Merge pull request #93 from cat-bro/failing-test-for-pulsar-user-scen…

…ario

Failing test for pulsar user scenario

docs/topics/tpv_by_example.rst

@@ -34,7 +34,7 @@ at each destination (optional). The tools are matched by tool id, and can be a r
 resource requirements can also be computed as python expressions. If resource requirements are defined at the
 destination, TPV will check whether the job will fit. For example, hisat2 will not schedule on `general_pulsar_1`
 as it has insufficient cores. If resource requirements are omitted in the tool or destination, it is considered a match.
-Note that TPV only considers destinations defined in its own config file, and ignore destinations in job_conf.yml.
+Note that TPV only considers destinations defined in its own config file, and ignores destinations in job_conf.yml.
 
 Default inheritance
 -------------------

tests/fixtures/mapping-destinations.yml

@@ -19,13 +19,19 @@ tools:
       accept:
       reject:
         - pulsar
+        - offline
     rules:
       - if: input_size < 2
         fail: Data size too small
   bwa:
     scheduling:
       require:
         - pulsar
+  toolshed_hifiasm:
+    cores: 1000
+    rules:
+      - if: input_size < 1000
+        cores: 2
   inheritance_test_tool:
     scheduling:
       accept:
@@ -100,6 +106,18 @@ tools:
       require:
         - test_of_min_mem_accepted
 
+users:
+  [email protected]:
+      rules:
+        - id: pulsar_user_mapping_rule
+          if: tool.id.startswith('toolshed') or tool.id.startswith('testtoolshed')
+          scheduling:
+            accept:
+              - pulsar # pulsar must be in require/prefer/accept for a job to be scheduled to pulsar
+              - offline # allow scheduling to a destination even when it is offline
+            require:
+              - pulsar-canberra
+
 destinations:
   local:
     runner: local
@@ -240,3 +258,9 @@ destinations:
     scheduling:
       require:
         - test_of_min_mem_accepted
+  pulsar-canberra:
+    runner: k8s
+    max_accepted_cores: 32
+    scheduling:
+      accept:
+        - pulsar-canberra

tests/test_mapper_destinations.py

@@ -176,3 +176,13 @@ def test_min_accepted_mem_honoured(self):
         tool = mock_galaxy.Tool('tool_for_testing_min_mem_acceptance_match')
         destination = self._map_to_destination(tool, user, datasets, tpv_config_paths=[config])
         self.assertEqual(destination.id, "destination_with_min_mem_accepted")
+
+    def test_user_map_to_destination_accepting_offline(self):
+        user = mock_galaxy.User('albo', '[email protected]')
+
+        config = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-destinations.yml')
+
+        tool = mock_galaxy.Tool('toolshed_hifiasm')
+        datasets = [mock_galaxy.DatasetAssociation("test", mock_galaxy.Dataset("test.txt", file_size=12 * 1024 ** 3))]
+        destination = self._map_to_destination(tool, user, datasets, tpv_config_paths=[config])
+        self.assertEqual(destination.id, "pulsar-canberra")

tpv/core/entities.py

@@ -485,9 +485,9 @@ def evaluate(self, context):
             if rule.is_matching(context):
                 rule = rule.evaluate(context)
                 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.gpus = rule.gpus or new_entity.gpus
+                new_entity.cores = rule.cores or new_entity.cores
+                new_entity.mem = rule.mem or new_entity.mem
                 new_entity.id = f"{new_entity.id}, Rule: {rule.id}"
                 context.update({
                     'entity': new_entity