Missing vg:Step type

graph-genome · Nov 22, 2019 · 4dce0de · 4dce0de
1 parent 15a1e0e
commit 4dce0de
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Showing 3 changed files with 16 additions and 4 deletions.
diff --git a/spodgi/OdgiStore.py b/spodgi/OdgiStore.py
@@ -16,7 +16,7 @@
 knownTypes = [VG.Node, VG.Path, VG.Step, FALDO.Region, FALDO.ExactPosition, FALDO.Position]
 knownPredicates = [RDF.value, VG.rank, VG.position, VG.step, VG.path, VG.linksForwardToForward, VG.linksForwardToReverse, VG.linksReverseToForward, VG.linksReverseToReverse, VG.links, VG.reverseOfNode, VG.node, FALDO.begin, FALDO.end, FALDO.reference, FALDO.position]
 nodeRelatedPredicates = [VG.linksForwardToForward, VG.linksForwardToReverse, VG.linksReverseToForward, VG.linksReverseToReverse, VG.links, RDF.value]
-stepAssociatedTypes = [FALDO.Region, FALDO.ExactPosition, FALDO.Position]
+stepAssociatedTypes = [FALDO.Region, FALDO.ExactPosition, FALDO.Position, VG.Step]
 stepAssociatedPredicates = [VG.rank, VG.position, VG.path, VG.node, VG.reverseOfNode, FALDO.begin, FALDO.end, FALDO.reference, FALDO.position]
 
 __all__ = [ 'OdgiStore' ]

diff --git a/spodgi/term.py b/spodgi/term.py
@@ -89,7 +89,7 @@ def __hash__(self):
 class NodeIriRef(URIRef):
     __slots__ = ("_nodeHandle", "_base", "_odgi")
 
-    def __new__(cls, nodeHandle, base, odgi):
+    def __new__(cls, nodeHandle, base=None, odgi=None):
          inst =  str.__new__(cls)
          inst._nodeHandle = nodeHandle
          inst._base = base
@@ -98,7 +98,7 @@ def __new__(cls, nodeHandle, base, odgi):
 
     def __eq__(self, other):
         if type(self) == type(other):
-            return self._odgi.get_id(self._nodeHandle) == self._odgi.get_id(other._nodeHandle) and self._base == other._base
+            return self._odgi.get_id(self._nodeHandle) == other._odgi.get_id(other._nodeHandle) and self._base == other._base
         elif (type(other) == URIRef):
             return URIRef(self.unicode()) == other
         else:
@@ -125,7 +125,8 @@ def toPython(self):
         return self.unicode()
 
     def unicode(self):
-        return f'{self._base}{self._odgi.get_id(self._nodeHandle)}'
+        nid = self._odgi.get_id(self._nodeHandle);
+        return f'{self._base}{nid}'
 
     def __str__(self):
         return self.unicode()

diff --git a/test/test_select.py b/test/test_select.py
@@ -44,3 +44,14 @@ def test_select_specific_step():
 
     spodgi.close()
     assert True
+
+def test_select_specific_sequence():
+    plugin.register('OdgiStore', Store,'spodgi.OdgiStore', 'OdgiStore')
+    s = plugin.get('OdgiStore', Store)(base="http://example.org/test/")
+    spodgi = Graph(store=s)
+    spodgi.open('./test/t.odgi', create=False)
+    for r in spodgi.query('SELECT ?sequence WHERE {<node/2> rdf:value ?sequence}'):
+        assert r[0].value == 'A'
+
+    spodgi.close()
+    assert True