def init_registry(self, registry_filename=None):
if registry_filename is not None:
self._registry = core.db.io.open_registry(registry_filename)
self._registry.set_global()
else:
self._registry = ModuleRegistry()
self._registry.set_global()
def setup_basic_package():
# setup basic package
basic_package = self.add_package('basic_modules')
self._registry._default_package = basic_package
prefix_dictionary = {'basic_modules': 'core.modules.'}
self.initialize_packages(prefix_dictionary)
setup_basic_package()
self._abstraction_pkg = self.add_package('abstraction', False)
# FIXME need to get this info from the package, but cannot
# do this since controller isn't imported yet
self._abstraction_pkg.identifier = 'local.abstractions'
self._abstraction_pkg.name = 'My SubWorkflows'
self._abstraction_pkg.version = '1.6'
self._registry.add_package(self._abstraction_pkg)
def make_registry(self):
reg_module = \
registry.get_descriptor_by_name('edu.utah.sci.vistrails.basic',
self.name).module
self._registry = ModuleRegistry()
self._registry.add_hierarchy(registry, self)
for module in self.pipeline.module_list:
if module.name == 'OutputPort':
port = self.make_port_from_module(module, 'source')
self._registry.add_port(reg_module, PortEndPoint.Source, port)
elif module.name == 'InputPort':
port = self.make_port_from_module(module, 'destination')
self._registry.add_port(reg_module, PortEndPoint.Destination,
port)
def add_port_to_registry(self, port_spec):
module = \
registry.get_descriptor_by_name(self.package, self.name, self.namespace).module
if self.registry is None:
self.registry = ModuleRegistry()
self.registry.add_hierarchy(registry, self)
if port_spec.type == 'input':
endpoint = PortEndPoint.Destination
else:
endpoint = PortEndPoint.Source
portSpecs = port_spec.spec[1:-1].split(',')
signature = [registry.get_descriptor_from_name_only(spec).module
for spec in portSpecs]
port = Port()
port.name = port_spec.name
port.spec = core.modules.module_registry.PortSpec(signature)
self.registry.add_port(module, endpoint, port)
def init_registry(self, registry_filename=None):
if registry_filename is not None:
self._registry = core.db.io.open_registry(registry_filename)
self._registry.set_global()
else:
self._registry = ModuleRegistry()
self._registry.set_global()
def setup_basic_package():
# setup basic package
basic_package = self.add_package('basic_modules')
self._registry._default_package = basic_package
prefix_dictionary = {'basic_modules': 'core.modules.'}
self.initialize_packages(prefix_dictionary)
setup_basic_package()
self._abstraction_pkg = self.add_package('abstraction', False)
# FIXME need to get this info from the package, but cannot
# do this since controller isn't imported yet
self._abstraction_pkg.identifier = 'local.abstractions'
self._abstraction_pkg.name = 'My SubWorkflows'
self._abstraction_pkg.version = '1.6'
self._registry.add_package(self._abstraction_pkg)
class PackageManager(object):
# # add_package_menu_signal is emitted with a tuple containing the package
# # identifier, package name and the menu item
# add_package_menu_signal = QtCore.SIGNAL("add_package_menu")
# # remove_package_menu_signal is emitted with the package identifier
# remove_package_menu_signal = QtCore.SIGNAL("remove_package_menu")
# # package_error_message_signal is emitted with the package identifier,
# # package name and the error message
# package_error_message_signal = QtCore.SIGNAL("package_error_message_signal")
# # reloading_package_signal is emitted when a package reload has disabled
# # the packages, but has not yet enabled them
# reloading_package_signal = QtCore.SIGNAL("reloading_package_signal")
class DependencyCycle(Exception):
def __init__(self, p1, p2):
self._package_1 = p1
self._package_2 = p2
def __str__(self):
return ("Packages '%s' and '%s' have cyclic dependencies" %
(self._package_1, self._package_2))
class MissingPackage(Exception):
def __init__(self, n):
self._package_name = n
def __str__(self):
return "Package '%s' is missing." % self._package_name
class PackageInternalError(Exception):
def __init__(self, n, d):
self._package_name = n
self._description = d
def __str__(self):
return "Package '%s' has a bug: %s" % (self._package_name,
self._description)
def import_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._packages is not None:
return self._packages
# Imports standard packages directory
conf = self._configuration
old_sys_path = copy.copy(sys.path)
if conf.check('packageDirectory'):
sys.path.insert(0, conf.packageDirectory)
try:
import packages
except ImportError:
debug.critical('ImportError: "packages" sys.path: %s' % sys.path)
raise
finally:
sys.path = old_sys_path
self._packages = packages
return packages
def import_user_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._userpackages is not None:
return self._userpackages
# Imports user packages directory
conf = self._configuration
old_sys_path = copy.copy(sys.path)
if conf.check('userPackageDirectory'):
sys.path.insert(
0, os.path.join(conf.userPackageDirectory, os.path.pardir))
try:
import userpackages
except ImportError:
debug.critical('ImportError: "userpackages" sys.path: %s' %
sys.path)
raise
finally:
sys.path = old_sys_path
self._userpackages = userpackages
return userpackages
def __init__(self, configuration):
"""__init__(configuration: ConfigurationObject) -> PackageManager
configuration is the persistent configuration object of the application.
