Merge pull request #24 from workflowhub-eu/refactor-workflow

Add Snakemake workflow

Author: OliverWoolland

Dockerfile

@@ -1,25 +1,29 @@
-# Docker container with poetry for python package management
+FROM python:3.11-slim
 
-FROM python:3.10-slim
-
-# Install poetry
 RUN pip install poetry
 
 # Set the working directory
 WORKDIR /app
 
-# Copy the pyproject.toml
+# Install build tools for Snakemake (gcc, make, etc.)
+RUN apt-get update && apt-get install -y build-essential
+
+# Copy the pyproject.toml file
 COPY pyproject.toml /app/
 
 # Install the dependencies
 RUN poetry install --no-root
 
-# Copy the rest of the files
+# Copy the rest of the application files
 COPY . /app
 
 # Install the package
 RUN poetry install
 
-# Run the application
-CMD ["help"]
+# Install Snakemake using Poetry
+RUN poetry add snakemake
+
+# Set the entry point for the container
 ENTRYPOINT ["poetry", "run"]
+
+CMD ["help"]

Snakefile

@@ -0,0 +1,67 @@
+# TODO - Refactor to input args to the Snakemake file
+WORKFLOW_IDS = range(1,11)
+VERSIONS = ['1']
+OUTPUT_DIRS = "data"
+MERGED_FILE = "merged.ttl"
+
+
+def list_expected_files():
+    files = []
+    for wf_id in WORKFLOW_IDS:
+        for ver in VERSIONS:
+            files.append(f"{OUTPUT_DIRS}/{wf_id}_{ver}_ro-crate-metadata.json")
+    return files
+
+rule all:
+    input:
+        MERGED_FILE
+
+rule source_ro_crates:
+    output:
+        "created_files.json"
+    shell:
+        """
+        # Create the output directory if it doesn't exist:
+        mkdir -p {OUTPUT_DIRS}
+
+        # Run the source_crates script to download the RO Crate metadata:
+        python workflowhub_graph/source_crates.py  --workflow-ids 1-10 --prod --all-versions
+
+        # After sourcing, check which files were actually created:
+        python workflowhub_graph/check_outputs.py --workflow-ids 1-10 --versions {VERSIONS} --output-dir {OUTPUT_DIRS}
+        """
+
+rule report_created_files:
+    input:
+        "created_files.json"
+    shell:
+        """
+        echo "Files created:"
+        cat created_files.json
+        """
+
+rule merge_files:
+    input:
+        "created_files.json"
+    output:
+        MERGED_FILE
+    run:
+        import json
+        import os
+
+        # Load the list of created files:
+        with open("created_files.json") as f:
+            created_files = json.load(f)
+
+        files_to_merge = [f"data/{os.path.basename(file)}" for file in created_files]
+
+        # If no files are available to merge, raise an exception:
+        if not files_to_merge:
+            raise ValueError("No files in to merge in data directory.")
+
+        file_patterns = " ".join(files_to_merge)
+
+        # Merge the JSON-LD files into a single RDF graph and output as a TTL file
+        shell(f"""
+            python workflowhub_graph/merge.py {output[0]} -p "data/*.json"
+        """)