def registerPlugin(cls, name):
""" Register a new plugin. This function should only be called when
creating a class with __metaclass__=PluginMeta that will trigger this.
"""
m = importlib.import_module(name)
# Define variables
m.Plugin._defineVariables()
m.Domain = cls # Register the domain class for this module
# TODO avoid loading bibtex here and make a lazy load like the rest.
# Load bibtex
m._bibtex = {}
bib = cls.__getSubmodule(name, 'bibtex')
if bib is not None:
if hasattr(bib, "_bibtex"):
print("WARNING FOR DEVELOPERS: %s/%s._bibtex unnecessarily declared. Just the doc string is enough." % (name, "bibtex"))
else:
try:
m._bibtex = pwutils.LazyDict(lambda: pwutils.parseBibTex(bib.__doc__))
except Exception:
pass
cls._plugins[name] = m # Register the name to as a plugin
def registerPlugin(cls, name):
""" Register a new plugin. This function should only be called
when creating a class with __metaclass__=PluginMeta that will
trigger this.
"""
m = importlib.import_module(name)
cls._plugins[name] = m # Register the name to as a plugin
# TODO: Load subclasses (protocols, viewers, wizards)
# Define variables
m.Plugin._defineVariables()
# Load bibtex
m._bibtex = {}
bib = cls.__getSubmodule(name, 'bibtex')
if bib is not None:
try:
m._bibtex = pwutils.parseBibTex(bib.__doc__)
except Exception:
pass
return m
number = "",
pages = "",
year = "",
note = "submitted",
issn = "",
doi = "",
url = "",
author = "Marabini et al.",
keywords = "Contrast transfer function"
}
@article{Sorzano2015b,
title = "Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.",
author = "Sorzano, C O S. and Alcorlo, M. and de la Rosa-Trevin, J. M. and Melero, R. and Foche, I. and Zaldivar-Peraza, A. and del Cano, L. and Vargas, J. and Abrishami, V. and Oton, J. and Marabini, R. and Carazo, J. M.",
journal = "Scientific Reports",
year = "2015",
pages = "14290",
volume = "5",
doi = "http://dx.doi.org/10.1038/srep14290",
url = "http://dx.doi.org/10.1038/srep14290"
}
"""
from pyworkflow.utils import parseBibTex
_bibtex = parseBibTex(_bibtexStr)
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
"""
Bibtex string file for Xmipp package.
"""
_bibtexStr = """
@article{Heymann2007,
title = "Bsoft: Image processing and molecular modeling for electron microscopy ",
journal = "Journal of Structural Biology ",
volume = "157",
number = "1",
pages = "3 - 18",
year = "2007",
issn = "1047-8477",
doi = "http://dx.doi.org/10.1016/j.jsb.2006.06.006",
url = "http://www.sciencedirect.com/science/article/pii/S1047847706001997",
author = "J. Bernard Heymann and David M. Belnap",
keywords = "Single particle analysis Tomography",
}
"""
from pyworkflow.utils import parseBibTex
_bibtex = parseBibTex(_bibtexStr)
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))
version = PluginInfo('scipion-em-%s' % pluginName).pipVersion
bin = PluginInfo('scipion-em-%s' % pluginName).printBinInfoStr()
print("Plugin name: %s, version: %s" % (pluginName, version))
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:
