Merge pull request #91 from cat-bro/helpers-for-tool-version-comparison

Add helpers for tool version comparison

tests/fixtures/mapping-rule-tool-limits.yml

@@ -26,7 +26,20 @@ tools:
         execute: |
           from galaxy.jobs.mapper import JobNotReadyException
           raise JobNotReadyException()
-
+  toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/.*:
+    rules:
+      - if: helpers.tool_version_gte(tool, '2.15.1+galaxy0')
+        env:
+          version_gte_2.15.1+galaxy0: true
+      - if: helpers.tool_version_gt(tool, '2.15.1+galaxy0')
+        env:
+          version_gt_2.15.1+galaxy0: true
+      - if: helpers.tool_version_lt(tool, '2.10.1+galaxy7')
+        env:
+          version_lt_2.10.1+galaxy7: true
+      - if: helpers.tool_version_lte(tool, '2.10.1+galaxy7')
+        env:
+          version_lte_2.10.1+galaxy7: true
 
 destinations:
   local:

tests/test_mapper_rules.py

@@ -226,3 +226,42 @@ def create_job(app, mock_user, mock_tool):
         with self.assertRaises(JobNotReadyException):
             tpv_config = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-rule-tool-limits.yml')
             self._map_to_destination(tool_total_limit_3, user_roosta, datasets, tpv_config_files=[tpv_config], app=app)
+
+    def test_tool_version_comparison_helpers(self):
+        tpv_config = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-rule-tool-limits.yml')
+        user = mock_galaxy.User('ford', '[email protected]')
+        datasets = [mock_galaxy.DatasetAssociation("test", mock_galaxy.Dataset("test.txt", file_size=1*1024**3))]
+
+        def mock_trinity_with_version(version):
+            return mock_galaxy.Tool(
+                id=f'toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/{version}',
+                version=version
+            )
+
+        env_keys = [ # env keys that may be added by cooked trinity rules
+            'version_gte_2.15.1+galaxy0',
+            'version_gt_2.15.1+galaxy0',
+            'version_lt_2.10.1+galaxy7',
+            'version_lte_2.10.1+galaxy7',
+        ]
+        # trinity version 3.15.1+galaxy0
+        tool = mock_trinity_with_version('3.15.1+galaxy0')
+        destination = self._map_to_destination(tool, user, datasets, tpv_config_files=[tpv_config])
+        self.assertCountEqual(
+            [e.get('name') for e in destination.env if e.get('name') in env_keys],
+            ['version_gte_2.15.1+galaxy0', 'version_gt_2.15.1+galaxy0'],
+        )
+        # trinity version 2.15.1+galaxy0
+        tool = mock_trinity_with_version('2.15.1+galaxy0')
+        destination = self._map_to_destination(tool, user, datasets, tpv_config_files=[tpv_config])
+        self.assertCountEqual(
+            [e.get('name') for e in destination.env if e.get('name') in env_keys],
+            ['version_gte_2.15.1+galaxy0'],
+        )
+        # trinity version 2.10.1+galaxy6
+        tool = mock_trinity_with_version('2.10.1+galaxy6')
+        destination = self._map_to_destination(tool, user, datasets, tpv_config_files=[tpv_config])
+        self.assertCountEqual(
+            [e.get('name') for e in destination.env if e.get('name') in env_keys],
+            ['version_lt_2.10.1+galaxy7', 'version_lte_2.10.1+galaxy7'],
+        )

tpv/commands/test/mock_galaxy.py

@@ -44,9 +44,10 @@ def __init__(self, file_name, file_size):
 
 # Tool mock and helpers=========================================
 class Tool:
-    def __init__(self, id):
+    def __init__(self, id, version=None):
         self.id = id
         self.old_id = id
+        self.version = version
         self.installed_tool_dependencies = []
 
 

tpv/core/helpers.py

@@ -1,3 +1,4 @@
+import packaging.version
 import random
 from functools import reduce
 from galaxy import model
@@ -85,3 +86,19 @@ def tag_values_match(entity, match_tag_values=[], exclude_tag_values=[]):
         all([any(entity.tpv_tags.filter(tag_value=tag_value)) for tag_value in match_tag_values])
         and not any([any(entity.tpv_tags.filter(tag_value=tag_value)) for tag_value in exclude_tag_values])
     )
+
+
+def tool_version_lte(tool, version):
+    return packaging.version.parse(tool.version) <= packaging.version.parse(version)
+
+
+def tool_version_lt(tool, version):
+    return packaging.version.parse(tool.version) < packaging.version.parse(version)
+
+
+def tool_version_gte(tool, version):
+    return packaging.version.parse(tool.version) >= packaging.version.parse(version)
+
+
+def tool_version_gt(tool, version):
+    return packaging.version.parse(tool.version) > packaging.version.parse(version)