def populateProtTree(tree, obj):
emProtocolsDict = em.getProtocols()
for sub in obj:
text = sub.text.get()
value = sub.value.get(text)
tag = sub.tag.get('')
icon = sub.icon.get('')
openItem = sub.openItem.get()
item = TreeItem(text, tag, icon, openItem)
tree.childs.append(item)
# If have tag 'protocol_base', fill dynamically with protocol sub-classes
protClassName = value.split('.')[-1] # Take last part
if sub.value.hasValue() and tag == 'protocol_base':
prot = emProtocolsDict.get(protClassName, None)
if prot is not None:
for k, v in emProtocolsDict.iteritems():
if not v is prot and issubclass(v, prot):
protItem = TreeItem(k, 'protocol_class',
'python_file.gif', None,
protClassName, v)
item.childs.append(protItem)
else:
item.protClass = protClassName
populateProtTree(item, sub)
def loadProtocolProject(request, requestType=POST):
""" Retrieve the project and protocol from this request.
Return:
(project, protocol) tuple
Parameters
----------
requestType
request
"""
requestDict = getattr(request, requestType)
protId = requestDict.get("protocolId")
protClass = requestDict.get("protocolClass")
# Load the project
project = loadProject(request)
# Create the protocol object
if protId and protId != 'None': # Case of existing protocol
protId = requestDict.get('protocolId', None)
protocol = project.getProtocol(int(protId))
# Remove this and create loadProtocol method in project class
protocol.setProject(project)
# Create a new protocol (added from the menu)
else:
protocolClass = em.getProtocols().get(protClass, None)
protocol = project.newProtocol(protocolClass)
loadProtocolConf(protocol)
return project, protocol
def loadProtocolProject(request, requestType='POST'):
""" Retrieve the project and protocol from this request.
Return:
(project, protocol) tuple
"""
requestDict = getattr(request, requestType)
projectName = request.session['projectName']
#print "projectName %s"%projectName
protId = requestDict.get("protocolId")
protClass = requestDict.get("protocolClass")
# Load the project
project = loadProject(request)
# Create the protocol object
if protId and protId != 'None': # Case of new protocol
protId = requestDict.get('protocolId', None)
protocol = project.getProtocol(int(protId))
# Remove this and create loadProtocol method in project class
protocol.setProject(project)
else:
protocolClass = em.getProtocols().get(protClass, None)
protocol = project.newProtocol(protocolClass)
return (project, protocol)
def loadProtocolProject(request, requestType='POST'):
""" Retrieve the project and protocol from this request.
Return:
(project, protocol) tuple
"""
requestDict = getattr(request, requestType)
projectName = request.session['projectName']
#print "projectName %s"%projectName
protId = requestDict.get("protocolId")
protClass = requestDict.get("protocolClass")
# Load the project
project = loadProject(request)
# Create the protocol object
if protId and protId != 'None': # Case of new protocol
protId = requestDict.get('protocolId', None)
protocol = project.getProtocol(int(protId))
# Remove this and create loadProtocol method in project class
protocol.setProject(project)
else:
protocolClass = em.getProtocols().get(protClass, None)
protocol = project.newProtocol(protocolClass)
return (project, protocol)
def browse_protocol_class(request):
if request.is_ajax():
protClassName = request.GET.get('protClassName')
from pyworkflow.em import findSubClasses, getProtocols
objs = findSubClasses(getProtocols(), protClassName).keys()
jsonStr = json.dumps({'objects' : objs},ensure_ascii=False)
return HttpResponse(jsonStr, mimetype='application/javascript')
def browse_protocol_class(request):
if request.is_ajax():
protClassName = request.GET.get('protClassName')
from pyworkflow.em import findSubClasses, getProtocols
objs = findSubClasses(getProtocols(), protClassName).keys()
jsonStr = json.dumps({'objects': objs}, ensure_ascii=False)
return HttpResponse(jsonStr, mimetype='application/javascript')
