def convert(_group):
if _group.__class__ == Group:
return
_group.__class__ = Group
if _group.db_location:
Location.convert(_group.db_location)
if _group.db_workflow:
from vistrails.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)
_group.set_defaults()
def get_workflow_diff_with_connections(vt_pair_1, vt_pair_2):
"""get_workflow_diff_with_connections
Similar to get_workflow_diff but with connection pairings.
"""
from vistrails.core.vistrail.pipeline import Pipeline
(v1, v2, m_pairs, m_heuristic, v1_only, v2_only, param_changes, \
c_pairs, c_heuristic, c1_only, c2_only) = \
vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2, False)
Pipeline.convert(v1)
Pipeline.convert(v2)
return (v1, v2, m_pairs, m_heustric, v1_only, v2_only, param_changes,
c_pairs, c_heuristic, c1_only, c2_only)
def get_workflow_diff(vt_pair_1, vt_pair_2):
"""get_workflow_diff( tuple(Vistrail, id), tuple(Vistrail, id) ) ->
Pipeline, Pipeline, [tuple(id, id)], [tuple(id, id)],
[id], [id], [tuple(id, id, list)]
Return a difference between two workflows referenced as vistrails.
"""
from vistrails.core.vistrail.pipeline import Pipeline
(v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes, \
_, _, _, _) = \
vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2, True)
Pipeline.convert(v1)
Pipeline.convert(v2)
return (v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes)
def get_workflow_diff_with_connections(vt_pair_1, vt_pair_2):
"""get_workflow_diff_with_connections
Similar to get_workflow_diff but with connection pairings.
"""
from vistrails.core.vistrail.pipeline import Pipeline
(v1, v2, m_pairs, m_heuristic, v1_only, v2_only, param_changes,
cparam_changes, annot_changes, c_pairs, c_heuristic, c1_only, c2_only) =\
vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2,
False)
Pipeline.convert(v1)
Pipeline.convert(v2)
return (v1, v2, m_pairs, m_heuristic, v1_only, v2_only, param_changes,
cparam_changes, annot_changes, c_pairs, c_heuristic, c1_only,
c2_only)
def convert(_group):
if _group.__class__ == Group:
return
_group.__class__ = Group
if _group.db_location:
Location.convert(_group.db_location)
if _group.db_workflow:
from vistrails.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)
for _control_parameter in _group.db_get_controlParameters():
ModuleControlParam.convert(_control_parameter)
_group.set_defaults()
def get_workflow_diff(vt_pair_1, vt_pair_2):
"""get_workflow_diff( tuple(Vistrail, id), tuple(Vistrail, id) ) ->
Pipeline, Pipeline, [tuple(id, id)], [tuple(id, id)],
[id], [id], [tuple(id, id, list)]
Return a difference between two workflows referenced as vistrails.
"""
from vistrails.core.vistrail.pipeline import Pipeline
(v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes,
cparam_changes, annot_changes, _, _, _, _) = \
vistrails.db.services.vistrail.getWorkflowDiff(vt_pair_1, vt_pair_2,
True)
Pipeline.convert(v1)
Pipeline.convert(v2)
return (v1, v2, pairs, heuristic_pairs, v1_only, v2_only, param_changes,
cparam_changes, annot_changes)
def serialize_module(self, module):
"""
Serializes a module to be executed in parallel.
"""
def process_group(group):
group.pipeline.id = None
for module in group.pipeline.module_list:
if module.is_group():
process_group(module)
pipeline = Pipeline(version=vistrails.db.versions.currentVersion)
if module.is_group():
process_group(module)
module = module.do_copy()
pipeline.add_module(module)
return serialize(pipeline)
def serialize_module(self, module):
"""
Serializes a module to be executed in parallel.
"""
def process_group(group):
group.pipeline.id = None
for module in group.pipeline.module_list:
if module.is_group():
process_group(module)
pipeline = Pipeline(version=vistrails.db.versions.currentVersion)
if module.is_group():
process_group(module)
module = module.do_copy()
pipeline.add_module(module)
return serialize(pipeline)
def open_workflow(filename):
from vistrails.core.vistrail.pipeline import Pipeline
workflow = vistrails.db.services.io.open_workflow_from_xml(filename)
Pipeline.convert(workflow)
return workflow
def get_workflow(vt, version):
from vistrails.core.vistrail.pipeline import Pipeline
workflow = vistrails.db.services.vistrail.materializeWorkflow(vt, version)
Pipeline.convert(workflow)
return workflow
def __init__(self, parent=None):
QPipelineView.__init__(self, parent)
self.setBackgroundBrush(CurrentTheme.QUERY_BACKGROUND_BRUSH)
self.scene().current_pipeline = Pipeline()
self.query_controller = None
def execute(modules, connections=[], add_port_specs=[],
enable_pkg=True, full_results=False):
"""Build a pipeline and execute it.
This is useful to simply build a pipeline in a test case, and run it. When
doing that, intercept_result() can be used to check the results of each
module.
modules is a list of module tuples describing the modules to be created,
with the following format:
[('ModuleName', 'package.identifier', [
# Functions
('port_name', [
# Function parameters
('Signature', 'value-as-string'),
]),
])]
connections is a list of tuples describing the connections to make, with
the following format:
[
(source_module_index, 'source_port_name',
dest_module_index, 'dest_module_name'),
]
add_port_specs is a list of specs to add to modules, with the following
format:
[
(mod_id, 'input'/'output', 'portname',
'(port_sig)'),
]
It is useful to test modules that can have custom ports through a
configuration widget.
The function returns the 'errors' dict it gets from the interpreter, so you
should use a construct like self.assertFalse(execute(...)) if the execution
is not supposed to fail.
For example, this creates (and runs) an Integer module with its value set
to 44, connected to a PythonCalc module, connected to a StandardOutput:
self.assertFalse(execute([
('Float', 'org.vistrails.vistrails.basic', [
('value', [('Float', '44.0')]),
]),
('PythonCalc', 'org.vistrails.vistrails.pythoncalc', [
('value2', [('Float', '2.0')]),
('op', [('String', '-')]),
]),
('StandardOutput', 'org.vistrails.vistrails.basic', []),
],
[
(0, 'value', 1, 'value1'),
(1, 'value', 2, 'value'),
]))
"""
from vistrails.core.db.locator import XMLFileLocator
from vistrails.core.modules.module_registry import MissingPackage
from vistrails.core.packagemanager import get_package_manager
from vistrails.core.utils import DummyView
from vistrails.core.vistrail.connection import Connection
from vistrails.core.vistrail.module import Module
from vistrails.core.vistrail.module_function import ModuleFunction
from vistrails.core.vistrail.module_param import ModuleParam
from vistrails.core.vistrail.pipeline import Pipeline
from vistrails.core.vistrail.port import Port
from vistrails.core.vistrail.port_spec import PortSpec
from vistrails.core.interpreter.noncached import Interpreter
pm = get_package_manager()
port_spec_per_module = {} # mod_id -> [portspec: PortSpec]
j = 0
for i, (mod_id, inout, name, sig) in enumerate(add_port_specs):
mod_specs = port_spec_per_module.setdefault(mod_id, [])
ps = PortSpec(id=i,
name=name,
type=inout,
sigstring=sig,
sort_key=-1)
for psi in ps.port_spec_items:
psi.id = j
j += 1
mod_specs.append(ps)
pipeline = Pipeline()
module_list = []
for i, (name, identifier, functions) in enumerate(modules):
function_list = []
try:
pkg = pm.get_package(identifier)
except MissingPackage:
if not enable_pkg:
raise
pkg = pm.identifier_is_available(identifier)
if pkg:
pm.late_enable_package(pkg.codepath)
pkg = pm.get_package(identifier)
for func_name, params in functions:
param_list = []
for param_type, param_val in params:
param_list.append(ModuleParam(type=param_type,
val=param_val))
function_list.append(ModuleFunction(name=func_name,
parameters=param_list))
name = name.rsplit('|', 1)
if len(name) == 2:
namespace, name = name
else:
namespace = None
name, = name
module = Module(name=name,
namespace=namespace,
package=identifier,
version=pkg.version,
id=i,
functions=function_list)
for port_spec in port_spec_per_module.get(i, []):
module.add_port_spec(port_spec)
pipeline.add_module(module)
module_list.append(module)
for i, (sid, sport, did, dport) in enumerate(connections):
s_sig = module_list[sid].get_port_spec(sport, 'output').sigstring
d_sig = module_list[did].get_port_spec(dport, 'input').sigstring
pipeline.add_connection(Connection(
id=i,
ports=[
Port(id=i*2,
type='source',
moduleId=sid,
name=sport,
signature=s_sig),
Port(id=i*2+1,
type='destination',
moduleId=did,
name=dport,
signature=d_sig),
]))
interpreter = Interpreter.get()
result = interpreter.execute(
pipeline,
locator=XMLFileLocator('foo.xml'),
current_version=1,
view=DummyView())
if full_results:
return result
else:
# Allows to do self.assertFalse(execute(...))
return result.errors
def execute(modules,
connections=[],
add_port_specs=[],
enable_pkg=True,
full_results=False):
"""Build a pipeline and execute it.
