Merge pull request #154 from fair-workflows/bug-steps-without-uri2

Fix bug: #130 Steps without URI are reffered to as <None> in workflow RDF

Author: svenvanderburg

fairworkflows/config.py

@@ -8,3 +8,5 @@
 # Generated workflow directory names
 PYTHON_DIR = 'scripts'
 PLEX_DIR = 'plex'
+
+DUMMY_FAIRWORKFLOWS_URI = 'http://fairworkflows.org'

fairworkflows/fairstep.py

@@ -9,6 +9,7 @@
 from rdflib import RDF, RDFS, DCTERMS
 
 from fairworkflows import namespaces
+from fairworkflows.config import DUMMY_FAIRWORKFLOWS_URI
 from fairworkflows.rdf_wrapper import RdfWrapper, replace_in_rdf
 
 
@@ -93,6 +94,11 @@ def __init__(self, label: str = None, description: str = None, uri=None,
             self.inputs = inputs
         if outputs is not None:
             self.outputs = outputs
+        # Set temporary URI to refer to this step in workflows
+        # (i.e. 'http://fairworkflows.org#8769029329049')
+        if uri is None:
+            self._uri = DUMMY_FAIRWORKFLOWS_URI + '#step' + str(hash(self))
+
         self._is_modified = False
         self._workflows = set()
 

tests/test_fairworkflow.py

@@ -68,6 +68,13 @@ def test_build(self, test_step1, test_step2, test_step3):
         assert len(workflow.__str__()) > 0
         assert workflow.rdf is not None
 
+    def test_build_including_step_without_uri(self):
+        step1 = FairStep()
+        workflow = FairWorkflow()
+        workflow.add(step1)
+        assert (rdflib.URIRef('None'), None, None) not in workflow.rdf
+        assert (None, None, rdflib.URIRef('None')) not in workflow.rdf
+
     def test_construct_from_rdf_uri_not_in_subjects(self):
         rdf = read_rdf_test_resource('test_workflow.trig')
         # This URI is not in the subject of this RDF: