From aa525c434a94e1931a3e85fb20130ab94f945610 Mon Sep 17 00:00:00 2001
From: Bryan Bartley <bryan.a.bartley@raytheon.com>
Date: Mon, 25 Apr 2022 09:08:31 -0700
Subject: [PATCH 1/2] Support PAML

---
 .gitmodules           | 3 +++
 setup.py              | 6 ++++--
 test/test_ontology.py | 4 ++++
 tyto/__init__.py      | 2 ++
 tyto/ontologies/paml  | 1 +
 tyto/paml.py          | 6 ++++++
 tyto/uml.py           | 6 ++++++
 7 files changed, 26 insertions(+), 2 deletions(-)
 create mode 160000 tyto/ontologies/paml
 create mode 100644 tyto/paml.py
 create mode 100644 tyto/uml.py

diff --git a/.gitmodules b/.gitmodules
index 7264e4c..b89ab87 100644
--- a/.gitmodules
+++ b/.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 = git@github.com:bioprotocols/paml.git
diff --git a/setup.py b/setup.py
index e08afa1..f0b61af 100644
--- a/setup.py
+++ b/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',
diff --git a/test/test_ontology.py b/test/test_ontology.py
index a4e8ce0..200c0c7 100644
--- a/test/test_ontology.py
+++ b/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()
diff --git a/tyto/__init__.py b/tyto/__init__.py
index e13accd..3fec9f1 100644
--- a/tyto/__init__.py
+++ b/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
diff --git a/tyto/ontologies/paml b/tyto/ontologies/paml
new file mode 160000
index 0000000..96fdd66
--- /dev/null
+++ b/tyto/ontologies/paml
@@ -0,0 +1 @@
+Subproject commit 96fdd666991a68a34db1f71774fb7f72952ac93a
diff --git a/tyto/paml.py b/tyto/paml.py
new file mode 100644
index 0000000..430cd0a
--- /dev/null
+++ b/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#')
+
diff --git a/tyto/uml.py b/tyto/uml.py
new file mode 100644
index 0000000..2fcf390
--- /dev/null
+++ b/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#')
+

From 83afcc055c569b93095c55e361a553c42e5739e0 Mon Sep 17 00:00:00 2001
From: Bryan Bartley <bryan.a.bartley@raytheon.com>
Date: Mon, 25 Apr 2022 09:28:11 -0700
Subject: [PATCH 2/2] Configure GraphEndpoint to parse turtle

---
 tyto/endpoint/endpoint.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tyto/endpoint/endpoint.py b/tyto/endpoint/endpoint.py
index a1bf08b..d86335e 100644
--- a/tyto/endpoint/endpoint.py
+++ b/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