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Refactor DependencyManager to walk dependencies resolvers first, then requirements.

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Invert previous loop to give resolvers a chance to resolve everything at once in subsequent commits.
This commit is contained in:
John Chilton
2017-01-08 08:24:15 -05:00
parent dad4c60d85
commit caf9bf21de
1 changed files with 44 additions and 22 deletions
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lib/galaxy/tools/deps/__init__.py
+44 -22
View File
@@ -14,6 +14,7 @@ from galaxy.util import (
plugin_config
)
from .requirements import ToolRequirement
from .resolvers import NullDependency
from .resolvers.conda import CondaDependencyResolver, DEFAULT_ENSURE_CHANNELS
from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver
@@ -107,20 +108,46 @@ class DependencyManager( object ):
def requirements_to_dependencies(self, requirements, **kwds):
"""
Takes a list of requirements and returns a dictionary
with requirements as key and dependencies as value.
with requirements as key and dependencies as value caching
these on the tool instance if supplied.
"""
requirement_to_dependency = OrderedDict()
for requirement in requirements:
if requirement.type in [ 'package', 'set_environment' ]:
dependency = self.find_dep( name=requirement.name,
version=requirement.version,
type=requirement.type,
**kwds )
log.debug(dependency.resolver_msg)
if dependency.dependency_type:
requirement_to_dependency[requirement] = dependency
requirement_to_dependency = self._requirements_to_dependencies_dict(requirements, **kwds)
if 'tool_instance' in kwds:
kwds['tool_instance'].dependencies = [dep.to_dict() for dep in requirement_to_dependency.values()]
return requirement_to_dependency
def _requirements_to_dependencies_dict(self, requirements, **kwds):
"""Build simple requirements to dependencies dict for resolution."""
requirement_to_dependency = OrderedDict()
index = kwds.get('index', None)
require_exact = kwds.get('exact', False)
resolvable_requirements = []
for requirement in requirements:
if requirement.type in ['package', 'set_environment']:
resolvable_requirements.append(requirement)
else:
log.debug("Unresolvable requirement type [%s] found, will be ignored." % requirement.type)
for i, resolver in enumerate(self.dependency_resolvers):
if index is not None and i != index:
continue
for requirement in resolvable_requirements:
if requirement in requirement_to_dependency:
continue
if requirement.type in ['package', 'set_environment']:
dependency = resolver.resolve( requirement.name, requirement.version, requirement.type, **kwds )
if require_exact and not dependency.exact:
continue
log.debug(dependency.resolver_msg)
if not isinstance(dependency, NullDependency):
requirement_to_dependency[requirement] = dependency
return requirement_to_dependency
def uses_tool_shed_dependencies(self):
@@ -128,17 +155,12 @@ class DependencyManager( object ):
def find_dep( self, name, version=None, type='package', **kwds ):
log.debug('Find dependency %s version %s' % (name, version))
index = kwds.get('index', None)
require_exact = kwds.get('exact', False)
for i, resolver in enumerate(self.dependency_resolvers):
if index is not None and i != index:
continue
dependency = resolver.resolve( name, version, type, **kwds )
if require_exact and not dependency.exact:
continue
if not isinstance(dependency, NullDependency):
return dependency
return NullDependency(version=version, name=name)
requirement = ToolRequirement(name=name, version=version, type=type)
dep_dict = self._requirements_to_dependencies_dict([requirement], **kwds)
if len(dep_dict) > 0:
return dep_dict.values()[0]
else:
return NullDependency(name=name, version=version)
def __build_dependency_resolvers( self, conf_file ):
if not conf_file: