Example RO crate

Addresses #37

ro-crate-metadata/Snakefile

@@ -0,0 +1,101 @@
+from snakemake.io import directory
+
+VERSIONS = ['1']
+OUTPUT_DIRS = "data"
+MERGED_FILE = "merged.ttl"
+ro_crate_metadata_dir = "ro-crate-metadata/"
+
+rule all:
+    input:
+        "ro-crate-metadata"
+
+rule source_ro_crates:
+    output:
+        "created_files.json"
+    shell:
+        """
+        # Create the output directory if it doesn't exist:
+        mkdir -p {OUTPUT_DIRS}
+        
+        # Add the current directory to PYTHONPATH, creating it if it doesn't exist
+        export PYTHONPATH="${{PYTHONPATH:+$PYTHONPATH:}}$(pwd)"
+
+        # Run the source_crates script to download the RO Crate metadata, 
+        # then check the output files and generate created_files.json:
+        
+        # - all versions of all workflows:
+        python workflowhub_graph/source_crates.py --prod --all-versions
+        python workflowhub_graph/check_outputs.py --versions {VERSIONS} --output-dir {OUTPUT_DIRS}
+        
+        # - all versions of first 10 workflows:
+        # python workflowhub_graph/source_crates.py --workflow-ids 1-20 --prod --all-versions
+        # python workflowhub_graph/check_outputs.py --workflow-ids 1-20 --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"
+        """)
+
+rule create_ro_crate:
+    input:
+        MERGED_FILE
+    params:
+        workflow_file = "Snakefile"
+    output:
+        directory("ro-crate-metadata/")
+    shell:
+        """
+        # Create a new virtual environment
+        python -m venv rocrate_env
+
+        # Activate the virtual environment
+        source rocrate_env/bin/activate
+
+        # Upgrade pip to avoid any potential issues
+        pip install --upgrade pip
+        
+        # pip uninstall urllib3
+
+        # Install required packages
+        pip install requests urllib3 rocrate rocrate-zenodo
+
+        # Run the create_ro_crate script
+        python workflowhub_graph/create_ro_crate.py {input} {params.workflow_file} {output}
+    
+        # Deactivate the virtual environment
+        deactivate
+
+        # Remove the virtual environment to clean up
+        rm -rf rocrate_env
+        """