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
#TODO: REMOVE THE USE OF globals() here
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
return SqliteMapper(sqliteFn, classesDict)
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
#TODO: REMOVE THE USE OF globals() here
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
return SqliteMapper(sqliteFn, classesDict)
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
classesDict = pwobj.Dict(default=pwprot.LegacyProtocol)
classesDict.update(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
return SqliteMapper(sqliteFn, classesDict)
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
mapper = SqliteMapper(sqliteFn, classesDict)
if not self.chdir:
mapper.setWorkingDir(self.path)
return mapper
def get_protocols(request):
search = request.GET.get('search', None)
result = []
emProtocolsDict = getProtocols()
for key, prot in emProtocolsDict.iteritems():
label = prot.getClassLabel()
className = prot.__name__
if search is None or search in label:
result.append((label, className))
jsonStr = json.dumps(result, ensure_ascii=False)
return HttpResponse(jsonStr, mimetype='application/javascript')
def get_protocols(request):
search = request.GET.get('search', None)
result = []
emProtocolsDict = getProtocols()
for key, prot in emProtocolsDict.iteritems():
label = prot.getClassLabel()
className = prot.__name__
if search is None or search in label:
result.append((label, className))
jsonStr = json.dumps(result, ensure_ascii=False)
return HttpResponse(jsonStr, mimetype='application/javascript')
def addItem(item):
# If it is a protocol
if item["tag"] == "protocol":
# Get the class name and then if it is disabled
protClassName = item["value"]
protClass = em.getProtocols().get(protClassName)
if protClass is None:
return False
else:
return not protClass.isDisabled()
else:
return True
def loadProtocols(self, filename=None, jsonStr=None):
""" Load protocols generated in the same format as self.exportProtocols.
Params:
filename: the path of the file where to read the workflow.
jsonStr: read the protocols from a string instead of file.
Note: either filename or jsonStr should be not None.
"""
f = open(filename)
protocolsList = json.load(f)
emProtocols = em.getProtocols()
newDict = {}
# First iteration: create all protocols and setup parameters
for protDict in protocolsList:
protClassName = protDict['object.className']
protId = protDict['object.id']
protClass = emProtocols.get(protClassName, None)
if protClass is None:
print "ERROR: protocol class name '%s' not found" % protClassName
else:
prot = self.newProtocol(protClass,
objLabel=protDict.get('object.label', None),
objComment=protDict.get('object.comment', None))
newDict[protId] = prot
for paramName, attr in prot.iterDefinitionAttributes():
if not attr.isPointer():
if paramName in protDict:
attr.set(protDict[paramName])
self.saveProtocol(prot)
# Second iteration: update pointers values
for protDict in protocolsList:
protId = protDict['object.id']
if protId in newDict:
prot = newDict[protId]
for paramName, attr in prot.iterDefinitionAttributes():
if attr.isPointer() and paramName in protDict:
parts = protDict[paramName].split('.')
if parts[0] in newDict:
attr.set(newDict[parts[0]]) # set pointer to correct created protocol
if len(parts) > 1: # set extended attribute part
attr._extended.set(parts[1])
else:
attr.set(None)
self.mapper.store(prot)
f.close()
self.mapper.commit()
def addAllProtocols(protocols):
# Add all protocols
from pyworkflow.em import getProtocols
allProts = getProtocols()
# Sort the dictionary
allProtsSorted = OrderedDict(
sorted(allProts.items(), key=lambda e: e[1].getClassLabel()))
allProtMenu = ProtocolConfig("All")
packages = {}
# Group protocols by package name
for k, v in allProtsSorted.iteritems():
if isAFinalProtocol(v, k):
packageName = v.getClassPackageName()
# Get the package submenu
packageMenu = packages.get(packageName)
# If no package menu available
if packageMenu is None:
