ent_as_s_attr(vrt_lines):
+        for line in vrt_lines:
+            if line.startswith('<ent'):
+                return True
+        return False
+
+
+    def pos_attrs_to_string_1(pos_attrs):
+        return f'{pos_attrs[0]}\t{pos_attrs[3]}\t{pos_attrs[1]}\t{pos_attrs[2]}\n'
+
+
+    def pos_attrs_to_string_2(pos_attrs):
+        return f'{pos_attrs[0]}\t{pos_attrs[1]}\t{pos_attrs[2]}\t{pos_attrs[3]}\n'
+
     current_app.logger.info(f'Converting {input_file}...')
 
-    with input_file.open() as f:
+    with open(input_file) as f:
         input_vrt_lines = f.readlines()
 
-    pos_attr_order = _check_pos_attribute_order(input_vrt_lines)
-    has_ent_as_s_attr = _check_has_ent_as_s_attr(input_vrt_lines)
+    pos_attr_order = check_pos_attribute_order(input_vrt_lines)
+    has_ent_as_s_attr = check_has_ent_as_s_attr(input_vrt_lines)
 
     current_app.logger.info(f'Detected pos_attr_order: [{",".join(pos_attr_order)}]')
     current_app.logger.info(f'Detected has_ent_as_s_attr: {has_ent_as_s_attr}')
 
     if pos_attr_order == ['word', 'lemma', 'simple_pos', 'pos', 'ner']:
-        pos_attrs_to_string_function = _pos_attrs_to_string_1
+        pos_attrs_to_string_function = pos_attrs_to_string_1
     elif pos_attr_order == ['word', 'pos', 'lemma', 'simple_pos', 'ner']:
-        pos_attrs_to_string_function = _pos_attrs_to_string_2
+        pos_attrs_to_string_function = pos_attrs_to_string_2
     elif pos_attr_order == ['word', 'pos', 'lemma', 'simple_pos']:
-        pos_attrs_to_string_function = _pos_attrs_to_string_2
+        pos_attrs_to_string_function = pos_attrs_to_string_2
     else:
         raise Exception('Can not handle format')
 
@@ -69,49 +113,5 @@ def normalize_vrt_file(input_file: Path, output_file: Path):
                     current_ent = pos_attrs[4]
         output_vrt += pos_attrs_to_string_function(pos_attrs)
 
-    with output_file.open(mode='w') as f:
+    with open(output_file, 'w') as f:
         f.write(output_vrt)
-
-
-def _check_pos_attribute_order(vrt_lines: list[str]) -> list[str]:
-    # The following orders are possible:
-    # since 26.02.2019: 'word,lemma,simple_pos,pos,ner'
-    # since 26.03.2021: 'word,pos,lemma,simple_pos,ner'
-    # since 27.01.2022: 'word,pos,lemma,simple_pos'
-    # This Function tries to find out which order we have by looking at the
-    # number of attributes and the position of the simple_pos attribute
-    SIMPLE_POS_LABELS = [
-        'ADJ', 'ADP', 'ADV', 'AUX', 'CONJ', 'DET', 'INTJ', 'NOUN', 'NUM',
-        'PART', 'PRON', 'PROPN', 'PUNCT', 'SCONJ', 'SYM', 'VERB', 'X'
-    ]
-    for line in vrt_lines:
-        if line.startswith('<'):
-            continue
-        pos_attrs = line.rstrip('\n').split('\t')
-        num_pos_attrs = len(pos_attrs)
-        if num_pos_attrs == 4:
-            if pos_attrs[3] in SIMPLE_POS_LABELS:
-                return ['word', 'pos', 'lemma', 'simple_pos']
-            continue
-        elif num_pos_attrs == 5:
-            if pos_attrs[2] in SIMPLE_POS_LABELS:
-                return ['word', 'lemma', 'simple_pos', 'pos', 'ner']
-            elif pos_attrs[3] in SIMPLE_POS_LABELS:
-                return ['word', 'pos', 'lemma', 'simple_pos', 'ner']
-            continue
-    # TODO: raise exception "can't determine attribute order"
-
-
-def _check_has_ent_as_s_attr(vrt_lines: list[str]) -> bool:
-    for line in vrt_lines:
-        if line.startswith('<ent'):
-            return True
-    return False
-
-
-def _pos_attrs_to_string_1(pos_attrs: list[str]) -> str:
-    return f'{pos_attrs[0]}\t{pos_attrs[3]}\t{pos_attrs[1]}\t{pos_attrs[2]}\n'
-
-
-def _pos_attrs_to_string_2(pos_attrs: list[str]) -> str:
-    return f'{pos_attrs[0]}\t{pos_attrs[1]}\t{pos_attrs[2]}\t{pos_attrs[3]}\n'

app/corpora/cqi_over_sio/__init__.py

@@ -1,16 +1,17 @@
 from cqi import CQiClient
 from cqi.errors import CQiException
 from cqi.status import CQiStatus
-from flask import current_app
+from docker.models.containers import Container
+from flask import current_app, session
 from flask_login import current_user
 from flask_socketio import Namespace
 from inspect import signature
 from threading import Lock
+from typing import Callable, Dict, List, Optional
 from app import db, docker_client, hashids, socketio
 from app.decorators import socketio_login_required
 from app.models import Corpus, CorpusStatus
-from . import cqi_extensions
-from .utils import CQiOverSocketIOSessionManager
+from . import extensions
 
 
 '''
@@ -18,7 +19,7 @@ This package tunnels the Corpus Query interface (CQi) protocol through
 Socket.IO (SIO) by tunneling CQi API calls through an event called "exec".
 
 Basic concept:
-1. A client connects to the namespace.
+1. A client connects to the "/cqi_over_sio" namespace.
 2. The client emits the "init" event and provides a corpus id for the corpus
    that should be analysed in this session.
      1.1 The analysis session counter of the corpus is incremented.
@@ -27,17 +28,17 @@ Basic concept:
      1.4 Connect the CQiClient to the server.
      1.5 Save the CQiClient, the Lock and the corpus id in the session for
          subsequential use.
-3. The client emits "exec" events, within which it provides the name of a CQi
-   API function and the corresponding arguments.
-     3.1 The "exec" event handler will execute the function, make sure that
-         the result is serializable and returns the result back to the client.
-4. The client disconnects from the namespace
-     4.1 The analysis session counter of the corpus is decremented.
-     4.2 The CQiClient and (Mutex) Lock belonging to it are teared down.
+2. The client emits the "exec" event provides the name of a CQi API function
+   arguments (optional).
+     - The event "exec" handler will execute the function, make sure that the
+       result is serializable and returns the result back to the client.
+4. Wait for more events
+5. The client disconnects from the "/cqi_over_sio" namespace
+     1.1 The analysis session counter of the corpus is decremented.
+     1.2 The CQiClient and (Mutex) Lock belonging to it are teared down.
 '''
 
-
-CQI_API_FUNCTION_NAMES = [
+CQI_API_FUNCTION_NAMES: List[str] = [
     'ask_feature_cl_2_3',
     'ask_feature_cqi_1_0',
     'ask_feature_cqp_2_3',
@@ -85,80 +86,68 @@ CQI_API_FUNCTION_NAMES = [
 ]
 
 
-class CQiOverSocketIONamespace(Namespace):
+class CQiNamespace(Namespace):
     @socketio_login_required
     def on_connect(self):
         pass
 
     @socketio_login_required
-    def on_init(self, corpus_hashid: str) -> dict:
-        corpus_id = hashids.decode(corpus_hashid)
-
-        if not isinstance(corpus_id, int):
-            return {'code': 400, 'msg': 'Bad Request'}
-
-        corpus = Corpus.query.get(corpus_id)
-
-        if corpus is None:
+    def on_init(self, db_corpus_hashid: str):
+        db_corpus_id: int = hashids.decode(db_corpus_hashid)
+        db_corpus: Optional[Corpus] = Corpus.query.get(db_corpus_id)
+        if db_corpus is None:
             return {'code': 404, 'msg': 'Not Found'}
-
-        if not (
-            corpus.user == current_user
-            or current_user.is_following_corpus(corpus)
-            or current_user.is_administrator
-        ):
+        if not (db_corpus.user == current_user
+                or current_user.is_following_corpus(db_corpus)
+                or current_user.is_administrator()):
             return {'code': 403, 'msg': 'Forbidden'}
-
-        if corpus.status not in [
+        if db_corpus.status not in [
             CorpusStatus.BUILT,
             CorpusStatus.STARTING_ANALYSIS_SESSION,
             CorpusStatus.RUNNING_ANALYSIS_SESSION,
             CorpusStatus.CANCELING_ANALYSIS_SESSION
         ]:
             return {'code': 424, 'msg': 'Failed Dependency'}
-
-        corpus.num_analysis_sessions = Corpus.num_analysis_sessions + 1
+        if db_corpus.num_analysis_sessions is None:
+            db_corpus.num_analysis_sessions = 0
+            db.session.commit()
+        db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions + 1
         db.session.commit()
-        retry_counter = 20
-        while corpus.status != CorpusStatus.RUNNING_ANALYSIS_SESSION:
+        retry_counter: int = 20
+        while db_corpus.status != CorpusStatus.RUNNING_ANALYSIS_SESSION:
             if retry_counter == 0:
-                corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
+                db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
                 db.session.commit()
                 return {'code': 408, 'msg': 'Request Timeout'}
             socketio.sleep(3)
             retry_counter -= 1
-            db.session.refresh(corpus)
-
-        cqpserver_container_name = f'nopaque-cqpserver-{corpus_id}'
-        cqpserver_container = docker_client.containers.get(cqpserver_container_name)
-        cqpserver_ip_address = cqpserver_container.attrs['NetworkSettings']['Networks'][current_app.config['NOPAQUE_DOCKER_NETWORK_NAME']]['IPAddress']
-        cqi_client = CQiClient(cqpserver_ip_address)
-        cqi_client_lock = Lock()
-
-        CQiOverSocketIOSessionManager.setup()
-        CQiOverSocketIOSessionManager.set_corpus_id(corpus_id)
-        CQiOverSocketIOSessionManager.set_cqi_client(cqi_client)
-        CQiOverSocketIOSessionManager.set_cqi_client_lock(cqi_client_lock)
-
+            db.session.refresh(db_corpus)
+        # cqi_client: CQiClient = CQiClient(f'cqpserver_{db_corpus_id}')
+        cqpserver_container_name: str = f'cqpserver_{db_corpus_id}'
+        cqpserver_container: Container = docker_client.containers.get(cqpserver_container_name)
+        cqpserver_host: str = cqpserver_container.attrs['NetworkSettings']['Networks'][current_app.config['NOPAQUE_DOCKER_NETWORK_NAME']]['IPAddress']
+        cqi_client: CQiClient = CQiClient(cqpserver_host)
+        session['cqi_over_sio'] = {
+            'cqi_client': cqi_client,
+            'cqi_client_lock': Lock(),
+            'db_corpus_id': db_corpus_id
+        }
         return {'code': 200, 'msg': 'OK'}
 
