Merge stable changes forward.

lib/galaxy/jobs/runners/__init__.py

@@ -35,6 +35,8 @@ JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE = "Invalid job runner parameter for this pl
 JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = "Job runner parameter '%s' value '%s' could not be converted to the correct type"
 JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE = "Job runner parameter %s failed validation"
 
+GALAXY_LIB_ADJUST_TEMPLATE = """GALAXY_LIB="%s"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi;"""
+
 
 class RunnerParams( ParamsWithSpecs ):
 
@@ -253,11 +255,13 @@ class BaseJobRunner( object ):
         #this is terminate-able when output dataset/job is deleted
         #so that long running set_meta()s can be canceled without having to reboot the server
         if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths:
+            lib_adjust = GALAXY_LIB_ADJUST_TEMPLATE % job_wrapper.galaxy_lib_dir
             external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(),
                                                                             set_extension=True,
                                                                             tmp_dir=job_wrapper.working_directory,
                                                                             #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
                                                                             kwds={ 'overwrite' : False } )
+            external_metadata_script = "%s %s" % (lib_adjust, external_metadata_script)
             if resolve_requirements:
                 dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands()
                 if dependency_shell_commands:

lib/galaxy/jobs/runners/tasks.py

@@ -124,19 +124,7 @@ class TaskedJobRunner( BaseJobRunner ):
         #run the metadata setting script here
         #this is terminate-able when output dataset/job is deleted
         #so that long running set_meta()s can be canceled without having to reboot the server
-        if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths:
-            external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(),
-                                                                            set_extension=True,
-                                                                            kwds={ 'overwrite' : False } )  # we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
-            log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) )
-            external_metadata_proc = subprocess.Popen( args=external_metadata_script,
-                                         shell=True,
-                                         env=os.environ,
-                                         preexec_fn=os.setpgrp )
-            job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session )
-            external_metadata_proc.wait()
-            log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id )
-
+        self._handle_metadata_externally(job_wrapper, resolve_requirements=True )
         # Finish the job
         try:
             job_wrapper.finish( stdout, stderr, job_exit_code )

lib/galaxy/tools/__init__.py

@@ -2456,7 +2456,8 @@ class Tool( object, Dictifiable ):
                 elif input.type == 'conditional':
                     if 'test_param' in tool_dict:
                         test_param = tool_dict['test_param']
-                        test_param['value'] = jsonify(group_state.get(test_param['name'], None))
+                        test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values))
+                        test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value']))
                         for i in range (len ( tool_dict['cases'] ) ):
                             current_state = {}
                             if i == group_state.get('__current_case__', None):

lib/galaxy/tools/parameters/basic.py

@@ -696,7 +696,7 @@ class BaseURLToolParameter( ToolParameter ):
         return form_builder.HiddenField( self.name, self.get_value( trans ) )
 
     def get_initial_value( self, trans, context, history=None ):
-        return self.value
+        return self.get_value( trans )
 
     def get_label( self ):
         # BaseURLToolParameters are ultimately "hidden" parameters