Merge pull request #98 from biosimulators/lps-warning-consolidation-plus

Fix for #96: consolidate warnings

biosimulators_utils/__main__.py

@@ -203,7 +203,7 @@ def _default(self):
         errors, warnings, _ = biosimulators_utils.sedml.validation.validate_model_with_language(filename, language, config=config)
 
         if warnings:
-            msg = 'The model file `{}` may be invalid.\n  {}'.format(
+            msg = 'The model file `{}` has warnings.\n  {}'.format(
                 filename, flatten_nested_list_of_strings(warnings).replace('\n', '\n  '))
             warn(msg, BioSimulatorsWarning)
 
@@ -249,7 +249,7 @@ def _default(self):
                 raise
 
         if reader.warnings:
-            msg = 'The SED-ML file `{}` may be invalid.\n  {}'.format(
+            msg = 'The SED-ML file `{}` has warnings.\n  {}'.format(
                 args.filename, flatten_nested_list_of_strings(reader.warnings).replace('\n', '\n  '))
             warn(msg, BioSimulatorsWarning)
 
@@ -289,7 +289,7 @@ def _default(self):
         _, errors, warnings = biosimulators_utils.omex_meta.io.read_omex_meta_file(args.filename)
 
         if warnings:
-            msg = 'The OMEX Metadata file `{}` may be invalid.\n  {}'.format(
+            msg = 'The OMEX Metadata file `{}` has warnings.\n  {}'.format(
                 args.filename, flatten_nested_list_of_strings(warnings).replace('\n', '\n  '))
             warn(msg, BioSimulatorsWarning)
 
@@ -345,7 +345,7 @@ def _default(self):
             config=config,
         )
         if warnings:
-            msg = 'The COMBINE/OMEX archive may be invalid.\n  {}'.format(
+            msg = 'The COMBINE/OMEX archive has warnings.\n  {}'.format(
                 flatten_nested_list_of_strings(warnings).replace('\n', '\n  '))
             warn(msg, BioSimulatorsWarning)
 

biosimulators_utils/combine/exec.py

@@ -125,7 +125,7 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
             # validate archive
             errors, warnings = validate(archive, archive_tmp_dir, config=config)
             if warnings:
-                msg = 'The COMBINE/OMEX archive may be invalid.\n  {}'.format(
+                msg = 'The COMBINE/OMEX archive has warnings.\n  {}'.format(
                     flatten_nested_list_of_strings(warnings).replace('\n', '\n  '))
                 warn(msg, BioSimulatorsWarning)
 

biosimulators_utils/combine/io.py

@@ -78,7 +78,7 @@ def run(self, archive, in_dir, out_file):
         self.warnings.extend(warnings)
 
         if self.warnings:
-            warn('COMBINE/OMEX archive may be invalid.\n  ' + flatten_nested_list_of_strings(self.warnings).replace('\n', '\n  '),
+            warn('COMBINE/OMEX archive has warnings.\n  ' + flatten_nested_list_of_strings(self.warnings).replace('\n', '\n  '),
                  BioSimulatorsWarning)
         if self.errors:
             raise ValueError('COMBINE/OMEX archive is invalid.\n  ' + flatten_nested_list_of_strings(self.errors).replace('\n', '\n  '))
@@ -105,7 +105,7 @@ def write_manifest(self, contents, filename):
 
         errors, warnings = get_combine_errors_warnings(manifest)
         if warnings:
-            msg = 'COMBINE/OMEX archive may be invalid.\n  ' + flatten_nested_list_of_strings(warnings).replace('\n', '\n  ')
+            msg = 'COMBINE/OMEX archive has warnings.\n  ' + flatten_nested_list_of_strings(warnings).replace('\n', '\n  ')
             warn(msg, BioSimulatorsWarning)
         if errors:
             msg = 'COMBINE/OMEX archive is invalid.\n  ' + flatten_nested_list_of_strings(errors).replace('\n', '\n  ')
@@ -237,7 +237,7 @@ def run(self, in_file, out_dir, include_omex_metadata_files=True, config=None):
 
