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Revert "Try next dep. resolver if building env failed"

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This reverts commit e821d469e6.
This commit is contained in:
Nate Coraor
2018-02-07 13:16:18 -05:00
parent 04e4da0d31
commit 11ec4ee93d
2 changed files with 27 additions and 36 deletions
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lib/galaxy/tools/deps/__init__.py
+25 -34
View File
@@ -109,26 +109,25 @@ class DependencyManager(object):
def dependency_shell_commands(self, requirements, **kwds):
requirements_to_dependencies = self.requirements_to_dependencies(requirements, **kwds)
shell_commands = []
for dependencies in requirements_to_dependencies:
ordered_dependencies = OrderedSet(dependencies.values())
try:
shell_commands = [dependency.shell_commands() for dependency in ordered_dependencies]
if 'tool_instance' in kwds:
# We log the dependencies on the tool instance,
# which subsequently is used to log the used dependencies for this job.
kwds['tool_instance'].dependencies = [dep.to_dict() for dep in ordered_dependencies]
except Exception as e:
log.exception(e)
return shell_commands
ordered_dependencies = OrderedSet(requirements_to_dependencies.values())
return [dependency.shell_commands() for dependency in ordered_dependencies]
def requirements_to_dependencies(self, requirements, **kwds):
"""
Takes a list of requirements and returns a list of dictionaries
with requirements as key and dependencies as value.
Each dictionary corresponds to one dependency resolver.
Takes a list of requirements and returns a dictionary
with requirements as key and dependencies as value caching
these on the tool instance if supplied.
"""
resolver_requirements = []
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)
return_null_dependencies = kwds.get('return_null', False)
@@ -136,15 +135,12 @@ class DependencyManager(object):
resolvable_requirements = requirements.resolvable
for i, resolver in enumerate(self.dependency_resolvers):
requirement_to_dependency = OrderedDict()
if index is not None and i != index:
continue
if len(requirement_to_dependency) == len(resolvable_requirements):
# Shortcut - resolution complete.
resolver_requirements.append(requirement_to_dependency)
continue
break
# Check requirements all at once
all_unmet = len(requirement_to_dependency) == 0
@@ -157,9 +153,8 @@ class DependencyManager(object):
log.debug(dependency.resolver_msg)
requirement_to_dependency[requirement] = dependency
# Shortcut - resolution complete for this resolver.
resolver_requirements.append(requirement_to_dependency)
continue
# Shortcut - resolution complete.
break
# Check individual requirements
for requirement in resolvable_requirements:
@@ -176,12 +171,8 @@ class DependencyManager(object):
elif return_null_dependencies and (resolver == self.dependency_resolvers[-1] or i == index):
log.debug(dependency.resolver_msg)
requirement_to_dependency[requirement] = dependency
if requirement_to_dependency:
resolver_requirements.append(requirement_to_dependency)
if not resolver_requirements:
# Have at least a single empty dict
resolver_requirements.append(OrderedDict())
return resolver_requirements
return requirement_to_dependency
def uses_tool_shed_dependencies(self):
return any(map(lambda r: isinstance(r, ToolShedPackageDependencyResolver), self.dependency_resolvers))
@@ -189,9 +180,9 @@ class DependencyManager(object):
def find_dep(self, name, version=None, type='package', **kwds):
log.debug('Find dependency %s version %s' % (name, version))
requirements = ToolRequirements([ToolRequirement(name=name, version=version, type=type)])
dependencies = self.requirements_to_dependencies(requirements, **kwds)[0]
if len(dependencies) > 0:
return dependencies.values()[0]
dep_dict = self._requirements_to_dependencies_dict(requirements, **kwds)
if len(dep_dict) > 0:
return dep_dict.values()[0]
else:
return NullDependency(name=name, version=version)
@@ -230,7 +221,7 @@ class CachedDependencyManager(DependencyManager):
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)[0]
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 os.path.exists(hashed_dependencies_dir):
@@ -253,7 +244,7 @@ class CachedDependencyManager(DependencyManager):
If cached environment exists or is successfully created, will generate
commands to activate it.
"""
resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)[0]
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.get_app_option("precache_dependencies", False):
lib/galaxy/tools/deps/views.py
+2 -2
View File
@@ -52,7 +52,7 @@ class DependencyResolversView(object):
kwds = {'install': False,
'return_null': True,
'installed_tool_dependencies': installed_tool_dependencies}
dependencies_per_tool = {tool: self._dependency_manager.requirements_to_dependencies(requirements, **kwds)[0] for tool, requirements in tool_requirements_d.items()}
dependencies_per_tool = {tool: self._dependency_manager.requirements_to_dependencies(requirements, **kwds) for tool, requirements in tool_requirements_d.items()}
return dependencies_per_tool
def uninstall_dependencies(self, index=None, **payload):
@@ -101,7 +101,7 @@ class DependencyResolversView(object):
return list(removed_environments)
def install_dependencies(self, requirements):
return self._dependency_manager.requirements_to_dependencies(requirements, **{'install': True})
return self._dependency_manager._requirements_to_dependencies_dict(requirements, **{'install': True})
def install_dependency(self, index=None, **payload):
"""