.dockerignore

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

.env.tpl

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

.flaskenv

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

.gitignore

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

.vscode/settings.json

@@ -1,17 +1,9 @@
 {
     "editor.rulers": [79],
-    "editor.tabSize": 4,
-    "emmet.includeLanguages": {
-        "jinja-html": "html"
-    },
-    "files.associations": {
-        ".flaskenv": "env",
-        "*.env.tpl": "env",
-        "*.txt.j2": "jinja"
-    },
     "files.insertFinalNewline": true,
-    "files.trimFinalNewlines": true,
+    "[css]": {
-    "files.trimTrailingWhitespace": true,
+        "editor.tabSize": 2
+    },
     "[html]": {
         "editor.tabSize": 2
     },
@@ -20,5 +12,8 @@
     },
     "[jinja-html]": {
         "editor.tabSize": 2
+    },
+    "[scss]": {
+        "editor.tabSize": 2
     }
 }

Dockerfile

@@ -4,13 +4,11 @@ FROM python:3.10.13-slim-bookworm
 LABEL authors="Patrick Jentsch <p.jentsch@uni-bielefeld.de>"
 
 
-# Set environment variables
 ENV LANG="C.UTF-8"
 ENV PYTHONDONTWRITEBYTECODE="1"
 ENV PYTHONUNBUFFERED="1"
 
 
-# Install system dependencies
 RUN apt-get update \
  && apt-get install --no-install-recommends --yes \
       build-essential \
@@ -19,39 +17,37 @@ RUN apt-get update \
  && rm --recursive /var/lib/apt/lists/*
 
 
-# Create a non-root user
 RUN useradd --create-home --no-log-init nopaque \
  && groupadd docker \
  && usermod --append --groups docker nopaque
 
+
 USER nopaque
 WORKDIR /home/nopaque
 
 
-# Create a Python virtual environment
 ENV NOPAQUE_PYTHON3_VENV_PATH="/home/nopaque/.venv"
 RUN python3 -m venv "${NOPAQUE_PYTHON3_VENV_PATH}"
 ENV PATH="${NOPAQUE_PYTHON3_VENV_PATH}/bin:${PATH}"
 
 
-# Install Python dependencies
-COPY --chown=nopaque:nopaque requirements.freezed.txt requirements.freezed.txt
-RUN python3 -m pip install --requirement requirements.freezed.txt \
- && rm requirements.freezed.txt
-
-
-# Install the application
-COPY docker-nopaque-entrypoint.sh /usr/local/bin/
 COPY --chown=nopaque:nopaque app app
 COPY --chown=nopaque:nopaque migrations migrations
 COPY --chown=nopaque:nopaque tests tests
-COPY --chown=nopaque:nopaque boot.sh config.py wsgi.py ./
+COPY --chown=nopaque:nopaque .flaskenv boot.sh config.py nopaque.py requirements.txt ./
 
 
-EXPOSE 5000
+RUN python3 -m pip install --requirement requirements.txt \
+ && mkdir logs
 
 
 USER root
 
 
+COPY docker-nopaque-entrypoint.sh /usr/local/bin/
+
+
+EXPOSE 5000
+
+
 ENTRYPOINT ["docker-nopaque-entrypoint.sh"]

README.md

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

app/TesseractOCRPipelineModel.defaults.yml

@@ -10,7 +10,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Amharic'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/amh.traineddata'
@@ -23,7 +22,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Arabic'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ara.traineddata'
@@ -36,7 +34,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Assamese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/asm.traineddata'
@@ -49,7 +46,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Azerbaijani'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/aze.traineddata'
@@ -62,7 +58,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Azerbaijani - Cyrillic'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/aze_cyrl.traineddata'
@@ -75,7 +70,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Belarusian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/bel.traineddata'
@@ -88,7 +82,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Bengali'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ben.traineddata'
@@ -101,7 +94,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Tibetan'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/bod.traineddata'
@@ -114,7 +106,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Bosnian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/bos.traineddata'
@@ -127,7 +118,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Bulgarian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/bul.traineddata'
@@ -140,7 +130,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Catalan; Valencian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/cat.traineddata'
@@ -153,7 +142,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Cebuano'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ceb.traineddata'
@@ -166,7 +154,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Czech'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ces.traineddata'
@@ -179,7 +166,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Chinese - Simplified'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/chi_sim.traineddata'
@@ -192,7 +178,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Chinese - Traditional'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/chi_tra.traineddata'
@@ -205,7 +190,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Cherokee'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/chr.traineddata'
@@ -218,7 +202,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Welsh'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/cym.traineddata'
@@ -231,7 +214,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Danish'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/dan.traineddata'
@@ -244,7 +226,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'German'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/deu.traineddata'
@@ -257,7 +238,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Dzongkha'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/dzo.traineddata'
@@ -270,7 +250,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Greek, Modern (1453-)'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ell.traineddata'
@@ -283,7 +262,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'English'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/eng.traineddata'
@@ -296,7 +274,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'English, Middle (1100-1500)'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/enm.traineddata'
@@ -309,7 +286,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Esperanto'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/epo.traineddata'
@@ -322,7 +298,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Estonian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/est.traineddata'
@@ -335,7 +310,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Basque'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/eus.traineddata'
@@ -348,7 +322,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Persian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/fas.traineddata'
@@ -361,7 +334,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Finnish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/fin.traineddata'
@@ -374,7 +346,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'French'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/fra.traineddata'
@@ -387,7 +358,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'German Fraktur'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/frk.traineddata'
@@ -400,7 +370,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'French, Middle (ca. 1400-1600)'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/frm.traineddata'
@@ -413,7 +382,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Irish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/gle.traineddata'
@@ -426,7 +394,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Galician'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/glg.traineddata'
@@ -439,7 +406,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Greek, Ancient (-1453)'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/grc.traineddata'
@@ -452,7 +418,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Gujarati'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/guj.traineddata'
@@ -465,7 +430,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Haitian; Haitian Creole'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/hat.traineddata'
@@ -478,7 +442,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Hebrew'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/heb.traineddata'
@@ -491,7 +454,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Hindi'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/hin.traineddata'
@@ -504,7 +466,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Croatian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/hrv.traineddata'
@@ -517,7 +478,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Hungarian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/hun.traineddata'
@@ -530,7 +490,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Inuktitut'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/iku.traineddata'
@@ -543,7 +502,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Indonesian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ind.traineddata'
@@ -556,7 +514,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Icelandic'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/isl.traineddata'
@@ -569,7 +526,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Italian'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ita.traineddata'
@@ -582,7 +538,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'Italian - Old'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ita_old.traineddata'
@@ -595,7 +550,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Javanese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/jav.traineddata'
@@ -608,7 +562,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Japanese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/jpn.traineddata'
@@ -621,7 +574,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Kannada'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kan.traineddata'
@@ -634,7 +586,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Georgian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kat.traineddata'
@@ -647,7 +598,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Georgian - Old'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kat_old.traineddata'
@@ -660,7 +610,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Kazakh'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kaz.traineddata'
@@ -673,7 +622,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Central Khmer'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/khm.traineddata'
@@ -686,7 +634,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Kirghiz; Kyrgyz'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kir.traineddata'
@@ -699,7 +646,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Korean'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kor.traineddata'
@@ -712,7 +658,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Kurdish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/kur.traineddata'
@@ -725,7 +670,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Lao'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/lao.traineddata'
@@ -738,7 +682,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Latin'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/lat.traineddata'
@@ -751,7 +694,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Latvian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/lav.traineddata'
@@ -764,7 +706,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Lithuanian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/lit.traineddata'
@@ -777,7 +718,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Malayalam'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/mal.traineddata'
@@ -790,7 +730,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Marathi'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/mar.traineddata'
@@ -803,7 +742,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Macedonian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/mkd.traineddata'
@@ -816,7 +754,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Maltese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/mlt.traineddata'
@@ -829,7 +766,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Malay'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/msa.traineddata'
@@ -842,7 +778,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Burmese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/mya.traineddata'
@@ -855,7 +790,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Nepali'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/nep.traineddata'
@@ -868,7 +802,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Dutch; Flemish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/nld.traineddata'
@@ -881,7 +814,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Norwegian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/nor.traineddata'
@@ -894,7 +826,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Oriya'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ori.traineddata'
@@ -907,7 +838,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Panjabi; Punjabi'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/pan.traineddata'
@@ -920,7 +850,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Polish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/pol.traineddata'
@@ -933,7 +862,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Portuguese'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/por.traineddata'
@@ -946,7 +874,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Pushto; Pashto'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/pus.traineddata'
@@ -959,7 +886,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Romanian; Moldavian; Moldovan'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ron.traineddata'
@@ -972,7 +898,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Russian'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/rus.traineddata'
@@ -985,7 +910,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Sanskrit'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/san.traineddata'
@@ -998,7 +922,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Sinhala; Sinhalese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/sin.traineddata'
@@ -1011,7 +934,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Slovak'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/slk.traineddata'
@@ -1024,7 +946,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Slovenian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/slv.traineddata'
@@ -1037,7 +958,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 - title: 'Spanish; Castilian'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/spa.traineddata'
@@ -1050,7 +970,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 - title: 'Spanish; Castilian - Old'
   description: ''
   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/spa_old.traineddata'
@@ -1063,7 +982,6 @@
     - '0.1.0'
     - '0.1.1'
     - '0.1.2'
-    - '0.1.3b'
 # - title: 'Albanian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/sqi.traineddata'
@@ -1076,7 +994,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Serbian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/srp.traineddata'
@@ -1089,7 +1006,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Serbian - Latin'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/srp_latn.traineddata'
@@ -1102,7 +1018,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Swahili'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/swa.traineddata'
@@ -1115,7 +1030,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Swedish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/swe.traineddata'
@@ -1128,7 +1042,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Syriac'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/syr.traineddata'
@@ -1141,7 +1054,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Tamil'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tam.traineddata'
@@ -1154,7 +1066,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Telugu'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tel.traineddata'
@@ -1167,7 +1078,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Tajik'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tgk.traineddata'
@@ -1180,7 +1090,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Tagalog'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tgl.traineddata'
@@ -1193,7 +1102,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Thai'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tha.traineddata'
@@ -1206,7 +1114,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Tigrinya'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tir.traineddata'
@@ -1219,7 +1126,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Turkish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/tur.traineddata'
@@ -1232,7 +1138,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Uighur; Uyghur'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/uig.traineddata'
@@ -1245,7 +1150,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Ukrainian'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/ukr.traineddata'
@@ -1258,7 +1162,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Urdu'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/urd.traineddata'
@@ -1271,7 +1174,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Uzbek'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/uzb.traineddata'
@@ -1284,7 +1186,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Uzbek - Cyrillic'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/uzb_cyrl.traineddata'
@@ -1297,7 +1198,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Vietnamese'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/vie.traineddata'
@@ -1310,7 +1210,6 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'
 # - title: 'Yiddish'
 #   description: ''
 #   url: 'https://github.com/tesseract-ocr/tessdata/raw/4.1.0/yid.traineddata'
@@ -1323,4 +1222,3 @@
 #     - '0.1.0'
 #     - '0.1.1'
 #     - '0.1.2'
-#     - '0.1.3b'

app/__init__.py

@@ -2,9 +2,9 @@ from apifairy import APIFairy
 from config import Config
 from docker import DockerClient
 from flask import Flask
-from flask.logging import default_handler
 from flask_apscheduler import APScheduler
 from flask_assets import Environment
+from flask_breadcrumbs import Breadcrumbs, default_breadcrumb_root
 from flask_login import LoginManager
 from flask_mail import Mail
 from flask_marshmallow import Marshmallow
@@ -13,142 +13,95 @@ from flask_paranoid import Paranoid
 from flask_socketio import SocketIO
 from flask_sqlalchemy import SQLAlchemy
 from flask_hashids import Hashids
-from logging import Formatter, StreamHandler
-from werkzeug.middleware.proxy_fix import ProxyFix
 
 
-docker_client = DockerClient.from_env()
-
 apifairy = APIFairy()
 assets = Environment()
+breadcrumbs = Breadcrumbs()
 db = SQLAlchemy()
+docker_client = DockerClient()
 hashids = Hashids()
 login = LoginManager()
+login.login_view = 'auth.login'
+login.login_message = 'Please log in to access this page.'
 ma = Marshmallow()
 mail = Mail()
 migrate = Migrate(compare_type=True)
 paranoid = Paranoid()
+paranoid.redirect_view = '/'
 scheduler = APScheduler()
 socketio = SocketIO()
 
 
 def create_app(config: Config = Config) -> Flask:
-    ''' Creates an initialized Flask object. '''
+    ''' Creates an initialized Flask (WSGI Application) object. '''
-
     app = Flask(__name__)
     app.config.from_object(config)
-
+    config.init_app(app)
-    # region Logging
-    log_formatter = Formatter(
-        fmt=app.config['NOPAQUE_LOG_FORMAT'],
-        datefmt=app.config['NOPAQUE_LOG_DATE_FORMAT']
-    )
-
-    log_handler = StreamHandler()
-    log_handler.setFormatter(log_formatter)
-    log_handler.setLevel(app.config['NOPAQUE_LOG_LEVEL'])
-
-    app.logger.setLevel('DEBUG')
-    app.logger.removeHandler(default_handler)
-    app.logger.addHandler(log_handler)
-    # endregion Logging
-
-    # region Middlewares
-    if app.config['NOPAQUE_PROXY_FIX_ENABLED']:
-        app.wsgi_app = ProxyFix(
-            app.wsgi_app,
-            x_for=app.config['NOPAQUE_PROXY_FIX_X_FOR'],
-            x_host=app.config['NOPAQUE_PROXY_FIX_X_HOST'],
-            x_port=app.config['NOPAQUE_PROXY_FIX_X_PORT'],
-            x_prefix=app.config['NOPAQUE_PROXY_FIX_X_PREFIX'],
-            x_proto=app.config['NOPAQUE_PROXY_FIX_X_PROTO']
-        )
-    # endregion Middlewares
-
-    # region Extensions
     docker_client.login(
         app.config['NOPAQUE_DOCKER_REGISTRY_USERNAME'],
         password=app.config['NOPAQUE_DOCKER_REGISTRY_PASSWORD'],
         registry=app.config['NOPAQUE_DOCKER_REGISTRY']
     )
 
-    from .models import AnonymousUser, User
-
     apifairy.init_app(app)
     assets.init_app(app)
+    breadcrumbs.init_app(app)
     db.init_app(app)
     hashids.init_app(app)
     login.init_app(app)
-    login.anonymous_user = AnonymousUser
-    login.login_view = 'auth.login'
-    login.user_loader(lambda user_id: User.query.get(int(user_id)))
     ma.init_app(app)
     mail.init_app(app)
     migrate.init_app(app, db)
     paranoid.init_app(app)
-    paranoid.redirect_view = '/'
     scheduler.init_app(app)
-    socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])
+    socketio.init_app(app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])  # noqa
-    # endregion Extensions
 
-    # region Blueprints
+    from .admin import bp as admin_blueprint
-    from .blueprints.admin import bp as admin_blueprint
+    default_breadcrumb_root(admin_blueprint, '.admin')
     app.register_blueprint(admin_blueprint, url_prefix='/admin')
 
-    from .blueprints.api import bp as api_blueprint
+    from .api import bp as api_blueprint
     app.register_blueprint(api_blueprint, url_prefix='/api')
 
-    from .blueprints.auth import bp as auth_blueprint
+    from .auth import bp as auth_blueprint
+    default_breadcrumb_root(auth_blueprint, '.')
     app.register_blueprint(auth_blueprint)
 
-    from .blueprints.contributions import bp as contributions_blueprint
+    from .contributions import bp as contributions_blueprint
+    default_breadcrumb_root(contributions_blueprint, '.contributions')
     app.register_blueprint(contributions_blueprint, url_prefix='/contributions')
 
-    from .blueprints.corpora import bp as corpora_blueprint
+    from .corpora import bp as corpora_blueprint
+    from .corpora.cqi_over_sio import CQiNamespace
+    default_breadcrumb_root(corpora_blueprint, '.corpora')
     app.register_blueprint(corpora_blueprint, cli_group='corpus', url_prefix='/corpora')
+    socketio.on_namespace(CQiNamespace('/cqi_over_sio'))
 
-    from .blueprints.errors import bp as errors_bp
+    from .errors import bp as errors_bp
     app.register_blueprint(errors_bp)
 
-    from .blueprints.jobs import bp as jobs_blueprint
+    from .jobs import bp as jobs_blueprint
+    default_breadcrumb_root(jobs_blueprint, '.jobs')
     app.register_blueprint(jobs_blueprint, url_prefix='/jobs')
 
-    from .blueprints.main import bp as main_blueprint
+    from .main import bp as main_blueprint
+    default_breadcrumb_root(main_blueprint, '.')
     app.register_blueprint(main_blueprint, cli_group=None)
 
