Merge branch 'release_19.09' into dev

lib/galaxy/jobs/__init__.py

@@ -1654,7 +1654,7 @@ class JobWrapper(HasResourceParameters):
         # Certain tools require tasks to be completed after job execution
         # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
         param_dict = self.get_param_dict(job)
-        self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job)
+        self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         # Call 'exec_after_process' hook
         self.tool.call_hook('exec_after_process', self.app, inp_data=inp_data,
                             out_data=out_data, param_dict=param_dict,

lib/galaxy/tool_util/deps/docker_util.py

@@ -225,6 +225,12 @@ def _docker_prefix(
 
 
 def parse_port_text(port_text):
+    """
+
+    >>> slurm_ports = parse_port_text("8888/tcp -> 0.0.0.0:32769")
+    >>> slurm_ports[8888]['host']
+    '0.0.0.0'
+    """
     ports = None
     if port_text is not None:
         ports = {}

lib/galaxy/tools/__init__.py

@@ -43,6 +43,7 @@ from galaxy.tool_util.loader import (
     raw_tool_xml_tree,
     template_macro_params
 )
+from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.tool_util.parser import (
     get_tool_source,
     get_tool_source_from_representation,
@@ -1750,7 +1751,7 @@ class Tool(Dictifiable):
     def exec_before_job(self, app, inp_data, out_data, param_dict={}):
         pass
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
         pass
 
     def job_failed(self, job_wrapper, message, exception=False):
@@ -2421,7 +2422,7 @@ class SetMetadataTool(Tool):
                 history.id, job.user, incoming={'input1': hda}, overwrite=False
             )
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
         working_directory = app.object_store.get_filename(
             job, base_dir='job_work', dir_only=True, obj_dir=True
         )
@@ -2505,17 +2506,13 @@ class DataManagerTool(OutputParameterJSONTool):
         if self.data_manager_id is None:
             self.data_manager_id = self.id
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, final_job_state=None, **kwds):
         assert self.allow_user_access(job.user), "You must be an admin to access this tool."
+        if final_job_state != DETECTED_JOB_STATE.OK:
+            return
         # run original exec_after_process
         super(DataManagerTool, self).exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
         # process results of tool
-        if job and job.state == job.states.ERROR:
-            return
-        # Job state may now be 'running' instead of previous 'error', but datasets are still set to e.g. error
-        for dataset in out_data.values():
-            if dataset.state != dataset.states.OK:
-                return
         data_manager_id = job.data_manager_association.data_manager_id
         data_manager = self.app.data_managers.get_manager(data_manager_id, None)
         assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % (data_manager_id)

lib/galaxy/tools/cache.py

@@ -151,7 +151,9 @@ class ToolShedRepositoryCache(object):
     def rebuild(self):
         self.repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).options(
             defer(self.app.install_model.ToolShedRepository.metadata),
-            joinedload('tool_dependencies'),
+            joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
+                defer(self.app.install_model.ToolShedRepository.metadata)
+            ),
         ).all()
         repos_by_tuple = defaultdict(list)
         for repository in self.repositories + self.local_repositories:

lib/galaxy/webapps/galaxy/api/folder_contents.py

@@ -129,6 +129,9 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
                                         tags=ldda_tags))
                 if content_item.library_dataset_dataset_association.message:
                     return_item.update(dict(message=content_item.library_dataset_dataset_association.message))
+                elif content_item.library_dataset_dataset_association.info:
+                    # There is no message but ldda info contains something so we display that instead.
+                    return_item.update(dict(message=content_item.library_dataset_dataset_association.info))
 
             # For every item include the default metadata
             return_item.update(dict(id=encoded_id,

lib/galaxy_ext/container_monitor/monitor.py

@@ -41,12 +41,17 @@ def main():
         try:
             ports_raw = parse_ports(container_name, connection_configuration)
             if ports_raw is not None:
-                host_ip = socket.gethostbyname(socket.gethostname())
+                try:
+                    host_ip = socket.gethostbyname(socket.gethostname())
+                except Exception:
+                    # doesn't work on OS X
+                    host_ip = None
                 with open("container_runtime.json", "w") as f:
-                    # Override the IPs
                     ports = docker_util.parse_port_text(ports_raw)
-                    for key in ports:
-                        ports[key]['host'] = host_ip
+                    if host_ip is not None:
+                        for key in ports:
+                            if ports[key]['host'] == '0.0.0.0':
+                                ports[key]['host'] = host_ip
                     json.dump(ports, f)
                 break
             else:

test/functional/tools/data_manager.xml

@@ -2,13 +2,15 @@
     <configfiles>
         <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "newvalue", "path": "newvalue.txt"}]}}</configfile>
     </configfiles>
-    <command>
+    <command detect_errors="exit_code">
         mkdir $out_file.files_path ;
-        echo "A new value" > $out_file.files_path/newvalue.txt;
-        cp $static_test_data $out_file
+        echo "A new value" > '$out_file.files_path/newvalue.txt';
+        cp '$static_test_data' '$out_file';
+        exit $exit_code
     </command>
     <inputs>
         <param type="text" name="ignored_value" value="" label="Ignored" />
+        <param type="integer" name="exit_code" value="0" label="Exit code"/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>

test/functional/tools/data_manager_add.xml

@@ -1,14 +1,16 @@
-<tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1">
+<tool id="data_manager_add_test" name="Test Data Manager add" tool_type="manage_data" version="0.0.1">
     <configfiles>
         <configfile name="static_test_data">{"data_tables": {"testbeta": { "add": [{"value": "newvalue", "path": "newvalue.txt"}]}}}</configfile>
     </configfiles>
-    <command>
+    <command detect_errors="exit_code">
         mkdir $out_file.files_path ;
-        echo "A new value" > $out_file.files_path/newvalue.txt;
-        cp $static_test_data $out_file
+        echo "A new value" > '$out_file.files_path/newvalue.txt';
+        cp '$static_test_data' '$out_file';
+        exit $exit_code
     </command>
     <inputs>
         <param type="text" name="ignored_value" value="" label="Ignored" />
+        <param type="integer" name="exit_code" value="0" label="Exit code"/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>

test/functional/tools/data_manager_add_remove.xml

@@ -1,14 +1,16 @@
-<tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1">
+<tool id="data_manager_add_remove_test" name="Test Data Manager add and remove" tool_type="manage_data" version="0.0.1">
     <configfiles>
         <configfile name="static_test_data">{"data_tables": {"testbeta": { "add": [{"value": "newvalue", "path": "newvalue.txt"}, {"value": "newvalue2", "path": "newvalue2.txt"}], "remove": [{"value": "newvalue", "path": "newvalue.txt"}]}}}</configfile>
     </configfiles>
-    <command>
+    <command detect_errors="exit_code">
         mkdir $out_file.files_path ;
-        echo "A new value" > $out_file.files_path/newvalue.txt;
-        cp $static_test_data $out_file
+        echo "A new value" > '$out_file.files_path/newvalue.txt';
+        cp '$static_test_data' '$out_file';
+        exit $exit_code
     </command>
     <inputs>
         <param type="text" name="ignored_value" value="" label="Ignored" />
+        <param type="integer" name="exit_code" value="0" label="Exit Code" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>