From fbe27016f7028fa4980d5c49014c99f8b961bf92 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 17 Aug 2014 18:43:54 -0400
Subject: [PATCH] Dynamic destinations - pass job_conf.xml params to rule
 functions. In other words, send extra job destination parameters to dynamic
 rule functions as arguments (in addition to those dynamically populated by
 Galaxy itself). This enables greater parameterization of rule functions and
 should lead to cleaner separation of logic and data (i.e. sites can program
 rules that restrict access to users, but which users can be populated at a
 higher level in `job_conf.xml`).

For example the following dynamic job rule:

    def cluster1(app, memory="4096", cores="1", hours="48"):
        native_spec = "--time=%s:00:00 --nodes=1 --ntasks=%s --mem=%s" % ( hours, cores, memory )
        return JobDestination( "cluster1", params=dict( native_specification=native_spec ) )

Could then be called with various parameters in job_conf.xml as follows:

    <destination id="short_job" type="dyanmic">
      <param id="function">cluster1</param>
      <param id="hours">1</param>
    </destination>

    <destination id="big_job" type="dynamic">
      <param id="function">cluster1</param>
      <param id="cores">8</param>
      <param id="memory">32768</param>
    </destination>
---
 lib/galaxy/jobs/mapper.py            | 13 +++++++++----
 test/unit/jobs/test_mapper.py        |  6 ++++++
 test/unit/jobs/test_rules/10_site.py |  5 +++++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index 62c30c61914..fa51fb4a547 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -69,7 +69,7 @@ class JobRunnerMapper( object ):
                 names.append( rule_module_name )
         return names
 
-    def __invoke_expand_function( self, expand_function ):
+    def __invoke_expand_function( self, expand_function, destination_params ):
         function_arg_names = inspect.getargspec( expand_function ).args
         app = self.job_wrapper.app
         possible_args = {
@@ -83,6 +83,11 @@ class JobRunnerMapper( object ):
 
         actual_args = {}
 
+        # Send through any job_conf.xml defined args to function
+        for destination_param in destination_params.keys():
+            if destination_param in function_arg_names:
+                actual_args[ destination_param ] = destination_params[ destination_param ]
+
         # Populate needed args
         for possible_arg_name in possible_args:
             if possible_arg_name in function_arg_names:
@@ -179,12 +184,12 @@ class JobRunnerMapper( object ):
                 raise Exception( message )
 
             expand_function = self.__get_expand_function( expand_function_name )
-            return self.__handle_rule( expand_function )
+            return self.__handle_rule( expand_function, destination )
         else:
             raise Exception( "Unhandled dynamic job runner type specified - %s" % expand_type )
 
-    def __handle_rule( self, rule_function ):
-        job_destination = self.__invoke_expand_function( rule_function )
+    def __handle_rule( self, rule_function, destination ):
+        job_destination = self.__invoke_expand_function( rule_function, destination.params )
         if not isinstance(job_destination, galaxy.jobs.JobDestination):
             job_destination_rep = str(job_destination)  # Should be either id or url
             if '://' in job_destination_rep:
diff --git a/test/unit/jobs/test_mapper.py b/test/unit/jobs/test_mapper.py
index 73bf03f049d..f0a00ff1bc6 100644
--- a/test/unit/jobs/test_mapper.py
+++ b/test/unit/jobs/test_mapper.py
@@ -46,6 +46,12 @@ def test_dynamic_mapping_defaults_to_tool_id_as_rule():
     assert mapper.job_config.rule_response == "tool1_dest_id"
 
 
+def test_dynamic_mapping_job_conf_params():
+    mapper = __mapper( __dynamic_destination( dict( function="check_job_conf_params", param1="7" ) ) )
+    assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION
+    assert mapper.job_config.rule_response == "sent_7_dest_id"
+
+
 def test_dynamic_mapping_function_parameters():
     mapper = __mapper( __dynamic_destination( dict( function="check_rule_params" ) ) )
     assert mapper.get_job_destination( {} ) is DYNAMICALLY_GENERATED_DESTINATION
diff --git a/test/unit/jobs/test_rules/10_site.py b/test/unit/jobs/test_rules/10_site.py
index 5f9d558a7f8..779d4edbdd1 100644
--- a/test/unit/jobs/test_rules/10_site.py
+++ b/test/unit/jobs/test_rules/10_site.py
@@ -40,6 +40,11 @@ def check_rule_params(
     return "all_passed"
 
 
+def check_job_conf_params( param1 ):
+    assert param1 == "7"
+    return "sent_7_dest_id"
+
+
 def check_resource_params( resource_params ):
     assert resource_params["memory"] == "8gb"
     return "have_resource_params"