-    from .blueprints.services import bp as services_blueprint
+    from .services import bp as services_blueprint
+    default_breadcrumb_root(services_blueprint, '.services')
     app.register_blueprint(services_blueprint, url_prefix='/services')
 
-    from .blueprints.settings import bp as settings_blueprint
+    from .settings import bp as settings_blueprint
+    default_breadcrumb_root(settings_blueprint, '.settings')
     app.register_blueprint(settings_blueprint, url_prefix='/settings')
 
-    from .blueprints.users import bp as users_blueprint
+    from .users import bp as users_blueprint
+    default_breadcrumb_root(users_blueprint, '.users')
     app.register_blueprint(users_blueprint, cli_group='user', url_prefix='/users')
 
-    from .blueprints.workshops import bp as workshops_blueprint
+    from .workshops import bp as workshops_blueprint
     app.register_blueprint(workshops_blueprint, url_prefix='/workshops')
-    # endregion Blueprints
-
-    # region SocketIO Namespaces
-    from .namespaces.cqi_over_sio import CQiOverSocketIONamespace
-    socketio.on_namespace(CQiOverSocketIONamespace('/cqi_over_sio'))
-
-    from .namespaces.users import UsersNamespace
-    socketio.on_namespace(UsersNamespace('/users'))
-    # endregion SocketIO Namespaces
-
-    # region Database event Listeners
-    from .models.event_listeners import register_event_listeners
-    register_event_listeners()
-    # endregion Database event Listeners
-
-    # region Add scheduler jobs
-    if app.config['NOPAQUE_IS_PRIMARY_INSTANCE']:
-        from .jobs import handle_corpora
-        scheduler.add_job('handle_corpora', handle_corpora, seconds=3, trigger='interval')
-
-        from .jobs import handle_jobs
-        scheduler.add_job('handle_jobs', handle_jobs, seconds=3, trigger='interval')
-    # endregion Add scheduler jobs
 
     return app

app/admin/json_routes.py

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

app/admin/routes.py

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

app/api/jobs.py

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

app/api/schemas.py

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

app/api/users.py

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

app/auth/__init__.py

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

app/auth/forms.py

@@ -60,11 +60,7 @@ class RegistrationForm(FlaskForm):
 
     def validate_username(self, field):
         if User.query.filter_by(username=field.data).first():
-            raise ValidationError('Username already registered')
+            raise ValidationError('Username already in use')
-
-    def validate_terms_of_use_accepted(self, field):
-        if not field.data:
-            raise ValidationError('Terms of Use not accepted')
 
 
 class LoginForm(FlaskForm):

app/auth/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, request, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user, login_user, login_required, logout_user
 from app import db
 from app.email import create_message, send
@@ -12,7 +13,24 @@ from .forms import (
 )
 
 
+@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'))
@@ -49,6 +67,7 @@ def register():
 
 
 @bp.route('/login', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.login', 'Login')
 def login():
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))
@@ -79,6 +98,7 @@ def logout():
 
 
 @bp.route('/unconfirmed')
+@register_breadcrumb(bp, '.unconfirmed', 'Unconfirmed')
 @login_required
 def unconfirmed():
     if current_user.confirmed:
@@ -121,6 +141,7 @@ def confirm(token):
 
 
 @bp.route('/reset-password-request', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.reset_password_request', 'Password Reset')
 def reset_password_request():
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))
@@ -150,6 +171,7 @@ def reset_password_request():
 
 
 @bp.route('/reset-password/<token>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.reset_password', 'Password Reset')
 def reset_password(token):
     if current_user.is_authenticated:
         return redirect(url_for('main.dashboard'))

app/blueprints/auth/__init__.py

@@ -1,29 +0,0 @@
-from flask import Blueprint, redirect, request, url_for
-from flask_login import current_user
-from app import db
-
-
-bp = Blueprint('auth', __name__)
-
-
-@bp.before_app_request
-def before_request():
-    if not current_user.is_authenticated:
-        return
-
-    current_user.ping()
-    db.session.commit()
-
-    if (
-        not current_user.confirmed
-        and request.endpoint
-        and request.blueprint != 'auth'
-        and request.endpoint != 'static'
-    ):
-        return redirect(url_for('auth.unconfirmed'))
-
-    if not current_user.terms_of_use_accepted:
-        return redirect(url_for('main.terms_of_use'))
-
-
-from . import routes

app/blueprints/contributions/__init__.py

@@ -1,25 +0,0 @@
-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
-
-
-from .spacy_nlp_pipeline_models import bp as spacy_nlp_pipeline_models_bp
-bp.register_blueprint(spacy_nlp_pipeline_models_bp, url_prefix='/spacy-nlp-pipeline-models')
-
-from .tesseract_ocr_pipeline_models import bp as tesseract_ocr_pipeline_models_bp
-bp.register_blueprint(tesseract_ocr_pipeline_models_bp, url_prefix='/tesseract-ocr-pipeline-models')

app/blueprints/contributions/routes.py

@@ -1,7 +0,0 @@
-from flask import render_template
-from . import bp
-
-
-@bp.route('')
-def index():
-    return render_template('contributions/index.html.j2', title='Contributions')

app/blueprints/contributions/spacy_nlp_pipeline_models/__init__.py

@@ -1,18 +0,0 @@
-from flask import current_app, Blueprint
-from flask_login import login_required
-
-
-bp = Blueprint('spacy_nlp_pipeline_models', __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/blueprints/jobs/__init__.py

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

app/contributions/__init__.py

@@ -2,7 +2,7 @@ from flask import Blueprint
 from flask_login import login_required
 
 
-bp = Blueprint('tesseract_ocr_pipeline_models', __name__)
+bp = Blueprint('contributions', __name__)
 
 
 @bp.before_request
@@ -15,4 +15,9 @@ def before_request():
     pass
 
 
-from . import json_routes, routes
+from . import (
+    routes,
+    spacy_nlp_pipeline_models,
+    tesseract_ocr_pipeline_models,
+    transkribus_htr_pipeline_models
+)

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/forms.py

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

app/contributions/spacy_nlp_pipeline_models/json_routes.py

@@ -1,14 +1,13 @@
 from flask import abort, current_app, request
-from flask_login import current_user, login_required
+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
+from .. import bp
 
 
-@bp.route('/<hashid:spacy_nlp_pipeline_model_id>', methods=['DELETE'])
+@bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['DELETE'])
-@login_required
 @content_negotiation(produces='application/json')
 def delete_spacy_model(spacy_nlp_pipeline_model_id):
     def _delete_spacy_model(app, spacy_nlp_pipeline_model_id):
@@ -16,9 +15,9 @@ def delete_spacy_model(spacy_nlp_pipeline_model_id):
             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):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_spacy_model,
@@ -32,7 +31,7 @@ def delete_spacy_model(spacy_nlp_pipeline_model_id):
     return response_data, 202
 
 
-@bp.route('/<hashid:spacy_nlp_pipeline_model_id>/is_public', methods=['PUT'])
+@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):
@@ -40,7 +39,7 @@ def update_spacy_nlp_pipeline_model_is_public(spacy_nlp_pipeline_model_id):
     if not isinstance(is_public, bool):
         abort(400)
     snpm = SpaCyNLPPipelineModel.query.get_or_404(spacy_nlp_pipeline_model_id)
-    if not (snpm.user == current_user or current_user.is_administrator):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     snpm.is_public = is_public
     db.session.commit()

app/contributions/spacy_nlp_pipeline_models/routes.py

@@ -1,5 +1,6 @@
 from flask import abort, flash, redirect, render_template, url_for
-from flask_login import current_user, login_required
+from flask_breadcrumbs import register_breadcrumb
+from flask_login import current_user
 from app import db
 from app.models import SpaCyNLPPipelineModel
 from . import bp
@@ -7,17 +8,23 @@ from .forms import (
     CreateSpaCyNLPPipelineModelForm,
     UpdateSpaCyNLPPipelineModelForm
 )
+from .utils import (
+    spacy_nlp_pipeline_model_dlc as spacy_nlp_pipeline_model_dlc
+)
 
 
-@bp.route('/')
+@bp.route('/spacy-nlp-pipeline-models')
-@login_required
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models', 'SpaCy NLP Pipeline Models')
-def index():
+def spacy_nlp_pipeline_models():
-    return redirect(url_for('contributions.index', _anchor='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('/create', methods=['GET', 'POST'])
+@bp.route('/spacy-nlp-pipeline-models/create', methods=['GET', 'POST'])
-@login_required
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models.create', 'Create')
-def create():
+def create_spacy_nlp_pipeline_model():
     form = CreateSpaCyNLPPipelineModelForm()
     if form.is_submitted():
         if not form.validate():
@@ -41,7 +48,7 @@ def create():
             abort(500)
         db.session.commit()
         flash(f'SpaCy NLP Pipeline model "{snpm.title}" created')
-        return {}, 201, {'Location': url_for('.index')}
+        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',
@@ -49,11 +56,11 @@ def create():
     )
 
 
-@bp.route('/<hashid:spacy_nlp_pipeline_model_id>', methods=['GET', 'POST'])
+@bp.route('/spacy-nlp-pipeline-models/<hashid:spacy_nlp_pipeline_model_id>', methods=['GET', 'POST'])
-@login_required
+@register_breadcrumb(bp, '.spacy_nlp_pipeline_models.entity', '', dynamic_list_constructor=spacy_nlp_pipeline_model_dlc)
-def entity(spacy_nlp_pipeline_model_id):
+def spacy_nlp_pipeline_model(spacy_nlp_pipeline_model_id):
     snpm = SpaCyNLPPipelineModel.query.get_or_404(spacy_nlp_pipeline_model_id)
-    if not (snpm.user == current_user or current_user.is_administrator):
+    if not (snpm.user == current_user or current_user.is_administrator()):
         abort(403)
     form = UpdateSpaCyNLPPipelineModelForm(data=snpm.to_json_serializeable())
     if form.validate_on_submit():
@@ -61,9 +68,9 @@ def entity(spacy_nlp_pipeline_model_id):
         if db.session.is_modified(snpm):
             flash(f'SpaCy NLP Pipeline model "{snpm.title}" updated')
             db.session.commit()
-        return redirect(url_for('.index'))
+        return redirect(url_for('.spacy_nlp_pipeline_models'))
     return render_template(
-        'contributions/spacy_nlp_pipeline_models/entity.html.j2',
+        '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/forms.py

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

app/contributions/tesseract_ocr_pipeline_models/json_routes.py

@@ -7,7 +7,7 @@ from app.models import TesseractOCRPipelineModel
 from . import bp
 
 
-@bp.route('/<hashid:tesseract_ocr_pipeline_model_id>', methods=['DELETE'])
+@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):
@@ -17,7 +17,7 @@ def delete_tesseract_model(tesseract_ocr_pipeline_model_id):
             db.session.commit()
 
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_tesseract_ocr_pipeline_model,
@@ -31,7 +31,7 @@ def delete_tesseract_model(tesseract_ocr_pipeline_model_id):
     return response_data, 202
 
 
-@bp.route('/<hashid:tesseract_ocr_pipeline_model_id>/is_public', methods=['PUT'])
+@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):
@@ -39,7 +39,7 @@ def update_tesseract_ocr_pipeline_model_is_public(tesseract_ocr_pipeline_model_i
     if not isinstance(is_public, bool):
         abort(400)
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     topm.is_public = is_public
     db.session.commit()

app/contributions/tesseract_ocr_pipeline_models/routes.py

@@ -1,4 +1,5 @@
 from flask import abort, flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user
 from app import db
 from app.models import TesseractOCRPipelineModel
@@ -7,15 +8,23 @@ from .forms import (
     CreateTesseractOCRPipelineModelForm,
     UpdateTesseractOCRPipelineModelForm
 )
+from .utils import (
+    tesseract_ocr_pipeline_model_dlc as tesseract_ocr_pipeline_model_dlc
+)
 
 
-@bp.route('/')
+@bp.route('/tesseract-ocr-pipeline-models')
-def index():
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline_models', 'Tesseract OCR Pipeline Models')
-    return redirect(url_for('contributions.index', _anchor='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('/create', methods=['GET', 'POST'])
+@bp.route('/tesseract-ocr-pipeline-models/create', methods=['GET', 'POST'])
-def create():
+@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():
@@ -38,7 +47,7 @@ def create():
             abort(500)
         db.session.commit()
         flash(f'Tesseract OCR Pipeline model "{topm.title}" created')
-        return {}, 201, {'Location': url_for('.index')}
+        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',
@@ -46,10 +55,11 @@ def create():
     )
 
 
-@bp.route('/<hashid:tesseract_ocr_pipeline_model_id>', methods=['GET', 'POST'])
+@bp.route('/tesseract-ocr-pipeline-models/<hashid:tesseract_ocr_pipeline_model_id>', methods=['GET', 'POST'])
-def entity(tesseract_ocr_pipeline_model_id):
+@register_breadcrumb(bp, '.tesseract_ocr_pipeline_models.entity', '', dynamic_list_constructor=tesseract_ocr_pipeline_model_dlc)
+def tesseract_ocr_pipeline_model(tesseract_ocr_pipeline_model_id):
     topm = TesseractOCRPipelineModel.query.get_or_404(tesseract_ocr_pipeline_model_id)
-    if not (topm.user == current_user or current_user.is_administrator):
+    if not (topm.user == current_user or current_user.is_administrator()):
         abort(403)
     form = UpdateTesseractOCRPipelineModelForm(data=topm.to_json_serializeable())
     if form.validate_on_submit():
@@ -57,9 +67,9 @@ def entity(tesseract_ocr_pipeline_model_id):
         if db.session.is_modified(topm):
             flash(f'Tesseract OCR Pipeline model "{topm.title}" updated')
             db.session.commit()
-        return redirect(url_for('.index'))
+        return redirect(url_for('.tesseract_ocr_pipeline_models'))
     return render_template(
-        'contributions/tesseract_ocr_pipeline_models/entity.html.j2',
+        '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/sandpaper.py

@@ -1,69 +1,81 @@
-from datetime import datetime
 from flask import current_app
-from pathlib import Path
-import json
-import shutil
 from app import db
 from app.models import User, Corpus, CorpusFile
+from datetime import datetime
+import json
+import os
+import shutil
 
 
 class SandpaperConverter:
-    def __init__(self, json_db_file: Path, data_dir: Path):
+    def __init__(self, json_db_file, data_dir):
         self.json_db_file = json_db_file
         self.data_dir = data_dir
 
     def run(self):
-        with self.json_db_file.open('r') as f:
+        with open(self.json_db_file, 'r') as f:
-            json_db: list[dict] = json.load(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 = self.data_dir / f'{json_user["id"]}'
+            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: dict, user_dir: Path):
+    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 = User.create(
+            user.makedirs()
-                confirmed=json_user['confirmed'],
+        except OSError as e:
-                email=json_user['email'],
+            current_app.logger.error(e)
-                last_seen=datetime.fromtimestamp(json_user['last_seen']),
+            db.session.rollback()
-                member_since=datetime.fromtimestamp(json_user['member_since']),
-                password_hash=json_user['password_hash'],  # TODO: Needs to be added manually
-                username=json_user['username']
-            )
-        except OSError:
             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 = user_dir / 'corpora' / f'{json_corpus["id"]}'
+            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: dict, user: User, corpus_dir: Path):
+    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 = Corpus.create(
+            corpus.makedirs()
-                user=user,
+        except OSError as e:
-                creation_date=datetime.fromtimestamp(json_corpus['creation_date']),
+            current_app.logger.error(e)
-                description=json_corpus['description'],
+            db.session.rollback()
-                title=json_corpus['title']
-            )
-        except OSError:
             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: dict, corpus: Corpus, corpus_dir: Path):
+    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,
@@ -87,13 +99,13 @@ class SandpaperConverter:
         db.session.refresh(corpus_file)
         try:
             shutil.copy2(
-                corpus_dir / json_corpus_file['filename'],
+                os.path.join(corpus_dir, json_corpus_file['filename']),
                 corpus_file.path
             )
         except:
             current_app.logger.warning(
                 'Can not convert corpus file: '
-                f'{corpus_dir / json_corpus_file["filename"]}'
+                f'{os.path.join(corpus_dir, json_corpus_file["filename"])}'
                 ' -> '
                 f'{corpus_file.path}'
             )

app/converters/vrt.py

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

app/corpora/cli.py

@@ -1,7 +1,7 @@
-from flask import current_app
+from app.models import Corpus, CorpusStatus
+import os
 import shutil
 from app import db
-from app.models import Corpus, CorpusStatus
 from . import bp
 
 
@@ -18,17 +18,10 @@ def reset():
     ]
     for corpus in [x for x in Corpus.query.all() if x.status in status]:
         print(f'Resetting corpus {corpus}')
-        corpus_cwb_dir = corpus.path / 'cwb'
+        shutil.rmtree(os.path.join(corpus.path, 'cwb'), ignore_errors=True)
-        corpus_cwb_data_dir = corpus_cwb_dir / 'data'
+        os.mkdir(os.path.join(corpus.path, 'cwb'))
-        corpus_cwb_registry_dir = corpus_cwb_dir / 'registry'
+        os.mkdir(os.path.join(corpus.path, 'cwb', 'data'))
-        try:
+        os.mkdir(os.path.join(corpus.path, 'cwb', 'registry'))
-            shutil.rmtree(corpus.path / 'cwb', ignore_errors=True)
-            corpus_cwb_dir.mkdir()
-            corpus_cwb_data_dir.mkdir()
-            corpus_cwb_registry_dir.mkdir()
-        except OSError as e:
-            current_app.logger.error(e)
-            raise
         corpus.status = CorpusStatus.UNPREPARED
         corpus.num_analysis_sessions = 0
     db.session.commit()

app/corpora/cqi_over_sio/__init__.py

@@ -1,16 +1,17 @@
 from cqi import CQiClient
 from cqi.errors import CQiException
 from cqi.status import CQiStatus
-from flask import current_app
+from docker.models.containers import Container
+from flask import current_app, session
 from flask_login import current_user
 from flask_socketio import Namespace
 from inspect import signature
 from threading import Lock
+from typing import Callable, Dict, List, Optional
 from app import db, docker_client, hashids, socketio
 from app.decorators import socketio_login_required
 from app.models import Corpus, CorpusStatus
-from . import cqi_extension_functions
+from . import extensions
-from .utils import SessionManager
 
 
 '''
@@ -18,7 +19,7 @@ This package tunnels the Corpus Query interface (CQi) protocol through
 Socket.IO (SIO) by tunneling CQi API calls through an event called "exec".
 
