simplify decompression and decoding

update breadcrumbs

.dockerignore

@@ -0,0 +1,12 @@
+# Exclude everything
+*
+
+# Include what we need
+!app
+!migrations
+!tests
+!.flaskenv
+!boot.sh
+!config.py
+!nopaque.py
+!requirements.txt

.env.tpl

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+################################################################################
+# Docker                                                                       #
+################################################################################
+# DEFAULT: ./data
+# NOTE: Use `.` as <project-basedir>
+# HOST_DATA_DIR=
+
+# Example: 1000
+# HINT: Use this bash command `id -u`
+HOST_UID=
+
+# Example: 1000
+# HINT: Use this bash command `id -g`
+HOST_GID=
+
+# Example: 999
+# HINT: Use this bash command `getent group docker | cut -d: -f3`
+HOST_DOCKER_GID=
+
+# DEFAULT: ./logs
+# NOTES: Use `.` as <project-basedir>
+# HOST_LOG_DIR=
+
+# DEFAULT: nopaque_default
+# DOCKER_NETWORK_NAME=
+
+################################################################################
+# Flask                                                                        #
+# https://flask.palletsprojects.com/en/1.1.x/config/                           #
+################################################################################
+# CHOOSE ONE: http, https
+# DEFAULT: http
+# PREFERRED_URL_SCHEME=
+
+# DEFAULT: hard to guess string
+# HINT: Use this bash command `python -c "import uuid; print(uuid.uuid4().hex)"`
+# SECRET_KEY=
+
+# DEFAULT: localhost:5000
+# Example: nopaque.example.com/nopaque.example.com:5000
+# HINT: If your instance is publicly available on a different Port then 80/443,
+#       you will have to add this to the server name
+# SERVER_NAME=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# HINT: Set to true if you redirect http to https
+# SESSION_COOKIE_SECURE=
+
+
+################################################################################
+# Flask-Assets                                                                 #
+# https://webassets.readthedocs.io/en/latest/                                  #
+################################################################################
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# ASSETS_DEBUG=
+
+
+################################################################################
+# Flask-Hashids                                                                #
+# https://github.com/Pevtrick/Flask-Hashids                                    #
+################################################################################
+# DEFAULT: 16
+# HASHIDS_MIN_LENGTH=
+
+# NOTE: Use this bash command `python -c "import uuid; print(uuid.uuid4().hex)"`
+#       It is strongly recommended that this is NEVER the same as the SECRET_KEY
+HASHIDS_SALT=
+
+
+################################################################################
+# Flask-Login                                                                  #
+# https://flask-login.readthedocs.io/en/latest/                                #
+################################################################################
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# HINT: Set to true if you redirect http to https
+# REMEMBER_COOKIE_SECURE=
+
+
+################################################################################
+# Flask-Mail                                                                   #
+# https://pythonhosted.org/Flask-Mail/                                         #
+################################################################################
+# EXAMPLE: nopaque Admin <nopaque@example.com>
+MAIL_DEFAULT_SENDER=
+
+MAIL_PASSWORD=
+
+# EXAMPLE: smtp.example.com
+MAIL_SERVER=
+
+# EXAMPLE: 587
+MAIL_PORT=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# MAIL_USE_SSL=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# MAIL_USE_TLS=
+
+# EXAMPLE: nopaque@example.com
+MAIL_USERNAME=
+
+
+################################################################################
+# Flask-SQLAlchemy                                                             #
+# https://flask-sqlalchemy.palletsprojects.com/en/2.x/config/                  #
+################################################################################
+# DEFAULT: 'sqlite:///<nopaque-basedir>/data.sqlite'
+# NOTE: Use `.` as <nopaque-basedir>,
+#       Don't use a SQLite database when using Docker
+# SQLALCHEMY_DATABASE_URI=
+
+
+################################################################################
+# nopaque                                                                      #
+################################################################################
+# An account is registered with this email adress gets automatically assigned
+# the administrator role.
+# EXAMPLE: admin.nopaque@example.com
+NOPAQUE_ADMIN=
+
+# DEFAULT: /mnt/nopaque
+# NOTE: This must be a network share and it must be available on all Docker
+#       Swarm nodes
+# NOPAQUE_DATA_DIR=
+
+# CHOOSE ONE: False, True
+# DEFAULT: True
+# NOPAQUE_IS_PRIMARY_INSTANCE=
+
+# transport://[userid:password]@hostname[:port]/[virtual_host]
+NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI=
+
+# NOTE: Get these from the nopaque development team
+NOPAQUE_DOCKER_REGISTRY_USERNAME=
+NOPAQUE_DOCKER_REGISTRY_PASSWORD=
+
+# DEFAULT: %Y-%m-%d %H:%M:%S
+# NOPAQUE_LOG_DATE_FORMAT=
+
+# DEFAULT: [%(asctime)s] %(levelname)s in %(pathname)s (function: %(funcName)s, line: %(lineno)d): %(message)s
+# NOPAQUE_LOG_FORMAT=
+
+# DEFAULT: INFO
+# CHOOSE ONE: CRITICAL, ERROR, WARNING, INFO, DEBUG
+# NOPAQUE_LOG_LEVEL=
+
+# CHOOSE ONE: False, True
+# DEFAULT: True
+# NOPAQUE_LOG_FILE_ENABLED=
+
+# DEFAULT: <nopaque-basedir>/logs
+# NOTE: Use `.` as <nopaque-basedir>
+# NOPAQUE_LOG_FILE_DIR=
+
+# DEFAULT: NOPAQUE_LOG_LEVEL
+# CHOOSE ONE: CRITICAL, ERROR, WARNING, INFO, DEBUG
+# NOPAQUE_LOG_FILE_LEVEL=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# NOPAQUE_LOG_STDERR_ENABLED=
+
+# CHOOSE ONE: CRITICAL, ERROR, WARNING, INFO, DEBUG
+# DEFAULT: NOPAQUE_LOG_LEVEL
+# NOPAQUE_LOG_STDERR_LEVEL=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# HINT: Set this to True only if you are using a proxy in front of nopaque
+# NOPAQUE_PROXY_FIX_ENABLED=
+
+# DEFAULT: 0
+# Number of values to trust for X-Forwarded-For
+# NOPAQUE_PROXY_FIX_X_FOR=
+
+# DEFAULT: 0
+# Number of values to trust for X-Forwarded-Host
+# NOPAQUE_PROXY_FIX_X_HOST=
+
+# DEFAULT: 0
+# Number of values to trust for X-Forwarded-Port
+# NOPAQUE_PROXY_FIX_X_PORT=
+
+# DEFAULT: 0
+# Number of values to trust for X-Forwarded-Prefix
+# NOPAQUE_PROXY_FIX_X_PREFIX=
+
+# DEFAULT: 0
+# Number of values to trust for X-Forwarded-Proto
+# NOPAQUE_PROXY_FIX_X_PROTO=
+
+# CHOOSE ONE: False, True
+# DEFAULT: False
+# NOPAQUE_TRANSKRIBUS_ENABLED=
+
+# READ-COOP account data: https://readcoop.eu/
+# NOPAQUE_READCOOP_USERNAME=
+# NOPAQUE_READCOOP_PASSWORD=

.flaskenv

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+FLASK_APP=nopaque.py

.gitignore

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+# nopaque specifics
+app/static/gen/
+data/
+docker-compose.override.yml
+logs/
+!logs/dummy
+*.env
+
+*.pjentsch-testing
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+    "recommendations": [
+        "samuelcolvin.jinjahtml",
+        "ms-azuretools.vscode-docker",
+        "ms-python.python"
+    ]
+}

.vscode/settings.json

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+{
+    "editor.rulers": [79],
+    "files.insertFinalNewline": true,
+    "python.terminal.activateEnvironment": false,
+    "[css]": {
+        "editor.tabSize": 2
+    },
+    "[scss]": {
+        "editor.tabSize": 2
+    },
+    "[html]": {
+        "editor.tabSize": 2
+    },
+    "[javascript]": {
+        "editor.tabSize": 2
+    },
+    "[jinja-html]": {
+        "editor.tabSize": 2
+    },
+    "[jinja-js]": {
+        "editor.tabSize": 2
+    }
+}

Dockerfile

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+FROM python:3.8.10-slim-buster
+
+
+LABEL authors="Patrick Jentsch <p.jentsch@uni-bielefeld.de>"
+
+
+ARG DOCKER_GID
+ARG UID
+ARG GID
+
+
+ENV LANG="C.UTF-8"
+ENV PYTHONDONTWRITEBYTECODE="1"
+ENV PYTHONUNBUFFERED="1"
+
+
+RUN apt-get update \
+ && apt-get install --no-install-recommends --yes \
+      build-essential \
+      libpq-dev \
+ && rm --recursive /var/lib/apt/lists/*
+
+
+RUN groupadd --gid "${DOCKER_GID}" docker \
+ && groupadd --gid "${GID}" nopaque \
+ && useradd --create-home --gid nopaque --groups "${DOCKER_GID}" --no-log-init --uid "${UID}" nopaque
+USER nopaque
+WORKDIR /home/nopaque
+
+
+ENV PYTHON3_VENV_PATH="/home/nopaque/venv"
+RUN python3 -m venv "${PYTHON3_VENV_PATH}"
+ENV PATH="${PYTHON3_VENV_PATH}/bin:${PATH}"
+
+
+COPY --chown=nopaque:nopaque requirements.txt .
+RUN python3 -m pip install --requirement requirements.txt \
+ && rm requirements.txt
+
+
+COPY --chown=nopaque:nopaque app app
+COPY --chown=nopaque:nopaque migrations migrations
+COPY --chown=nopaque:nopaque tests tests
+COPY --chown=nopaque:nopaque .flaskenv boot.sh config.py nopaque.py ./
+
+
+EXPOSE 5000
+
+
+ENTRYPOINT ["./boot.sh"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Bielefeld University - CRC 1288 - INF
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# nopaque
+
+nopaque bundles various tools and services that provide humanities scholars with DH methods and thus can support their various individual research processes. Using nopaque, researchers can subject digitized sources to Optical Character Recognition (OCR). The resulting text files can then be used as a data basis for Natural Language Processing (NLP). The texts are automatically subjected to various linguistic annotations. The data processed via NLP can then be summarized in the web application as corpora and analyzed by means of an information retrieval system through complex search queries. The range of functions of the web application will be successively extended according to the needs of the researchers.
+
+## Prerequisites and requirements
+
+1. Install docker for your system. Following the official instructions.
+2. Install docker-compose. Following the official instructions.
+
+
+## Configuration and startup
+
+### **Create Docker swarm**
+
+The generated computational workload is handled by a [Docker](https://docs.docker.com/) swarm. A swarm is a group of machines that are running Docker and joined into a cluster. It consists out of two different kinds of members, manager and worker nodes. The swarm setup process is described best in the [Docker documentation](https://docs.docker.com/engine/swarm/swarm-tutorial/).
+
+### **Create network storage**
+
+A shared network space is necessary so that all swarm members have access to all the data. To achieve this a [samba](https://www.samba.org/) share can be used.
+
+You can create a samba share by using [this](https://hub.docker.com/r/dperson/samba/) Docker image.
+
+``` bash
+# Mount the Samba share on all swarm nodes (managers and workers)
+username@hostname:~$ sudo mkdir /mnt/nopaque
+username@hostname:~$ sudo mount --types cifs --options gid=${USER},password=nopaque,uid=${USER},user=nopaque,vers=3.0 //<SAMBA-SERVER-IP>/<SAMBA-SHARE-NAME> /mnt/nopaque
+```
+
+### **Download, configure and build nopaque**
+
+``` bash
+# Clone the nopaque repository
+username@hostname:~$ git clone https://gitlab.ub.uni-bielefeld.de/sfb1288inf/nopaque.git
+# Create data directories
+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.
+username@hostname:~$ <YOUR EDITOR> db.env
+username@hostname:~$ <YOUR EDITOR> .env
+# Create docker-compose.override.yml file
+username@hostname:~$ touch docker-compose.override.yml
+# Tweak the docker-compose.override.yml to satisfy your needs. (You can find examples inside the docker-compose directory)
+username@hostname:~$ <YOUR EDITOR> docker-compose.override.yml
+# Build docker images
+username@hostname:~$ docker-compose build
+```
+
+### Start your instance
+``` bash
+# For background execution add the -d flag
+docker-compose up
+# To scale your app use the following command after starting it normally
+docker-compose \
+  -f docker-compose.yml \
+  -f docker-compose.override.yml \
+  -f docker-compose.scale.yml \
+  up \
+    -d \
+    --no-recreate \
+    --scale nopaque=<NUM_INSTANCES>
+```

app/SpaCyNLPPipelineModel.defaults.yml

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+- title: 'Catalan'
+  description: 'Catalan pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/ca_core_news_md-3.2.0/ca_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/ca_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'ca_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0' 
+- title: 'German'
+  description: 'German pipeline optimized for CPU. Components: tok2vec, tagger, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/de_core_news_md-3.2.0/de_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/de_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'de_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0' 
+- title: 'Greek'
+  description: 'Greek pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/el_core_news_md-3.2.0/el_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/el_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'el_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'English'
+  description: 'English pipeline optimized for CPU. Components: tok2vec, tagger, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/en_core_web_md-3.2.0/en_core_web_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/en_core_web_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'en_core_web_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'Spanish'
+  description: 'Spanish pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/es_core_news_md-3.2.0/es_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/es_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'es_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'French'
+  description: 'French pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/fr_core_news_md-3.2.0/fr_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/fr_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'fr_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'Italian'
+  description: 'Italian pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/it_core_news_md-3.2.0/it_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/it_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'it_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'Polish'
+  description: 'Polish pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/pl_core_news_md-3.2.0/pl_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/pl_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'pl_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'Russian'
+  description: 'Russian pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/ru_core_news_md-3.2.0/ru_core_news_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/ru_core_news_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'ru_core_news_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+- title: 'Chinese'
+  description: 'Chinese pipeline optimized for CPU. Components: tok2vec, tagger, parser, senter, ner, attribute_ruler.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/zh_core_web_md-3.2.0/zh_core_web_md-3.2.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/zh_core_web_md-3.2.0'
+  publishing_year: 2021
+  pipeline_name: 'zh_core_web_md'
+  version: '3.2.0'
+  compatible_service_versions:
+    - '0.1.0'
+
+- title: 'Catalan'
+  description: 'Catalan pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/ca_core_news_md-3.4.0/ca_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/ca_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'ca_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'German'
+  description: 'German pipeline optimized for CPU. Components: tok2vec, tagger, morphologizer, parser, lemmatizer (trainable_lemmatizer), senter, ner.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/de_core_news_md-3.4.0/de_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/de_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'de_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'Greek'
+  description: 'Greek pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, lemmatizer (trainable_lemmatizer), senter, ner, attribute_ruler.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/el_core_news_md-3.4.0/el_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/el_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'el_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'English'
+  description: 'English pipeline optimized for CPU. Components: tok2vec, tagger, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/en_core_web_md-3.4.1/en_core_web_md-3.4.1.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/en_core_web_md-3.4.1'
+  publishing_year: 2022
+  pipeline_name: 'en_core_web_md'
+  version: '3.4.1'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'Spanish'
+  description: 'Spanish pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/es_core_news_md-3.4.0/es_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/es_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'es_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'French'
+  description: 'French pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/fr_core_news_md-3.4.0/fr_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/fr_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'fr_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2' 
+- title: 'Italian'
+  description: 'Italian pipeline optimized for CPU. Components: tok2vec, morphologizer, tagger, parser, lemmatizer (trainable_lemmatizer), senter, ner'
+  url: 'https://github.com/explosion/spacy-models/releases/download/it_core_news_md-3.4.0/it_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/it_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'it_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'Polish'
+  description: 'Polish pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, lemmatizer (trainable_lemmatizer), tagger, senter, ner.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/pl_core_news_md-3.4.0/pl_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/pl_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'pl_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'Russian'
+  description: 'Russian pipeline optimized for CPU. Components: tok2vec, morphologizer, parser, senter, ner, attribute_ruler, lemmatizer.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/ru_core_news_md-3.4.0/ru_core_news_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/ru_core_news_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'ru_core_news_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'
+- title: 'Chinese'
+  description: 'Chinese pipeline optimized for CPU. Components: tok2vec, tagger, parser, senter, ner, attribute_ruler.'
+  url: 'https://github.com/explosion/spacy-models/releases/download/zh_core_web_md-3.4.0/zh_core_web_md-3.4.0.tar.gz'
+  publisher: 'Explosion'
+  publisher_url: 'https://github.com/explosion'
+  publishing_url: 'https://github.com/explosion/spacy-models/releases/tag/zh_core_web_md-3.4.0'
+  publishing_year: 2022
+  pipeline_name: 'zh_core_web_md'
+  version: '3.4.0'
+  compatible_service_versions:
+    - '0.1.1'
+    - '0.1.2'

app/__init__.py

@@ -0,0 +1,103 @@
+from apifairy import APIFairy
+from config import Config
+from docker import DockerClient
+from flask import Flask
+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
+from flask_migrate import Migrate
+from flask_paranoid import Paranoid
+from flask_socketio import SocketIO
+from flask_sqlalchemy import SQLAlchemy
+from flask_hashids import Hashids
+from werkzeug.exceptions import HTTPException
+
+
+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 (WSGI Application) object. '''
+    app = Flask(__name__)
+    app.config.from_object(config)
+    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']
+    )
+
+    apifairy.init_app(app)
+    assets.init_app(app)
+    breadcrumbs.init_app(app)
+    db.init_app(app)
+    hashids.init_app(app)
+    login.init_app(app)
+    ma.init_app(app)
+    mail.init_app(app)
+    migrate.init_app(app, db)
+    paranoid.init_app(app)
+    scheduler.init_app(app)
+    socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])  # noqa
+
+    from .admin import bp as admin_blueprint
+    default_breadcrumb_root(admin_blueprint, '.admin')
+    app.register_blueprint(admin_blueprint, url_prefix='/admin')
+
+    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
+    default_breadcrumb_root(corpora_blueprint, '.corpora')
+    app.register_blueprint(corpora_blueprint, cli_group='corpus', url_prefix='/corpora')
+
+    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, url_prefix='/users')
+
+    return app

app/admin/__init__.py

@@ -0,0 +1,20 @@
+from flask import Blueprint
+from flask_login import login_required
+from app.decorators import admin_required
+
+
+bp = Blueprint('admin', __name__)
+
+
+@bp.before_request
+@login_required
+@admin_required
+def before_request():
+    '''
+    Ensures that the routes in this package can be visited only by users with
+    administrator privileges (login_required and admin_required).
+    '''
+    pass
+
+
+from . import json_routes, routes

app/admin/forms.py

@@ -0,0 +1,16 @@
+from flask_wtf import FlaskForm
+from wtforms import SelectField, SubmitField
+from app.models import Role
+
+
+class UpdateUserForm(FlaskForm):
+    role = SelectField('Role')
+    submit = SubmitField()
+
+    def __init__(self, user, *args, **kwargs):
+        if 'data' not in kwargs:
+            kwargs['data'] = {'role': user.role.hashid}
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'update-user-form'
+        super().__init__(*args, **kwargs)
+        self.role.choices = [(x.hashid, x.name) for x in Role.query.all()]

app/admin/json_routes.py

@@ -0,0 +1,23 @@
+from flask import abort, request
+from app import db
+from app.decorators import content_negotiation
+from app.models import User
+from . import bp
+
+
+@bp.route('/users/<hashid:user_id>/confirmed', methods=['PUT'])
+@content_negotiation(consumes='application/json', produces='application/json')
+def update_user_role(user_id):
+    confirmed = request.json
+    if not isinstance(confirmed, bool):
+        abort(400)
+    user = User.query.get_or_404(user_id)
+    user.confirmed = confirmed
+    db.session.commit()
+    response_data = {
+        'message': (
+            f'User "{user.username}" is now '
+            f'{"confirmed" if confirmed else "unconfirmed"}'
+        )
+    }
+    return response_data, 200

