Merge pull request #2243 from djarecka/cmtk_errors

adding import error in cmtk.nbs and imprve KeyError when specific att…

Author: satra

nipype/interfaces/cmtk/nbs.py

@@ -32,7 +32,10 @@ def ntwks_to_matrices(in_files, edge_key):
     for idx, name in enumerate(in_files):
         graph = nx.read_gpickle(name)
         for u, v, d in graph.edges(data=True):
-            graph[u][v]['weight'] = d[edge_key]  # Setting the edge requested edge value as weight value
+            try:
+                graph[u][v]['weight'] = d[edge_key]  # Setting the edge requested edge value as weight value
+            except:
+                raise KeyError("the graph edges do not have {} attribute".format(edge_key))
         matrix[:, :, idx] = nx.to_numpy_matrix(graph)  # Retrieve the matrix
     return matrix
 
@@ -77,6 +80,10 @@ class NetworkBasedStatistic(BaseInterface):
     output_spec = NetworkBasedStatisticOutputSpec
 
     def _run_interface(self, runtime):
+
+        if not have_cv:
+            raise ImportError("cviewer library is not available")
+
         THRESH = self.inputs.threshold
         K = self.inputs.number_of_permutations
         TAIL = self.inputs.t_tail

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -0,0 +1,58 @@
+from __future__ import unicode_literals
+from ..nbs import NetworkBasedStatistic
+from ....utils.misc import package_check
+import numpy as np
+import networkx as nx
+import pytest
+
+have_cv = True
+try:
+    package_check('cviewer')
+except Exception as e:
+    have_cv = False
+
+@pytest.fixture()
+def creating_graphs(tmpdir):
+    graphlist = []
+    graphnames = ["name"+str(i) for i in range(6)]
+    for idx, name in enumerate(graphnames):
+        graph = np.random.rand(10,10)
+        G = nx.from_numpy_matrix(graph)
+        out_file = str(tmpdir) + graphnames[idx] + '.pck'
+        # Save as pck file
+        nx.write_gpickle(G, out_file)
+        graphlist.append(out_file)
+    return graphlist
+
+
+@pytest.mark.skipif(have_cv, reason="tests for import error, cviewer available")
+def test_importerror(creating_graphs):
+    graphlist = creating_graphs
+    group1 = graphlist[:3]
+    group2 = graphlist[3:]
+    
+    nbs = NetworkBasedStatistic()
+    nbs.inputs.in_group1 = group1
+    nbs.inputs.in_group2 = group2
+    nbs.inputs.edge_key = "weight"
+    
+    with pytest.raises(ImportError) as e:
+        nbs.run()
+    assert "cviewer library is not available" == str(e.value)
+
+
+@pytest.mark.skipif(not have_cv, reason="cviewer has to be available")
+def test_keyerror(creating_graphs):
+    graphlist =creating_graphs
+
+    group1 = graphlist[:3]
+    group2 = graphlist[3:]
+
+    nbs = NetworkBasedStatistic()
+    nbs.inputs.in_group1 = group1
+    nbs.inputs.in_group2 = group2
+    nbs.inputs.edge_key = "Your_edge"
+
+    with pytest.raises(KeyError) as e:
+        nbs.run()
+    assert "the graph edges do not have Your_edge attribute" in str(e.value)