Refactor PlantDB client/server: env vars, auth, URLs, deps #81

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Merged

jlegrand62 merged 101 commits into dev from feature/authentication

Jan 26, 2026

.github/workflows/gh-pages.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,9 +2,12 @@ @@
     name: Build & Deploy documentation
-    # Triggers workflow on any push to the repository
     on:
-      - push
+      # Automatic trigger on release
+      release:
+        types: [ published ]
+      # Enables manual triggering from the Action tab
+      workflow_dispatch:
     jobs:
       docs:
@@ Expand Down @@

.github/workflows/pull_request.yml

            
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    @@ -1,49 +1,26 @@
  
    # GitHub workflow that build the Docker image, run python unit tests & clean-up

    # pull_request.yml

    name: CI UnitTests

    on: pull_request

    on:

      pull_request:

    jobs:

      # Build a Docker image with the current code

      docker-build:

        runs-on: ubuntu-latest

      build-and-test:

        runs-on: ubuntu-22.04

        steps:

          # Step 1: Check out repository code including submodules

          - name: Checkout

            uses: actions/checkout@v4

            with:

              submodules: true

          # Step 2: Build the Dockerfile

          - name: Build Dockerfile

          # Build the Docker image, targeting the test stage

          - name: Build Docker image

            run: |

              # Clean up any dangling containers before build

              docker container prune -f

              # Build Docker image using commit SHA as tag with clean cache

              ./docker/build.sh -t ${{ github.sha }} --no-cache

      # Run unit tests in the Docker container

      unit-tests:

        runs-on: ubuntu-latest

        # Ensure Docker image is built before running tests

        needs: docker-build

        steps:

          - name: Run Unit Tests

            run: |

              # Execute tests using the previously built Docker image

              ./docker/run.sh -t ${{ github.sha }} --unittest

              docker build -f docker/Dockerfile --target test -t plantdb-test:${{ github.sha }} .

      # Cleanup Docker resources after tests complete

      docker-clean:

        runs-on: ubuntu-latest

        # Run after tests complete, regardless of test outcome

        needs: unit-tests

        if: always()

        steps:

          - name: Remove Docker Image

          # Clean up

          - name: Remove Docker image

            if: always()

            run: |

              # Remove any unused containers

              docker container prune -f

              # Force remove the image created for this workflow run

              docker image rm roboticsmicrofarms/plantdb:${{ github.sha }} --force
      
              docker image rm plantdb-test:${{ github.sha }} --force

README.md

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -73,7 +73,7 @@ The `plantdb` packages are available through:
  
    To create a new conda environment for PlantDB:

    ``` shell

    conda create -n plantdb 'python=3.10' ipython

    conda create -n plantdb 'python<3.13' ipython

    ```

    ## Installation

    @@ -191,7 +191,7 @@ import os
  
    db_path = os.environ['ROMI_DB']

    # Use it to connect to DB:

    from plantdb.commons.fsdb import FSDB

    from plantdb.commons.fsdb.core import FSDB

    db = FSDB(db_path)

    db.connect()

