Merge branch 'release_16.04' into dev

mariabernard · Jul 19, 2016 · e1e0a3b · e1e0a3b
2 parents d351121 + 8a5042d
commit e1e0a3b
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py
@@ -427,13 +427,20 @@ def execute(cls, app, sa_session, action, job, replacement_dict):
                 else:
                     log.debug("No job found yet for wfi_step %s, (step %s)" % (wfi_step, wfi_step.workflow_step))
             for j2c in jobs_to_check:
-                sa_session.refresh(j2c)
                 creating_jobs = []
                 for input_dataset in j2c.input_datasets:
+                    if not input_dataset.dataset:
+                        log.debug("PJA Async Issue: No dataset attached to input_dataset %s during handling of workflow invocation %s" % (input_dataset.id, wfi))
+                    elif not input_dataset.dataset.creating_job:
+                        log.debug("PJA Async Issue: No creating job attached to dataset %s during handling of workflow invocation %s" % (input_dataset.dataset.id, wfi))
+                    else:
+                        creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
+                for (input_dataset, creating_job) in creating_jobs:
+                    sa_session.refresh(creating_job)
                     sa_session.refresh(input_dataset)
-                    sa_session.refresh(input_dataset.dataset.creating_job)
-                    creating_jobs.append( (input_dataset, input_dataset.dataset.creating_job) )
                 for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
+                    # note that the above input_dataset is a reference to a
+                    # job.input_dataset.dataset at this point
                     safe_to_delete = True
                     for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
                         if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]:

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -650,7 +650,7 @@ def prepare_step( self, tool_dependency, action_elem, action_dict, install_envir
             url_template_elem = tool_dependency_util.get_download_url_for_platform( url_template_elems, platform_info_dict )
         else:
             url_template_elem = url_template_elems[ 0 ]
-        action_dict[ 'url' ] = Template( url_template_elem.text ).safe_substitute( platform_info_dict )
+        action_dict[ 'url' ] = Template( url_template_elem.text.strip() ).safe_substitute( platform_info_dict )
         action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None )
         action_dict.update( self.get_elem_checksums( action_elem ) )
         return action_dict
@@ -1175,7 +1175,7 @@ class SetupPerlEnvironment( Download, RecipeStep ):
 
     def __init__( self, app ):
         self.app = app
-        self.type = 'setup_purl_environment'
+        self.type = 'setup_perl_environment'
 
     def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
                       install_environment, work_dir, current_dir=None, initial_download=False ):