def save_protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
try:
project.saveProtocol(protocol)
protId = protocol.getObjId()
res = {"success": protId}
except Exception, ex:
errors = [parseText(str(ex))]
res = {"errors": errors}
def save_protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
try:
project.saveProtocol(protocol)
protId = protocol.getObjId()
res = {'success' : protId}
except Exception, ex:
errors = [parseText(str(ex))]
res = {'errors' : errors}
def protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
errors = protocol.validate()
if len(errors) == 0:
# No errors, launch the protocol
try:
project.launchProtocol(protocol)
except Exception, ex:
errors = [parseText(str(ex))]
def protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
errors = protocol.validate()
if len(errors) == 0:
# No errors, launch the protocol
try:
project.launchProtocol(protocol)
except Exception, ex:
errors = [parseText(str(ex))]
def delete_protocol(request):
if request.is_ajax():
project = loadProject(request)
list_id = request.GET.get('id', None).split(",")
list_protocols = []
for id in list_id:
protocol = project.getProtocol(int(id))
list_protocols.append(protocol)
try:
project.deleteProtocol(*list_protocols)
res = {'success' : 'Protocol deleted successful'}
except Exception, ex:
errors = [parseText(str(ex))]
res = {'errors' : errors}
def delete_protocol(request):
if request.is_ajax():
projectName = request.session["projectName"]
project = loadProject(request)
list_id = request.GET.get("id", None).split(",")
list_protocols = []
for id in list_id:
protocol = project.getProtocol(int(id))
list_protocols.append(protocol)
try:
project.deleteProtocol(*list_protocols)
res = {"success": "Protocol deleted successful"}
except Exception, ex:
errors = [parseText(str(ex))]
res = {"errors": errors}
def copy_protocol(request):
if request.is_ajax():
projectName = request.session['projectName']
project = loadProject(request)
list_id = request.GET.get('id', None).split(",")
list_protocols = []
for id in list_id:
protocol = project.getProtocol(int(id))
list_protocols.append(protocol)
try:
protocol = project.copyProtocol(list_protocols)
res = {'success' : 'Protocol copied successful'}
except Exception, ex:
errors = [parseText(str(ex))]
res = {'errors' : errors}
def contextForm(request):
from views_base import base_form
from django.core.context_processors import csrf
from views_util import getResourceCss, getResourceIcon, getResourceJs, getResourceLogo
from pyworkflow.protocol.params import Group, Line
project, protocol = loadProtocolProject(request, requestType='GET')
action = request.GET.get('action', None)
paramProt = request.GET.get('paramProt', None)
protRunIdViewer = request.GET.get('protRunIdViewer', None)
# Patch : to fix the relion dynamic way to generate the viewer form
# For this is necessary to call setProtocol method
if protRunIdViewer is not None:
protocol_parent = project.getProtocol(int(protRunIdViewer))
protocol.setProtocol(protocol_parent)
hosts = project.getHostNames()
print "Host in the project: ", hosts
visualize = 0
viewerDict = None
if action == 'visualize':
visualize = 1
viewerDict = protocol._getVisualizeDict()
elif action == 'protSimple':
visualize = 2
elif action == 'copy':
protocol = project.copyProtocol(protocol)
package = protocol.getClassPackage()
logoPath = ''
path = getattr(package, '_logo', '')
if path != '':
logoPath = getResourceLogo(path)
wizards = findWizardsWeb(protocol)
protocol.htmlCitations = parseText(protocol.citations())
protocol.htmlDoc = parseText(protocol.getDoc())
for section in protocol._definition.iterSections():
for paramName, param in section.iterParams():
protVar = getattr(protocol, paramName, None)
if protVar is None:
# raise Exception("_fillSection: param '%s' not found in protocol" % paramName)
# GROUP PARAM
if isinstance(param, Group):
for paramGroupName, paramGroup in param.iterParams():
protVar = getattr(protocol, paramGroupName, None)
# LINE PARAM
if isinstance(paramGroup, Line):
for paramLineName, paramLine in paramGroup.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in paramGroup.iterParams():
wizParamName = name
if wizParamName in wizards:
paramGroup.hasWizard = True
paramGroup.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramGroupName in viewerDict:
paramGroup.hasViewer = True
if not paramGroup.help.empty():
paramGroup.htmlHelp = parseText(paramGroup.help.get())
paramGroup.htmlCond = paramGroup.condition.get()
paramGroup.htmlDepend = ','.join(paramGroup._dependants)
paramGroup.htmlCondParams = ','.join(paramGroup._conditionParams)
elif protVar is None:
pass
else:
paramGroup = PreprocessParamForm(request, paramGroup, paramGroupName, wizards, viewerDict, visualize, protVar)
param.htmlCond = param.condition.get()
param.htmlDepend = ','.join(param._dependants)
param.htmlCondParams = ','.join(param._conditionParams)
# LINE PARAM
if isinstance(param, Line):
for paramLineName, paramLine in param.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in param.iterParams():
wizParamName = name
if wizParamName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
param.htmlCond = param.condition.get()
param.htmlDepend = ','.join(param._dependants)
param.htmlCondParams = ','.join(param._conditionParams)
else:
# OTHER PARAM
param = PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar)
context = {SERVICE_NAME: getVarFromRequest(request, SERVICE_NAME),
CTX_PROJECT_NAME: project.getShortName(),
'protocol': protocol,
'package_logo': logoPath,
'protRunIdViewer': protRunIdViewer,
'definition': protocol._definition,
'visualize': visualize,
'paramProt': paramProt,
'favicon': getResourceIcon('favicon'),
'comment': getResourceIcon('edit_toolbar'),
'jquery_ui_css': getResourceCss('jquery_ui'),
'wizard': getResourceIcon('wizard'),
'protocol_form_utils': getResourceJs('protocol_form_utils'),
'hosts': hosts,
'comment': parseText(protocol.getObjComment()),