This is useful to simply build a pipeline in a test case, and run it. When
doing that, intercept_result() can be used to check the results of each
module.
modules is a list of module tuples describing the modules to be created,
with the following format:
[('ModuleName', 'package.identifier', [
# Functions
('port_name', [
# Function parameters
('Signature', 'value-as-string'),
]),
])]
connections is a list of tuples describing the connections to make, with
the following format:
[
(source_module_index, 'source_port_name',
dest_module_index, 'dest_module_name'),
]
add_port_specs is a list of specs to add to modules, with the following
format:
[
(mod_id, 'input'/'output', 'portname',
'(port_sig)'),
]
It is useful to test modules that can have custom ports through a
configuration widget.
The function returns the 'errors' dict it gets from the interpreter, so you
should use a construct like self.assertFalse(execute(...)) if the execution
is not supposed to fail.
For example, this creates (and runs) an Integer module with its value set
to 44, connected to a PythonCalc module, connected to a StandardOutput:
self.assertFalse(execute([
('Float', 'org.vistrails.vistrails.basic', [
('value', [('Float', '44.0')]),
]),
('PythonCalc', 'org.vistrails.vistrails.pythoncalc', [
('value2', [('Float', '2.0')]),
('op', [('String', '-')]),
]),
('StandardOutput', 'org.vistrails.vistrails.basic', []),
],
[
(0, 'value', 1, 'value1'),
(1, 'value', 2, 'value'),
]))
"""
from vistrails.core.db.locator import XMLFileLocator
from vistrails.core.modules.module_registry import MissingPackage
from vistrails.core.packagemanager import get_package_manager
from vistrails.core.utils import DummyView
from vistrails.core.vistrail.connection import Connection
from vistrails.core.vistrail.module import Module
from vistrails.core.vistrail.module_function import ModuleFunction
from vistrails.core.vistrail.module_param import ModuleParam
from vistrails.core.vistrail.pipeline import Pipeline
from vistrails.core.vistrail.port import Port
from vistrails.core.vistrail.port_spec import PortSpec
from vistrails.core.interpreter.noncached import Interpreter
pm = get_package_manager()
port_spec_per_module = {} # mod_id -> [portspec: PortSpec]
j = 0
for i, (mod_id, inout, name, sig) in enumerate(add_port_specs):
mod_specs = port_spec_per_module.setdefault(mod_id, [])
ps = PortSpec(id=i, name=name, type=inout, sigstring=sig, sort_key=-1)
for psi in ps.port_spec_items:
psi.id = j
j += 1
mod_specs.append(ps)
pipeline = Pipeline()
module_list = []
for i, (name, identifier, functions) in enumerate(modules):
function_list = []
try:
pkg = pm.get_package(identifier)
except MissingPackage:
if not enable_pkg:
raise
dep_graph = pm.build_dependency_graph([identifier])
for pkg_id in pm.get_ordered_dependencies(dep_graph):
pkg = pm.identifier_is_available(pkg_id)
if pkg is None:
raise
pm.late_enable_package(pkg.codepath)
pkg = pm.get_package(identifier)
for func_name, params in functions:
param_list = []
for j, (param_type, param_val) in enumerate(params):
param_list.append(
ModuleParam(pos=j, type=param_type, val=param_val))
function_list.append(
ModuleFunction(name=func_name, parameters=param_list))
name = name.rsplit('|', 1)
if len(name) == 2:
namespace, name = name
else:
namespace = None
name, = name
module = Module(name=name,
namespace=namespace,
package=identifier,
version=pkg.version,
id=i,
functions=function_list)
for port_spec in port_spec_per_module.get(i, []):
module.add_port_spec(port_spec)
pipeline.add_module(module)
module_list.append(module)
for i, (sid, sport, did, dport) in enumerate(connections):
s_sig = module_list[sid].get_port_spec(sport, 'output').sigstring
d_sig = module_list[did].get_port_spec(dport, 'input').sigstring
pipeline.add_connection(
Connection(id=i,
ports=[
Port(id=i * 2,
type='source',
moduleId=sid,
name=sport,
signature=s_sig),
Port(id=i * 2 + 1,
type='destination',
moduleId=did,
name=dport,
signature=d_sig),
]))
interpreter = Interpreter.get()
result = interpreter.execute(pipeline,
locator=XMLFileLocator('foo.xml'),
current_version=1,
view=DummyView())
if full_results:
return result
else:
# Allows to do self.assertFalse(execute(...))
return result.errors