     @socketio_login_required
-    def on_exec(self, fn_name: str, fn_args: dict = {}) -> dict:
+    def on_exec(self, fn_name: str, fn_args: Dict = {}):
         try:
-            cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
-            cqi_client_lock = CQiOverSocketIOSessionManager.get_cqi_client_lock()
+            cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+            cqi_client_lock: Lock = session['cqi_over_sio']['cqi_client_lock']
         except KeyError:
             return {'code': 424, 'msg': 'Failed Dependency'}
-
         if fn_name in CQI_API_FUNCTION_NAMES:
-            fn = getattr(cqi_client.api, fn_name)
-        elif fn_name in cqi_extensions.CQI_EXTENSION_FUNCTION_NAMES:
-            fn = getattr(cqi_extensions, fn_name)
+            fn: Callable = getattr(cqi_client.api, fn_name)
+        elif fn_name in extensions.CQI_EXTENSION_FUNCTION_NAMES:
+            fn: Callable = getattr(extensions, fn_name)
         else:
             return {'code': 400, 'msg': 'Bad Request'}
-
         for param in signature(fn).parameters.values():
-            # Check if the parameter is optional or required
             if param.default is param.empty:
                 if param.name not in fn_args:
                     return {'code': 400, 'msg': 'Bad Request'}
@@ -167,7 +156,6 @@ class CQiOverSocketIONamespace(Namespace):
                     continue
             if type(fn_args[param.name]) is not param.annotation:
                 return {'code': 400, 'msg': 'Bad Request'}
-
         cqi_client_lock.acquire()
         try:
             fn_return_value = fn(**fn_args)
@@ -185,7 +173,6 @@ class CQiOverSocketIONamespace(Namespace):
             }
         finally:
             cqi_client_lock.release()
-
         if isinstance(fn_return_value, CQiStatus):
             payload = {
                 'code': fn_return_value.code,
@@ -193,31 +180,27 @@ class CQiOverSocketIONamespace(Namespace):
             }
         else:
             payload = fn_return_value
-
         return {'code': 200, 'msg': 'OK', 'payload': payload}
 
     def on_disconnect(self):
         try:
-            corpus_id = CQiOverSocketIOSessionManager.get_corpus_id()
-            cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
-            cqi_client_lock = CQiOverSocketIOSessionManager.get_cqi_client_lock()
-            CQiOverSocketIOSessionManager.teardown()
+            cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+            cqi_client_lock: Lock = session['cqi_over_sio']['cqi_client_lock']
+            db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
         except KeyError:
             return
-
         cqi_client_lock.acquire()
-
+        try:
+            session.pop('cqi_over_sio')
+        except KeyError:
+            pass
         try:
             cqi_client.api.ctrl_bye()
         except (BrokenPipeError, CQiException):
             pass
-
         cqi_client_lock.release()
-
-        corpus = Corpus.query.get(corpus_id)
-
-        if corpus is None:
+        db_corpus: Optional[Corpus] = Corpus.query.get(db_corpus_id)
+        if db_corpus is None:
             return
-
-        corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
+        db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
         db.session.commit()

app/corpora/cqi_over_sio/extensions.py

@@ -1,17 +1,23 @@
 from collections import Counter
+from cqi import CQiClient
 from cqi.models.corpora import Corpus as CQiCorpus
 from cqi.models.subcorpora import Subcorpus as CQiSubcorpus
+from cqi.models.attributes import (
+    PositionalAttribute as CQiPositionalAttribute,
+    StructuralAttribute as CQiStructuralAttribute
+)
 from cqi.status import StatusOk as CQiStatusOk
-from flask import current_app
+from flask import session
+from typing import Dict, List
 import gzip
 import json
 import math
 from app import db
 from app.models import Corpus
-from .utils import CQiOverSocketIOSessionManager
+from .utils import lookups_by_cpos, partial_export_subcorpus, export_subcorpus
 
 
-CQI_EXTENSION_FUNCTION_NAMES = [
+CQI_EXTENSION_FUNCTION_NAMES: List[str] = [
     'ext_corpus_update_db',
     'ext_corpus_static_data',
     'ext_corpus_paginate_corpus',
@@ -22,28 +28,28 @@ CQI_EXTENSION_FUNCTION_NAMES = [
 
 
 def ext_corpus_update_db(corpus: str) -> CQiStatusOk:
-    corpus_id = CQiOverSocketIOSessionManager.get_corpus_id()
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
-    db_corpus = Corpus.query.get(corpus_id)
-    cqi_corpus = cqi_client.corpora.get(corpus)
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+    db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
+    db_corpus: Corpus = Corpus.query.get(db_corpus_id)
+    cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
     db_corpus.num_tokens = cqi_corpus.size
     db.session.commit()
     return CQiStatusOk()
 
 
-def ext_corpus_static_data(corpus: str) -> dict:
-    corpus_id = CQiOverSocketIOSessionManager.get_corpus_id()
-    db_corpus = Corpus.query.get(corpus_id)
+def ext_corpus_static_data(corpus: str) -> Dict:
+    db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
+    db_corpus: Corpus = Corpus.query.get(db_corpus_id)
 
     static_data_file_path = db_corpus.path / 'cwb' / 'static.json.gz'
     if static_data_file_path.exists():
         with static_data_file_path.open('rb') as f:
             return f.read()
 
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
-    cqi_corpus = cqi_client.corpora.get(corpus)
-    cqi_p_attrs = cqi_corpus.positional_attributes.list()
-    cqi_s_attrs = cqi_corpus.structural_attributes.list()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+    cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
+    cqi_p_attrs: List[CQiPositionalAttribute] = cqi_corpus.positional_attributes.list()
+    cqi_s_attrs: List[CQiStructuralAttribute] = cqi_corpus.structural_attributes.list()
 
     static_data = {
         'corpus': {
@@ -56,21 +62,21 @@ def ext_corpus_static_data(corpus: str) -> dict:
     }
 
     for p_attr in cqi_p_attrs:
-        current_app.logger.info(f'corpus.freqs.{p_attr.name}')
+        print(f'corpus.freqs.{p_attr.name}')
         static_data['corpus']['freqs'][p_attr.name] = []
-        p_attr_id_list = list(range(p_attr.lexicon_size))
+        p_attr_id_list: List[int] = list(range(p_attr.lexicon_size))
         static_data['corpus']['freqs'][p_attr.name].extend(p_attr.freqs_by_ids(p_attr_id_list))
         del p_attr_id_list
 
-        current_app.logger.info(f'p_attrs.{p_attr.name}')
+        print(f'p_attrs.{p_attr.name}')
         static_data['p_attrs'][p_attr.name] = []
-        cpos_list = list(range(cqi_corpus.size))
+        cpos_list: List[int] = list(range(cqi_corpus.size))
         static_data['p_attrs'][p_attr.name].extend(p_attr.ids_by_cpos(cpos_list))
         del cpos_list
 
-        current_app.logger.info(f'values.p_attrs.{p_attr.name}')
+        print(f'values.p_attrs.{p_attr.name}')
         static_data['values']['p_attrs'][p_attr.name] = []
-        p_attr_id_list = list(range(p_attr.lexicon_size))
+        p_attr_id_list: List[int] = list(range(p_attr.lexicon_size))
         static_data['values']['p_attrs'][p_attr.name].extend(p_attr.values_by_ids(p_attr_id_list))
         del p_attr_id_list
 
@@ -86,9 +92,9 @@ def ext_corpus_static_data(corpus: str) -> dict:
             # Note: Needs more testing, don't use it in production       #
             ##############################################################
             cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
-            cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
-            first_match = 0
-            last_match = cqi_subcorpus.size - 1
+            cqi_subcorpus: CQiSubcorpus = cqi_corpus.subcorpora.get('Last')
+            first_match: int = 0
+            last_match: int = cqi_subcorpus.size - 1
             match_boundaries = zip(
                 range(first_match, last_match + 1),
                 cqi_subcorpus.dump(
@@ -106,7 +112,7 @@ def ext_corpus_static_data(corpus: str) -> dict:
             del cqi_subcorpus, first_match, last_match
             for id, lbound, rbound in match_boundaries:
                 static_data['s_attrs'][s_attr.name]['lexicon'].append({})
-                current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
+                print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
                 static_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
             del match_boundaries
 
@@ -118,33 +124,33 @@ def ext_corpus_static_data(corpus: str) -> dict:
             # This is a very slow operation, thats why we only use it for
             # the text attribute
             lbound, rbound = s_attr.cpos_by_id(id)
-            current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
+            print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
             static_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
             static_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'] = {}
-            cpos_list = list(range(lbound, rbound + 1))
+            cpos_list: List[int] = list(range(lbound, rbound + 1))
             for p_attr in cqi_p_attrs:
-                p_attr_ids = []
+                p_attr_ids: List[int] = []
                 p_attr_ids.extend(p_attr.ids_by_cpos(cpos_list))
-                current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.freqs.{p_attr.name}')
+                print(f's_attrs.{s_attr.name}.lexicon.{id}.freqs.{p_attr.name}')
                 static_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr_ids))
                 del p_attr_ids
             del cpos_list
 
-        sub_s_attrs = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
-        current_app.logger.info(f's_attrs.{s_attr.name}.values')
+        sub_s_attrs: List[CQiStructuralAttribute] = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
+        print(f's_attrs.{s_attr.name}.values')
         static_data['s_attrs'][s_attr.name]['values'] = [
             sub_s_attr.name[(len(s_attr.name) + 1):]
             for sub_s_attr in sub_s_attrs
         ]
-        s_attr_id_list = list(range(s_attr.size))
-        sub_s_attr_values = []
+        s_attr_id_list: List[int] = list(range(s_attr.size))
+        sub_s_attr_values: List[str] = []
         for sub_s_attr in sub_s_attrs:
             tmp = []
             tmp.extend(sub_s_attr.values_by_ids(s_attr_id_list))
             sub_s_attr_values.append(tmp)
             del tmp
         del s_attr_id_list
-        current_app.logger.info(f'values.s_attrs.{s_attr.name}')
+        print(f'values.s_attrs.{s_attr.name}')
         static_data['values']['s_attrs'][s_attr.name] = [
             {
                 s_attr_value_name: sub_s_attr_values[s_attr_value_name_idx][s_attr_id]
@@ -154,11 +160,11 @@ def ext_corpus_static_data(corpus: str) -> dict:
             } for s_attr_id in range(0, s_attr.size)
         ]
         del sub_s_attr_values
-    current_app.logger.info('Saving static data to file')
+    print('Saving static data to file')
     with gzip.open(static_data_file_path, 'wt') as f:
         json.dump(static_data, f)
     del static_data
-    current_app.logger.info('Sending static data to client')
+    print('Sending static data to client')
     with open(static_data_file_path, 'rb') as f:
         return f.read()
 
@@ -167,8 +173,8 @@ def ext_corpus_paginate_corpus(
     corpus: str,
     page: int = 1,
     per_page: int = 20
-) -> dict:
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
+) -> Dict:
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus)
     # Sanity checks
     if (
@@ -183,7 +189,7 @@ def ext_corpus_paginate_corpus(
     first_cpos = (page - 1) * per_page
     last_cpos = min(cqi_corpus.size, first_cpos + per_page)
     cpos_list = [*range(first_cpos, last_cpos)]
-    lookups = _lookups_by_cpos(cqi_corpus, cpos_list)
+    lookups = lookups_by_cpos(cqi_corpus, cpos_list)
     payload = {}
     # the items for the current page
     payload['items'] = [cpos_list]
@@ -213,9 +219,9 @@ def ext_cqp_paginate_subcorpus(
     context: int = 50,
     page: int = 1,
     per_page: int = 20
-) -> dict:
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
     # Sanity checks
@@ -230,7 +236,7 @@ def ext_cqp_paginate_subcorpus(
         return {'code': 416, 'msg': 'Range Not Satisfiable'}
     offset = (page - 1) * per_page
     cutoff = per_page
-    cqi_results_export = _export_subcorpus(
+    cqi_results_export = export_subcorpus(
         cqi_subcorpus, context=context, cutoff=cutoff, offset=offset)
     payload = {}
     # the items for the current page
@@ -260,147 +266,22 @@ def ext_cqp_partial_export_subcorpus(
     subcorpus: str,
     match_id_list: list,
     context: int = 50
-) -> dict:
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
-    cqi_subcorpus_partial_export = _partial_export_subcorpus(cqi_subcorpus, match_id_list, context=context)
+    cqi_subcorpus_partial_export = partial_export_subcorpus(cqi_subcorpus, match_id_list, context=context)
     return cqi_subcorpus_partial_export
 
