Merge pull request #179 from fair-workflows/auto-publish-steps

Reintroduce autopublishing of steps

Author: svenvanderburg

fairworkflows/fairworkflow.py

@@ -431,7 +431,7 @@ def draw(self, filepath):
                 'Cannot produce visualization of RDF, you need to install '
                 'graphviz dependency https://graphviz.org/')
 
-    def publish_as_nanopub(self, use_test_server=False, **kwargs):
+    def publish_as_nanopub(self, use_test_server=False, publish_steps=False, **kwargs):
         """Publish to nanopub server.
 
         Publish the workflow as nanopublication to the nanopub server.
@@ -441,6 +441,9 @@ def publish_as_nanopub(self, use_test_server=False, **kwargs):
 
         Args:
             use_test_server (bool): Toggle using the test nanopub server.
+            publish_steps (bool): Toggle publishing publishing all unpublished steps first before
+                publishing the workflow. (Otherwise an exception is raised and unpublished steps
+                need to be published manually first)
             kwargs: Keyword arguments to be passed to [nanopub.Publication.from_assertion](
                 https://nanopub.readthedocs.io/en/latest/reference/publication.html#
                 nanopub.publication.Publication.from_assertion).
@@ -453,7 +456,11 @@ def publish_as_nanopub(self, use_test_server=False, **kwargs):
         for step in self:
             if step.is_modified or not step._is_published:
                 self._is_modified = True  # If one of the steps is modified the workflow is too.
-                raise RuntimeError(f'{step} was not published yet, please publish steps first')
+                if publish_steps:
+                    step.publish_as_nanopub(use_test_server=use_test_server, **kwargs)
+                else:
+                    raise RuntimeError(f'{step} was not published yet, please publish steps first, '
+                                       f'or use force=True')
 
         return self._publish_as_nanopub(use_test_server=use_test_server, **kwargs)
 

tests/test_fairworkflow.py

@@ -277,12 +277,10 @@ def test_publish_as_nanopub(self, mock_publish, test_workflow):
             {'concept_uri': test_published_uris[3]}   # Last call
         ]
         with pytest.raises(RuntimeError):
-            # 'Publishing a workflow with unpublished steps must raise RunTimeError'
+            # 'Publishing a workflow with unpublished steps must raise RunTimeError...'
             test_workflow.publish_as_nanopub()
-        # First publish the steps
-        for step in test_workflow:
-            step.publish_as_nanopub()
-        pubinfo = test_workflow.publish_as_nanopub()
+        # ...unless using pubish_steps=True
+        pubinfo = test_workflow.publish_as_nanopub(publish_steps=True)
         assert pubinfo['concept_uri'] == 'www.example.org/published_workflow#workflow'
         assert mock_publish.call_count == 4  # 1 workflow, 3 steps
         for step in test_workflow: