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Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes

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[17.01] Fix cached dependency manager.
This commit is contained in:
Nicola Soranzo
2017-01-24 11:51:06 +00:00
committed by GitHub
parent 0bf7efb89a df8be3add7
commit dc49b1c220
2 changed files with 16 additions and 11 deletions
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lib/galaxy/tools/deps/__init__.py
+15 -10
View File
@@ -36,7 +36,6 @@ def build_dependency_manager( config ):
'app_config': config,
}
if getattr(config, "use_cached_dependency_manager", False):
dependency_manager_kwds['tool_dependency_cache_dir'] = config.tool_dependency_cache_dir
dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
else:
dependency_manager = DependencyManager( **dependency_manager_kwds )
@@ -92,15 +91,20 @@ class DependencyManager( object ):
global_key = "%s_%s" % (config_prefix, key)
value = explicit_resolver_options.get(key, CONFIG_VAL_NOT_FOUND)
if value is CONFIG_VAL_NOT_FOUND:
if isinstance(self.__app_config, dict):
value = self.__app_config.get(global_key, CONFIG_VAL_NOT_FOUND)
else:
value = getattr(self.__app_config, global_key, CONFIG_VAL_NOT_FOUND)
value = self.get_app_option(global_key, default)
return value
def get_app_option(self, key, default=None):
value = CONFIG_VAL_NOT_FOUND
if isinstance(self.__app_config, dict):
value = self.__app_config.get(key, CONFIG_VAL_NOT_FOUND)
else:
value = getattr(self.__app_config, key, CONFIG_VAL_NOT_FOUND)
if value is CONFIG_VAL_NOT_FOUND and hasattr(self.__app_config, "config_dict"):
value = self.__app_config.config_dict.get(global_key, CONFIG_VAL_NOT_FOUND)
value = self.__app_config.config_dict.get(key, CONFIG_VAL_NOT_FOUND)
if value is CONFIG_VAL_NOT_FOUND:
value = default
return value
def dependency_shell_commands( self, requirements, **kwds ):
@@ -210,8 +214,9 @@ class DependencyManager( object ):
class CachedDependencyManager(DependencyManager):
def __init__(self, default_base_path, conf_file=None, app_config={}):
def __init__(self, default_base_path, conf_file=None, app_config={}, tool_dependency_cache_dir=None):
super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, conf_file=conf_file, app_config=app_config)
self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir")
def build_cache(self, requirements, **kwds):
resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
@@ -240,7 +245,7 @@ class CachedDependencyManager(DependencyManager):
resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable]
hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies)
if not os.path.exists(hashed_dependencies_dir) and self.__app_config.getattr("precache_dependencies", False):
if not os.path.exists(hashed_dependencies_dir) and self.get_app_option("precache_dependencies", False):
# Cache not present, try to create it
self.build_cache(requirements, **kwds)
if os.path.exists(hashed_dependencies_dir):
@@ -265,4 +270,4 @@ class CachedDependencyManager(DependencyManager):
:rtype: str
"""
req_hashes = self.hash_dependencies(resolved_dependencies)
return os.path.abspath(os.path.join(self.extra_config['tool_dependency_cache_dir'], req_hashes))
return os.path.abspath(os.path.join(self.tool_dependency_cache_dir, req_hashes))
test/integration/test_resolvers.py
+1 -1
View File
@@ -20,7 +20,7 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
@classmethod
def handle_galaxy_config_kwds(cls, config):
cls.conda_tmp_prefix = mkdtemp()
config["use_cached_dep_manager"] = True
config["use_cached_dependency_manager"] = True
config["conda_auto_init"] = True
config["conda_prefix"] = os.path.join(cls.conda_tmp_prefix, 'conda')