Merge branch 'release_16.07' into dev

galaxyproject · Aug 4, 2016 · 3206a54 · 3206a54
2 parents 7efa1e0 + 8b0d88b
commit 3206a54
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Showing 4 changed files with 16 additions and 54 deletions.
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
@@ -83,48 +83,3 @@ def display_peek( self, dataset ):
 
     def sniff( self, filename ):
         return False
-
-
-class HubAssembly( Html ):
-    """
-    derived class for BioC data structures in Galaxy
-    """
-
-    file_ext = 'huba'
-    composite_type = 'auto_primary_file'
-
-    def __init__(self, **kwd):
-        Html.__init__(self, **kwd)
-
-    def generate_primary_file( self, dataset=None ):
-        """
-        This is called only at upload to write the html file
-        cannot rename the datasets here - they come with the default unfortunately
-        """
-        rval = [
-            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
-            This composite dataset is composed of the following files:<p/><ul>' % (
-                self.file_ext)]
-        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).items():
-            opt_text = ''
-            if composite_file.optional:
-                opt_text = ' (optional)'
-            rval.append('<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text) )
-        rval.append('</ul></html>')
-        return "\n".join(rval)
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        if not dataset.dataset.purged:
-            dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-
-    def display_peek( self, dataset ):
-        try:
-            return dataset.peek
-        except:
-            return "Track Hub structure: Visualization in UCSC Track Hub"
-
-    def sniff( self, filename ):
-        return False
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
@@ -207,13 +207,18 @@ def build_command_line( self, job_wrapper, include_metadata=False, include_work_
             container=container
         )
 
-    def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ):
+    def get_work_dir_outputs( self, job_wrapper, job_working_directory=None, tool_working_directory=None ):
         """
         Returns list of pairs (source_file, destination) describing path
         to work_dir output file and ultimate destination.
         """
-        if not job_working_directory:
-            job_working_directory = os.path.abspath( job_wrapper.working_directory )
+        if tool_working_directory is not None and job_working_directory is not None:
+            raise Exception("get_work_dir_outputs called with both a job and tool working directory, only one may be specified")
+
+        if tool_working_directory is None:
+            if not job_working_directory:
+                job_working_directory = os.path.abspath( job_wrapper.working_directory )
+            tool_working_directory = os.path.join(job_working_directory, "working")
 
         # Set up dict of dataset id --> output path; output path can be real or
         # false depending on outputs_to_working_directory
@@ -234,9 +239,9 @@ def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ):
                 if hda_tool_output and hda_tool_output.from_work_dir:
                     # Copy from working dir to HDA.
                     # TODO: move instead of copy to save time?
-                    source_file = os.path.join( job_working_directory, 'working', hda_tool_output.from_work_dir )
+                    source_file = os.path.join( tool_working_directory, hda_tool_output.from_work_dir )
                     destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] )
-                    if in_directory( source_file, job_working_directory ):
+                    if in_directory( source_file, tool_working_directory ):
                         output_pairs.append( ( source_file, destination ) )
                     else:
                         # Security violation.

diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
@@ -661,7 +661,7 @@ def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, r
             # each work_dir output substitute the effective path on the Pulsar
             # server relative to the remote working directory as the
             # false_path to send the metadata command generation module.
-            work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory)
+            work_dir_outputs = self.get_work_dir_outputs(job_wrapper, tool_working_directory=working_directory)
             outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)]
             for output in outputs:
                 for pulsar_workdir_path, real_path in work_dir_outputs:

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
@@ -707,9 +707,11 @@ def __init__( self, params, sanitize=True ):
                 # name. Anything relying on NEVER_SANITIZE should be
                 # changed to not require this and NEVER_SANITIZE should be
                 # removed.
-                if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for
-                                                                    nonsanitize_parameter in self.NEVER_SANITIZE ]:
-                    self.__dict__[ key ] = sanitize_param( value )
+                if (value is not None and
+                    key not in self.NEVER_SANITIZE and
+                    True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for
+                                  nonsanitize_parameter in self.NEVER_SANITIZE ]):
+                        self.__dict__[ key ] = sanitize_param( value )
                 else:
                     self.__dict__[ key ] = value
         else: