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Merge pull request #441 from Christian-B/unlinked_dependencies
Added unlinked dependency resolver
This commit is contained in:
John Chilton
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"""
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Backup resolvers for when dependencies can not be loaded from the database.
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Mainly suited for testing stage.
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Ideally all dependencies will be stored in the database
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when a tool is added from a Tool Shed.
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That should remain the preferred way of locating dependencies.
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In cases where that is not possible
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for example during testing this resolver can act as a backup.
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This resolver looks not just for manually added dependencies
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but also ones added from a Tool Shed.
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This tool is still under development so the default behaviour could change.
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It has been tested when placed in the same directory as galaxy_packages.py
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At the time of writing July 3 2015 this resolver has to be plugged in.
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See bottom for instructions on how to add this resolver.
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"""
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from os import listdir
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from os.path import join, exists, getmtime
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from .galaxy_packages import GalaxyPackageDependencyResolver
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from ..resolvers import INDETERMINATE_DEPENDENCY
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import logging
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log = logging.getLogger( __name__ )
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MANUAL = "manual"
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PREFERRED_OWNERS = MANUAL + ",iuc,devteam"
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class UnlinkedToolShedPackageDependencyResolver(GalaxyPackageDependencyResolver):
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resolver_type = "unlinked_tool_shed_packages"
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def __init__(self, dependency_manager, **kwds):
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super(UnlinkedToolShedPackageDependencyResolver, self).__init__(dependency_manager, **kwds)
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# Provide a list of preferred owners whose dependency to use
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self.preferred_owners = kwds.get('preferred_owners', PREFERRED_OWNERS).split(",")
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# Option to ignore owner and just use last modified time
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self.select_by_owner = str(kwds.get('select_by_owner', "true")).lower() != "false"
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def _find_dep_versioned( self, name, version, type='package', **kwds ):
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try:
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possibles = self._find_possible_depenencies(name, version, type)
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if len(possibles) == 0:
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log.debug("Unable to find dependency,'%s' '%s' '%s'", name, version, type)
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return INDETERMINATE_DEPENDENCY
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elif len(possibles) == 1:
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# Only one candidate found so ignore any preference rules
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return possibles[0].dependency
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else:
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# Pick the preferred one
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return self._select_preferred_dependency(possibles).dependency
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except:
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log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
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return INDETERMINATE_DEPENDENCY
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# Finds all possible dependency to use
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# Should be extended as required
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# Returns CandidateDepenency objects with data for preference picking
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def _find_possible_depenencies(self, name, version, type):
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possibles = []
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if exists(self.base_path):
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path = join( self.base_path, name, version )
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if exists(path):
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# First try the way without owner/name/revision
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package = self._galaxy_package_dep(path, version)
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if package != INDETERMINATE_DEPENDENCY:
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log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, path)
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possibles.append(CandidateDepenency(package, path))
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# now try with an owner/name/revision
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for owner in listdir(path):
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owner_path = join(path, owner)
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for package_name in listdir(owner_path):
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if package_name.startswith("package_" + name):
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package_path = join(owner_path, package_name)
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for revision in listdir(package_path):
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revision_path = join(package_path, revision)
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package = self._galaxy_package_dep(revision_path, version)
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if package != INDETERMINATE_DEPENDENCY:
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log.debug("Found dependency '%s' '%s' '%s' at '%s'", name, version, type, revision_path)
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possibles.append(CandidateDepenency(package, package_path, owner))
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return possibles
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def _select_preferred_dependency(self, possibles, by_owner=None):
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if by_owner is None:
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by_owner = self.select_by_owner
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preferred = []
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if by_owner:
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for owner in self.preferred_owners:
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for candidate in possibles:
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if candidate.owner == owner:
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preferred.append(candidate)
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if len(preferred) == 1:
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log.debug("Picked dependency based on owner '%s'", owner)
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return preferred[0]
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elif len(preferred) > 1:
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log.debug("Multiple dependency found with owner '%s'", owner)
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break
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if len(preferred) == 0:
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preferred = possibles
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latest_modified = 0
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for candidate in preferred:
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modified = getmtime(candidate.path)
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if latest_modified < modified:
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latest_candidate = candidate
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latest_modified = modified
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log.debug("Picking dependency at '%s' as it was the last modified", latest_candidate.path)
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return latest_candidate
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"""
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#Currently no need has been found for expand the verionsless method
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#This is an example of how it could be done
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def _find_dep_default( self, name, type='package', **kwds ):
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try:
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possibles = TODO
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if len(possibles) == 0:
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log.debug("Unable to find dependency,'%s' default '%s'", name, type)
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return INDETERMINATE_DEPENDENCY
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elif len(possibles) == 1:
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#Only one candidate found so ignore any preference rules
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return possibles[0].dependency
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else:
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#Pick the preferred one
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return self._select_preferred_dependency(possibles, by_owner=False).dependency
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except:
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log.exception("Unexpected error hunting for dependency '%s' default '%s'", name, type)
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return INDETERMINATE_DEPENDENCY
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"""
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class CandidateDepenency():
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def __init__(self, dependency, path, owner=MANUAL):
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self.dependency = dependency
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self.path = path
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self.owner = owner
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__all__ = ['UnlinkedToolShedPackageDependencyResolver']
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"""
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At the time of writing July 3 2015 this resolver has to be plugged in.
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Adding resolver instructions:
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1. create a dependency_resolvers_config.xml file
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<dependency_resolvers>
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<tool_shed_packages />
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<galaxy_packages />
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<galaxy_packages versionless="true" />
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<unlinked_tool_shed_packages />
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</dependency_resolvers>
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1a. ALWAYS add <tool_shed_packages /> first!!!!
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1b. <galaxy_packages /> is optional as
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this resolver will also find dependency found by that resolver
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1bi Current default is to use a dependency to find that way first!
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1bii So an alternative version of dependency_resolvers_config.xml
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<dependency_resolvers>
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<tool_shed_packages />
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<unlinked_tool_shed_packages />
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<unlinked_tool_shed_packages versionless="true" />
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</dependency_resolvers>
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1c. See __init__ for optional config values
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1ci versionless currently is handled by the super class
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GalaxyPackageDependencyResolver
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2. Add a parameter to config.ini
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dependency_resolvers_config_file = ./config/dependency_resolvers_config.xml
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2a. File name/path can be different
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2b. config key must be dependency_resolvers_config_file
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3. For planemo it may be required to specify:
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--dependency_resolvers_config_file (xml file described in 1 above)
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--tool_dependency_dir (root of dependencies typically galaxy/dependency_dir)
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See planemo test --help for more information
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"""
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