"""
global _package_manager
if _package_manager:
m = "Package manager can only be constructed once."
raise VistrailsInternalError(m)
_package_manager = self
self._configuration = configuration
self._package_list = {}
self._package_versions = {}
self._dependency_graph = core.data_structures.graph.Graph()
self._registry = None
self._userpackages = None
self._packages = None
self._abstraction_pkg = None
def init_registry(self, registry_filename=None):
if registry_filename is not None:
self._registry = core.db.io.open_registry(registry_filename)
self._registry.set_global()
else:
self._registry = ModuleRegistry()
self._registry.set_global()
def setup_basic_package():
# setup basic package
basic_package = self.add_package('basic_modules')
self._registry._default_package = basic_package
prefix_dictionary = {'basic_modules': 'core.modules.'}
self.initialize_packages(prefix_dictionary)
setup_basic_package()
self._abstraction_pkg = self.add_package('abstraction', False)
# FIXME need to get this info from the package, but cannot
# do this since controller isn't imported yet
self._abstraction_pkg.identifier = 'local.abstractions'
self._abstraction_pkg.name = 'My SubWorkflows'
self._abstraction_pkg.version = '1.6'
self._registry.add_package(self._abstraction_pkg)
def finalize_packages(self):
"""Finalizes all installed packages. Call this only prior to
exiting VisTrails."""
for package in self._package_list.itervalues():
package.finalize()
self._package_list = {}
self._package_versions = {}
global _package_manager
_package_manager = None
def add_package(self, codepath, add_to_package_list=True):
"""Adds a new package to the manager. This does not initialize it.
To do so, call initialize_packages()"""
package = self._registry.create_package(codepath)
if add_to_package_list:
self.add_to_package_list(codepath, package)
return package
def add_to_package_list(self, codepath, package):
self._package_list[codepath] = package
def initialize_abstraction_pkg(self, prefix_dictionary):
if self._abstraction_pkg is None:
raise Exception("Subworkflows packages is None")
self.add_to_package_list(self._abstraction_pkg.codepath,
self._abstraction_pkg)
self.late_enable_package(self._abstraction_pkg.codepath,
prefix_dictionary, False)
def remove_package(self, codepath):
"""remove_package(name): Removes a package from the system."""
pkg = self._package_list[codepath]
self._dependency_graph.delete_vertex(pkg.identifier)
del self._package_versions[pkg.identifier][pkg.version]
if len(self._package_versions[pkg.identifier]) == 0:
del self._package_versions[pkg.identifier]
self.remove_menu_items(pkg)
pkg.finalize()
del self._package_list[codepath]
self._registry.remove_package(pkg)
app = get_vistrails_application()
app.send_notification("package_removed", codepath)
def has_package(self, identifier, version=None):
"""has_package(identifer: string) -> Boolean.
Returns true if given package identifier is present."""
if identifier in self._package_versions:
return (version is None
or version in self._package_versions[identifier])
return False
def look_at_available_package(self, codepath):
"""look_at_available_package(codepath: string) -> Package
Returns a Package object for an uninstalled package. This does
NOT install a package.
"""
return self._registry.create_package(codepath, False)
def get_package(self, identifier, version=None):
package_versions = self._package_versions[identifier]
if version is not None:
return package_versions[version]
max_version = '0'
max_pkg = None
for version, pkg in package_versions.iteritems():
if versions_increasing(max_version, version):
max_version = version
max_pkg = pkg
return max_pkg
def get_package_by_codepath(self, codepath):
"""get_package_by_codepath(codepath: string) -> Package.
Returns a package with given codepath if it is enabled,
otherwise throws exception
"""
if codepath not in self._package_list:
raise self.MissingPackage(codepath)
else:
return self._package_list[codepath]
def get_package_by_identifier(self, identifier):
"""get_package_by_identifier(identifier: string) -> Package.
Returns a package with given identifier if it is enabled,
otherwise throws exception
"""
if identifier not in self._registry.packages:
raise self.MissingPackage(identifier)
return self._registry.packages[identifier]
def get_package_configuration(self, codepath):
"""get_package_configuration(codepath: string) ->
ConfigurationObject or None
Returns the configuration object for the package, if existing,
or None. Throws MissingPackage if package doesn't exist.
"""
pkg = self.get_package_by_codepath(codepath)
if not hasattr(pkg.module, 'configuration'):
return None
else:
c = pkg.module.configuration
if not isinstance(c, ConfigurationObject):
d = "'configuration' attribute should be a ConfigurationObject"
raise self.PackageInternalError(codepath, d)
return c
def check_dependencies(self, package, deps):
# want to check that necessary version also exists, if specified
missing_deps = []
for dep in deps:
min_version = None
max_version = None
if type(dep) == tuple:
identifier = dep[0]
if len(dep) > 1:
min_version = dep[1]
if len(dep) > 2:
max_version = dep[2]
else:
identifier = dep
if identifier not in self._package_versions:
missing_deps.append((identifier, None, None))
else:
if min_version is None and max_version is None:
continue
found_version = False
for version, pkg in \
self._package_versions[identifier].iteritems():
if ((min_version is None
or versions_increasing(min_version, version)) and
(max_version is None
or versions_increasing(version, max_version))):
found_version = True
if not found_version:
missing_deps.append((identifier, min_version, max_version))
if len(missing_deps) > 0:
raise Package.MissingDependency(package, missing_deps)
return True
def add_dependencies(self, package):
"""add_dependencies(package) -> None. Register all
dependencies a package contains by calling the appropriate
callback.
Does not add multiple dependencies - if a dependency is already there,
add_dependencies ignores it.
"""
deps = package.dependencies()
# FIXME don't hardcode this
from core.modules.basic_modules import identifier as basic_pkg
if package.identifier != basic_pkg:
deps.append(basic_pkg)
self.check_dependencies(package, deps)
for dep in deps:
if type(dep) == tuple:
dep_name = dep[0]
else:
dep_name = dep
if not self._dependency_graph.has_edge(package.identifier,
dep_name):
self._dependency_graph.add_edge(package.identifier, dep_name)
def late_enable_package(self,
package_codepath,
prefix_dictionary={},
needs_add=True):
"""late_enable_package enables a package 'late', that is,
after VisTrails initialization. All dependencies need to be
already enabled.
"""
if needs_add:
if package_codepath in self._package_list:
msg = 'duplicate package identifier: %s' % package_codepath
raise VistrailsInternalError(msg)
self.add_package(package_codepath)
pkg = self.get_package_by_codepath(package_codepath)
try:
pkg.load(prefix_dictionary.get(pkg.codepath, None))
except Exception, e:
# invert self.add_package
del self._package_list[package_codepath]
raise
self._dependency_graph.add_vertex(pkg.identifier)
if pkg.identifier not in self._package_versions:
self._package_versions[pkg.identifier] = {}
self._package_versions[pkg.identifier][pkg.version] = pkg
try:
self.add_dependencies(pkg)
#check_requirements is now called in pkg.initialize()
#pkg.check_requirements()
self._registry.initialize_package(pkg)
self._registry.signals.emit_new_package(pkg.identifier, True)
app = get_vistrails_application()
app.send_notification("package_added", package_codepath)
self.add_menu_items(pkg)
except Exception, e:
del self._package_versions[pkg.identifier][pkg.version]
if len(self._package_versions[pkg.identifier]) == 0:
del self._package_versions[pkg.identifier]
self._dependency_graph.delete_vertex(pkg.identifier)
# invert self.add_package
del self._package_list[package_codepath]
# if we adding the package to the registry, make sure we
# remove it if initialization fails
try:
self._registry.remove_package(pkg)
except MissingPackage:
pass
raise e
class PackageManager(object):
# # add_package_menu_signal is emitted with a tuple containing the package
# # identifier, package name and the menu item
# add_package_menu_signal = QtCore.SIGNAL("add_package_menu")
# # remove_package_menu_signal is emitted with the package identifier
# remove_package_menu_signal = QtCore.SIGNAL("remove_package_menu")
# # package_error_message_signal is emitted with the package identifier,
# # package name and the error message
# package_error_message_signal = QtCore.SIGNAL("package_error_message_signal")
# # reloading_package_signal is emitted when a package reload has disabled
# # the packages, but has not yet enabled them
# reloading_package_signal = QtCore.SIGNAL("reloading_package_signal")
class DependencyCycle(Exception):
def __init__(self, p1, p2):
self._package_1 = p1
self._package_2 = p2
def __str__(self):
return ("Packages '%s' and '%s' have cyclic dependencies" %
(self._package_1,
self._package_2))
class MissingPackage(Exception):
def __init__(self, n):
self._package_name = n
def __str__(self):
return "Package '%s' is missing." % self._package_name
class PackageInternalError(Exception):
def __init__(self, n, d):
self._package_name = n
self._description = d
def __str__(self):
return "Package '%s' has a bug: %s" % (self._package_name,
self._description)
def import_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._packages is not None:
return self._packages
# Imports standard packages directory
conf = self._configuration
old_sys_path = copy.copy(sys.path)
if conf.check('packageDirectory'):
sys.path.insert(0, conf.packageDirectory)
try:
import packages
except ImportError:
debug.critical('ImportError: "packages" sys.path: %s' % sys.path)
raise
finally:
sys.path = old_sys_path
self._packages = packages
return packages
def import_user_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._userpackages is not None:
return self._userpackages
# Imports user packages directory
conf = self._configuration
old_sys_path = copy.copy(sys.path)
if conf.check('userPackageDirectory'):
sys.path.insert(0, os.path.join(conf.userPackageDirectory,
os.path.pardir))
try:
import userpackages
except ImportError:
debug.critical('ImportError: "userpackages" sys.path: %s' % sys.path)
raise
finally:
sys.path = old_sys_path
self._userpackages = userpackages
return userpackages
def __init__(self, configuration):
"""__init__(configuration: ConfigurationObject) -> PackageManager
configuration is the persistent configuration object of the application.
