Merge pull request #89 from cat-bro/show-fastqc-with-rules

If a tool has file size rules, a role rule has no access to tool's scheduling tags

tests/fixtures/mapping-role.yml

@@ -28,6 +28,23 @@ tools:
         - pulsar-training-large
       require:
         - pulsar
+  fastqc:
+    cores: 8
+    mem: 30.7
+    env:
+      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+    scheduling:
+      require:
+      - pulsar
+    rules:
+    - id: fastqc_small_input_rule
+      if: input_size < 0.01
+      cores: 2
+      mem: 7.6
+    - id: fastqc_medium_input_rule
+      if: 0.01 <= input_size < 2
+      cores: 4
+      mem: 15.3
 users:
   default:
     max_cores: 3

tests/test_mapper_role.py

@@ -58,7 +58,7 @@ def test_map_role_training_matching_tag_values(self):
         self.assertEqual(destination.params['native_spec'], '--mem 1 --cores 1')
 
         # test training small pulsar rule
-        tool = mock_galaxy.Tool('bwa')
+        tool = mock_galaxy.Tool('fastqc')
         destination = self._map_to_destination(tool, user)
         self.assertEqual(destination.params['native_spec'], '--mem 2 --cores 2')
 

tpv/core/entities.py

@@ -484,14 +484,14 @@ def evaluate(self, context):
         for rule in self.rules.values():
             if rule.is_matching(context):
                 rule = rule.evaluate(context)
-                context.update({
-                    'entity': rule
-                })
                 new_entity = rule.inherit(new_entity)
                 new_entity.gpus = rule.gpus or self.gpus
                 new_entity.cores = rule.cores or self.cores
                 new_entity.mem = rule.mem or self.mem
                 new_entity.id = f"{new_entity.id}, Rule: {rule.id}"
+                context.update({
+                    'entity': new_entity
+                })
         return super(EntityWithRules, new_entity).evaluate(context)
 
     def __repr__(self):