diff --git a/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py new file mode 100644 index 00000000000..1414b5ac941 --- /dev/null +++ b/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py @@ -0,0 +1,184 @@ +""" +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. + +""" + +from os import listdir +from os.path import join, exists, getmtime + +from .galaxy_packages import GalaxyPackageDependencyResolver +from ..resolvers import INDETERMINATE_DEPENDENCY + +import logging +log = logging.getLogger( __name__ ) + +MANUAL = "manual" +PREFERRED_OWNERS = MANUAL + ",iuc,devteam" + + +class UnlinkedToolShedPackageDependencyResolver(GalaxyPackageDependencyResolver): + resolver_type = "unlinked_tool_shed_packages" + + def __init__(self, dependency_manager, **kwds): + super(UnlinkedToolShedPackageDependencyResolver, self).__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_depenencies(name, version, type) + if len(possibles) == 0: + log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type) + return INDETERMINATE_DEPENDENCY + 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: + log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type) + return INDETERMINATE_DEPENDENCY + + # Finds all possible dependency to use + # Should be extended as required + # Returns CandidateDepenency objects with data for preference picking + def _find_possible_depenencies(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) + if package != INDETERMINATE_DEPENDENCY: + log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, path) + possibles.append(CandidateDepenency(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.startswith("package_" + name): + 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) + if package != INDETERMINATE_DEPENDENCY: + log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path) + possibles.append(CandidateDepenency(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 + + """ + #Currently no need has been found for expand the verionsless method + #This is an example of how it could be done + def _find_dep_default( self, name, type='package', **kwds ): + try: + possibles = TODO + if len(possibles) == 0: + log.debug("Unable to find dependency,'%s' default '%s'", name, type) + return INDETERMINATE_DEPENDENCY + 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, by_owner=False).dependency + except: + log.exception("Unexpected error hunting for dependency '%s' default '%s'", name, type) + return INDETERMINATE_DEPENDENCY + """ + + +class CandidateDepenency(): + + def __init__(self, dependency, path, owner=MANUAL): + self.dependency = dependency + self.path = path + self.owner = owner + +__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 + + + + + + + + +1a. ALWAYS add first!!!! + +1b. 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 + + + + + + +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 +"""