implemented rsmetacheck dockerization & somef configuration script

.dockerignore

@@ -0,0 +1,12 @@
+.git
+.github
+.venv
+__pycache__
+*.pyc
+.pytest_cache
+.mypy_cache
+.ruff_cache
+somef_outputs
+pitfalls_outputs
+analysis_results.json
+.env

.env.example

@@ -0,0 +1,27 @@
+# Optional API tokens. Leave blank to skip a provider.
+# Example: github_pat_xxxxxxxxxxxxxxxxxxxx
+GITHUB_API_TOKEN=
+# Example: glpat-xxxxxxxxxxxxxxxxxxxx
+GITLAB_API_TOKEN=
+# Example: xxxxxxxxxxxxxxxxxxxx
+CODEBERG_TOKEN=
+# Example: ATBBxxxxxxxxxxxxxxxxxxxx
+BITBUCKET_API_TOKEN=
+# Example: user@example.org
+BITBUCKET_EMAIL=
+
+# Classifier model files. Leave blank to use the models installed with somef.
+# Example: /usr/local/lib/python3.11/site-packages/somef/models/description.p
+SOMEF_DESCRIPTION_MODEL=
+# Example: /usr/local/lib/python3.11/site-packages/somef/models/invocation.p
+SOMEF_INVOCATION_MODEL=
+# Example: /usr/local/lib/python3.11/site-packages/somef/models/installation.p
+SOMEF_INSTALLATION_MODEL=
+# Example: /usr/local/lib/python3.11/site-packages/somef/models/citation.p
+SOMEF_CITATION_MODEL=
+
+# RDF/base metadata configuration.
+# Example: https://w3id.org/okn/i/
+SOMEF_BASE_URI=
+# Example: 1000
+SOMEF_DOWNLOAD_LIMIT_MB=1000

.gitignore

@@ -83,6 +83,7 @@ poetry.lock
 .env
 .env.*
 *.env
+!.env.example
 
 # Logs
 *.log
@@ -139,4 +140,4 @@ uv.lock
 results_*/
 
 # Backup directory 
-BACKUP/
+BACKUP/

Dockerfile

@@ -0,0 +1,39 @@
+FROM python:3.11-slim
+
+# Runtime defaults: no Poetry venv, non-interactive installs, and SoMEF config values.
+ENV PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    POETRY_VIRTUALENVS_CREATE=false \
+    POETRY_NO_INTERACTION=1 \
+    DEBIAN_FRONTEND=noninteractive \
+    NLTK_DATA=/usr/local/share/nltk_data \
+    SOMEF_CONFIGURATION_FILE=/root/.somef/config.json \
+    SOMEF_BASE_URI=https://w3id.org/okn/i/ \
+    SOMEF_DOWNLOAD_LIMIT_MB=1000
+
+WORKDIR /app
+
+# System packages needed to install Python packages with native extensions and clone repos.
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends build-essential git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Poetry globally; dependencies will still go into the container Python.
+RUN pip install poetry
+
+# Install project dependencies first to keep Docker layer caching useful.
+COPY pyproject.toml poetry.lock ./
+RUN poetry install --only main --no-root --no-ansi
+
+# Pre-download NLTK resources used by SoMEF so runtime does not configure interactively.
+RUN python -m nltk.downloader -d /usr/local/share/nltk_data \
+    wordnet omw-1.4 punkt punkt_tab stopwords
+
+# Copy the application and install only the rsmetacheck package itself.
+COPY . .
+RUN poetry install --only-root --no-ansi \
+    && chmod +x /app/docker-somef-config.sh
+
+# Configure SoMEF from environment variables, then run rsmetacheck through Poetry.
+ENTRYPOINT ["/app/docker-somef-config.sh"]
+CMD ["rsmetacheck", "--help"]

docker-somef-config.sh

@@ -0,0 +1,19 @@
+#!/bin/sh
+set -e
+
+echo "configuring somef..."
+printf "%s\n" \
+    "${GITHUB_API_TOKEN:-}" \
+    "${GITLAB_API_TOKEN:-}" \
+    "${CODEBERG_TOKEN:-}" \
+    "${BITBUCKET_API_TOKEN:-}" \
+    "${BITBUCKET_EMAIL:-}" \
+    "${SOMEF_DESCRIPTION_MODEL:-}" \
+    "${SOMEF_INVOCATION_MODEL:-}" \
+    "${SOMEF_INSTALLATION_MODEL:-}" \
+    "${SOMEF_CITATION_MODEL:-}" \
+    "${SOMEF_BASE_URI:-}" \
+    "${SOMEF_DOWNLOAD_LIMIT_MB:-1000}" \
+    | somef configure
+
+exec "$@"