reverting to the previous workflow.config setup

Author: dtyagi

benchmarks/common/summarize_results.py

@@ -6,8 +6,8 @@ def create_summary(configurations: list[str],
                    mesh_files: list[str],
                    solution_metrics: list[str],
                    solution_field_data: list[str],
-                   benchmark_and_tool_metadata: str,
-                   tool: str,
+                   benchmark: str,
+                   benchmark_uri: str,
                    summary_json: str) -> None:
 
     """
@@ -19,25 +19,17 @@ def create_summary(configurations: list[str],
         mesh_files: List of paths to mesh files
         solution_metrics: List of paths to metrics JSON files
         solution_field_data: List of paths to solution field data files
-        benchmark_and_tool_metadata: Path to the benchmark and tool metadata file
+        benchmark: Name of the benchmark
+        benchmark_uri: URI of the benchmark
         summary_json: Output path for the summary JSON file
     """
 
-    with open(benchmark_and_tool_metadata, "r") as metadata_file:
-        metadata = json.load(metadata_file)
-        benchmark = metadata["benchmark"]
-        benchmark_uri = metadata["benchmark_uri"]
-        tool_uri = metadata.get(tool).get("tool_uri")
-        tool_version = metadata.get(tool).get("tool_version")
-
+    
     all_summaries = []
     for idx, config in enumerate(configurations):
         summary = {}
         summary["benchmark"] = benchmark
         summary["benchmark_uri"] = benchmark_uri
-        summary["tool"] = tool
-        summary["tool_version"] = tool_version
-        summary["tool_uri"] = tool_uri
         with open(parameter_files[idx], "r") as param_file:
             summary["parameters"] = json.load(param_file)
         summary["mesh"] = f"{config}/mesh"
@@ -60,10 +52,7 @@ def create_summary(configurations: list[str],
     parser.add_argument("--input_mesh_file", nargs="+", type=str, required=True, help="Path to the mesh file (input)")
     parser.add_argument("--input_solution_metrics", nargs="+", type=str, required=True, help="Path to the metrics JSON file (input)")
     parser.add_argument("--input_solution_field_data", nargs="+", type=str, required=True, help="Path to the zipped solution files (input)")
-    parser.add_argument("--input_benchmark_and_tool_metadata", required=True, type=str, help="Path to the benchmark and tool metadata file (input)")
-    parser.add_argument("--input_tool", required=True, type=str, help="Name of the tool (input)")
-    #parser.add_argument("--input_benchmark", required=True, type=str, help="Name of the benchmark (input)")
-    #parser.add_argument("--input_benchmark_uri", required=True, type=str, help="URI of the benchmark (input)")
+    parser.add_argument("--input_benchmark", required=True, type=str, help="Name of the benchmark (input)")
     parser.add_argument("--output_summary_json", required=True, type=str, help="Path to the summary JSON file (output)")
     args = parser.parse_args()
     create_summary(
@@ -72,7 +61,6 @@ def create_summary(configurations: list[str],
         args.input_mesh_file,
         args.input_solution_metrics,
         args.input_solution_field_data,
-        args.input_benchmark_and_tool_metadata,
-        args.input_tool,
+        args.input_benchmark,
         args.output_summary_json
     )

benchmarks/linear-elastic-plate-with-hole/Snakefile

@@ -6,6 +6,7 @@ configuration_to_parameter_file = config["configuration_to_parameter_file"]
 configurations = config["configurations"]
 tools = config["tools"]
 benchmark = config["benchmark"]
+benchmark_uri = config["benchmark_uri"]
 
 
 rule all:
@@ -52,7 +53,6 @@ rule summary:
             f"{result_dir}/{{tool}}/solution_field_data_{{configuration}}.zip",
             tool=[wildcards.tool], configuration=configurations
         ),
-        benchmark_and_tool_metadata_file = f"benchmark_and_tool_metadata.json",
     output:
         summary_json = f"{result_dir}/{{tool}}/summary.json",
     conda: "environment_postprocessing.yml",
@@ -64,8 +64,8 @@ rule summary:
             --input_mesh_file {input.mesh} \
             --input_solution_metrics {input.metrics} \
             --input_solution_field_data {input.solution_field_data} \
-            --input_benchmark_and_tool_metadata {input.benchmark_and_tool_metadata_file} \
-            --input_tool {wildcards.tool} \
+            --input_benchmark {benchmark} \
+            --input_benchmark_uri {benchmark_uri} \
             --output_summary_json {output.summary_json}
         """
 

benchmarks/linear-elastic-plate-with-hole/generate_config.py

@@ -40,8 +40,6 @@ def get_configuration(file):
 configuration_to_parameter_file = {v: str(k) for k, v in configurations.items()}
 
 tools = ["fenics", "kratos"]
-tools_uri = ["https://github.com/FEniCS/dolfinx", "https://github.com/KratosMultiphysics/Kratos"]
-software_versions = ["0.9", "10.3.1"]
 benchmark = "linear-elastic-plate-with-hole"
 benchmark_uri = "https://portal.mardi4nfdi.de/wiki/Model:6775296"
 
@@ -51,27 +49,9 @@ def get_configuration(file):
     "configurations": list(configurations.values()),
     "tools": tools,
     "benchmark": benchmark,
+    "benchmark_uri": benchmark_uri
 }
 
 # Write workflow configuration file
 with open("workflow_config.json", "w") as f:
-    json.dump(workflow_config, f, indent=4)
-
-benchmark_and_tool_metadata = {}
-
-# Create tool entries using loops
-for i, tool in enumerate(tools):
-    benchmark_and_tool_metadata[tool] = {
-        "tool_uri": tools_uri[i],
-        "tool_version": software_versions[i]
-    }
-
-# Add the remaining metadata
-benchmark_and_tool_metadata.update({
-    "benchmark": benchmark,
-    "benchmark_uri": benchmark_uri,
-})
-
-# Write benchmark_and_tool_metadata configuration file
-with open("benchmark_and_tool_metadata.json", "w") as f:
-    json.dump(benchmark_and_tool_metadata, f, indent=4)
+    json.dump(workflow_config, f, indent=4)

benchmarks/linear-elastic-plate-with-hole/main.nf

@@ -33,7 +33,8 @@ process summary{
     val mesh_file
     val solution_metrics
     val solution_field_data
-    path benchmark_and_tool_metadata
+    val benchmark
+    val benchmark_uri
     val tool
 
     output:
@@ -47,8 +48,8 @@ process summary{
         --input_mesh_file ${mesh_file.join(' ')} \
         --input_solution_metrics ${solution_metrics.join(' ')} \
         --input_solution_field_data ${solution_field_data.join(' ')} \
-        --input_benchmark_and_tool_metadata ${benchmark_and_tool_metadata} \
-        --input_tool ${tool} \
+        --input_benchmark ${benchmark} \
+        --input_benchmark_uri ${benchmark_uri} \
         --output_summary_json "summary.json"
 
     """
@@ -137,17 +138,17 @@ workflow {
     input_summary_metrics = fenics_summary_metrics.concat(kratos_summary_metrics)
 
     //Summarizing results
-    //def ch_benchmark = Channel.value(params.benchmark)
-    //def ch_benchmark_uri = Channel.value(params.benchmark_uri)
-    def ch_benchmark_and_tool_metadata_file = Channel.value(file('benchmark_and_tool_metadata.json'))
+    def ch_benchmark = Channel.value(params.benchmark)
+    def ch_benchmark_uri = Channel.value(params.benchmark_uri)
     def ch_summarize_python_script = Channel.value(file('../common/summarize_results.py'))
     summary(ch_summarize_python_script, \
             input_summary_configuration, \
             input_summary_parameter_file, \
             input_summary_mesh, \
             input_summary_metrics, \
             input_summary_solution_field, \
-            ch_benchmark_and_tool_metadata_file, \
+            ch_benchmark, \
+            ch_benchmark_uri, \
             ch_tools)
 
 }
@@ -169,4 +170,4 @@ be matched with their corresponding inputs using a common key.
 
 Information on channel operations: https://www.nextflow.io/docs/latest/reference/operator.html
 Information on channels: https://training.nextflow.io/2.2/basic_training/channels/
-*/
+*/ 

docs/getting_started/benchmark_addition_guide.md

@@ -24,13 +24,12 @@ The steps are as follows:
 
 4. **Create a script for discovering the configurations**
 
-    - Create the script `generate_config.py` in `benchmarks/problem/`.
-    - The script should:
-        - Discover all the parameter configuration JSON files.
-        - Extract configurations.
-        - List the simulation tools for each configuration, cf. [generate_config.py](https://github.com/BAMresearch/NFDI4IngModelValidationPlatform/blob/main/benchmarks/linear-elastic-plate-with-hole/generate_config.py).
+    - Copy the script `benchmarks/linear-elastic-plate-with-hole/generate_config.py` to `benchmarks/problem_name/`.
+    - Modify the list of simulation tools for the benchmark, cf. [generate_config.py](https://github.com/BAMresearch/NFDI4IngModelValidationPlatform/blob/main/benchmarks/linear-elastic-plate-with-hole/generate_config.py).
 
-        **Note:** The simulation-tool-specific keywords are used by the main workflow to call the corresponding sub-workflows.
+    **Note:** The simulation-tool-specific keywords are used by the main workflow to call the corresponding sub-workflows.
+
+    **Note:** In the future, the file will be moved to the `benchmarks/common/`folder and the list of simulation tools which is benchmark-specific will be provided separately.
 
 5. **Create the mesh generation script**
 

mkdocs.yml

@@ -31,11 +31,6 @@ markdown_extensions:
       enable_dollar_delimiter: true
   - pymdownx.tasklist:
   - pymdownx.superfences
-  #- pymdownx.snippets:
-  #    check_paths: true
-  #- pymdownx.inlinehilite
-  #    custom_checkbox: true
-  #- markdown_checklist.extension
 
 nav:
   - index.md