def explore(ctx, name, ids, recalculate=None, **kwargs):
kwargs.update(ctx.parent.objs)
engine = kwargs['engine']
config = kwargs['config']
mod.reflect(engine)
try:
setup.expand_stage_pattern(name, 'recalculate', kwargs)
setup.expand_stage_pattern(name, 'skip_stage', kwargs)
except introspect.UnknownStageError as err:
click.secho("Unknown stage %s" % err.args, err=True, fg='red')
ctx.exit(1)
if not ids:
ids = setup.pdbs(config, kwargs)
kwargs['exclude'] = kwargs.get('skip_stage')
dispatcher = Dispatcher(name, config, sessionmaker(engine), **kwargs)
result = []
for stage in dispatcher.stages(name):
recalc = ''
if recalculate is True or stage.name in recalculate:
recalc = 'Will Recalculate'
result.append((stage.name, recalc))
formatter = click.HelpFormatter(width=90)
formatter.write_dl(result)
click.echo(formatter.getvalue(), nl=False)
def explore(ctx, name, ids, recalculate=None, **kwargs):
kwargs.update(ctx.parent.objs)
engine = kwargs['engine']
config = kwargs['config']
mod.reflect(engine)
try:
setup.expand_stage_pattern(name, 'recalculate', kwargs)
setup.expand_stage_pattern(name, 'skip_stage', kwargs)
except introspect.UnknownStageError as err:
click.secho("Unknown stage %s" % err.args, err=True, fg='red')
ctx.exit(1)
if not ids:
ids = setup.pdbs(config, kwargs)
kwargs['exclude'] = kwargs.get('skip_stage')
dispatcher = Dispatcher(name, config, sessionmaker(engine), **kwargs)
result = []
for stage in dispatcher.stages(name):
recalc = ''
if recalculate is True or stage.name in recalculate:
recalc = 'Will Recalculate'
result.append((stage.name, recalc))
formatter = click.HelpFormatter(width=90)
formatter.write_dl(result)
click.echo(formatter.getvalue(), nl=False)
def test_can_exclude_stages_in_container(self):
dispatcher = Dispatcher('motifs.loader', CONFIG, Session,
skip_dependencies=True,
exclude=['motifs.release'])
val = [o.name for o in dispatcher.stages('motifs.loader')]
assert 'motifs.release' not in val
assert val == [
'motifs.discrepancies',
'motifs.info',
'motifs.assignments',
'motifs.loop_order',
'motifs.loop_positions',
]
class StagesTest(ut.TestCase):
def setUp(self):
self.dispatcher = Dispatcher('units.info', CONFIG, Session)
def stages(self, *args):
return [o.name for o in self.dispatcher.stages(*args)]
def test_can_load_requested_stages(self):
assert self.stages('units.info') == [
'download',
'pdbs.info',
'units.info',
]
def test_when_skipping_produces_container_stages_in_correct_order(self):
self.dispatcher.skip_dependencies = True
assert self.stages('units.loader') == [
'units.info',
'units.centers',
'units.coordinates',
'units.distances',
'units.incomplete',
'units.rotation',
]
def test_it_can_load_stage_container(self):
assert self.stages('units.loader') == [
'download',
'pdbs.info',
'units.info',
'units.centers',
'units.coordinates',
'units.distances',
'units.incomplete',
'units.rotation',
]
def test_can_exclude_specific_stages(self):
self.dispatcher.exclude = set(['units.distances'])
val = self.stages('units.loader')
assert 'units.distances' not in val
assert val == [
'download',
'pdbs.info',
'units.info',
'units.centers',
'units.coordinates',
'units.incomplete',
'units.rotation',
]
def test_can_exclude_a_stage_collection(self):
self.dispatcher.exclude = set(['pdbs.loader', 'units.distances'])
assert self.stages('units.loader') == [
'download',
'units.info',
'units.centers',
'units.coordinates',
'units.incomplete',
'units.rotation',
]
@pytest.mark.xfail(reason="Haven't worked on yet")
def test_complains_if_nothing_to_run(self):
self.dispatcher.skip_dependencies = True
self.dispatcher.exclude.add('units.info')
with pytest.raises(core.InvalidState):
self.stages('units.info')
def test_can_get_one_stage_built(self):
self.dispatcher.skip_dependencies = True
assert self.stages('units.info') == ['units.info']
def test_running_with_nested_container_dependencies(self):
val = self.stages('ife.loader')
assert val.index('interactions.pairwise') < val.index('ife.info')
assert val == [
'download',
'pdbs.info',
'export.cifatom',
'pdbs.obsolete',
'units.info',
'chains.info',
'mat_files',
'units.centers',
'units.coordinates',
'units.distances',
'units.incomplete',
'units.rotation',
'interactions.flanking',
'interactions.pairwise',
'species_mapping',
'chains.species',
'interactions.summary',
'ife.info',
]