chore: merging

biosimulators_test_suite/_version.py

@@ -1 +1 @@
-__version__ = '0.1.48'
+__version__ = '0.1.49'

examples/bngl/test-bngl/manifest.xml

@@ -4,8 +4,6 @@
   <content location="./test.sedml" format="http://identifiers.org/combine.specifications/sed-ml" master="true"/>
   <content location="." format="http://identifiers.org/combine.specifications/omex"/>
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
-  <content location="metadata_1.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
-  <content location="metadata_2.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
 </omexManifest>

examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf

@@ -15,7 +15,7 @@
     <prism:keyword>metabolism</prism:keyword>
 
     <!-- thumbnail image -->
-    <collex:thumbnail rdf:resource="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Figure1.png"/>
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Figure1.jpg"/>
 
     <!-- long description -->
     <dc:description>Iron is an essential element of most living organisms but is a dangerous substance when poorly liganded in solution. The hormone hepcidin regulates the export of iron from tissues to the plasma contributing to iron homeostasis and also restricting its availability to infectious agents. Disruption of iron regulation in mammals leads to disorders such as anemia and hemochromatosis, and contributes to the etiology of several other diseases such as cancer and neurodegenerative diseases. Here we test the hypothesis that hepcidin alone is able to regulate iron distribution in different dietary regimes in the mouse using a computational model of iron distribution calibrated with radioiron tracer data.</dc:description>

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn] >= 0.1.95
+biosimulators_utils[containers,bngl,cellml,lems,neuroml,sbml,smoldyn] >= 0.1.97
 cement
 docker
 natsort

tests/test_examples.py

@@ -1,6 +1,7 @@
 from biosimulators_utils.combine.io import CombineArchiveReader
 from biosimulators_utils.combine.data_model import CombineArchiveContentFormat
 from biosimulators_utils.combine.validation import validate
+from biosimulators_utils.omex_meta.data_model import OmexMetaSchema
 from biosimulators_utils.report.data_model import ReportFormat
 from biosimulators_utils.report.io import ReportReader
 from biosimulators_utils.sedml.io import SedmlSimulationReader
@@ -25,7 +26,8 @@ def tearDown(self):
 
     def test(self):
         examples_dir = os.path.join(os.path.dirname(__file__), '..', 'examples')
-        for example_filename in glob.glob(os.path.join(examples_dir, '**', '*.omex')):
+        example_filenames = glob.glob(os.path.join(examples_dir, '**', '*.omex'))
+        for example_filename in example_filenames:
             example_specs_filename = os.path.join(example_filename[0:-5], 'expected-results.json')
 
             example_base_dir = os.path.join(os.path.dirname(example_filename))
@@ -41,7 +43,8 @@ def test(self):
             archive = CombineArchiveReader().run(archive_filename, archive_dirname)
 
             errors, _ = validate(archive, archive_dirname,
-                                 formats_to_validate=list(CombineArchiveContentFormat.__members__.values()))
+                                 formats_to_validate=list(CombineArchiveContentFormat.__members__.values()),
+                                 metadata_schema=OmexMetaSchema.biosimulations)
             if errors:
                 msg = 'COMBINE/OMEX archive `{}` is invalid.\n  {}'.format(
                     archive_filename,