 Basic concept:
-1. A client connects to the namespace.
+1. A client connects to the "/cqi_over_sio" namespace.
 2. The client emits the "init" event and provides a corpus id for the corpus
    that should be analysed in this session.
      1.1 The analysis session counter of the corpus is incremented.
@@ -27,17 +28,17 @@ Basic concept:
      1.4 Connect the CQiClient to the server.
      1.5 Save the CQiClient, the Lock and the corpus id in the session for
          subsequential use.
-3. The client emits "exec" events, within which it provides the name of a CQi
+2. The client emits the "exec" event provides the name of a CQi API function
-   API function and the corresponding arguments.
+   arguments (optional).
-     3.1 The "exec" event handler will execute the function, make sure that
+     - The event "exec" handler will execute the function, make sure that the
-         the result is serializable and returns the result back to the client.
+       result is serializable and returns the result back to the client.
-4. The client disconnects from the namespace
+4. Wait for more events
-     4.1 The analysis session counter of the corpus is decremented.
+5. The client disconnects from the "/cqi_over_sio" namespace
-     4.2 The CQiClient and (Mutex) Lock belonging to it are teared down.
+     1.1 The analysis session counter of the corpus is decremented.
+     1.2 The CQiClient and (Mutex) Lock belonging to it are teared down.
 '''
 
-
+CQI_API_FUNCTION_NAMES: List[str] = [
-CQI_API_FUNCTION_NAMES = [
     'ask_feature_cl_2_3',
     'ask_feature_cqi_1_0',
     'ask_feature_cqp_2_3',
@@ -85,90 +86,68 @@ CQI_API_FUNCTION_NAMES = [
 ]
 
 
-CQI_EXTENSION_FUNCTION_NAMES = [
+class CQiNamespace(Namespace):
-    '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',
-]
-
-
-class CQiOverSocketIONamespace(Namespace):
     @socketio_login_required
     def on_connect(self):
         pass
 
     @socketio_login_required
-    def on_init(self, corpus_hashid: str) -> dict:
+    def on_init(self, db_corpus_hashid: str):
-        corpus_id = hashids.decode(corpus_hashid)
+        db_corpus_id: int = hashids.decode(db_corpus_hashid)
-
+        db_corpus: Optional[Corpus] = Corpus.query.get(db_corpus_id)
-        if not isinstance(corpus_id, int):
+        if db_corpus is None:
-            return {'code': 400, 'msg': 'Bad Request'}
-
-        corpus = Corpus.query.get(corpus_id)
-
-        if corpus is None:
             return {'code': 404, 'msg': 'Not Found'}
-
+        if not (db_corpus.user == current_user
-        if not (
+                or current_user.is_following_corpus(db_corpus)
-            corpus.user == current_user
+                or current_user.is_administrator()):
-            or current_user.is_following_corpus(corpus)
-            or current_user.is_administrator
-        ):
             return {'code': 403, 'msg': 'Forbidden'}
-
+        if db_corpus.status not in [
-        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'}
-
+        if db_corpus.num_analysis_sessions is None:
-        corpus.num_analysis_sessions = Corpus.num_analysis_sessions + 1
+            db_corpus.num_analysis_sessions = 0
+            db.session.commit()
+        db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions + 1
         db.session.commit()
-        retry_counter = 20
+        retry_counter: int = 20
-        while corpus.status != CorpusStatus.RUNNING_ANALYSIS_SESSION:
+        while db_corpus.status != CorpusStatus.RUNNING_ANALYSIS_SESSION:
             if retry_counter == 0:
-                corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
+                db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
                 db.session.commit()
                 return {'code': 408, 'msg': 'Request Timeout'}
             socketio.sleep(3)
             retry_counter -= 1
-            db.session.refresh(corpus)
+            db.session.refresh(db_corpus)
-
+        # cqi_client: CQiClient = CQiClient(f'cqpserver_{db_corpus_id}')
-        cqpserver_container_name = f'nopaque-cqpserver-{corpus_id}'
+        cqpserver_container_name: str = f'cqpserver_{db_corpus_id}'
-        cqpserver_container = docker_client.containers.get(cqpserver_container_name)
+        cqpserver_container: Container = docker_client.containers.get(cqpserver_container_name)
-        cqpserver_ip_address = cqpserver_container.attrs['NetworkSettings']['Networks'][current_app.config['NOPAQUE_DOCKER_NETWORK_NAME']]['IPAddress']
+        cqpserver_host: str = cqpserver_container.attrs['NetworkSettings']['Networks'][current_app.config['NOPAQUE_DOCKER_NETWORK_NAME']]['IPAddress']
-        cqi_client = CQiClient(cqpserver_ip_address)
+        cqi_client: CQiClient = CQiClient(cqpserver_host)
-        cqi_client_lock = Lock()
+        session['cqi_over_sio'] = {
-
+            'cqi_client': cqi_client,
-        SessionManager.setup()
+            'cqi_client_lock': Lock(),
-        SessionManager.set_corpus_id(corpus_id)
+            'db_corpus_id': db_corpus_id
-        SessionManager.set_cqi_client(cqi_client)
+        }
-        SessionManager.set_cqi_client_lock(cqi_client_lock)
-
         return {'code': 200, 'msg': 'OK'}
 
     @socketio_login_required
-    def on_exec(self, fn_name: str, fn_args: dict = {}) -> dict:
+    def on_exec(self, fn_name: str, fn_args: Dict = {}):
         try:
-            cqi_client = SessionManager.get_cqi_client()
+            cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
-            cqi_client_lock = SessionManager.get_cqi_client_lock()
+            cqi_client_lock: Lock = session['cqi_over_sio']['cqi_client_lock']
         except KeyError:
             return {'code': 424, 'msg': 'Failed Dependency'}
-
         if fn_name in CQI_API_FUNCTION_NAMES:
-            fn = getattr(cqi_client.api, fn_name)
+            fn: Callable = getattr(cqi_client.api, fn_name)
-        elif fn_name in CQI_EXTENSION_FUNCTION_NAMES:
+        elif fn_name in extensions.CQI_EXTENSION_FUNCTION_NAMES:
-            fn = getattr(cqi_extension_functions, fn_name)
+            fn: Callable = getattr(extensions, fn_name)
         else:
             return {'code': 400, 'msg': 'Bad Request'}
-
         for param in signature(fn).parameters.values():
-            # Check if the parameter is optional or required
             if param.default is param.empty:
                 if param.name not in fn_args:
                     return {'code': 400, 'msg': 'Bad Request'}
@@ -177,7 +156,6 @@ class CQiOverSocketIONamespace(Namespace):
                     continue
             if type(fn_args[param.name]) is not param.annotation:
                 return {'code': 400, 'msg': 'Bad Request'}
-
         cqi_client_lock.acquire()
         try:
             fn_return_value = fn(**fn_args)
@@ -195,7 +173,6 @@ class CQiOverSocketIONamespace(Namespace):
             }
         finally:
             cqi_client_lock.release()
-
         if isinstance(fn_return_value, CQiStatus):
             payload = {
                 'code': fn_return_value.code,
@@ -203,31 +180,27 @@ class CQiOverSocketIONamespace(Namespace):
             }
         else:
             payload = fn_return_value
-
         return {'code': 200, 'msg': 'OK', 'payload': payload}
 
     def on_disconnect(self):
         try:
-            corpus_id = SessionManager.get_corpus_id()
+            cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
-            cqi_client = SessionManager.get_cqi_client()
+            cqi_client_lock: Lock = session['cqi_over_sio']['cqi_client_lock']
-            cqi_client_lock = SessionManager.get_cqi_client_lock()
+            db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
-            SessionManager.teardown()
         except KeyError:
             return
-
         cqi_client_lock.acquire()
-
+        try:
+            session.pop('cqi_over_sio')
+        except KeyError:
+            pass
         try:
             cqi_client.api.ctrl_bye()
         except (BrokenPipeError, CQiException):
             pass
-
         cqi_client_lock.release()
-
+        db_corpus: Optional[Corpus] = Corpus.query.get(db_corpus_id)
-        corpus = Corpus.query.get(corpus_id)
+        if db_corpus is None:
-
-        if corpus is None:
             return
-
+        db_corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
-        corpus.num_analysis_sessions = Corpus.num_analysis_sessions - 1
         db.session.commit()

app/corpora/cqi_over_sio/extensions.py

@@ -1,39 +1,56 @@
 from collections import Counter
+from cqi import CQiClient
 from cqi.models.corpora import Corpus as CQiCorpus
 from cqi.models.subcorpora import Subcorpus as CQiSubcorpus
+from cqi.models.attributes import (
+    PositionalAttribute as CQiPositionalAttribute,
+    StructuralAttribute as CQiStructuralAttribute
+)
 from cqi.status import StatusOk as CQiStatusOk
-from flask import current_app
+from flask import session
+from typing import Dict, List
 import gzip
 import json
 import math
+import os
 from app import db
 from app.models import Corpus
-from .utils import SessionManager
+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:
-    corpus_id = SessionManager.get_corpus_id()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
-    cqi_client = SessionManager.get_cqi_client()
+    db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
-    db_corpus = Corpus.query.get(corpus_id)
+    db_corpus: Corpus = Corpus.query.get(db_corpus_id)
-    cqi_corpus = cqi_client.corpora.get(corpus)
+    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:
+def ext_corpus_static_data(corpus: str) -> Dict:
-    corpus_id = SessionManager.get_corpus_id()
+    db_corpus_id: int = session['cqi_over_sio']['db_corpus_id']
-    db_corpus = Corpus.query.get(corpus_id)
+    db_corpus: Corpus = Corpus.query.get(db_corpus_id)
 
-    static_data_file_path = db_corpus.path / 'cwb' / 'static.json.gz'
+    static_data_file_path: str = os.path.join(db_corpus.path, 'cwb', 'static.json.gz')
-    if static_data_file_path.exists():
+    if os.path.exists(static_data_file_path):
-        with static_data_file_path.open('rb') as f:
+        with open(static_data_file_path, 'rb') as f:
             return f.read()
 
-    cqi_client = SessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
-    cqi_corpus = cqi_client.corpora.get(corpus)
+    cqi_corpus: CQiCorpus = cqi_client.corpora.get(corpus)
-    cqi_p_attrs = cqi_corpus.positional_attributes.list()
+    cqi_p_attrs: List[CQiPositionalAttribute] = cqi_corpus.positional_attributes.list()
-    cqi_s_attrs = cqi_corpus.structural_attributes.list()
+    cqi_s_attrs: List[CQiStructuralAttribute] = cqi_corpus.structural_attributes.list()
 
     static_data = {
         'corpus': {
@@ -46,21 +63,21 @@ def ext_corpus_static_data(corpus: str) -> dict:
     }
 
     for p_attr in cqi_p_attrs:
-        current_app.logger.info(f'corpus.freqs.{p_attr.name}')
+        print(f'corpus.freqs.{p_attr.name}')
         static_data['corpus']['freqs'][p_attr.name] = []
-        p_attr_id_list = list(range(p_attr.lexicon_size))
+        p_attr_id_list: List[int] = list(range(p_attr.lexicon_size))
         static_data['corpus']['freqs'][p_attr.name].extend(p_attr.freqs_by_ids(p_attr_id_list))
         del p_attr_id_list
 
-        current_app.logger.info(f'p_attrs.{p_attr.name}')
+        print(f'p_attrs.{p_attr.name}')
         static_data['p_attrs'][p_attr.name] = []
-        cpos_list = list(range(cqi_corpus.size))
+        cpos_list: List[int] = list(range(cqi_corpus.size))
         static_data['p_attrs'][p_attr.name].extend(p_attr.ids_by_cpos(cpos_list))
         del cpos_list
 
-        current_app.logger.info(f'values.p_attrs.{p_attr.name}')
+        print(f'values.p_attrs.{p_attr.name}')
         static_data['values']['p_attrs'][p_attr.name] = []
-        p_attr_id_list = list(range(p_attr.lexicon_size))
+        p_attr_id_list: List[int] = list(range(p_attr.lexicon_size))
         static_data['values']['p_attrs'][p_attr.name].extend(p_attr.values_by_ids(p_attr_id_list))
         del p_attr_id_list
 
@@ -76,9 +93,9 @@ def ext_corpus_static_data(corpus: str) -> dict:
             # Note: Needs more testing, don't use it in production       #
             ##############################################################
             cqi_corpus.query('Last', f'<{s_attr.name}> []* </{s_attr.name}>;')
-            cqi_subcorpus = cqi_corpus.subcorpora.get('Last')
+            cqi_subcorpus: CQiSubcorpus = cqi_corpus.subcorpora.get('Last')
-            first_match = 0
+            first_match: int = 0
-            last_match = cqi_subcorpus.size - 1
+            last_match: int = cqi_subcorpus.size - 1
             match_boundaries = zip(
                 range(first_match, last_match + 1),
                 cqi_subcorpus.dump(
@@ -96,7 +113,7 @@ def ext_corpus_static_data(corpus: str) -> dict:
             del cqi_subcorpus, first_match, last_match
             for id, lbound, rbound in match_boundaries:
                 static_data['s_attrs'][s_attr.name]['lexicon'].append({})
-                current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
+                print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
                 static_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
             del match_boundaries
 
@@ -108,33 +125,33 @@ def ext_corpus_static_data(corpus: str) -> dict:
             # This is a very slow operation, thats why we only use it for
             # the text attribute
             lbound, rbound = s_attr.cpos_by_id(id)
-            current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
+            print(f's_attrs.{s_attr.name}.lexicon.{id}.bounds')
             static_data['s_attrs'][s_attr.name]['lexicon'][id]['bounds'] = [lbound, rbound]
             static_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'] = {}
-            cpos_list = list(range(lbound, rbound + 1))
+            cpos_list: List[int] = list(range(lbound, rbound + 1))
             for p_attr in cqi_p_attrs:
-                p_attr_ids = []
+                p_attr_ids: List[int] = []
                 p_attr_ids.extend(p_attr.ids_by_cpos(cpos_list))
-                current_app.logger.info(f's_attrs.{s_attr.name}.lexicon.{id}.freqs.{p_attr.name}')
+                print(f's_attrs.{s_attr.name}.lexicon.{id}.freqs.{p_attr.name}')
                 static_data['s_attrs'][s_attr.name]['lexicon'][id]['freqs'][p_attr.name] = dict(Counter(p_attr_ids))
                 del p_attr_ids
             del cpos_list
 
-        sub_s_attrs = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
+        sub_s_attrs: List[CQiStructuralAttribute] = cqi_corpus.structural_attributes.list(filters={'part_of': s_attr})
-        current_app.logger.info(f's_attrs.{s_attr.name}.values')
+        print(f's_attrs.{s_attr.name}.values')
         static_data['s_attrs'][s_attr.name]['values'] = [
             sub_s_attr.name[(len(s_attr.name) + 1):]
             for sub_s_attr in sub_s_attrs
         ]
-        s_attr_id_list = list(range(s_attr.size))
+        s_attr_id_list: List[int] = list(range(s_attr.size))
-        sub_s_attr_values = []
+        sub_s_attr_values: List[str] = []
         for sub_s_attr in sub_s_attrs:
             tmp = []
             tmp.extend(sub_s_attr.values_by_ids(s_attr_id_list))
             sub_s_attr_values.append(tmp)
             del tmp
         del s_attr_id_list
-        current_app.logger.info(f'values.s_attrs.{s_attr.name}')
+        print(f'values.s_attrs.{s_attr.name}')
         static_data['values']['s_attrs'][s_attr.name] = [
             {
                 s_attr_value_name: sub_s_attr_values[s_attr_value_name_idx][s_attr_id]
@@ -144,11 +161,11 @@ def ext_corpus_static_data(corpus: str) -> dict:
             } for s_attr_id in range(0, s_attr.size)
         ]
         del sub_s_attr_values
-    current_app.logger.info('Saving static data to file')
+    print('Saving static data to file')
     with gzip.open(static_data_file_path, 'wt') as f:
         json.dump(static_data, f)
     del static_data
-    current_app.logger.info('Sending static data to client')
+    print('Sending static data to client')
     with open(static_data_file_path, 'rb') as f:
         return f.read()
 
