def __init__(self, **kwargs):
Protocol.__init__(self, **kwargs)
self.lastCheck = datetime.datetime.now()
self.lastIdSeen = 0
self._moviesWithSteps = []
def _insertChild(self, key, child):
if isinstance(child, Set):
child.write()
Protocol._insertChild(self, key, child)
def _insertChild(self, key, child):
if isinstance(child, Set):
child.write()
Protocol._insertChild(self, key, child)
def __init__(self, **kwargs):
Protocol.__init__(self, **kwargs)
def __init__(self, **kwargs):
Protocol.__init__(self, **kwargs)
def __init__(self, **args):
Protocol.__init__(self, **args)
self.stepsExecutionMode = params.STEPS_PARALLEL
def printPluginInfo(pluginName, verbosity):
""" Print info about a given plugin """
showBase = verbosity > 0
subclasses = {}
emCategories = [('Imports', em.ProtImport),
('Micrographs', em.ProtMicrographs),
('Particles', em.ProtParticles), ('2D', em.Prot2D),
('3D', em.Prot3D)]
plugin = Domain.getPlugin(pluginName)
version = PluginInfo('scipion-em-%s' % pluginName).pipVersion
print("Plugin name: %s, version: %s\n" % (pluginName, version))
print("Plugin binaries: ")
env = createEnvironment()
plugin.Plugin.defineBinaries(env)
print(env.printHelp())
# print bibtex
bib, error2 = getSubmodule(pluginName, 'bibtex')
if bib is None:
if error2 is None:
msg = " missing bibtex"
else:
msg = " error -> %s" % error2
else:
print("Plugin references:")
bibtex = pwutils.parseBibTex(bib.__doc__)
for citeStr in bibtex:
text = Protocol()._getCiteText(bibtex[citeStr])
print(text)
# print protocols
sub, error = getSubmodule(pluginName, 'protocols')
if sub is None:
if error is None:
msg = " missing protocols"
else:
msg = " error -> %s" % error
else:
for name in dir(sub):
attr = getattr(sub, name)
if inspect.isclass(attr) and issubclass(attr, Protocol):
# Set this special property used by Scipion
attr._package = plugin
subclasses[name] = attr
print("Plugin protocols:\n")
print("%-35s %-35s %-10s %-s" %
('NAME', 'LABEL', 'CATEGORY', 'DESCRIPTION'))
prots = OrderedDict(sorted(subclasses.items()))
for prot in prots:
label = prots[prot].getClassLabel()
desc = getFirstLine(prots[prot].__doc__)
cat = 'None'
for c in emCategories:
if issubclass(prots[prot], c[1]):
cat = c[0]
if prots[prot].isBase():
cat = 'Base prot'
# skip Base protocols if not requested
if prots[prot].isBase() and not showBase:
continue
else:
print("%-35s %-35s %-10s %-s" % (prot, label, cat, desc))
print("Plugin binaries: %s" % bin)
# print bibtex
bib, error2 = getSubmodule(plugin, pluginName, 'bibtex')
if bib is None:
if error2 is None:
msg = " missing bibtex"
else:
exitWithErrors = True
msg = " error -> %s" % error2
else:
print("Plugin references:")
bibtex = pwutils.parseBibTex(bib.__doc__)
for citeStr in bibtex:
text = Protocol()._getCiteText(bibtex[citeStr])
print(text)
# print protocols
sub, error = getSubmodule(plugin, pluginName, 'protocols')
if sub is None:
if error is None:
msg = " missing protocols"
else:
exitWithErrors = True
msg = " error -> %s" % error
else:
for name in dir(sub):
attr = getattr(sub, name)
if inspect.isclass(attr) and issubclass(attr, Protocol):
def __init__(self, **args):
Protocol.__init__(self, **args)
self.nClass = None