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

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 (

from . import (
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 """