Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore

client/galaxy/scripts/mvc/tool/tool-form-composite.js

@@ -372,7 +372,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                 Galaxy.emit.debug( 'tool-form-composite::submit()', 'Validation complete.', job_def );
                 Utils.request({
                     type    : 'POST',
-                    url     : Galaxy.root + 'api/workflows/' + this.model.id + '/run',
+                    url     : Galaxy.root + 'api_internal/workflows/' + this.model.id + '/run',
                     data    : job_def,
                     success : function( response ) {
                         Galaxy.emit.debug( 'tool-form-composite::submit', 'Submission successful.', response );
@@ -477,4 +477,4 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
     return {
         View: View
     };
-});
+});

lib/galaxy/datatypes/data.py

@@ -975,7 +975,7 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skip
     data_checked = False
     temp = open( file_name, "U" )
     last_line = ''
-    while count <= LINE_COUNT:
+    while count < LINE_COUNT:
         line = last_line + temp.readline( WIDTH - len( last_line ) )
         if line and not is_multi_byte and not data_checked:
             # See if we have a compressed or binary file
@@ -993,7 +993,7 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skip
         if not line_wrap:
             if '\n' in line:
                 i = line.index( '\n' )
-                last_line = line[i:]
+                last_line = line[i + 1:]
                 line = line[:i]
             else:
                 last_line = ''

lib/galaxy/jobs/actions/post.py

@@ -427,13 +427,20 @@ class DeleteIntermediatesAction(DefaultJobAction):
                 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]:

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -88,7 +88,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
     @expose_api
     def run( self, trans, workflow_id, payload, **kwd ):
         """
-        POST /api/workflows/{encoded_workflow_id}/run
+        POST /api_internal/workflows/{encoded_workflow_id}/run
 
         Run a workflow with a dictionary of prefixed_name/value pairs e.g.
             payload = { inputs: { step_0: { parameter_0|parameter_1 : value_0, ... }, ... } }

lib/galaxy/webapps/galaxy/buildapp.py

@@ -271,7 +271,7 @@ def populate_api_routes( webapp, app ):
     webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
     webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
     webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
-    webapp.mapper.connect( '/api/workflows/{workflow_id}/run', action='run', controller="workflows", conditions=dict( method=['POST'] ) )
+    webapp.mapper.connect( '/api_internal/workflows/{workflow_id}/run', action='run', controller="workflows", conditions=dict( method=['POST'] ) )
     webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
     webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
     webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -650,7 +650,7 @@ class DownloadBinary( Download, RecipeStep ):
             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 ):

test/unit/datatypes/test_data.py

@@ -0,0 +1,11 @@
+"""
+Unit tests for base DataTypes.
+.. seealso:: galaxy.datatypes.data
+"""
+
+from galaxy.datatypes.data import get_file_peek
+
+
+def test_get_file_peek( ):
+    # should get the first 5 lines of the file without a trailing newline character
+    assert get_file_peek('test-data/1.tabular', line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'