 
-def ext_cqp_export_subcorpus(subcorpus: str, context: int = 50) -> dict:
+def ext_cqp_export_subcorpus(
+    subcorpus: str,
+    context: int = 50
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = CQiOverSocketIOSessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
-    cqi_subcorpus_export = _export_subcorpus(cqi_subcorpus, context=context)
+    cqi_subcorpus_export = export_subcorpus(cqi_subcorpus, context=context)
     return cqi_subcorpus_export
-
-
-def _lookups_by_cpos(corpus: CQiCorpus, cpos_list: list[int]) -> dict:
-    lookups = {}
-    lookups['cpos_lookup'] = {cpos: {} for cpos in cpos_list}
-    for attr in corpus.positional_attributes.list():
-        cpos_attr_values = attr.values_by_cpos(cpos_list)
-        for i, cpos in enumerate(cpos_list):
-            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_values[i]
-    for attr in corpus.structural_attributes.list():
-        # We only want to iterate over non subattributes, identifiable by
-        # attr.has_values == False
-        if attr.has_values:
-            continue
-        cpos_attr_ids = attr.ids_by_cpos(cpos_list)
-        for i, cpos in enumerate(cpos_list):
-            if cpos_attr_ids[i] == -1:
-                continue
-            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_ids[i]
-        occured_attr_ids = [x for x in set(cpos_attr_ids) if x != -1]
-        if len(occured_attr_ids) == 0:
-            continue
-        subattrs = corpus.structural_attributes.list(filters={'part_of': attr})
-        if len(subattrs) == 0:
-            continue
-        lookup_name = f'{attr.name}_lookup'
-        lookups[lookup_name] = {}
-        for attr_id in occured_attr_ids:
-            lookups[lookup_name][attr_id] = {}
-        for subattr in subattrs:
-            subattr_name = subattr.name[(len(attr.name) + 1):]  # noqa
-            for i, subattr_value in enumerate(subattr.values_by_ids(occured_attr_ids)):  # noqa
-                lookups[lookup_name][occured_attr_ids[i]][subattr_name] = subattr_value  # noqa
-    return lookups
-
-
-def _partial_export_subcorpus(
-    subcorpus: CQiSubcorpus,
-    match_id_list: list[int],
-    context: int = 25
-) -> dict:
-    if subcorpus.size == 0:
-        return {'matches': []}
-    match_boundaries = []
-    for match_id in match_id_list:
-        if match_id < 0 or match_id >= subcorpus.size:
-            continue
-        match_boundaries.append(
-            (
-                match_id,
-                subcorpus.dump(subcorpus.fields['match'], match_id, match_id)[0],
-                subcorpus.dump(subcorpus.fields['matchend'], match_id, match_id)[0]
-            )
-        )
-    cpos_set = set()
-    matches = []
-    for match_boundary in match_boundaries:
-        match_num, match_start, match_end = match_boundary
-        c = (match_start, match_end)
-        if match_start == 0 or context == 0:
-            lc = None
-            cpos_list_lbound = match_start
-        else:
-            lc_lbound = max(0, (match_start - context))
-            lc_rbound = match_start - 1
-            lc = (lc_lbound, lc_rbound)
-            cpos_list_lbound = lc_lbound
-        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
-            rc = None
-            cpos_list_rbound = match_end
-        else:
-            rc_lbound = match_end + 1
-            rc_rbound = min(
-                (match_end + context),
-                (subcorpus.collection.corpus.size - 1)
-            )
-            rc = (rc_lbound, rc_rbound)
-            cpos_list_rbound = rc_rbound
-        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
-        matches.append(match)
-        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
-    lookups = _lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
-    return {'matches': matches, **lookups}
-
-
-def _export_subcorpus(
-    subcorpus: CQiSubcorpus,
-    context: int = 25,
-    cutoff: float = float('inf'),
-    offset: int = 0
-) -> dict:
-    if subcorpus.size == 0:
-        return {'matches': []}
-    first_match = max(0, offset)
-    last_match = min((offset + cutoff - 1), (subcorpus.size - 1))
-    match_boundaries = zip(
-        range(first_match, last_match + 1),
-        subcorpus.dump(subcorpus.fields['match'], first_match, last_match),
-        subcorpus.dump(subcorpus.fields['matchend'], first_match, last_match)
-    )
-    cpos_set = set()
-    matches = []
-    for match_num, match_start, match_end in match_boundaries:
-        c = (match_start, match_end)
-        if match_start == 0 or context == 0:
-            lc = None
-            cpos_list_lbound = match_start
-        else:
-            lc_lbound = max(0, (match_start - context))
-            lc_rbound = match_start - 1
-            lc = (lc_lbound, lc_rbound)
-            cpos_list_lbound = lc_lbound
-        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
-            rc = None
-            cpos_list_rbound = match_end
-        else:
-            rc_lbound = match_end + 1
-            rc_rbound = min(
-                (match_end + context),
-                (subcorpus.collection.corpus.size - 1)
-            )
-            rc = (rc_lbound, rc_rbound)
-            cpos_list_rbound = rc_rbound
-        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
-        matches.append(match)
-        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
-    lookups = _lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
-    return {'matches': matches, **lookups}

app/corpora/cqi_over_sio/utils.py

@@ -0,0 +1,131 @@
+from cqi.models.corpora import Corpus as CQiCorpus
+from cqi.models.subcorpora import Subcorpus as CQiSubcorpus
+from typing import Dict, List
+
+
+def lookups_by_cpos(corpus: CQiCorpus, cpos_list: List[int]) -> Dict:
+    lookups = {}
+    lookups['cpos_lookup'] = {cpos: {} for cpos in cpos_list}
+    for attr in corpus.positional_attributes.list():
+        cpos_attr_values: List[str] = attr.values_by_cpos(cpos_list)
+        for i, cpos in enumerate(cpos_list):
+            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_values[i]
+    for attr in corpus.structural_attributes.list():
+        # We only want to iterate over non subattributes, identifiable by
+        # attr.has_values == False
+        if attr.has_values:
+            continue
+        cpos_attr_ids: List[int] = attr.ids_by_cpos(cpos_list)
+        for i, cpos in enumerate(cpos_list):
+            if cpos_attr_ids[i] == -1:
+                continue
+            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_ids[i]
+        occured_attr_ids = [x for x in set(cpos_attr_ids) if x != -1]
+        if len(occured_attr_ids) == 0:
+            continue
+        subattrs = corpus.structural_attributes.list(filters={'part_of': attr})
+        if len(subattrs) == 0:
+            continue
+        lookup_name: str = f'{attr.name}_lookup'
+        lookups[lookup_name] = {}
+        for attr_id in occured_attr_ids:
+            lookups[lookup_name][attr_id] = {}
+        for subattr in subattrs:
+            subattr_name = subattr.name[(len(attr.name) + 1):]  # noqa
+            for i, subattr_value in enumerate(subattr.values_by_ids(occured_attr_ids)):  # noqa
+                lookups[lookup_name][occured_attr_ids[i]][subattr_name] = subattr_value  # noqa
+    return lookups
+
+
+def partial_export_subcorpus(
+    subcorpus: CQiSubcorpus,
+    match_id_list: List[int],
+    context: int = 25
+) -> Dict:
+    if subcorpus.size == 0:
+        return {"matches": []}
+    match_boundaries = []
+    for match_id in match_id_list:
+        if match_id < 0 or match_id >= subcorpus.size:
+            continue
+        match_boundaries.append(
+            (
+                match_id,
+                subcorpus.dump(subcorpus.fields['match'], match_id, match_id)[0],
+                subcorpus.dump(subcorpus.fields['matchend'], match_id, match_id)[0]
+            )
+        )
+    cpos_set = set()
+    matches = []
+    for match_boundary in match_boundaries:
+        match_num, match_start, match_end = match_boundary
+        c = (match_start, match_end)
+        if match_start == 0 or context == 0:
+            lc = None
+            cpos_list_lbound = match_start
+        else:
+            lc_lbound = max(0, (match_start - context))
+            lc_rbound = match_start - 1
+            lc = (lc_lbound, lc_rbound)
+            cpos_list_lbound = lc_lbound
+        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
+            rc = None
+            cpos_list_rbound = match_end
+        else:
+            rc_lbound = match_end + 1
+            rc_rbound = min(
+                (match_end + context),
+                (subcorpus.collection.corpus.size - 1)
+            )
+            rc = (rc_lbound, rc_rbound)
+            cpos_list_rbound = rc_rbound
+        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
+        matches.append(match)
+        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
+    lookups = lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
+    return {'matches': matches, **lookups}
+
+
+def export_subcorpus(
+    subcorpus: CQiSubcorpus,
+    context: int = 25,
+    cutoff: float = float('inf'),
+    offset: int = 0
+) -> Dict:
+    if subcorpus.size == 0:
+        return {"matches": []}
+    first_match = max(0, offset)
+    last_match = min((offset + cutoff - 1), (subcorpus.size - 1))
+    match_boundaries = zip(
+        range(first_match, last_match + 1),
+        subcorpus.dump(subcorpus.fields['match'], first_match, last_match),
+        subcorpus.dump(subcorpus.fields['matchend'], first_match, last_match)
+    )
+    cpos_set = set()
+    matches = []
+    for match_num, match_start, match_end in match_boundaries:
+        c = (match_start, match_end)
+        if match_start == 0 or context == 0:
+            lc = None
+            cpos_list_lbound = match_start
+        else:
+            lc_lbound = max(0, (match_start - context))
+            lc_rbound = match_start - 1
+            lc = (lc_lbound, lc_rbound)
+            cpos_list_lbound = lc_lbound
+        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
+            rc = None
+            cpos_list_rbound = match_end
+        else:
+            rc_lbound = match_end + 1
+            rc_rbound = min(
+                (match_end + context),
+                (subcorpus.collection.corpus.size - 1)
+            )
+            rc = (rc_lbound, rc_rbound)
+            cpos_list_rbound = rc_rbound
+        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
+        matches.append(match)
+        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
+    lookups = lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
+    return {'matches': matches, **lookups}

app/corpora/decorators.py

@@ -10,7 +10,7 @@ def corpus_follower_permission_required(*permissions):
         def decorated_function(*args, **kwargs):
             corpus_id = kwargs.get('corpus_id')
             corpus = Corpus.query.get_or_404(corpus_id)
-            if not (corpus.user == current_user or current_user.is_administrator):
+            if not (corpus.user == current_user or current_user.is_administrator()):
                 cfa = CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=current_user.id).first()
                 if cfa is None:
                     abort(403)
@@ -26,7 +26,7 @@ def corpus_owner_or_admin_required(f):
     def decorated_function(*args, **kwargs):
         corpus_id = kwargs.get('corpus_id')
         corpus = Corpus.query.get_or_404(corpus_id)
-        if not (corpus.user == current_user or current_user.is_administrator):
+        if not (corpus.user == current_user or current_user.is_administrator()):
             abort(403)
         return f(*args, **kwargs)
     return decorated_function

app/corpora/events.py

@@ -15,7 +15,7 @@ def get_corpus(corpus_hashid):
     if not (
         corpus.is_public
         or corpus.user == current_user
-        or current_user.is_administrator
+        or current_user.is_administrator()
     ):
         return {'options': {'status': 403, 'statusText': 'Forbidden'}}
     return {
@@ -38,7 +38,7 @@ def subscribe_corpus(corpus_hashid):
     if not (
         corpus.is_public
         or corpus.user == current_user
-        or current_user.is_administrator
+        or current_user.is_administrator()
     ):
         return {'options': {'status': 403, 'statusText': 'Forbidden'}}
     join_room(f'/corpora/{corpus.hashid}')

app/corpora/files/json_routes.py

@@ -1,7 +1,7 @@
-from flask import current_app
+from flask import abort, current_app
 from threading import Thread
-from app.decorators import content_negotiation
 from app import db
+from app.decorators import content_negotiation
 from app.models import CorpusFile
 from ..decorators import corpus_follower_permission_required
 from . import bp

app/corpora/files/routes.py

@@ -6,19 +6,24 @@ from flask import (
     send_from_directory,
     url_for
 )
+from flask_breadcrumbs import register_breadcrumb
 from app import db
 from app.models import Corpus, CorpusFile, CorpusStatus
 from ..decorators import corpus_follower_permission_required
+from ..utils import corpus_endpoint_arguments_constructor as corpus_eac
 from . import bp
 from .forms import CreateCorpusFileForm, UpdateCorpusFileForm
+from .utils import corpus_file_dynamic_list_constructor as corpus_file_dlc
 
