diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index bf6f279d..078eded2 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.8, 3.9, "3.10" ] + python-version: [ 3.9, "3.10" ] steps: - uses: actions/checkout@v4 @@ -49,17 +49,19 @@ jobs: cd SBML ./validateAll.sh - - name: Test test_suite output regeneration + - name: test omex file creation run: | - cd SBML - pip install pymetadata docker "requests<2.32.0" - python create_minimal_omex_archive.py + pip install "pymetadata>=0.4.2" docker "requests<2.32.0" + cd SBML + ./test_biosimulators_docker.py + - name: Test test_suite output regeneration run: | cd test_suite ./test_results_regeneration.sh + - name: Final version info run: | omv list -V # list installed engines diff --git a/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.sedml b/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.sedml new file mode 100644 index 00000000..31329888 --- /dev/null +++ b/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.sedml @@ -0,0 +1,92 @@ + + + +

+ +SED-ML export for: +Components: + fn1 (Type: fitzHughNagumoCell: I=0.8 (dimensionless) SEC=1.0 (SI time)) + net1 (Type: network) + sim1 (Type: Simulation: length=200.0 (SI time) step=0.01 (SI time)) + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + var_time_0 + + + + + + + + DISPLAY__d1_V_fnPop1_0_V + + + + + + + + DISPLAY__d1_W_fnPop1_0_W + + + + + + + + OUTPUT__of1_V_fnPop1_0_V + + + + + + + + OUTPUT__of1_W_fnPop1_0_W + + + + + + + + + + + + + + + + + + + + + diff --git a/SBML/test_biosimulators_docker.py b/SBML/test_biosimulators_docker.py new file mode 100755 index 00000000..473a6070 --- /dev/null +++ b/SBML/test_biosimulators_docker.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +''' +use pymetadata module to create a minimal valid combine archive +using LEMS_NML2_Ex9_FN.sbml and LEMS_NML2_Ex9_FN.sedml +''' + +import sys +sys.path.append("..") +import utils + +sbml_filepath = 'LEMS_NML2_Ex9_FN.sbml' +#sedml_filepath = 'LEMS_NML2_Ex9_FN.sedml' #xmlns:sbml added manually +sedml_filepath = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing +omex_filepath = utils.create_omex(sedml_filepath,sbml_filepath) + +utils.biosimulators_core('tellurium',omex_filepath) + +print('Finished') diff --git a/utils/__init__.py b/utils/__init__.py index 5aec8296..f594d21d 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -16,6 +16,7 @@ import yaml import libsbml import libsedml +import tempfile #define error categories for detailed error counting per engine # (currently only tellurium) @@ -71,84 +72,151 @@ def get_entry_format(file_path, file_type): return file_entry_format -def create_omex(sedml_file, sbml_file): + +def add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, output_filepath=None): ''' - wrap a sedml and an sbml filin a combine archive omex file - overwrite any existing omex file + add an xmlns:sbml attribute to the sedml file that matches the sbml file + raise an error if the attribute is already present + output fixed file to output_filepath which defaults to sedml_filepath ''' - if sedml_file.endswith('.sedml'): - omex_file = Path(sedml_file[:-6] + '.omex') - elif sedml_file.endswith('.xml'): - omex_file = Path(sedml_file[:-4] + '.omex') + # read the sedml file as a string + with open(sedml_filepath, 'r') as file: + sedstr = file.read() + + m = re.search(r']*>', sedstr) + + if m == None: + raise ValueError(f'Invalid SedML file: main tag not found in {sedml_filepath}') + + # read the sbml file as a string to add the xmlns attribute if it is missing + if "xmlns:sbml" in m.group(): + raise ValueError(f'xmlns:sbml attribute already present in file {sedml_filepath}') + + with open(sbml_filepath, 'r') as file: + sbml_str = file.read() + + sbml_xmlns = re.search(r'xmlns="([^"]*)"', sbml_str).group(1) + missing_sbml_attribute = 'xmlns:sbml="' + sbml_xmlns + '"' + + sedstr = re.sub(r']*>', sedstr) + + if m == None: + raise ValueError(f'Invalid SedML file: main tag not found in {sedml_filepath}') + + if "xmlns:sbml" not in m.group(): + return True else: - omex_file = Path(sedml_file+'.omex') + return False + +def get_temp_file(): + ''' + create a temporary filename in the current working directory + ''' + return f"tmp{random.randrange(1000000)}" - sbml_file_entry_format = get_entry_format(sbml_file, 'SBML') - sedml_file_entry_format = get_entry_format(sedml_file, 'SEDML') +def create_omex(sedml_filepath, sbml_filepath, omex_filepath=None, silent_overwrite=True, add_missing_xmlns=True): + ''' + wrap a sedml and an sbml file in a combine archive omex file + overwrite any existing omex file + ''' + + #provide an omex filepath if not specified + if not omex_filepath: + if sedml_filepath.endswith('.sedml'): + omex_filepath = Path(sedml_filepath[:-6] + '.omex') + elif sedml_filepath.endswith('.xml'): + omex_filepath = Path(sedml_filepath[:-4] + '.omex') + else: + omex_filepath = Path(sedml_filepath+'.omex') + + #suppress pymetadata "file exists" warning by preemptively removing existing omex file + if os.path.exists(omex_filepath) and silent_overwrite: + os.remove(omex_filepath) + + tmp_sedml_filepath = None + if add_missing_xmlns: + if xmlns_sbml_attribute_missing(sedml_filepath): + #create a temporary sedml file with the missing attribute added + tmp_sedml_filepath = get_temp_file() + add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, tmp_sedml_filepath) + sedml_filepath = tmp_sedml_filepath + + sbml_file_entry_format = get_entry_format(sbml_filepath, 'SBML') + sedml_file_entry_format = get_entry_format(sedml_filepath, 'SEDML') #wrap sedml+sbml files into an omex combine archive om = omex.Omex() om.add_entry( entry = omex.ManifestEntry( - location = sedml_file, + location = sedml_filepath, format = getattr(omex.EntryFormat, sedml_file_entry_format), master = True, ), - entry_path = Path(os.path.basename(sedml_file)) + entry_path = Path(os.path.basename(sedml_filepath)) ) om.add_entry( entry = omex.ManifestEntry( - location = sbml_file, + location = sbml_filepath, format = getattr(omex.EntryFormat, sbml_file_entry_format), master = False, ), - entry_path = Path(os.path.basename(sbml_file)) + entry_path = Path(os.path.basename(sbml_filepath)) ) - om.to_omex(Path(omex_file)) + om.to_omex(Path(omex_filepath)) - data_dir = os.path.dirname(os.path.abspath(sedml_file)) + if tmp_sedml_filepath: + os.remove(tmp_sedml_filepath) - return data_dir, omex_file + return omex_filepath -def read_log_yml(data_dir): - log_yml = os.path.join(data_dir,"log.yml") - if not os.path.isfile(log_yml): +def read_log_yml(log_filepath): + ''' + read the log YAML file if it exists + return the exception message as a string + ''' + if not os.path.isfile(log_filepath): return None - with open(log_yml) as f: + with open(log_filepath) as f: ym = yaml.safe_load(f) return ym['exception']['message'] -def run_biosimulators_docker(engine,sedml_file,sbml_file,error_categories=error_categories): +def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir=None,error_categories=error_categories): ''' - try to run the sedml+sbml combo using biosimulators - after wrapping the input files into a combine archive - calls biosimulators via docker locally - assumes local docker is setup - engine can be any string that matches a biosimulators docker "URI": - ghcr.io/biosimulators/{engine} + put the sedml and sbml file into an omex archive + run it locally using a biosimulators docker + categorise an error message in the log file ''' #put the sedml and sbml into a combine archive - data_dir,omex_file = create_omex(sedml_file,sbml_file) - - #create mounts to share files with the container - mount_in = docker.types.Mount("/root/in",data_dir,type="bind",read_only=True) - mount_out = docker.types.Mount("/root/out",data_dir,type="bind") - - client = docker.from_env() + omex_filepath = create_omex(sedml_filepath,sbml_filepath) try: - client.containers.run(f"ghcr.io/biosimulators/{engine}", - mounts=[mount_in,mount_out], - command=f"-i /root/in/{omex_file} -o /root/out") + biosimulators_core(engine,omex_filepath,output_dir=output_dir) return "pass" #no errors except Exception as e: #capture the error as a string which won't break markdown tables error_str = safe_md_string(e) #try to load the cleaner error message from the log.yml file - log_str = read_log_yml(data_dir) + log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml")) if log_str: error_str = safe_md_string(log_str) @@ -160,6 +228,32 @@ def run_biosimulators_docker(engine,sedml_file,sbml_file,error_categories=error_ return ["other",f"```{error_str}```"] +def biosimulators_core(engine,omex_filepath,output_dir=None): + ''' + run the omex file using biosimulators + calls biosimulators via docker locally + assumes local docker is setup + engine can be any string that matches a biosimulators docker "URI": + ghcr.io/biosimulators/{engine} + ''' + + #directory containing omex file needs mapping into the container as the input folders + omex_dir = os.path.dirname(os.path.abspath(omex_filepath)) + omex_file = os.path.basename(os.path.abspath(omex_filepath)) + mount_in = docker.types.Mount("/root/in",omex_dir,type="bind",read_only=True) + + #we want the output folder to be different to the input folder + #to avoid the "file already exists" type error + if not output_dir: + output_dir = os.path.join(omex_dir,'output') + os.makedirs(output_dir,exist_ok=True) + + mount_out = docker.types.Mount("/root/out",output_dir,type="bind") + client = docker.from_env() + client.containers.run(f"ghcr.io/biosimulators/{engine}", + mounts=[mount_in,mount_out], + command=f"-i /root/in/{omex_file} -o /root/out") + def test_engine(engine,filename,error_categories=error_categories): ''' test running the file with the given engine