feat: handle zip lcms

.devcontainer/Dockerfile.devcontainer

@@ -0,0 +1,30 @@
+FROM python:3.12-slim AS base
+
+# Install any additional OS packages you want in addition to sudo, git and nano
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked,id=apt-cache \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked,id=apt-lib \
+    apt-get update && \
+    apt-get install -y --no-install-recommends \
+    sudo git nano \
+# required 
+    gcc g++ libxrender1 libxext6 libglib2.0-0
+
+ARG USERNAME=debian
+
+# add default user with no password and sudo privilege
+RUN useradd -m --shell /bin/bash $USERNAME && passwd -d ${USERNAME} && adduser ${USERNAME} sudo
+
+USER $USERNAME
+WORKDIR /home/${USERNAME}
+
+ENV PIP_CACHE_DIR=./.cache/pip
+ENV PIP_USER=1
+ENV PIP_NO_WARN_SCRIPT_LOCATION=1
+
+RUN mkdir -p ${PIP_CACHE_DIR}
+
+# to be replaced later by ADD git#branch if needed
+COPY pyproject.toml .
+
+RUN --mount=type=cache,target=${PIP_CACHE_DIR},sharing=locked,id=pip-cache \
+    touch README.md && pip install --upgrade pip && pip install .[dev] && rm -rf README.md pyproject.toml build *.egg-info

.devcontainer/devcontainer.json

@@ -0,0 +1,35 @@
+{
+  "name": "ChemSpectraApp",
+  "build": {
+    "dockerfile": "Dockerfile.devcontainer",
+    "context": ".."
+  },
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  "forwardPorts": [
+    3007 // Port for the web server
+  ],
+  // Ensure the environment
+  "postStartCommand": "pip install --upgrade pip && pip install --upgrade .[dev] && pip freeze > dependencies.list",
+  "remoteUser": "debian",
+  "workspaceMount": "source=${localWorkspaceFolder},target=/home/debian/chem_spectra,type=bind",
+  "workspaceFolder": "/home/debian/chem_spectra",
+  // Configure tool-specific properties.
+  "customizations": {
+    // Configure properties specific to VS Code.
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.autopep8",
+        "ms-python.vscode-pylance",
+        "github.vscode-github-actions"
+      ],
+      "settings": {
+        "[python]": {
+          "python.defaultInterpreterPath": "/usr/local/bin/python",
+          "editor.defaultFormatter": "ms-python.autopep8"
+        },
+        "editor.formatOnSave": true
+      }
+    }
+  }
+}

.github/workflows/unit_test.yml

@@ -6,19 +6,28 @@ jobs:
   run-unit-tests:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
-        python-version: 3.8
+        check-latest: true
+        cache: "pip"
+        python-version: "3.12"
     - name: Install dependencies
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        activate-environment: python-v38
-        environment-file: environment.yml
-        miniforge-version: latest
+      run: |
+        pip install --upgrade pip
+        pip install .[dev]   
+    - name: Create tmp directory with permissions
+      run: |
+        mkdir -p chem_spectra/tmp
+        chmod -R 777 chem_spectra/tmp
+    - name: Start msconvert Docker container
+      run: |
+        docker run --detach --name msconvert_docker \
+          --rm -it \
+          -e WINEDEBUG=-all \
+          -v ${{ github.workspace }}/chem_spectra/tmp:/data \
+          proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses bash
     - name: Test with pytest
       shell: bash -el {0}
       run: |
-        conda activate python-v38
         python -m pytest

.gitignore

@@ -1,4 +1,5 @@
-venv/
+.venv/
+.cache/
 
 *.pyc
 __pycache__/

Dockerfile.p2d

@@ -0,0 +1,46 @@
+FROM python:3.12-slim AS base
+
+# Install any additional OS packages you want in addition to sudo, git and nano
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked,id=apt-cache \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked,id=apt-lib \
+    apt-get update \
+    && apt-get install -y --no-install-recommends \
+    sudo git nano curl \
+    gcc g++ libxrender1 libxext6 libglib2.0-0 # required
+
+ADD --chmod=755 https://payload.chemserv.scc.kit.edu/fake-docker.py /bin/docker
+ADD https://payload.chemserv.scc.kit.edu/spectra_config.py /app/instance/config.py
+
+WORKDIR /app
+
+RUN mkdir -p /var/cache/pip
+
+ENV PIP_CACHE_DIR=/var/cache/pip \
+    PIP_ROOT_USER_ACTION=ignore
+
+COPY pyproject.toml .
+
+RUN --mount=type=cache,target=/var/cache/pip,sharing=locked,id=pip-cache \
+    pip install --upgrade pip && pip install .
+
+COPY ./chem_spectra /app/chem_spectra
+COPY ./server.py /app/server.py
+
+# Finalize app setup
+RUN mkdir -p /shared /app/instance && \
+    ln -s /shared /app/chem_spectra/tmp
+
+ENV FLASK_ENV=production \
+    FLASK_DEBUG=0 \
+    MSC_HOST=msconvert \
+    MSC_PORT=4000 \
+    MSC_VALIDATE=true \
+    SPECTRA_PORT=4000
+
+EXPOSE 4000
+
+CMD ["gunicorn", "--timeout", "600", "-w", "4", "-b", "0.0.0.0:4000", "server:app"]
+# i.e the command: gunicorn --timeout 600 -w 4 -b 0.0.0.0:4000 server:app
+
+HEALTHCHECK --interval=5s --timeout=3s --start-period=30s --retries=3 \
+    CMD curl --fail http://localhost:4000/ping || exit 1

INSTALL.md

@@ -4,86 +4,56 @@ This guidance is tested on Linux Ubuntu 18.04 & Ubuntu 20.04
 
 ## 1. Installation
 
-### 1.1. Install Anaconda & Docker
+### 1.1. Install Python
 
-Please refer to [https://www.anaconda.com/] & [https://docs.docker.com/install/].
+Use the file pyproject.toml to determine the version of Python required.
 
-You can follow [unofficial Anaconda & Docker installations for Dummies](INSTALL_BASIC.md) for a test installation.
+### 1.2. Clone repository and create env
 
-However, it is highly recommended to refer to official websites.
-
-### 1.2. Create env
-
-_Logout & login to load installations._
-
-```
-$ conda create --name chem-spectra python=3.8
-$ source activate chem-spectra
-```
-
-```
-$ sudo apt-get install gcc libxrender1 libxext-dev pkg-config g++
-```
-
-```
-$ git clone https://github.com/ComPlat/chem-spectra-app.git
-$ cd chem-spectra-app
-$ pip install -r requirements.txt
+```sh
+git clone https://github.com/ComPlat/chem-spectra-app.git
+cd chem-spectra-app
 ```
 
-The project is in `~/chem-spectra-app`.
-
-
-### 1.3. Use msconvert in Docker
+ALL the **FOLLOWING** commands are assumed to be executed while inside this
+`chem-spectra-app` folder.
 
 ```
-$ docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
+python3 -m venv .venv && .venv/bin/pip install --upgrade pip
+source .venv/bin/activate
+pip install .
 ```
 
-__Make sure you are in the `chem-spectra-app` folder.__
-```
-$ cd ~/chem-spectra-app
-```
+### 1.3. Use docker to run a supporting service
 
-```
-$ mkdir chem_spectra/tmp
-$ sudo chmod -R 755 chem_spectra/tmp
-```
-To running docker for converting Mass spectrum, run this command:
-```
-$ docker run --detach --name msconvert_docker \
-    --rm -it \
-    -e WINEDEBUG=-all \
-    -v [YOUR LOCATION TO chem-spectra-app]/chem_spectra/tmp:/data \
-    chambm/pwiz-skyline-i-agree-to-the-vendor-licenses bash
-```
-
-For example, if your location of `chem-spectra-app` is `/home/ubuntu/chem-spectra-app`
-```
-$ docker run --detach --name msconvert_docker \
+```sh
+docker pull proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses
+mkdir -p chem_spectra/tmp
+chmod -R 755 chem_spectra/tmp
+docker run --detach --name msconvert_docker \
     --rm -it \
     -e WINEDEBUG=-all \
-    -v /home/ubuntu/chem-spectra-app/chem_spectra/tmp:/data \
-    chambm/pwiz-skyline-i-agree-to-the-vendor-licenses bash
+    -v ./chem_spectra/tmp:/data \
+    proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses bash
 ```
 
 ### 1.4. Add `config.py`
 
 Generate a secret key.
 
-```
-$ python -c 'import os; print(os.urandom(16))'
+```sh
+python -c 'import os; print(os.urandom(16))'
 >> b'T\x1d\xb3\xfe\xb6q\xef\xbf\x7f\xcaj\xcbZ\x84\x1ee'
 ```
 
 Create `config.py`.
 
-```
-$ mkdir -p ./instance && touch ./instance/config.py
-$ vim ./instance/config.py
+```sh
+mkdir -p ./instance && touch ./instance/config.py
+nano ./instance/config.py
 ```
 
-Add content.
+Add the following content.
 
 ```python
 # ./instance/config.py
@@ -99,23 +69,22 @@ MAX_ZIP_SIZE = 100 #maximum size of a zip file in MB to prevent zip bomb, defaul
 
 Using only "one" of following commands.
 
-```
+```sh
 # run on the production server
-$ gunicorn -w 4 -b 0.0.0.0:3007 server:app --daemon
+gunicorn -w 4 -b 0.0.0.0:3007 server:app --daemon
 ```
 
-
-```
+```sh
 # for local development only
-$ export FLASK_APP=chem_spectra && export FLASK_DEBUG=true && flask run --host=0.0.0.0 --port=3007
+export FLASK_APP=chem_spectra && export FLASK_DEBUG=true && flask run --host=0.0.0.0 --port=3007
 ```
 
 ### 1.6 Quick test
 
 You should receive `pong` when executing the following command from another machine.
 
-```
-$ curl xxx.xxx.xxx.xxx:3007/ping
+```sh
+curl xxx.xxx.xxx.xxx:3007/ping
 ```
 
 ## 2. Usage
@@ -130,63 +99,45 @@ body = { file: target.jdx }
 ```
 
 ### 2.1. Logging
-By default, the logging file is at 
-```
-./instance/logging.log
-```
+
+By default, the logging file is at `./instance/logging.log`.
 
 ### 2.2. Implement a new log message
+
 Import `logging` package at where you want to write your log message
+
 ```
 import logging
 ```
 
 Write log message as
+
 ```
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.ERROR) //levels: DEBUG, INFO, ERROR, WARNING, CRITICAL
 logger.error('message to log')
 ```
-Note: You need to use function as the same as your logger level, which named as lowercased of level's name, to write your log message to the logs file
 
+Note: You need to use function as the same as your logger level, which named as lowercased of level's name, to write your log message to the logs file
 
 ### 2.3. Automatic startup in crontab
 
 To make sure ChemSpectra is started on reboot you can use this BASH script in your root crontab (if required, adapt Chemotion ELN username and home directory):
 
 ```sh
 #!/bin/bash
-
-sudo -H -u production bash -c "cd /home/production/chem-spectra-app && \
-  source /home/production/anaconda3/bin/activate chem-spectra && \
-  gunicorn -w 4 -b 0.0.0.0:3007 server:app --daemon"
-
-# Remember to modify path according to your installation
+cd /path/to/chem-spectra-app
+source .venv/bin/activate
 docker run --detach --name msconvert_docker \
     --rm -it \
     -e WINEDEBUG=-all \
-    -v /home/production/chem-spectra-app/chem_spectra/tmp:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \
+    -v ./chem_spectra/tmp:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses \
     bash
+gunicorn -w 4 -b 0.0.0.0:3007 server:app --daemon
 ```
 
 ## 3. Run test
 
-```
-$ coverage run -m pytest --disable-pytest-warnings
-$ coverage report
-```
-
-## 4. Linting
-
-```
-$ flake8
-```
-
-
-## DEBUG
-
-### msconvert_docker
-
-```
-$ docker exec -it msconvert_docker wine msconvert --help
+```sh
+python -m pytest
 ```