switching no SED-ML in COMBINE archive from warning to error; closes #26

biosimulators · Mar 3, 2021 · b07d921 · b07d921
1 parent d1376cc
commit b07d921
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Showing 4 changed files with 12 additions and 16 deletions.
diff --git a/biosimulators_utils/combine/exceptions.py b/biosimulators_utils/combine/exceptions.py
@@ -10,9 +10,15 @@
 
 __all__ = [
     'CombineArchiveExecutionError',
+    'NoSedmlError',
 ]
 
 
 class CombineArchiveExecutionError(BioSimulatorsException):
     """ Error that a SED document could not be executed """
     pass  # pragma: no cover
+
+
+class NoSedmlError(BioSimulatorsException):
+    """ Error that a COMBINE/OMEX archive does not contain any SED-ML files """
+    pass  # pragma: no cover
diff --git a/biosimulators_utils/combine/exec.py b/biosimulators_utils/combine/exec.py
@@ -16,11 +16,9 @@
 from ..sedml.data_model import (SedDocument, Task, Output, Report, DataSet, Plot2D, Curve,  # noqa: F401
                                 Plot3D, Surface, Variable)
 from ..sedml.io import SedmlSimulationReader  # noqa: F401
-from ..warnings import warn
-from .exceptions import CombineArchiveExecutionError
+from .exceptions import CombineArchiveExecutionError, NoSedmlError
 from .io import CombineArchiveReader
 from .utils import get_sedml_contents, get_summary_sedml_contents
-from .warnings import NoSedmlWarning
 import datetime
 import glob
 import os
@@ -116,7 +114,8 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
     # determine files to execute
     sedml_contents = get_sedml_contents(archive)
     if not sedml_contents:
-        warn("COMBINE/OMEX archive '{}' does not contain any executing SED-ML files".format(archive_filename), NoSedmlWarning)
+        msg = "COMBINE/OMEX archive '{}' does not contain any executing SED-ML files".format(archive_filename)
+        raise NoSedmlError(msg)
 
     # print summary of SED documents
     print(get_summary_sedml_contents(archive, archive_tmp_dir))

diff --git a/biosimulators_utils/combine/warnings.py b/biosimulators_utils/combine/warnings.py
@@ -6,12 +6,4 @@
 :License: MIT
 """
 
-from ..warnings import BioSimulatorsWarning
-
-
-__all__ = ['NoSedmlWarning']
-
-
-class NoSedmlWarning(BioSimulatorsWarning):
-    """ Warning that a COMBINE/OMEX archive does not contain any SED-ML files """
-    pass  # pragma: no cover
+__all__ = []
diff --git a/tests/combine/test_combine_exec.py b/tests/combine/test_combine_exec.py
@@ -1,9 +1,8 @@
 from biosimulators_utils.archive.io import ArchiveReader
 from biosimulators_utils.combine import exec
 from biosimulators_utils.combine.data_model import CombineArchive, CombineArchiveContent
-from biosimulators_utils.combine.exceptions import CombineArchiveExecutionError
+from biosimulators_utils.combine.exceptions import CombineArchiveExecutionError, NoSedmlError
 from biosimulators_utils.combine.io import CombineArchiveWriter
-from biosimulators_utils.combine.warnings import NoSedmlWarning
 from biosimulators_utils.log import utils as log_utils
 from biosimulators_utils.log.warnings import StandardOutputNotLoggedWarning
 from biosimulators_utils.plot.data_model import PlotFormat
@@ -87,7 +86,7 @@ def exec_sed_doc(task_executer, filename, working_dir, base_out_dir,
 
         archive.contents[0].format = 'unknown'
         CombineArchiveWriter().run(archive, in_dir, archive_filename)
-        with self.assertWarnsRegex(NoSedmlWarning, 'does not contain any executing SED-ML files'):
+        with self.assertRaisesRegex(NoSedmlError, 'does not contain any executing SED-ML files'):
             with mock.patch('biosimulators_utils.sedml.exec.exec_sed_doc', side_effect=exec_sed_doc):
                 sed_doc_executer = functools.partial(exec_sed_doc, sed_task_executer)
                 exec.exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,