"""
global _package_manager
if _package_manager:
m = "Package manager can only be constructed once."
raise VistrailsInternalError(m)
_package_manager = self
self._configuration = configuration
self._package_list = {}
self._package_versions = {}
self._dependency_graph = core.data_structures.graph.Graph()
self._registry = None
self._userpackages = None
self._packages = None
self._abstraction_pkg = None
def init_registry(self, registry_filename=None):
if registry_filename is not None:
self._registry = core.db.io.open_registry(registry_filename)
self._registry.set_global()
else:
self._registry = ModuleRegistry()
self._registry.set_global()
def setup_basic_package():
# setup basic package
basic_package = self.add_package('basic_modules')
self._registry._default_package = basic_package
prefix_dictionary = {'basic_modules': 'core.modules.'}
self.initialize_packages(prefix_dictionary)
setup_basic_package()
self._abstraction_pkg = self.add_package('abstraction', False)
# FIXME need to get this info from the package, but cannot
# do this since controller isn't imported yet
self._abstraction_pkg.identifier = 'local.abstractions'
self._abstraction_pkg.name = 'My SubWorkflows'
self._abstraction_pkg.version = '1.6'
self._registry.add_package(self._abstraction_pkg)
def finalize_packages(self):
"""Finalizes all installed packages. Call this only prior to
exiting VisTrails."""
for package in self._package_list.itervalues():
package.finalize()
self._package_list = {}
self._package_versions = {}
global _package_manager
_package_manager = None
def add_package(self, codepath, add_to_package_list=True):
"""Adds a new package to the manager. This does not initialize it.
To do so, call initialize_packages()"""
package = self._registry.create_package(codepath)
if add_to_package_list:
self.add_to_package_list(codepath, package)
app = get_vistrails_application()
app.send_notification("package_added", codepath)
return package
def add_to_package_list(self, codepath, package):
self._package_list[codepath] = package
def initialize_abstraction_pkg(self, prefix_dictionary):
if self._abstraction_pkg is None:
raise Exception("Subworkflows packages is None")
self.add_to_package_list(self._abstraction_pkg.codepath,
self._abstraction_pkg)
self.late_enable_package(self._abstraction_pkg.codepath,
prefix_dictionary, False)
def remove_package(self, codepath):
"""remove_package(name): Removes a package from the system."""
pkg = self._package_list[codepath]
self._dependency_graph.delete_vertex(pkg.identifier)
del self._package_versions[pkg.identifier][pkg.version]
if len(self._package_versions[pkg.identifier]) == 0:
del self._package_versions[pkg.identifier]
self.remove_menu_items(pkg)
pkg.finalize()
del self._package_list[codepath]
self._registry.remove_package(pkg)
app = get_vistrails_application()
app.send_notification("package_removed", codepath)
def has_package(self, identifier, version=None):
"""has_package(identifer: string) -> Boolean.
Returns true if given package identifier is present."""
if identifier in self._package_versions:
return (version is None or
version in self._package_versions[identifier])
return False
def look_at_available_package(self, codepath):
"""look_at_available_package(codepath: string) -> Package
Returns a Package object for an uninstalled package. This does
NOT install a package.
"""
return self._registry.create_package(codepath, False)
def get_package(self, identifier, version=None):
package_versions = self._package_versions[identifier]
if version is not None:
return package_versions[version]
max_version = '0'
max_pkg = None
for version, pkg in package_versions.iteritems():
if versions_increasing(max_version, version):
max_version = version
max_pkg = pkg
return max_pkg
def get_package_by_codepath(self, codepath):
"""get_package_by_codepath(codepath: string) -> Package.
Returns a package with given codepath if it is enabled,
otherwise throws exception
"""
if codepath not in self._package_list:
raise self.MissingPackage(codepath)
else:
return self._package_list[codepath]
def get_package_by_identifier(self, identifier):
"""get_package_by_identifier(identifier: string) -> Package.
Returns a package with given identifier if it is enabled,
otherwise throws exception
"""
if identifier not in self._registry.packages:
raise self.MissingPackage(identifier)
return self._registry.packages[identifier]
def get_package_configuration(self, codepath):
"""get_package_configuration(codepath: string) ->
ConfigurationObject or None
Returns the configuration object for the package, if existing,
or None. Throws MissingPackage if package doesn't exist.
"""
pkg = self.get_package_by_codepath(codepath)
if not hasattr(pkg.module, 'configuration'):
return None
else:
c = pkg.module.configuration
if not isinstance(c, ConfigurationObject):
d = "'configuration' attribute should be a ConfigurationObject"
raise self.PackageInternalError(codepath, d)
return c
def check_dependencies(self, package, deps):
# want to check that necessary version also exists, if specified
missing_deps = []
for dep in deps:
min_version = None
max_version = None
if type(dep) == tuple:
identifier = dep[0]
if len(dep) > 1:
min_version = dep[1]
if len(dep) > 2:
max_version = dep[2]
else:
identifier = dep
if identifier not in self._package_versions:
missing_deps.append((identifier, None, None))
else:
if min_version is None and max_version is None:
continue
found_version = False
for version, pkg in \
self._package_versions[identifier].iteritems():
if ((min_version is None or
versions_increasing(min_version, version)) and
(max_version is None or
versions_increasing(version, max_version))):
found_version = True
if not found_version:
missing_deps.append((identifier, min_version, max_version))
if len(missing_deps) > 0:
raise Package.MissingDependency(package, missing_deps)
return True
def add_dependencies(self, package):
"""add_dependencies(package) -> None. Register all
dependencies a package contains by calling the appropriate
callback.
Does not add multiple dependencies - if a dependency is already there,
add_dependencies ignores it.
"""
deps = package.dependencies()
# FIXME don't hardcode this
from core.modules.basic_modules import identifier as basic_pkg
if package.identifier != basic_pkg:
deps.append(basic_pkg)
self.check_dependencies(package, deps)
for dep in deps:
if type(dep) == tuple:
dep_name = dep[0]
else:
dep_name = dep
if not self._dependency_graph.has_edge(package.identifier,
dep_name):
self._dependency_graph.add_edge(package.identifier, dep_name)
def late_enable_package(self, package_codepath, prefix_dictionary={},
needs_add=True):
"""late_enable_package enables a package 'late', that is,
after VisTrails initialization. All dependencies need to be
already enabled.
"""
if needs_add:
if package_codepath in self._package_list:
msg = 'duplicate package identifier: %s' % package_codepath
raise VistrailsInternalError(msg)
self.add_package(package_codepath)
pkg = self.get_package_by_codepath(package_codepath)
try:
pkg.load(prefix_dictionary.get(pkg.codepath, None))
except Exception, e:
# invert self.add_package
del self._package_list[package_codepath]
raise
self._dependency_graph.add_vertex(pkg.identifier)
if pkg.identifier not in self._package_versions:
self._package_versions[pkg.identifier] = {}
self._package_versions[pkg.identifier][pkg.version] = pkg
try:
self.add_dependencies(pkg)
#check_requirements is now called in pkg.initialize()
#pkg.check_requirements()
self._registry.initialize_package(pkg)
# FIXME Empty packages still need to be added, but currently they are not
# because newPackage is typically only called for the first module inside
# a package.
from core.modules.abstraction import identifier as abstraction_identifier
if pkg.identifier == abstraction_identifier:
self._registry.signals.emit_new_package(abstraction_identifier, True)
except Exception, e:
del self._package_versions[pkg.identifier][pkg.version]
if len(self._package_versions[pkg.identifier]) == 0:
del self._package_versions[pkg.identifier]
self._dependency_graph.delete_vertex(pkg.identifier)
# invert self.add_package
del self._package_list[package_codepath]
# if we adding the package to the registry, make sure we
# remove it if initialization fails
try:
self._registry.remove_package(pkg)
except MissingPackage:
pass
raise e
class Module(DBModule):
""" Represents a module from a Pipeline """
##########################################################################
# Constructor and copy
def __init__(self, *args, **kwargs):
DBModule.__init__(self, *args, **kwargs)
if self.cache is None:
self.cache = 1
if self.id is None:
self.id = -1
if self.location is None:
self.location = Location(x=-1.0, y=-1.0)
if self.name is None:
self.name = ''
if self.package is None:
self.package = ''
if self.version is None:
self.version = ''
self.portVisible = set()
self.registry = None
def __copy__(self):
"""__copy__() -> Module - Returns a clone of itself"""
return Module.do_copy(self)
def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
cp = DBModule.do_copy(self, new_ids, id_scope, id_remap)
cp.__class__ = Module
# cp.registry = copy.copy(self.registry)
cp.registry = None
for port_spec in cp.db_portSpecs:
cp.add_port_to_registry(port_spec)
cp.portVisible = copy.copy(self.portVisible)
return cp
@staticmethod
def convert(_module):
_module.__class__ = Module
_module.registry = None
for _port_spec in _module.db_portSpecs:
PortSpec.convert(_port_spec)
_module.add_port_to_registry(_port_spec)
if _module.db_location:
Location.convert(_module.db_location)
for _function in _module.db_functions:
ModuleFunction.convert(_function)
for _annotation in _module.db_get_annotations():
Annotation.convert(_annotation)
_module.portVisible = set()
##########################################################################
id = DBModule.db_id
cache = DBModule.db_cache
annotations = DBModule.db_annotations
location = DBModule.db_location
center = DBModule.db_location
name = DBModule.db_name
label = DBModule.db_name
namespace = DBModule.db_namespace
package = DBModule.db_package
tag = DBModule.db_tag
version = DBModule.db_version
# type check this (list, hash)
def _get_functions(self):
self.db_functions.sort(key=lambda x: x.db_pos)
return self.db_functions
def _set_functions(self, functions):
