1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/b69b84f67337/ changeset: r5034:b69b84f67337 user: natefoo date: 2011-02-09 22:31:43 summary: More comprehensive conflict resolution for eggs that are dependencies of other eggs, and eggs which conflict with system versions. affected #: 1 file (1.8 KB)

--- a/lib/galaxy/eggs/__init__.py Wed Feb 09 16:29:50 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Wed Feb 09 16:31:43 2011 -0500 @@ -36,12 +36,13 @@ """ Contains information about locating and downloading eggs. """ - def __init__( self, name=None, version=None, tag=None, url=None, platform=None ): + def __init__( self, name=None, version=None, tag=None, url=None, platform=None, crate=None ): self.name = name self.version = version self.tag = tag self.url = url self.platform = platform + self.crate = crate self.distribution = None self.dir = None if self.name is not None and self.version is not None: @@ -145,37 +146,68 @@ log.debug( "Removed conflicting egg: %s" % doppelganger ) def resolve( self ): try: - return pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + rval = [] + # resolve this egg and its dependencies + dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + for dist in dists: + # if any of the resolved dependencies should be managed eggs but are being pulled from the wrong path, fix them + if dist.project_name in self.crate.all_names and not os.path.realpath( dist.location ).startswith( os.path.realpath( self.dir ) ): + # TODO: like eggs.require(), this breaks requirement versioning + subdists = self.version_conflict( dist, dist.as_requirement() ) + if type( subdists ) == list: + rval.extend( subdists ) + else: + rval.append( subdists ) + else: + rval.append( dist ) + return rval except pkg_resources.DistributionNotFound, e: # If this statement is true, it means we do have the requested egg, # just not one (or more) of its deps. if e.args[0].project_name != self.distribution.project_name: - log.warning( "Warning: %s (a dependant egg of %s) cannot be fetched" % ( e.args[0].project_name, self.distribution.project_name ) ) + log.warning( "Warning: %s (a dependent egg of %s) cannot be fetched" % ( e.args[0].project_name, self.distribution.project_name ) ) return ( self.distribution, ) else: raise EggNotFetchable( self ) except pkg_resources.VersionConflict, e: # there's a conflicting egg on the path, remove it - dist = e.args[0] - # use the canonical path for comparisons - location = os.path.realpath( dist.location ) - for entry in pkg_resources.working_set.entries: - if os.path.realpath( entry ) == location: - pkg_resources.working_set.entries.remove( entry ) - break - else: - location = entry = None - del pkg_resources.working_set.by_key[dist.key] - if entry is not None: - pkg_resources.working_set.entry_keys[entry] = [] - if entry in sys.path: - sys.path.remove(entry) - r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) - if location is not None and not location.endswith( '.egg' ): - # re-add the path if it's a non-egg dir, in case more deps live there - pkg_resources.working_set.entries.append( location ) - sys.path.append( location ) - return r + return self.version_conflict( e.args[0], e.args[1] ) + def version_conflict( self, conflict_dist, conflict_req ): + # since this conflict may be for a dependent egg, find the correct egg from the crate + if conflict_dist.project_name == self.distribution.project_name: + egg = self + dist = egg.distribution + elif conflict_dist.project_name in self.crate.all_names: + egg = self.crate[conflict_dist.project_name] + dist = egg.distribution + else: + # should not happen, but just in case + egg = None + dist = conflict_dist + # use the canonical path to locate and remove the conflict from the working set + location = os.path.realpath( conflict_dist.location ) + for entry in pkg_resources.working_set.entries: + if os.path.realpath( entry ) == location: + pkg_resources.working_set.entries.remove( entry ) + break + else: + location = entry = None + del pkg_resources.working_set.by_key[conflict_dist.key] + # remove the conflict from sys.path + if entry is not None: + pkg_resources.working_set.entry_keys[entry] = [] + if entry in sys.path: + sys.path.remove(entry) + # if the conflict is a dpeendent egg, fetch that specific egg + if egg: + r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) + else: + r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env ) + # re-add the path if it's a non-egg dir, in case more deps live there + if location is not None and not location.endswith( '.egg' ): + pkg_resources.working_set.entries.append( location ) + sys.path.append( location ) + return r def require( self ): try: dists = self.resolve() @@ -215,7 +247,7 @@ platform = self.platform or '-'.join( ( py, pkg_resources.get_platform() ) ) else: platform = self.py_platform or py - egg = egg_class( name, version, tag, url, platform ) + egg = egg_class( name=name, version=version, tag=tag, url=url, platform=platform, crate=self ) self.eggs[name] = egg @property def config_missing( self ): @@ -331,7 +363,7 @@ return False

def get_env(): - env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) + env = pkg_resources.Environment( search_path='', platform=pkg_resources.get_platform() ) for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir, 'eggs' ), False ): env.add( dist ) return env @@ -340,6 +372,8 @@ def require( req_str ): c = Crate() req = pkg_resources.Requirement.parse( req_str ) + # TODO: This breaks egg version requirements. Not currently a problem, but + # it could become one. try: return c[req.project_name].require() except KeyError:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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