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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 (

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 """