app/admin/routes.py

@@ -0,0 +1,146 @@
+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.users.settings.forms import (
+    UpdateAvatarForm,
+    UpdatePasswordForm,
+    UpdateNotificationsForm,
+    UpdateAccountInformationForm,
+    UpdateProfileInformationForm
+)
+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',
+        title='Administration'
+    )
+
+
+@bp.route('/corpora')
+@register_breadcrumb(bp, '.corpora', 'Corpora')
+def corpora():
+    corpora = Corpus.query.all()
+    return render_template(
+        'admin/corpora.html.j2',
+        title='Corpora',
+        corpora=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(
+        'admin/users.html.j2',
+        title='Users',
+        users=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()
+    return render_template(
+        'admin/user.html.j2',
+        title=user.username,
+        user=user,
+        corpora=corpora
+    )
+
+
+@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)
+    update_profile_information_form = UpdateProfileInformationForm(user)
+    update_avatar_form = UpdateAvatarForm()
+    update_password_form = UpdatePasswordForm(user)
+    update_notifications_form = UpdateNotificationsForm(user)
+    update_user_form = UpdateUserForm(user)
+
+    # region handle update profile information form
+    if update_profile_information_form.submit.data and update_profile_information_form.validate():
+        user.about_me = update_profile_information_form.about_me.data
+        user.location = update_profile_information_form.location.data
+        user.organization = update_profile_information_form.organization.data
+        user.website = update_profile_information_form.website.data
+        user.full_name = update_profile_information_form.full_name.data
+        db.session.commit()
+        flash('Your changes have been saved')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update profile information form
+
+    # region handle update avatar form
+    if update_avatar_form.submit.data and update_avatar_form.validate():
+        try:
+            Avatar.create(
+                update_avatar_form.avatar.data,
+                user=user
+            )
+        except (AttributeError, OSError):
+            abort(500)
+        db.session.commit()
+        flash('Your changes have been saved')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update avatar form
+
+    # region handle update account information form
+    if update_account_information_form.submit.data and update_account_information_form.validate():
+        user.email = update_account_information_form.email.data
+        user.username = update_account_information_form.username.data
+        db.session.commit()
+        flash('Profile settings updated')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update account information form
+
+    # region handle update password form
+    if update_password_form.submit.data and update_password_form.validate():
+        user.password = update_password_form.new_password.data
+        db.session.commit()
+        flash('Your changes have been saved')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update password form
+
+    # region handle update notifications form
+    if update_notifications_form.submit.data and update_notifications_form.validate():
+        user.setting_job_status_mail_notification_level = \
+            update_notifications_form.job_status_mail_notification_level.data
+        db.session.commit()
+        flash('Your changes have been saved')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update notifications form
+
+    # region handle update user form
+    if update_user_form.submit.data and update_user_form.validate():
+        role_id = hashids.decode(update_user_form.role.data)
+        user.role = Role.query.get(role_id)
+        db.session.commit()
+        flash('Your changes have been saved')
+        return redirect(url_for('.user_settings', user_id=user.id))
+    # endregion handle update user form
+
+    return render_template(
+        'admin/user_settings.html.j2',
+        title='Settings',
+        update_account_information_form=update_account_information_form,
+        update_avatar_form=update_avatar_form,
+        update_notifications_form=update_notifications_form,
+        update_password_form=update_password_form,
+        update_profile_information_form=update_profile_information_form,
+        update_user_form=update_user_form,
+        user=user
+    )

app/api/__init__.py

@@ -0,0 +1,14 @@
+from flask import Blueprint
+
+
+bp = Blueprint('api', __name__)
+
+
+from .tokens import bp as tokens_blueprint
+bp.register_blueprint(tokens_blueprint, url_prefix='/tokens')
+
+from .users import bp as users_blueprint
+bp.register_blueprint(users_blueprint, url_prefix='/users')
+
+from .jobs import bp as jobs_blueprint
+bp.register_blueprint(jobs_blueprint, url_prefix='/jobs')

app/api/auth.py

@@ -0,0 +1,48 @@
+from flask_httpauth import HTTPBasicAuth, HTTPTokenAuth
+from werkzeug.exceptions import Forbidden, Unauthorized
+from app.models import User
+
+
+basic_auth = HTTPBasicAuth()
+token_auth = HTTPTokenAuth()
+auth_error_responses = {
+    Unauthorized.code: Unauthorized.description,
+    Forbidden.code: Forbidden.description
+}
+
+@basic_auth.verify_password
+def verify_password(email_or_username, password):
+    user = User.query.filter((User.email == email_or_username.lower()) | (User.username == email_or_username)).first()
+    if user is not None and user.verify_password(password):
+        return user
+
+
+@basic_auth.error_handler
+def basic_auth_error(status):
+    error = (Forbidden if status == 403 else Unauthorized)()
+    return {
+        'code': error.code,
+        'message': error.name,
+        'description': error.description,
+    }, error.code, {'WWW-Authenticate': 'Form'}
+
+
+@token_auth.verify_token
+def verify_token(token):
+    return User.verify_access_token(token) if token else None
+
+
+@token_auth.error_handler
+def token_auth_error(status):
+    error = (Forbidden if status == 403 else Unauthorized)()
+    return {
+        'code': error.code,
+        'message': error.name,
+        'description': error.description,
+    }, error.code
+
+
+@basic_auth.get_user_roles
+@token_auth.get_user_roles
+def get_user_roles(user):
+    return [user.role.name]

app/api/jobs.py

@@ -0,0 +1,102 @@
+
+from apifairy import authenticate, response
+from apifairy.decorators import body, other_responses
+from flask import abort, Blueprint
+from werkzeug.exceptions import InternalServerError
+from app import db, hashids
+from app.models import Job, JobInput, JobStatus, TesseractOCRPipelineModel
+from .schemas import EmptySchema, JobSchema, SpaCyNLPPipelineJobSchema, TesseractOCRPipelineJobSchema, TesseractOCRPipelineModelSchema
+from .auth import auth_error_responses, token_auth
+
+
+bp = Blueprint('jobs', __name__)
+job_schema = JobSchema()
+jobs_schema = JobSchema(many=True)
+spacy_nlp_pipeline_job_schema = SpaCyNLPPipelineJobSchema()
+tesseract_ocr_pipeline_job_schema = TesseractOCRPipelineJobSchema()
+tesseract_ocr_pipeline_model_schema = TesseractOCRPipelineModelSchema()
+tesseract_ocr_pipeline_models_schema = TesseractOCRPipelineModelSchema(many=True)
+
+
+@bp.route('', methods=['GET'])
+@authenticate(token_auth, role='Administrator')
+@response(jobs_schema)
+@other_responses(auth_error_responses)
+def get_jobs():
+    """Get all jobs"""
+    return Job.query.all()
+
+
+@bp.route('/tesseract-ocr-pipeline', methods=['POST'])
+@authenticate(token_auth)
+@body(tesseract_ocr_pipeline_job_schema, location='form')
+@response(job_schema)
+@other_responses({**auth_error_responses, InternalServerError.code: InternalServerError.description})
+def create_tesseract_ocr_pipeline_job(args):
+    """Create a new Tesseract OCR Pipeline job"""
+    current_user = token_auth.current_user()
+    try:
+        job = Job.create(
+            title=args['title'],
+            description=args['description'],
+            service='tesseract-ocr-pipeline',
+            service_args={
+                'model': hashids.decode(args['model_id']),
+                'binarization': args['binarization']
+            },
+            service_version=args['service_version'],
+            user=current_user
+        )
+    except OSError:
+        abort(500)
+    try:
+        JobInput.create(args['pdf'], job=job)
+    except OSError:
+        abort(500)
+    job.status = JobStatus.SUBMITTED
+    db.session.commit()
+    return job, 201
+
+
+@bp.route('/tesseract-ocr-pipeline/models', methods=['GET'])
+@authenticate(token_auth)
+@response(tesseract_ocr_pipeline_models_schema)
+@other_responses(auth_error_responses)
+def get_tesseract_ocr_models():
+    """Get all Tesseract OCR Models"""
+    return TesseractOCRPipelineModel.query.all()
+
+
+@bp.route('/<hashid:job_id>', methods=['DELETE'])
+@authenticate(token_auth)
+@response(EmptySchema, status_code=204)
+@other_responses(auth_error_responses)
+def delete_job(job_id):
+    """Delete a job by id"""
+    current_user = token_auth.current_user()
+    job = Job.query.get(job_id)
+    if job is None:
+        abort(404)
+    if not (job.user == current_user or current_user.is_administrator()):
+        abort(403)
+    try:
+        job.delete()
+    except OSError as e:
+        abort(500)
+    db.session.commit()
+    return {}, 204
+
+
+@bp.route('/<hashid:job_id>', methods=['GET'])
+@authenticate(token_auth)
+@response(job_schema)
+@other_responses(auth_error_responses)
+def get_job(job_id):
+    """Get a job by id"""
+    current_user = token_auth.current_user()
+    job = Job.query.get(job_id)
+    if job is None:
+        abort(404)
+    if not (job.user == current_user or current_user.is_administrator()):
+        abort(403)
+    return job

app/api/schemas.py

@@ -0,0 +1,173 @@
+from apifairy.fields import FileField
+from marshmallow import validate, validates, ValidationError
+from marshmallow.decorators import post_dump
+from app import ma
+from app.models import (
+    Job,
+    JobStatus,
+    TesseractOCRPipelineModel,
+    Token,
+    User,
+    UserSettingJobStatusMailNotificationLevel
+)
+from app.services import SERVICES
+
+
+
+class EmptySchema(ma.Schema):
+    pass
+
+
+class TokenSchema(ma.SQLAlchemySchema):
+    class Meta:
+        model = Token
+        ordered = True
+
+    access_token = ma.String(required=True)
+    refresh_token = ma.String()
+
+
+class TesseractOCRPipelineModelSchema(ma.SQLAlchemySchema):
+    class Meta:
+        model = TesseractOCRPipelineModel
+        ordered = True
+
+    hashid = ma.String(data_key='id', dump_only=True)
+    user_hashid = ma.String(data_key='user_id', dump_only=True)
+    title = ma.auto_field(
+        required=True,
+        validate=validate.Length(min=1, max=64)
+    )
+    description = ma.auto_field(
+        required=True,
+        validate=validate.Length(min=1, max=255)
+    )
+    version = ma.String(
+        required=True,
+        validate=validate.Length(min=1, max=16)
+    )
+    compatible_service_versions = ma.List(
+        ma.String(required=True, validate=validate.Length(min=1, max=16)),
+        required=True,
+        validate=validate.Length(min=1, max=255)
+    )
+    publisher = ma.String(
+        required=True,
+        validate=validate.Length(min=1, max=128)
+    )
+    publisher_url = ma.String(
+        validate=[validate.URL(), validate.Length(min=1, max=512)]
+    )
+    publishing_url = ma.String(
+        required=True,
+        validate=[validate.URL(), validate.Length(min=1, max=512)]
+    )
+    publishing_year = ma.Int(
+        required=True
+    )
+    is_public = ma.Boolean(required=True)
+
+
+class JobSchema(ma.SQLAlchemySchema):
+    class Meta:
+        model = Job
+        ordered = True
+
+    hashid = ma.String(data_key='id', dump_only=True)
+    user_hashid = ma.String(data_key='user_id', dump_only=True)
+    title = ma.auto_field(
+        required=True,
+        validate=validate.Length(min=1, max=32)
+    )
+    description = ma.auto_field(
+        required=True,
+        validate=validate.Length(min=1, max=255)
+    )
+    creation_date = ma.auto_field(dump_only=True)
+    end_date = ma.auto_field(dump_only=True)
+    service = ma.String(
+        dump_only=True,
+        validate=validate.OneOf(SERVICES.keys())
+    )
+    service_args = ma.Dict(dump_only=True)
+    service_version = ma.String(dump_only=True)
+    status = ma.String(
+        dump_only=True,
+        validate=validate.OneOf(list(JobStatus.__members__.keys()))
+    )
+
+    @post_dump(pass_original=True)
+    def post_dump(self, serialized_job, job, **kwargs):
+        serialized_job['status'] = job.status.name
+        return serialized_job
+
+
+class TesseractOCRPipelineJobSchema(JobSchema):
+    binarization = ma.Boolean(load_only=True, missing=False)
+    model_id = ma.String(required=True, load_only=True)
+    service_version = ma.auto_field(
+        required=True,
+        validate=[validate.Length(min=1, max=16), validate.OneOf(list(SERVICES['tesseract-ocr-pipeline']['versions'].keys()))]
+    )
+    pdf = FileField()
+
+    @validates('pdf')
+    def validate_pdf(self, value):
+        if value.mimetype != 'application/pdf':
+            raise ValidationError('PDF files only!')
+
+
+class SpaCyNLPPipelineJobSchema(JobSchema):
+    binarization = ma.Boolean(load_only=True, missing=False)
+    model_id = ma.String(required=True, load_only=True)
+    service_version = ma.auto_field(
+        required=True,
+        validate=[validate.Length(min=1, max=16), validate.OneOf(list(SERVICES['tesseract-ocr-pipeline']['versions'].keys()))]
+    )
+    txt = FileField(required=True)
+
+    @validates('txt')
+    def validate_txt(self, value):
+        if value.mimetype != 'text/plain':
+            raise ValidationError('Plain text files only!')
+
+
+class UserSchema(ma.SQLAlchemySchema):
+    class Meta:
+        model = User
+        ordered = True
+
+    hashid = ma.String(data_key='id', dump_only=True)
+    username = ma.auto_field(
+        validate=[
+            validate.Length(min=1, max=64),
+            validate.Regexp(
+                User.username_pattern,
+                error='Usernames must have only letters, numbers, dots or underscores'
+            )
+        ]
+    )
+    email = ma.auto_field(validate=validate.Email())
+    member_since = ma.auto_field(dump_only=True)
+    last_seen = ma.auto_field(dump_only=True)
+    password = ma.String(load_only=True)
+    last_seen = ma.auto_field(dump_only=True)
+    setting_job_status_mail_notification_level = ma.String(
+        validate=validate.OneOf(list(UserSettingJobStatusMailNotificationLevel.__members__.keys()))
+    )
+
+    @validates('email')
+    def validate_email(self, email):
+        if User.query.filter(User.email == email).first():
+            raise ValidationError('Email already registered')
+
+    @validates('username')
+    def validate_username(self, username):
+        if User.query.filter(User.username == username).first():
+            raise ValidationError('Username already in use')
+
+    @post_dump(pass_original=True)
+    def post_dump(self, serialized_user, user, **kwargs):
+        serialized_user['setting_job_status_mail_notification_level'] = \
+            user.setting_job_status_mail_notification_level.name
+        return serialized_user

app/api/tokens.py

@@ -0,0 +1,58 @@
+from apifairy import authenticate, body, response, other_responses
+from flask import Blueprint, request, abort
+from app import db
+from app.models import Token, User
+from .auth import basic_auth
+from .schemas import EmptySchema, TokenSchema
+
+
+bp = Blueprint('tokens', __name__)
+token_schema = TokenSchema()
+
+
+@bp.route('', methods=['DELETE'])
+@response(EmptySchema, status_code=204, description='Token revoked')
+@other_responses({401: 'Invalid access token'})
+def delete_token():
+    """Revoke an access token"""
+    access_token = request.headers['Authorization'].split()[1]
+    token = Token.query.filter(Token.access_token == access_token).first()
+    if token is None:  # pragma: no cover
+        abort(401)
+    token.expire()
+    db.session.commit()
+    return {}
+
+
+@bp.route('', methods=['POST'])
+@authenticate(basic_auth)
+@response(token_schema)
+@other_responses({401: 'Invalid username or password'})
+def create_token():
+    """Create new access and refresh tokens"""
+    user = basic_auth.current_user()
+    token = user.generate_auth_token()
+    db.session.add(token)
+    Token.clean()  # keep token table clean of old tokens
+    db.session.commit()
+    return token, 200
+
+
+@bp.route('', methods=['PUT'])
+@body(token_schema)
+@response(token_schema, description='Newly issued access and refresh tokens')
+@other_responses({401: 'Invalid access or refresh token'})
+def refresh_token(args):
+    """Refresh an access token"""
+    access_token = args.get('access_token')
+    refresh_token = args.get('refresh_token')
+    if access_token is None or refresh_token is None:
+        abort(401)
+    token = User.verify_refresh_token(refresh_token, access_token)
+    if token is None:
+        abort(401)
+    token.expire()
+    new_token = token.user.generate_auth_token()
+    db.session.add_all([token, new_token])
+    db.session.commit()
+    return new_token, 200

app/api/users.py

@@ -0,0 +1,99 @@
+
+from apifairy import authenticate, body, response
+from apifairy.decorators import other_responses
+from flask import abort, Blueprint
+from werkzeug.exceptions import InternalServerError
+from app import db
+from app.email import create_message, send
+from app.models import User
+from .schemas import EmptySchema, UserSchema
+from .auth import auth_error_responses, token_auth
+
+
+bp = Blueprint('users', __name__)
+user_schema = UserSchema()
+users_schema = UserSchema(many=True)
+
+
+@bp.route('', methods=['GET'])
+@authenticate(token_auth, role='Administrator')
+@response(users_schema)
+@other_responses(auth_error_responses)
+def get_users():
+    """Get all users"""
+    return User.query.all()
+
+
+@bp.route('', methods=['POST'])
+@body(user_schema)
+@response(user_schema, 201)
+@other_responses({InternalServerError.code: InternalServerError.description})
+def create_user(args):
+    """Create a new user"""
+    try:
+        user = User.create(
+            email=args['email'].lower(),
+            password=args['password'],
+            username=args['username']
+        )
+    except OSError:
+        abort(500)
+    msg = create_message(
+        user.email,
+        'Confirm Your Account',
+        'auth/email/confirm',
+        token=user.generate_confirm_token(),
+        user=user
+    )
+    send(msg)
+    db.session.commit()
+    return user, 201
+
+
+@bp.route('/<hashid:user_id>', methods=['DELETE'])
+@authenticate(token_auth)
+@response(EmptySchema, status_code=204)
+@other_responses(auth_error_responses)
+def delete_user(user_id):
+    """Delete a user by id"""
+    current_user = token_auth.current_user()
+    user = User.query.get(user_id)
+    if user is None:
+        abort(404)
+    if not (user == current_user or current_user.is_administrator()):
+        abort(403)
+    user.delete()
+    db.session.commit()
+    return {}, 204
+
+
+@bp.route('/<hashid:user_id>', methods=['GET'])
+@authenticate(token_auth)
+@response(user_schema)
+@other_responses(auth_error_responses)
+@other_responses({404: 'User not found'})
+def get_user(user_id):
+    """Retrieve a user by id"""
+    current_user = token_auth.current_user()
+    user = User.query.get(user_id)
+    if user is None:
+        abort(404)
+    if not (user == current_user or current_user.is_administrator()):
+        abort(403)
+    return user
+
+
+@bp.route('/<username>', methods=['GET'])
+@authenticate(token_auth)
+@response(user_schema)
+@other_responses(auth_error_responses)
+@other_responses({404: 'User not found'})
+def get_user_by_username(username):
+    """Retrieve a user by username"""
+    current_user = token_auth.current_user()
+    user = User.query.filter(User.username == username).first()
+    if user is None:
+        abort(404)
+    if not (user == current_user or current_user.is_administrator()):
+        abort(403)
+    return user

app/auth/__init__.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+
+
+bp = Blueprint('auth', __name__)
+from . import routes

app/auth/forms.py

@@ -0,0 +1,108 @@
+from flask_wtf import FlaskForm
+from wtforms import (
+    BooleanField,
+    PasswordField,
+    StringField,
+    SubmitField,
+    ValidationError
+)
+from wtforms.validators import InputRequired, Email, EqualTo, Length, Regexp
+from app.models import User
+
+
+class RegistrationForm(FlaskForm):
+    email = StringField(
+        'Email',
+        validators=[InputRequired(), Email(), Length(max=254)]
+    )
+    username = StringField(
+        'Username',
+        validators=[
+            InputRequired(),
+            Length(max=64),
+            Regexp(
+                User.username_pattern,
+                message=(
+                    'Usernames must have only letters, numbers, dots or '
+                    'underscores'
+                )
+            )
+       ]
+    )
+    password = PasswordField(
+        'Password',
+        validators=[
+            InputRequired(),
+            EqualTo('password_2', message='Passwords must match')
+        ]
+    )
+    password_2 = PasswordField(
+        'Password confirmation',
+        validators=[
+            InputRequired(),
+            EqualTo('password', message='Passwords must match')
+        ]
+    )
+    terms_of_use_accepted = BooleanField(
+        'I have read and accept the terms of use',
+        validators=[InputRequired()]
+    )
+    submit = SubmitField()
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'registration-form'
+        super().__init__(*args, **kwargs)
+
+    def validate_email(self, field):
+        if User.query.filter_by(email=field.data.lower()).first():
+            raise ValidationError('Email already registered')
+
+    def validate_username(self, field):
+        if User.query.filter_by(username=field.data).first():
+            raise ValidationError('Username already in use')
+
+
+class LoginForm(FlaskForm):
+    user = StringField('Email or username', validators=[InputRequired()])
+    password = PasswordField('Password', validators=[InputRequired()])
+    remember_me = BooleanField('Keep me logged in')
+    submit = SubmitField()
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'login-form'
+        super().__init__(*args, **kwargs)
+
+
+class ResetPasswordRequestForm(FlaskForm):
+    email = StringField('Email', validators=[InputRequired(), Email()])
+    submit = SubmitField()
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'reset-password-request-form'
+        super().__init__(*args, **kwargs)
+
+
+class ResetPasswordForm(FlaskForm):
+    password = PasswordField(
+        'New password',
+        validators=[
+            InputRequired(),
+            EqualTo('password_2', message='Passwords must match')
+        ]
+    )
+    password_2 = PasswordField(
+        'New password confirmation',
+        validators=[
+            InputRequired(),
+            EqualTo('password', message='Passwords must match')
+        ]
+    )
+    submit = SubmitField()
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'reset-password-form'
+        super().__init__(*args, **kwargs)

app/auth/routes.py

@@ -0,0 +1,190 @@
+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
+from app.models import User
+from . import bp
+from .forms import (
+    LoginForm,
+    ResetPasswordForm,
+    ResetPasswordRequestForm,
+    RegistrationForm
+)
+
+
+@bp.before_app_request
+def before_request():
+    """
+    Checks if a user is unconfirmed when visiting specific sites. Redirects to
+    unconfirmed view if user is unconfirmed.
+    """
+    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'))
+    form = RegistrationForm()
+    if form.validate_on_submit():
+        try:
+            user = User.create(
+                email=form.email.data.lower(),
+                password=form.password.data,
+                username=form.username.data,
+                terms_of_use_accepted=form.terms_of_use_accepted.data
+            )
+        except OSError:
+            flash('Internal Server Error', category='error')
+            abort(500)
+        flash(f'User "{user.username}" created')
+        token = user.generate_confirm_token()
+        msg = create_message(
+            user.email,
+            'Confirm Your Account',
+            'auth/email/confirm',
+            token=token,
+            user=user
+        )
+        send(msg)
+        flash('A confirmation email has been sent to you by email')
+        db.session.commit()
+        return redirect(url_for('.login'))
+    return render_template(
+        'auth/register.html.j2',
+        title='Register',
+        form=form
+    )
+
+
+@bp.route('/login', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.login', 'Login')
+def login():
+    if current_user.is_authenticated:
+        return redirect(url_for('main.dashboard'))
+    form = LoginForm()
+    if form.validate_on_submit():
+        user = User.query.filter((User.email == form.user.data.lower()) | (User.username == form.user.data)).first()
+        if user and user.verify_password(form.password.data):
+            login_user(user, form.remember_me.data)
+            next = request.args.get('next')
+            if next is None or not next.startswith('/'):
+                next = url_for('main.dashboard')
+            flash('You have been logged in')
+            return redirect(next)
+        flash('Invalid email/username or password', category='error')
+    return render_template(
+        'auth/login.html.j2',
+        title='Log in',
+        form=form
+    )
+
+
+@bp.route('/logout')
+@login_required
+def logout():
+    logout_user()
+    flash('You have been logged out')
+    return redirect(url_for('main.index'))
+
+
+@bp.route('/unconfirmed')
+@register_breadcrumb(bp, '.unconfirmed', 'Unconfirmed')
+@login_required
+def unconfirmed():
+    if current_user.confirmed:
+        return redirect(url_for('main.dashboard'))
+    return render_template(
+        'auth/unconfirmed.html.j2',
+        title='Unconfirmed'
+    )
+
+
+@bp.route('/confirm-request')
+@login_required
+def confirm_request():
+    if current_user.confirmed:
+        return redirect(url_for('main.dashboard'))
+    token = current_user.generate_confirm_token()
+    msg = create_message(
+        current_user.email,
+        'Confirm Your Account',
+        'auth/email/confirm',
+        token=token,
+        user=current_user
+    )
+    send(msg)
+    flash('A new confirmation email has been sent to you by email')
+    return redirect(url_for('.unconfirmed'))
+
+
+@bp.route('/confirm/<token>')
+@login_required
+def confirm(token):
+    if current_user.confirmed:
+        return redirect(url_for('main.dashboard'))
+    if current_user.confirm(token):
+        db.session.commit()
+        flash('You have confirmed your account')
+        return redirect(url_for('main.dashboard'))
+    flash('The confirmation link is invalid or has expired', category='error')
+    return redirect(url_for('.unconfirmed'))
+
+
+@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'))
+    form = ResetPasswordRequestForm()
+    if form.validate_on_submit():
+        user = User.query.filter_by(email=form.email.data.lower()).first()
+        if user is not None:
+            token = user.generate_reset_password_token()
+            msg = create_message(
+                user.email,
+                'Reset Your Password',
+                'auth/email/reset_password',
+                token=token,
+                user=user
+            )
+            send(msg)
+        flash(
+            'An email with instructions to reset your password has been sent '
+            'to you'
+        )
+        return redirect(url_for('.login'))
+    return render_template(
+        'auth/reset_password_request.html.j2',
+        title='Password Reset',
+        form=form
+    )
+
+
+@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'))
+    form = ResetPasswordForm()
+    if form.validate_on_submit():
+        if User.reset_password(token, form.password.data):
+            db.session.commit()
+            flash('Your password has been updated')
+            return redirect(url_for('.login'))
+        return redirect(url_for('main.index'))
+    return render_template(
+        'auth/reset_password.html.j2',
+        title='Password Reset',
+        form=form,
+        token=token
+    )

app/contributions/__init__.py

@@ -0,0 +1,23 @@
+from flask import Blueprint
+from flask_login import login_required
+
+
+bp = Blueprint('contributions', __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,
+    spacy_nlp_pipeline_models,
+    tesseract_ocr_pipeline_models,
+    transkribus_htr_pipeline_models
+)

app/contributions/forms.py

@@ -0,0 +1,47 @@
+from flask_wtf import FlaskForm
+from wtforms import (
+    StringField,
+    SubmitField,
+    SelectMultipleField,
+    IntegerField
+)
+from wtforms.validators import InputRequired, Length
+
+
+class ContributionBaseForm(FlaskForm):
+    title = StringField(
+        'Title',
+        validators=[InputRequired(), Length(max=64)]
+    )
+    description = StringField(
+        'Description',
+        validators=[InputRequired(), Length(max=255)]
+    )
+    version = StringField(
+        'Version',
+        validators=[InputRequired(), Length(max=16)]
+    )
+    publisher = StringField(
+        'Publisher',
+        validators=[InputRequired(), Length(max=128)]
+    )
+    publisher_url = StringField(
+        'Publisher URL',
+        validators=[InputRequired(), Length(max=512)]
+    )
+    publishing_url = StringField(
+        'Publishing URL',
+        validators=[InputRequired(), Length(max=512)]
+    )
+    publishing_year = IntegerField(
+        'Publishing year',
+        validators=[InputRequired()]
+    )
+    compatible_service_versions = SelectMultipleField(
+        'Compatible service versions'
+    )
+    submit = SubmitField()
+
+
+class UpdateContributionBaseForm(ContributionBaseForm):
+    pass

app/contributions/routes.py

@@ -0,0 +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/__init__.py

@@ -0,0 +1,2 @@
+from .. import bp
+from . import json_routes, routes

app/contributions/spacy_nlp_pipeline_models/forms.py

@@ -0,0 +1,48 @@
+from flask_wtf.file import FileField, FileRequired
+from wtforms import StringField, ValidationError
+from wtforms.validators import InputRequired, Length
+from app.services import SERVICES
+from ..forms import ContributionBaseForm, UpdateContributionBaseForm
+
+
+class CreateSpaCyNLPPipelineModelForm(ContributionBaseForm):
+    spacy_model_file = FileField(
+        'File',
+        validators=[FileRequired()]
+    )
+    pipeline_name = StringField(
+        'Pipeline name',
+        validators=[InputRequired(), Length(max=64)]
+    )
+
+    def validate_spacy_model_file(self, field):
+        if not field.data.filename.lower().endswith('.tar.gz'):
+            raise ValidationError('.tar.gz files only!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-spacy-nlp-pipeline-model-form'
+        super().__init__(*args, **kwargs)
+        service_manifest = SERVICES['spacy-nlp-pipeline']
+        self.compatible_service_versions.choices = [('', 'Choose your option')]
+        self.compatible_service_versions.choices += [
+            (x, x) for x in service_manifest['versions'].keys()
+        ]
+        self.compatible_service_versions.default = ''
+
+
+class UpdateSpaCyNLPPipelineModelForm(UpdateContributionBaseForm):
+    pipeline_name = StringField(
+        'Pipeline name',
+        validators=[InputRequired(), Length(max=64)]
+    )
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'edit-spacy-nlp-pipeline-model-form'
+        super().__init__(*args, **kwargs)
+        service_manifest = SERVICES['spacy-nlp-pipeline']
+        self.compatible_service_versions.choices = [('', 'Choose your option')]
+        self.compatible_service_versions.choices += [
+            (x, x) for x in service_manifest['versions'].keys()
+        ]
+        self.compatible_service_versions.default = ''

app/contributions/spacy_nlp_pipeline_models/json_routes.py

@@ -0,0 +1,52 @@
+from flask import abort, current_app, request
+from flask_login import current_user
+from threading import Thread
+from app import db
+from app.decorators import content_negotiation, permission_required
+from app.models import SpaCyNLPPipelineModel
+from .. import bp
+
+
+@bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['DELETE'])
+@content_negotiation(produces='application/json')
+def delete_spacy_model(spacy_nlp_pipeline_model_id):
+    def _delete_spacy_model(app, spacy_nlp_pipeline_model_id):
+        with app.app_context():
+            snpm = SpaCyNLPPipelineModel.query.get(spacy_nlp_pipeline_model_id)
+            snpm.delete()
+            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()):
+        abort(403)
+    thread = Thread(
+        target=_delete_spacy_model,
+        args=(current_app._get_current_object(), snpm.id)
+    )
+    thread.start()
+    response_data = {
+        'message': \
+            f'SpaCy NLP Pipeline Model "{snpm.title}" marked for deletion'
+    }
+    return response_data, 202
+
+
+@bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>/is_public', methods=['PUT'])
+@permission_required('CONTRIBUTE')
+@content_negotiation(consumes='application/json', produces='application/json')
+def update_spacy_nlp_pipeline_model_is_public(spacy_nlp_pipeline_model_id):
+    is_public = request.json
+    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()):
+        abort(403)
+    snpm.is_public = is_public
+    db.session.commit()
+    response_data = {
+        'message': (
+            f'SpaCy NLP Pipeline Model "{snpm.title}"'
+            f' is now {"public" if is_public else "private"}'
+        )
+    }
+    return response_data, 200

app/contributions/spacy_nlp_pipeline_models/routes.py

@@ -0,0 +1,77 @@
+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
+from . import bp
+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',
+        title='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():
+        if not form.validate():
+            return {'errors': form.errors}, 400
+        try:
+            snpm = SpaCyNLPPipelineModel.create(
+                form.spacy_model_file.data,
+                compatible_service_versions=form.compatible_service_versions.data,
+                description=form.description.data,
+                pipeline_name=form.pipeline_name.data,
+                publisher=form.publisher.data,
+                publisher_url=form.publisher_url.data,
+                publishing_url=form.publishing_url.data,
+                publishing_year=form.publishing_year.data,
+                is_public=False,
+                title=form.title.data,
+                version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        db.session.commit()
+        flash(f'SpaCy NLP Pipeline model "{snpm.title}" created')
+        return {}, 201, {'Location': url_for('.spacy_nlp_pipeline_models')}
+    return render_template(
+        'contributions/spacy_nlp_pipeline_models/create.html.j2',
+        title='Create SpaCy NLP Pipeline Model',
+        form=form
+    )
+
+
+@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()):
+        abort(403)
+    form = UpdateSpaCyNLPPipelineModelForm(data=snpm.to_json_serializeable())
+    if form.validate_on_submit():
+        form.populate_obj(snpm)
+        if db.session.is_modified(snpm):
+            flash(f'SpaCy NLP Pipeline model "{snpm.title}" updated')
+            db.session.commit()
+        return redirect(url_for('.spacy_nlp_pipeline_models'))
+    return render_template(
+        'contributions/spacy_nlp_pipeline_models/spacy_nlp_pipeline_model.html.j2',
+        title=f'{snpm.title} {snpm.version}',
+        form=form,
+        spacy_nlp_pipeline_model=snpm
+    )

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/__init__.py

@@ -0,0 +1,2 @@
+from .. import bp
+from . import json_routes, routes

app/contributions/tesseract_ocr_pipeline_models/forms.py

@@ -0,0 +1,39 @@
+from flask_wtf.file import FileField, FileRequired
+from wtforms import ValidationError
+from app.services import SERVICES
+from ..forms import ContributionBaseForm, UpdateContributionBaseForm
+
+
+class CreateTesseractOCRPipelineModelForm(ContributionBaseForm):
+    tesseract_model_file = FileField(
+        'File',
+        validators=[FileRequired()]
+    )
+    
+    def validate_tesseract_model_file(self, field):
+        if not field.data.filename.lower().endswith('.traineddata'):
+            raise ValidationError('traineddata files only!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-tesseract-ocr-pipeline-model-form'
+        service_manifest = SERVICES['tesseract-ocr-pipeline']
+        super().__init__(*args, **kwargs)
+        self.compatible_service_versions.choices = [('', 'Choose your option')]
+        self.compatible_service_versions.choices += [
+            (x, x) for x in service_manifest['versions'].keys()
+        ]
+        self.compatible_service_versions.default = ''
+
+
+class UpdateTesseractOCRPipelineModelForm(UpdateContributionBaseForm):
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'edit-tesseract-ocr-pipeline-model-form'
+        service_manifest = SERVICES['tesseract-ocr-pipeline']
+        super().__init__(*args, **kwargs)
+        self.compatible_service_versions.choices = [('', 'Choose your option')]
+        self.compatible_service_versions.choices += [
+            (x, x) for x in service_manifest['versions'].keys()
+        ]
+        self.compatible_service_versions.default = ''

app/contributions/tesseract_ocr_pipeline_models/json_routes.py

@@ -0,0 +1,52 @@
+from flask import abort, current_app, request
+from flask_login import current_user
+from threading import Thread
+from app import db
+from app.decorators import content_negotiation, permission_required
+from app.models import TesseractOCRPipelineModel
+from . import bp
+
+
+@bp.route('/tesseract-ocr-pipeline-models/<hashid:tesseract_ocr_pipeline_model_id>', methods=['DELETE'])
+@content_negotiation(produces='application/json')
+def delete_tesseract_model(tesseract_ocr_pipeline_model_id):
+    def _delete_tesseract_ocr_pipeline_model(app, tesseract_ocr_pipeline_model_id):
+        with app.app_context():
+            topm = TesseractOCRPipelineModel.query.get(tesseract_ocr_pipeline_model_id)
+            topm.delete()
+            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()):
+        abort(403)
+    thread = Thread(
+        target=_delete_tesseract_ocr_pipeline_model,
+        args=(current_app._get_current_object(), topm.id)
+    )
+    thread.start()
+    response_data = {
+        'message': \
+            f'Tesseract OCR Pipeline Model "{topm.title}" marked for deletion'
+    }
+    return response_data, 202
+
+
+@bp.route('/tesseract-ocr-pipeline-models/<hashid:tesseract_ocr_pipeline_model_id>/is_public', methods=['PUT'])
+@permission_required('CONTRIBUTE')
+@content_negotiation(consumes='application/json', produces='application/json')
+def update_tesseract_ocr_pipeline_model_is_public(tesseract_ocr_pipeline_model_id):
+    is_public = request.json
+    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()):
+        abort(403)
+    topm.is_public = is_public
+    db.session.commit()
+    response_data = {
+        'message': (
+            f'Tesseract OCR Pipeline Model "{topm.title}"'
+            f' is now {"public" if is_public else "private"}'
+        )
+    }
+    return response_data, 200

app/contributions/tesseract_ocr_pipeline_models/routes.py

@@ -0,0 +1,76 @@
+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
+from . import bp
+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',
+        title='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():
+        if not form.validate():
+            return {'errors': form.errors}, 400
+        try:
+            topm = TesseractOCRPipelineModel.create(
+                form.tesseract_model_file.data,
+                compatible_service_versions=form.compatible_service_versions.data,
+                description=form.description.data,
+                publisher=form.publisher.data,
+                publisher_url=form.publisher_url.data,
+                publishing_url=form.publishing_url.data,
+                publishing_year=form.publishing_year.data,
+                is_public=False,
+                title=form.title.data,
+                version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        db.session.commit()
+        flash(f'Tesseract OCR Pipeline model "{topm.title}" created')
+        return {}, 201, {'Location': url_for('.tesseract_ocr_pipeline_models')}
+    return render_template(
+        'contributions/tesseract_ocr_pipeline_models/create.html.j2',
+        title='Create Tesseract OCR Pipeline Model',
+        form=form
+    )
+
+
+@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()):
+        abort(403)
+    form = UpdateTesseractOCRPipelineModelForm(data=topm.to_json_serializeable())
+    if form.validate_on_submit():
+        form.populate_obj(topm)
+        if db.session.is_modified(topm):
+            flash(f'Tesseract OCR Pipeline model "{topm.title}" updated')
+            db.session.commit()
+        return redirect(url_for('.tesseract_ocr_pipeline_models'))
+    return render_template(
+        'contributions/tesseract_ocr_pipeline_models/tesseract_ocr_pipeline_model.html.j2',
+        title=f'{topm.title} {topm.version}',
+        form=form,
+        tesseract_ocr_pipeline_model=topm
+    )

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/contributions/transkribus_htr_pipeline_models/__init__.py

@@ -0,0 +1,2 @@
+from .. import bp
+from . import routes

app/contributions/transkribus_htr_pipeline_models/routes.py

@@ -0,0 +1,7 @@
+from flask import abort
+from . import bp
+
+
+@bp.route('/transkribus_htr_pipeline_models')
+def transkribus_htr_pipeline_models():
+    return abort(503)

app/converters/cli.py

@@ -0,0 +1,22 @@
+import click
+from . import bp
+from .sandpaper import SandpaperConverter
+
+
+@bp.cli.group('converter')
+def converter():
+    ''' Converter commands. '''
+    pass
+
+@converter.group('sandpaper')
+def sandpaper_converter():
+    ''' Sandpaper converter commands. '''
+    pass
+
+@sandpaper_converter.command('run')
+@click.argument('json_db_file')
+@click.argument('data_dir')
+def run_sandpaper_converter(json_db_file, data_dir):
+    ''' Run the sandpaper converter. '''
+    sandpaper_converter = SandpaperConverter(json_db_file, data_dir)
+    sandpaper_converter.run()

app/converters/sandpaper.py

@@ -0,0 +1,112 @@
+from flask import current_app
+from app import db
+from app.models import User, Corpus, CorpusFile
+from datetime import datetime
+import json
+import os
+import shutil
+
+
+class SandpaperConverter:
+    def __init__(self, json_db_file, data_dir):
+        self.json_db_file = json_db_file
+        self.data_dir = data_dir
+
+    def run(self):
+        with open(self.json_db_file, 'r') as f:
+            json_db = json.loads(f.read())
+
+        for json_user in json_db:
+            if not json_user['confirmed']:
+                current_app.logger.info(f'Skip unconfirmed user {json_user["username"]}')
+                continue
+            user_dir = os.path.join(self.data_dir, str(json_user['id']))
+            self.convert_user(json_user, user_dir)
+            db.session.commit()
+
+
+    def convert_user(self, json_user, user_dir):
+        current_app.logger.info(f'Create User {json_user["username"]}...')
+        user = User(
+            confirmed=json_user['confirmed'],
+            email=json_user['email'],
+            last_seen=datetime.fromtimestamp(json_user['last_seen']),
+            member_since=datetime.fromtimestamp(json_user['member_since']),
+            password_hash=json_user['password_hash'],  # TODO: Needs to be added manually
+            username=json_user['username']
+        )
+        db.session.add(user)
+        db.session.flush(objects=[user])
+        db.session.refresh(user)
+        try:
+            user.makedirs()
+        except OSError as e:
+            current_app.logger.error(e)
+            db.session.rollback()
+            raise Exception('Internal Server Error')
+        for json_corpus in json_user['corpora'].values():
+            if not json_corpus['files'].values():
+                current_app.logger.info(f'Skip empty corpus {json_corpus["title"]}')
+                continue
+            corpus_dir = os.path.join(user_dir, 'corpora', str(json_corpus['id']))
+            self.convert_corpus(json_corpus, user, corpus_dir)
+        current_app.logger.info('Done')
+
+
+    def convert_corpus(self, json_corpus, user, corpus_dir):
+        current_app.logger.info(f'Create Corpus {json_corpus["title"]}...')
+        corpus = Corpus(
+            user=user,
+            creation_date=datetime.fromtimestamp(json_corpus['creation_date']),
+            description=json_corpus['description'],
+            title=json_corpus['title']
+        )
+        db.session.add(corpus)
+        db.session.flush(objects=[corpus])
+        db.session.refresh(corpus)
+        try:
+            corpus.makedirs()
+        except OSError as e:
+            current_app.logger.error(e)
+            db.session.rollback()
+            raise Exception('Internal Server Error')
+        for json_corpus_file in json_corpus['files'].values():
+            self.convert_corpus_file(json_corpus_file, corpus, corpus_dir)
+        current_app.logger.info('Done')
+
+
+    def convert_corpus_file(self, json_corpus_file, corpus, corpus_dir):
+        current_app.logger.info(f'Create CorpusFile {json_corpus_file["title"]}...')
+        corpus_file = CorpusFile(
+            corpus=corpus,
+            address=json_corpus_file['address'],
+            author=json_corpus_file['author'],
+            booktitle=json_corpus_file['booktitle'],
+            chapter=json_corpus_file['chapter'],
+            editor=json_corpus_file['editor'],
+            filename=json_corpus_file['filename'],
+            institution=json_corpus_file['institution'],
+            journal=json_corpus_file['journal'],
+            mimetype='application/vrt+xml',
+            pages=json_corpus_file['pages'],
+            publisher=json_corpus_file['publisher'],
+            publishing_year=json_corpus_file['publishing_year'],
+            school=json_corpus_file['school'],
+            title=json_corpus_file['title']
+        )
+        db.session.add(corpus_file)
+        db.session.flush(objects=[corpus_file])
+        db.session.refresh(corpus_file)
+        try:
+            shutil.copy2(
+                os.path.join(corpus_dir, json_corpus_file['filename']),
+                corpus_file.path
+            )
+        except:
+            current_app.logger.warning(
+                'Can not convert corpus file: '
+                f'{os.path.join(corpus_dir, json_corpus_file["filename"])}'
+                ' -> '
+                f'{corpus_file.path}'
+            )
+        current_app.logger.info('Done')

app/converters/vrt.py

@@ -0,0 +1,117 @@
+from flask import current_app
+
+
+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 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)
+
+    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
+    elif pos_attr_order == ['word', 'pos', 'lemma', 'simple_pos', 'ner']:
+        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
+    else:
+        raise Exception('Can not handle format')
+
+    current_ent = None
+    multi_line_tag_definition = False
+    output_vrt = ''
+    for line in input_vrt_lines:
+        if line.strip() == '':
+            continue
+        if line.startswith('<'):
+            if not has_ent_as_s_attr:
+                if current_ent is not None:
+                    output_vrt += '</ent>\n'
+                    current_ent = None
+            if not line.rstrip().endswith('>'):
+                multi_line_tag_definition = True
+            if line.startswith('<text'):
+                output_vrt += '<text>\n'
+            if line.startswith('</text>'):
+                output_vrt += '</text>\n'
+            elif line.startswith('<s'):
+                output_vrt += '<s>\n'
+            elif line.startswith('</s>'):
+                output_vrt += '</s>\n'
+            elif line.startswith('<ent'):
+                output_vrt += line
+            elif line.startswith('</ent>'):
+                output_vrt += line
+            continue
+        if multi_line_tag_definition and line.rstrip().endswith('>'):
+            multi_line_tag_definition = False
+            continue
+        pos_attrs = line.rstrip('\n').split('\t')
+        if not has_ent_as_s_attr and len(pos_attrs) > 4:
+            if pos_attrs[4].lower() in ['null', 'none']:
+                if current_ent:
+                    output_vrt += '</ent>\n'
+                    current_ent = None
+            else:
+                if current_ent is None:
+                    output_vrt += f'<ent type="{pos_attrs[4]}">\n'
+                    current_ent = pos_attrs[4]
+                elif current_ent != pos_attrs[4]:
+                    output_vrt += '</ent>\n'
+                    current_ent = None
+                    output_vrt += f'<ent type="{pos_attrs[4]}">\n'
+                    current_ent = pos_attrs[4]
+        output_vrt += pos_attrs_to_string_function(pos_attrs)
+
+    with open(output_file, 'w') as f:
+        f.write(output_vrt)

app/corpora/__init__.py

@@ -0,0 +1,19 @@
+from flask import Blueprint
+from flask_login import login_required
+
+
+bp = Blueprint('corpora', __name__)
+bp.cli.short_help = 'Corpus commands.'
+
+
+@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 cli, cqi_over_sio, files, followers, routes, json_routes

app/corpora/cli.py

@@ -0,0 +1,27 @@
+from app.models import Corpus, CorpusStatus
+import os
+import shutil
+from app import db
+from . import bp
+
+
+@bp.cli.command('reset')
+def reset():
+    ''' Reset built corpora. '''
+    status = [
+        CorpusStatus.QUEUED,
+        CorpusStatus.BUILDING,
+        CorpusStatus.BUILT,
+        CorpusStatus.STARTING_ANALYSIS_SESSION,
+        CorpusStatus.RUNNING_ANALYSIS_SESSION,
+        CorpusStatus.CANCELING_ANALYSIS_SESSION
+    ]
+    for corpus in [x for x in Corpus.query.all() if x.status in status]:
+        print(f'Resetting corpus {corpus}')
+        shutil.rmtree(os.path.join(corpus.path, 'cwb'), ignore_errors=True)
+        os.mkdir(os.path.join(corpus.path, 'cwb'))
+        os.mkdir(os.path.join(corpus.path, 'cwb', 'data'))
+        os.mkdir(os.path.join(corpus.path, 'cwb', 'registry'))
+        corpus.status = CorpusStatus.UNPREPARED
+        corpus.num_analysis_sessions = 0
+    db.session.commit()

app/corpora/cqi_over_sio/__init__.py

@@ -0,0 +1,113 @@
+from cqi import CQiClient
+from cqi.errors import CQiException
+from flask import session
+from flask_login import current_user
+from flask_socketio import ConnectionRefusedError
+from threading import Lock
+from app import db, hashids, socketio
+from app.decorators import socketio_login_required
+from app.models import Corpus, CorpusStatus
+import math
+
+
+'''
+This package tunnels the Corpus Query interface (CQi) protocol through
+Socket.IO (SIO) by wrapping each CQi function in a seperate SIO event.
+
+This module only handles the SIO connect/disconnect, which handles the setup
+and teardown of necessary ressources for later use. Each CQi function has a
+corresponding SIO event. The event handlers are spread across the different
+modules within this package.
+
+Basic concept:
+1. A client connects to the SIO namespace and provides the id of a corpus to be
+   analysed.
+     1.1 The analysis session counter of the corpus is incremented.
+     1.2 A CQiClient and a (Mutex) Lock belonging to it is created.
+     1.3 Wait until the CQP server is running.
+     1.4 Connect the CQiClient to the server.
+     1.5 Save the CQiClient and the Lock in the session for subsequential use.
+2. A client emits an event and may provide a single json object with necessary
+   arguments for the targeted CQi function.
+3. A SIO event handler (decorated with cqi_over_socketio) gets executed.
+     - The event handler function defines all arguments. Hence the client
+       is sent as a single json object, the decorator decomposes it to fit
+       the functions signature. This also includes type checking and proper
+       use of the lock (acquire/release) mechanism.
+4. Wait for more events
+5. The client disconnects from the 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.
+'''
+
+
+NAMESPACE = '/cqi_over_sio'
+
+
+from .cqi import *  # noqa
+
+
+@socketio.on('connect', namespace=NAMESPACE)
+@socketio_login_required
+def connect(auth):
+    # the auth variable is used in a hacky way. It contains the corpus id for
+    # which a corpus analysis session should be started.
+    corpus_id = hashids.decode(auth['corpus_id'])
+    corpus = Corpus.query.get(corpus_id)
+    if corpus is None:
+        # return {'code': 404, 'msg': 'Not Found'}
+        raise ConnectionRefusedError('Not Found')
+    if not (corpus.user == current_user
+            or current_user.is_following_corpus(corpus)
+            or current_user.is_administrator()):
+        # return {'code': 403, 'msg': 'Forbidden'}
+        raise ConnectionRefusedError('Forbidden')
+    if corpus.status not in [
+        CorpusStatus.BUILT,
+        CorpusStatus.STARTING_ANALYSIS_SESSION,
+        CorpusStatus.RUNNING_ANALYSIS_SESSION,
+        CorpusStatus.CANCELING_ANALYSIS_SESSION
+    ]:
+        # return {'code': 424, 'msg': 'Failed Dependency'}
+        raise ConnectionRefusedError('Failed Dependency')
+    if corpus.num_analysis_sessions is None:
+        corpus.num_analysis_sessions = 0
+        db.session.commit()
+    corpus.num_analysis_sessions = Corpus.num_analysis_sessions + 1
+    db.session.commit()
+    retry_counter = 20
+    while corpus.status != CorpusStatus.RUNNING_ANALYSIS_SESSION:
+        if retry_counter == 0:
+            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)
+    cqi_client = CQiClient(f'cqpserver_{corpus_id}', timeout=math.inf)
+    session['cqi_over_sio'] = {
+        'corpus_id': corpus_id,
+        'cqi_client': cqi_client,
+        'cqi_client_lock': Lock(),
+    }
+    # return {'code': 200, 'msg': 'OK'}
+
+
+@socketio.on('disconnect', namespace=NAMESPACE)
+def disconnect():
+    try:
+        cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+        cqi_client_lock: Lock = session['cqi_over_sio']['cqi_client_lock']
+    except KeyError:
+        return
+    cqi_client_lock.acquire()
+    try:
+        cqi_client.api.ctrl_bye()
+    except (BrokenPipeError, CQiException):
+        pass
+    cqi_client_lock.release()
+    corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
+    corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
+    db.session.commit()
+    session.pop('cqi_over_sio')
+    # return {'code': 200, 'msg': 'OK'}

app/corpora/cqi_over_sio/cqi.py

@@ -0,0 +1,110 @@
+from cqi import CQiClient
+from cqi.errors import CQiException
+from cqi.status import CQiStatus
+from flask import session
+from inspect import signature
+from threading import Lock
+from typing import Callable, Dict, List
+from app import socketio
+from app.decorators import socketio_login_required
+from . import NAMESPACE as ns
+from .extensions import CQI_EXTENSION_FUNCTION_NAMES
+from . import extensions as extensions_module
+
+
+CQI_FUNCTION_NAMES: List[str] = [
+    'ask_feature_cl_2_3',
+    'ask_feature_cqi_1_0',
+    'ask_feature_cqp_2_3',
+    'cl_alg2cpos',
+    'cl_attribute_size',
+    'cl_cpos2alg',
+    'cl_cpos2id',
+    'cl_cpos2lbound',
+    'cl_cpos2rbound',
+    'cl_cpos2str',
+    'cl_cpos2struc',
+    'cl_drop_attribute',
+    'cl_id2cpos',
+    'cl_id2freq',
+    'cl_id2str',
+    'cl_idlist2cpos',
+    'cl_lexicon_size',
+    'cl_regex2id',
+    'cl_str2id',
+    'cl_struc2cpos',
+    'cl_struc2str',
+    'corpus_alignment_attributes',
+    'corpus_charset',
+    'corpus_drop_corpus',
+    'corpus_full_name',
+    'corpus_info',
+    'corpus_list_corpora',
+    'corpus_positional_attributes',
+    'corpus_properties',
+    'corpus_structural_attribute_has_values',
+    'corpus_structural_attributes',
+    'cqp_drop_subcorpus',
+    'cqp_dump_subcorpus',
+    'cqp_fdist_1',
+    'cqp_fdist_2',
+    'cqp_list_subcorpora',
+    'cqp_query',
+    'cqp_subcorpus_has_field',
+    'cqp_subcorpus_size',
+    'ctrl_bye',
+    'ctrl_connect',
+    'ctrl_last_general_error',
+    'ctrl_ping',
+    'ctrl_user_abort'
+]
+
+
+@socketio.on('cqi', namespace=ns)
+@socketio_login_required
+def cqi_over_sio(fn_name: str, fn_args: Dict = {}):
+    try:
+        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_FUNCTION_NAMES:
+        fn: Callable = getattr(cqi_client.api, fn_name)
+    elif fn_name in CQI_EXTENSION_FUNCTION_NAMES:
+        fn: Callable = getattr(extensions_module, fn_name)
+    else:
+        return {'code': 400, 'msg': 'Bad Request'}
+    for param in signature(fn).parameters.values():
+        if param.default is param.empty:
+            if param.name not in fn_args:
+                return {'code': 400, 'msg': 'Bad Request'}
+        else:
+            if param.name not in fn_args:
+                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)
+    except BrokenPipeError as e:
+        return {'code': 500, 'msg': 'Internal Server Error'}
+    except CQiException as e:
+        return {
+            'code': 502,
+            'msg': 'Bad Gateway',
+            'payload': {
+                'code': e.code,
+                'desc': e.description,
+                'msg': e.__class__.__name__
+            }
+        }
+    finally:
+        cqi_client_lock.release()
+    if isinstance(fn_return_value, CQiStatus):
+        payload = {
+            'code': fn_return_value.code,
+            'msg': fn_return_value.__class__.__name__
+        }
+    else:
+        payload = fn_return_value
+    return {'code': 200, 'msg': 'OK', 'payload': payload}