@@ -157,8 +174,8 @@ def ext_corpus_paginate_corpus(
     corpus: str,
     page: int = 1,
     per_page: int = 20
-) -> dict:
+) -> Dict:
-    cqi_client = SessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus)
     # Sanity checks
     if (
@@ -173,7 +190,7 @@ def ext_corpus_paginate_corpus(
     first_cpos = (page - 1) * per_page
     last_cpos = min(cqi_corpus.size, first_cpos + per_page)
     cpos_list = [*range(first_cpos, last_cpos)]
-    lookups = _lookups_by_cpos(cqi_corpus, cpos_list)
+    lookups = lookups_by_cpos(cqi_corpus, cpos_list)
     payload = {}
     # the items for the current page
     payload['items'] = [cpos_list]
@@ -203,9 +220,9 @@ def ext_cqp_paginate_subcorpus(
     context: int = 50,
     page: int = 1,
     per_page: int = 20
-) -> dict:
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = SessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
     # Sanity checks
@@ -220,7 +237,7 @@ def ext_cqp_paginate_subcorpus(
         return {'code': 416, 'msg': 'Range Not Satisfiable'}
     offset = (page - 1) * per_page
     cutoff = per_page
-    cqi_results_export = _export_subcorpus(
+    cqi_results_export = export_subcorpus(
         cqi_subcorpus, context=context, cutoff=cutoff, offset=offset)
     payload = {}
     # the items for the current page
@@ -250,147 +267,22 @@ def ext_cqp_partial_export_subcorpus(
     subcorpus: str,
     match_id_list: list,
     context: int = 50
-) -> dict:
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = SessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
-    cqi_subcorpus_partial_export = _partial_export_subcorpus(cqi_subcorpus, match_id_list, context=context)
+    cqi_subcorpus_partial_export = partial_export_subcorpus(cqi_subcorpus, match_id_list, context=context)
     return cqi_subcorpus_partial_export
 
 
-def ext_cqp_export_subcorpus(subcorpus: str, context: int = 50) -> dict:
+def ext_cqp_export_subcorpus(
+    subcorpus: str,
+    context: int = 50
+) -> Dict:
     corpus_name, subcorpus_name = subcorpus.split(':', 1)
-    cqi_client = SessionManager.get_cqi_client()
+    cqi_client: CQiClient = session['cqi_over_sio']['cqi_client']
     cqi_corpus = cqi_client.corpora.get(corpus_name)
     cqi_subcorpus = cqi_corpus.subcorpora.get(subcorpus_name)
-    cqi_subcorpus_export = _export_subcorpus(cqi_subcorpus, context=context)
+    cqi_subcorpus_export = export_subcorpus(cqi_subcorpus, context=context)
     return cqi_subcorpus_export
-
-
-def _lookups_by_cpos(corpus: CQiCorpus, cpos_list: list[int]) -> dict:
-    lookups = {}
-    lookups['cpos_lookup'] = {cpos: {} for cpos in cpos_list}
-    for attr in corpus.positional_attributes.list():
-        cpos_attr_values = attr.values_by_cpos(cpos_list)
-        for i, cpos in enumerate(cpos_list):
-            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_values[i]
-    for attr in corpus.structural_attributes.list():
-        # We only want to iterate over non subattributes, identifiable by
-        # attr.has_values == False
-        if attr.has_values:
-            continue
-        cpos_attr_ids = attr.ids_by_cpos(cpos_list)
-        for i, cpos in enumerate(cpos_list):
-            if cpos_attr_ids[i] == -1:
-                continue
-            lookups['cpos_lookup'][cpos][attr.name] = cpos_attr_ids[i]
-        occured_attr_ids = [x for x in set(cpos_attr_ids) if x != -1]
-        if len(occured_attr_ids) == 0:
-            continue
-        subattrs = corpus.structural_attributes.list(filters={'part_of': attr})
-        if len(subattrs) == 0:
-            continue
-        lookup_name = f'{attr.name}_lookup'
-        lookups[lookup_name] = {}
-        for attr_id in occured_attr_ids:
-            lookups[lookup_name][attr_id] = {}
-        for subattr in subattrs:
-            subattr_name = subattr.name[(len(attr.name) + 1):]  # noqa
-            for i, subattr_value in enumerate(subattr.values_by_ids(occured_attr_ids)):  # noqa
-                lookups[lookup_name][occured_attr_ids[i]][subattr_name] = subattr_value  # noqa
-    return lookups
-
-
-def _partial_export_subcorpus(
-    subcorpus: CQiSubcorpus,
-    match_id_list: list[int],
-    context: int = 25
-) -> dict:
-    if subcorpus.size == 0:
-        return {'matches': []}
-    match_boundaries = []
-    for match_id in match_id_list:
-        if match_id < 0 or match_id >= subcorpus.size:
-            continue
-        match_boundaries.append(
-            (
-                match_id,
-                subcorpus.dump(subcorpus.fields['match'], match_id, match_id)[0],
-                subcorpus.dump(subcorpus.fields['matchend'], match_id, match_id)[0]
-            )
-        )
-    cpos_set = set()
-    matches = []
-    for match_boundary in match_boundaries:
-        match_num, match_start, match_end = match_boundary
-        c = (match_start, match_end)
-        if match_start == 0 or context == 0:
-            lc = None
-            cpos_list_lbound = match_start
-        else:
-            lc_lbound = max(0, (match_start - context))
-            lc_rbound = match_start - 1
-            lc = (lc_lbound, lc_rbound)
-            cpos_list_lbound = lc_lbound
-        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
-            rc = None
-            cpos_list_rbound = match_end
-        else:
-            rc_lbound = match_end + 1
-            rc_rbound = min(
-                (match_end + context),
-                (subcorpus.collection.corpus.size - 1)
-            )
-            rc = (rc_lbound, rc_rbound)
-            cpos_list_rbound = rc_rbound
-        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
-        matches.append(match)
-        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
-    lookups = _lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
-    return {'matches': matches, **lookups}
-
-
-def _export_subcorpus(
-    subcorpus: CQiSubcorpus,
-    context: int = 25,
-    cutoff: float = float('inf'),
-    offset: int = 0
-) -> dict:
-    if subcorpus.size == 0:
-        return {'matches': []}
-    first_match = max(0, offset)
-    last_match = min((offset + cutoff - 1), (subcorpus.size - 1))
-    match_boundaries = zip(
-        range(first_match, last_match + 1),
-        subcorpus.dump(subcorpus.fields['match'], first_match, last_match),
-        subcorpus.dump(subcorpus.fields['matchend'], first_match, last_match)
-    )
-    cpos_set = set()
-    matches = []
-    for match_num, match_start, match_end in match_boundaries:
-        c = (match_start, match_end)
-        if match_start == 0 or context == 0:
-            lc = None
-            cpos_list_lbound = match_start
-        else:
-            lc_lbound = max(0, (match_start - context))
-            lc_rbound = match_start - 1
-            lc = (lc_lbound, lc_rbound)
-            cpos_list_lbound = lc_lbound
-        if match_end == (subcorpus.collection.corpus.size - 1) or context == 0:
-            rc = None
-            cpos_list_rbound = match_end
-        else:
-            rc_lbound = match_end + 1
-            rc_rbound = min(
-                (match_end + context),
-                (subcorpus.collection.corpus.size - 1)
-            )
-            rc = (rc_lbound, rc_rbound)
-            cpos_list_rbound = rc_rbound
-        match = {'num': match_num, 'lc': lc, 'c': c, 'rc': rc}
-        matches.append(match)
-        cpos_set.update(range(cpos_list_lbound, cpos_list_rbound + 1))
-    lookups = _lookups_by_cpos(subcorpus.collection.corpus, list(cpos_set))
-    return {'matches': matches, **lookups}

app/corpora/cqi_over_sio/utils.py

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

app/corpora/decorators.py

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

app/corpora/events.py

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

app/corpora/files/__init__.py

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

app/corpora/files/json_routes.py

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

app/corpora/files/routes.py

@@ -6,19 +6,25 @@ from flask import (
     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)
@@ -60,6 +66,7 @@ def create_corpus_file(corpus_id):
 
 
 @bp.route('/<hashid:corpus_id>/files/<hashid:corpus_file_id>', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.entity.files.entity', '', dynamic_list_constructor=corpus_file_dlc)
 @corpus_follower_permission_required('MANAGE_FILES')
 def corpus_file(corpus_id, corpus_file_id):
     corpus_file = CorpusFile.query.filter_by(corpus_id=corpus_id, id=corpus_file_id).first_or_404()
@@ -85,9 +92,9 @@ def corpus_file(corpus_id, corpus_file_id):
 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(
-        corpus_file.path.parent,
+        os.path.dirname(corpus_file.path),
-        corpus_file.path.name,
+        os.path.basename(corpus_file.path),
         as_attachment=True,
-        download_name=corpus_file.filename,
+        attachment_filename=corpus_file.filename,
         mimetype=corpus_file.mimetype
     )

app/corpora/files/utils.py

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

app/corpora/followers/json_routes.py

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

app/corpora/routes.py

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

app/corpora/utils.py

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

app/daemon/__init__.py

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

app/daemon/corpus_utils.py

@@ -1,16 +1,12 @@
+from app import docker_client
+from app.models import Corpus, CorpusStatus
 from flask import current_app
 import docker
 import os
 import shutil
-from app import db, docker_client, scheduler
-from app.models import Corpus, CorpusStatus
 
 
-def handle_corpora():
+def check_corpora():
-    with scheduler.app.app_context():
-        _handle_corpora()
-
-def _handle_corpora():
     corpora = Corpus.query.all()
     for corpus in [x for x in corpora if x.status == CorpusStatus.SUBMITTED]:
         _create_build_corpus_service(corpus)
@@ -21,14 +17,13 @@ def _handle_corpora():
     for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION and x.num_analysis_sessions == 0]:
         corpus.status = CorpusStatus.CANCELING_ANALYSIS_SESSION
     for corpus in [x for x in corpora if x.status == CorpusStatus.RUNNING_ANALYSIS_SESSION]:
-        _checkout_cqpserver_container(corpus)
+        _checkout_analysing_corpus_container(corpus)
     for corpus in [x for x in corpora if x.status == CorpusStatus.STARTING_ANALYSIS_SESSION]:
         _create_cqpserver_container(corpus)
     for corpus in [x for x in corpora if x.status == CorpusStatus.CANCELING_ANALYSIS_SESSION]:
         _remove_cqpserver_container(corpus)
-    db.session.commit()
 
-def _create_build_corpus_service(corpus: Corpus):
+def _create_build_corpus_service(corpus):
     ''' # Docker service settings # '''
     ''' ## Command ## '''
     command = ['bash', '-c']
@@ -50,10 +45,12 @@ def _create_build_corpus_service(corpus: Corpus):
     ''' ## Constraints ## '''
     constraints = ['node.role==worker']
     ''' ## Image ## '''
-    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1887'
+    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1879'
     ''' ## Labels ## '''
     labels = {
-        'nopaque.server_name': current_app.config['SERVER_NAME']
+        'origin': current_app.config['SERVER_NAME'],
+        'type': 'corpus.build',
+        'corpus_id': str(corpus.id)
     }
     ''' ## Mounts ## '''
     mounts = []
@@ -98,7 +95,7 @@ def _create_build_corpus_service(corpus: Corpus):
         return
     corpus.status = CorpusStatus.QUEUED
 
-def _checkout_build_corpus_service(corpus: Corpus):
+def _checkout_build_corpus_service(corpus):
     service_name = f'build-corpus_{corpus.id}'
     try:
         service = docker_client.services.get(service_name)
@@ -126,7 +123,8 @@ def _checkout_build_corpus_service(corpus: Corpus):
     except docker.errors.DockerException as e:
         current_app.logger.error(f'Remove service "{service_name}" failed: {e}')
 
-def _create_cqpserver_container(corpus: Corpus):
+def _create_cqpserver_container(corpus):
+    ''' # Docker container settings # '''
     ''' ## Command ## '''
     command = []
     command.append(
@@ -141,9 +139,9 @@ def _create_cqpserver_container(corpus: Corpus):
     ''' ## Entrypoint ## '''
     entrypoint = ['bash', '-c']
     ''' ## Image ## '''
-    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1887'
+    image = f'{current_app.config["NOPAQUE_DOCKER_IMAGE_PREFIX"]}cwb:r1879'
     ''' ## Name ## '''
-    name = f'nopaque-cqpserver-{corpus.id}'
+    name = f'cqpserver_{corpus.id}'
     ''' ## Network ## '''
     network = f'{current_app.config["NOPAQUE_DOCKER_NETWORK_NAME"]}'
     ''' ## Volumes ## '''
@@ -200,8 +198,8 @@ def _create_cqpserver_container(corpus: Corpus):
         return
     corpus.status = CorpusStatus.RUNNING_ANALYSIS_SESSION
 
-def _checkout_cqpserver_container(corpus: Corpus):
+def _checkout_analysing_corpus_container(corpus):
-    container_name = f'nopaque-cqpserver-{corpus.id}'
+    container_name = f'cqpserver_{corpus.id}'
     try:
         docker_client.containers.get(container_name)
     except docker.errors.NotFound as e:
@@ -211,8 +209,8 @@ def _checkout_cqpserver_container(corpus: Corpus):
     except docker.errors.DockerException as e:
         current_app.logger.error(f'Get container "{container_name}" failed: {e}')
 
-def _remove_cqpserver_container(corpus: Corpus):
+def _remove_cqpserver_container(corpus):
-    container_name = f'nopaque-cqpserver-{corpus.id}'
+    container_name = f'cqpserver_{corpus.id}'
     try:
         container = docker_client.containers.get(container_name)
     except docker.errors.NotFound:

app/daemon/job_utils.py

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

app/decorators.py

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

app/email.py

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

app/extensions/nopaque_sqlalchemy_extras/__init__.py

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

app/extensions/nopaque_sqlalchemy_extras/types.py

@@ -1,42 +0,0 @@
-import json
-from app import db
-
-
-class ContainerColumn(db.TypeDecorator):
-    impl = db.String
-
-    def __init__(self, container_type, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.container_type = container_type
-
-    def process_bind_param(self, value, dialect):
-        if isinstance(value, self.container_type):
-            return json.dumps(value)
-        elif isinstance(value, str) and isinstance(json.loads(value), self.container_type):
-            return value
-        else:
-            return TypeError()
-
-    def process_result_value(self, value, dialect):
-        return json.loads(value)
-
-
-class IntEnumColumn(db.TypeDecorator):
-    impl = db.Integer
-
-    def __init__(self, enum_type, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.enum_type = enum_type
-
-    def process_bind_param(self, value, dialect):
-        if isinstance(value, self.enum_type) and isinstance(value.value, int):
-            return value.value
-        elif isinstance(value, int):
-            return self.enum_type(value).value
-        elif isinstance(value, str):
-            return self.enum_type[value].value
-        else:
-            return TypeError()
-
-    def process_result_value(self, value, dialect):
-        return self.enum_type(value)

app/jobs/__init__.py

@@ -1,2 +1,18 @@
-from .handle_corpora import handle_corpora
+from flask import Blueprint
-from .handle_jobs import handle_jobs
+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

@@ -1,6 +1,7 @@
 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
@@ -17,7 +18,7 @@ def delete_job(job_id):
             db.session.commit()
 
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     thread = Thread(
         target=_delete_job,
@@ -38,7 +39,7 @@ def job_log(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(job.path / 'pipeline_data' / 'logs' / 'pyflow_log.txt') as log_file:
+    with open(os.path.join(job.path, 'pipeline_data', 'logs', 'pyflow_log.txt')) as log_file:
         log = log_file.read()
     response_data = {
         'jobLog': log
@@ -56,7 +57,7 @@ def restart_job(job_id):
             db.session.commit()
 
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     if job.status == JobStatus.FAILED:
         response = {'errors': {'message': 'Job status is not "failed"'}}

app/jobs/routes.py

@@ -5,20 +5,25 @@ from flask import (
     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('')
-def jobs():
+@register_breadcrumb(bp, '.', '<i class="nopaque-icons left">J</i>My Jobs')
+def corpora():
     return redirect(url_for('main.dashboard', _anchor='jobs'))
 
