Merge pull request #17 from galaxyproject/add_sample

Add sample vortex config and map to first available destination

docs/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# GalaxyCloudRunner documentation build configuration file, created by
+# total-perspective-vortex documentation build configuration file, created by
 # sphinx-quickstart on Sat Nov 10 18:16:35 2018.
 #
 # This file is execfile()d with the current directory set to its

tests/fixtures/mapping-sample.yml

@@ -0,0 +1,12 @@
+global:
+  default_inherits: default
+
+tools:
+  default:
+    cores: 2
+    mem: cores * 2
+    params:
+      local_slots: "{cores}"
+
+destinations:
+  local:

tests/test_mapper_inheritance.py

@@ -57,3 +57,11 @@ def test_map_inherit_no_default(self):
         self.assertEqual(destination.id, "local")
         self.assertFalse([env['value'] for env in destination.env if env['name'] == 'TEST_JOB_SLOTS'])
         self.assertEqual(destination.params['another_spec'], '--gpus 4')
+
+    def test_map_inherit_no_default_no_tool_def(self):
+        tool = mock_galaxy.Tool('some_random_tool')
+        user = mock_galaxy.User('gargravarr', '[email protected]')
+        vortex_config_path = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-inheritance-no-default.yml')
+
+        destination = self._map_to_destination(tool, user, datasets=[], vortex_config_path=vortex_config_path)
+        self.assertEqual(destination.id, "local")

tests/test_mapper_sample.py

@@ -0,0 +1,22 @@
+import os
+import unittest
+from vortex.rules import gateway
+from . import mock_galaxy
+
+
+class TestMapperSample(unittest.TestCase):
+
+    @staticmethod
+    def _map_to_destination(tool):
+        galaxy_app = mock_galaxy.App()
+        job = mock_galaxy.Job()
+        user = mock_galaxy.User('gargravarr', '[email protected]')
+        vortex_config = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-sample.yml')
+        gateway.ACTIVE_DESTINATION_MAPPER = None
+        return gateway.map_tool_to_destination(galaxy_app, job, tool, user, vortex_config_files=[vortex_config])
+
+    def test_map_sample_tool(self):
+        tool = mock_galaxy.Tool('sometool')
+        destination = self._map_to_destination(tool)
+        self.assertEqual(destination.id, "local")
+        self.assertEqual(destination.params['local_slots'], '2')

vortex/core/loader.py

@@ -80,6 +80,8 @@ def validate_entities(self, entity_class: type, entity_list: dict) -> dict:
         validated = {}
         for entity_id, entity_dict in entity_list.items():
             try:
+                if not entity_dict:
+                    entity_dict = {}
                 entity_dict['id'] = entity_id
                 entity_class.from_dict(self, entity_dict)
                 validated[entity_id] = entity_class.from_dict(self, entity_dict)

vortex/core/mapper.py

@@ -2,6 +2,7 @@
 import logging
 import re
 
+from .entities import Tool
 from .loader import VortexConfigLoader
 
 log = logging.getLogger(__name__)
@@ -60,6 +61,8 @@ def find_best_match(self, entity, destinations, context):
 
     def _find_matching_entities(self, tool, user):
         tool_entity = self._find_entity_by_id_regex(self.tools, tool.id)
+        if not tool_entity:
+            tool_entity = Tool.from_dict(self.loader, {'id': tool.id})
 
         entity_list = [tool_entity]
 
@@ -116,7 +119,8 @@ def map_to_destination(self, app, tool, user, job):
         # 7. Return destination with params
         if destination:
             destination = app.job_config.get_destination(destination.id)
-            destination.env += [dict(name=k, value=v) for (k, v) in evaluated.env.items()]
+            if evaluated.env:
+                destination.env += [dict(name=k, value=v) for (k, v) in evaluated.env.items()]
             destination.params.update(evaluated.params or {})
             return destination
         else: