Merge branch 'release_16.04' into dev

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -65,7 +65,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     >>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
     False
     >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', headers='#PBS -test')
-    >>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
+    >>> script.startswith('#!/bin/bash\\n\\n#PBS -test\\n')
     True
     >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', slots_statement='GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"')
     >>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\\nexport GALAXY_SLOTS\\n') > 0
@@ -76,7 +76,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     job_instrumenter = kwds.get("job_instrumenter", None)
     if job_instrumenter:
         del kwds["job_instrumenter"]
-        working_directory = kwds["working_directory"]
+        working_directory = kwds.get("metadata_directory", kwds["working_directory"])
         kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or ''
         kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ''
 

lib/galaxy/tools/__init__.py

@@ -1099,6 +1099,8 @@ class Tool( object, Dictifiable ):
         for expanded_incoming in expanded_incomings:
             params = {}
             errors = {}
+            if self.input_translator:
+                self.input_translator.translate( expanded_incoming )
             if not self.check_values:
                 # If `self.check_values` is false we don't do any checking or
                 # processing on input  This is used to pass raw values

lib/galaxy/tools/parameters/basic.py

@@ -1673,13 +1673,16 @@ class BaseDataToolParameter( ToolParameter ):
     def to_json( self, value, app ):
         def single_to_json( value ):
             src = None
-            if isinstance( value, galaxy.model.DatasetCollectionElement ):
+            if isinstance( value, dict ) and 'src' in value and 'id' in value:
+                return value
+            elif isinstance( value, galaxy.model.DatasetCollectionElement ):
                 src = 'dce'
             elif isinstance( value, app.model.HistoryDatasetCollectionAssociation ):
                 src = 'hdca'
-            else:
+            elif hasattr( value, 'id' ):
                 src = 'hda'
-            return { 'id' : app.security.encode_id( value.id ), 'src' : src }
+            if src is not None:
+                return { 'id' : app.security.encode_id( value.id ), 'src' : src }
 
         if value not in [ None, '', 'None' ]:
             if isinstance( value, list ) and len( value ) > 0:

lib/galaxy/util/sanitize_html.py

@@ -194,7 +194,7 @@ class _BaseHTMLProcessor(sgmllib.SGMLParser):
 
     def output(self):
         '''Return processed HTML as a single string'''
-        return ''.join([str(p) for p in self.pieces])
+        return ''.join(self.pieces)
 
 
 class _HTMLSanitizer(_BaseHTMLProcessor):

lib/galaxy/util/validation.py

@@ -5,20 +5,20 @@ TODO: Refactor BaseController references to similar methods to use this module.
 from galaxy import exceptions
 from galaxy.util.sanitize_html import sanitize_html
 
-from six import string_types, text_type
+from six import string_types
 
 
 def validate_and_sanitize_basestring( key, val ):
     if not isinstance( val, string_types ):
         raise exceptions.RequestParameterInvalidException( '%s must be a string or unicode: %s'
                                                            % ( key, str( type( val ) ) ) )
-    return text_type( sanitize_html( val, 'utf-8', 'text/html' ), 'utf-8' )
+    return sanitize_html( val, 'utf-8', 'text/html' )
 
 
 def validate_and_sanitize_basestring_list( key, val ):
     try:
         assert isinstance( val, list )
-        return [ text_type( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ]
+        return [ sanitize_html( t, 'utf-8', 'text/html' ) for t in val ]
     except ( AssertionError, TypeError ):
         raise exceptions.RequestParameterInvalidException( '%s must be a list of strings: %s'
                                                            % ( key, str( type( val ) ) ) )

tools/data_source/biomart.xml

@@ -8,10 +8,10 @@
     everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
 -->
 <tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
-	<description>Central server</description>
+	<description>Ensembl server</description>
 	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-	<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
-		<display>go to BioMart Central $GALAXY_URL</display>
+	<inputs action="http://www.ensembl.org/biomart/martview" check_values="false" method="get" target="_top">
+		<display>go to BioMart Ensembl $GALAXY_URL</display>
 		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
     </inputs>
     <request_param_translation>