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 __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