Allow more rich container description in job_conf.xml.

lib/galaxy/jobs/__init__.py

@@ -469,13 +469,20 @@ class JobConfiguration( object ):
         rval = {}
         for param in parent.findall('param'):
             key = param.get('id')
-            param_value = param.text
+            if key in ["container", "container_override"]:
+                from galaxy.tools.deps import requirements
+                containers = map(requirements.container_from_element, list(param))
+                param_value = map(lambda c: c.to_dict(), containers)
+            else:
+                param_value = param.text
+
             if 'from_environ' in param.attrib:
                 environ_var = param.attrib['from_environ']
                 param_value = os.environ.get(environ_var, param_value)
             elif 'from_config' in param.attrib:
                 config_val = param.attrib['from_config']
                 param_value = self.app.config.config_dict.get(config_val, param_value)
+
             rval[key] = param_value
         return rval
 

lib/galaxy/tools/deps/containers.py

@@ -9,6 +9,7 @@ import six
 
 from galaxy.util import asbool
 from ..deps import docker_util
+from .requirements import ContainerDescription
 
 import logging
 log = logging.getLogger(__name__)
@@ -59,6 +60,13 @@ class ContainerFinder(object):
             )
             return container
 
+        if "container_override" in destination_info:
+            container_description = ContainerDescription.from_dict(destination_info["container_override"][0])
+            if container_description:
+                container = __destination_container(container_description)
+                if container:
+                    return container
+
         # Is destination forcing Galaxy to use a particular container do it,
         # this is likely kind of a corner case. For instance if deployers
         # do not trust the containers annotated in tools.
@@ -90,6 +98,13 @@ class ContainerFinder(object):
 
         # If we still don't have a container, check to see if any container
         # types define a default container id and use that.
+        if "container" in destination_info:
+            container_description = ContainerDescription.from_dict(destination_info["container"][0])
+            if container_description:
+                container = __destination_container(container_description)
+                if container:
+                    return container
+
         for container_type in CONTAINER_CLASSES.keys():
             container_id = self.__default_container_id(container_type, destination_info)
             if container_id:

lib/galaxy/tools/deps/requirements.py

@@ -92,11 +92,16 @@ def parse_requirements_from_xml( xml_root ):
     if requirements_elem is not None:
         container_elems = requirements_elem.findall( 'container' )
 
-    containers = []
-    for container_elem in container_elems:
-        identifier = xml_text( container_elem )
-        type = container_elem.get( "type", DEFAULT_CONTAINER_TYPE )
-        container = ContainerDescription( identifier=identifier, type=type )
-        containers.append( container )
+    containers = map(container_from_element, container_elems)
 
     return requirements, containers
+
+
+def container_from_element(container_elem):
+    identifier = xml_text(container_elem)
+    type = container_elem.get("type", DEFAULT_CONTAINER_TYPE)
+    container = ContainerDescription(
+        identifier=identifier,
+        type=type,
+    )
+    return container