 
 @bp.route('/<hashid:job_id>')
+@register_breadcrumb(bp, '.entity', '', dynamic_list_constructor=job_dlc)
 def job(job_id):
     job = Job.query.get_or_404(job_id)
-    if not (job.user == current_user or current_user.is_administrator):
+    if not (job.user == current_user or current_user.is_administrator()):
         abort(403)
     return render_template(
         'jobs/job.html.j2',
@@ -30,13 +35,13 @@ def job(job_id):
 @bp.route('/<hashid:job_id>/inputs/<hashid:job_input_id>/download')
 def download_job_input(job_id, job_input_id):
     job_input = JobInput.query.filter_by(job_id=job_id, id=job_input_id).first_or_404()
-    if not (job_input.job.user == current_user or current_user.is_administrator):
+    if not (job_input.job.user == current_user or current_user.is_administrator()):
         abort(403)
     return send_from_directory(
-        job_input.path.parent,
+        os.path.dirname(job_input.path),
-        job_input.path.name,
+        os.path.basename(job_input.path),
         as_attachment=True,
-        download_name=job_input.filename,
+        attachment_filename=job_input.filename,
         mimetype=job_input.mimetype
     )
 
@@ -44,12 +49,12 @@ def download_job_input(job_id, job_input_id):
 @bp.route('/<hashid:job_id>/results/<hashid:job_result_id>/download')
 def download_job_result(job_id, job_result_id):
     job_result = JobResult.query.filter_by(job_id=job_id, id=job_result_id).first_or_404()
-    if not (job_result.job.user == current_user or current_user.is_administrator):
+    if not (job_result.job.user == current_user or current_user.is_administrator()):
         abort(403)
     return send_from_directory(
-        job_result.path.parent,
+        os.path.dirname(job_result.path),
-        job_result.path.name,
+        os.path.basename(job_result.path),
         as_attachment=True,
-        download_name=job_result.filename,
+        attachment_filename=job_result.filename,
         mimetype=job_result.mimetype
     )

app/jobs/utils.py

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

app/main/cli.py

@@ -1,9 +1,7 @@
 from flask import current_app
 from flask_migrate import upgrade
-from pathlib import Path
+import os
-from app import db
 from app.models import (
-    Corpus,
     CorpusFollowerRole,
     Role,
     SpaCyNLPPipelineModel,
@@ -16,22 +14,25 @@ from . import bp
 @bp.cli.command('deploy')
 def deploy():
     ''' Run deployment tasks. '''
-
+    # Make default directories
     print('Make default directories')
     base_dir = current_app.config['NOPAQUE_DATA_DIR']
-    default_dirs: list[Path] = [
+    default_dirs = [
-        base_dir / 'tmp',
+        os.path.join(base_dir, 'tmp'),
-        base_dir / 'users'
+        os.path.join(base_dir, 'users')
     ]
-    for default_dir in default_dirs:
+    for dir in default_dirs:
-        if not default_dir.exists():
+        if os.path.exists(dir):
-            default_dir.mkdir()
+            if not os.path.isdir(dir):
-        if not default_dir.is_dir():
+                raise NotADirectoryError(f'{dir} is not a directory')
-            raise NotADirectoryError(f'{default_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')
@@ -43,9 +44,4 @@ def deploy():
     print('Insert/Update default TesseractOCRPipelineModels')
     TesseractOCRPipelineModel.insert_defaults()
 
-    print('Stop running analysis sessions')
-    for corpus in Corpus.query.all():
-        corpus.num_analysis_sessions = 0
-    db.session.commit()
-
     # TODO: Implement checks for if the nopaque network exists

app/main/routes.py

@@ -1,11 +1,14 @@
 from flask import flash, redirect, render_template, url_for
+from flask_breadcrumbs import register_breadcrumb
 from flask_login import current_user, login_required, login_user
-from app.blueprints.auth.forms import LoginForm
+from app.auth.forms import LoginForm
 from app.models import Corpus, User
+from sqlalchemy import or_
 from . import bp
 
 
 @bp.route('/', methods=['GET', 'POST'])
+@register_breadcrumb(bp, '.', '<i class="material-icons">home</i>')
 def index():
     form = LoginForm()
     if form.validate_on_submit():
@@ -24,6 +27,7 @@ def index():
 
 
 @bp.route('/faq')
+@register_breadcrumb(bp, '.faq', 'Frequently Asked Questions')
 def faq():
     return render_template(
         'main/faq.html.j2',
@@ -32,6 +36,7 @@ def faq():
 
 
 @bp.route('/dashboard')
+@register_breadcrumb(bp, '.dashboard', '<i class="material-icons left">dashboard</i>Dashboard')
 @login_required
 def dashboard():
     return render_template(
@@ -40,15 +45,8 @@ def dashboard():
     )
 
 
-@bp.route('/manual')
-def manual():
-    return render_template(
-        'main/manual.html.j2',
-        title='Manual'
-    )
-
-
 @bp.route('/news')
+@register_breadcrumb(bp, '.news', '<i class="material-icons left">email</i>News')
 def news():
     return render_template(
         'main/news.html.j2',
@@ -57,6 +55,7 @@ def news():
 
 
 @bp.route('/privacy_policy')
+@register_breadcrumb(bp, '.privacy_policy', 'Private statement (GDPR)')
 def privacy_policy():
     return render_template(
         'main/privacy_policy.html.j2',
@@ -65,6 +64,7 @@ def privacy_policy():
 
 
 @bp.route('/terms_of_use')
+@register_breadcrumb(bp, '.terms_of_use', 'Terms of Use')
 def terms_of_use():
     return render_template(
         'main/terms_of_use.html.j2',
@@ -72,14 +72,17 @@ def terms_of_use():
     )
 
 
-@bp.route('/social')
+@bp.route('/social-area')
+@register_breadcrumb(bp, '.social_area', '<i class="material-icons left">group</i>Social Area')
 @login_required
-def social():
+def social_area():
+    print('test')
     corpora = Corpus.query.filter(Corpus.is_public == True, Corpus.user != current_user).all()
+    print(corpora)
     users = User.query.filter(User.is_public == True, User.id != current_user.id).all()
     return render_template(
-        'main/social.html.j2',
+        'main/social_area.html.j2',
-        title='Social',
+        title='Social Area',
         corpora=corpora,
         users=users
     )

app/models/__init__.py

@@ -1,14 +0,0 @@
-from .anonymous_user import *
-from .avatar import *
-from .corpus_file import *
-from .corpus_follower_association import *
-from .corpus_follower_role import *
-from .corpus import *
-from .job_input import *
-from .job_result import *
-from .job import *
-from .role import *
-from .spacy_nlp_pipeline_model import *
-from .tesseract_ocr_pipeline_model import *
-from .token import *
-from .user import *

app/models/anonymous_user.py

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

app/models/avatar.py

@@ -1,40 +0,0 @@
-from flask import current_app
-from flask_hashids import HashidMixin
-from pathlib import Path
-from app import db
-from .file_mixin import FileMixin
-
-
-class Avatar(HashidMixin, FileMixin, db.Model):
-    __tablename__ = 'avatars'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Relationships
-    user = db.relationship('User', back_populates='avatar')
-
-    @property
-    def path(self) -> Path:
-        return self.user.path / 'avatar'
-        # return os.path.join(self.user.path, 'avatar')
-
-    def delete(self):
-        try:
-            self.path.unlink(missing_ok=True)
-        except OSError as e:
-            current_app.logger.error(e)
-            raise
-        db.session.delete(self)
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            **self.file_mixin_to_json_serializeable()
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/corpus.py

@@ -1,199 +0,0 @@
-from datetime import datetime
-from enum import IntEnum
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from sqlalchemy.ext.associationproxy import association_proxy
-from pathlib import Path
-import shutil
-import xml.etree.ElementTree as ET
-from app import db
-from app.converters.vrt import normalize_vrt_file
-from app.extensions.nopaque_sqlalchemy_extras import IntEnumColumn
-from .corpus_follower_association import CorpusFollowerAssociation
-
-
-class CorpusStatus(IntEnum):
-    UNPREPARED = 1
-    SUBMITTED = 2
-    QUEUED = 3
-    BUILDING = 4
-    BUILT = 5
-    FAILED = 6
-    STARTING_ANALYSIS_SESSION = 7
-    RUNNING_ANALYSIS_SESSION = 8
-    CANCELING_ANALYSIS_SESSION = 9
-
-    @staticmethod
-    def get(corpus_status: 'CorpusStatus | int | str') -> 'CorpusStatus':
-        if isinstance(corpus_status, CorpusStatus):
-            return corpus_status
-        if isinstance(corpus_status, int):
-            return CorpusStatus(corpus_status)
-        if isinstance(corpus_status, str):
-            return CorpusStatus[corpus_status]
-        raise TypeError('corpus_status must be CorpusStatus, int, or str')
-
-
-class Corpus(HashidMixin, db.Model):
-    '''
-    Class to define a corpus.
-    '''
-    __tablename__ = 'corpora'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Fields
-    creation_date = db.Column(db.DateTime(), default=datetime.utcnow)
-    description = db.Column(db.String(255))
-    status = db.Column(
-        IntEnumColumn(CorpusStatus),
-        default=CorpusStatus.UNPREPARED
-    )
-    title = db.Column(db.String(32))
-    num_analysis_sessions = db.Column(db.Integer, default=0)
-    num_tokens = db.Column(db.Integer, default=0)
-    is_public = db.Column(db.Boolean, default=False)
-    # Relationships
-    files = db.relationship(
-        'CorpusFile',
-        back_populates='corpus',
-        lazy='dynamic',
-        cascade='all, delete-orphan'
-    )
-    corpus_follower_associations = db.relationship(
-        'CorpusFollowerAssociation',
-        back_populates='corpus',
-        cascade='all, delete-orphan'
-    )
-    followers = association_proxy(
-        'corpus_follower_associations',
-        'follower',
-        creator=lambda u: CorpusFollowerAssociation(follower=u)
-    )
-    user = db.relationship('User', back_populates='corpora')
-    # "static" attributes
-    max_num_tokens = 2_147_483_647
-
-    def __repr__(self):
-        return f'<Corpus {self.title}>'
-
-    @property
-    def analysis_url(self):
-        return url_for('corpora.analysis', corpus_id=self.id)
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.user.jsonpatch_path}/corpora/{self.hashid}'
-
-    @property
-    def path(self) -> Path:
-        return self.user.path / 'corpora' / f'{self.id}'
-
-    @property
-    def url(self):
-        return url_for('corpora.corpus', corpus_id=self.id)
-
-    @property
-    def user_hashid(self):
-        return self.user.hashid
-
-    @staticmethod
-    def create(**kwargs):
-        corpus = Corpus(**kwargs)
-        db.session.add(corpus)
-        db.session.flush(objects=[corpus])
-        db.session.refresh(corpus)
-        corpus_files_dir = corpus.path / 'files'
-        corpus_cwb_dir = corpus.path / 'cwb'
-        corpus_cwb_data_dir = corpus_cwb_dir / 'data'
-        corpus_cwb_registry_dir = corpus_cwb_dir / 'registry'
-        try:
-            corpus.path.mkdir()
-            corpus_files_dir.mkdir()
-            corpus_cwb_dir.mkdir()
-            corpus_cwb_data_dir.mkdir()
-            corpus_cwb_registry_dir.mkdir()
-        except OSError as e:
-            # TODO: Potential leftover cleanup
-            current_app.logger.error(e)
-            db.session.rollback()
-            raise
-        return corpus
-
-    def build(self):
-        corpus_cwb_dir = self.path / 'cwb'
-        corpus_cwb_data_dir = corpus_cwb_dir / 'data'
-        corpus_cwb_registry_dir = corpus_cwb_dir / 'registry'
-        try:
-            shutil.rmtree(corpus_cwb_dir, ignore_errors=True)
-            corpus_cwb_dir.mkdir()
-            corpus_cwb_data_dir.mkdir()
-            corpus_cwb_registry_dir.mkdir()
-        except OSError as e:
-            current_app.logger.error(e)
-            self.status = CorpusStatus.FAILED
-            raise
-        corpus_element = ET.fromstring('<corpus>\n</corpus>')
-        for corpus_file in self.files:
-            normalized_vrt_path = corpus_cwb_dir / f'{corpus_file.id}.norm.vrt'
-            try:
-                normalize_vrt_file(corpus_file.path, normalized_vrt_path)
-            except:
-                self.status = CorpusStatus.FAILED
-                return
-            element_tree = ET.parse(normalized_vrt_path)
-            text_element = element_tree.getroot()
-            text_element.set('author', corpus_file.author)
-            text_element.set('title', corpus_file.title)
-            text_element.set(
-                'publishing_year',
-                f'{corpus_file.publishing_year}'
-            )
-            text_element.set('address', corpus_file.address or 'NULL')
-            text_element.set('booktitle', corpus_file.booktitle or 'NULL')
-            text_element.set('chapter', corpus_file.chapter or 'NULL')
-            text_element.set('editor', corpus_file.editor or 'NULL')
-            text_element.set('institution', corpus_file.institution or 'NULL')
-            text_element.set('journal', corpus_file.journal or 'NULL')
-            text_element.set('pages', f'{corpus_file.pages}' or 'NULL')
-            text_element.set('publisher', corpus_file.publisher or 'NULL')
-            text_element.set('school', corpus_file.school or 'NULL')
-            text_element.tail = '\n'
-            # corpus_element.insert(1, text_element)
-            corpus_element.append(text_element)
-        ET.ElementTree(corpus_element).write(
-            corpus_cwb_dir / 'corpus.vrt',
-            encoding='utf-8'
-        )
-        self.status = CorpusStatus.SUBMITTED
-
-    def delete(self):
-        shutil.rmtree(self.path, ignore_errors=True)
-        db.session.delete(self)
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'creation_date': f'{self.creation_date.isoformat()}Z',
-            'description': self.description,
-            'max_num_tokens': self.max_num_tokens,
-            'num_analysis_sessions': self.num_analysis_sessions,
-            'num_tokens': self.num_tokens,
-            'status': self.status.name,
-            'title': self.title,
-            'is_public': self.is_public
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            json_serializeable['corpus_follower_associations'] = {
-                x.hashid: x.to_json_serializeable()
-                for x in self.corpus_follower_associations
-            }
-            json_serializeable['files'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.files
-            }
-        return json_serializeable

app/models/corpus_file.py

@@ -1,102 +0,0 @@
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from pathlib import Path
-from app import db
-from .corpus import CorpusStatus
-from .file_mixin import FileMixin
-
-
-class CorpusFile(FileMixin, HashidMixin, db.Model):
-    __tablename__ = 'corpus_files'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    corpus_id = db.Column(db.Integer, db.ForeignKey('corpora.id'))
-    # Fields
-    author = db.Column(db.String(255))
-    description = db.Column(db.String(255))
-    publishing_year = db.Column(db.Integer)
-    title = db.Column(db.String(255))
-    address = db.Column(db.String(255))
-    booktitle = db.Column(db.String(255))
-    chapter = db.Column(db.String(255))
-    editor = db.Column(db.String(255))
-    institution = db.Column(db.String(255))
-    journal = db.Column(db.String(255))
-    pages = db.Column(db.String(255))
-    publisher = db.Column(db.String(255))
-    school = db.Column(db.String(255))
-    # Relationships
-    corpus = db.relationship(
-        'Corpus',
-        back_populates='files'
-    )
-
-    @property
-    def download_url(self):
-        return url_for(
-            'corpora.download_corpus_file',
-            corpus_id=self.corpus_id,
-            corpus_file_id=self.id
-        )
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.corpus.jsonpatch_path}/files/{self.hashid}'
-
-    @property
-    def path(self) -> Path:
-        return self.corpus.path / 'files' / f'{self.id}'
-
-    @property
-    def url(self):
-        return url_for(
-            'corpora.corpus_file',
-            corpus_id=self.corpus_id,
-            corpus_file_id=self.id
-        )
-
-    @property
-    def user_hashid(self):
-        return self.corpus.user.hashid
-
-    @property
-    def user_id(self):
-        return self.corpus.user_id
-
-    def delete(self):
-        try:
-            self.path.unlink(missing_ok=True)
-        except OSError as e:
-            current_app.logger.error(e)
-            raise
-        db.session.delete(self)
-        self.corpus.status = CorpusStatus.UNPREPARED
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'address': self.address,
-            'author': self.author,
-            'description': self.description,
-            'booktitle': self.booktitle,
-            'chapter': self.chapter,
-            'editor': self.editor,
-            'institution': self.institution,
-            'journal': self.journal,
-            'pages': self.pages,
-            'publisher': self.publisher,
-            'publishing_year': self.publishing_year,
-            'school': self.school,
-            'title': self.title,
-            **self.file_mixin_to_json_serializeable(
-                backrefs=backrefs,
-                relationships=relationships
-            )
-        }
-        if backrefs:
-            json_serializeable['corpus'] = \
-                self.corpus.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/corpus_follower_association.py

@@ -1,47 +0,0 @@
-from flask_hashids import HashidMixin
-from app import db
-from .corpus_follower_role import CorpusFollowerRole
-
-
-class CorpusFollowerAssociation(HashidMixin, db.Model):
-    __tablename__ = 'corpus_follower_associations'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    corpus_id = db.Column(db.Integer, db.ForeignKey('corpora.id'))
-    follower_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    role_id = db.Column(db.Integer, db.ForeignKey('corpus_follower_roles.id'))
-    # Relationships
-    corpus = db.relationship(
-        'Corpus',
-        back_populates='corpus_follower_associations'
-    )
-    follower = db.relationship(
-        'User',
-        back_populates='corpus_follower_associations'
-    )
-    role = db.relationship(
-        'CorpusFollowerRole',
-        back_populates='corpus_follower_associations'
-    )
-
-    def __init__(self, **kwargs):
-        if 'role' not in kwargs:
-            kwargs['role'] = CorpusFollowerRole.query.filter_by(default=True).first()
-        super().__init__(**kwargs)
-
-    def __repr__(self):
-        return f'<CorpusFollowerAssociation {self.follower.__repr__()} ~ {self.role.__repr__()} ~ {self.corpus.__repr__()}>'
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'corpus': self.corpus.to_json_serializeable(backrefs=True),
-            'follower': self.follower.to_json_serializeable(),
-            'role': self.role.to_json_serializeable()
-        }
-        if backrefs:
-            pass
-        if relationships:
-            pass
-        return json_serializeable

app/models/corpus_follower_role.py

@@ -1,106 +0,0 @@
-from flask_hashids import HashidMixin
-from enum import IntEnum
-from app import db
-
-
-class CorpusFollowerPermission(IntEnum):
-    VIEW = 1
-    MANAGE_FILES = 2
-    MANAGE_FOLLOWERS = 4
-    MANAGE_CORPUS = 8
-
-    @staticmethod
-    def get(corpus_follower_permission: 'CorpusFollowerPermission | int | str') -> 'CorpusFollowerPermission':
-        if isinstance(corpus_follower_permission, CorpusFollowerPermission):
-            return corpus_follower_permission
-        if isinstance(corpus_follower_permission, int):
-            return CorpusFollowerPermission(corpus_follower_permission)
-        if isinstance(corpus_follower_permission, str):
-            return CorpusFollowerPermission[corpus_follower_permission]
-        raise TypeError('corpus_follower_permission must be CorpusFollowerPermission, int, or str')
-
-
-class CorpusFollowerRole(HashidMixin, db.Model):
-    __tablename__ = 'corpus_follower_roles'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Fields
-    name = db.Column(db.String(64), unique=True)
-    default = db.Column(db.Boolean, default=False, index=True)
-    permissions = db.Column(db.Integer, default=0)
-    # Relationships
-    corpus_follower_associations = db.relationship(
-        'CorpusFollowerAssociation',
-        back_populates='role'
-    )
-
-    def __repr__(self):
-        return f'<CorpusFollowerRole {self.name}>'
-
-    def has_permission(self, permission: CorpusFollowerPermission | int | str):
-        perm = CorpusFollowerPermission.get(permission)
-        return self.permissions & perm.value == perm.value
-
-    def add_permission(self, permission: CorpusFollowerPermission | int | str):
-        perm = CorpusFollowerPermission.get(permission)
-        if not self.has_permission(perm):
-            self.permissions += perm.value
-
-    def remove_permission(self, permission: CorpusFollowerPermission | int | str):
-        perm = CorpusFollowerPermission.get(permission)
-        if self.has_permission(perm):
-            self.permissions -= perm.value
-
-    def reset_permissions(self):
-        self.permissions = 0
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'default': self.default,
-            'name': self.name,
-            'permissions': [
-                x.name
-                for x in CorpusFollowerPermission
-                if self.has_permission(x)
-            ]
-        }
-        if backrefs:
-            pass
-        if relationships:
-            json_serializeable['corpus_follower_association'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.corpus_follower_association
-            }
-        return json_serializeable
-
-    @staticmethod
-    def insert_defaults():
-        roles = {
-            'Anonymous': [],
-            'Viewer': [
-                CorpusFollowerPermission.VIEW
-            ],
-            'Contributor': [
-                CorpusFollowerPermission.VIEW,
-                CorpusFollowerPermission.MANAGE_FILES
-            ],
-            'Administrator': [
-                CorpusFollowerPermission.VIEW,
-                CorpusFollowerPermission.MANAGE_FILES,
-                CorpusFollowerPermission.MANAGE_FOLLOWERS,
-                CorpusFollowerPermission.MANAGE_CORPUS
-
-            ]
-        }
-        default_role_name = 'Viewer'
-        for role_name, permissions in roles.items():
-            role = CorpusFollowerRole.query.filter_by(name=role_name).first()
-            if role is None:
-                role = CorpusFollowerRole(name=role_name)
-            role.reset_permissions()
-            for permission in permissions:
-                role.add_permission(permission)
-            role.default = role.name == default_role_name
-            db.session.add(role)
-        db.session.commit()

app/models/event_listeners.py

@@ -1,138 +0,0 @@
-from datetime import datetime
-from enum import Enum
-from app import db, mail, socketio
-from app.email import create_message
-from .corpus_file import CorpusFile
-from .corpus_follower_association import CorpusFollowerAssociation
-from .corpus import Corpus
-from .job_input import JobInput
-from .job_result import JobResult
-from .job import Job, JobStatus
-from .spacy_nlp_pipeline_model import SpaCyNLPPipelineModel
-from .tesseract_ocr_pipeline_model import TesseractOCRPipelineModel
-from .user import UserSettingJobStatusMailNotificationLevel
-
-
-def register_event_listeners():
-    resources = [
-        Corpus,
-        CorpusFile,
-        Job,
-        JobInput,
-        JobResult,
-        SpaCyNLPPipelineModel,
-        TesseractOCRPipelineModel
-    ]
-
-    for resource in resources:
-        db.event.listen(resource, 'after_delete', resource_after_delete)
-        db.event.listen(resource, 'after_insert', resource_after_insert)
-        db.event.listen(resource, 'after_update', resource_after_update)
-
-    db.event.listen(CorpusFollowerAssociation, 'after_delete', cfa_after_delete)
-    db.event.listen(CorpusFollowerAssociation, 'after_insert', cfa_after_insert)
-
-    db.event.listen(Job, 'after_update', job_after_update)
-
-
-def resource_after_delete(mapper, connection, resource):
-    jsonpatch = [
-        {
-            'op': 'remove',
-            'path': resource.jsonpatch_path
-        }
-    ]
-    namespace = '/users'
-    room = f'/users/{resource.user_hashid}'
-    socketio.emit('patch', jsonpatch, namespace=namespace, room=room)
-
-
-def cfa_after_delete(mapper, connection, cfa):
-    jsonpatch_path = f'/users/{cfa.corpus.user.hashid}/corpora/{cfa.corpus.hashid}/corpus_follower_associations/{cfa.hashid}'
-    jsonpatch = [
-        {
-            'op': 'remove',
-            'path': jsonpatch_path
-        }
-    ]
-    namespace = '/users'
-    room = f'/users/{cfa.corpus.user.hashid}'
-    socketio.emit('patch', jsonpatch, namespace=namespace, room=room)
-
-
-def resource_after_insert(mapper, connection, resource):
-    jsonpatch_value = resource.to_json_serializeable()
-    for attr in mapper.relationships:
-        jsonpatch_value[attr.key] = {}
-    jsonpatch = [
-        {
-            'op': 'add',
-            'path': resource.jsonpatch_path,
-            'value': jsonpatch_value
-        }
-    ]
-    namespace = '/users'
-    room = f'/users/{resource.user_hashid}'
-    socketio.emit('patch', jsonpatch, namespace=namespace, room=room)
-
-
-def cfa_after_insert(mapper, connection, cfa):
-    jsonpatch_value = cfa.to_json_serializeable()
-    jsonpatch_path = f'/users/{cfa.corpus.user.hashid}/corpora/{cfa.corpus.hashid}/corpus_follower_associations/{cfa.hashid}'
-    jsonpatch = [
-        {
-            'op': 'add',
-            'path': jsonpatch_path,
-            'value': jsonpatch_value
-        }
-    ]
-    namespace = '/users'
-    room = f'/users/{cfa.corpus.user.hashid}'
-    socketio.emit('patch', jsonpatch, namespace=namespace, room=room)
-
-
-def resource_after_update(mapper, connection, resource):
-    jsonpatch = []
-    for attr in db.inspect(resource).attrs:
-        if attr.key in mapper.relationships:
-            continue
-        if not attr.load_history().has_changes():
-            continue
-        jsonpatch_path = f'{resource.jsonpatch_path}/{attr.key}'
-        if isinstance(attr.value, datetime):
-            jsonpatch_value = f'{attr.value.isoformat()}Z'
-        elif isinstance(attr.value, Enum):
-            jsonpatch_value = attr.value.name
-        else:
-            jsonpatch_value = attr.value
-        jsonpatch.append(
-            {
-                'op': 'replace',
-                'path': jsonpatch_path,
-                'value': jsonpatch_value
-            }
-        )
-    if jsonpatch:
-        namespace = '/users'
-        room = f'/users/{resource.user_hashid}'
-        socketio.emit('patch', jsonpatch, namespace=namespace, room=room)
-
-
-def job_after_update(mapper, connection, job):
-    for attr in db.inspect(job).attrs:
-        if attr.key != 'status':
-            continue
-        if not attr.load_history().has_changes():
-            return
-        if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.NONE:
-            return
-        if job.user.setting_job_status_mail_notification_level == UserSettingJobStatusMailNotificationLevel.END:
-            if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
-                return
-        msg = create_message(
-            job.user.email,
-            f'Status update for your Job "{job.title}"',
-            'tasks/email/notification',
-            job=job
-        )
-        mail.send(msg)

app/models/file_mixin.py

@@ -1,40 +0,0 @@
-from datetime import datetime
-from flask import current_app
-from werkzeug.utils import secure_filename
-from app import db
-
-
-class FileMixin:
-    '''
-    Mixin for db.Model classes. All file related models should use this.
-    '''
-    creation_date = db.Column(db.DateTime, default=datetime.utcnow)
-    filename = db.Column(db.String(255))
-    mimetype = db.Column(db.String(255))
-
-    def file_mixin_to_json_serializeable(self, backrefs=False, relationships=False):
-        return {
-            'creation_date': f'{self.creation_date.isoformat()}Z',
-            'filename': self.filename,
-            'mimetype': self.mimetype
-        }
-    
-    @classmethod
-    def create(cls, file_storage, **kwargs):
-        filename = kwargs.pop('filename', file_storage.filename)
-        mimetype = kwargs.pop('mimetype', file_storage.mimetype)
-        obj = cls(
-            filename=secure_filename(filename),
-            mimetype=mimetype,
-            **kwargs
-        )
-        db.session.add(obj)
-        db.session.flush(objects=[obj])
-        db.session.refresh(obj)
-        try:
-            file_storage.save(obj.path)
-        except (AttributeError, OSError) as e:
-            current_app.logger.error(e)
-            db.session.rollback()
-            raise e
-        return obj

app/models/job.py

@@ -1,171 +0,0 @@
-from datetime import datetime
-from enum import IntEnum
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from time import sleep
-from pathlib import Path
-import shutil
-from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn, IntEnumColumn
-
-
-class JobStatus(IntEnum):
-    INITIALIZING = 1
-    SUBMITTED = 2
-    QUEUED = 3
-    RUNNING = 4
-    CANCELING = 5
-    CANCELED = 6
-    COMPLETED = 7
-    FAILED = 8
-
-    @staticmethod
-    def get(job_status: 'JobStatus | int | str') -> 'JobStatus':
-        if isinstance(job_status, JobStatus):
-            return job_status
-        if isinstance(job_status, int):
-            return JobStatus(job_status)
-        if isinstance(job_status, str):
-            return JobStatus[job_status]
-        raise TypeError('job_status must be JobStatus, int, or str')
-
-
-class Job(HashidMixin, db.Model):
-    '''
-    Class to define Jobs.
-    '''
-    __tablename__ = 'jobs'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Fields
-    creation_date = \
-        db.Column(db.DateTime(), default=datetime.utcnow)
-    description = db.Column(db.String(255))
-    end_date = db.Column(db.DateTime())
-    service = db.Column(db.String(64))
-    service_args = db.Column(ContainerColumn(dict, 255))
-    service_version = db.Column(db.String(16))
-    status = db.Column(
-        IntEnumColumn(JobStatus),
-        default=JobStatus.INITIALIZING
-    )
-    title = db.Column(db.String(32))
-    # Relationships
-    inputs = db.relationship(
-        'JobInput',
-        back_populates='job',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    results = db.relationship(
-        'JobResult',
-        back_populates='job',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    user = db.relationship(
-        'User',
-        back_populates='jobs'
-    )
-
-    def __repr__(self):
-        return f'<Job {self.title}>'
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.user.jsonpatch_path}/jobs/{self.hashid}'
-
-    @property
-    def path(self) -> Path:
-        return self.user.path / 'jobs' / f'{self.id}'
-
-    @property
-    def url(self):
-        return url_for('jobs.job', job_id=self.id)
-
-    @property
-    def user_hashid(self):
-        return self.user.hashid
-
-    @staticmethod
-    def create(**kwargs):
-        job = Job(**kwargs)
-        db.session.add(job)
-        db.session.flush(objects=[job])
-        db.session.refresh(job)
-        job_inputs_dir = job.path / 'inputs'
-        job_pipeline_data_dir = job.path / 'pipeline_data'
-        job_results_dir = job.path / 'results'
-        try:
-            job.path.mkdir()
-            job_inputs_dir.mkdir()
-            job_pipeline_data_dir.mkdir()
-            job_results_dir.mkdir()
-        except OSError as e:
-            # TODO: Potential leftover cleanup
-            current_app.logger.error(e)
-            db.session.rollback()
-            raise
-        return job
-
-    def delete(self):
-        ''' Delete the job and its inputs and results from the database. '''
-        if self.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:  # noqa
-            self.status = JobStatus.CANCELING
-            db.session.commit()
-            while self.status != JobStatus.CANCELED:
-                # In case the daemon handled a job in any way
-                if self.status != JobStatus.CANCELING:
-                    self.status = JobStatus.CANCELING
-                    db.session.commit()
-                sleep(1)
-                db.session.refresh(self)
-        try:
-            shutil.rmtree(self.path)
-        except OSError as e:
-            current_app.logger.error(e)
-            db.session.rollback()
-            raise e
-        db.session.delete(self)
-
-    def restart(self):
-        ''' Restart a job - only if the status is failed '''
-        if self.status != JobStatus.FAILED:
-            raise Exception('Job status is not "failed"')
-        shutil.rmtree(self.path / 'results', ignore_errors=True)
-        shutil.rmtree(self.path / 'pyflow.data', ignore_errors=True)
-        for result in self.results:
-            db.session.delete(result)
-        self.end_date = None
-        self.status = JobStatus.SUBMITTED
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'creation_date': f'{self.creation_date.isoformat()}Z',
-            'description': self.description,
-            'end_date': (
-                None if self.end_date is None
-                else f'{self.end_date.isoformat()}Z'
-            ),
-            'service': self.service,
-            'service_args': self.service_args,
-            'service_version': self.service_version,
-            'status': self.status.name,
-            'title': self.title
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            json_serializeable['inputs'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.inputs
-            }
-            json_serializeable['results'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.results
-            }
-        return json_serializeable

app/models/job_input.py

@@ -1,65 +0,0 @@
-from flask import url_for
-from flask_hashids import HashidMixin
-from pathlib import Path
-from app import db
-from .file_mixin import FileMixin
-
-
-class JobInput(FileMixin, HashidMixin, db.Model):
-    __tablename__ = 'job_inputs'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
-    # Relationships
-    job = db.relationship(
-        'Job',
-        back_populates='inputs'
-    )
-
-    def __repr__(self):
-        return f'<JobInput {self.filename}>'
-
-    @property
-    def content_url(self):
-        return url_for(
-            'jobs.download_job_input',
-            job_id=self.job.id,
-            job_input_id=self.id
-        )
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.job.jsonpatch_path}/inputs/{self.hashid}'
-
-    @property
-    def path(self) -> Path:
-        return self.job.path / 'inputs' / f'{self.id}'
-
-    @property
-    def url(self):
-        return url_for(
-            'jobs.job',
-            job_id=self.job_id,
-            _anchor=f'job-{self.job.hashid}-input-{self.hashid}'
-        )
-
-    @property
-    def user_hashid(self):
-        return self.job.user.hashid
-
-    @property
-    def user_id(self):
-        return self.job.user.id
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            **self.file_mixin_to_json_serializeable()
-        }
-        if backrefs:
-            json_serializeable['job'] = \
-                self.job.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/job_result.py

@@ -1,71 +0,0 @@
-from flask import url_for
-from flask_hashids import HashidMixin
-from pathlib import Path
-from app import db
-from .file_mixin import FileMixin
-
-
-class JobResult(FileMixin, HashidMixin, db.Model):
-    __tablename__ = 'job_results'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
-    # Fields
-    description = db.Column(db.String(255))
-    # Relationships
-    job = db.relationship(
-        'Job',
-        back_populates='results'
-    )
-
-    def __repr__(self):
-        return f'<JobResult {self.filename}>'
-
-    @property
-    def download_url(self):
-        return url_for(
-            'jobs.download_job_result',
-            job_id=self.job_id,
-            job_result_id=self.id
-        )
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.job.jsonpatch_path}/results/{self.hashid}'
-
-    @property
-    def path(self) -> Path:
-        return self.job.path / 'results' / f'{self.id}'
-
-    @property
-    def url(self):
-        return url_for(
-            'jobs.job',
-            job_id=self.job_id,
-            _anchor=f'job-{self.job.hashid}-result-{self.hashid}'
-        )
-
-    @property
-    def user_hashid(self):
-        return self.job.user.hashid
-
-    @property
-    def user_id(self):
-        return self.job.user.id
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'description': self.description,
-            **self.file_mixin_to_json_serializeable(
-                backrefs=backrefs,
-                relationships=relationships
-            )
-        }
-        if backrefs:
-            json_serializeable['job'] = \
-                self.job.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/role.py

@@ -1,99 +0,0 @@
-from enum import IntEnum
-from flask_hashids import HashidMixin
-from app import db
-
-
-class Permission(IntEnum):
-    '''
-    Defines User permissions as integers by the power of 2. User permission
-    can be evaluated using the bitwise operator &.
-    '''
-    ADMINISTRATE = 1
-    CONTRIBUTE = 2
-    USE_API = 4
-
-    @staticmethod
-    def get(permission: 'Permission | int | str') -> 'Permission':
-        if isinstance(permission, Permission):
-            return permission
-        if isinstance(permission, int):
-            return Permission(permission)
-        if isinstance(permission, str):
-            return Permission[permission]
-        raise TypeError('permission must be Permission, int, or str')
-
-
-class Role(HashidMixin, db.Model):
-    __tablename__ = 'roles'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Fields
-    name = db.Column(db.String(64), unique=True)
-    default = db.Column(db.Boolean, default=False, index=True)
-    permissions = db.Column(db.Integer, default=0)
-    # Relationships
-    users = db.relationship('User', back_populates='role', lazy='dynamic')
-
-    def __repr__(self):
-        return f'<Role {self.name}>'
-
-    def has_permission(self, permission: Permission | int | str):
-        p = Permission.get(permission)
-        return self.permissions & p.value == p.value
-
-    def add_permission(self, permission: Permission | int | str):
-        p = Permission.get(permission)
-        if not self.has_permission(p):
-            self.permissions += p.value
-
-    def remove_permission(self, permission: Permission | int | str):
-        p = Permission.get(permission)
-        if self.has_permission(p):
-            self.permissions -= p.value
-
-    def reset_permissions(self):
-        self.permissions = 0
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'default': self.default,
-            'name': self.name,
-            'permissions': [
-                x.name for x in Permission
-                if self.has_permission(x.value)
-            ]
-        }
-        if backrefs:
-            pass
-        if relationships:
-            json_serializeable['users'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.users
-            }
-        return json_serializeable
-
-    @staticmethod
-    def insert_defaults():
-        roles = {
-            'User': [],
-            'API user': [Permission.USE_API],
-            'Contributor': [Permission.CONTRIBUTE],
-            'Administrator': [
-                Permission.ADMINISTRATE,
-                Permission.CONTRIBUTE,
-                Permission.USE_API
-            ],
-            'System user': []
-        }
-        default_role_name = 'User'
-        for role_name, permissions in roles.items():
-            role = Role.query.filter_by(name=role_name).first()
-            if role is None:
-                role = Role(name=role_name)
-            role.reset_permissions()
-            for permission in permissions:
-                role.add_permission(permission)
-            role.default = role.name == default_role_name
-            db.session.add(role)
-        db.session.commit()

app/models/spacy_nlp_pipeline_model.py

@@ -1,136 +0,0 @@
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from tqdm import tqdm
-from pathlib import Path
-import requests
-import yaml
-from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn
-from .file_mixin import FileMixin
-from .user import User
-
-
-class SpaCyNLPPipelineModel(FileMixin, HashidMixin, db.Model):
-    __tablename__ = 'spacy_nlp_pipeline_models'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Fields
-    title = db.Column(db.String(64))
-    description = db.Column(db.String(255))
-    version = db.Column(db.String(16))
-    compatible_service_versions = db.Column(ContainerColumn(list, 255))
-    publisher = db.Column(db.String(128))
-    publisher_url = db.Column(db.String(512))
-    publishing_url = db.Column(db.String(512))
-    publishing_year = db.Column(db.Integer)
-    pipeline_name = db.Column(db.String(64))
-    is_public = db.Column(db.Boolean, default=False)
-    # Relationships
-    user = db.relationship('User', back_populates='spacy_nlp_pipeline_models')
-
-    @property
-    def path(self) -> Path:
-        return self.user.path / 'spacy_nlp_pipeline_models' / f'{self.id}'
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.user.jsonpatch_path}/spacy_nlp_pipeline_models/{self.hashid}'
-
-    @property
-    def url(self):
-        return url_for(
-            'contributions.spacy_nlp_pipeline_models.entity',
-            spacy_nlp_pipeline_model_id=self.id
-        )
-
-    @property
-    def user_hashid(self):
-        return self.user.hashid
-
-    @staticmethod
-    def insert_defaults(force_download=False):
-        nopaque_user = User.query.filter_by(username='nopaque').first()
-        default_records_file = Path(__file__).parent / 'default_records' / 'spacy_nlp_pipeline_model.yml'
-        with default_records_file.open('r') as f:
-            default_records = yaml.safe_load(f)
-        for m in default_records:
-            model = SpaCyNLPPipelineModel.query.filter_by(title=m['title'], version=m['version']).first()  # noqa
-            if model is not None:
-                model.compatible_service_versions = m['compatible_service_versions']
-                model.description = m['description']
-                model.filename = m['url'].split('/')[-1]
-                model.publisher = m['publisher']
-                model.publisher_url = m['publisher_url']
-                model.publishing_url = m['publishing_url']
-                model.publishing_year = m['publishing_year']
-                model.is_public = True
-                model.title = m['title']
-                model.version = m['version']
-                model.pipeline_name = m['pipeline_name']
-            else:
-                model = SpaCyNLPPipelineModel(
-                    compatible_service_versions=m['compatible_service_versions'],
-                    description=m['description'],
-                    filename=m['url'].split('/')[-1],
-                    publisher=m['publisher'],
-                    publisher_url=m['publisher_url'],
-                    publishing_url=m['publishing_url'],
-                    publishing_year=m['publishing_year'],
-                    is_public=True,
-                    title=m['title'],
-                    user=nopaque_user,
-                    version=m['version'],
-                    pipeline_name=m['pipeline_name']
-                )
-                db.session.add(model)
-                db.session.flush(objects=[model])
-                db.session.refresh(model)
-            if not model.path.exists() or force_download:
-                r = requests.get(m['url'], stream=True)
-                pbar = tqdm(
-                    desc=f'{model.title} ({model.filename})',
-                    unit="B",
-                    unit_scale=True,
-                    unit_divisor=1024,
-                    total=int(r.headers['Content-Length'])
-                )
-                pbar.clear()
-                with open(model.path, 'wb') as f:
-                    for chunk in r.iter_content(chunk_size=1024):
-                        if chunk:  # filter out keep-alive new chunks
-                            pbar.update(len(chunk))
-                            f.write(chunk)
-                    pbar.close()
-        db.session.commit()
-
-    def delete(self):
-        try:
-            self.path.unlink(missing_ok=True)
-        except OSError as e:
-            current_app.logger.error(e)
-            raise
-        db.session.delete(self)
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'compatible_service_versions': self.compatible_service_versions,
-            'description': self.description,
-            'publisher': self.publisher,
-            'publisher_url': self.publisher_url,
-            'publishing_url': self.publishing_url,
-            'publishing_year': self.publishing_year,
-            'pipeline_name': self.pipeline_name,
-            'is_public': self.is_public,
-            'title': self.title,
-            'version': self.version,
-            **self.file_mixin_to_json_serializeable()
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/tesseract_ocr_pipeline_model.py

@@ -1,132 +0,0 @@
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from tqdm import tqdm
-from pathlib import Path
-import requests
-import yaml
-from app import db
-from app.extensions.nopaque_sqlalchemy_extras import ContainerColumn
-from .file_mixin import FileMixin
-from .user import User
-
-
-class TesseractOCRPipelineModel(FileMixin, HashidMixin, db.Model):
-    __tablename__ = 'tesseract_ocr_pipeline_models'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Fields
-    title = db.Column(db.String(64))
-    description = db.Column(db.String(255))
-    version = db.Column(db.String(16))
-    compatible_service_versions = db.Column(ContainerColumn(list, 255))
-    publisher = db.Column(db.String(128))
-    publisher_url = db.Column(db.String(512))
-    publishing_url = db.Column(db.String(512))
-    publishing_year = db.Column(db.Integer)
-    is_public = db.Column(db.Boolean, default=False)
-    # Relationships
-    user = db.relationship('User', back_populates='tesseract_ocr_pipeline_models')
-
-    @property
-    def path(self) -> Path:
-        return self.user.path / 'tesseract_ocr_pipeline_models' / f'{self.id}'
-
-    @property
-    def jsonpatch_path(self):
-        return f'{self.user.jsonpatch_path}/tesseract_ocr_pipeline_models/{self.hashid}'
-
-    @property
-    def url(self):
-        return url_for(
-            'contributions.tesseract_ocr_pipeline_models.entity',
-            tesseract_ocr_pipeline_model_id=self.id
-        )
-
-    @property
-    def user_hashid(self):
-        return self.user.hashid
-
-    @staticmethod
-    def insert_defaults(force_download=False):
-        nopaque_user = User.query.filter_by(username='nopaque').first()
-        default_records_file = Path(__file__).parent / 'default_records' / 'tesseract_ocr_pipeline_model.yml'
-        with default_records_file.open('r') as f:
-            default_records = yaml.safe_load(f)
-        for m in default_records:
-            model = TesseractOCRPipelineModel.query.filter_by(title=m['title'], version=m['version']).first()  # noqa
-            if model is not None:
-                model.compatible_service_versions = m['compatible_service_versions']
-                model.description = m['description']
-                model.filename = f'{model.id}.traineddata'
-                model.publisher = m['publisher']
-                model.publisher_url = m['publisher_url']
-                model.publishing_url = m['publishing_url']
-                model.publishing_year = m['publishing_year']
-                model.is_public = True
-                model.title = m['title']
-                model.version = m['version']
-            else:
-                model = TesseractOCRPipelineModel(
-                    compatible_service_versions=m['compatible_service_versions'],
-                    description=m['description'],
-                    publisher=m['publisher'],
-                    publisher_url=m['publisher_url'],
-                    publishing_url=m['publishing_url'],
-                    publishing_year=m['publishing_year'],
-                    is_public=True,
-                    title=m['title'],
-                    user=nopaque_user,
-                    version=m['version']
-                )
-                db.session.add(model)
-                db.session.flush(objects=[model])
-                db.session.refresh(model)
-                model.filename = f'{model.id}.traineddata'
-            if not model.path.exists() or force_download:
-                r = requests.get(m['url'], stream=True)
-                pbar = tqdm(
-                    desc=f'{model.title} ({model.filename})',
-                    unit="B",
-                    unit_scale=True,
-                    unit_divisor=1024,
-                    total=int(r.headers['Content-Length'])
-                )
-                pbar.clear()
-                with open(model.path, 'wb') as f:
-                    for chunk in r.iter_content(chunk_size=1024):
-                        if chunk:  # filter out keep-alive new chunks
-                            pbar.update(len(chunk))
-                            f.write(chunk)
-                    pbar.close()
-        db.session.commit()
-
-    def delete(self):
-        try:
-            self.path.unlink(missing_ok=True)
-        except OSError as e:
-            current_app.logger.error(e)
-            raise
-        db.session.delete(self)
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'compatible_service_versions': self.compatible_service_versions,
-            'description': self.description,
-            'publisher': self.publisher,
-            'publisher_url': self.publisher_url,
-            'publishing_url': self.publishing_url,
-            'publishing_year': self.publishing_year,
-            'is_public': self.is_public,
-            'title': self.title,
-            'version': self.version,
-            **self.file_mixin_to_json_serializeable()
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable

app/models/token.py

@@ -1,48 +0,0 @@
-from datetime import datetime, timedelta
-from app import db
-
-
-class Token(db.Model):
-    __tablename__ = 'tokens'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
-    # Fields
-    access_token = db.Column(db.String(64), index=True)
-    access_expiration = db.Column(db.DateTime)
-    refresh_token = db.Column(db.String(64), index=True)
-    refresh_expiration = db.Column(db.DateTime)
-    # Relationships
-    user = db.relationship('User', back_populates='tokens')
-
-    def expire(self):
-        self.access_expiration = datetime.utcnow()
-        self.refresh_expiration = datetime.utcnow()
-
-    def to_json_serializeable(self, backrefs=False, relationships=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'access_token': self.access_token,
-            'access_expiration': (
-                None if self.access_expiration is None
-                else f'{self.access_expiration.isoformat()}Z'
-            ),
-            'refresh_token': self.refresh_token,
-            'refresh_expiration': (
-                None if self.refresh_expiration is None
-                else f'{self.refresh_expiration.isoformat()}Z'
-            )
-        }
-        if backrefs:
-            json_serializeable['user'] = \
-                self.user.to_json_serializeable(backrefs=True)
-        if relationships:
-            pass
-        return json_serializeable
-
-    @staticmethod
-    def clean():
-        """Remove any tokens that have been expired for more than a day."""
-        yesterday = datetime.utcnow() - timedelta(days=1)
-        Token.query.filter(Token.refresh_expiration < yesterday).delete()