         # raise warnings and errors
         if self.warnings:
-            warn('COMBINE/OMEX archive may be invalid.\n  ' + flatten_nested_list_of_strings(self.warnings).replace('\n', '\n  '),
+            warn('COMBINE/OMEX archive has warnings.\n  ' + flatten_nested_list_of_strings(self.warnings).replace('\n', '\n  '),
                  BioSimulatorsWarning)
         if self.errors:
             raise ValueError('`{}` is not a valid COMBINE/OMEX archive.\n  {}'.format(

biosimulators_utils/combine/validation.py

@@ -281,7 +281,7 @@ def validate_content(content, archive_dirname,
         ]]
     if warnings:
         warnings = [[
-            'The {} file at location `{}` may be invalid.'.format(file_type, content.location),
+            'The {} file at location `{}` has warnings.'.format(file_type, content.location),
             warnings,
         ]]
 

biosimulators_utils/model_lang/sbml/validation.py

@@ -37,12 +37,33 @@ def validate_model(filename, name=None, validate_consistency=True, config=None):
             if validate_consistency:
                 doc.checkConsistency()
 
+            warning_map = {}
             for i_error in range(doc.getNumErrors()):
                 sbml_error = doc.getError(i_error)
                 if sbml_error.isInfo() or sbml_error.isWarning():
-                    warnings.append([sbml_error.getMessage()])
+                    err_id = sbml_error.getErrorId()
+                    if err_id not in warning_map:
+                        warning_map[err_id] = [
+                            0,
+                            sbml_error.getCategoryAsString(),
+                            sbml_error.getMessage().strip(),
+                            sbml_error.getLine(),
+                            sbml_error.getColumn(),
+                            sbml_error.getSeverityAsString().lower(),
+                        ]
+                    warning_map[err_id][0] += 1
                 else:
-                    errors.append([sbml_error.getMessage()])
+                    errors.append(['{} ({}) at line {}, column {}: {}'.format(
+                        sbml_error.getCategoryAsString(), sbml_error.getErrorId(),
+                        sbml_error.getLine(), sbml_error.getColumn(),
+                        sbml_error.getMessage())
+                    ])
+            for err_id, (count, category, first_msg, line, column, severity) in warning_map.items():
+                warnings.append([
+                    '{} {}{} of type {} ({}). The following is the first {} at line {}, column {}:'.format(
+                        count, severity, 's' if count > 1 else '', category, err_id, severity, line, column),
+                    [[first_msg]]
+                ])
 
         else:
             errors.append(['`{}` is not a file.'.format(filename or '')])

biosimulators_utils/omex_meta/io.py

@@ -340,7 +340,7 @@ def run(self, filename_or_filenames, archive=None, working_dir=None, config=None
 
             if temp_warnings:
                 if isinstance(filename_or_filenames, (tuple, list)):
-                    warnings.append(['The OMEX Metadata file at location `{}` may be invalid.'.format(error_filename), temp_warnings])
+                    warnings.append(['The OMEX Metadata file at location `{}` has warnings.'.format(error_filename), temp_warnings])
                 else:
                     warnings.extend(temp_warnings)
 
@@ -503,7 +503,7 @@ def run(self, filename_or_filenames, archive=None, working_dir=None, config=None
 
             if temp_warnings:
                 if isinstance(filename_or_filenames, (tuple, list)):
-                    warnings.append(['The OMEX Metadata file at location `{}` may be invalid.'.format(error_filename), temp_warnings])
+                    warnings.append(['The OMEX Metadata file at location `{}` has warnings.'.format(error_filename), temp_warnings])
                 else:
                     warnings.extend(temp_warnings)
 

biosimulators_utils/omex_meta/validation.py

@@ -53,7 +53,7 @@ def validate_biosimulations_metadata(metadata, archive=None, working_dir=None):
 
         if temp_warnings:
             el_uri = get_global_combine_archive_content_uri(el_metadata['uri'], el_metadata['combine_archive_uri'])
-            warnings.append(['The metadata for URI `{}` may be invalid.'.format(
+            warnings.append(['The metadata for URI `{}` has warnings.'.format(
                 el_uri),  temp_warnings])
 
     if not has_archive_metadata:

biosimulators_utils/sedml/data_model.py

@@ -603,6 +603,21 @@ def is_equal(self, other):
             and self.language == other.language \
             and are_lists_equal(self.changes, other.changes)
 
+    def has_structural_changes(self):
+        """ Check if there are structural model changes present.
+
+        * Add element
+        * Replace element
+        * Remove element
+
+        Returns:
+            :obj:`bool`: :obj:`True`, if structural model changes are present
+        """
+        for change in self.changes:
+            if isinstance(change, (AddElementModelChange, ReplaceElementModelChange, RemoveElementModelChange)):
+                return True
+        return False
+
 
 class ModelChange(SedBase, SedIdGroupMixin, TargetGroupMixin):
     """ A change to a model