added higher level conversion function to exec method

.gitignore

@@ -19,3 +19,6 @@ docs/.buildinfo
 docs/.doctrees/
 docs/_raw_sources/
 docs/_sources/
+
+# test files (to be deleted)
+test_spatial_exec.py

biosimulators_utils/combine/data_model.py

@@ -11,6 +11,8 @@
 import abc
 import datetime  # noqa: F401
 import enum
+from typing import List
+
 
 __all__ = [
     'CombineArchiveBase',
@@ -40,7 +42,7 @@ def __init__(self, contents=None):
         """
         self.contents = contents or []
 
-    def get_master_content(self):
+    def get_master_content(self) -> List:
         """ Get the master content of an archive
 
         Returns:

biosimulators_utils/combine/exec.py

@@ -29,19 +29,27 @@
 import os
 import tempfile
 import shutil
-import types  # noqa: F401
+from typing import Optional, Tuple
+from types import FunctionType  # noqa: F401
+
 
 __all__ = [
     'exec_sedml_docs_in_archive',
 ]
 
 
-def exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir, apply_xml_model_changes=False,
-                               sed_doc_executer_supported_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
-                               sed_doc_executer_logged_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
-                               log_level=StandardOutputErrorCapturerLevel.c,
-                               config=None):
-    """ Execute the SED-ML files in a COMBINE/OMEX archive (execute tasks and save outputs)
+def exec_sedml_docs_in_archive(
+        sed_doc_executer,
+        archive_filename: str,
+        out_dir: str,
+        apply_xml_model_changes=False,
+        sed_doc_executer_supported_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
+        sed_doc_executer_logged_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
+        log_level=StandardOutputErrorCapturerLevel.c,
+        config: Optional[Config] = None
+        ) -> Tuple[SedDocumentResults, CombineArchiveLog]:
+    """ Execute the SED-ML files in a COMBINE/OMEX archive (execute tasks and save outputs). If 'smoldyn' is detected
+        in the archive, a simularium file will automatically be generated.
 
     Args:
         sed_doc_executer (:obj:`types.FunctionType`): function to execute each SED document in the archive.
@@ -53,8 +61,10 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
                     ''' Execute the tasks specified in a SED document and generate the specified outputs
 
                     Args:
-                        doc (:obj:`SedDocument` of :obj:`str`): SED document or a path to SED-ML file which defines a SED document
-                        working_dir (:obj:`str`): working directory of the SED document (path relative to which models are located)
+                        doc (:obj:`SedDocument` of :obj:`str`): SED document or a
+                            path to SED-ML file which defines a SED document
+                        working_dir (:obj:`str`): working directory of the
+                            SED document (path relative to which models are located)
 
                         out_path (:obj:`str`): path to store the outputs
 
@@ -64,7 +74,8 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
                               with reports at keys ``{rel_out_path}/{report.id}`` within the HDF5 file
 
                         rel_out_path (:obj:`str`, optional): path relative to :obj:`out_path` to store the outputs
-                        apply_xml_model_changes (:obj:`bool`, optional): if :obj:`True`, apply any model changes specified in the SED-ML file
+                        apply_xml_model_changes (:obj:`bool`, optional): if :obj:`True`,
+                            apply any model changes specified in the SED-ML file
                         log (:obj:`SedDocumentLog`, optional): execution status of document
                         log_level (:obj:`StandardOutputErrorCapturerLevel`, optional): level at which to log output
                         indent (:obj:`int`, optional): degree to indent status messages
@@ -77,14 +88,17 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
             * CSV: directory in which to save outputs to files
               ``{ out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv``
             * HDF5: directory in which to save a single HDF5 file (``{ out_dir }/reports.h5``),
-              with reports at keys ``{ relative-path-to-SED-ML-file-within-archive }/{ report.id }`` within the HDF5 file
-
-        apply_xml_model_changes (:obj:`bool`): if :obj:`True`, apply any model changes specified in the SED-ML files before
-            calling :obj:`task_executer`.
-        sed_doc_executer_supported_features (:obj:`list` of :obj:`type`, optional): list of the types of elements that the
-            SED document executer supports. Default: tasks, reports, plots, data sets, curves, and surfaces.
-        sed_doc_executer_logged_features (:obj:`list` of :obj:`type`, optional): list of the types fo elements which that
-            the SED document executer logs. Default: tasks, reports, plots, data sets, curves, and surfaces.
+              with reports at keys ``{ relative-path-to-SED-ML-file-within-archive }/{ report.id }``
+              within the HDF5 file
+
+        apply_xml_model_changes (:obj:`bool`): if :obj:`True`, apply any model changes specified in the
+            SED-ML files before calling :obj:`task_executer`.
+        sed_doc_executer_supported_features (:obj:`list` of :obj:`type`, optional): list of the types
+            of elements that the SED document executer supports. Default: tasks, reports, plots, data sets,
+            curves, and surfaces.
+        sed_doc_executer_logged_features (:obj:`list` of :obj:`type`, optional): list of the types of elements
+            which that the SED document executer logs. Default: tasks, reports,
+            plots, data sets, curves, and surfaces.
         log_level (:obj:`StandardOutputErrorCapturerLevel`, optional): level at which to log output
         config (:obj:`Config`): configuration
 
@@ -225,6 +239,34 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
                         results[content.location] = doc_results
                     if config.LOG:
                         doc_log.status = Status.SUCCEEDED
+
+                    # check the manifest for a smoldyn model
+                    for file_contents in archive.contents:
+                        if 'smoldyn' in file_contents.location:
+                            config.SPATIAL = True
+                            print('There is spatial!')
+
+                    # generate simularium file if spatial
+                    if config.SPATIAL:
+                        import biosimulators_simularium as biosimularium
+                        simularium_filename = os.path.join(out_dir, 'output')
+                        spatial_archive = biosimularium.SmoldynCombineArchive(
+                            rootpath=out_dir,
+                            simularium_filename=simularium_filename
+                        )
+                        # check if modelout file exists
+                        if not os.path.exists(spatial_archive.model_output_filename):
+                            generate_model_output_file = True
+                        else:
+                            generate_model_output_file = False
+                        # construct converter
+                        converter = biosimularium.SmoldynDataConverter(
+                            archive=spatial_archive,
+                            generate_model_output=generate_model_output_file
+                        )
+                        # generate simularium file
+                        converter.generate_simularium_file(io_format='json')
+
                 except Exception as exception:
                     if config.DEBUG:
                         raise
@@ -241,40 +283,47 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
 
         print('')
 
-        # handle smoldyn output/simularium conversion
-        # arch = SmoldynCombineArchive(rootpath=archive_tmp_dir)
-        # if arch.verify_smoldyn_in_manifest():
-        #     converter = SmoldynDataConverter(arch)
-        #     simularium_fp = os.path.join(arch.rootpath, 'simularium_output')
-        #     arch.simularium_filename = simularium_fp
-        #     converter.generate_simularium_file()
-
         if config.BUNDLE_OUTPUTS:
             print('Bundling outputs ...')
 
             # bundle CSV files of reports into zip archive
             report_formats = config.REPORT_FORMATS
-            archive_paths = [os.path.join(out_dir, '**', '*.' + format.value) for format in report_formats if format != ReportFormat.h5]
+            archive_paths = [
+                os.path.join(out_dir, '**', '*.' + f.value)
+                for f in report_formats if f != ReportFormat.h5
+            ]
             archive = build_archive_from_paths(archive_paths, out_dir)
             if archive.files:
                 ArchiveWriter().run(archive, os.path.join(out_dir, config.REPORTS_PATH))
 