app/corpora/cqi_over_sio/extensions.py

@@ -0,0 +1,314 @@
+from collections import Counter
+from cqi import CQiClient
+from cqi.models.corpora import Corpus as CQiCorpus
+from cqi.models.attributes import (
+    PositionalAttribute as CQiPositionalAttribute,
+    StructuralAttribute as CQiStructuralAttribute
+)
+from cqi.status import StatusOk as CQiStatusOk
+from flask import session
+from typing import Dict, List
+import gzip
+import json
+import math
+import os
+from app import db
+from app.models import Corpus
+from .utils import lookups_by_cpos, partial_export_subcorpus, export_subcorpus
+
+
+CQI_EXTENSION_FUNCTION_NAMES: List[str] = [
+    'ext_corpus_update_db',
+    'ext_corpus_static_data',
+    'ext_corpus_paginate_corpus',
+    'ext_cqp_paginate_subcorpus',
+    'ext_cqp_partial_export_subcorpus',
+    'ext_cqp_export_subcorpus',
+]
+
+
+def ext_corpus_update_db(corpus: str) -> CQiStatusOk:
+    db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+    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:
+    db_corpus = Corpus.query.get(session['cqi_over_sio']['corpus_id'])
+    static_corpus_data_file = os.path.join(db_corpus.path, 'cwb', 'static.json.gz')
+    if os.path.exists(static_corpus_data_file):
+        with open(static_corpus_data_file, 'rb') as f:
+            return f.read()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+    cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
+    cqi_p_attrs: Dict[str, CQiPositionalAttribute] = {
+        p_attr.name: p_attr
+        for p_attr in cqi_corpus.positional_attributes.list()
+    }
+    cqi_s_attrs: Dict[str, CQiStructuralAttribute] = {
+        s_attr.name: s_attr
+        for s_attr in cqi_corpus.structural_attributes.list()
+    }
+    static_corpus_data = {
+        'corpus': {
+            'bounds': [0, cqi_corpus.size - 1],
+            'counts': {
+                'token': cqi_corpus.size
+            },
+            'freqs': {}
+        },
+        'p_attrs': {},
+        's_attrs': {},
+        'values': {'p_attrs': {}, 's_attrs': {}}
+    }
+    for p_attr in cqi_p_attrs.values():
+        static_corpus_data['corpus']['freqs'][p_attr.name] = {}
+        chunk_size = 10000
+        p_attr_id_list = list(range(p_attr.lexicon_size))
+        chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
+        del p_attr_id_list
+        for chunk in chunks:
+            # print(f'corpus.freqs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
+            static_corpus_data['corpus']['freqs'][p_attr.name].update(
+                dict(zip(chunk, p_attr.freqs_by_ids(chunk)))
+            )
+        del chunks
+        static_corpus_data['p_attrs'][p_attr.name] = {}
+        cpos_list = list(range(cqi_corpus.size))
+        chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
+        del cpos_list
+        for chunk in chunks:
+            # print(f'p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
+            static_corpus_data['p_attrs'][p_attr.name].update(
+                dict(zip(chunk, p_attr.ids_by_cpos(chunk)))
+            )
+        del chunks
+        static_corpus_data['values']['p_attrs'][p_attr.name] = {}
+        p_attr_id_list = list(range(p_attr.lexicon_size))
+        chunks = [p_attr_id_list[i:i+chunk_size] for i in range(0, len(p_attr_id_list), chunk_size)]
+        del p_attr_id_list
+        for chunk in chunks:
+            # print(f'values.p_attrs.{p_attr.name}: {chunk[0]} - {chunk[-1]}')
+            static_corpus_data['values']['p_attrs'][p_attr.name].update(
+                dict(zip(chunk, p_attr.values_by_ids(chunk)))
+            )
+        del chunks
+    for s_attr in cqi_s_attrs.values():
+        if s_attr.has_values:
+            continue
+        static_corpus_data['corpus']['counts'][s_attr.name] = s_attr.size
+        static_corpus_data['s_attrs'][s_attr.name] = {'lexicon': {}, 'values': None}
+        static_corpus_data['values']['s_attrs'][s_attr.name] = {}
+        ##########################################################################
+        # A faster way to get cpos boundaries for smaller s_attrs                #
+        ##########################################################################
+        # if s_attr.name in ['s', 'ent']:
+        #     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
+        #     match_boundaries = zip(
+        #         range(first_match, last_match + 1),
+        #         cqi_subcorpus.dump(cqi_subcorpus.fields['match'], first_match, last_match),
+        #         cqi_subcorpus.dump(cqi_subcorpus.fields['matchend'], first_match, last_match)
+        #     )
+        #     for id, lbound, rbound in match_boundaries:
+        #         static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {}
+        #         static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
+        #         static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
+        #         static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
+        #     cqi_subcorpus.drop()
+        for id in range(0, s_attr.size):
+            # print(f's_attrs.{s_attr.name}.lexicon.{id}')
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id] = {
+                'bounds': None,
+                'counts': None,
+                'freqs': None
+            }
+            if s_attr.name != 'text':
+                continue
+            lbound, rbound = s_attr.cpos_by_id(id)
+            # print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
+            # print(f's_attrs.{s_attr.name}.lexicon.{id}.counts')
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts'] = {}
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['token'] = rbound - lbound + 1
+            cpos_list = list(range(lbound, rbound + 1))
+            chunks = [cpos_list[i:i+chunk_size] for i in range(0, len(cpos_list), chunk_size)]
+            del cpos_list
+            ent_ids = set()
+            for chunk in chunks:
+                # print(f'Gather ent_ids from cpos: {chunk[0]} - {chunk[-1]}')
+                ent_ids.update({x for x in cqi_s_attrs['ent'].ids_by_cpos(chunk) if x != -1})
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['ent'] = len(ent_ids)
+            del ent_ids
+            s_ids = set()
+            for chunk in chunks:
+                # print(f'Gather s_ids from cpos: {chunk[0]} - {chunk[-1]}')
+                s_ids.update({x for x in cqi_s_attrs['s'].ids_by_cpos(chunk) if x != -1})
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['counts']['s'] = len(s_ids)
+            del s_ids
+            # print(f's_attrs.{s_attr.name}.lexicon.{id}.freqs')
+            static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'] = {}
+            for p_attr in cqi_p_attrs.values():
+                p_attr_ids = []
+                for chunk in chunks:
+                    # print(f'Gather p_attr_ids from cpos: {chunk[0]} - {chunk[-1]}')
+                    p_attr_ids.extend(p_attr.ids_by_cpos(chunk))
+                static_corpus_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr_ids))
+                del p_attr_ids
+            del chunks
+        sub_s_attrs = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
+        s_attr_value_names: List[str] = [
+            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))
+        chunks = [s_attr_id_list[i:i+chunk_size] for i in range(0, len(s_attr_id_list), chunk_size)]
+        del s_attr_id_list
+        sub_s_attr_values = []
+        for sub_s_attr in sub_s_attrs:
+            tmp = []
+            for chunk in chunks:
+                tmp.extend(sub_s_attr.values_by_ids(chunk))
+            sub_s_attr_values.append(tmp)
+            del tmp
+        del chunks
+        # print(f's_attrs.{s_attr.name}.values')
+        static_corpus_data['s_attrs'][s_attr.name]['values'] = s_attr_value_names
+        # print(f'values.s_attrs.{s_attr.name}')
+        static_corpus_data['values']['s_attrs'][s_attr.name] = {
+            s_attr_id: {
+                s_attr_value_name: sub_s_attr_values[s_attr_value_name_idx][s_attr_id_idx]
+                for s_attr_value_name_idx, s_attr_value_name in enumerate(
+                    static_corpus_data['s_attrs'][s_attr.name]['values']
+                )
+            } for s_attr_id_idx, s_attr_id in enumerate(range(0, s_attr.size))
+        }
+        del sub_s_attr_values
+    with gzip.open(static_corpus_data_file, 'wt') as f:
+        json.dump(static_corpus_data, f)
+    del static_corpus_data
+    with open(static_corpus_data_file, 'rb') as f:
+        return f.read()
+
+
+def ext_corpus_paginate_corpus(
+    corpus: str,
+    page: int = 1,
+    per_page: int = 20
+) -> Dict:
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
+    cqi_corpus = cqi_client.corpora.get(corpus)
+    # Sanity checks
+    if (
+        per_page < 1
+        or page < 1
+        or (
+            cqi_corpus.size > 0
+            and page > math.ceil(cqi_corpus.size / per_page)
+        )
+    ):
+        return {'code': 416, 'msg': 'Range Not Satisfiable'}
+    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)
+    payload = {}
+    # the items for the current page
+    payload['items'] = [cpos_list]
+    # the lookups for the items
+    payload['lookups'] = lookups
+    # the total number of items matching the query
+    payload['total'] = cqi_corpus.size
+    # the number of items to be displayed on a page.
+    payload['per_page'] = per_page
+    # The total number of pages
+    payload['pages'] = math.ceil(payload['total'] / payload['per_page'])
+    # the current page number (1 indexed)
+    payload['page'] = page if payload['pages'] > 0 else None
+    # True if a previous page exists
+    payload['has_prev'] = payload['page'] > 1 if payload['page'] else False
+    # True if a next page exists.
+    payload['has_next'] = payload['page'] < payload['pages'] if payload['page'] else False  # noqa
+    # Number of the previous page.
+    payload['prev_num'] = payload['page'] - 1 if payload['has_prev'] else None
+    # Number of the next page
+    payload['next_num'] = payload['page'] + 1 if payload['has_next'] else None
+    return payload
+
+
+def ext_cqp_paginate_subcorpus(
+    subcorpus: str,
+    context: int = 50,
+    page: int = 1,
+    per_page: int = 20
+) -> Dict:
+    corpus_name, subcorpus_name = subcorpus.split(':', 1)
+    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
+    if (
+        per_page < 1
+        or page < 1
+        or (
+            cqi_subcorpus.size > 0
+            and page > math.ceil(cqi_subcorpus.size / per_page)
+        )
+    ):
+        return {'code': 416, 'msg': 'Range Not Satisfiable'}
+    offset = (page - 1) * per_page
+    cutoff = per_page
+    cqi_results_export = export_subcorpus(
+        cqi_subcorpus, context=context, cutoff=cutoff, offset=offset)
+    payload = {}
+    # the items for the current page
+    payload['items'] = cqi_results_export.pop('matches')
+    # the lookups for the items
+    payload['lookups'] = cqi_results_export
+    # the total number of items matching the query
+    payload['total'] = cqi_subcorpus.size
+    # the number of items to be displayed on a page.
+    payload['per_page'] = per_page
+    # The total number of pages
+    payload['pages'] = math.ceil(payload['total'] / payload['per_page'])
+    # the current page number (1 indexed)
+    payload['page'] = page if payload['pages'] > 0 else None
+    # True if a previous page exists
+    payload['has_prev'] = payload['page'] > 1 if payload['page'] else False
+    # True if a next page exists.
+    payload['has_next'] = payload['page'] < payload['pages'] if payload['page'] else False  # noqa
+    # Number of the previous page.
+    payload['prev_num'] = payload['page'] - 1 if payload['has_prev'] else None
+    # Number of the next page
+    payload['next_num'] = payload['page'] + 1 if payload['has_next'] else None
+    return payload
+
+
+def ext_cqp_partial_export_subcorpus(
+    subcorpus: str,
+    match_id_list: list,
+    context: int = 50
+) -> Dict:
+    corpus_name, subcorpus_name = subcorpus.split(':', 1)
+    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)
+    return cqi_subcorpus_partial_export
+
+
+def ext_cqp_export_subcorpus(
+    subcorpus: str,
+    context: int = 50
+) -> Dict:
+    corpus_name, subcorpus_name = subcorpus.split(':', 1)
+    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)
+    return cqi_subcorpus_export

app/corpora/cqi_over_sio/utils.py

@@ -0,0 +1,133 @@
+from cqi.models.corpora import Corpus
+from cqi.models.subcorpora import Subcorpus
+from typing import Dict, List
+from app.models import Corpus
+
+
+def lookups_by_cpos(corpus: Corpus, 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.attrs['name']] = \
+                cpos_attr_values[i]
+    for attr in corpus.structural_attributes.list():
+        # We only want to iterate over non subattributes, identifiable by
+        # attr.attrs['has_values'] == False
+        if attr.attrs['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.attrs['name']] = cpos_attr_ids[i]
+        occured_attr_ids = [x for x in set(cpos_attr_ids) if x != -1]
+        if not occured_attr_ids:
+            continue
+        subattrs = corpus.structural_attributes.list(filters={'part_of': attr})
+        if not subattrs:
+            continue
+        lookup_name = f'{attr.attrs["name"]}_lookup'
+        lookups[lookup_name] = {}
+        for attr_id in occured_attr_ids:
+            lookups[lookup_name][attr_id] = {}
+        for subattr in subattrs:
+            subattr_name = subattr.attrs['name'][(len(attr.attrs['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: Subcorpus,
+    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: Subcorpus,
+    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

@@ -0,0 +1,33 @@
+from flask import abort
+from flask_login import current_user
+from functools import wraps
+from app.models import Corpus, CorpusFollowerAssociation
+
+
+def corpus_follower_permission_required(*permissions):
+    def decorator(f):
+        @wraps(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()):
+                cfa = CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=current_user.id).first()
+                if cfa is None:
+                    abort(403)
+                if not all([cfa.role.has_permission(p) for p in permissions]):
+                    abort(403)
+            return f(*args, **kwargs)
+        return decorated_function
+    return decorator
+
+
+def corpus_owner_or_admin_required(f):
+    @wraps(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()):
+            abort(403)
+        return f(*args, **kwargs)
+    return decorated_function
+

app/corpora/events.py

@@ -0,0 +1,45 @@
+from flask_login import current_user
+from flask_socketio import join_room
+from app import hashids, socketio
+from app.decorators import socketio_login_required
+from app.models import Corpus
+
+
+@socketio.on('GET /corpora/<corpus_id>')
+@socketio_login_required
+def get_corpus(corpus_hashid):
+    corpus_id = hashids.decode(corpus_hashid)
+    corpus = Corpus.query.get(corpus_id)
+    if corpus is None:
+        return {'options': {'status': 404, 'statusText': 'Not found'}}
+    if not (
+        corpus.is_public
+        or corpus.user == current_user
+        or current_user.is_administrator()
+    ):
+        return {'options': {'status': 403, 'statusText': 'Forbidden'}}
+    return {
+        'body': corpus.to_json_serializable(),
+        'options': {
+            'status': 200,
+            'statusText': 'OK',
+            'headers': {'Content-Type: application/json'}
+        }
+    }
+
+
+@socketio.on('SUBSCRIBE /corpora/<corpus_id>')
+@socketio_login_required
+def subscribe_corpus(corpus_hashid):
+    corpus_id = hashids.decode(corpus_hashid)
+    corpus = Corpus.query.get(corpus_id)
+    if corpus is None:
+        return {'options': {'status': 404, 'statusText': 'Not found'}}
+    if not (
+        corpus.is_public
+        or corpus.user == current_user
+        or current_user.is_administrator()
+    ):
+        return {'options': {'status': 403, 'statusText': 'Forbidden'}}
+    join_room(f'/corpora/{corpus.hashid}')
+    return {'options': {'status': 200, 'statusText': 'OK'}}

app/corpora/files/__init__.py

@@ -0,0 +1,2 @@
+from .. import bp
+from . import json_routes, routes

app/corpora/files/forms.py

@@ -0,0 +1,54 @@
+from flask_wtf import FlaskForm
+from flask_wtf.file import FileField, FileRequired
+from wtforms import (
+    StringField,
+    SubmitField,
+    ValidationError,
+    IntegerField
+)
+from wtforms.validators import InputRequired, Length
+
+
+class CorpusFileBaseForm(FlaskForm):
+    author = StringField(
+        'Author',
+        validators=[InputRequired(), Length(max=255)]
+    )
+    publishing_year = IntegerField(
+        'Publishing year',
+        validators=[InputRequired()]
+    )
+    title = StringField(
+        'Title',
+        validators=[InputRequired(), Length(max=255)]
+    )
+    address = StringField('Adress', validators=[Length(max=255)])
+    booktitle = StringField('Booktitle', validators=[Length(max=255)])
+    chapter = StringField('Chapter', validators=[Length(max=255)])
+    editor = StringField('Editor', validators=[Length(max=255)])
+    institution = StringField('Institution', validators=[Length(max=255)])
+    journal = StringField('Journal', validators=[Length(max=255)])
+    pages = StringField('Pages', validators=[Length(max=255)])
+    publisher = StringField('Publisher', validators=[Length(max=255)])
+    school = StringField('School', validators=[Length(max=255)])
+    submit = SubmitField()
+
+
+class CreateCorpusFileForm(CorpusFileBaseForm):
+    vrt = FileField('File', validators=[FileRequired()])
+
+    def validate_vrt(self, field):
+        if not field.data.filename.lower().endswith('.vrt'):
+            raise ValidationError('VRT files only!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-corpus-file-form'
+        super().__init__(*args, **kwargs)
+
+
+class UpdateCorpusFileForm(CorpusFileBaseForm):
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'update-corpus-file-form'
+        super().__init__(*args, **kwargs)

app/corpora/files/json_routes.py

@@ -0,0 +1,30 @@
+from flask import abort, current_app
+from threading import Thread
+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
+
+
+@bp.route('/<hashid:corpus_id>/files/<hashid:corpus_file_id>', methods=['DELETE'])
+@corpus_follower_permission_required('MANAGE_FILES')
+@content_negotiation(produces='application/json')
+def delete_corpus_file(corpus_id, corpus_file_id):
+    def _delete_corpus_file(app, corpus_file_id):
+        with app.app_context():
+            corpus_file = CorpusFile.query.get(corpus_file_id)
+            corpus_file.delete()
+            db.session.commit()
+
+    corpus_file = CorpusFile.query.filter_by(corpus_id=corpus_id, id=corpus_file_id).first_or_404()
+    thread = Thread(
+        target=_delete_corpus_file,
+        args=(current_app._get_current_object(), corpus_file.id)
+    )
+    thread.start()
+    response_data = {
+        'message': f'Corpus File "{corpus_file.title}" marked for deletion',
+        'category': 'corpus'
+    }
+    return response_data, 202

app/corpora/files/routes.py

@@ -0,0 +1,100 @@
+from flask import (
+    abort,
+    flash,
+    redirect,
+    render_template,
+    send_from_directory,
+    url_for
+)
+from flask_breadcrumbs import register_breadcrumb
+import os
+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)
+    form = CreateCorpusFileForm()
+    if form.is_submitted():
+        if not form.validate():
+            response = {'errors': form.errors}
+            return response, 400
+        try:
+            corpus_file = CorpusFile.create(
+                form.vrt.data,
+                address=form.address.data,
+                author=form.author.data,
+                booktitle=form.booktitle.data,
+                chapter=form.chapter.data,
+                editor=form.editor.data,
+                institution=form.institution.data,
+                journal=form.journal.data,
+                pages=form.pages.data,
+                publisher=form.publisher.data,
+                publishing_year=form.publishing_year.data,
+                school=form.school.data,
+                title=form.title.data,
+                mimetype='application/vrt+xml',
+                corpus=corpus
+            )
+        except (AttributeError, OSError):
+            abort(500)
+        corpus.status = CorpusStatus.UNPREPARED
+        db.session.commit()
+        flash(f'Corpus File "{corpus_file.filename}" added', category='corpus')
+        return '', 201, {'Location': corpus.url}
+    return render_template(
+        'corpora/files/create.html.j2',
+        title='Add corpus file',
+        form=form,
+        corpus=corpus
+    )
+
+
+@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()
+    form = UpdateCorpusFileForm(data=corpus_file.to_json_serializeable())
+    if form.validate_on_submit():
+        form.populate_obj(corpus_file)
+        if db.session.is_modified(corpus_file):
+            corpus_file.corpus.status = CorpusStatus.UNPREPARED
+            db.session.commit()
+            flash(f'Corpus file "{corpus_file.filename}" updated', category='corpus')
+        return redirect(corpus_file.corpus.url)
+    return render_template(
+        'corpora/files/corpus_file.html.j2',
+        title='Edit corpus file',
+        form=form,
+        corpus=corpus_file.corpus,
+        corpus_file=corpus_file
+    )
+
+
+@bp.route('/<hashid:corpus_id>/files/<hashid:corpus_file_id>/download')
+@corpus_follower_permission_required('VIEW')
+def download_corpus_file(corpus_id, corpus_file_id):
+    corpus_file = CorpusFile.query.filter_by(corpus_id=corpus_id, id=corpus_file_id).first_or_404()
+    return send_from_directory(
+        os.path.dirname(corpus_file.path),
+        os.path.basename(corpus_file.path),
+        as_attachment=True,
+        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/__init__.py

@@ -0,0 +1,2 @@
+from .. import bp
+from . import json_routes

app/corpora/followers/json_routes.py

@@ -0,0 +1,76 @@
+from flask import abort, flash, jsonify, make_response, request
+from flask_login import current_user
+from app import db
+from app.decorators import content_negotiation
+from app.models import (
+    Corpus,
+    CorpusFollowerAssociation,
+    CorpusFollowerRole,
+    User
+)
+from ..decorators import corpus_follower_permission_required
+from . import bp
+
+
+# @bp.route('/<hashid:corpus_id>/followers', methods=['POST'])
+# @corpus_follower_permission_required('MANAGE_FOLLOWERS')
+# @content_negotiation(consumes='application/json', produces='application/json')
+# def create_corpus_followers(corpus_id):
+#     usernames = request.json
+#     if not (isinstance(usernames, list) or all(isinstance(u, str) for u in usernames)):
+#         abort(400)
+#     corpus = Corpus.query.get_or_404(corpus_id)
+#     for username in usernames:
+#         user = User.query.filter_by(username=username, is_public=True).first_or_404()
+#         user.follow_corpus(corpus)
+#     db.session.commit()
+#     response_data = {
+#         'message': f'Users are now following "{corpus.title}"',
+#         'category': 'corpus'
+#     }
+#     return response_data, 200
+
+
+# @bp.route('/<hashid:corpus_id>/followers/<hashid:follower_id>/role', methods=['PUT'])
+# @corpus_follower_permission_required('MANAGE_FOLLOWERS')
+# @content_negotiation(consumes='application/json', produces='application/json')
+# def update_corpus_follower_role(corpus_id, follower_id):
+#     role_name = request.json
+#     if not isinstance(role_name, str):
+#         abort(400)
+#     cfr = CorpusFollowerRole.query.filter_by(name=role_name).first()
+#     if cfr is None:
+#         abort(400)
+#     cfa = CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=follower_id).first_or_404()
+#     cfa.role = cfr
+#     db.session.commit()
+#     response_data = {
+#         'message': f'User "{cfa.follower.username}" is now {cfa.role.name}',
+#         'category': 'corpus'
+#     }
+#     return response_data, 200
+
+
+# @bp.route('/<hashid:corpus_id>/followers/<hashid:follower_id>', methods=['DELETE'])
+# def delete_corpus_follower(corpus_id, follower_id):
+#     cfa = CorpusFollowerAssociation.query.filter_by(corpus_id=corpus_id, follower_id=follower_id).first_or_404()
+#     if not (
+#         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()):
+#         abort(403)
+#     if current_user.id == follower_id:
+#         flash(f'You are no longer following "{cfa.corpus.title}"', 'corpus')
+#         response = make_response()
+#         response.status_code = 204
+#     else:
+#         response_data = {
+#             'message': f'"{cfa.follower.username}" is not following "{cfa.corpus.title}" anymore',
+#             'category': 'corpus'
+#         }
+#         response = jsonify(response_data)
+#         response.status_code = 200
+#     cfa.follower.unfollow_corpus(cfa.corpus)
+#     db.session.commit()
+#     return response

app/corpora/forms.py

@@ -0,0 +1,33 @@
+from flask_wtf import FlaskForm
+from wtforms import StringField, SubmitField, TextAreaField
+from wtforms.validators import InputRequired, Length
+
+
+class CorpusBaseForm(FlaskForm):
+    description = TextAreaField(
+        'Description',
+        validators=[InputRequired(), Length(max=255)]
+    )
+    title = StringField('Title', validators=[InputRequired(), Length(max=32)])
+    submit = SubmitField()
+
+
+class CreateCorpusForm(CorpusBaseForm):
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-corpus-form'
+        super().__init__(*args, **kwargs)
+
+
+class UpdateCorpusForm(CorpusBaseForm):
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'update-corpus-form'
+        super().__init__(*args, **kwargs)
+
+
+class ImportCorpusForm(FlaskForm):
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'import-corpus-form'
+        super().__init__(*args, **kwargs)

app/corpora/json_routes.py

@@ -0,0 +1,125 @@
+from datetime import datetime
+from flask import abort, current_app, request, url_for
+from flask_login import current_user
+from threading import Thread
+from app import db
+from app.decorators import content_negotiation
+from app.models import Corpus, CorpusFollowerRole
+from . import bp
+from .decorators import corpus_follower_permission_required, corpus_owner_or_admin_required
+import nltk
+from string import punctuation
+
+
+@bp.route('/<hashid:corpus_id>', methods=['DELETE'])
+@corpus_owner_or_admin_required
+@content_negotiation(produces='application/json')
+def delete_corpus(corpus_id):
+    def _delete_corpus(app, corpus_id):
+        with app.app_context():
+            corpus = Corpus.query.get(corpus_id)
+            corpus.delete()
+            db.session.commit()
+
+    corpus = Corpus.query.get_or_404(corpus_id)
+    thread = Thread(
+        target=_delete_corpus,
+        args=(current_app._get_current_object(), corpus.id)
+    )
+    thread.start()
+    response_data = {
+        'message': f'Corpus "{corpus.title}" marked for deletion',
+        'category': 'corpus'
+    }
+    return response_data, 200
+
+
+@bp.route('/<hashid:corpus_id>/build', methods=['POST'])
+@corpus_follower_permission_required('MANAGE_FILES')
+@content_negotiation(produces='application/json')
+def build_corpus(corpus_id):
+    def _build_corpus(app, corpus_id):
+        with app.app_context():
+            corpus = Corpus.query.get(corpus_id)
+            corpus.build()
+            db.session.commit()
+
+    corpus = Corpus.query.get_or_404(corpus_id)
+    if len(corpus.files.all()) == 0:
+        abort(409)
+    thread = Thread(
+        target=_build_corpus,
+        args=(current_app._get_current_object(), corpus_id)
+    )
+    thread.start()
+    response_data = {
+        'message': f'Corpus "{corpus.title}" marked for building',
+        'category': 'corpus'
+    }
+    return response_data, 202
+
+@bp.route('/stopwords')
+@content_negotiation(produces='application/json')
+def get_stopwords():
+    nltk.download('stopwords')
+    languages = ["german", "english", "catalan", "greek", "spanish", "french", "italian", "russian", "chinese"]
+    stopwords = {}
+    for language in languages:
+        stopwords[language] = nltk.corpus.stopwords.words(language)
+    stopwords['punctuation'] = list(punctuation) + ['—', '|']
+    stopwords['user_stopwords'] = []
+    response_data = stopwords
+    return response_data, 202
+
+# @bp.route('/<hashid:corpus_id>/generate-share-link', methods=['POST'])
+# @corpus_follower_permission_required('MANAGE_FOLLOWERS')
+# @content_negotiation(consumes='application/json', produces='application/json')
+# def generate_corpus_share_link(corpus_id):
+#     data = request.json
+#     if not isinstance(data, dict):
+#         abort(400)
+#     expiration = data.get('expiration')
+#     if not isinstance(expiration, str):
+#         abort(400)
+#     role_name = data.get('role')
+#     if not isinstance(role_name, str):
+#         abort(400)
+#     expiration_date = datetime.strptime(expiration, '%b %d, %Y')
+#     cfr = CorpusFollowerRole.query.filter_by(name=role_name).first()
+#     if cfr is None:
+#         abort(400)
+#     corpus = Corpus.query.get_or_404(corpus_id)
+#     token = current_user.generate_follow_corpus_token(corpus.hashid, role_name, expiration_date)
+#     corpus_share_link = url_for(
+#         'corpora.follow_corpus',
+#         corpus_id=corpus_id,
+#         token=token,
+#         _external=True
+#     )
+#     response_data = {
+#         'message': 'Corpus share link generated',
+#         'category': 'corpus',
+#         'corpusShareLink': corpus_share_link
+#     }
+#     return response_data, 200
+    
+
+
+# @bp.route('/<hashid:corpus_id>/is_public', methods=['PUT'])
+# @corpus_owner_or_admin_required
+# @content_negotiation(consumes='application/json', produces='application/json')
+# def update_corpus_is_public(corpus_id):
+#     is_public = request.json
+#     if not isinstance(is_public, bool):
+#         abort(400)
+#     corpus = Corpus.query.get_or_404(corpus_id)
+#     corpus.is_public = is_public
+#     db.session.commit()
+#     response_data = {
+#         'message': (
+#             f'Corpus "{corpus.title}" is now'
+#             f' {"public" if is_public else "private"}'
+#         ),
+#         'category': 'corpus'
+#     }
+#     return response_data, 200

app/corpora/routes.py

@@ -0,0 +1,121 @@
+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 (
+    Corpus,
+    CorpusFollowerAssociation,
+    CorpusFollowerRole,
+    User
+)
+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():
+        try:
+            corpus = Corpus.create(
+                title=form.title.data,
+                description=form.description.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        db.session.commit()
+        flash(f'Corpus "{corpus.title}" created', 'corpus')
+        return redirect(corpus.url)
+    return render_template(
+        'corpora/create.html.j2',
+        title='Create corpus',
+        form=form
+    )
+
+
+@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()
+    # TODO: Better solution for filtering admin
+    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():
+            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():
+        return render_template(
+            'corpora/corpus.html.j2',
+            title=corpus.title,
+            corpus=corpus,
+            cfr=cfr,
+            cfrs=cfrs,
+            users = users
+        )
+    if (current_user.is_following_corpus(corpus) or corpus.is_public):
+        abort(404)
+        # cfas = CorpusFollowerAssociation.query.filter(Corpus.id == corpus_id, CorpusFollowerAssociation.follower_id != corpus.user.id).all()
+        # return render_template(
+        #     'corpora/public_corpus.html.j2',
+        #     title=corpus.title,
+        #     corpus=corpus,
+        #     cfrs=cfrs,
+        #     cfr=cfr,
+        #     cfas=cfas,
+        #     users = users
+        # )
+    abort(403)
+
+
+
+@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(
+        'corpora/analysis.html.j2',
+        corpus=corpus,
+        title=f'Analyse Corpus {corpus.title}'
+    )
+
+
+# @bp.route('/<hashid:corpus_id>/follow/<token>')
+# def follow_corpus(corpus_id, token):
+#     corpus = Corpus.query.get_or_404(corpus_id)
+#     if current_user.follow_corpus_by_token(token):
+#         db.session.commit()
+#         flash(f'You are following "{corpus.title}" now', category='corpus')
+#         return redirect(url_for('corpora.corpus', corpus_id=corpus_id))
+#     abort(403)
+
+
+@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

@@ -0,0 +1,225 @@
+from app import docker_client
+from app.models import Corpus, CorpusStatus
+from flask import current_app
+import docker
+import os
+import shutil
+
+
+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)
+    for corpus in [x for x in corpora if x.status in [CorpusStatus.QUEUED, CorpusStatus.BUILDING]]:
+        _checkout_build_corpus_service(corpus)
+    for corpus in [x for x in corpora if x.status == CorpusStatus.BUILT and x.num_analysis_sessions > 0]:
+        corpus.status = CorpusStatus.STARTING_ANALYSIS_SESSION
+    for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION and x.num_analysis_sessions == 0]:
+        corpus.status = CorpusStatus.CANCELING_ANALYSIS_SESSION
+    for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION]:
+        _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)
+
+def _create_build_corpus_service(corpus):
+    ''' # Docker service settings # '''
+    ''' ## Command ## '''
+    command = ['bash', '-c']
+    command.append(
+        f'mkdir /corpora/data/nopaque-{corpus.hashid.lower()}'
+        ' && '
+        'cwb-encode'
+        ' -c utf8'
+        f' -d /corpora/data/nopaque-{corpus.hashid.lower()}'
+        ' -f /root/files/corpus.vrt'
+        f' -R /usr/local/share/cwb/registry/nopaque-{corpus.hashid.lower()}'
+        ' -P pos -P lemma -P simple_pos'
+        ' -S ent:0+type -S s:0'
+        ' -S text:0+address+author+booktitle+chapter+editor+institution+journal+pages+publisher+publishing_year+school+title'
+        ' -xsB -9'
+        ' && '
+        f'cwb-make -V NOPAQUE-{corpus.hashid.upper()}'
+    )
+    ''' ## Constraints ## '''
+    constraints = ['node.role==worker']
+    ''' ## Image ## '''
+    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1702'
+    ''' ## Labels ## '''
+    labels = {
+        'origin': current_app.config['SERVER_NAME'],
+        'type': 'corpus.build',
+        'corpus_id': str(corpus.id)
+    }
+    ''' ## Mounts ## '''
+    mounts = []
+    ''' ### Data mount ### '''
+    data_mount_source = os.path.join(corpus.path, 'cwb', 'data')
+    data_mount_target = '/corpora/data'
+    data_mount = f'{data_mount_source}:{data_mount_target}:rw'
+    # Make sure that their is no data in the data directory
+    shutil.rmtree(data_mount_source, ignore_errors=True)
+    os.makedirs(data_mount_source)
+    mounts.append(data_mount)
+    ''' ### File mount ### '''
+    file_mount_source = os.path.join(corpus.path, 'cwb', 'corpus.vrt')
+    file_mount_target = '/root/files/corpus.vrt'
+    file_mount = f'{file_mount_source}:{file_mount_target}:ro'
+    mounts.append(file_mount)
+    ''' ### Registry mount ### '''
+    registry_mount_source = os.path.join(corpus.path, 'cwb', 'registry')
+    registry_mount_target = '/usr/local/share/cwb/registry'
+    registry_mount = f'{registry_mount_source}:{registry_mount_target}:rw'
+    # Make sure that their is no data in the registry directory
+    shutil.rmtree(registry_mount_source, ignore_errors=True)
+    os.makedirs(registry_mount_source)
+    mounts.append(registry_mount)
+    ''' ## Name ## '''
+    name = f'build-corpus_{corpus.id}'
+    ''' ## Restart policy ## '''
+    restart_policy = docker.types.RestartPolicy()
+    try:
+        docker_client.services.create(
+            image,
+            command=command,
+            constraints=constraints,
+            labels=labels,
+            mounts=mounts,
+            name=name,
+            restart_policy=restart_policy,
+            user='0:0'
+        )
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Create service "{name}" failed: {e}')
+        return
+    corpus.status = CorpusStatus.QUEUED
+
+def _checkout_build_corpus_service(corpus):
+    service_name = f'build-corpus_{corpus.id}'
+    try:
+        service = docker_client.services.get(service_name)
+    except docker.errors.NotFound as e:
+        current_app.logger.error(f'Get service "{service_name}" failed: {e}')
+        corpus.status = CorpusStatus.FAILED
+        return
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get service "{service_name}" failed: {e}')
+    service_tasks = service.tasks()
+    if not service_tasks:
+        return
+    task_state = service_tasks[0].get('Status').get('State')
+    if corpus.status == CorpusStatus.QUEUED and task_state != 'pending':
+        corpus.status = CorpusStatus.BUILDING
+        return
+    elif corpus.status == CorpusStatus.BUILDING and task_state == 'complete':
+        corpus.status = CorpusStatus.BUILT
+    elif corpus.status == CorpusStatus.BUILDING and task_state == 'failed':
+        corpus.status = CorpusStatus.FAILED
+    else:
+        return
+    try:
+        service.remove()
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
+
+def _create_cqpserver_container(corpus):
+    ''' # Docker container settings # '''
+    ''' ## Command ## '''
+    command = []
+    command.append(
+        'echo "host *;" > cqpserver.init'
+        ' && '
+        'echo "user anonymous \\"\\";" >> cqpserver.init'
+        ' && '
+        'cqpserver -I cqpserver.init'
+    )
+    ''' ## Detach ## '''
+    detach = True
+    ''' ## Entrypoint ## '''
+    entrypoint = ['bash', '-c']
+    ''' ## Image ## '''
+    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1702'
+    ''' ## Name ## '''
+    name = f'cqpserver_{corpus.id}'
+    ''' ## Network ## '''
+    network = f'{current_app.config["DOCKER_NETWORK_NAME"]}'
+    ''' ## Volumes ## '''
+    volumes = []
+    ''' ### Corpus data volume ### '''
+    data_volume_source = os.path.join(corpus.path, 'cwb', 'data')
+    data_volume_target = '/corpora/data'
+    # data_volume_source = os.path.join(corpus.path, 'cwb', 'data', f'nopaque_{corpus.id}')
+    # data_volume_target = f'/corpora/data/nopaque_{corpus.hashid.lower()}'
+    data_volume = f'{data_volume_source}:{data_volume_target}:rw'
+    volumes.append(data_volume)
+    ''' ### Corpus registry volume ### '''
+    registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry')
+    registry_volume_target = '/usr/local/share/cwb/registry'
+    # registry_volume_source = os.path.join(corpus.path, 'cwb', 'registry', f'nopaque_{corpus.id}')
+    # registry_volume_target = f'/usr/local/share/cwb/registry/nopaque_{corpus.hashid.lower()}'
+    registry_volume = f'{registry_volume_source}:{registry_volume_target}:rw'
+    volumes.append(registry_volume)
+    # Check if a cqpserver container already exists. If this is the case,
+    # remove it and create a new one
+    try:
+        container = docker_client.containers.get(name)
+    except docker.errors.NotFound:
+        pass
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get container "{name}" failed: {e}')
+        return
+    else:
+        try:
+            container.remove(force=True)
+        except docker.errors.DockerException as e:
+            current_app.logger.error(f'Remove container "{name}" failed: {e}')
+            return
+    try:
+        docker_client.containers.run(
+            image,
+            command=command,
+            detach=detach,
+            entrypoint=entrypoint,
+            name=name,
+            network=network,
+            user='0:0',
+            volumes=volumes
+        )
+    except docker.errors.ImageNotFound as e:
+        current_app.logger.error(
+            f'Run container "{name}" failed '
+            f'due to "docker.errors.ImageNotFound" error: {e}'
+        )
+        corpus.status = CorpusStatus.FAILED
+        return
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Run container "{name}" failed: {e}')
+        return
+    corpus.status = CorpusStatus.RUNNING_ANALYSIS_SESSION
+
+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:
+        current_app.logger.error(f'Get container "{container_name}" failed: {e}')
+        corpus.num_analysis_sessions = 0
+        corpus.status = CorpusStatus.BUILT
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get container "{container_name}" failed: {e}')
+
+def _remove_cqpserver_container(corpus):
+    container_name = f'cqpserver_{corpus.id}'
+    try:
+        container = docker_client.containers.get(container_name)
+    except docker.errors.NotFound:
+        corpus.status = CorpusStatus.BUILT
+        return
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get container "{container_name}" failed: {e}')
+        return
+    try:
+        container.remove(force=True)
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Remove container "{container_name}" failed: {e}')

app/daemon/job_utils.py

@@ -0,0 +1,234 @@
+from app import db, docker_client, hashids
+from app.models import (
+    Job,
+    JobResult,
+    JobStatus,
+    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 check_jobs():
+    jobs = Job.query.all()
+    for job in [x for x in jobs if x.status == JobStatus.SUBMITTED]:
+        _create_job_service(job)
+    for job in [x for x in jobs if x.status in [JobStatus.QUEUED, JobStatus.RUNNING]]:
+        _checkout_job_service(job)
+    for job in [x for x in jobs if x.status == JobStatus.CANCELING]:
+        _remove_job_service(job)
+
+def _create_job_service(job):
+    ''' # Docker service settings # '''
+    ''' ## Service specific settings ## '''
+    if job.service == 'file-setup-pipeline':
+        mem_mb = 512
+        n_cores = 2
+        executable = 'file-setup-pipeline'
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}file-setup-pipeline:v{job.service_version}'
+    elif job.service == 'tesseract-ocr-pipeline':
+        mem_mb = 1024
+        n_cores = 4
+        executable = 'tesseract-ocr-pipeline'
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}tesseract-ocr-pipeline:v{job.service_version}'
+    elif job.service == 'transkribus-htr-pipeline':
+        mem_mb = 1024
+        n_cores = 4
+        executable = 'transkribus-htr-pipeline'
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}transkribus-htr-pipeline:v{job.service_version}'
+    elif job.service == 'spacy-nlp-pipeline':
+        mem_mb = 1024
+        n_cores = 1
+        executable = 'spacy-nlp-pipeline'
+        image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}spacy-nlp-pipeline:v{job.service_version}'
+    ''' ## Command ## '''
+    command = f'{executable} -i /input -o /output'
+    command += ' --log-dir /logs'
+    command += f' --mem-mb {mem_mb}'
+    command += f' --n-cores {n_cores}'
+    if job.service == 'spacy-nlp-pipeline':
+        model_id = hashids.decode(job.service_args['model'])
+        model = SpaCyNLPPipelineModel.query.get(model_id)
+        if model is None:
+            job.status = JobStatus.FAILED
+            return
+        command += f' -m {model.pipeline_name}'
+        if 'encoding_detection' in job.service_args and job.service_args['encoding_detection']:
+            command += ' --check-encoding'
+    elif job.service == 'tesseract-ocr-pipeline':
+        command += f' -m {job.service_args["model"]}'
+        if 'binarization' in job.service_args and job.service_args['binarization']:
+            command += ' --binarize'
+        if 'ocropus_nlbin_threshold' in job.service_args and job.service_args['ocropus_nlbin_threshold']:
+            value = job.service_args['ocropus_nlbin_threshold']
+            command += f' --ocropus-nlbin-threshold {value}'
+    elif job.service == 'transkribus-htr-pipeline':
+        transkribus_htr_pipeline_model_id = job.service_args['model']
+        command += f' -m {transkribus_htr_pipeline_model_id}'
+        readcoop_username = current_app.config.get('NOPAQUE_READCOOP_USERNAME')
+        command += f' --readcoop-username "{readcoop_username}"'
+        readcoop_password = current_app.config.get('NOPAQUE_READCOOP_PASSWORD')
+        command += f' --readcoop-password "{readcoop_password}"'
+        if 'binarization' in job.service_args and job.service_args['binarization']:
+            command += ' --binarize'
+    ''' ## Constraints ## '''
+    constraints = ['node.role==worker']
+    ''' ## Labels ## '''
+    labels = {
+        'origin': current_app.config['SERVER_NAME'],
+        'type': 'job',
+        'job_id': str(job.id)
+    }
+    ''' ## Mounts ## '''
+    mounts = []
+    ''' ### Input mount(s) ### '''
+    input_mount_target_base = '/input'
+    if job.service == 'file-setup-pipeline':
+        input_mount_target_base += f'/{secure_filename(job.title)}'
+    for job_input in job.inputs:
+        input_mount_source = job_input.path
+        input_mount_target = f'{input_mount_target_base}/{job_input.filename}'
+        input_mount = f'{input_mount_source}:{input_mount_target}:ro'
+        mounts.append(input_mount)
+    if job.service == 'tesseract-ocr-pipeline':
+        if isinstance(job.service_args['model'], str):
+            model_id = hashids.decode(job.service_args['model'])
+        elif isinstance(job.service_args['model'], int):
+            model_id = job.service_args['model']
+        else:
+            job.status = JobStatus.FAILED
+            return
+        model = TesseractOCRPipelineModel.query.get(model_id)
+        if model is None:
+            job.status = JobStatus.FAILED
+            return
+        models_mount_source = model.path
+        models_mount_target = f'/usr/local/share/tessdata/{model.id}.traineddata'
+        models_mount = f'{models_mount_source}:{models_mount_target}:ro'
+        mounts.append(models_mount)
+    elif job.service == 'spacy-nlp-pipeline':
+        model_id = hashids.decode(job.service_args['model'])
+        model = SpaCyNLPPipelineModel.query.get(model_id)
+        if model is None:
+            job.status = JobStatus.FAILED
+            return
+        models_mount_source = model.path
+        models_mount_target = f'/usr/local/share/spacy/models/{model.filename}'
+        models_mount = f'{models_mount_source}:{models_mount_target}:ro'
+        mounts.append(models_mount)
+    ''' ### Output mount ### '''
+    output_mount_source = os.path.join(job.path, 'results')
+    output_mount_target = '/output'
+    output_mount = f'{output_mount_source}:{output_mount_target}:rw'
+    # Make sure that their is no data in the output directory
+    shutil.rmtree(output_mount_source, ignore_errors=True)
+    os.makedirs(output_mount_source)
+    mounts.append(output_mount)
+    ''' ### Pipeline data mount ### '''
+    pyflow_data_mount_source = os.path.join(job.path, 'pipeline_data')
+    pyflow_data_mount_target = '/logs/pyflow.data'
+    pyflow_data_mount = f'{pyflow_data_mount_source}:{pyflow_data_mount_target}:rw'
+    # Make sure that their is no data in the output directory
+    shutil.rmtree(pyflow_data_mount_source, ignore_errors=True)
+    os.makedirs(pyflow_data_mount_source)
+    mounts.append(pyflow_data_mount)
+    ''' ## Name ## '''
+    name = f'job_{job.id}'
+    ''' ## Resources ## '''
+    resources = docker.types.Resources(
+        cpu_reservation=n_cores * (10 ** 9),
+        mem_reservation=mem_mb * (10 ** 6)
+    )
+    ''' ## Restart policy ## '''
+    restart_policy = docker.types.RestartPolicy()
+    try:
+        docker_client.services.create(
+            image,
+            command=command,
+            constraints=constraints,
+            labels=labels,
+            mounts=mounts,
+            name=name,
+            resources=resources,
+            restart_policy=restart_policy,
+            user='0:0'
+        )
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Create service "{name}" failed: {e}')
+        return
+    job.status = JobStatus.QUEUED
+
+def _checkout_job_service(job):
+    service_name = f'job_{job.id}'
+    try:
+        service = docker_client.services.get(service_name)
+    except docker.errors.NotFound as e:
+        current_app.logger.error(f'Get service "{service_name}" failed: {e}')
+        job.status = JobStatus.FAILED
+        return
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get service "{service_name}" failed: {e}')
+        return
+    service_tasks = service.tasks()
+    if not service_tasks:
+        return
+    task_state = service_tasks[0].get('Status').get('State')
+    if job.status == JobStatus.QUEUED and task_state != 'pending':
+        job.status = JobStatus.RUNNING
+        return
+    elif job.status == JobStatus.RUNNING and task_state == 'complete':
+        job.status = JobStatus.COMPLETED
+        results_dir = os.path.join(job.path, 'results')
+        with open(os.path.join(results_dir, 'outputs.json')) as f:
+            outputs = json.load(f)
+        for output in outputs:
+            filename = os.path.basename(output['file'])
+            job_result = JobResult(
+                filename=filename,
+                job=job,
+                mimetype=output['mimetype']
+            )
+            if 'description' in output:
+                job_result.description = output['description']
+            db.session.add(job_result)
+            db.session.flush(objects=[job_result])
+            db.session.refresh(job_result)
+            os.rename(
+                os.path.join(results_dir, output['file']),
+                job_result.path
+            )
+    elif job.status == JobStatus.RUNNING and task_state == 'failed':
+        job.status = JobStatus.FAILED
+    else:
+        return
+    job.end_date = datetime.utcnow()
+    try:
+        service.remove()
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
+
+def _remove_job_service(job):
+    service_name = f'job_{job.id}'
+    try:
+        service = docker_client.services.get(service_name)
+    except docker.errors.NotFound:
+        job.status = JobStatus.CANCELED
+        return
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Get service "{service_name}" failed: {e}')
+        return
+    try:
+        service.update(mounts=None)
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Update service "{service_name}" failed: {e}')
+        return
+    try:
+        service.remove()
+    except docker.errors.DockerException as e:
+        current_app.logger.error(f'Remove "{service_name}" service failed: {e}')

app/decorators.py

@@ -0,0 +1,99 @@
+from flask import abort, current_app, request
+from flask_login import current_user
+from functools import wraps
+from threading import Thread
+from typing import List, Union
+from werkzeug.exceptions import NotAcceptable
+from app.models import Permission
+
+
+def permission_required(permission):
+    def decorator(f):
+        @wraps(f)
+        def decorated_function(*args, **kwargs):
+            if not current_user.can(permission):
+                abort(403)
+            return f(*args, **kwargs)
+        return decorated_function
+    return decorator
+
+
+def admin_required(f):
+    return permission_required(Permission.ADMINISTRATE)(f)
+
+
+def socketio_login_required(f):
+    @wraps(f)
+    def decorated_function(*args, **kwargs):
+        if current_user.is_authenticated:
+            return f(*args, **kwargs)
+        else:
+            return {'code': 401, 'msg': 'Unauthorized'}
+    return decorated_function
+
+
+def socketio_permission_required(permission):
+    def decorator(f):
+        @wraps(f)
+        def decorated_function(*args, **kwargs):
+            if not current_user.can(permission):
+                return {'code': 403, 'msg': 'Forbidden'}
+            return f(*args, **kwargs)
+        return decorated_function
+    return decorator
+
+
+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: Union[str, List[str], None] = None,
+    consumes: Union[str, List[str], None] = None
+):
+    def decorator(f):
+        @wraps(f)
+        def decorated_function(*args, **kwargs):
+            provided = request.mimetype
+            if consumes is None:
+                consumeables = None
+            elif isinstance(consumes, str):
+                consumeables = {consumes}
+            elif isinstance(consumes, list) and all(isinstance(x, str) for x in consumes):
+                consumeables = {*consumes}
+            else:
+                raise TypeError()
+            accepted = {*request.accept_mimetypes.values()}
+            if produces is None:
+                produceables = None
+            elif isinstance(produces, str):
+                produceables = {produces}
+            elif isinstance(produces, list) and all(isinstance(x, str) for x in produces):
+                produceables = {*produces}
+            else:
+                raise TypeError()
+            if produceables is not None and len(produceables & accepted) == 0:
+                raise NotAcceptable()
+            if consumeables is not None and provided not in consumeables:
+                raise NotAcceptable()
+            return f(*args, **kwargs)
+        return decorated_function
+    return decorator

app/email.py

@@ -0,0 +1,25 @@
+from flask import current_app, render_template
+from flask_mail import Message
+from threading import Thread
+from app import mail
+
+
+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'{subject_prefix} {subject}'
+    )
+    return msg
+
+
+def send(msg, *args, **kwargs):
+    def _send(app, msg):
+        with app.app_context():
+            mail.send(msg)
+
+    thread = Thread(target=_send, args=[current_app._get_current_object(), msg])
+    thread.start()
+    return thread

app/errors/__init__.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+
+
+bp = Blueprint('errors', __name__)
+from . import handlers

app/errors/handlers.py

@@ -0,0 +1,14 @@
+from flask import jsonify, render_template, request
+from werkzeug.exceptions import HTTPException
+from . import bp
+
+
+@bp.app_errorhandler(HTTPException)
+def handle_http_exception(error):
+    ''' Generic HTTP exception handler '''
+    accept_json = request.accept_mimetypes.accept_json
+    accept_html = request.accept_mimetypes.accept_html
+    if accept_json and not accept_html:
+        response = jsonify(str(error))
+        return response, error.code
+    return render_template('errors/error.html.j2', error=error), error.code

app/jobs/__init__.py

@@ -0,0 +1,18 @@
+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

@@ -0,0 +1,73 @@
+from flask import abort, current_app
+from flask_login import current_user
+from threading import Thread
+import os
+from app import db
+from app.decorators import admin_required, content_negotiation
+from app.models import Job, JobStatus
+from . import bp
+
+
+@bp.route('/<hashid:job_id>', methods=['DELETE'])
+@content_negotiation(produces='application/json')
+def delete_job(job_id):
+    def _delete_job(app, job_id):
+        with app.app_context():
+            job = Job.query.get(job_id)
+            job.delete()
+            db.session.commit()
+
+    job = Job.query.get_or_404(job_id)
+    if not (job.user == current_user or current_user.is_administrator()):
+        abort(403)
+    thread = Thread(
+        target=_delete_job,
+        args=(current_app._get_current_object(), job_id)
+    )
+    thread.start()
+    response_data = {
+        'message': f'Job "{job.title}" marked for deletion'
+    }
+    return response_data, 202
+
+
+@bp.route('/<hashid:job_id>/log')
+@admin_required
+@content_negotiation(produces='application/json')
+def job_log(job_id):
+    job = Job.query.get_or_404(job_id)
+    if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
+        response = {'errors': {'message': 'Job status is not completed or failed'}}
+        return response, 409
+    with open(os.path.join(job.path, 'pipeline_data', 'logs', 'pyflow_log.txt')) as log_file:
+        log = log_file.read()
+    response_data = {
+        'jobLog': log
+    }
+    return response_data, 200
+
+
+@bp.route('/<hashid:job_id>/restart', methods=['POST'])
+@content_negotiation(produces='application/json')
+def restart_job(job_id):
+    def _restart_job(app, job_id):
+        with app.app_context():
+            job = Job.query.get(job_id)
+            job.restart()
+            db.session.commit()
+
+    job = Job.query.get_or_404(job_id)
+    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"'}}
+        return response, 409
+    thread = Thread(
+        target=_restart_job,
+        args=(current_app._get_current_object(), job_id)
+    )
+    thread.start()
+    response_data = {
+        'message': f'Job "{job.title}" marked for restarting'
+    }
+    return response_data, 202

app/jobs/routes.py

@@ -0,0 +1,60 @@
+from flask import (
+    abort,
+    redirect,
+    render_template,
+    send_from_directory,
+    url_for
+)
+from flask_breadcrumbs import register_breadcrumb
+from flask_login import current_user
+import os
+from app.models import Job, JobInput, JobResult
+from . import bp
+from .utils import job_dynamic_list_constructor as job_dlc
+
+
+@bp.route('')
+@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()):
+        abort(403)
+    return render_template(
+        'jobs/job.html.j2',
+        title='Job',
+        job=job
+    )
+
+
+@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()):
+        abort(403)
+    return send_from_directory(
+        os.path.dirname(job_input.path),
+        os.path.basename(job_input.path),
+        as_attachment=True,
+        attachment_filename=job_input.filename,
+        mimetype=job_input.mimetype
+    )
+
+
+@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()):
+        abort(403)
+    return send_from_directory(
+        os.path.dirname(job_result.path),
+        os.path.basename(job_result.path),
+        as_attachment=True,
+        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/__init__.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+
+
+bp = Blueprint('main', __name__, cli_group=None)
+from . import cli, routes

app/main/cli.py

@@ -0,0 +1,45 @@
+from flask import current_app
+from flask_migrate import upgrade
+import os
+from app.models import (
+    CorpusFollowerRole,
+    Role,
+    SpaCyNLPPipelineModel,
+    TesseractOCRPipelineModel,
+    User
+)
+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 = [
+        os.path.join(base_dir, 'tmp'),
+        os.path.join(base_dir, 'users')
+    ]
+    for dir in default_dirs:
+        if os.path.exists(dir):
+            if not os.path.isdir(dir):
+                raise NotADirectoryError(f'{dir} is not a directory')
+        else:
+            os.mkdir(dir)
+
+    # 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')
+    User.insert_defaults()
+    print('Insert/Update default CorpusFollowerRoles')
+    CorpusFollowerRole.insert_defaults()
+    print('Insert/Update default SpaCyNLPPipelineModels')
+    SpaCyNLPPipelineModel.insert_defaults()
+    print('Insert/Update default TesseractOCRPipelineModels')
+    TesseractOCRPipelineModel.insert_defaults()

app/main/routes.py

@@ -0,0 +1,92 @@
+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.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():
+        user = User.query.filter((User.email == form.user.data.lower()) | (User.username == form.user.data)).first()
+        if user and user.verify_password(form.password.data):
+            login_user(user, form.remember_me.data)
+            flash('You have been logged in')
+            return redirect(url_for('.dashboard'))
+        flash('Invalid email/username or password', category='error')
+        redirect(url_for('.index'))
+    return render_template(
+        'main/index.html.j2',
+        title='nopaque',
+        form=form
+    )
+
+
+@bp.route('/faq')
+@register_breadcrumb(bp, '.faq', 'Frequently Asked Questions')
+def faq():
+    return render_template(
+        'main/faq.html.j2',
+        title='Frequently Asked Questions'
+    )
+
+
+@bp.route('/dashboard')
+@register_breadcrumb(bp, '.dashboard', '<i class="material-icons left">dashboard</i>Dashboard')
+@login_required
+def dashboard():
+    return render_template(
+        'main/dashboard.html.j2',
+        title='Dashboard'
+    )
+
+
+# @bp.route('/user_manual')
+# @register_breadcrumb(bp, '.user_manual', '<i class="material-icons left">help</i>User manual')
+# def user_manual():
+#     return render_template('main/user_manual.html.j2', title='User 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',
+        title='News'
+    )
+
+
+@bp.route('/privacy_policy')
+@register_breadcrumb(bp, '.privacy_policy', 'Private statement (GDPR)')
+def privacy_policy():
+    return render_template(
+        'main/privacy_policy.html.j2',
+        title='Privacy statement (GDPR)'
+    )
+
+
+@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',
+        title='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():
+#     corpora = Corpus.query.filter(Corpus.is_public == True, Corpus.user != current_user).all()
+#     users = User.query.filter(User.is_public == True, User.id != current_user.id).all()
+#     return render_template(
+#         'main/social_area.html.j2',
+#         title='Social Area',
+#         corpora=corpora,
+#         users=users
+#     )

app/services/__init__.py

@@ -0,0 +1,25 @@
+from flask import Blueprint
+from flask_login import login_required
+import os
+import yaml
+
+
+services_file = \
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), 'services.yml')
+with open(services_file, 'r') as f:
+    SERVICES = yaml.safe_load(f)
+
+bp = Blueprint('services', __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  # noqa

app/services/forms.py

@@ -0,0 +1,192 @@
+from flask_wtf import FlaskForm
+from flask_login import current_user
+from flask_wtf.file import FileField, FileRequired
+from wtforms import (
+    BooleanField,
+    DecimalRangeField,
+    MultipleFileField,
+    SelectField,
+    StringField,
+    SubmitField,
+    ValidationError
+)
+from wtforms.validators import InputRequired, Length
+from app.models import SpaCyNLPPipelineModel, TesseractOCRPipelineModel
+from . import SERVICES
+
+
+class CreateJobBaseForm(FlaskForm):
+    description = StringField(
+        'Description',
+        validators=[InputRequired(), Length(max=255)]
+    )
+    title = StringField(
+        'Title',
+        validators=[InputRequired(), Length(max=32)]
+    )
+    version = SelectField('Version', validators=[InputRequired()])
+    submit = SubmitField()
+
+
+class CreateFileSetupPipelineJobForm(CreateJobBaseForm):
+    images = MultipleFileField('File(s)', validators=[InputRequired()])
+
+    def validate_images(form, field):
+        valid_mimetypes = ['image/jpeg', 'image/png', 'image/tiff']
+        for image in field.data:
+            if image.mimetype not in valid_mimetypes:
+                raise ValidationError('JPEG, PNG and TIFF files only!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-file-setup-pipeline-job-form'
+        service_manifest = SERVICES['file-setup-pipeline']
+        version = kwargs.pop('version', service_manifest['latest_version'])
+        super().__init__(*args, **kwargs)
+        self.version.choices = [(x, x) for x in service_manifest['versions']]
+        self.version.data = version
+        self.version.default = service_manifest['latest_version']
+
+
+class CreateTesseractOCRPipelineJobForm(CreateJobBaseForm):
+    binarization = BooleanField('Binarization')
+    pdf = FileField('File', validators=[FileRequired()])
+    model = SelectField('Model', validators=[InputRequired()])
+    ocropus_nlbin_threshold = DecimalRangeField(
+        render_kw={'min': 0, 'max': 1, 'step': 0.1, 'start': [0.5], 'disabled': True}
+    )
+
+    def validate_binarization(self, field):
+        service_info = SERVICES['tesseract-ocr-pipeline']['versions'][self.version.data]
+        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!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-tesseract-ocr-pipeline-job-form'
+        service_manifest = SERVICES['tesseract-ocr-pipeline']
+        version = kwargs.pop('version', service_manifest['latest_version'])
+        super().__init__(*args, **kwargs)
+        service_info = service_manifest['versions'][version]
+        if self.binarization.render_kw is None:
+            self.binarization.render_kw = {}
+        self.binarization.render_kw['disabled'] = True
+        if self.ocropus_nlbin_threshold.render_kw is None:
+            self.ocropus_nlbin_threshold.render_kw = {}
+        self.ocropus_nlbin_threshold.render_kw['disabled'] = True
+        if 'methods' in service_info:
+            if 'binarization' in service_info['methods']:
+                del self.binarization.render_kw['disabled']
+                if 'ocropus_nlbin_threshold' in service_info['methods']:
+                    del self.ocropus_nlbin_threshold.render_kw['disabled']
+        user_models = [
+            x for x in current_user.tesseract_ocr_pipeline_models.order_by(TesseractOCRPipelineModel.title).all()
+        ]
+        models = [
+            x for x in TesseractOCRPipelineModel.query.order_by(TesseractOCRPipelineModel.title).all()
+            if version in x.compatible_service_versions and (x.is_public == True or x.user == current_user)
+        ]
+        self.model.choices = {
+            '': [('', 'Choose your option')],
+            'Your models': [(x.hashid, f'{x.title} [{x.version}]') for x in user_models] if user_models else [(0, 'Nothing here yet...')],
+            'Public models': [(x.hashid, f'{x.title} [{x.version}]') for x in models]
+        }
+        self.model.default = ''
+        self.version.choices = [(x, x) for x in service_manifest['versions']]
+        self.version.data = version
+        self.version.default = service_manifest['latest_version']
+
+
+class CreateTranskribusHTRPipelineJobForm(CreateJobBaseForm):
+    binarization = BooleanField('Binarization')
+    pdf = FileField('File', validators=[FileRequired()])
+    model = SelectField('Model', validators=[InputRequired()])
+
+    def validate_binarization(self, field):
+        service_info = SERVICES['transkribus-htr-pipeline']['versions'][self.version.data]
+        if field.data:
+            if(
+                'methods' not in service_info
+                or 'binarization' not 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!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-transkribus-htr-pipeline-job-form'
+        transkribus_htr_pipeline_models = kwargs.pop('transkribus_htr_pipeline_models', [])
+        service_manifest = SERVICES['transkribus-htr-pipeline']
+        version = kwargs.pop('version', service_manifest['latest_version'])
+        super().__init__(*args, **kwargs)
+        service_info = service_manifest['versions'][version]
+        if self.binarization.render_kw is None:
+            self.binarization.render_kw = {}
+        self.binarization.render_kw['disabled'] = True
+        if 'methods' in service_info:
+            if 'binarization' in service_info['methods']:
+                del self.binarization.render_kw['disabled']
+        self.model.choices = [('', 'Choose your option')]
+        self.model.choices += [(x['modelId'], x['name']) for x in transkribus_htr_pipeline_models]
+        self.model.default = ''
+        self.version.choices = [(x, x) for x in service_manifest['versions']]
+        self.version.data = version
+        self.version.default = service_manifest['latest_version']
+
+
+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:
+            if(
+                'methods' not in service_info
+                or 'encoding_detection' not in service_info['methods']
+            ):
+                raise ValidationError('Encoding detection is not available')
+
+    def validate_txt(form, field):
+        if field.data.mimetype != 'text/plain':
+            raise ValidationError('Plain text files only!')
+
+    def __init__(self, *args, **kwargs):
+        if 'prefix' not in kwargs:
+            kwargs['prefix'] = 'create-spacy-nlp-pipeline-job-form'
+        service_manifest = SERVICES['spacy-nlp-pipeline']
+        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
+        if 'methods' in service_info:
+            if 'encoding_detection' in service_info['methods']:
+                del self.encoding_detection.render_kw['disabled']
+        user_models = [
+            x for x in current_user.spacy_nlp_pipeline_models.order_by(SpaCyNLPPipelineModel.title).all()
+        ]
+        models = [
+            x for x in SpaCyNLPPipelineModel.query.filter(SpaCyNLPPipelineModel.user != current_user, SpaCyNLPPipelineModel.is_public == True).order_by(SpaCyNLPPipelineModel.title).all()
+            if version in x.compatible_service_versions
+        ]
+        self.model.choices = {
+            '': [('', 'Choose your option')],
+            'Your models': [(x.hashid, f'{x.title} [{x.version}]') for x in user_models] if user_models else [(0, 'Nothing here yet...')],
+            'Public models': [(x.hashid, f'{x.title} [{x.version}]') for x in models]
+        }
+        self.model.default = ''
+        self.version.choices = [(x, x) for x in service_manifest['versions']]
+        self.version.data = version
+        self.version.default = version

app/services/routes.py

@@ -0,0 +1,231 @@
+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,
+    JobStatus,
+    TesseractOCRPipelineModel,
+    SpaCyNLPPipelineModel
+)
+from . import bp, SERVICES
+from .forms import (
+    CreateFileSetupPipelineJobForm,
+    CreateTesseractOCRPipelineJobForm,
+    CreateTranskribusHTRPipelineJobForm,
+    CreateSpacyNLPPipelineJobForm
+)
+
+
+@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]
+    version = request.args.get('version', service_manifest['latest_version'])
+    if version not in service_manifest['versions']:
+        abort(404)
+    form = CreateFileSetupPipelineJobForm(prefix='create-job-form', version=version)
+    if form.is_submitted():
+        if not form.validate():
+            response = {'errors': form.errors}
+            return response, 400
+        try:
+            job = Job.create(
+                title=form.title.data,
+                description=form.description.data,
+                service=service,
+                service_args={},
+                service_version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        for input_file in form.images.data:
+            try:
+                JobInput.create(input_file, job=job)
+            except (AttributeError, OSError):
+                abort(500)
+        job.status = JobStatus.SUBMITTED
+        db.session.commit()
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
+        flash(message, 'job')
+        return {}, 201, {'Location': job.url}
+    return render_template(
+        'services/file_setup_pipeline.html.j2',
+        title=service_manifest['name'],
+        form=form
+    )
+
+
+@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)
+    form = CreateTesseractOCRPipelineJobForm(prefix='create-job-form', version=version)
+    if form.is_submitted():
+        if not form.validate():
+            response = {'errors': form.errors}
+            return response, 400
+        try:
+            job = Job.create(
+                title=form.title.data,
+                description=form.description.data,
+                service=service_name,
+                service_args={
+                    'binarization': form.binarization.data,
+                    'model': hashids.decode(form.model.data),
+                    'ocropus_nlbin_threshold': float(form.ocropus_nlbin_threshold.data)
+                },
+                service_version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        try:
+            JobInput.create(form.pdf.data, job=job)
+        except (AttributeError, OSError):
+            abort(500)
+        job.status = JobStatus.SUBMITTED
+        db.session.commit()
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
+        flash(message, 'job')
+        return {}, 201, {'Location': job.url}
+    tesseract_ocr_pipeline_models = [
+        x for x in TesseractOCRPipelineModel.query.all()
+        if version in x.compatible_service_versions and (x.is_public == True or x.user == current_user)
+    ]
+    user_tesseract_ocr_pipeline_models_count = len(current_user.tesseract_ocr_pipeline_models.all())
+    return render_template(
+        'services/tesseract_ocr_pipeline.html.j2',
+        title=service_manifest['name'],
+        form=form,
+        tesseract_ocr_pipeline_models=tesseract_ocr_pipeline_models,
+        user_tesseract_ocr_pipeline_models_count=user_tesseract_ocr_pipeline_models_count
+    )
+
+
+@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)
+    service = 'transkribus-htr-pipeline'
+    service_manifest = SERVICES[service]
+    version = request.args.get('version', service_manifest['latest_version'])
+    if version not in service_manifest['versions']:
+        abort(404)
+    r = requests.get(
+        'https://transkribus.eu/TrpServer/rest/models/text',
+        headers={'Accept': 'application/json'}
+    )
+    if r.status_code != 200:
+        abort(500)
+    transkribus_htr_pipeline_models = r.json()['trpModelMetadata']
+    transkribus_htr_pipeline_models.append({'modelId': 48513, 'name': 'Caroline Minuscle', 'language': 'lat', 'isoLanguages': ['lat']})
+    form = CreateTranskribusHTRPipelineJobForm(
+        prefix='create-job-form',
+        transkribus_htr_pipeline_models=transkribus_htr_pipeline_models,
+        version=version
+    )
+    if form.is_submitted():
+        if not form.validate():
+            response = {'errors': form.errors}
+            return response, 400
+        try:
+            job = Job.create(
+                title=form.title.data,
+                description=form.description.data,
+                service=service,
+                service_args={
+                    'binarization': form.binarization.data,
+                    'model': form.model.data
+                },
+                service_version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        try:
+            JobInput.create(form.pdf.data, job=job)
+        except (AttributeError, OSError):
+            abort(500)
+        job.status = JobStatus.SUBMITTED
+        db.session.commit()
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
+        flash(message, 'job')
+        return {}, 201, {'Location': job.url}
+    return render_template(
+        'services/transkribus_htr_pipeline.html.j2',
+        title=service_manifest['name'],
+        form=form,
+        transkribus_htr_pipeline_models=transkribus_htr_pipeline_models
+    )
+
+
+@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]
+    version = request.args.get('version', SERVICES[service]['latest_version'])
+    if version not in service_manifest['versions']:
+        abort(404)
+    form = CreateSpacyNLPPipelineJobForm(prefix='create-job-form', version=version)
+    spacy_nlp_pipeline_models = SpaCyNLPPipelineModel.query.all()
+    user_spacy_nlp_pipeline_models_count = len(current_user.spacy_nlp_pipeline_models.all())
+    if form.is_submitted():
+        if not form.validate():
+            response = {'errors': form.errors}
+            return response, 400
+        try:
+            job = Job.create(
+                title=form.title.data,
+                description=form.description.data,
+                service=service,
+                service_args={
+                    'encoding_detection': form.encoding_detection.data,
+                    'model': form.model.data
+                },
+                service_version=form.version.data,
+                user=current_user
+            )
+        except OSError:
+            abort(500)
+        try:
+            JobInput.create(form.txt.data, job=job)
+        except (AttributeError, OSError):
+            abort(500)
+        job.status = JobStatus.SUBMITTED
+        db.session.commit()
+        message = Markup(f'Job "<a href="{job.url}">{job.title}</a>" created')
+        flash(message, 'job')
+        return {}, 201, {'Location': job.url}
+    return render_template(
+        'services/spacy_nlp_pipeline.html.j2',
+        title=service_manifest['name'],
+        form=form,
+        spacy_nlp_pipeline_models=spacy_nlp_pipeline_models,
+        user_spacy_nlp_pipeline_models_count=user_spacy_nlp_pipeline_models_count
+    )
+
+
+@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',
+        title='Corpus Analysis'
+    )

app/services/services.yml

@@ -0,0 +1,60 @@
+# TODO: This could also be done via GitLab/GitHub APIs
+file-setup-pipeline:
+  name: 'File Setup Pipeline'
+  publisher: 'Bielefeld University - CRC 1288 - INF'
+  latest_version: '0.1.0'
+  versions:
+    0.1.0:
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/file-setup-pipeline/-/releases/v0.1.0'
+tesseract-ocr-pipeline:
+  name: 'Tesseract OCR Pipeline'
+  publisher: 'Bielefeld University - CRC 1288 - INF'
+  latest_version: '0.1.1'
+  versions:
+    0.1.0:
+      methods:
+        - 'binarization'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/tesseract-ocr-pipeline/-/releases/v0.1.0'
+    0.1.1:
+      methods:
+        - 'binarization'
+        - 'ocropus_nlbin_threshold'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/tesseract-ocr-pipeline/-/releases/v0.1.1'
+transkribus-htr-pipeline:
+  name: 'Transkribus HTR Pipeline'
+  publisher: 'Bielefeld University - CRC 1288 - INF'
+  latest_version: '0.1.1'
+  versions:
+    0.1.0:
+      methods:
+        - 'binarization'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/transkribus-htr-pipeline/-/releases/v0.1.0'
+    0.1.1:
+      methods:
+        - 'binarization'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/transkribus-htr-pipeline/-/releases/v0.1.1'
+spacy-nlp-pipeline:
+  name: 'SpaCy NLP Pipeline'
+  publisher: 'Bielefeld University - CRC 1288 - INF'
+  latest_version: '0.1.2'
+  versions:
+    0.1.0:
+      methods:
+        - 'encoding_detection'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/spacy-nlp-pipeline/-/releases/v0.1.0'
+    0.1.1:
+      methods:
+        - 'encoding_detection'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/spacy-nlp-pipeline/-/releases/v0.1.1'
+    0.1.2:
+      methods:
+        - 'encoding_detection'
+      publishing_year: 2022
+      url: 'https://gitlab.ub.uni-bielefeld.de/sfb1288inf/spacy-nlp-pipeline/-/releases/v0.1.2'

app/settings/__init__.py

@@ -0,0 +1,18 @@
+from flask import Blueprint
+from flask_login import login_required
+
+
+bp = Blueprint('settings', __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

app/settings/routes.py

@@ -0,0 +1,12 @@
+from flask import g, url_for
+from flask_breadcrumbs import register_breadcrumb
+from flask_login import current_user
+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/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/materialize/fixes.css

@@ -0,0 +1,8 @@
+.parallax-container .parallax {
+  z-index: 0;
+}
+
+.autocomplete-content {
+  width: 100% !important;
+  left: 0 !important;
+}

app/static/css/materialize/sidenav_fixed.css

@@ -0,0 +1,12 @@
+/*
+ * The sidenav-fixed class is used which causes the sidenav to be fixed and open
+ * on large screens and hides to the regular functionality on smaller screens.
+ * In order to prevent the sidenav to overlap the content, the content (in our
+ * case header, main and footer) gets an offset equal to the width of the
+ * sidenav.
+ */
+@media only screen and (min-width : 993px) {
+  header, main, footer {padding-left: 300px;}
+  .modal:not(.bottom-sheet) {left: 300px;}
+  .navbar-fixed > nav {width: calc(100% - 300px)}
+}

app/static/css/materialize/sticky_footer.css

@@ -0,0 +1,18 @@
+/*
+ * Sticky Footer: https://materializecss.com/footer.html#sticky-footer
+ * A sticky footer always stays on the bottom of the page regardless of how
+ * little content is on the page. However, this footer will be pushed down if
+ * there is a lot of content, so it is different from a fixed footer.
+ *
+ * Note: This may cause issues in Internet Explorer which has weak support for
+ *       flexbox.
+ */
+body {
+  display: flex;
+  flex-direction: column;
+  min-height: 100vh;
+}
+
+main {
+  flex: 1 0 auto;
+}

app/static/css/nopaque_icons.css

@@ -0,0 +1,33 @@
+@font-face {
+  font-family: 'Nopaque Icons';
+  font-style: normal;
+  font-weight: 400;
+  src: local('nopaque Icons'),
+    local('NopaqueIcons-Regular'),
+    url(../fonts/nopaque_icons/NopaqueIcons-Regular.otf) format('opentype');
+}
+
+.nopaque-icons {
+  font-family: 'Nopaque Icons';
+  font-weight: normal;
+  font-style: normal;
+  font-size: 24px;  /* Preferred icon size */
+  display: inline-block;
+  line-height: 1;
+  text-transform: none;
+  letter-spacing: normal;
+  word-wrap: normal;
+  white-space: nowrap;
+  direction: ltr;
+
+  /* Support for all WebKit browsers. */
+  -webkit-font-smoothing: antialiased;
+  /* Support for Safari and Chrome. */
+  text-rendering: optimizeLegibility;
+
+  /* Support for Firefox. */
+  -moz-osx-font-smoothing: grayscale;
+
+  /* Support for IE. */
+  font-feature-settings: 'liga';
+}

app/static/css/queryBuilder.css

@@ -0,0 +1,146 @@
+.modal-conent {
+  overflow-x: hidden;
+}
+
+#concordance-query-builder {
+  width: 70%;
+}
+
+#concordance-query-builder nav {
+  background-color: #6B3F89;
+  margin-top: -25px;
+  margin-left: -25px;
+  width: 105%;
+}
+
+#query-builder-nav{
+  padding-left: 15px;
+}
+
+#close-query-builder {
+  margin-right: 50px;
+  cursor: pointer;
+}
+
+#general-options-query-builder-tutorial-info-icon {
+  color: black;
+}
+
+#your-query {
+  border-bottom-style: solid;
+  border-bottom-width: 1px;
+}
+
+#insert-query-button {
+  background-color: #00426f;
+  text-align: center;
+}
+
+#structural-attr h6 {
+  margin-left: 15px;
+}
+
+#add-structural-attribute-tutorial-info-icon {
+  color: black;
+}
+
+#sentence {
+  background-color:#FD9720;
+}
+
+#entity {
+  background-color: #A6E22D;
+}
+
+#text-annotation {
+  background-color: #2FBBAB;
+}
+
+#no-value-metadata-message {
+  padding-top: 25px;
+  margin-left: -20px;
+}
+
+#token-kind-selector {
+  background-color: #f2eff7;
+  padding: 15px;
+  border-top-style: solid;
+  border-color: #6B3F89;
+}
+
+#token-kind-selector.s5 {
+  margin-top: 15px;
+}
+
+#token-kind-selector h6 {
+  margin-left: 15px;
+}
+
+#token-tutorial-info-icon {
+  color: black;
+}
+
+#no-value-message {
+  padding-top: 25px;
+  margin-left: -20px;
+}
+
+#token-edit-options h6 {
+  margin-left: 15px;
+}
+
+#edit-options-tutorial-info-icon {
+  color: black;
+}
+
+#incidence-modifiers-button a{
+  background-color: #2FBBAB;
+}
+
+#incidence-modifiers a{
+  background-color: white;
+}
+
+#ignore-case {
+  margin-left: 5px;
+}
+
+#or, #and {
+  background-color: #fc0;
+}
+
+#betweenNM {
+  width: 60%;
+}
+
+#query-builder-tutorial-modal {
+  width: 60%;
+}
+
+#query-builder-tutorial-modal ul {
+  margin-top: 10px;
+}
+
+#query-builder-tutorial {
+  padding:15px;
+}
+
+#scroll-up-button-query-builder-tutorial {
+  background-color: #28B3D1;
+}
+
+[data-type="start-sentence"], [data-type="end-sentence"] {
+  background-color: #FD9720;
+}
+
+[data-type="start-empty-entity"], [data-type="start-entity"], [data-type="end-entity"] {
+  background-color: #A6E22D;
+}
+
+[data-type="start-text-annotation"]{
+  background-color: #2FBBAB;
+}
+
+[data-type="token"] {
+  background-color: #28B3D1;
+}

app/static/css/style.css

@@ -0,0 +1,67 @@
+/* Change navbar height bacause an extended and fixed navbar is used */
+.navbar-fixed {
+  height: 112px;
+}
+
+/* Change placholdertext color of file uplaod fields */
+::placeholder {
+  color: #9e9e9e;
+  opacity: 1;
+}
+
+/*
+ * changes preoloader size etc. to fit visually better with the chip status
+ * indicator of jobs
+ */
+.status-spinner {
+  margin-bottom: -10px;
+  width: 30px !important;
+  height: 30px !important;
+}
+
+#manual-modal .manual-chapter-title {
+  display: none;
+}
+
+.show-if-only-child:not(:only-child) {
+  display: none !important;
+}
+
+.btn-scale-x2 {
+  transform: scale(2);
+}
+
+.btn-scale-x2 .nopaque-icons.service-icons {
+  font-size: 2.5rem;
+}
+
+/* Fix material icon vertical alignment when nested in various elements */
+h1 .nopaque-icons, h2 .nopaque-icons, h3 .nopaque-icons, h4 .nopaque-icons, .tab .nopaque-icons, .tab .material-icons {
+  line-height: inherit;
+}
+
+
+.corpus-status-text, .job-status-text {text-transform: lowercase;}
+.corpus-status-text[data-status]:empty::before, .job-status-text[data-status]:empty::before {content: attr(data-status);}
+
+.service-scheme[data-service="file-setup-pipeline"] .nopaque-icons.service-icons[data-service="inherit"]:empty::before {content: "E";}
+.service-scheme[data-service="tesseract-ocr-pipeline"] .nopaque-icons.service-icons[data-service="inherit"]:empty::before {content: "F";}
+.service-scheme[data-service="transkribus-htr-pipeline"] .nopaque-icons.service-icons[data-service="inherit"]:empty::before {content: "F";}
+.service-scheme[data-service="spacy-nlp-pipeline"] .nopaque-icons.service-icons[data-service="inherit"]:empty::before {content: "G";}
+.service-scheme[data-service="corpus-analysis"] .nopaque-icons.service-icons[data-service="inherit"]:empty::before {content: "H";}
+
+.nopaque-icons.service-icons[data-service="file-setup-pipeline"]:empty::before {content: "E";}
+.nopaque-icons.service-icons[data-service="tesseract-ocr-pipeline"]:empty::before {content: "F";}
+.nopaque-icons.service-icons[data-service="transkribus-htr-pipeline"]:empty::before {content: "F";}
+.nopaque-icons.service-icons[data-service="spacy-nlp-pipeline"]:empty::before {content: "G";}
+.nopaque-icons.service-icons[data-service="corpus-analysis"]:empty::before {content: "H";}
+
+[draggable="true"] {cursor: move !important;}
+.clickable {cursor: pointer !important;}
+.chip.s-attr .chip.p-attr {background-color: inherit;}
+
+
+.width-25 {width: 25%;}
+.width-50 {width: 50%;}
+.width-75 {width: 75%;}
+.width-100 {width: 100%;}