# Add it to the menu ...
packageLine = {
"tag": "package",
"value": packageName,
"text": packageName
}
packageMenu = addToTree(allProtMenu, packageLine)
# Store it in the dict
packages[packageName] = packageMenu
# Add the protocol
protLine = {
"tag": "protocol",
"value": k,
"text": v.getClassLabel(prependPackageName=False)
}
# If it's a new protocol
if v.isNew():
# add the new icon
protLine["icon"] = "newProt.png"
addToTree(packageMenu, protLine)
protocols["All"] = allProtMenu
def addAllProtocols(protocols):
# Add all protocols
from pyworkflow.em import getProtocols
allProts = getProtocols()
# Sort the dictionary
allProtsSorted = OrderedDict(sorted(allProts.items(), key= lambda e: e[1].getClassLabel()))
allProtMenu = ProtocolConfig(ALL_PROTOCOLS)
packages = {}
# Group protocols by package name
for k, v in allProtsSorted.iteritems():
if isAFinalProtocol(v, k):
packageName = v.getClassPackageName()
# Get the package submenu
packageMenu = packages.get(packageName)
# If no package menu available
if packageMenu is None:
# Add it to the menu ...
packageLine = {"tag": "package", "value": packageName,
"text": packageName}
packageMenu = addToTree(allProtMenu, packageLine)
# Store it in the dict
packages[packageName] = packageMenu
# Add the protocol
tag = getProtocolTag(v.isInstalled())
protLine = {"tag": tag, "value": k,
"text": v.getClassLabel(prependPackageName=False)}
# If it's a new protocol
if v.isNew() and v.isInstalled():
# add the new icon
protLine["icon"] = "newProt.png"
addToTree(packageMenu, protLine)
protocols[ALL_PROTOCOLS] = allProtMenu
def handle(self):
try:
project = self.server.project
window = self.server.window
msg = self.request.recv(1024)
tokens = shlex.split(msg)
if msg.startswith('run protocol'):
protocolName = tokens[2]
from pyworkflow.em import getProtocols
protocolClass = getProtocols()[protocolName]
# Create the new protocol instance and set the input values
protocol = project.newProtocol(protocolClass)
for token in tokens[3:]:
#print token
param, value = token.split('=')
attr = getattr(protocol, param, None)
if param == 'label':
protocol.setObjLabel(value)
elif attr.isPointer():
obj = project.getObject(int(value))
attr.set(obj)
elif value:
attr.set(value)
#project.launchProtocol(protocol)
# We need to enqueue the action of execute a new protocol
# to be run in the same GUI thread and avoid concurrent
# access to the project sqlite database
window.getViewWidget().executeProtocol(protocol)
if msg.startswith('run function'):
functionName = tokens[2]
functionPointer = getattr(window, functionName)
functionPointer(*tokens[3:])
else:
answer = 'no answer available'
self.request.sendall(answer + '\n')
except Exception as e:
print e
import traceback
traceback.print_stack()
def handle(self):
try:
project = self.server.project
window = self.server.window
msg = self.request.recv(1024)
tokens = shlex.split(msg)
if msg.startswith('run protocol'):
protocolName = tokens[2]
from pyworkflow.em import getProtocols
protocolClass = getProtocols()[protocolName]
# Create the new protocol instance and set the input values
protocol = project.newProtocol(protocolClass)
for token in tokens[3:]:
#print token
param, value = token.split('=')
attr = getattr(protocol, param, None)
if param == 'label':
protocol.setObjLabel(value)
elif attr.isPointer():
obj = project.getObject(int(value))
attr.set(obj)
elif value:
attr.set(value)
#project.launchProtocol(protocol)
# We need to enqueue the action of execute a new protocol
# to be run in the same GUI thread and avoid concurrent
# access to the project sqlite database
window.getViewWidget().executeProtocol(protocol)
if msg.startswith('run function'):
functionName = tokens[2]
functionPointer = getattr(window, functionName)
functionPointer(*tokens[3:])
else:
answer = 'no answer available'
self.request.sendall(answer + '\n')
except Exception as e:
print e
import traceback
traceback.print_stack()
def populateProtTree(tree, obj):
emProtocolsDict = em.getProtocols()
for sub in obj:
text = sub.text.get()
value = sub.value.get(text)
tag = sub.tag.get('')
icon = sub.icon.get('')
openItem = sub.openItem.get()
item = TreeItem(text, tag, icon, openItem)
tree.childs.append(item)
# If have tag 'protocol_base', fill dynamically with protocol sub-classes
protClassName = value.split('.')[-1] # Take last part
if sub.value.hasValue() and tag == 'protocol_base':
prot = emProtocolsDict.get(protClassName, None)
if prot is not None:
for k, v in emProtocolsDict.iteritems():
if not v is prot and issubclass(v, prot):
protItem = TreeItem(k, 'protocol_class', '/python_file.gif', None, protClassName, v)
item.childs.append(protItem)
else:
item.protClass = protClassName
populateProtTree(item, sub)
def loadProtocols(self, filename=None, jsonStr=None):
""" Load protocols generated in the same format as self.exportProtocols.
Params:
filename: the path of the file where to read the workflow.
jsonStr: read the protocols from a string instead of file.
Note: either filename or jsonStr should be not None.
"""
f = open(filename)
protocolsList = json.load(f)
emProtocols = em.getProtocols()
newDict = OrderedDict()
# First iteration: create all protocols and setup parameters
for protDict in protocolsList:
protClassName = protDict['object.className']
protId = protDict['object.id']
protClass = emProtocols.get(protClassName, None)
if protClass is None:
print "ERROR: protocol class name '%s' not found" % protClassName
else:
prot = self.newProtocol(protClass,
objLabel=protDict.get('object.label',
None),
objComment=protDict.get(
'object.comment', None))
newDict[protId] = prot
self.saveProtocol(prot)
# Second iteration: update pointers values
def _setPointer(pointer, value):
# Properly setup the pointer value checking if the
# id is already present in the dictionary
parts = value.split('.')
target = newDict.get(parts[0], None)
pointer.set(target)
if not pointer.pointsNone():
pointer.setExtendedParts(parts[1:])
for protDict in protocolsList:
protId = protDict['object.id']
if protId in newDict:
prot = newDict[protId]
for paramName, attr in prot.iterDefinitionAttributes():
if paramName in protDict:
# If the attribute is a pointer, we should look
# if the id is already in the dictionary and
# set the extended property
if attr.isPointer():
_setPointer(attr, protDict[paramName])
# This case is similar to Pointer, but the values
# is a list and we will setup a pointer for each value
elif isinstance(attr, pwobj.PointerList):
for value in protDict[paramName]:
p = pwobj.Pointer()
_setPointer(p, value)
attr.append(p)
# For "normal" parameters we just set the string value
else:
attr.set(protDict[paramName])
self.mapper.store(prot)
f.close()
self.mapper.commit()
return newDict
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
"""
List all existing protocols within Scipion
"""
import sys
from pyworkflow.em import getProtocols
if __name__ == '__main__':
count = 0
withDoc = '--with-doc' in sys.argv
emProtocolsDict = getProtocols()
protDict = {}
# Group protocols by package name
for k, v in emProtocolsDict.iteritems():
packageName = v.getClassPackageName()
if packageName not in protDict:
protDict[packageName] = []
protDict[packageName].append((k, v))
for group, prots in protDict.iteritems():
print "-" * 100
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 ''
if __name__ == '__main__':
count = 0
withDoc = '--with-doc' in sys.argv
asciidoc = '--asciidoc' in sys.argv
emProtocolsDict = em.getProtocols()
emCategories = [('Imports', em.ProtImport, []),
('Micrographs', em.ProtMicrographs, []),
('Particles', em.ProtParticles, []),
('2D', em.Prot2D, []),
('3D', em.Prot3D, [])]
protDict = {}
# Group protocols by package name
for k, v in emProtocolsDict.iteritems():
packageName = v.getClassPackageName()
if packageName not in protDict:
protDict[packageName] = []
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 = em.getProtocols()
emCategories = [('Imports', em.ProtImport, []),
('Micrographs', em.ProtMicrographs, []),
('Particles', em.ProtParticles, []),
('2D', em.Prot2D, []),
('3D', em.Prot3D, [])]
protDict = {}
# Group protocols by package name
for k, v in emProtocolsDict.iteritems():
packageName = v.getClassPackageName()
if packageName not in protDict:
protDict[packageName] = []
if not issubclass(v, Viewer) and not v.isBase():
