Merge branch 'master' into experimental

.github/workflows/non-omv-remote.yml

@@ -34,12 +34,18 @@ jobs:
         omv install jneuroml
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
 
+
     - name: Final version info
       run: |
         omv list -V # list installed engines
         pip list
         env
 
+    - name: Check health status of biosimulations API
+      run: |
+        cd SBML/tests
+        python ./test_biosimulators_api.py
+
     - name: Test remote biosimulators compatibility table creation
       run: |
         cd SBML/tests

.github/workflows/non-omv.yml

@@ -6,7 +6,7 @@ on:
     branches: [ master, development, experimental, test*, feature/* ]
   pull_request:
     branches: [ master, development, experimental, test*, feature/* ]
-
+      
 jobs:
   build:
 
@@ -64,4 +64,9 @@ jobs:
       run: |
         omv list -V # list installed engines
         pip list
-        env
+        env
+
+    - name: Create results table
+      run: |
+        cd SBML/tests
+        python ./test_creation_combined_results_table.py

SBML/tests/test_biosimulators_api.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+"""Test health status of the BioSimulators API."""
+
+import requests 
+import sys
+
+biosimulations_api_url = "https://api.biosimulations.org/health"
+
+r = requests.get(biosimulations_api_url)  
+r_status = r.json()["status"]
+
+if r_status == "ok":
+    exit_status = 0
+else:
+    exit_status = 1
+
+sys.exit(exit_status)

SBML/tests/test_biosimulators_local.py

@@ -2,18 +2,15 @@
 
 """
 This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
-It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
-The results are then displayed in a table and saved to a markdown file.
+It runs each engine and saves a JSON file with the log.yml file (as a dict), and the d1 plot for each engine.
 """
 
 import sys
 import os
 sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
 import utils
 import argparse
-
-engines = utils.engines
-types_dict = utils.types_dict
+import json
 
 # Save the current working directory
 cwd = os.getcwd()
@@ -41,8 +38,15 @@
 
 print('d1 plots will be saved in:', d1_plots_local_dir)
 
-results_local = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, 
+engine_keys = list(utils.ENGINES.keys())
+
+results_local = utils.run_biosimulators_locally(engine_keys,
+                                    sedml_file_name=sedml_file_name, 
                                     sbml_file_name=sbml_file_name,
                                     d1_plots_local_dir=d1_plots_local_dir, 
-                                    engines=engines, test_folder=test_folder)
+                                    test_folder=test_folder)
+
+results_local_path = os.path.join(path_to_sbml_folder, 'tests', 'results_local.json')
+with open(results_local_path, 'w') as fp:
+    json.dump(results_local, fp, indent=4)
 

SBML/tests/test_biosimulators_remote.py

@@ -2,18 +2,17 @@
 
 """
 This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file.
-It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation.
-The results are then displayed in a table and saved to a markdown file.
+It runs each engine and saves the d1 plots, and a JSON file containing the log.yml file (as dict) and the 
+links for accessing the remote results, for each engine.
 """
 
 import sys
 import os
 sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
 import utils
 import argparse
+import json
 
-engines = utils.engines
-types_dict = utils.types_dict
 
 # Save the current working directory
 cwd = os.getcwd()
@@ -41,8 +40,14 @@
 
 print('d1 plots will be saved in:', d1_plots_remote_dir)
 
-results_remote = utils.run_biosimulators_remotely(sedml_file_name=sedml_file_name, 
+engine_keys = list(utils.ENGINES.keys())
+
+results_remote = utils.run_biosimulators_remotely(engine_keys, sedml_file_name=sedml_file_name, 
                                     sbml_file_name=sbml_file_name,
                                     d1_plots_remote_dir=d1_plots_remote_dir, 
-                                    engines=engines, test_folder=test_folder)
+                                    test_folder=test_folder)
+
+results_remote_path = os.path.join(path_to_sbml_folder, 'tests', 'results_remote.json')
+with open(results_remote_path, 'w') as fp:
+    json.dump(results_remote, fp, indent=4)
 

SBML/tests/test_compatibility_biosimulators.py

@@ -12,8 +12,8 @@
 import utils
 import argparse
 
-engines = utils.engines
-types_dict = utils.types_dict
+engines = utils.ENGINES
+types_dict = utils.TYPES
 
 # Save the current working directory
 cwd = os.getcwd()
@@ -42,8 +42,11 @@
 
 print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir)
 
-utils.run_biosimulators_remotely_and_locally(sedml_file_name, 
+engine_keys = list(utils.ENGINES.keys())
+
+utils.run_biosimulators_remotely_and_locally(engine_keys,
+                                 sedml_file_name, 
                                  sbml_file_name,
                                  d1_plots_remote_dir, 
                                  d1_plots_local_dir,
-                                 engines=engines, test_folder=test_folder)
+                                 test_folder=test_folder)

SBML/tests/test_creation_combined_results_table.py

@@ -0,0 +1,54 @@
+import sys
+import os
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils
+import utils
+import argparse
+import json
+
+engines = utils.ENGINES
+
+# Save the current working directory
+cwd = os.getcwd()
+print('Current working directory:', cwd)
+
+# SBML folder is one folder up relative to cwd
+path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir))
+print('Path to SBML folder:', path_to_sbml_folder)
+
+# change the working directory to the SBML folder (because here the SBML and SED-ML files are located)
+os.chdir(path_to_sbml_folder)
+print('Changed working directory to:', os.getcwd())
+
+sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml'
+sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing
+
+# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues)
+parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines')
+parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved')
+args = parser.parse_args()
+
+test_folder = 'tests'
+
+d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local')
+d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote')
+
+results_paths = {
+    "local": os.path.join(path_to_sbml_folder, 'tests', 'results_local.json'),
+    "remote": os.path.join(path_to_sbml_folder, 'tests', 'results_remote.json')
+}
+
+results = {}
+for key, path in results_paths.items():
+    with open(path, 'r') as f:
+        results[key] = json.load(f)
+
+results_table = utils.create_combined_results_table(results["remote"], 
+                                  results["local"], 
+                                  sedml_file_name, 
+                                  sbml_file_name, 
+                                  d1_plots_local_dir, 
+                                  d1_plots_remote_dir,
+                                  test_folder='tests')
+
+print(results_table)
+

test_suite/test_test_suite_compatibility_biosimulators.py

@@ -134,7 +134,7 @@ def process_cases(args):
                                  os.path.basename(sbml_file_path),
                                  os.path.join(test_folder,'d1_plots_remote'), 
                                  os.path.join(test_folder,'d1_plots_local'),
-                                 engines=engines, test_folder=test_folder)
+                                 test_folder=test_folder)
 
 
 if __name__ == "__main__":