use example data from fixtures and assert every node and 'edge' has a…

… type relationship and that all nodes have property "id".

test/write/graph/test_rdf.py

@@ -1,74 +1,41 @@
 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]
+from rdflib import RDF, Graph, Namespace
+import pytest
 
 
 @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)
+    nodes = bw_rdf.write_nodes(nodes)
+    edges = bw_rdf.write_edges(edges)
 
     # check if the writing of the nodes went okay.
-    assert all([node_type_1, node_type_2, edge_1])
+    assert all([nodes, edges])
 
     tmp_path = bw_rdf.outdir
 
     rdf_files_path = os.path.join(tmp_path, "*.xml")
     rdf_files = glob.glob(rdf_files_path)
 
-    g = Graph()
+    graph = Graph()
     for file in rdf_files:
         with open(file) as f:
-            g_temp = Graph().parse(data=f.read(), format="xml")
-            g += g_temp
+            temp_graph = Graph().parse(data=f.read(), format="xml")
+            graph += temp_graph
+            for node in temp_graph:
+                print(node)
+
+    biocypher_namespace = Namespace("https://biocypher.org/biocypher#")
+
+    # All nodes should have an identifier
+    assert len(set(graph.subjects(biocypher_namespace["id"]))) == 8
+
+    # everything should have a type assigned
+    assert len(set(graph.subjects(RDF.type))) == 20
 
-    # 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'.
+    # check if all the nodes have assigned their properties
+    assert len(set(graph.subject_objects())) == 92