updating for refactoring of wc_lang.io

KarrLab · Jan 7, 2019 · ca93376 · ca93376
1 parent a27bea9
commit ca93376
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 10 deletions.
diff --git a/rand_wc_model_gen/__main__.py b/rand_wc_model_gen/__main__.py
@@ -12,8 +12,10 @@
 import rand_wc_model_gen
 import rand_wc_model_gen.analysis
 import rand_wc_model_gen.config
-import wc_kb_gen.random
+import wc_kb
 import wc_kb.io
+import wc_kb_gen.random
+import wc_lang
 import wc_lang.io
 import wc_model_gen.prokaryote
 import wc_sim.multialgorithm.run_results
@@ -60,14 +62,13 @@ def _default(self):
             os.makedirs(os.path.dirname(config['kb']['path']['core']))
         if not os.path.isdir(os.path.dirname(config['kb']['path']['seq'])):
             os.makedirs(os.path.dirname(config['kb']['path']['seq']))
-        wc_kb.io.Writer().run(kb,
-                              config['kb']['path']['core'], config['kb']['path']['seq'],
+        wc_kb.io.Writer().run(config['kb']['path']['core'], kb,
+                              seq_path=config['kb']['path']['seq'],
                               set_repo_metadata_from_path=config['kb_gen']['set_repo_metadata_from_path'])
 
         if not os.path.isdir(os.path.dirname(config['model']['path'])):
             os.makedirs(os.path.dirname(config['model']['path']))
-        wc_lang.io.Writer().run(model,
-                                config['model']['path'],
+        wc_lang.io.Writer().run(config['model']['path'], model,
                                 set_repo_metadata_from_path=config['model_gen']['set_repo_metadata_from_path'])
 
 
@@ -89,7 +90,7 @@ def _default(self):
         args = self.app.pargs
         config = rand_wc_model_gen.config.get_config(extra_path=args.config_path)['rand_wc_model_gen']
 
-        model = wc_lang.io.Reader().run(config['model']['path'])
+        model = wc_lang.io.Reader().run(config['model']['path'])[wc_lang.Model][0]
 
         seed = args.seed
         if seed is None:
@@ -122,8 +123,8 @@ class Meta:
     def _default(self):
         args = self.app.pargs
         config = rand_wc_model_gen.config.get_config(extra_path=args.config_path)['rand_wc_model_gen']
-        kb = wc_kb.io.Reader().run(config['kb']['path']['core'], config['kb']['path']['seq'])
-        model = wc_lang.io.Reader().run(config['model']['path'])
+        kb = wc_kb.io.Reader().run(config['kb']['path']['core'], config['kb']['path']['seq'])[wc_kb.KnowledgeBase][0]
+        model = wc_lang.io.Reader().run(config['model']['path'])[wc_lang.Model][0]
         runner = rand_wc_model_gen.analysis.AnalysisRunner(kb, model, config['sim_results']['path'],
                                                            out_path=config['analysis']['path'],
                                                            options=config['analysis'])

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -105,8 +105,8 @@ def test_generate(self):
         self.assertTrue(os.path.isfile(self.kb_core_path))
         self.assertTrue(os.path.isfile(self.kb_seq_path))
         self.assertTrue(os.path.isfile(self.model_path))
-        kb = wc_kb.io.Reader().run(self.kb_core_path, self.kb_seq_path)
-        model = wc_lang.io.Reader().run(self.model_path)
+        kb = wc_kb.io.Reader().run(self.kb_core_path, self.kb_seq_path)[wc_kb.KnowledgeBase][0]
+        model = wc_lang.io.Reader().run(self.model_path)[wc_lang.Model][0]
 
     @unittest.skipIf(os.getenv('CIRCLECI', '0') in ['1', 'true'], 'Too long for CircleCI')
     def test_simulate(self):