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

Conflicts:
	extra/ucsc_encode_submission/ucsc_gather.py
	htsworkflow/submission/test/test_daf.py

Also merging the conflict was made more difficult by needing
to work around changes in the older version of librdf on 10.04

diff --cc extra/ucsc_encode_submission/ucsc_gather.py
index 6172df70a5b11947505bede7bc5a51dc9179754d,3877379c1de838e3762f4b6ccedd2c76cd0d25f4..ddd1fad63512c79f0ea9394931f0a381ad099579
--- 1/extra/ucsc_encode_submission/ucsc_gather.py
--- 2/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@@ -46,9 -49,11 +49,12 @@@ def main(cmdline=None)
      apidata = api.make_auth_from_opts(opts, parser)
  
      model = get_model(opts.load_model)
 -    mapper = DAFMapper(opts.name, opts.daf,  model)
 -    submission_uri = get_submission_uri(opts.name)
 +    if opts.name:
 +        mapper = DAFMapper(opts.name, opts.daf,  model)
 +        submission_uri = get_submission_uri(opts.name)
+ 
+     if opts.library_url is not None:
+         mapper.library_url = opts.library_url
          
      if opts.load_rdf is not None:
          load_into_model(model, 'turtle', opts.load_rdf, submission_uri)

diff --cc htsworkflow/submission/daf.py
index e1a9b1f113927dd431fcc43512918ea46f20f104,a3e3c3547f7dc552f45bc98542da8ba3ad901568..9429a3818bf93fb4e2093add094a0848db97d948
--- 1/htsworkflow/submission/daf.py
--- 2/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@@ -263,8 -268,14 +268,12 @@@ class DAFMapper(object)
          if str(view) == str(libraryOntology['ignore']):
              return None
  
-         submissionName = toTypedNode(self.make_submission_name(submission_dir))
+         submission_name = self.make_submission_name(submission_dir)
          submissionNode = self.get_submission_node(submission_dir)
 -        submission_uri = submissionNode.uri
 -        print "submission:", str(submission_name), str(submissionNode), str(submission_uri)
 -
++        submission_uri = str(submissionNode.uri)
+         view_name = fromTypedNode(self.model.get_target(view, dafTermOntology['name']))
 -        submissionView = RDF.Node(RDF.Uri(str(submission_uri) + '/' + view_name))
++        submissionView = RDF.Node(RDF.Uri(submission_uri + '/' + view_name))
+ 
          self.model.add_statement(
              RDF.Statement(self.submissionSet, dafTermOntology['has_submission'], submissionNode))
  

diff --cc htsworkflow/submission/test/test_daf.py
index cefc78f1541c05247058e146b7bbbd83b1e60c78,a7515b05374ac59a87cf6d845b2cfa073d26dc9d..5da4dc2faff3217fdf7386849add99c089ccc2d8
--- 1/htsworkflow/submission/test/test_daf.py
--- 2/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@@ -65,11 -66,10 +66,11 @@@ class TestDAF(unittest.TestCase)
          daf.add_to_model(model, parsed, name)
  
          signal_view_node = RDF.Node(subNS['/view/Signal'].uri)
+ 
          writer = get_serializer()
          turtle =  writer.serialize_model_to_string(model)
-         #print turtle
 -        self.failUnless(str(signal_view_node) in turtle)
 +
 +        self.failUnless(str(signal_view_node.uri) in turtle)
  
          statements = list(model.find_statements(
              RDF.Statement(
@@@ -175,10 -170,20 +171,18 @@@ class TestDAFMapper(unittest.TestCase)
          
          daf_mapper.construct_file_attributes('/tmp/analysis1', libNode, 'filename.bam')
          source = daf_mapper.model.get_source(rdfNS['type'], submissionOntology['submission'])
 -        self.failUnlessEqual(str(source), "<http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1>")
 +        self.failUnlessEqual(str(source.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1")
          view = daf_mapper.model.get_target(source, submissionOntology['has_view'])
-         self.failUnlessEqual(str(view.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/view/Signal")
 -        self.failUnlessEqual(str(view), "<http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1/Signal>")
 -
++        self.failUnlessEqual(str(view.uri), "http://jumpgate.caltech.edu/wiki/SubmissionsLog/testfind/analysis1/Signal")
  
 -
+     def test_library_url(self):
+         daf_mapper = load_daf_mapper('urltest')
+ 
+         self.failUnlessEqual(daf_mapper.library_url,
+                              'http://jumpgate.caltech.edu/library/')
+         daf_mapper.library_url = 'http://google.com'
+         self.failUnlessEqual(daf_mapper.library_url, 'http://google.com' )
+         
  def suite():
      suite = unittest.makeSuite(TestDAF, 'test')
      suite.addTest(unittest.makeSuite(TestDAFMapper, 'test'))