def _selectItemByClass(self, item, className):
if not item.node.isRoot():
data = item.node.pointer.get()
self.toggleItemSelection(
item, isinstance(data,
Domain.getObjects()[className]))
def _loadSet(self, dbName, dbPreffix):
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=dbName, tablePrefix=dbPreffix)
if dbPreffix:
setClassName = "SetOf%ss" % db.getSelfClassName()
else:
setClassName = db.getProperty('self') # get the set class name
# FIXME: Check why the import is here
from pyworkflow.em import Domain
setObj = Domain.getObjects()[setClassName](filename=dbName, prefix=dbPreffix)
return setObj
def checkPlugins():
""" Discover all plugins and print some info.
"""
plugins = Domain.getPlugins()
env = createEnvironment()
print("Plugins:")
for k, plugin in plugins.iteritems():
print("-", plugin.__name__)
plugin.Plugin.defineBinaries(env)
print("\nDefined binaries: ")
print(env.printHelp())
if args.verbosity > 0:
print("Objects")
pwutils.prettyDict(Domain.getObjects())
print("Protocols")
pwutils.prettyDict(Domain.getProtocols())
print("Viewers")
pwutils.prettyDict(Domain.getViewers())
def evalParamCondition(self, paramName):
"""Evaluate if a condition is True for a give param
with the values of a particular Protocol"""
param = self.getParam(paramName)
if not param.hasCondition():
return True
condStr = param.condition.get()
localDict = {}
globalDict = dict(globals())
# FIXME: Check why this import is here
from pyworkflow.em import Domain
globalDict.update(Domain.getObjects())
for t in param._conditionParams:
if self.hasParam(t) or self._protocol.hasAttribute(t):
localDict[t] = self._protocol.getAttributeValue(t)
return eval(condStr, globalDict, localDict)
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))
help="Show plugin summary (protocols, citations, etc). "
"If verbosity > 0, base protocol classes will be shown. ")
add("--install",
nargs='+',
help="Specify a binary version to install. "
"If you pass a second argument, it should a path to the installation"
"and a link will be created. ")
add("-v", "--verbosity", action="count", default=0)
args = parser.parse_args()
pluginName = args.plugin
if not pluginName: # List all plugins
checkPlugins()
else:
plugin = Domain.getPlugin(pluginName)
print("Plugin: %s" % pluginName)
if args.install:
if len(args.install) > 2:
print("ERROR: --install option should have one or two arguments. ")
installBinary(plugin, target=args.install[0])
if len(args.install) > 1:
print(
"TODO: Installation via a symbolic link is not yet implemented. "
)
else:
if args.check:
checkPlugin(pluginName)
if args.info:
""" Get the first non empty line from doc. """
if doc:
for lines in doc.split('\n'):
l = lines.strip()
if l:
return l
return ''
n = len(sys.argv)
if n > 4:
usage("Incorrect number of input parameters")
if n == 1: # List all plugins
plugins = Domain.getPlugins()
print("Plugins:")
for k, v in iteritems(plugins):
print("-", k)
print("Objects")
pwutils.prettyDict(Domain.getObjects())
print("Protocols")
pwutils.prettyDict(Domain.getProtocols())
print("Viewers")
pwutils.prettyDict(Domain.getViewers())
elif n == 2:
if sys.argv[1] in ['-h', '--help', 'help']: