create basic unit test. add dummy nodes and edges and check nr of nod…

…es and edges written to xml file

biocypher/write/graph/_rdf.py

@@ -169,6 +169,9 @@ def _write_single_edge_list_to_file(
                                         g.add((self.namespaces["biocypher"][rdf_predicate], self.namespaces["biocypher"][key], Literal(v)))
                                 except (SyntaxError, ValueError, TypeError):
                                     g.add((self.namespaces["biocypher"][rdf_predicate], self.namespaces["biocypher"][key], Literal(value)))
+                            else:
+                                g.add((self.namespaces["biocypher"][rdf_predicate], self.namespaces["biocypher"][key], Literal(value)))
+
                         else:
                             g.add((self.namespaces["biocypher"][rdf_predicate], self.namespaces["biocypher"][key], Literal(value)))
 
@@ -288,6 +291,7 @@ def write_nodes(self, nodes, batch_size: int = int(1e6)):
         if not passed:
             logger.error('Error while writing node data.')
             return False
+        return True
 
     def write_edges(
         self,
@@ -315,6 +319,8 @@ def write_edges(
         if not passed:
             logger.error('Error while writing edge data.')
             return False
+
+        return True
 
     def _construct_import_call(self) -> bool:
         """

test/fixtures/rdf.py

@@ -0,0 +1,21 @@
+import os
+
+import pytest
+
+from biocypher.write.graph._rdf import _RDFwriter
+
+
+@pytest.fixture(scope="function")
+def bw_rdf(translator, deduplicator, tmp_path_session):
+    bw_rdf = _RDFwriter(
+        translator=translator,
+        deduplicator=deduplicator,
+        output_directory=tmp_path_session,
+        delimiter=",",
+    )
+    bw_rdf.rdf_format = "xml"
+    yield bw_rdf
+
+    # teardown
+    for f in os.listdir(tmp_path_session):
+        os.remove(os.path.join(tmp_path_session, f))

test/write/graph/test_rdf.py

@@ -0,0 +1,75 @@
+import os
+import pytest
+from rdflib import Graph
+from biocypher.write import _batch_writer
+from biocypher.write.graph._rdf import _RDFwriter
+from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
+import glob
+
+def nodes_and_edges():
+    nodes_type_1 = []
+    nodes_type_2 = []
+    edges = []
+    number_of_items = 4
+    for i in range(number_of_items):
+        node1 = BioCypherNode(
+            f"EFO:{i+1}",
+            node_label="disease",
+            properties= {"name": f"disease{i+1}"}
+        )
+        node2 = BioCypherNode(
+            f"ensembl:ENS{i+1}",
+            node_label="gene",
+        )
+        edge_1 = BioCypherEdge(
+            source_id=f"EFO:{i+1}",
+            target_id=f"ensembl:ENS{i+1}",
+            relationship_label="gene_disease_relationship",
+            properties = {"score": "0.3"}
+        )
+        nodes_type_1.append(node1)
+        nodes_type_2.append(node2)
+        edges.append(edge_1)
+
+    return [[nodes_type_1, nodes_type_2], edges]
+
+@pytest.fixture
+def _get_nodes():
+    # return a list of nodes
+    return nodes_and_edges()[0]
+
+@pytest.fixture
+def _get_edges():
+    # return a list of edges
+    return nodes_and_edges()[1]
+
+
+@pytest.mark.parametrize("length", [4], scope="function")
+def test_rdf_write_data(bw_rdf, length, _get_nodes, _get_edges):
+    # writer = _get_writer
+    # writer.rdf_format = "xml"
+    nodes = _get_nodes
+    edges = _get_edges
+
+    node_type_1 = bw_rdf.write_nodes(nodes[0])
+    node_type_2 = bw_rdf.write_nodes(nodes[1])
+    edge_1 = bw_rdf.write_edges(edges)
+
+    # check if the writing of the nodes went okay.
+    assert all([node_type_1, node_type_2, edge_1])
+
+    tmp_path = bw_rdf.outdir
+
+    rdf_files_path = os.path.join(tmp_path, "*.xml")
+    rdf_files = glob.glob(rdf_files_path)
+
+    g = Graph()
+    for file in rdf_files:
+        print(file)
+        with open(file) as f:
+            g_temp = Graph().parse(data=f.read(), format="xml")
+            g += g_temp
+
+    # check if the number of nodes and relations are correct
+    assert len(set(g.subjects())) == 15  # generated 4 nodes per type (8 in total) and 4 'edges'. together with the class definition (+3) makes 15 in total
+    assert len(set(g.subject_objects())) == 47 # all the triples; between nodes, but also the converted properties of nodes and the 'edges'.