Merge pull request #63 from SynBioDex/feature-support_paml

Support PAML

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "tyto/ontologies/sbol-owl"]
 	path = tyto/ontologies/sbol-owl
 	url = https://github.com/dissys/sbol-owl.git
+[submodule "tyto/ontologies/paml"]
+	path = tyto/ontologies/paml
+	url = [email protected]:bioprotocols/paml.git

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 setup(name='tyto',
-      version='1.1',
+      version='1.2',
       description='Automatically generates Python symbols for ontology terms',
       python_requires='>=3.6',
       url='https://github.com/SynBioDex/tyto',
@@ -33,7 +33,9 @@
                               'ontologies/*.rdf',
                               'ontologies/*.ttl',
                               'ontologies/sbol-owl3/sbolowl3.rdf',
-                              'ontologies/sbol-owl/sbol.rdf']},
+                              'ontologies/sbol-owl/sbol.rdf',
+                              'ontologies/paml/paml/paml.ttl',
+                              'ontologies/paml/uml/uml.ttl']},
       include_package_data=True,
       install_requires=[
             'rdflib>=5.0',

test/test_ontology.py

@@ -181,6 +181,10 @@ def test_pubchem(self):
             # Ambiguous term matches many SIDs
             PubChem['water']
 
+class TestPAML(unittest.TestCase):
+
+    def test_paml(self):
+        self.assertEqual(PAML.SampleArray, 'http://bioprotocols.org/paml#SampleArray')
 
 if __name__ == '__main__':
     unittest.main()

tyto/__init__.py

@@ -9,3 +9,5 @@
 from .sbol3 import SBOL3
 from .edam import EDAM
 from .pubchem import PubChem
+from .paml import PAML
+from .uml import UML

tyto/endpoint/endpoint.py

@@ -242,7 +242,10 @@ def is_loaded(self):
         return bool(self.graph)
 
     def load(self):
-        self.graph.parse(self.path)
+        if self.path.split('.')[-1] == 'ttl':
+            self.graph.parse(self.path, format='ttl')
+        else:
+            self.graph.parse(self.path)
 
     def query(self, ontology, sparql, err_msg):
         sparql_final = sparql.format(from_clause='')  # Because only one ontology per file, delete the from clause

tyto/paml.py

@@ -0,0 +1,6 @@
+from .tyto import Ontology, installation_path
+
+
+PAML = Ontology(path=installation_path('ontologies/paml/paml/paml.ttl'),
+                uri='http://bioprotocols.org/paml#')
+

tyto/uml.py

@@ -0,0 +1,6 @@
+from .tyto import Ontology, installation_path
+
+
+UML = Ontology(path=installation_path('ontologies/paml/uml/uml.ttl'),
+                uri='http://bioprotocols.org/uml#')
+