docker/Dockerfile

-Original file line number
+Diff line change
@@ Expand Up / @@ -8,7 +8,9 @@ ENV PYTHONUNBUFFERED=1 @@
     ENV PATH="/root/.local/bin:${PATH}"
     # Install build dependencies
-    RUN apt-get update && \
+    RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+        --mount=type=cache,target=/var/lib/apt,sharing=locked \
+        apt-get update && \
         apt-get install -yq --no-install-recommends \
             # Install python3.10 & pip
             python3 python3-pip python3-dev \
@@ Expand All / @@ -27,11 +29,13 @@ COPY src/commons commons/ @@
     COPY src/server server/
     # Build uwsgi & Python packages
-    RUN python3 -m pip install --no-cache-dir --user \
+    RUN --mount=type=cache,target=/root/.cache/pip \
+        python3 -m pip install --no-cache-dir --user \
             wheel setuptools pip --upgrade && \
         python3 -m pip install --no-cache-dir --user \
             uwsgi \
             commons/.[io] \
+            open3d \
             server/. && \
         # Remove pip cache and unnecessary files
         python3 -m pip cache purge
@@ Expand All / @@ -40,23 +44,33 @@ RUN python3 -m pip install --no-cache-dir --user \ @@
     FROM builder AS test
     # Update package manager & install requirements:
-    RUN apt-get update && \
+    RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+        --mount=type=cache,target=/var/lib/apt,sharing=locked \
+        apt-get update && \
         apt-get install -yq --no-install-recommends \
             # Install Open3D system dependencies
             libegl1 libgl1 libgomp1
+    COPY src/client client/
     # Install test dependencies
-    RUN echo "\n\n# Installing 'plantdb.commons' test dependencies..." && \
+    RUN --mount=type=cache,target=/root/.cache/pip \
+        echo "\n\n# Installing 'plantdb.commons' test dependencies..." && \
         python3 -m pip install --no-cache-dir --user \
             commons/[test] && \
         echo "\n\n# Installing 'plantdb.server' test dependencies..." && \
         python3 -m pip install --no-cache-dir --user \
-            server/[test]
+            server/[test] && \
+        echo "\n\n# Installing 'plantdb.client' test dependencies..." && \
+        python3 -m pip install --no-cache-dir --user \
+            client/[test]
     # Run tests
     RUN echo "\n\n# Running 'plantdb.commons' tests..." && \
         nose2 -v -s commons/tests/ && \
-        echo "\n\n# Running 'plantdb.commons' tests..." && \
-        nose2 -v -s server/tests/
+        echo "\n\n# Running 'plantdb.server' tests..." && \
+        nose2 -v -s server/tests/ && \
+        echo "\n\n# Running 'plantdb.client' tests..." && \
+        nose2 -v -s client/tests/
     # ============= Final stage =============
     FROM ubuntu:22.04 AS runtime
@@ Expand Down Expand Up / @@ -91,7 +105,9 @@ ENV ROMI_DB="/myapp/db" @@
     SHELL ["/bin/bash", "-c"]
     # Update package manager & install requirements:
-    RUN apt-get update && \
+    RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+        --mount=type=cache,target=/var/lib/apt,sharing=locked \
+        apt-get update && \
         apt-get install -yq --no-install-recommends \
             # Install curl to performs healthcheck
             curl \
@@ Expand Down Expand Up / @@ -127,7 +143,8 @@ WORKDIR /home/${USER_NAME} @@
     # Copy Python packages from builder (including uwsgi)
     COPY --chown=${USER_NAME} --from=builder /root/.local /home/${USER_NAME}/.local
-    RUN echo "\n\n# Installing 'plantdb.commons', 'plantdb.server' & uwsgi..." && \
+    RUN --mount=type=cache,target=/root/.cache/pip \
+        echo "\n\n# Installing 'plantdb.commons', 'plantdb.server' & uwsgi..." && \
         python3 -m pip install --no-cache-dir --user plantdb.commons plantdb.server uwsgi && \
         # Clean pip cache:
         python3 -m pip cache purge && \
@@ Expand Down @@

docker/run.sh

            
                      Original file line number
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    @@ -1,9 +1,8 @@
  
    #!/bin/bash

    # --------------------------------

    # ------------------------------------------

    # Functions for colors and messages

    # --------------------------------

    # ------------------------------------------

    setup_colors() {

      RED="\033[0;31m"    # Define red color code

      GREEN="\033[0;32m"  # Define green color code

    @@ -38,9 +37,9 @@ log_debug() {
  
      fi

    }

    # --------------------------------

    # ------------------------------------------

    # Functions for script initialization

    # --------------------------------

    # ------------------------------------------

    initialize_variables() {

      # Image tag to use, 'latest' by default:

      vtag="latest"

    @@ -54,6 +53,8 @@ initialize_variables() {
  
      DEBUG_MODE=false

      # Production mode is disabled by default

      PRODUCTION_MODE=false

      # Unit‑test mode is disabled by default

      UNITTEST_MODE=false

      # If the `ROMI_DB` variable is set, use it as default database location, else set it to empty:

      if [ -z ${ROMI_DB+x} ]; then

    @@ -63,9 +64,9 @@ initialize_variables() {
  
      fi

    }

    # --------------------------------

    # ------------------------------------------

    # Usage information function

    # --------------------------------

    # ------------------------------------------

    show_usage() {

      echo -e "$(bold USAGE):"

      echo "  ./docker/run.sh [OPTIONS]"

    @@ -93,13 +94,15 @@ show_usage() {
  
      # -- Debug option:

      echo "  --debug

        Enable debug mode to print additional debug information."

      echo "  --unittest

        Run all unit tests in src/server/tests, src/commons/tests and src/client/tests and exit."

      echo "  -h, --help

        Output a usage message and exit."

    }

    # --------------------------------

    # ------------------------------------------

    # Command line parsing function

    # --------------------------------

    # ------------------------------------------

    parse_arguments() {

      while [ "$1" != "" ]; do

        case $1 in

    @@ -132,6 +135,9 @@ parse_arguments() {
  
          DEBUG_MODE=true

          log_debug "Debug mode enabled!"

          ;;

        --unittest)

          UNITTEST_MODE=true

          ;;

        -h | --help)

          show_usage

          exit 0

    @@ -145,9 +151,31 @@ parse_arguments() {
  
      done

    }

    # --------------------------------

    # ------------------------------------------

    # Unit‑test helper

    # ------------------------------------------

    run_unittests() {

      log_info "Running unit tests for src/server/tests, src/commons/tests and src/client/tests"

      # Use python -m unittest discover for each test directory

      for test_dir in src/server/tests src/commons/tests src/client/tests; do

        if [ -d "$test_dir" ]; then

          log_info "Discovering tests in $test_dir"

          python -m unittest discover -s "$test_dir"

          test_status=$?

          if [ $test_status -ne 0 ]; then

            log_error "Tests failed in $test_dir (status $test_status)"

            exit $test_status

          fi

        else

          log_warning "Test directory $test_dir does not exist, skipping."

        fi

      done

      log_info "All tests passed successfully."

    }

    # ------------------------------------------

    # Database setup functions

    # --------------------------------

    # ------------------------------------------

    check_database_environment() {

      if [ -z ${ROMI_DB+x} ] ; then

        log_warning "Environment variable 'ROMI_DB' is not defined, set it to use as default database location!"

    @@ -177,9 +205,9 @@ setup_user_group() {
  
      fi

    }

    # --------------------------------

    # ------------------------------------------

    # Check if netstat is available

    # --------------------------------

    # ------------------------------------------

    check_netstat_installed() {

      if ! command -v netstat &> /dev/null; then

        log_warning "netstat command not found. This is required to find available ports."

    @@ -190,9 +218,9 @@ check_netstat_installed() {
  
      return 0

    }

    # --------------------------------

    # ------------------------------------------

    # Port finder function

    # --------------------------------

    # ------------------------------------------

    find_available_port() {

      if [ ${port_specified} -eq 0 ]; then

        log_info "Finding available port in range 5000-5100..."

    @@ -226,9 +254,9 @@ find_available_port() {
  
      fi

    }

    # --------------------------------

    # ------------------------------------------

    # Terminal handling function

    # --------------------------------

    # ------------------------------------------

    check_terminal() {

      if [ -t 1 ]; then

        USE_TTY="-t"

    @@ -237,9 +265,9 @@ check_terminal() {
  
      fi

    }

    # --------------------------------

    # ------------------------------------------

    # Docker run functions

    # --------------------------------

    # ------------------------------------------

    create_docker_run_cmd() {

      # Base docker run command

      docker_cmd="docker run"

    @@ -271,7 +299,7 @@ create_docker_run_cmd() {
  
      if [ "$1" = "development" ]; then

        docker_cmd+=" \"fsdb_rest_api --port 5000\""

      elif [ "$1" = "production" ]; then

      # Run uWSGI to serve the application on port 5000.

        # Run uWSGI to serve the application on port 5000.

        docker_cmd+=" \"uwsgi --http :5000 --module plantdb.server.cli.wsgi:application --callable application --master\""

      elif [ "$1" = "command" ]; then

        docker_cmd+=" \"${cmd}\""

    @@ -329,7 +357,7 @@ run_docker_command() {
  
      # Print the full command that will be executed

      log_debug "Executing command: ${docker_cmd}"

      # Get the date to estimate command execution time:

      # Get date to estimate command execution time:

      start_time=$(date +%s)

      # Execute the docker run command

    @@ -349,14 +377,18 @@ run_docker_command() {
  
      exit ${cmd_status}

    }

    # --------------------------------

    # ------------------------------------------

    # Main script execution

    # --------------------------------

    # ------------------------------------------

    main() {

      setup_colors

      initialize_variables

      parse_arguments "$@"

      if [ "${UNITTEST_MODE}" = true ]; then

        run_unittests

        exit 0

      fi

      check_database_environment

      setup_database_mount

      setup_user_group

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