 
 @bp.route('/<hashid:corpus_id>/files')
+@register_breadcrumb(bp, '.entity.files', 'Files', endpoint_arguments_constructor=corpus_eac)
 def corpus_files(corpus_id):
     return redirect(url_for('.corpus', _anchor='files', corpus_id=corpus_id))
 
 
 @bp.route('/<hashid:corpus_id>/files/create', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.entity.files.create', 'Create', endpoint_arguments_constructor=corpus_eac)
 @corpus_follower_permission_required('MANAGE_FILES')
 def create_corpus_file(corpus_id):
     corpus = Corpus.query.get_or_404(corpus_id)
@@ -60,6 +65,7 @@ def create_corpus_file(corpus_id):
 
 
 @bp.route('/<hashid:corpus_id>/files/<hashid:corpus_file_id>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.entity.files.entity', '', dynamic_list_constructor=corpus_file_dlc)
 @corpus_follower_permission_required('MANAGE_FILES')
 def corpus_file(corpus_id, corpus_file_id):
     corpus_file = CorpusFile.query.filter_by(corpus_id=corpus_id, id=corpus_file_id).first_or_404()
@@ -88,6 +94,6 @@ def download_corpus_file(corpus_id, corpus_file_id):
         corpus_file.path.parent,
         corpus_file.path.name,
         as_attachment=True,
-        download_name=corpus_file.filename,
+        attachment_filename=corpus_file.filename,
         mimetype=corpus_file.mimetype
     )

app/corpora/files/utils.py

@@ -0,0 +1,15 @@
+from flask import request, url_for
+from app.models import CorpusFile
+from ..utils import corpus_endpoint_arguments_constructor as corpus_eac
+
+
+def corpus_file_dynamic_list_constructor():
+    corpus_id = request.view_args['corpus_id']
+    corpus_file_id = request.view_args['corpus_file_id']
+    corpus_file = CorpusFile.query.filter_by(corpus_id=corpus_id, id=corpus_file_id).first_or_404()
+    return [
+        {
+            'text': f'{corpus_file.author}: {corpus_file.title} ({corpus_file.publishing_year})',
+            'url': url_for('.corpus_file', corpus_id=corpus_id, corpus_file_id=corpus_file_id)
+        }
+    ]

app/corpora/followers/json_routes.py

@@ -58,7 +58,7 @@ def delete_corpus_follower(corpus_id, follower_id):
         current_user.id == follower_id
         or current_user == cfa.corpus.user 
         or CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=current_user.id).first().role.has_permission('MANAGE_FOLLOWERS')
-        or current_user.is_administrator):
+        or current_user.is_administrator()):
         abort(403)
     if current_user.id == follower_id:
         flash(f'You are no longer following "{cfa.corpus.title}"', 'corpus')

app/corpora/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 from app import db
 from app.models import (
@@ -10,14 +11,20 @@ from app.models import (
 from . import bp
 from .decorators import corpus_follower_permission_required
 from .forms import CreateCorpusForm
+from .utils import (
+    corpus_endpoint_arguments_constructor as corpus_eac,
+    corpus_dynamic_list_constructor as corpus_dlc
+)
 
 
 @bp.route('')
+@register_breadcrumb(bp, '.', '<i class="nopaque-icons left">I</i>My Corpora')
 def corpora():
     return redirect(url_for('main.dashboard', _anchor='corpora'))
 
 
 @bp.route('/create', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.create', 'Create')
 def create_corpus():
     form = CreateCorpusForm()
     if form.validate_on_submit():
@@ -40,6 +47,7 @@ def create_corpus():
 
 
 @bp.route('/<hashid:corpus_id>')
+@register_breadcrumb(bp, '.entity', '', dynamic_list_constructor=corpus_dlc)
 def corpus(corpus_id):
     corpus = Corpus.query.get_or_404(corpus_id)
     cfrs = CorpusFollowerRole.query.all()
@@ -47,13 +55,13 @@ def corpus(corpus_id):
     users = User.query.filter(User.is_public == True, User.id != current_user.id, User.id != corpus.user.id, User.role_id < 4).all()
     cfa = CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=current_user.id).first()
     if cfa is None:
-        if corpus.user == current_user or current_user.is_administrator:
+        if corpus.user == current_user or current_user.is_administrator():
             cfr = CorpusFollowerRole.query.filter_by(name='Administrator').first()
         else:
             cfr = CorpusFollowerRole.query.filter_by(name='Anonymous').first()
     else:
         cfr = cfa.role
-    if corpus.user == current_user or current_user.is_administrator:
+    if corpus.user == current_user or current_user.is_administrator():
         return render_template(
             'corpora/corpus.html.j2',
             title=corpus.title,
@@ -79,6 +87,7 @@ def corpus(corpus_id):
 
 @bp.route('/<hashid:corpus_id>/analysis')
 @corpus_follower_permission_required('VIEW')
+@register_breadcrumb(bp, '.entity.analysis', 'Analysis', endpoint_arguments_constructor=corpus_eac)
 def analysis(corpus_id):
     corpus = Corpus.query.get_or_404(corpus_id)
     return render_template(
@@ -99,11 +108,13 @@ def follow_corpus(corpus_id, token):
 
 
 @bp.route('/import', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.import', 'Import')
 def import_corpus():
     abort(503)
 
 
 @bp.route('/<hashid:corpus_id>/export')
 @corpus_follower_permission_required('VIEW')
+@register_breadcrumb(bp, '.entity.export', 'Export', endpoint_arguments_constructor=corpus_eac)
 def export_corpus(corpus_id):
     abort(503)

app/corpora/utils.py

@@ -0,0 +1,17 @@
+from flask import request, url_for
+from app.models import Corpus
+
+
+def corpus_endpoint_arguments_constructor():
+    return {'corpus_id': request.view_args['corpus_id']}
+
+
+def corpus_dynamic_list_constructor():
+    corpus_id = request.view_args['corpus_id']
+    corpus = Corpus.query.get_or_404(corpus_id)
+    return [
+        {
+            'text': f'<i class="material-icons left">book</i>{corpus.title}',
+            'url': url_for('.corpus', corpus_id=corpus_id)
+        }
+    ]

app/daemon/__init__.py

@@ -0,0 +1,11 @@
+from app import db
+from flask import Flask
+from .corpus_utils import check_corpora
+from .job_utils import check_jobs
+
+
+def daemon(app: Flask):
+    with app.app_context():
+        check_corpora()
+        check_jobs()
+        db.session.commit()

app/daemon/corpus_utils.py

@@ -1,16 +1,12 @@
+from app import docker_client
+from app.models import Corpus, CorpusStatus
 from flask import current_app
 import docker
 import os
 import shutil
-from app import db, docker_client, scheduler
-from app.models import Corpus, CorpusStatus
 
 
-def handle_corpora():
-    with scheduler.app.app_context():
-        _handle_corpora()
-
-def _handle_corpora():
+def check_corpora():
     corpora = Corpus.query.all()
     for corpus in [x for x in corpora if x.status == CorpusStatus.SUBMITTED]:
         _create_build_corpus_service(corpus)
@@ -21,14 +17,13 @@ def _handle_corpora():
     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]:
-        _checkout_cqpserver_container(corpus)
+        _checkout_analysing_corpus_container(corpus)
     for corpus in [x for x in corpora if x.status == CorpusStatus.STARTING_ANALYSIS_SESSION]:
         _create_cqpserver_container(corpus)
     for corpus in [x for x in corpora if x.status == CorpusStatus.CANCELING_ANALYSIS_SESSION]:
         _remove_cqpserver_container(corpus)
-    db.session.commit()
 
-def _create_build_corpus_service(corpus: Corpus):
+def _create_build_corpus_service(corpus):
     ''' # Docker service settings # '''
     ''' ## Command ## '''
     command = ['bash', '-c']
@@ -53,7 +48,9 @@ def _create_build_corpus_service(corpus: Corpus):
     image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1879'
     ''' ## Labels ## '''
     labels = {
-        'nopaque.server_name': current_app.config['SERVER_NAME']
+        'origin': current_app.config['SERVER_NAME'],
+        'type': 'corpus.build',
+        'corpus_id': str(corpus.id)
     }
     ''' ## Mounts ## '''
     mounts = []
@@ -98,7 +95,7 @@ def _create_build_corpus_service(corpus: Corpus):
         return
     corpus.status = CorpusStatus.QUEUED
 
-def _checkout_build_corpus_service(corpus: Corpus):
+def _checkout_build_corpus_service(corpus):
     service_name = f'build-corpus_{corpus.id}'
     try:
         service = docker_client.services.get(service_name)
@@ -126,7 +123,8 @@ def _checkout_build_corpus_service(corpus: Corpus):
     except docker.errors.DockerException as e:
         current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
 
-def _create_cqpserver_container(corpus: Corpus):
+def _create_cqpserver_container(corpus):
+    ''' # Docker container settings # '''
     ''' ## Command ## '''
     command = []
     command.append(
@@ -143,7 +141,7 @@ def _create_cqpserver_container(corpus: Corpus):
     ''' ## Image ## '''
     image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1879'
     ''' ## Name ## '''
-    name = f'nopaque-cqpserver-{corpus.id}'
+    name = f'cqpserver_{corpus.id}'
     ''' ## Network ## '''
     network = f'{current_app.config["NOPAQUE_DOCKER_NETWORK_NAME"]}'
     ''' ## Volumes ## '''
@@ -200,8 +198,8 @@ def _create_cqpserver_container(corpus: Corpus):
         return
     corpus.status = CorpusStatus.RUNNING_ANALYSIS_SESSION
 
-def _checkout_cqpserver_container(corpus: Corpus):
-    container_name = f'nopaque-cqpserver-{corpus.id}'
+def _checkout_analysing_corpus_container(corpus):
+    container_name = f'cqpserver_{corpus.id}'
     try:
         docker_client.containers.get(container_name)
     except docker.errors.NotFound as e:
@@ -211,8 +209,8 @@ def _checkout_cqpserver_container(corpus: Corpus):
     except docker.errors.DockerException as e:
         current_app.logger.error(f'Get container "{container_name}" failed: {e}')
 
-def _remove_cqpserver_container(corpus: Corpus):
-    container_name = f'nopaque-cqpserver-{corpus.id}'
+def _remove_cqpserver_container(corpus):
+    container_name = f'cqpserver_{corpus.id}'
     try:
         container = docker_client.containers.get(container_name)
     except docker.errors.NotFound:

app/daemon/job_utils.py

@@ -1,11 +1,4 @@
-from datetime import datetime
-from flask import current_app
-from werkzeug.utils import secure_filename
-import docker
-import json
-import os
-import shutil
-from app import db, docker_client, hashids, scheduler
+from app import db, docker_client, hashids
 from app.models import (
     Job,
     JobResult,
@@ -13,13 +6,16 @@ from app.models import (
     TesseractOCRPipelineModel,
     SpaCyNLPPipelineModel
 )
+from datetime import datetime
+from flask import current_app
+from werkzeug.utils import secure_filename
+import docker
+import json
+import os
+import shutil
 
 
-def handle_jobs():
-    with scheduler.app.app_context():
-        _handle_jobs()
-
-def _handle_jobs():
+def check_jobs():
     jobs = Job.query.all()
     for job in [x for x in jobs if x.status == JobStatus.SUBMITTED]:
         _create_job_service(job)
@@ -27,9 +23,8 @@ def _handle_jobs():
         _checkout_job_service(job)
     for job in [x for x in jobs if x.status == JobStatus.CANCELING]:
         _remove_job_service(job)
-    db.session.commit()
 
-def _create_job_service(job: Job):
+def _create_job_service(job):
     ''' # Docker service settings # '''
     ''' ## Service specific settings ## '''
     if job.service == 'file-setup-pipeline':
@@ -86,7 +81,9 @@ def _create_job_service(job: Job):
     constraints = ['node.role==worker']
     ''' ## Labels ## '''
     labels = {
-        'origin': current_app.config['SERVER_NAME']
+        'origin': current_app.config['SERVER_NAME'],
+        'type': 'job',
+        'job_id': str(job.id)
     }
     ''' ## Mounts ## '''
     mounts = []
@@ -167,7 +164,7 @@ def _create_job_service(job: Job):
         return
     job.status = JobStatus.QUEUED
 
-def _checkout_job_service(job: Job):
+def _checkout_job_service(job):
     service_name = f'job_{job.id}'
     try:
         service = docker_client.services.get(service_name)
@@ -216,7 +213,7 @@ def _checkout_job_service(job: Job):
     except docker.errors.DockerException as e:
         current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
 
-def _remove_job_service(job: Job):
+def _remove_job_service(job):
     service_name = f'job_{job.id}'
     try:
         service = docker_client.services.get(service_name)

app/decorators.py

@@ -1,7 +1,8 @@
-from flask import abort, request
+from flask import abort, current_app, request
 from flask_login import current_user
 from functools import wraps
-from typing import Optional
+from threading import Thread
+from typing import List, Union
 from werkzeug.exceptions import NotAcceptable
 from app.models import Permission
 
@@ -23,21 +24,22 @@ def admin_required(f):
 
 def socketio_login_required(f):
     @wraps(f)
-    def wrapper(*args, **kwargs):
+    def decorated_function(*args, **kwargs):
         if current_user.is_authenticated:
             return f(*args, **kwargs)
-        return {'code': 401, 'body': 'Unauthorized'}
-    return wrapper
+        else:
+            return {'code': 401, 'msg': 'Unauthorized'}
+    return decorated_function
 
 
 def socketio_permission_required(permission):
     def decorator(f):
         @wraps(f)
-        def wrapper(*args, **kwargs):
+        def decorated_function(*args, **kwargs):
             if not current_user.can(permission):
-                return {'code': 403, 'body': 'Forbidden'}
+                return {'code': 403, 'msg': 'Forbidden'}
             return f(*args, **kwargs)
-        return wrapper
+        return decorated_function
     return decorator
 
 
@@ -45,9 +47,27 @@ def socketio_admin_required(f):
     return socketio_permission_required(Permission.ADMINISTRATE)(f)
 
 
+def background(f):
+    '''
+    ' This decorator executes a function in a Thread.
+    ' Decorated functions need to be executed within a code block where an
+    ' app context exists.
+    '
+    ' NOTE: An app object is passed as a keyword argument to the decorated
+    '       function.
+    '''
+    @wraps(f)
+    def wrapped(*args, **kwargs):
+        kwargs['app'] = current_app._get_current_object()
+        thread = Thread(target=f, args=args, kwargs=kwargs)
+        thread.start()
+        return thread
+    return wrapped
+
+
 def content_negotiation(
-    produces: Optional[str | list[str]] = None,
-    consumes: Optional[str | list[str]] = None
+    produces: Union[str, List[str], None] = None,
+    consumes: Union[str, List[str], None] = None
 ):
     def decorator(f):
         @wraps(f)

app/email.py

@@ -1,32 +1,25 @@
-from flask import current_app, Flask, render_template
+from flask import current_app, render_template
 from flask_mail import Message
 from threading import Thread
 from app import mail
 
 
-def create_message(
-    recipient: str,
-    subject: str,
-    template: str,
-    **context
-) -> Message:
-    message = Message(
-        body=render_template(f'{template}.txt.j2', **context),
-        html=render_template(f'{template}.html.j2', **context),
+def create_message(recipient, subject, template, **kwargs):
+    subject_prefix: str = current_app.config['NOPAQUE_MAIL_SUBJECT_PREFIX']
+    msg: Message = Message(
+        body=render_template(f'{template}.txt.j2', **kwargs),
+        html=render_template(f'{template}.html.j2', **kwargs),
         recipients=[recipient],
-        subject=f'[nopaque] {subject}'
+        subject=f'{subject_prefix} {subject}'
     )
-    return message
+    return msg
 
 
-def send(message: Message) -> Thread:
-    def _send(app: Flask, message: Message):
+def send(msg, *args, **kwargs):
+    def _send(app, msg):
         with app.app_context():
-            mail.send(message)
+            mail.send(msg)
 
-    thread = Thread(
-        target=_send,
-        args=[current_app._get_current_object(), message]
-    )
+    thread = Thread(target=_send, args=[current_app._get_current_object(), msg])
     thread.start()
     return thread

app/ext/flask_sqlalchemy/__init__.py

@@ -0,0 +1,2 @@
+from .container_column import ContainerColumn
+from .int_enum_column import IntEnumColumn

app/ext/flask_sqlalchemy/container_column.py

@@ -0,0 +1,21 @@
+import json
+from app import db
+
+
+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/ext/flask_sqlalchemy/int_enum_column.py

@@ -1,26 +1,6 @@
-import json
 from app import db
 
 
-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)
-
-
 class IntEnumColumn(db.TypeDecorator):
     impl = db.Integer
 

app/extensions/nopaque_sqlalchemy_extras/__init__.py

@@ -1,2 +0,0 @@
-from .types import ContainerColumn
-from .types import IntEnumColumn

app/jobs/__init__.py

@@ -1,2 +1,18 @@
-from .handle_corpora import handle_corpora
-from .handle_jobs import handle_jobs
+from flask import Blueprint
+from flask_login import login_required
+
+
+bp = Blueprint('jobs', __name__)
+
+
+@bp.before_request
+@login_required
+def before_request():
+    '''
+    Ensures that the routes in this package can only be visited by users that
+    are logged in.
+    '''
+    pass
+
+
+from . import routes, json_routes

app/jobs/json_routes.py

@@ -17,7 +17,7 @@ def delete_job(job_id):
             db.session.commit()
 
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_job,
@@ -56,7 +56,7 @@ def restart_job(job_id):
             db.session.commit()
 
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     if job.status == JobStatus.FAILED:
         response = {'errors': {'message': 'Job status is not "failed"'}}

app/jobs/routes.py

@@ -5,20 +5,24 @@ from flask import (
     send_from_directory,
     url_for
 )
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 from app.models import Job, JobInput, JobResult
 from . import bp
+from .utils import job_dynamic_list_constructor as job_dlc
 
 
 @bp.route('')
-def jobs():
+@register_breadcrumb(bp, '.', '<i class="nopaque-icons left">J</i>My Jobs')
+def corpora():
     return redirect(url_for('main.dashboard', _anchor='jobs'))
 
 
 @bp.route('/<hashid:job_id>')
+@register_breadcrumb(bp, '.entity', '', dynamic_list_constructor=job_dlc)
 def job(job_id):
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     return render_template(
         'jobs/job.html.j2',
@@ -30,13 +34,13 @@ def job(job_id):
 @bp.route('/<hashid:job_id>/inputs/<hashid:job_input_id>/download')
 def download_job_input(job_id, job_input_id):
     job_input = JobInput.query.filter_by(job_id=job_id, id=job_input_id).first_or_404()
-    if not (job_input.job.user == current_user or current_user.is_administrator):
+    if not (job_input.job.user == current_user or current_user.is_administrator()):
         abort(403)
     return send_from_directory(
         job_input.path.parent,
         job_input.path.name,
         as_attachment=True,
-        download_name=job_input.filename,
+        attachment_filename=job_input.filename,
         mimetype=job_input.mimetype
     )
 
@@ -44,12 +48,12 @@ def download_job_input(job_id, job_input_id):
 @bp.route('/<hashid:job_id>/results/<hashid:job_result_id>/download')
 def download_job_result(job_id, job_result_id):
     job_result = JobResult.query.filter_by(job_id=job_id, id=job_result_id).first_or_404()
-    if not (job_result.job.user == current_user or current_user.is_administrator):
+    if not (job_result.job.user == current_user or current_user.is_administrator()):
         abort(403)
     return send_from_directory(
         job_result.path.parent,
         job_result.path.name,
         as_attachment=True,
-        download_name=job_result.filename,
+        attachment_filename=job_result.filename,
         mimetype=job_result.mimetype
     )

app/jobs/utils.py

@@ -0,0 +1,13 @@
+from flask import request, url_for
+from app.models import Job
+
+
+def job_dynamic_list_constructor():
+    job_id = request.view_args['job_id']
+    job = Job.query.get_or_404(job_id)
+    return [
+        {
+            'text': f'<i class="nopaque-icons left service-icons" data-service="{job.service}"></i>{job.title}',
+            'url': url_for('.job', job_id=job_id)
+        }
+    ]

app/main/cli.py

@@ -1,9 +1,8 @@
 from flask import current_app
 from flask_migrate import upgrade
 from pathlib import Path
-from app import db
+from typing import List
 from app.models import (
-    Corpus,
     CorpusFollowerRole,
     Role,
     SpaCyNLPPipelineModel,
@@ -16,10 +15,10 @@ from . import bp
 @bp.cli.command('deploy')
 def deploy():
     ''' Run deployment tasks. '''
-
+    # Make default directories
     print('Make default directories')
     base_dir = current_app.config['NOPAQUE_DATA_DIR']
-    default_dirs: list[Path] = [
+    default_dirs: List[Path] = [
         base_dir / 'tmp',
         base_dir / 'users'
     ]
@@ -29,9 +28,11 @@ def deploy():
         if not default_dir.is_dir():
             raise NotADirectoryError(f'{default_dir} is not a directory')
 
+    # migrate database to latest revision
     print('Migrate database to latest revision')
     upgrade()
 
+    # Insert/Update default database values
     print('Insert/Update default Roles')
     Role.insert_defaults()
     print('Insert/Update default Users')
@@ -43,9 +44,4 @@ def deploy():
     print('Insert/Update default TesseractOCRPipelineModels')
     TesseractOCRPipelineModel.insert_defaults()
 
-    print('Stop running analysis sessions')
-    for corpus in Corpus.query.all():
-        corpus.num_analysis_sessions = 0
-    db.session.commit()
-
     # TODO: Implement checks for if the nopaque network exists

app/main/routes.py

@@ -1,11 +1,14 @@
 from flask import flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user, login_required, login_user
-from app.blueprints.auth.forms import LoginForm
+from app.auth.forms import LoginForm
 from app.models import Corpus, User
+from sqlalchemy import or_
 from . import bp
 
 
 @bp.route('/', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.', '<i class="material-icons">home</i>')
 def index():
     form = LoginForm()
     if form.validate_on_submit():
@@ -24,6 +27,7 @@ def index():
 
 
 @bp.route('/faq')
+@register_breadcrumb(bp, '.faq', 'Frequently Asked Questions')
 def faq():
     return render_template(
         'main/faq.html.j2',
@@ -32,6 +36,7 @@ def faq():
 
 
 @bp.route('/dashboard')
+@register_breadcrumb(bp, '.dashboard', '<i class="material-icons left">dashboard</i>Dashboard')
 @login_required
 def dashboard():
     return render_template(
@@ -40,15 +45,8 @@ def dashboard():
     )
 
 
-@bp.route('/manual')
-def manual():
-    return render_template(
-        'main/manual.html.j2',
-        title='Manual'
-    )
-
-
 @bp.route('/news')
+@register_breadcrumb(bp, '.news', '<i class="material-icons left">email</i>News')
 def news():
     return render_template(
         'main/news.html.j2',
@@ -57,6 +55,7 @@ def news():
 
 
 @bp.route('/privacy_policy')
+@register_breadcrumb(bp, '.privacy_policy', 'Private statement (GDPR)')
 def privacy_policy():
     return render_template(
         'main/privacy_policy.html.j2',
@@ -65,6 +64,7 @@ def privacy_policy():
 
 
 @bp.route('/terms_of_use')
+@register_breadcrumb(bp, '.terms_of_use', 'Terms of Use')
 def terms_of_use():
     return render_template(
         'main/terms_of_use.html.j2',
@@ -73,9 +73,12 @@ def terms_of_use():
 
 
 @bp.route('/social-area')
+@register_breadcrumb(bp, '.social_area', '<i class="material-icons left">group</i>Social Area')
 @login_required
 def social_area():
+    print('test')
     corpora = Corpus.query.filter(Corpus.is_public == True, Corpus.user != current_user).all()
+    print(corpora)
     users = User.query.filter(User.is_public == True, User.id != current_user.id).all()
     return render_template(
         'main/social_area.html.j2',

app/models/__init__.py

@@ -1,4 +1,3 @@
-from .anonymous_user import *
 from .avatar import *
 from .corpus_file import *
 from .corpus_follower_association import *
@@ -12,3 +11,9 @@ from .spacy_nlp_pipeline_model import *
 from .tesseract_ocr_pipeline_model import *
 from .token import *
 from .user import *
+from app import login
+
+
+@login.user_loader
+def load_user(user_id):
+    return User.query.get(int(user_id))

app/models/anonymous_user.py

@@ -1,10 +0,0 @@
-from flask_login import AnonymousUserMixin
-
-
-class AnonymousUser(AnonymousUserMixin):
-    def can(self, permissions):
-        return False
-
-    @property
-    def is_administrator(self):
-        return False

app/models/corpus.py

@@ -3,12 +3,13 @@ from enum import IntEnum
 from flask import current_app, url_for
 from flask_hashids import HashidMixin
 from sqlalchemy.ext.associationproxy import association_proxy
+from typing import Union
 from pathlib import Path
 import shutil
 import xml.etree.ElementTree as ET
 from app import db
 from app.converters.vrt import normalize_vrt_file
-from app.extensions.nopaque_sqlalchemy_extras import IntEnumColumn
+from app.ext.flask_sqlalchemy import IntEnumColumn
 from .corpus_follower_association import CorpusFollowerAssociation
 
 
@@ -24,7 +25,7 @@ class CorpusStatus(IntEnum):
     CANCELING_ANALYSIS_SESSION = 9
 
     @staticmethod
-    def get(corpus_status: 'CorpusStatus | int | str') -> 'CorpusStatus':
+    def get(corpus_status: Union['CorpusStatus', int, str]) -> 'CorpusStatus':
         if isinstance(corpus_status, CorpusStatus):
             return corpus_status
         if isinstance(corpus_status, int):

app/models/corpus_follower_role.py

@@ -1,5 +1,6 @@
 from flask_hashids import HashidMixin
 from enum import IntEnum
+from typing import Union
 from app import db
 
 
@@ -10,7 +11,7 @@ class CorpusFollowerPermission(IntEnum):
     MANAGE_CORPUS = 8
 
     @staticmethod
-    def get(corpus_follower_permission: 'CorpusFollowerPermission | int | str') -> 'CorpusFollowerPermission':
+    def get(corpus_follower_permission: Union['CorpusFollowerPermission', int, str]) -> 'CorpusFollowerPermission':
         if isinstance(corpus_follower_permission, CorpusFollowerPermission):
             return corpus_follower_permission
         if isinstance(corpus_follower_permission, int):
@@ -37,16 +38,16 @@ class CorpusFollowerRole(HashidMixin, db.Model):
     def __repr__(self):
         return f'<CorpusFollowerRole {self.name}>'
 
-    def has_permission(self, permission: CorpusFollowerPermission | int | str):
+    def has_permission(self, permission: Union[CorpusFollowerPermission, int, str]):
         perm = CorpusFollowerPermission.get(permission)
         return self.permissions & perm.value == perm.value
-
-    def add_permission(self, permission: CorpusFollowerPermission | int | str):
+    
+    def add_permission(self, permission: Union[CorpusFollowerPermission, int, str]):
         perm = CorpusFollowerPermission.get(permission)
         if not self.has_permission(perm):
             self.permissions += perm.value
-
-    def remove_permission(self, permission: CorpusFollowerPermission | int | str):
+    
+    def remove_permission(self, permission: Union[CorpusFollowerPermission, int, str]):
         perm = CorpusFollowerPermission.get(permission)
         if self.has_permission(perm):
             self.permissions -= perm.value

app/models/event_listeners.py

@@ -43,7 +43,7 @@ def resource_after_delete(mapper, connection, resource):
         }
     ]
     room = f'/users/{resource.user_hashid}'
-    socketio.emit('patch_user', jsonpatch, namespace='/users', room=room)
+    socketio.emit('PATCH', jsonpatch, room=room)
 
 
 def cfa_after_delete(mapper, connection, cfa):
@@ -55,7 +55,7 @@ def cfa_after_delete(mapper, connection, cfa):
         }
     ]
     room = f'/users/{cfa.corpus.user.hashid}'
-    socketio.emit('patch_user', jsonpatch, namespace='/users', room=room)
+    socketio.emit('PATCH', jsonpatch, room=room)
 
 
 def resource_after_insert(mapper, connection, resource):
@@ -70,7 +70,7 @@ def resource_after_insert(mapper, connection, resource):
         }
     ]
     room = f'/users/{resource.user_hashid}'
-    socketio.emit('patch_user', jsonpatch, namespace='/users', room=room)
+    socketio.emit('PATCH', jsonpatch, room=room)
 
 
 def cfa_after_insert(mapper, connection, cfa):
@@ -84,7 +84,7 @@ def cfa_after_insert(mapper, connection, cfa):
         }
     ]
     room = f'/users/{cfa.corpus.user.hashid}'
-    socketio.emit('patch_user', jsonpatch, namespace='/users', room=room)
+    socketio.emit('PATCH', jsonpatch, room=room)
 
 
 def resource_after_update(mapper, connection, resource):
@@ -110,7 +110,7 @@ def resource_after_update(mapper, connection, resource):
         )
     if jsonpatch:
         room = f'/users/{resource.user_hashid}'
-        socketio.emit('patch_user', jsonpatch, namespace='/users', room=room)
+        socketio.emit('PATCH', jsonpatch, room=room)
 
 
 def job_after_update(mapper, connection, job):

app/models/job.py

@@ -3,10 +3,11 @@ from enum import IntEnum
 from flask import current_app, url_for
 from flask_hashids import HashidMixin
 from time import sleep
+from typing import Union
 from pathlib import Path
 import shutil
 from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn, IntEnumColumn
+from app.ext.flask_sqlalchemy import ContainerColumn, IntEnumColumn
 
 
 class JobStatus(IntEnum):
@@ -20,7 +21,7 @@ class JobStatus(IntEnum):
     FAILED = 8
 
     @staticmethod
-    def get(job_status: 'JobStatus | int | str') -> 'JobStatus':
+    def get(job_status: Union['JobStatus', int, str]) -> 'JobStatus':
         if isinstance(job_status, JobStatus):
             return job_status
         if isinstance(job_status, int):

app/models/role.py

@@ -1,5 +1,6 @@
 from enum import IntEnum
 from flask_hashids import HashidMixin
+from typing import Union
 from app import db
 
 
@@ -13,7 +14,7 @@ class Permission(IntEnum):
     USE_API = 4
 
     @staticmethod
-    def get(permission: 'Permission | int | str') -> 'Permission':
+    def get(permission: Union['Permission', int, str]) -> 'Permission':
         if isinstance(permission, Permission):
             return permission
         if isinstance(permission, int):
@@ -37,16 +38,16 @@ class Role(HashidMixin, db.Model):
     def __repr__(self):
         return f'<Role {self.name}>'
 
-    def has_permission(self, permission: Permission | int | str):
+    def has_permission(self, permission: Union[Permission, int, str]):
         p = Permission.get(permission)
         return self.permissions & p.value == p.value
-
-    def add_permission(self, permission: Permission | int | str):
+    
+    def add_permission(self, permission: Union[Permission, int, str]):
         p = Permission.get(permission)
         if not self.has_permission(p):
             self.permissions += p.value
-
-    def remove_permission(self, permission: Permission | int | str):
+    
+    def remove_permission(self, permission: Union[Permission, int, str]):
         p = Permission.get(permission)
         if self.has_permission(p):
             self.permissions -= p.value

app/models/spacy_nlp_pipeline_model.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import requests
 import yaml
 from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn
+from app.ext.flask_sqlalchemy import ContainerColumn
 from .file_mixin import FileMixin
 from .user import User
 
@@ -104,7 +104,7 @@ class SpaCyNLPPipelineModel(FileMixin, HashidMixin, db.Model):
                             f.write(chunk)
                     pbar.close()
         db.session.commit()
-
+    
     def delete(self):
         try:
             self.path.unlink(missing_ok=True)

app/models/tesseract_ocr_pipeline_model.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import requests
 import yaml
 from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn
+from app.ext.flask_sqlalchemy import ContainerColumn
 from .file_mixin import FileMixin
 from .user import User
 

app/models/user.py

@@ -5,13 +5,14 @@ from flask_hashids import HashidMixin
 from flask_login import UserMixin
 from sqlalchemy.ext.associationproxy import association_proxy
 from pathlib import Path
+from typing import Union
 from werkzeug.security import generate_password_hash, check_password_hash
 import jwt
 import re
 import secrets
 import shutil
 from app import db, hashids
-from app.extensions.nopaque_sqlalchemy_extras import IntEnumColumn
+from app.ext.flask_sqlalchemy import IntEnumColumn
 from .corpus import Corpus
 from .corpus_follower_association import CorpusFollowerAssociation
 from .corpus_follower_role import CorpusFollowerRole
@@ -25,7 +26,7 @@ class ProfilePrivacySettings(IntEnum):
     SHOW_MEMBER_SINCE = 4
 
     @staticmethod
-    def get(profile_privacy_setting: 'ProfilePrivacySettings | int | str') -> 'ProfilePrivacySettings':
+    def get(profile_privacy_setting: Union['ProfilePrivacySettings', int, str]) -> 'ProfilePrivacySettings':
         if isinstance(profile_privacy_setting, ProfilePrivacySettings):
             return profile_privacy_setting
         if isinstance(profile_privacy_setting, int):
@@ -131,10 +132,6 @@ class User(HashidMixin, UserMixin, db.Model):
     def __repr__(self):
         return f'<User {self.username}>'
 
-    @property
-    def is_administrator(self):
-        return self.can(Permission.ADMINISTRATE)
-
     @property
     def jsonpatch_path(self):
         return f'/users/{self.hashid}'
@@ -145,8 +142,7 @@ class User(HashidMixin, UserMixin, db.Model):
 
     @password.setter
     def password(self, password):
-        #pbkdf2:sha256
-        self.password_hash = generate_password_hash(password, method='pbkdf2')
+        self.password_hash = generate_password_hash(password)
 
     @property
     def path(self) -> Path:
@@ -298,6 +294,9 @@ class User(HashidMixin, UserMixin, db.Model):
             algorithm='HS256'
         )
 
+    def is_administrator(self):
+        return self.can(Permission.ADMINISTRATE)
+
     def ping(self):
         self.last_seen = datetime.utcnow()
 