             # bundle PDF files of plots into zip archive
             viz_formats = config.VIZ_FORMATS
-            archive_paths = [os.path.join(out_dir, '**', '*.' + format.value) for format in viz_formats]
+            archive_paths = [os.path.join(out_dir, '**', '*.' + f.value) for f in viz_formats]
             archive = build_archive_from_paths(archive_paths, out_dir)
             if archive.files:
                 ArchiveWriter().run(archive, os.path.join(out_dir, config.PLOTS_PATH))
 
+            # bundle Simularium file into zip archive
+            if config.SPATIAL:
+                simularium_format = ['simularium']
+                archive_paths = [os.path.join(out_dir, '**', '*.' + f) for f in simularium_format]
+                archive = build_archive_from_paths(archive_paths, out_dir)
+                if archive.files:
+                    ArchiveWriter().run(archive, os.path.join(out_dir, 'simularium.zip'))
+
+
         # cleanup temporary files
         print('Cleaning up ...')
         if not config.KEEP_INDIVIDUAL_OUTPUTS:
 
             report_formats = config.REPORT_FORMATS
             viz_formats = config.VIZ_FORMATS
             path_patterns = (
-                [os.path.join(out_dir, '**', '*.' + format.value) for format in report_formats if format != ReportFormat.h5]
-                + [os.path.join(out_dir, '**', '*.' + format.value) for format in viz_formats]
+                [
+                    os.path.join(out_dir, '**', '*.' + f.value)
+                    for f in report_formats if format != ReportFormat.h5
+                ]
+                + [os.path.join(out_dir, '**', '*.' + f.value) for f in viz_formats]
             )
             for path_pattern in path_patterns:
                 for path in glob.glob(path_pattern, recursive=True):
@@ -330,3 +379,9 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
 
     # return results and log
     return (results, log)
+
+
+
+
+
+

biosimulators_utils/config.py

@@ -28,9 +28,13 @@
 DEFAULT_BIOSIMULATIONS_API_ENDPOINT = 'https://api.biosimulations.org/'
 DEFAULT_BIOSIMULATIONS_API_AUTH_ENDPOINT = 'https://auth.biosimulations.org/oauth/token'
 DEFAULT_BIOSIMULATIONS_API_AUDIENCE = 'api.biosimulations.org'
+DEFAULT_SUPPORTED_SPATIAL_SIMULATOR = 'smoldyn'
 
 
+# noinspection PyPep8Naming,PyDefaultArgument
 class Config(object):
+    SUPPORTED_SPATIAL_SIMULATOR: str
+
     """ Configuration
 
     Attributes:
@@ -65,6 +69,8 @@ class Config(object):
         BIOSIMULATIONS_API_AUDIENCE (:obj:`str`): audience for the BioSimulations API
         VERBOSE (:obj:`bool`): whether to display the detailed output of the execution of each task
         DEBUG (:obj:`bool`): whether to raise exceptions rather than capturing them
+        SUPPORTED_SPATIAL_SIMULATOR (:obj:`strl`, optional): spatial simulator that this config supports. Currently
+                only `'smoldyn'` is supported.
     """
 
