Merge pull request #9 from jmchilton/chemical_datatypes

Fix datatype sniff test to use sample and revert molecule registry ha…

lib/galaxy/datatypes/registry.py

@@ -11,7 +11,6 @@ from . import data
 from . import tabular
 from . import interval
 from . import images
-from . import molecules
 from . import sequence
 from . import qualityscore
 from . import xml
@@ -739,7 +738,6 @@ class Registry( object ):
                 binary.MzSQlite(),
                 binary.IdpDB(),
                 binary.SQlite(),
-                molecules.CML(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),
@@ -760,11 +758,6 @@ class Registry( object ):
                 interval.Interval(),
                 tabular.Sam(),
                 tabular.Eland(),
-                molecules.SDF(),
-                molecules.FPS(),
-                molecules.InChI(),
-                molecules.MOL2(),
-                molecules.PDB(),
                 tabular.CSV()
             ]
 

lib/galaxy/datatypes/sniff.py

@@ -263,8 +263,9 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
 
     >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
     >>> from galaxy.datatypes import registry
+    >>> sample_conf = os.path.join(util.galaxy_directory(), "config", "datatypes_conf.xml.sample")
     >>> datatypes_registry = registry.Registry()
-    >>> datatypes_registry.load_datatypes()
+    >>> datatypes_registry.load_datatypes(root_dir=util.galaxy_directory(), config=sample_conf)
     >>> sniff_order = datatypes_registry.sniff_order
     >>> guess_ext(fname, sniff_order)
     'xml'