@@ -314,7 +313,7 @@ class User(HashidMixin, UserMixin, db.Model):
     def has_profile_privacy_setting(self, setting):
         s = ProfilePrivacySettings.get(setting)
         return self.profile_privacy_settings & s.value == s.value
-
+    
     def add_profile_privacy_setting(self, setting):
         s = ProfilePrivacySettings.get(setting)
         if not self.has_profile_privacy_setting(s):
@@ -349,7 +348,7 @@ class User(HashidMixin, UserMixin, db.Model):
 
     def is_following_corpus(self, corpus):
         return corpus in self.followed_corpora
-
+    
     def generate_follow_corpus_token(self, corpus_hashid, role_name, expiration=7):
         now = datetime.utcnow()
         payload = {
@@ -365,7 +364,7 @@ class User(HashidMixin, UserMixin, db.Model):
             current_app.config['SECRET_KEY'],
             algorithm='HS256'
         )
-
+    
     def follow_corpus_by_token(self, token):
         try:
             payload = jwt.decode(

app/namespaces/cqi_over_sio/utils.py

@@ -1,37 +0,0 @@
-from cqi import CQiClient
-from threading import Lock
-from flask import session
-
-
-class CQiOverSocketIOSessionManager:
-    @staticmethod
-    def setup():
-        session['cqi_over_sio'] = {}
-
-    @staticmethod
-    def teardown():
-        session.pop('cqi_over_sio')
-
-    @staticmethod
-    def set_corpus_id(corpus_id: int):
-        session['cqi_over_sio']['corpus_id'] = corpus_id
-
-    @staticmethod
-    def get_corpus_id() -> int:
-        return session['cqi_over_sio']['corpus_id']
-
-    @staticmethod
-    def set_cqi_client(cqi_client: CQiClient):
-        session['cqi_over_sio']['cqi_client'] = cqi_client
-
-    @staticmethod
-    def get_cqi_client() -> CQiClient:
-        return session['cqi_over_sio']['cqi_client']
-
-    @staticmethod
-    def set_cqi_client_lock(cqi_client_lock: Lock):
-        session['cqi_over_sio']['cqi_client_lock'] = cqi_client_lock
-
-    @staticmethod
-    def get_cqi_client_lock() -> Lock:
-        return session['cqi_over_sio']['cqi_client_lock']

app/namespaces/users/__init__.py

@@ -1,78 +0,0 @@
-from flask_login import current_user
-from flask_socketio import join_room, leave_room, Namespace
-from app import hashids
-from app.decorators import socketio_login_required
-from app.models import User
-
-
-class UsersNamespace(Namespace):
-    @socketio_login_required
-    def on_get_user(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'code': 400, 'msg': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        return {
-            'body': user.to_json_serializeable(
-                backrefs=True,
-                relationships=True
-            ),
-            'status': 200,
-            'statusText': 'OK'
-        }
-
-    @socketio_login_required
-    def on_subscribe_user(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'code': 400, 'msg': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        join_room(f'/users/{user.hashid}')
-
-        return {'status': 200, 'statusText': 'OK'}
-
-    @socketio_login_required
-    def on_unsubscribe_user(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'code': 400, 'msg': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        leave_room(f'/users/{user.hashid}')
-
-        return {'status': 200, 'statusText': 'OK'}

app/services/forms.py

@@ -61,7 +61,7 @@ class CreateTesseractOCRPipelineJobForm(CreateJobBaseForm):
         if field.data:
             if not('methods' in service_info and 'binarization' in service_info['methods']):
                 raise ValidationError('Binarization is not available')
-
+              
     def validate_pdf(self, field):
         if field.data.mimetype != 'application/pdf':
             raise ValidationError('PDF files only!')
@@ -146,7 +146,7 @@ class CreateSpacyNLPPipelineJobForm(CreateJobBaseForm):
     encoding_detection = BooleanField('Encoding detection', render_kw={'disabled': True})
     txt = FileField('File', validators=[FileRequired()])
     model = SelectField('Model', validators=[InputRequired()])
-
+    
     def validate_encoding_detection(self, field):
         service_info = SERVICES['spacy-nlp-pipeline']['versions'][self.version.data]
         if field.data:
@@ -167,6 +167,7 @@ class CreateSpacyNLPPipelineJobForm(CreateJobBaseForm):
         version = kwargs.pop('version', service_manifest['latest_version'])
         super().__init__(*args, **kwargs)
         service_info = service_manifest['versions'][version]
+        print(service_info)
         if self.encoding_detection.render_kw is None:
             self.encoding_detection.render_kw = {}
         self.encoding_detection.render_kw['disabled'] = True

app/services/routes.py

@@ -1,10 +1,12 @@
-from flask import abort, current_app, flash, redirect, render_template, request, url_for
+from flask import abort, current_app, flash, Markup, redirect, render_template, request, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 import requests
 from app import db, hashids
 from app.models import (
     Job,
     JobInput,
+    JobResult,
     JobStatus,
     TesseractOCRPipelineModel,
     SpaCyNLPPipelineModel
@@ -19,11 +21,13 @@ from .forms import (
 
 
 @bp.route('/services')
+@register_breadcrumb(bp, '.', 'Services')
 def services():
     return redirect(url_for('main.dashboard'))
 
 
 @bp.route('/file-setup-pipeline', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.file_setup_pipeline', '<i class="nopaque-icons service-icons left" data-service="file-setup-pipeline"></i>File Setup')
 def file_setup_pipeline():
     service = 'file-setup-pipeline'
     service_manifest = SERVICES[service]
@@ -53,7 +57,7 @@ def file_setup_pipeline():
                 abort(500)
         job.status = JobStatus.SUBMITTED
         db.session.commit()
-        message = f'Job "<a href="{job.url}">{job.title}</a>" created'
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
         flash(message, 'job')
         return {}, 201, {'Location': job.url}
     return render_template(
@@ -64,12 +68,15 @@ def file_setup_pipeline():
 
 
 @bp.route('/tesseract-ocr-pipeline', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline', '<i class="nopaque-icons service-icons left" data-service="tesseract-ocr-pipeline"></i>Tesseract OCR Pipeline')
 def tesseract_ocr_pipeline():
     service_name = 'tesseract-ocr-pipeline'
     service_manifest = SERVICES[service_name]
     version = request.args.get('version', service_manifest['latest_version'])
     if version not in service_manifest['versions']:
         abort(404)
+    job_results = JobResult.query.all()
+    choosable_job_ids = [job_result.job.hashid for job_result in job_results if job_result.job.service == "file-setup-pipeline" and job_result.filename.endswith('.pdf')]
     form = CreateTesseractOCRPipelineJobForm(prefix='create-job-form', version=version)
     if form.is_submitted():
         if not form.validate():
@@ -96,7 +103,7 @@ def tesseract_ocr_pipeline():
             abort(500)
         job.status = JobStatus.SUBMITTED
         db.session.commit()
-        message = f'Job "<a href="{job.url}">{job.title}</a>" created'
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
         flash(message, 'job')
         return {}, 201, {'Location': job.url}
     tesseract_ocr_pipeline_models = [
@@ -107,6 +114,7 @@ def tesseract_ocr_pipeline():
     return render_template(
         'services/tesseract_ocr_pipeline.html.j2',
         title=service_manifest['name'],
+        choosable_job_ids=choosable_job_ids,
         form=form,
         tesseract_ocr_pipeline_models=tesseract_ocr_pipeline_models,
         user_tesseract_ocr_pipeline_models_count=user_tesseract_ocr_pipeline_models_count
@@ -114,6 +122,7 @@ def tesseract_ocr_pipeline():
 
 
 @bp.route('/transkribus-htr-pipeline', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.transkribus_htr_pipeline', '<i class="nopaque-icons service-icons left" data-service="transkribus-htr-pipeline"></i>Transkribus HTR Pipeline')
 def transkribus_htr_pipeline():
     if not current_app.config.get('NOPAQUE_TRANSKRIBUS_ENABLED'):
         abort(404)
@@ -159,7 +168,7 @@ def transkribus_htr_pipeline():
             abort(500)
         job.status = JobStatus.SUBMITTED
         db.session.commit()
-        message = f'Job "<a href="{job.url}">{job.title}</a>" created'
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
         flash(message, 'job')
         return {}, 201, {'Location': job.url}
     return render_template(
@@ -171,6 +180,7 @@ def transkribus_htr_pipeline():
 
 
 @bp.route('/spacy-nlp-pipeline', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.spacy_nlp_pipeline', '<i class="nopaque-icons service-icons left" data-service="spacy-nlp-pipeline"></i>SpaCy NLP Pipeline')
 def spacy_nlp_pipeline():
     service = 'spacy-nlp-pipeline'
     service_manifest = SERVICES[service]
@@ -204,7 +214,7 @@ def spacy_nlp_pipeline():
             abort(500)
         job.status = JobStatus.SUBMITTED
         db.session.commit()
-        message = f'Job "<a href="{job.url}">{job.title}</a>" created'
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
         flash(message, 'job')
         return {}, 201, {'Location': job.url}
     return render_template(
@@ -217,6 +227,7 @@ def spacy_nlp_pipeline():
 
 
 @bp.route('/corpus-analysis')
+@register_breadcrumb(bp, '.corpus_analysis', '<i class="nopaque-icons service-icons left" data-service="corpus-analysis"></i>Corpus Analysis')
 def corpus_analysis():
     return render_template(
         'services/corpus_analysis.html.j2',

app/settings/routes.py

@@ -1,10 +1,12 @@
 from flask import g, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
-from app.blueprints.users.settings.routes import settings as settings_route
+from app.users.settings.routes import settings as settings_route
 from . import bp
 
 
 @bp.route('/settings', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.', '<i class="material-icons left">settings</i>Settings')
 def settings():
     g._nopaque_redirect_location_on_post = url_for('.settings')
     return settings_route(current_user.id)

app/static/css/colors.scss

@@ -0,0 +1,290 @@
+/// Map deep get
+/// @author Kitty Giraudel
+/// @access public
+/// @param {Map} $map - Map
+/// @param {Arglist} $keys - Key chain
+/// @return {*} - Desired value
+@function map-deep-get($map, $keys...) {
+    @each $key in $keys {
+        $map: map-get($map, $key);
+    }
+    @return $map;
+}
+
+
+$color: (
+  "baseline": (
+    "primary": #00426f,
+    "primary-variant": #1a5c89,
+    "secondary": #00426f,
+    "secondary-variant": #1a5c89,
+    "background": #ffffff,
+    "surface": #ffffff,
+    "error": #b00020
+  ),
+  "social-area": (
+    "base": #d6ae86,
+    "darken": #C98536,
+    "lighten": #EAE2DB
+  ),
+  "service": (
+    "corpus-analysis": (
+      "base": #aa9cc9,
+      "darken": #6b3f89,
+      "lighten": #ebe8f6
+    ),
+    "file-setup-pipeline": (
+      "base": #d5dc95,
+      "darken": #a1b300,
+      "lighten": #f2f3e1
+    ),
+    "spacy-nlp-pipeline": (
+      "base": #98acd2,
+      "darken": #0064a3,
+      "lighten": #e5e8f5
+    ),
+    "tesseract-ocr-pipeline": (
+      "base": #a9d8c8,
+      "darken": #00a58b,
+      "lighten": #e7f4f1
+    ),
+    "transkribus-htr-pipeline": (
+      "base": #607d8b,
+      "darken": #37474f,
+      "lighten": #cfd8dc
+    )
+  ),
+  "status": (
+    "corpus": (
+      "UNPREPARED": #9e9e9e,
+      "QUEUED": #2196f3,
+      "BUILDING": #ffc107,
+      "BUILT": #4caf50,
+      "FAILED": #f44336,
+      "STARTING_ANALYSIS_SESSION": #2196f3,
+      "RUNNING_ANALYSIS_SESSION": #4caf50,
+      "CANCELING_ANALYSIS_SESSION": #ff5722
+    ),
+    "job": (
+      "INITIALIZING": #9e9e9e,
+      "SUBMITTED": #9e9e9e,
+      "QUEUED": #2196f3,
+      "RUNNING": #ffc107,
+      "CANCELING": #ff5722,
+      "CANCELED": #ff5722,
+      "COMPLETED": #4caf50,
+      "FAILED": #f44336
+    )
+  ),
+  "s-attr": (
+    "PERSON": #a6e22d,
+    "PER": #a6e22d,
+    "NORP": #ef60b4,
+    "FACILITY": #43c6fc,
+    "ORG": #43c6fc,
+    "GPE": #fd9720,
+    "LOC": #fd9720,
+    "PRODUCT": #a99dfb,
+    "MISC": #a99dfb,
+    "EVENT": #fc0,
+    "WORK_OF_ART": #fc0,
+    "LANGUAGE": #fc0,
+    "DATE": #2fbbab,
+    "TIME": #2fbbab,
+    "PERCENT": #bbb,
+    "MONEY": #bbb,
+    "QUANTITY": #bbb,
+    "ORDINAL": #bbb,
+    "CARDINAL": #bbb
+  )
+);
+
+@each $key, $color-code in map-get($color, "baseline") {
+  .#{$key}-color {
+    background-color: $color-code !important;
+  }
+
+  .#{$key}-color-border {
+    border-color: $color-code !important;
+  }
+
+  .#{$key}-color-text {
+    color: $color-code !important;
+  }
+}
+
+@each $key, $color-code in map-get($color, "social-area") {
+  .social-area-color-#{$key} {
+    background-color: $color-code !important;
+  }
+
+  .social-area-color-border-#{$key} {
+    border-color: $color-code !important;
+  }
+}
+
+@each $service-name, $color-palette in map-get($color, "service") {
+  .service-color[data-service="#{$service-name}"] {
+    background-color: map-get($color-palette, "base") !important;
+
+    &.darken {
+      background-color: map-get($color-palette, "darken") !important;
+    }
+
+    &.lighten {
+      background-color: map-get($color-palette, "lighten") !important;
+    }
+  }
+
+  .service-color-border[data-service="#{$service-name}"] {
+    border-color: map-get($color-palette, "base") !important;
+
+    &.border-darken {
+      border-color: map-get($color-palette, "darken") !important;
+    }
+
+    &.border-lighten {
+      border-color: map-get($color-palette, "lighten") !important;
+    }
+  }
+
+  .service-color-text[data-service="#{$service-name}"] {
+    color: map-get($color-palette, "base") !important;
+
+    &.text-darken {
+      color: map-get($color-palette, "darken") !important;
+    }
+
+    &.text-lighten {
+      color: map-get($color-palette, "lighten") !important;
+    }
+  }
+
+  .service-scheme[data-service="#{$service-name}"] {
+    background-color: map-get($color-palette, "lighten");
+
+    .btn, .btn-small, .btn-large, .btn-floating {
+      background-color: map-get($color-palette, "darken");
+
+      &:hover {
+        background-color: map-get($color-palette, "base");
+      }
+    }
+
+    .pagination {
+      li.active {
+        background-color: map-get($color-palette, "darken");
+      }
+    }
+
+    .table-of-contents {
+      a.active, a:hover {
+        border-color: map-get($color-palette, "darken");
+      }
+    }
+
+    .tabs {
+      .tab {
+        &.disabled {
+          a {
+            color: inherit;
+
+            &:hover {
+              color: change-color(map-get($color-palette, "darken"), $alpha: 0.15);
+            }
+          }
+        }
+
+        a {
+          color: inherit;
+
+          &:focus, &:hover, &.active {
+            color: map-get($color-palette, "darken");
+          }
+
+          &:focus, &.active, &.active:focus {
+            background-color: change-color(map-get($color-palette, "darken"), $alpha: 0.15);
+          }
+        }
+      }
+      .indicator {
+        background-color: map-get($color-palette, "darken");
+      }
+    }
+  }
+}
+
+@each $ressource-name, $color-palette in map-get($color, "status") {
+  @each $key, $color-code in $color-palette {
+    .#{$ressource-name}-status-color[data-status="#{$key}"] {
+      background-color: $color-code !important;
+    }
+
+    .#{$ressource-name}-status-color-border[data-status="#{$key}"] {
+      border-color: $color-code !important;
+    }
+
+    .#{$ressource-name}-status-color-text[data-status="#{$key}"] {
+      color: $color-code !important;
+    }
+  }
+}
+
+
+@each $key, $color-code in map-get($color, "s-attr") {
+  .chip.s-attr[data-s-attr-type="ent"][data-s-attr-ent-type="#{$key}"] {
+    background-color: $color-code !important;
+  }
+}
+
+
+main {
+  .btn, .btn-small, .btn-large, .btn-floating {
+    background-color: map-deep-get($color, "baseline", "secondary");
+
+    &:hover {
+      background-color: map-deep-get($color, "baseline", "secondary-variant");
+    }
+  }
+
+  .pagination {
+    li.active {
+      background-color: map-deep-get($color, "baseline", "secondary");
+    }
+  }
+
+  .table-of-contents {
+    a.active, a:hover {
+      border-color: map-deep-get($color, "baseline", "secondary");
+    }
+  }
+
+  .tabs {
+    .tab {
+      &.disabled {
+        a {
+          color: inherit;
+
+          &:hover {
+            color: change-color(map-deep-get($color, "baseline", "secondary"), $alpha: 0.15);
+          }
+        }
+      }
+
+      a {
+        color: inherit;
+
+        &:focus, &:hover, &.active {
+          color: map-deep-get($color, "baseline", "secondary");
+        }
+
+        &:focus, &.active, &.active:focus {
+          background-color: change-color(map-deep-get($color, "baseline", "secondary"), $alpha: 0.15);
+        }
+      }
+    }
+    .indicator {
+      background-color: map-deep-get($color, "baseline", "secondary");
+    }
+  }
+}

app/static/css/corpus-status-colors.css

@@ -1,43 +0,0 @@
-[data-corpus-status="UNPREPARED"] {
-  --corpus-status-color: #9e9e9e;
-}
-
-[data-corpus-status="QUEUED"] {
-  --corpus-status-color: #2196f3;
-}
-
-[data-corpus-status="BUILDING"] {
-  --corpus-status-color: #ffc107;
-}
-
-[data-corpus-status="BUILT"] {
-  --corpus-status-color: #4caf50;
-}
-
-[data-corpus-status="FAILED"] {
-  --corpus-status-color: #f44336;
-}
-
-[data-corpus-status="STARTING_ANALYSIS_SESSION"] {
-  --corpus-status-color: #2196f3;
-}
-
-[data-corpus-status="RUNNING_ANALYSIS_SESSION"] {
-  --corpus-status-color: #4caf50;
-}
-
-[data-corpus-status="CANCELING_ANALYSIS_SESSION"] {
-  --corpus-status-color: #ff5722;
-}
-
-.corpus-status-color {
-  background-color: var(--corpus-status-color) !important;
-}
-
-.corpus-status-color-border {
-  border-color: var(--corpus-status-color) !important;
-}
-
-.corpus-status-color-text {
-  color: var(--corpus-status-color) !important;
-}

app/static/css/corpus-status-text.css

@@ -1,35 +0,0 @@
-[data-corpus-status="UNPREPARED"] {
-  --corpus-status-content: "unprepared";
-}
-
-[data-corpus-status="QUEUED"] {
-  --corpus-status-content: "queued";
-}
-
-[data-corpus-status="BUILDING"] {
-  --corpus-status-content: "building";
-}
-
-[data-corpus-status="BUILT"] {
-  --corpus-status-content: "built";
-}
-
-[data-corpus-status="FAILED"] {
-  --corpus-status-content: "failed";
-}
-
-[data-corpus-status="STARTING_ANALYSIS_SESSION"] {
-  --corpus-status-content: "starting analysis session";
-}
-
-[data-corpus-status="RUNNING_ANALYSIS_SESSION"] {
-  --corpus-status-content: "running analysis session";
-}
-
-[data-corpus-status="CANCELING_ANALYSIS_SESSION"] {
-  --corpus-status-content: "canceling analysis session";
-}
-
-.corpus-status-text:empty::before {
-  content: var(--corpus-status-content);
-}

app/static/css/helpers.scss

@@ -0,0 +1,31 @@
+/*
+ * Spacing
+ */
+$spacing-shortcuts: ("margin": "mg", "padding": "pd");
+$spacing-directions: ("top": "t", "right": "r", "bottom": "b", "left": "l");
+$spacing-values: ("0": 0, "1": 0.25rem, "2": 0.5rem, "3": 0.75rem, "4": 1rem, "5": 1.5rem, "6": 3rem, "auto": auto);
+
+@each $spacing-shortcut-name, $spacing-shortcut-value in $spacing-shortcuts {
+  @each $spacing-name, $spacing-value in $spacing-values {
+    // All directions
+    .#{$spacing-shortcut-value}-#{$spacing-name} {
+      #{$spacing-shortcut-name}: $spacing-value !important;
+    }
+    // Horizontal axis
+    .#{$spacing-shortcut-value}x-#{$spacing-name} {
+      #{$spacing-shortcut-name}-left: $spacing-value !important;
+      #{$spacing-shortcut-name}-right: $spacing-value !important;
+    }
+    // Vertical axis
+    .#{$spacing-shortcut-value}y-#{$spacing-name} {
+      #{$spacing-shortcut-name}-top: $spacing-value !important;
+      #{$spacing-shortcut-name}-bottom: $spacing-value !important;
+    }
+    // Cardinal directions
+    @each $spacing-direction-name, $spacing-direction-value in $spacing-directions {
+      .#{$spacing-shortcut-value}#{$spacing-direction-value}-#{$spacing-name} {
+        #{$spacing-shortcut-name}-#{$spacing-direction-name}: $spacing-value !important;
+      }
+    }
+  }
+}

app/static/css/job-status-colors.css

@@ -1,43 +0,0 @@
-[data-job-status="INITIALIZING"] {
-  --job-status-color: #9e9e9e;
-}
-
-[data-job-status="SUBMITTED"] {
-  --job-status-color: #9e9e9e;
-}
-
-[data-job-status="QUEUED"] {
-  --job-status-color: #2196f3;
-}
-
-[data-job-status="RUNNING"] {
-  --job-status-color: #ffc107;
-}
-
-[data-job-status="CANCELING"] {
-  --job-status-color: #ff5722;
-}
-
-[data-job-status="CANCELED"] {
-  --job-status-color: #ff5722;
-}
-
-[data-job-status="COMPLETED"] {
-  --job-status-color: #4caf50;
-}
-
-[data-job-status="FAILED"] {
-  --job-status-color: #f44336;
-}
-
-.job-status-color {
-  background-color: var(--job-status-color) !important;
-}
-
-.job-status-color-border {
-  border-color: var(--job-status-color) !important;
-}
-
-.job-status-color-text {
-  color: var(--job-status-color) !important;
-}

app/static/css/job-status-text.css

@@ -1,35 +0,0 @@
-[data-job-status="INITIALIZING"] {
-  --job-status-content: "initializing";
-}
-
-[data-job-status="SUBMITTED"] {
-  --job-status-content: "submitted";
-}
-
-[data-job-status="QUEUED"] {
-  --job-status-content: "queued";
-}
-
-[data-job-status="RUNNING"] {
-  --job-status-content: "running";
-}
-
-[data-job-status="CANCELING"] {
-  --job-status-content: "canceling";
-}
-
-[data-job-status="CANCELED"] {
-  --job-status-content: "canceled";
-}
-
-[data-job-status="COMPLETED"] {
-  --job-status-content: "completed";
-}
-
-[data-job-status="FAILED"] {
-  --job-status-content: "failed";
-}
-
-.job-status-text:empty::before {
-  content: var(--job-status-content);
-}