Source code for galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages
"""
Backup resolvers for when dependencies can not be loaded from the database.
Mainly suited for testing stage.
Ideally all dependencies will be stored in the database
when a tool is added from a Tool Shed.
That should remain the preferred way of locating dependencies.
In cases where that is not possible
for example during testing this resolver can act as a backup.
This resolver looks not just for manually added dependencies
but also ones added from a Tool Shed.
This tool is still under development so the default behaviour could change.
It has been tested when placed in the same directory as galaxy_packages.py
At the time of writing July 3 2015 this resolver has to be plugged in.
See bottom for instructions on how to add this resolver.
"""
import logging
from os import listdir
from os.path import (
exists,
getmtime,
join,
)
from . import (
Dependency,
NullDependency,
)
from .galaxy_packages import BaseGalaxyPackageDependencyResolver
log = logging.getLogger(__name__)
MANUAL = "manual"
PREFERRED_OWNERS = f"{MANUAL},iuc,devteam"
[docs]class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver):
dict_collection_visible_keys = BaseGalaxyPackageDependencyResolver.dict_collection_visible_keys + [
"preferred_owners",
"select_by_owner",
]
resolver_type = "unlinked_tool_shed_packages"
[docs] def __init__(self, dependency_manager, **kwds):
super().__init__(dependency_manager, **kwds)
# Provide a list of preferred owners whose dependency to use
self.preferred_owners = kwds.get("preferred_owners", PREFERRED_OWNERS).split(",")
# Option to ignore owner and just use last modified time
self.select_by_owner = str(kwds.get("select_by_owner", "true")).lower() != "false"
def _find_dep_versioned(self, name, version, type="package", **kwds):
try:
possibles = self._find_possible_dependencies(name, version, type)
if len(possibles) == 0:
log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type)
return NullDependency(version=version, name=name)
elif len(possibles) == 1:
# Only one candidate found so ignore any preference rules
return possibles[0].dependency
else:
# Pick the preferred one
return self._select_preferred_dependency(possibles).dependency
except Exception:
log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
return NullDependency(version=version, name=name)
# Finds all possible dependency to use
# Should be extended as required
# Returns CandidateDependency objects with data for preference picking
def _find_possible_dependencies(self, name, version, type):
possibles = []
if exists(self.base_path):
path = join(self.base_path, name, version)
if exists(path):
# First try the way without owner/name/revision
package = self._galaxy_package_dep(path, version, name, type, True)
if not isinstance(package, NullDependency):
log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, path)
possibles.append(CandidateDependency(package, path))
# now try with an owner/name/revision
for owner in listdir(path):
owner_path = join(path, owner)
for package_name in listdir(owner_path):
if package_name.lower().startswith(f"package_{name.lower()}"):
package_path = join(owner_path, package_name)
for revision in listdir(package_path):
revision_path = join(package_path, revision)
package = self._galaxy_package_dep(revision_path, version, name, type, True)
if not isinstance(package, NullDependency):
log.debug(
"Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path
)
possibles.append(CandidateDependency(package, package_path, owner))
return possibles
def _select_preferred_dependency(self, possibles, by_owner=None):
if by_owner is None:
by_owner = self.select_by_owner
preferred = []
if by_owner:
for owner in self.preferred_owners:
for candidate in possibles:
if candidate.owner == owner:
preferred.append(candidate)
if len(preferred) == 1:
log.debug("Picked dependency based on owner '%s'", owner)
return preferred[0]
elif len(preferred) > 1:
log.debug("Multiple dependency found with owner '%s'", owner)
break
if len(preferred) == 0:
preferred = possibles
latest_modified = 0
for candidate in preferred:
modified = getmtime(candidate.path)
if latest_modified < modified:
latest_candidate = candidate
latest_modified = modified
log.debug("Picking dependency at '%s' as it was the last modified", latest_candidate.path)
return latest_candidate
class CandidateDependency(Dependency):
dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ["dependency", "path", "owner"]
dependency_type = "unlinked_tool_shed_package"
@property
def exact(self):
return self.dependency.exact
def __init__(self, dependency, path, owner=MANUAL):
self.dependency = dependency
self.path = path
self.owner = owner
def shell_commands(self):
"""
Return shell commands to enable this dependency.
"""
return self.dependency.shell_commands()
__all__ = ("UnlinkedToolShedPackageDependencyResolver",)
"""
At the time of writing July 3 2015 this resolver has to be plugged in.
Adding resolver instructions:
1. create a dependency_resolvers_config.xml file
<dependency_resolvers>
<tool_shed_packages />
<galaxy_packages />
<galaxy_packages versionless="true" />
<unlinked_tool_shed_packages />
</dependency_resolvers>
1a. ALWAYS add <tool_shed_packages /> first!!!!
1b. <galaxy_packages /> is optional as
this resolver will also find dependency found by that resolver
1bi Current default is to use a dependency to find that way first!
1bii So an alternative version of dependency_resolvers_config.xml
<dependency_resolvers>
<tool_shed_packages />
<unlinked_tool_shed_packages />
<unlinked_tool_shed_packages versionless="true" />
</dependency_resolvers>
1c. See __init__ for optional config values
1ci versionless currently is handled by the super class
GalaxyPackageDependencyResolver
2. Add a parameter to config.ini
dependency_resolvers_config_file = ./config/dependency_resolvers_config.xml
2a. File name/path can be different
2b. config key must be dependency_resolvers_config_file
3. For planemo it may be required to specify:
--dependency_resolvers_config_file (xml file described in 1 above)
--tool_dependency_dir (root of dependencies typically galaxy/dependency_dir)
See planemo test --help for more information
"""