app/models/user.py

@@ -1,453 +0,0 @@
-from datetime import datetime, timedelta
-from enum import IntEnum
-from flask import current_app, url_for
-from flask_hashids import HashidMixin
-from flask_login import UserMixin
-from sqlalchemy.ext.associationproxy import association_proxy
-from pathlib import Path
-from werkzeug.security import generate_password_hash, check_password_hash
-import jwt
-import re
-import secrets
-import shutil
-from app import db, hashids
-from app.extensions.nopaque_sqlalchemy_extras import IntEnumColumn
-from .corpus import Corpus
-from .corpus_follower_association import CorpusFollowerAssociation
-from .corpus_follower_role import CorpusFollowerRole
-from .role import Permission, Role
-from .token import Token
-
-
-class ProfilePrivacySettings(IntEnum):
-    SHOW_EMAIL = 1
-    SHOW_LAST_SEEN = 2
-    SHOW_MEMBER_SINCE = 4
-
-    @staticmethod
-    def get(profile_privacy_setting: 'ProfilePrivacySettings | int | str') -> 'ProfilePrivacySettings':
-        if isinstance(profile_privacy_setting, ProfilePrivacySettings):
-            return profile_privacy_setting
-        if isinstance(profile_privacy_setting, int):
-            return ProfilePrivacySettings(profile_privacy_setting)
-        if isinstance(profile_privacy_setting, str):
-            return ProfilePrivacySettings[profile_privacy_setting]
-        raise TypeError('profile_privacy_setting must be ProfilePrivacySettings, int, or str')
-
-
-class UserSettingJobStatusMailNotificationLevel(IntEnum):
-    NONE = 1
-    END = 2
-    ALL = 3
-
-
-class User(HashidMixin, UserMixin, db.Model):
-    __tablename__ = 'users'
-    # Primary key
-    id = db.Column(db.Integer, primary_key=True)
-    # Foreign keys
-    role_id = db.Column(db.Integer, db.ForeignKey('roles.id'))
-    # Fields
-    email = db.Column(db.String(254), index=True, unique=True)
-    username = db.Column(db.String(64), index=True, unique=True)
-    username_pattern = re.compile(r'^[A-Za-zÄÖÜäöüß0-9_.]*$')
-    password_hash = db.Column(db.String(128))
-    confirmed = db.Column(db.Boolean, default=False)
-    terms_of_use_accepted = db.Column(db.Boolean, default=False)
-    member_since = db.Column(db.DateTime(), default=datetime.utcnow)
-    setting_job_status_mail_notification_level = db.Column(
-        IntEnumColumn(UserSettingJobStatusMailNotificationLevel),
-        default=UserSettingJobStatusMailNotificationLevel.END
-    )
-    last_seen = db.Column(db.DateTime())
-    full_name = db.Column(db.String(64))
-    about_me = db.Column(db.String(256))
-    location = db.Column(db.String(64))
-    website = db.Column(db.String(128))
-    organization = db.Column(db.String(128))
-    is_public = db.Column(db.Boolean, default=False)
-    profile_privacy_settings = db.Column(db.Integer(), default=0)
-    # Relationships
-    avatar = db.relationship(
-        'Avatar',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        uselist=False
-    )
-    corpora = db.relationship(
-        'Corpus',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    corpus_follower_associations = db.relationship(
-        'CorpusFollowerAssociation',
-        back_populates='follower',
-        cascade='all, delete-orphan'
-    )
-    followed_corpora = association_proxy(
-        'corpus_follower_associations',
-        'corpus',
-        creator=lambda c: CorpusFollowerAssociation(corpus=c)
-    )
-    jobs = db.relationship(
-        'Job',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    role = db.relationship(
-        'Role',
-        back_populates='users'
-    )
-    spacy_nlp_pipeline_models = db.relationship(
-        'SpaCyNLPPipelineModel',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    tesseract_ocr_pipeline_models = db.relationship(
-        'TesseractOCRPipelineModel',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-    tokens = db.relationship(
-        'Token',
-        back_populates='user',
-        cascade='all, delete-orphan',
-        lazy='dynamic'
-    )
-
-    def __init__(self, **kwargs):
-        if 'role' not in kwargs:
-            kwargs['role'] = (
-                Role.query.filter_by(name='Administrator').first()
-                if kwargs['email'] == current_app.config['NOPAQUE_ADMIN']
-                else Role.query.filter_by(default=True).first()
-            )
-        super().__init__(**kwargs)
-
-    def __repr__(self):
-        return f'<User {self.username}>'
-
-    @property
-    def is_administrator(self):
-        return self.can(Permission.ADMINISTRATE)
-
-    @property
-    def jsonpatch_path(self):
-        return f'/users/{self.hashid}'
-
-    @property
-    def password(self):
-        raise AttributeError('password is not a readable attribute')
-
-    @password.setter
-    def password(self, password):
-        #pbkdf2:sha256
-        self.password_hash = generate_password_hash(password, method='pbkdf2')
-
-    @property
-    def path(self) -> Path:
-        return current_app.config.get('NOPAQUE_DATA_DIR') / 'users' / f'{self.id}'
-
-    @staticmethod
-    def create(**kwargs):
-        user = User(**kwargs)
-        db.session.add(user)
-        db.session.flush(objects=[user])
-        db.session.refresh(user)
-        user_spacy_nlp_pipeline_models_dir = user.path / 'spacy_nlp_pipeline_models'
-        user_tesseract_ocr_pipeline_models_dir = user.path / 'tesseract_ocr_pipeline_models'
-        user_corpora_dir = user.path / 'corpora'
-        user_jobs_dir = user.path / 'jobs'
-        try:
-            user.path.mkdir()
-            user_spacy_nlp_pipeline_models_dir.mkdir()
-            user_tesseract_ocr_pipeline_models_dir.mkdir()
-            user_corpora_dir.mkdir()
-            user_jobs_dir.mkdir()
-        except OSError as e:
-            # TODO: Potential leftover cleanup
-            current_app.logger.error(e)
-            db.session.rollback()
-            raise
-        return user
-
-    @staticmethod
-    def insert_defaults():
-        nopaque_user = User.query.filter_by(username='nopaque').first()
-        system_user_role = Role.query.filter_by(name='System user').first()
-        if nopaque_user is None:
-            nopaque_user = User.create(
-                username='nopaque',
-                role=system_user_role
-            )
-            db.session.add(nopaque_user)
-        elif nopaque_user.role != system_user_role:
-            nopaque_user.role = system_user_role
-        db.session.commit()
-
-    @staticmethod
-    def reset_password(token, new_password):
-        try:
-            payload = jwt.decode(
-                token,
-                current_app.config['SECRET_KEY'],
-                algorithms=['HS256'],
-                issuer=current_app.config['SERVER_NAME'],
-                options={'require': ['exp', 'iat', 'iss', 'purpose', 'sub']}
-            )
-        except jwt.PyJWTError:
-            return False
-        if payload.get('purpose') != 'User.reset_password':
-            return False
-        user_hashid = payload.get('sub')
-        user_id = hashids.decode(user_hashid)
-        user = User.query.get(user_id)
-        if user is None:
-            return False
-        user.password = new_password
-        db.session.add(user)
-        return True
-
-    @staticmethod
-    def verify_access_token(access_token, refresh_token=None):
-        token = Token.query.filter(Token.access_token == access_token).first()
-        if token is not None:
-            if token.access_expiration > datetime.utcnow():
-                token.user.ping()
-                db.session.commit()
-                if token.user.role.name != 'System user':
-                    return token.user
-
-    @staticmethod
-    def verify_refresh_token(refresh_token, access_token):
-        token = Token.query.filter((Token.refresh_token == refresh_token) & (Token.access_token == access_token)).first()
-        if token is not None:
-            if token.refresh_expiration > datetime.utcnow():
-                return token
-            # someone tried to refresh with an expired token
-            # revoke all tokens from this user as a precaution
-            token.user.revoke_auth_tokens()
-            db.session.commit()
-
-    def can(self, permission):
-        return self.role is not None and self.role.has_permission(permission)
-
-    def confirm(self, confirmation_token):
-        try:
-            payload = jwt.decode(
-                confirmation_token,
-                current_app.config['SECRET_KEY'],
-                algorithms=['HS256'],
-                issuer=current_app.config['SERVER_NAME'],
-                options={'require': ['exp', 'iat', 'iss', 'purpose', 'sub']}
-            )
-        except jwt.PyJWTError:
-            return False
-        if payload.get('purpose') != 'user.confirm':
-            return False
-        if payload.get('sub') != self.hashid:
-            return False
-        self.confirmed = True
-        db.session.add(self)
-        return True
-
-    def delete(self):
-        shutil.rmtree(self.path, ignore_errors=True)
-        db.session.delete(self)
-
-    def generate_auth_token(self):
-        return Token(
-            access_token=secrets.token_urlsafe(),
-            access_expiration=datetime.utcnow() + timedelta(minutes=15),
-            refresh_token=secrets.token_urlsafe(),
-            refresh_expiration=datetime.utcnow() + timedelta(days=7),
-            user=self
-        )
-
-    def generate_confirm_token(self, expiration=3600):
-        now = datetime.utcnow()
-        payload = {
-            'exp': now + timedelta(seconds=expiration),
-            'iat': now,
-            'iss': current_app.config['SERVER_NAME'],
-            'purpose': 'user.confirm',
-            'sub': self.hashid
-        }
-        return jwt.encode(
-            payload,
-            current_app.config['SECRET_KEY'],
-            algorithm='HS256'
-        )
-
-    def generate_reset_password_token(self, expiration=3600):
-        now = datetime.utcnow()
-        payload = {
-            'exp': now + timedelta(seconds=expiration),
-            'iat': now,
-            'iss': current_app.config['SERVER_NAME'],
-            'purpose': 'User.reset_password',
-            'sub': self.hashid
-        }
-        return jwt.encode(
-            payload,
-            current_app.config['SECRET_KEY'],
-            algorithm='HS256'
-        )
-
-    def ping(self):
-        self.last_seen = datetime.utcnow()
-
-    def revoke_auth_tokens(self):
-        for token in self.tokens:
-            db.session.delete(token)
-
-    def verify_password(self, password):
-        if self.role.name == 'System user':
-            return False
-        return check_password_hash(self.password_hash, password)
-
-    #region Profile Privacy settings
-    def has_profile_privacy_setting(self, setting):
-        s = ProfilePrivacySettings.get(setting)
-        return self.profile_privacy_settings & s.value == s.value
-
-    def add_profile_privacy_setting(self, setting):
-        s = ProfilePrivacySettings.get(setting)
-        if not self.has_profile_privacy_setting(s):
-            self.profile_privacy_settings += s.value
-
-    def remove_profile_privacy_setting(self, setting):
-        s = ProfilePrivacySettings.get(setting)
-        if self.has_profile_privacy_setting(s):
-            self.profile_privacy_settings -= s.value
-
-    def reset_profile_privacy_settings(self):
-        self.profile_privacy_settings = 0
-    #endregion Profile Privacy settings
-
-    def follow_corpus(self, corpus, role=None):
-        if role is None:
-            cfr = CorpusFollowerRole.query.filter_by(default=True).first()
-        else:
-            cfr = role
-        if self.is_following_corpus(corpus):
-            cfa = CorpusFollowerAssociation.query.filter_by(corpus=corpus, follower=self).first()
-            if cfa.role != cfr:
-                cfa.role = cfr
-        else:
-            cfa = CorpusFollowerAssociation(corpus=corpus, role=cfr, follower=self)
-            db.session.add(cfa)
-
-    def unfollow_corpus(self, corpus):
-        if not self.is_following_corpus(corpus):
-            return
-        self.followed_corpora.remove(corpus)
-
-    def is_following_corpus(self, corpus):
-        return corpus in self.followed_corpora
-
-    def generate_follow_corpus_token(self, corpus_hashid, role_name, expiration=7):
-        now = datetime.utcnow()
-        payload = {
-            'exp': expiration,
-            'iat': now,
-            'iss': current_app.config['SERVER_NAME'],
-            'purpose': 'User.follow_corpus',
-            'role_name': role_name,
-            'sub': corpus_hashid
-        }
-        return jwt.encode(
-            payload,
-            current_app.config['SECRET_KEY'],
-            algorithm='HS256'
-        )
-
-    def follow_corpus_by_token(self, token):
-        try:
-            payload = jwt.decode(
-                token,
-                current_app.config['SECRET_KEY'],
-                algorithms=['HS256'],
-                issuer=current_app.config['SERVER_NAME'],
-                options={'require': ['exp', 'iat', 'iss', 'purpose', 'role_name', 'sub']}
-            )
-        except jwt.PyJWTError:
-            return False
-        if payload.get('purpose') != 'User.follow_corpus':
-            return False
-        corpus_hashid = payload.get('sub')
-        corpus_id = hashids.decode(corpus_hashid)
-        corpus = Corpus.query.get_or_404(corpus_id)
-        if corpus is None:
-            return False
-        role_name = payload.get('role_name')
-        role = CorpusFollowerRole.query.filter_by(name=role_name).first()
-        if role is None:
-            return False
-        self.follow_corpus(corpus, role)
-        # db.session.add(self)
-        return True
-
-    def to_json_serializeable(self, backrefs=False, relationships=False, filter_by_privacy_settings=False):
-        json_serializeable = {
-            'id': self.hashid,
-            'confirmed': self.confirmed,
-            'avatar': url_for('users.user_avatar', user_id=self.id),
-            'email': self.email,
-            'last_seen': (
-                None if self.last_seen is None
-                else f'{self.last_seen.isoformat()}Z'
-            ),
-            'member_since': f'{self.member_since.isoformat()}Z',
-            'username': self.username,
-            'full_name': self.full_name,
-            'about_me': self.about_me,
-            'website': self.website,
-            'location': self.location,
-            'organization': self.organization,
-            'job_status_mail_notification_level': \
-                    self.setting_job_status_mail_notification_level.name,
-            'profile_privacy_settings': {
-                'is_public': self.is_public,
-                'show_email': self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_EMAIL),
-                'show_last_seen': self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_LAST_SEEN),
-                'show_member_since': self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_MEMBER_SINCE)
-            }
-        }
-        if backrefs:
-            json_serializeable['role'] = \
-                self.role.to_json_serializeable(backrefs=True)
-        if relationships:
-            json_serializeable['corpus_follower_associations'] = {
-                x.hashid: x.to_json_serializeable()
-                for x in self.corpus_follower_associations
-            }
-            json_serializeable['corpora'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.corpora
-            }
-            json_serializeable['jobs'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.jobs
-            }
-            json_serializeable['tesseract_ocr_pipeline_models'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.tesseract_ocr_pipeline_models
-            }
-            json_serializeable['spacy_nlp_pipeline_models'] = {
-                x.hashid: x.to_json_serializeable(relationships=True)
-                for x in self.spacy_nlp_pipeline_models
-            }
-
-        if filter_by_privacy_settings:
-            if not self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_EMAIL):
-                json_serializeable.pop('email')
-            if not self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_LAST_SEEN):
-                json_serializeable.pop('last_seen')
-            if not self.has_profile_privacy_setting(ProfilePrivacySettings.SHOW_MEMBER_SINCE):
-                json_serializeable.pop('member_since')
-        return json_serializeable

app/namespaces/cqi_over_sio/utils.py

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

app/namespaces/jobs.py

@@ -1,109 +0,0 @@
-from flask import current_app, Flask
-from flask_login import current_user
-from flask_socketio import Namespace
-from app import db, hashids, socketio
-from app.decorators import socketio_admin_required, socketio_login_required
-from app.models import Job, JobStatus
-
-
-def _delete_job(app: Flask, job_id: int):
-    with app.app_context():
-        job = Job.query.get(job_id)
-        job.delete()
-        db.session.commit()
-
-
-def _restart_job(app, job_id):
-    with app.app_context():
-        job = Job.query.get(job_id)
-        job.restart()
-        db.session.commit()
-
-
-class UsersNamespace(Namespace):
-    @socketio_login_required
-    def on_delete(self, job_hashid: str) -> dict:
-        job_id = hashids.decode(job_hashid)
-
-        if not isinstance(job_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        job = Job.query.get(job_id)
-
-        if job is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            job.user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        socketio.start_background_task(
-            _delete_job,
-            current_app._get_current_object(),
-            job_id
-        )
-
-        return {
-            'body': f'Job "{job.title}" marked for deletion',
-            'status': 202,
-            'statusText': 'Accepted'
-        }
-
-    @socketio_admin_required
-    def on_log(self, job_hashid: str):
-        job_id = hashids.decode(job_hashid)
-
-        if not isinstance(job_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        job = Job.query.get(job_id)
-
-        if job is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if job.status not in [JobStatus.COMPLETED, JobStatus.FAILED]:
-            return {'status': 409, 'statusText': 'Conflict'}
-
-        with open(job.path / 'pipeline_data' / 'logs' / 'pyflow_log.txt') as log_file:
-            log = log_file.read()
-
-        return {
-            'body': log,
-            'status': 200,
-            'statusText': 'Forbidden'
-        }
-
-    socketio_login_required
-    def on_restart(self, job_hashid: str):
-        job_id = hashids.decode(job_hashid)
-
-        if not isinstance(job_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        job = Job.query.get(job_id)
-
-        if job is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            job.user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        if job.status == JobStatus.FAILED:
-            return {'status': 409, 'statusText': 'Conflict'}
-
-        socketio.start_background_task(
-            _restart_job,
-            current_app._get_current_object(),
-            job_id
-        )
-
-        return {
-            'body': f'Job "{job.title}" marked for restarting',
-            'status': 202,
-            'statusText': 'Accepted'
-        }

app/namespaces/users.py

@@ -1,116 +0,0 @@
-from flask import current_app, Flask
-from flask_login import current_user
-from flask_socketio import join_room, leave_room, Namespace
-from app import db, hashids, socketio
-from app.decorators import socketio_login_required
-from app.models import User
-
-
-def _delete_user(app: Flask, user_id: int):
-    with app.app_context():
-        user = User.query.get(user_id)
-        user.delete()
-        db.session.commit()
-
-
-class UsersNamespace(Namespace):
-    @socketio_login_required
-    def on_get(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        return {
-            'body': user.to_json_serializeable(
-                backrefs=True,
-                relationships=True
-            ),
-            'status': 200,
-            'statusText': 'OK'
-        }
-
-    @socketio_login_required
-    def on_subscribe(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        join_room(f'/users/{user.hashid}')
-
-        return {'status': 200, 'statusText': 'OK'}
-
-    @socketio_login_required
-    def on_unsubscribe(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        leave_room(f'/users/{user.hashid}')
-
-        return {'status': 200, 'statusText': 'OK'}
-
-    @socketio_login_required
-    def on_delete(self, user_hashid: str) -> dict:
-        user_id = hashids.decode(user_hashid)
-
-        if not isinstance(user_id, int):
-            return {'status': 400, 'statusText': 'Bad Request'}
-
-        user = User.query.get(user_id)
-
-        if user is None:
-            return {'status': 404, 'statusText': 'Not found'}
-
-        if not (
-            user == current_user
-            or current_user.is_administrator
-        ):
-            return {'status': 403, 'statusText': 'Forbidden'}
-
-        socketio.start_background_task(
-            _delete_user,
-            current_app._get_current_object(),
-            user.id
-        )
-
-        return {
-            'body': f'User "{user.username}" marked for deletion',
-            'status': 202,
-            'statusText': 'Accepted'
-        }