Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / htsworkflow / submission / test / test_daf.py

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index b730144d227af3a1bf7fc6b73783ede6a7f3a1ff..334a71a9203e7ca5d621b634a62bfc9b5fd299a6 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -5,7 +5,7 @@ import shutil
 import tempfile
 import unittest
 
-from htsworkflow.submission import daf
+from htsworkflow.submission import daf, results
 from htsworkflow.util.rdfhelp import \
      dafTermOntology, \
      fromTypedNode, \
@@ -15,6 +15,7 @@ from htsworkflow.util.rdfhelp import \
      get_model, \
      get_serializer
 
+from htsworkflow.submission.test import test_results
 import RDF
 
 test_daf = """# Lab and general info
@@ -155,7 +156,7 @@ def load_daf_mapper(name, extra_statements=None, ns=None, test_daf=test_daf):
                                        ns)
 
     test_daf_stream = StringIO(test_daf)
-    mapper = daf.DAFMapper(name, daf_file = test_daf_stream, model=model)
+    mapper = daf.UCSCSubmission(name, daf_file = test_daf_stream, model=model)
     return mapper
 
 def dump_model(model):
@@ -164,7 +165,14 @@ def dump_model(model):
     print turtle
 
 
-class TestDAFMapper(unittest.TestCase):
+class TestUCSCSubmission(unittest.TestCase):
+    def setUp(self):
+        test_results.generate_sample_results_tree(self)
+
+    def tearDown(self):
+        # see things created by temp_results.generate_sample_results_tree
+        shutil.rmtree(self.tempdir)
+
     def test_create_mapper_add_pattern(self):
         name = 'testsub'
         mapper = load_daf_mapper(name)
@@ -287,6 +295,26 @@ thisView:FastqRd1 dafTerm:filename_re ".*\\\\.fastq" ;
         self.failUnless('controlId' in variables)
 
 
+    def test_link_daf(self):
+        name = 'testsub'
+        submission = load_daf_mapper(name, test_daf=test_daf)
+        result_map = results.ResultMap()
+        result_dir = os.path.join(self.sourcedir,
+                                  test_results.S1_NAME)
+        result_map.add_result('1000', result_dir)
+
+        submission.link_daf(result_map)
+
+        # make sure daf gets linked
+        created_daf = os.path.join(result_dir, name+'.daf')
+        self.failUnless(os.path.exists(created_daf))
+        stream = open(created_daf,'r')
+        daf_body = stream.read()
+        stream.close()
+
+        self.failUnlessEqual(test_daf, daf_body)
+
+
 @contextmanager
 def mktempdir(prefix='tmp'):
     d = tempfile.mkdtemp(prefix=prefix)
@@ -304,7 +332,7 @@ def mktempfile(suffix='', prefix='tmp', dir=None):
 
 def suite():
     suite = unittest.makeSuite(TestDAF, 'test')
-    suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))
+    suite.addTest(unittest.makeSuite(TestUCSCSubmission, 'test'))
     return suite
 
 if __name__ == "__main__":