prepare for new trackster

.hgignore

@@ -27,3 +27,6 @@ run_functional_tests.html
 
 # Project files
 *.kpf
+
+# Chrom len files
+*.len

lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py

@@ -3,7 +3,7 @@
 from __future__ import division
 
 import sys
-
+from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.arrays.array_tree import *
 from bx.arrays.wiggle import IntervalReader

lib/galaxy/datatypes/data.py

@@ -223,7 +223,7 @@ class Data( object ):
         """Returns available converters by type for this dataset"""
         return datatypes_registry.get_converters_by_datatype(original_dataset.ext)
     def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ):
-        """Returns ( target_ext, exisiting converted dataset )"""
+        """Returns ( target_ext, existing converted dataset )"""
         return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd )
     def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True ):
         """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure."""

lib/galaxy/datatypes/registry.py

@@ -211,7 +211,7 @@ class Registry( object ):
         except KeyError:
             #datatype was never declared
             mimetype = 'application/octet-stream'
-            self.log.warning('unkown mimetype in data factory %s' % ext)
+            self.log.warning('unknown mimetype in data factory %s' % ext)
         return mimetype
     
     def get_datatype_by_extension(self, ext ):
@@ -265,10 +265,10 @@ class Registry( object ):
         tool_xml_text = """
             <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.0" tool_type="set_metadata">
               <type class="SetMetadataTool" module="galaxy.tools"/>
-              <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
+              <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
+              <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
               <inputs>
-                <param format="data" name="input1" type="data" label="File to set metadata on."/>
+                <param format="data" name="input1" type="data" label="File to set metadata on."/>
                 <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/>
                 <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/>
               </inputs>
@@ -326,7 +326,7 @@ class Registry( object ):
         return None
 
     def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ):
-        """Returns ( target_ext, exisiting converted dataset )"""
+        """Returns ( target_ext, existing converted dataset )"""
         for convert_ext in self.get_converters_by_datatype( dataset.ext ):
             if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ):
                 datasets = dataset.get_converted_files_by_type( convert_ext )
@@ -347,12 +347,12 @@ class Registry( object ):
         rval = {}
         for ext, d_type in self.datatypes_by_extension.iteritems():
             inputs = []
-            for meta_name, meta_spec in d_type.metadata_spec.iteritems():
-                if meta_spec.set_in_upload:
+            for meta_name, meta_spec in d_type.metadata_spec.iteritems():
+                if meta_spec.set_in_upload:
                     help_txt = meta_spec.desc
                     if not help_txt or help_txt == meta_name:
                         help_txt = ""
-                    inputs.append( '<param type="text" name="%s" label="Set metadata value for &quot;%s&quot;" value="%s" help="%s"/>' % ( meta_name, meta_name, meta_spec.default, help_txt ) )
+                    inputs.append( '<param type="text" name="%s" label="Set metadata value for &quot;%s&quot;" value="%s" help="%s"/>' % ( meta_name, meta_name, meta_spec.default, help_txt ) )
             rval[ ext ] = "\n".join( inputs )
         if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype
             rval[ 'auto' ] = rval[ 'txt' ]

lib/galaxy/web/controllers/tracks.py

@@ -33,7 +33,7 @@ messages = Bunch(
 )
 
 # Dataset type required for each track type. This needs to be more flexible,
-# there might be mutliple types of indexes that suffice for a given track type.
+# there might be multiple types of indexes that suffice for a given track type.
 track_type_to_dataset_type = {
     "line": "array_tree"
 }
@@ -158,7 +158,7 @@ class TracksController( BaseController ):
         converted_dataset_type = track_type_to_dataset_type[track_type]    
         converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type )
         # If at this point we still don't have an `array_tree_dataset`, there
-        # is now way we can display this data as an array tree
+        # is no way we can display this data as an array tree
         if converted_dataset is None:
             return messages.NO_DATA
         # Need to check states again for the converted version
@@ -186,7 +186,7 @@ class TracksController( BaseController ):
             return dataset
         # See if we can convert the dataset
         if type not in dataset.get_converter_types():
-            log.debug( "Conversion from '%s' to '%d' not possible", dataset.extension, type )
+            log.debug( "Conversion from '%s' to '%s' not possible", dataset.extension, type )
             return None
         # See if converted dataset already exists
         converted_datasets = dataset.get_converted_files_by_type( type )