     def __init__(self,
@@ -96,22 +102,26 @@ def __init__(self,
                  BIOSIMULATIONS_API_AUTH_ENDPOINT=DEFAULT_BIOSIMULATIONS_API_AUTH_ENDPOINT,
                  BIOSIMULATIONS_API_AUDIENCE=DEFAULT_BIOSIMULATIONS_API_AUDIENCE,
                  VERBOSE=False,
-                 DEBUG=False):
+                 DEBUG=False,
+                 SPATIAL=False):
         """
         Args:
-            OMEX_METADATA_INPUT_FORMAT (:obj:`OmexMetadataInputFormat`, optional): format to validate OMEX Metadata files against
+            OMEX_METADATA_INPUT_FORMAT (:obj:`OmexMetadataInputFormat`, optional): format to validate
+                OMEX Metadata files against
             OMEX_METADATA_OUTPUT_FORMAT (:obj:`OmexMetadataOutputFormat`, optional): format to export OMEX Metadata files
             OMEX_METADATA_SCHEMA (:obj:`OmexMetadataSchema`, optional): schema to validate OMEX Metadata files against
-            VALIDATE_OMEX_MANIFESTS (:obj:`bool`, optional): whether to validate OMEX manifests during the execution of COMBINE/OMEX archives
-            VALIDATE_SEDML (:obj:`bool`, optional): whether to validate SED-ML files during the execution of COMBINE/OMEX archives
-            VALIDATE_SEDML_MODELS (:obj:`bool`, optional): whether to validate models referenced by SED-ML files during the execution
+            VALIDATE_OMEX_MANIFESTS (:obj:`bool`, optional): whether to validate OMEX manifests during the execution
                 of COMBINE/OMEX archives
+            VALIDATE_SEDML (:obj:`bool`, optional): whether to validate SED-ML files during the execution of
+                COMBINE/OMEX archives
+            VALIDATE_SEDML_MODELS (:obj:`bool`, optional): whether to validate models referenced by SED-ML
+                files during the execution of COMBINE/OMEX archives
             VALIDATE_IMPORTED_MODEL_FILES (:obj:`bool`, optional): whether to validate files imported from models
             VALIDATE_OMEX_METADATA (:obj:`bool`, optional): whether to validate OMEX metadata (RDF files) during the execution of
                 COMBINE/OMEX archives
             VALIDATE_IMAGES (:obj:`bool`, optional): whether to validate the images in COMBINE/OMEX archives during their execution
             VALIDATE_RESULTS (:obj:`bool`, optional): whether to validate the results of simulations following their execution
-            ALGORITHM_SUBSTITUTION_POLICY (:obj:`str`, optional): algorithm substition policy
+            ALGORITHM_SUBSTITUTION_POLICY (:obj:`str`, optional): algorithm substitution policy
             COLLECT_COMBINE_ARCHIVE_RESULTS (:obj:`bool`, optional): whether to assemble an in memory data structure with all of the
                 simulation results of COMBINE/OMEX archives
             COLLECT_SED_DOCUMENT_RESULTS (:obj:`bool`, optional): whether to assemble an in memory data structure with all of the
@@ -132,6 +142,7 @@ def __init__(self,
             BIOSIMULATIONS_API_AUDIENCE (:obj:`str`, optional): audience for the BioSimulations API
             VERBOSE (:obj:`bool`, optional): whether to display the detailed output of the execution of each task
             DEBUG (:obj:`bool`, optional): whether to raise exceptions rather than capturing them
+            SPATIAL (:obj:`bool`, optional): whether the simulation is spatial in nature and able to be simularium-ed
         """
         self.OMEX_METADATA_INPUT_FORMAT = OMEX_METADATA_INPUT_FORMAT
         self.OMEX_METADATA_OUTPUT_FORMAT = OMEX_METADATA_OUTPUT_FORMAT
@@ -162,23 +173,34 @@ def __init__(self,
         self.BIOSIMULATIONS_API_AUDIENCE = BIOSIMULATIONS_API_AUDIENCE
         self.VERBOSE = VERBOSE
         self.DEBUG = DEBUG
+        self.SPATIAL = SPATIAL
+        self.SUPPORTED_SPATIAL_SIMULATOR = DEFAULT_SUPPORTED_SPATIAL_SIMULATOR
+        try:
+            assert self.SUPPORTED_SPATIAL_SIMULATOR == 'smoldyn'
+        except AssertionError:
+            raise ValueError(
+                """
+                The only spatial simulator that is currently supported is 'smoldyn'. Please set the value of 
+                    SUPPORTED_SPATIAL_SIMULATOR to 'smoldyn' and try again.
+                """
+            )
 
 
 def get_config():
-    """ Get the configuration
+    """ Factory for generating a new instance of `Config`.
 
     Returns:
         :obj:`Config`: configuration
     """
     report_formats = os.environ.get('REPORT_FORMATS', 'h5').strip()
     if report_formats:
-        report_formats = [ReportFormat(format.strip().lower()) for format in report_formats.split(',')]
+        report_formats = [ReportFormat(f.strip().lower()) for f in report_formats.split(',')]
     else:
         report_formats = []
 
     viz_formats = os.environ.get('VIZ_FORMATS', 'pdf').strip()
     if viz_formats:
-        viz_formats = [VizFormat(format.strip().lower()) for format in viz_formats.split(',')]
+        viz_formats = [VizFormat(f.strip().lower()) for f in viz_formats.split(',')]
     else:
         viz_formats = []
 
@@ -198,7 +220,8 @@ def get_config():
         VALIDATE_RESULTS=os.environ.get('VALIDATE_RESULTS', '1').lower() in ['1', 'true'],
         ALGORITHM_SUBSTITUTION_POLICY=AlgorithmSubstitutionPolicy(os.environ.get(
             'ALGORITHM_SUBSTITUTION_POLICY', DEFAULT_ALGORITHM_SUBSTITUTION_POLICY)),
-        COLLECT_COMBINE_ARCHIVE_RESULTS=os.environ.get('COLLECT_COMBINE_ARCHIVE_RESULTS', '0').lower() in ['1', 'true'],
+        COLLECT_COMBINE_ARCHIVE_RESULTS=os.environ.get('COLLECT_COMBINE_ARCHIVE_RESULTS',
+                                                       '0').lower() in ['1', 'true'],
         COLLECT_SED_DOCUMENT_RESULTS=os.environ.get('COLLECT_SED_DOCUMENT_RESULTS', '0').lower() in ['1', 'true'],
         SAVE_PLOT_DATA=os.environ.get('SAVE_PLOT_DATA', '1').lower() in ['1', 'true'],
         REPORT_FORMATS=report_formats,
@@ -212,10 +235,12 @@ def get_config():
         LOG_PATH=os.environ.get('LOG_PATH', DEFAULT_LOG_PATH),
         BIOSIMULATORS_API_ENDPOINT=os.environ.get('BIOSIMULATORS_API_ENDPOINT', DEFAULT_BIOSIMULATORS_API_ENDPOINT),
         BIOSIMULATIONS_API_ENDPOINT=os.environ.get('BIOSIMULATIONS_API_ENDPOINT', DEFAULT_BIOSIMULATIONS_API_ENDPOINT),
-        BIOSIMULATIONS_API_AUTH_ENDPOINT=os.environ.get('BIOSIMULATIONS_API_AUTH_ENDPOINT', DEFAULT_BIOSIMULATIONS_API_AUTH_ENDPOINT),
+        BIOSIMULATIONS_API_AUTH_ENDPOINT=os.environ.get('BIOSIMULATIONS_API_AUTH_ENDPOINT',
+                                                        DEFAULT_BIOSIMULATIONS_API_AUTH_ENDPOINT),
         BIOSIMULATIONS_API_AUDIENCE=os.environ.get('BIOSIMULATIONS_API_AUDIENCE', DEFAULT_BIOSIMULATIONS_API_AUDIENCE),
         VERBOSE=os.environ.get('VERBOSE', '1').lower() in ['1', 'true'],
         DEBUG=os.environ.get('DEBUG', '0').lower() in ['1', 'true'],
+        SPATIAL=os.environ.get('SPATIAL', '0').lower() in ['1', 'true']
     )
 
 

requirements.optional.txt

@@ -23,10 +23,10 @@ python_libsbml
 
 [smoldyn]
 smoldyn >= 2.66
-# simulariumio
 
-[simularium]
-simulariumio
+[spatial]
+smoldyn >= 2.66
+biosimulators_simularium
 
 #################################
 ## Visualization formats