#!/usr/bin/env python
# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
###
"""
List all existing protocols within Scipion
"""
import sys
from pwem.protocols import (ProtImport, ProtMicrographs, ProtParticles, Prot2D,
Prot3D)
from pyworkflow import Config
from pyworkflow.viewer import Viewer
from pyworkflow.protocol.protocol import Protocol
[docs]def getFirstLine(doc):
""" Get the first non empty line from doc. """
if doc:
for lines in doc.split('\n'):
l = lines.strip()
if l:
return l
return ''
[docs]def hasDoubleInheritance(classRef):
# loop while class has single parent
numParents = len(classRef.__bases__)
while numParents == 1 and classRef is not Protocol:
classRef = classRef.__bases__[0]
numParents = len(classRef.__bases__)
if numParents > 1:
return True
else:
return False
if __name__ == '__main__':
count = 0
withDoc = '--with-doc' in sys.argv
asciidoc = '--asciidoc' in sys.argv
extended = '--extended' in sys.argv
emProtocolsDict = Config.getDomain().getProtocols()
emCategories = [('Imports', ProtImport, []),
('Micrographs', ProtMicrographs, []),
('Particles', ProtParticles, []),
('2D', Prot2D, []),
('3D', Prot3D, [])]
protDict = {}
# Group protocols by package name
for k, v in emProtocolsDict.items():
packageName = v.getClassPackageName()
if packageName not in protDict:
protDict[packageName] = []
if not issubclass(v, Viewer) and not v.isBase():
if extended:
protTuple = (k, v, hasDoubleInheritance(v),
v().allowMpi, v().numberOfMpi,
v().allowThreads, v().numberOfThreads,
v().stepsExecutionMode)
else:
protTuple = (k, v)
protDict[packageName].append(protTuple)
for c in emCategories:
if issubclass(v, c[1]):
c[2].append(protTuple)
def iterGroups(protDict):
groups = list(protDict.keys())
groups.sort(key=lambda x: 1000-len(protDict[x]))
for g in groups:
yield g, protDict[g]
def printProtocols(prots):
protList = [(p[0], p[1], p[1].getClassLabel()) for p in prots]
protList.sort(key=lambda x: x[2])
for k, v, l in protList:
doc = getFirstLine(v.__doc__) if withDoc else ''
print("* link:%s[%s]: %s" % (k, l, doc))
if asciidoc:
print(":toc:\n:toc-placement!:\n\ntoc::[]\n")
print("\n== By Categories\n")
for c in emCategories:
print("\n=== %s\n" % c[0])
printProtocols(c[2])
print("\n== By Packages\n")
for group, prots in iterGroups(protDict):
print("\n=== ", group, "(%d protocols)\n" % len(prots))
printProtocols(prots)
elif withDoc:
for group, prots in iterGroups(protDict):
print("Package: ", group, "(%d protocols)" % len(prots))
for p in prots:
print(" %s ( %s ):" % (p[1].getClassLabel(), p[0]))
print(" ", p[1].__doc__)
print("-" * 100)
else:
if extended:
formatStr = "{:<15}\t{:<35}\t{:<35}" + "\t{:<20}" * 6
print(formatStr.format("PACKAGE", "PROTOCOL",
"LABEL", "DOUBLE_INHERITANCE",
"ALLOWS_MPI", "NUM_MPI",
"ALLOWS_THREADS", "NUM_THREADS",
"STEPS_EXEC_MODE"))
for group, prots in iterGroups(protDict):
for p in prots:
print(formatStr.format(group, p[0],
p[1].getClassLabel(), *p[2:]))
else:
formatStr = "{:<15}\t{:<35}\t{:<35}"
print(formatStr.format("PACKAGE", "PROTOCOL", "LABEL"))
for group, prots in iterGroups(protDict):
for k, v in prots:
print(formatStr.format(group, k, v.getClassLabel()))