build: use mamba to setup project in Docker

Dockerfile

@@ -9,50 +9,37 @@ RUN mkdir -p /sketch_map_tool/static/bundles
 RUN npm run build
 
 
-FROM ubuntu:22.04
+FROM condaforge/mambaforge:latest
+
 
-# install libzbar (neccessary for pyzbar to read the QR codes)
-# install gdal
-# install libgl1 (for openCV)
-# to reduce image size, clean up the apt cache by removing /var/lib/apt/lists.
 RUN apt-get update \
     && apt-get install -y --no-upgrade \
-        python3-pip \
-        libzbar0 \
-        libgdal-dev \
         libgl1 \
     && rm -rf /var/lib/apt/lists/*
-
-# update C env vars so compiler can find gdal
-ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
-ENV C_INCLUDE_PATH=/usr/include/gdal
-
+        # libzbar0 \
+        # libgdal-dev \
 # within docker container: run without root privileges
 RUN useradd -md /home/smt smt
 WORKDIR /opt/smt
 RUN chown smt:smt . -R
 USER smt:smt
 
-# make poetry binaries available to the docker container user
-ENV PATH=$PATH:/home/smt/.local/bin
+COPY --chown=smt:smt environment.yml environment.yml
+RUN mamba env create --file environment.yml
+
+# make RUN commands use the new environment:
+SHELL ["mamba", "run", "--no-capture-output", "--name", "smt", "/bin/bash", "-c"]
 
 COPY --chown=smt:smt pyproject.toml pyproject.toml
 COPY --chown=smt:smt poetry.lock poetry.lock
-COPY --chown=smt:smt setup.cfg setup.cfg
-# install Python dependencies
-RUN pip3 install --no-cache-dir poetry
-# these versions have to be fixed for now, since poetry and (py)gdal packages can't work together
-RUN python3 -m poetry run pip install numpy==1.23.5
-RUN python3 -m poetry run pip install pygdal==3.4.1.10
-RUN python3 -m poetry install --no-ansi --no-interaction --no-root
-
-# copy all the other files and install the project
+RUN which python
+RUN python -m poetry install --no-ansi --no-interaction --no-root
+
 COPY --chown=smt:smt sketch_map_tool sketch_map_tool
 COPY --chown=smt:smt data/ data/
-COPY --chown=smt:smt tests/ tests/
-RUN python3 -m poetry install --no-ansi --no-interaction
+RUN python -m poetry install --no-ansi --no-interaction
 
 # get JS dependencies
 COPY --from=bundler --chown=smt:smt /sketch_map_tool/static/bundles sketch_map_tool/static/bundles
 
-# Use entry-points defined in docker-compose file
+# use entry-points defined in docker-compose file

docker-compose.yaml

@@ -15,7 +15,16 @@ services:
       SMT-RESULT-BACKEND: "db+postgresql://smt:smt@postgres:5432"
     ports:
       - "127.0.0.1:8081:8080"
-    entrypoint: ["poetry", "run", "waitress-serve", "sketch_map_tool.routes:app"]
+    entrypoint:
+      [
+        "mamba",
+        "run",
+        "--no-capture-output",
+        "--name",
+        "smt",
+        "waitress-serve",
+        "sketch_map_tool.routes:app",
+      ]
   celery:
     # Task queue
     build:
@@ -28,7 +37,24 @@ services:
     environment:
       SMT-BROKER-URL: "redis://redis:6379"
       SMT-RESULT-BACKEND: "db+postgresql://smt:smt@postgres:5432"
-    entrypoint: ["poetry", "run", "celery", "--app", "sketch_map_tool.tasks", "worker", "--beat", "--concurrency", "4", "--loglevel", "INFO", "-E"]
+    entrypoint:
+      [
+        "mamba",
+        "run",
+        "--no-capture-output",
+        "--name",
+        "smt",
+        "celery",
+        "--app",
+        "sketch_map_tool.tasks",
+        "worker",
+        "--beat",
+        "--concurrency",
+        "4",
+        "--loglevel",
+        "INFO",
+        "-E",
+      ]
   flower:
     # Monitoring of Celery
     image: mher/flower
@@ -46,7 +72,7 @@ services:
     # dump redis db every 10 minutes (if 1 value changed)
     entrypoint: ["redis-server", "--save", "\"\""]
     volumes:
-        - redis_data:/data
+      - redis_data:/data
   postgres:
     # Result backend
     image: postgres:15
@@ -57,7 +83,7 @@ services:
     ports:
       - "5432:5432"
     volumes:
-        - pg_data:/var/lib/postgresql/data
+      - pg_data:/var/lib/postgresql/data
 volumes:
-    redis_data:
-    pg_data:
+  redis_data:
+  pg_data:

environment.yml

@@ -4,5 +4,6 @@ channels:
 dependencies:
   - python=3.10.*
   - poetry=1.*
-  - gdal=3.7.1  # same as in Dockerfile and pyproject.toml
-  - pyzbar=0.1.9  # same as in Dockerfile and pyproject.toml
+  - gdal=3.7.1
+  - pyzbar=0.1.9
+  - psycopg2=2.9.7

pyproject.toml

@@ -19,7 +19,6 @@ opencv-python = "^4.6.0"
 qrcode = "^7.3.1"
 svglib = "^1.4.1"
 PyMuPDF = {extras = ["Pillow"], version = "^1.21.0"}
-psycopg2 = "^2.9.5"
 plotly = "^5.15.0"
 kaleido = "0.2.1"  # Not working with '^', cf. https://github.com/plotly/Kaleido/issues/125
 geojson = "^2.5.0"

sketch_map_tool/__init__.py

@@ -23,7 +23,7 @@ def make_flask() -> Flask:
             "task_serializer": "pickle",
             "task_track_started": True,  # report ‘started’ status worker executes task
             "task_send_sent_event": True,
-            "result_serializer": "json",
+            "result_serializer": "pickle",
             "result_extended": True,  # save result attributes to backend (e.g. name)
             "result_compression": "gzip",
             "result_chord_join_timeout": 10.0,  # default: 3.0 seconds

sketch_map_tool/database/client_flask.py

@@ -1,5 +1,4 @@
 import json
-from datetime import datetime, timezone
 from uuid import UUID
 
 import psycopg2
@@ -31,16 +30,14 @@ def _insert_id_map(uuid: str, map_: dict):
     create_query = """
     CREATE TABLE IF NOT EXISTS uuid_map(
       uuid uuid PRIMARY KEY,
-      ts timestamptz;
       map json NOT NULL
     )
     """
-    insert_query = "INSERT INTO uuid_map(uuid, ts, map) VALUES (%s, %s, %s)"
+    insert_query = "INSERT INTO uuid_map(uuid, map) VALUES (%s, %s)"
     db_conn = open_connection()
     with db_conn.cursor() as curs:
         curs.execute(create_query)
-        dt = datetime.now(timezone.utc)
-        curs.execute(insert_query, [uuid, dt, json.dumps(map_)])
+        curs.execute(insert_query, [uuid, json.dumps(map_)])
 
 
 def _delete_id_map(uuid: str):