debug

tests/test_core.py

@@ -16,7 +16,7 @@ def test_KbGenerator(self):
         gen = wc_kb_gen.KbGenerator()
 
         self.assertEqual(gen.component_generators, [])
-        self.assertEqual(gen.options, {'id': None, 'name': None, 'version': None})
+        self.assertEqual(gen.options, {'id': None, 'name': None, 'version': None, 'input_kb': None})
 
     def test_ModelGenerator_run(self):
         gen = wc_kb_gen.KbGenerator(options={
@@ -36,6 +36,20 @@ def test_ModelGenerator_run(self):
         self.assertEqual(kb.id, 'test_kb')
         self.assertEqual(kb.version, '0.0.1')
 
+        kb_input = wc_kb.core.KnowledgeBase(id='kb_input')
+        kb_input.cell = wc_kb.core.Cell(id='kb_input_cell')
+        gen = wc_kb_gen.KbGenerator(options={
+            'id': 'test_kb',
+            'version': '0.0.1',
+            'input_kb': kb_input,
+        })
+        kb = gen.run()
+
+        self.assertEqual(kb.id, 'kb_input')
+        self.assertEqual(kb.version, '')
+        self.assertEqual(kb.cell.id, 'kb_input_cell')
+        self.assertTrue(kb.is_equal(kb_input))
+
     def test_ModelGenerator_run_with_components(self):
         class TestComponentGenerator1(wc_kb_gen.KbComponentGenerator):
             def get_data(self):

wc_kb_gen/core.py

@@ -15,9 +15,14 @@ class KbGenerator(object):
 
     Options:
 
-    * id
-    * name
-    * component
+    * id (:obj:`str`): id
+    * name (:obj:`str`): name
+    * version (:obj:`str`): version
+    * input_kb (:obj:`wc_kb.core.KnowledgeBase`, optional): knowledge base input if
+        one wants to build upon an existing knowledge base
+    * component (:obj:`dict`): dictionary of options whose keys are the names
+        of component generator classes and whose values are dictionaries of options
+        for the component generator classes
 
     Attributes:
         component_generators (:obj:`list` of :obj:`KbComponentGenerator`): component
@@ -61,6 +66,10 @@ def clean_and_validate_options(self):
         assert(isinstance(version, str) or version is None)
         options['version'] = version
 
+        input_kb = options.get('input_kb', None)
+        assert(isinstance(input_kb, wc_kb.core.KnowledgeBase) or input_kb is None)
+        options['input_kb'] = input_kb
+
     def run(self):
         """ Generate a knowledge base of experimental data for a whole-cell model