# want to convert functions to hash...?
self.db_functions = functions
functions = property(_get_functions, _set_functions)
def add_function(self, function):
self.db_add_function(function)
def add_annotation(self, annotation):
self.db_add_annotation(annotation)
def delete_annotation(self, annotation):
self.db_delete_annotation(annotation)
def has_annotation_with_key(self, key):
return self.db_has_annotation_with_key(key)
def get_annotation_by_key(self, key):
return self.db_get_annotation_by_key(key)
def _get_port_specs(self):
return self.db_portSpecs_id_index
port_specs = property(_get_port_specs)
def has_portSpec_with_name(self, name):
return self.db_has_portSpec_with_name(name)
def get_portSpec_by_name(self, name):
return self.db_get_portSpec_by_name(name)
def summon(self):
get = registry.get_descriptor_by_name
result = get(self.package, self.name, self.namespace).module()
if self.cache != 1:
result.is_cacheable = lambda *args: False
if hasattr(result, 'srcPortsOrder'):
result.srcPortsOrder = [p.name for p in self.destinationPorts()]
result.registry = self.registry or registry
return result
def getNumFunctions(self):
"""getNumFunctions() -> int - Returns the number of functions """
return len(self.functions)
def sourcePorts(self):
"""sourcePorts() -> list of Port
Returns list of source (output) ports module supports.
"""
ports = registry.module_source_ports(True, self.package, self.name, self.namespace)
if self.registry:
ports.extend(self.registry.module_source_ports(False, self.package, self.name, self.namespace))
return ports
def destinationPorts(self):
"""destinationPorts() -> list of Port
Returns list of destination (input) ports module supports
"""
ports = registry.module_destination_ports(True, self.package, self.name, self.namespace)
if self.registry:
ports.extend(self.registry.module_destination_ports(False, self.package, self.name, self.namespace))
return ports
def add_port_to_registry(self, port_spec):
module = \
registry.get_descriptor_by_name(self.package, self.name, self.namespace).module
if self.registry is None:
self.registry = ModuleRegistry()
self.registry.add_hierarchy(registry, self)
if port_spec.type == 'input':
endpoint = PortEndPoint.Destination
else:
endpoint = PortEndPoint.Source
portSpecs = port_spec.spec[1:-1].split(',')
signature = [registry.get_descriptor_from_name_only(spec).module
for spec in portSpecs]
port = Port()
port.name = port_spec.name
port.spec = core.modules.module_registry.PortSpec(signature)
self.registry.add_port(module, endpoint, port)
def delete_port_from_registry(self, id):
if not id in self.port_specs:
raise VistrailsInternalError("id missing in port_specs")
portSpec = self.port_specs[id]
portSpecs = portSpec.spec[1:-1].split(',')
signature = [registry.get_descriptor_from_name_only(spec).module
for spec in portSpecs]
port = Port(signature)
port.name = portSpec.name
port.spec = core.modules.module_registry.PortSpec(signature)
module = \
registry.get_descriptor_by_name(self.package, self.name, self.namespace).module
assert isinstance(self.registry, ModuleRegistry)
if portSpec.type == 'input':
self.registry.delete_input_port(module, port.name)
else:
self.registry.delete_output_port(module, port.name)
##########################################################################
# Debugging
def show_comparison(self, other):
if type(other) != type(self):
print "Type mismatch"
print type(self), type(other)
elif self.id != other.id:
print "id mismatch"
print self.id, other.id
elif self.name != other.name:
print "name mismatch"
print self.name, other.name
elif self.cache != other.cache:
print "cache mismatch"
print self.cache, other.cache
elif self.location != other.location:
print "location mismatch"
# FIXME Location has no show_comparison
# self.location.show_comparison(other.location)
elif len(self.functions) != len(other.functions):
print "function length mismatch"
print len(self.functions), len(other.functions)
else:
for f, g in izip(self.functions, other.functions):
if f != g:
print "function mismatch"
f.show_comparison(g)
return
print "No difference found"
assert self == other
##########################################################################
# Operators
def __str__(self):
"""__str__() -> str Returns a string representation of itself. """
return ("(Module '%s' id=%s functions:%s port_specs:%s)@%X" %
(self.name,
self.id,
[str(f) for f in self.functions],
[str(port_spec) for port_spec in self.db_portSpecs],
id(self)))
def __eq__(self, other):
""" __eq__(other: Module) -> boolean
Returns True if self and other have the same attributes. Used by ==
operator.
"""
if type(other) != type(self):
return False
if self.name != other.name:
return False
if self.cache != other.cache:
return False
if self.location != other.location:
return False
if len(self.functions) != len(other.functions):
return False
if len(self.annotations) != len(other.annotations):
return False
for f, g in izip(self.functions, other.functions):
if f != g:
return False
for f, g in izip(self.annotations, other.annotations):
if f != g:
return False
return True
def __ne__(self, other):
return not self.__eq__(other)
def open_registry(filename):
from core.modules.module_registry import ModuleRegistry
registry = db.services.io.open_registry_from_xml(filename)
ModuleRegistry.convert(registry)
return registry
class Group(DBGroup, Module):
##########################################################################
# Constructors and copy
def __init__(self, *args, **kwargs):
if 'pipeline' in kwargs:
kwargs['workflow'] = kwargs['pipeline']
del kwargs['pipeline']
DBGroup.__init__(self, *args, **kwargs)
if self.cache is None:
self.cache = 1
if self.id is None:
self.id = -1
if self.location is None:
self.location = Location(x=-1.0, y=-1.0)
if self.name is None:
self.name = ''
if self.package is None:
self.package = ''
if self.version is None:
self.version = ''
self.portVisible = set()
self._registry = None
def __copy__(self):
return Group.do_copy(self)
def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
cp = DBGroup.do_copy(self, new_ids, id_scope, id_remap)
cp.__class__ = Group
cp._registry = None
# for port_spec in cp.db_portSpecs:
# cp.add_port_to_registry(port_spec)
cp.portVisible = copy.copy(self.portVisible)
return cp
@staticmethod
def convert(_group):
if _group.__class__ == Group:
return
_group.__class__ = Group
_group._registry = None
_group.portVisible = set()
if _group.db_location:
Location.convert(_group.db_location)
if _group.db_workflow:
from core.vistrail.pipeline import Pipeline
Pipeline.convert(_group.db_workflow)
for _function in _group.db_functions:
ModuleFunction.convert(_function)
for _annotation in _group.db_get_annotations():
Annotation.convert(_annotation)
##########################################################################
# Properties
# We need to repeat these here because Module uses DBModule. ...
id = DBGroup.db_id
cache = DBGroup.db_cache
annotations = DBGroup.db_annotations
location = DBGroup.db_location
center = DBGroup.db_location
name = DBGroup.db_name
label = DBGroup.db_name
namespace = DBGroup.db_namespace
package = DBGroup.db_package
tag = DBGroup.db_tag
version = DBGroup.db_version
def summon(self):
# define this so that pipeline is copied over...
pass
def is_group(self):
return True
pipeline = DBGroup.db_workflow
def _get_registry(self):
if not self._registry:
# print 'making registry'
self.make_registry()
return self._registry
registry = property(_get_registry)
# override these from the Module class with defaults
def _get_port_specs(self):
return dict()
port_specs = property(_get_port_specs)
def has_portSpec_with_name(self, name):
return False
def get_portSpec_by_name(self, name):
return None
@staticmethod
def make_port_from_module(module, port_type):
for function in module.functions:
if function.name == 'name':
port_name = function.params[0].strValue
print ' port_name:', port_name
if function.name == 'spec':
port_spec = function.params[0].strValue
#print ' port_spec:', port_spec
port = Port(id=-1,
name=port_name,
type=port_type)
portSpecs = port_spec[1:-1].split(',')
signature = []
for s in portSpecs:
spec = s.split(':', 2)
signature.append(registry.get_descriptor_by_name(*spec).module)
port.spec = core.modules.module_registry.PortSpec(signature)
return port
def make_registry(self):
reg_module = \
registry.get_descriptor_by_name('edu.utah.sci.vistrails.basic',
self.name).module
self._registry = ModuleRegistry()
self._registry.add_hierarchy(registry, self)
for module in self.pipeline.module_list:
print 'module:', module.name
if module.name == 'OutputPort':
port = self.make_port_from_module(module, 'source')
self._registry.add_port(reg_module, PortEndPoint.Source, port)
elif module.name == 'InputPort':
port = self.make_port_from_module(module, 'destination')
self._registry.add_port(reg_module, PortEndPoint.Destination,
port)
def sourcePorts(self):
return self.registry.module_source_ports(False, self.package,
self.name, self.namespace)
def destinationPorts(self):
return self.registry.module_destination_ports(False, self.package,
self.name, self.namespace)
##########################################################################
# Operators
def __str__(self):
"""__str__() -> str - Returns a string representation of an
GroupModule object.
"""
rep = '<group id="%s" abstraction_id="%s" verion="%s">'
rep += str(self.location)
rep += str(self.functions)
rep += str(self.annotations)
rep += '</group>'
return rep % (str(self.id), str(self.abstraction_id),
str(self.version))
def __eq__(self, other):
""" __eq__(other: GroupModule) -> boolean
Returns True if self and other have the same attributes. Used by ==
operator.
"""
if type(other) != type(self):
return False
if self.location != other.location:
return False
if len(self.functions) != len(other.functions):
return False
if len(self.annotations) != len(other.annotations):
return False
for f,g in izip(self.functions, other.functions):
if f != g:
return False
for f,g in izip(self.annotations, other.annotations):
if f != g:
return False
return True
def __ne__(self, other):
return not self.__eq__(other)
class AbstractionModule(DBAbstractionRef):
##########################################################################
# Constructors and copy
def __init__(self, *args, **kwargs):
DBAbstractionRef.__init__(self, *args, **kwargs)
if self.id is None:
self.id = -1
self.portVisible = set()
self._registry = None
self.abstraction = None
# FIXME should we have a registry for an abstraction module?
def __copy__(self):
return AbstractionModule.do_copy(self)
def do_copy(self, new_ids=False, id_scope=None, id_remap=None):
cp = DBAbstractionRef.do_copy(self, new_ids, id_scope, id_remap)
cp.__class__ = AbstractionModule
cp.portVisible = copy.copy(self.portVisible)
cp._registry = self._registry
cp.abstraction = self.abstraction
return cp
@staticmethod
def convert(_abstraction_module):
if _abstraction_module.__class__ == AbstractionModule:
return
_abstraction_module.__class__ = AbstractionModule
if _abstraction_module.db_location:
Location.convert(_abstraction_module.db_location)
for _function in _abstraction_module.db_functions:
ModuleFunction.convert(_function)
for _annotation in _abstraction_module.db_get_annotations():
Annotation.convert(_annotation)
_abstraction_module.portVisible = set()
_abstraction_module._registry = None
_abstraction_module.abstraction = None
##########################################################################
# Properties
id = DBAbstractionRef.db_id
cache = DBAbstractionRef.db_cache
abstraction_id = DBAbstractionRef.db_abstraction_id
location = DBAbstractionRef.db_location
center = DBAbstractionRef.db_location
version = DBAbstractionRef.db_version
tag = DBAbstractionRef.db_name
label = DBAbstractionRef.db_name
name = 'Abstraction'
package = 'edu.utah.sci.vistrails.basic'
namespace = None
annotations = DBAbstractionRef.db_annotations
def _get_functions(self):
self.db_functions.sort(key=lambda x: x.db_pos)
return self.db_functions
def _set_functions(self, functions):
# want to convert functions to hash...?
self.db_functions = functions
functions = property(_get_functions, _set_functions)
def _get_pipeline(self):
from core.vistrail.pipeline import Pipeline
import db.services.vistrail
workflow = db.services.vistrail.materializeWorkflow(self.abstraction,
self.version)
Pipeline.convert(workflow)
return workflow
pipeline = property(_get_pipeline)
def _get_registry(self):
if not self._registry:
self.make_registry()
return self._registry
registry = property(_get_registry)
def add_annotation(self, annotation):
self.db_add_annotation(annotation)
def delete_annotation(self, annotation):
self.db_delete_annotation(annotation)
def has_annotation_with_key(self, key):
return self.db_has_annotation_with_key(key)
def get_annotation_by_key(self, key):
return self.db_get_annotation_by_key(key)
def getNumFunctions(self):
"""getNumFunctions() -> int - Returns the number of functions """
return len(self.functions)
def summon(self):
# we shouldn't ever call this since we're expanding abstractions
return None
@staticmethod
def make_port_from_module(module, port_type):
for function in module.functions:
if function.name == 'name':
port_name = function.params[0].strValue
if function.name == 'spec':
port_spec = function.params[0].strValue
port = Port(id=-1,
name=port_name,
type=port_type)
portSpecs = port_spec[1:-1].split(',')
signature = []
for s in portSpecs:
spec = s.split(':', 2)
signature.append(registry.get_descriptor_by_name(*spec).module)
port.spec = core.modules.module_registry.PortSpec(signature)
return port
def make_registry(self):
reg_module = \
registry.get_descriptor_by_name('edu.utah.sci.vistrails.basic',
self.name).module
self._registry = ModuleRegistry()
self._registry.add_hierarchy(registry, self)
for module in self.pipeline.module_list:
if module.name == 'OutputPort':
port = self.make_port_from_module(module, 'source')
self._registry.add_port(reg_module, PortEndPoint.Source, port)
elif module.name == 'InputPort':
port = self.make_port_from_module(module, 'destination')
self._registry.add_port(reg_module, PortEndPoint.Destination,
port)
def sourcePorts(self):
ports = []
for module in self.pipeline.module_list:
if module.name == 'OutputPort':
ports.append(self.make_port_from_module(module, 'source'))
return ports
def destinationPorts(self):
ports = []
for module in self.pipeline.module_list:
if module.name == 'InputPort':
ports.append(self.make_port_from_module(module, 'destination'))
return ports
##########################################################################
# Operators
def __str__(self):
"""__str__() -> str - Returns a string representation of an
AbstractionModule object.
"""
rep = '<abstraction_module id="%s" abstraction_id="%s" verion="%s">'
rep += str(self.location)
rep += str(self.functions)
rep += str(self.annotations)
rep += '</abstraction_module>'
return rep % (str(self.id), str(self.abstraction_id),
str(self.version))
def __eq__(self, other):
""" __eq__(other: AbstractionModule) -> boolean
Returns True if self and other have the same attributes. Used by ==
operator.
"""
if type(other) != type(self):
return False
if self.location != other.location:
return False
if len(self.functions) != len(other.functions):
return False
if len(self.annotations) != len(other.annotations):
return False
for f,g in izip(self.functions, other.functions):
if f != g:
return False
for f,g in izip(self.annotations, other.annotations):
if f != g:
return False
return True
def __ne__(self, other):
return not self.__eq__(other)