'showHost': True,
'showParallel': True
}
# Update the context dictionary with the special params
for paramName in SPECIAL_PARAMS:
context[paramName] = protocol.getAttributeValue(paramName, '')
# Cross Site Request Forgery protection is need it
context.update(csrf(request))
context = base_form(request, context)
return context
def PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar):
try:
# MULTI POINTER
if isinstance(param, MultiPointerParam):
htmlValueList = []
htmlIdValueList = []
for pointer in protVar:
htmlValue, htmlIdValue = getPointerHtml(pointer)
htmlValueList.append(htmlValue)
htmlIdValueList.append(htmlIdValue)
param.htmlValueIdZip = zip(htmlValueList,htmlIdValueList)
# POINTER
elif isinstance(param, PointerParam):
param.htmlValue, param.htmlIdValue = getPointerHtml(protVar, True)
# RELATION PARAM
elif isinstance(param, RelationParam):
param.htmlValue, param.htmlIdValue = getPointerHtml(protVar)
param.relationName = param.getName()
param.attributeName = param.getAttributeName()
param.direction = param.getDirection()
else:
param.htmlValue = protVar.get(param.default.get(""))
if isinstance(protVar, Boolean):
if param.htmlValue:
param.htmlValue = 'true'
else:
param.htmlValue = 'false'
if paramName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[paramName].__name__
# print "param: ", paramName, " has wizard", " view: "
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
# print "param: ", paramName, " has viewer"
param.htmlCond = param.condition.get()
param.htmlDepend = ','.join(param._dependants)
param.htmlCondParams = ','.join(param._conditionParams)
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
# param.htmlExpertLevel = param.expertLevel.get()
""" Workflow Addon """
valueURL = request.GET.get(paramName, None)
if valueURL is not None:
if valueURL is not param.htmlValue:
param.htmlValue = valueURL
return param
except Exception, ex:
print "ERROR with param: ", paramName
raise ex
# Method to launch a protocol #
def protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
errors = protocol.validate()
if len(errors) == 0:
# No errors, launch the protocol
try:
project.launchProtocol(protocol, chdir=False)
except Exception, ex:
errors = [parseText(str(ex))]
jsonStr = json.dumps({'errors' : parseText(errors)}, ensure_ascii=False)
return HttpResponse(jsonStr, content_type='application/javascript')
def updateProtocolParams(request, protocol, project):
""" Update the protocol values from the Web-form.
This function will be used from save_protocol and execute_protocol.
"""
# PARAMS
for paramName, param in protocol.iterDefinitionAttributes():
updateParam(request, project, protocol, paramName)
# SPECIAL_PARAMS
for paramName in SPECIAL_PARAMS:
updateParam(request, project, protocol, paramName)
def contextForm(request):
from views_base import base_form
from django.core.context_processors import csrf
from views_util import getResourceCss, getResourceIcon, getResourceJs, getResourceLogo
from pyworkflow.protocol.params import Group, Line
project, protocol = loadProtocolProject(request, requestType="GET")
action = request.GET.get("action", None)
paramProt = request.GET.get("paramProt", None)
protRunIdViewer = request.GET.get("protRunIdViewer", None)
# Patch : to fix the relion dynamic way to generate the viewer form
# For this is necessary to call setProtocol method
if protRunIdViewer is not None:
protocol_parent = project.getProtocol(int(protRunIdViewer))
protocol.setProtocol(protocol_parent)
hosts = project.getHostNames()
print "Host in the project: ", hosts
visualize = 0
viewerDict = None
if action == "visualize":
visualize = 1
viewerDict = protocol._getVisualizeDict()
elif action == "protSimple":
visualize = 2
elif action == "copy":
protocol = project.copyProtocol(protocol)
package = protocol.getClassPackage()
logoPath = ""
path = getattr(package, "_logo", "")
if path != "":
logoPath = getResourceLogo(path)
wizards = findWizardsWeb(protocol)
protocol.htmlCitations = parseText(protocol.citations())
protocol.htmlDoc = parseText(protocol.getDoc())
for section in protocol._definition.iterSections():
for paramName, param in section.iterParams():
protVar = getattr(protocol, paramName, None)
if protVar is None:
# raise Exception("_fillSection: param '%s' not found in protocol" % paramName)
# GROUP PARAM
if isinstance(param, Group):
for paramGroupName, paramGroup in param.iterParams():
protVar = getattr(protocol, paramGroupName, None)
# LINE PARAM
if isinstance(paramGroup, Line):
for paramLineName, paramLine in paramGroup.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(
request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar
)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in paramGroup.iterParams():
wizParamName = name
if wizParamName in wizards:
paramGroup.hasWizard = True
paramGroup.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramGroupName in viewerDict:
paramGroup.hasViewer = True
if not paramGroup.help.empty():
paramGroup.htmlHelp = parseText(paramGroup.help.get())
paramGroup.htmlCond = paramGroup.condition.get()
paramGroup.htmlDepend = ",".join(paramGroup._dependants)
paramGroup.htmlCondParams = ",".join(paramGroup._conditionParams)
elif protVar is None:
pass
else:
paramGroup = PreprocessParamForm(
request, paramGroup, paramGroupName, wizards, viewerDict, visualize, protVar
)
param.htmlCond = param.condition.get()
param.htmlDepend = ",".join(param._dependants)
param.htmlCondParams = ",".join(param._conditionParams)
# LINE PARAM
if isinstance(param, Line):
for paramLineName, paramLine in param.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(
request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar
)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in param.iterParams():
wizParamName = name
if wizParamName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
param.htmlCond = param.condition.get()
param.htmlDepend = ",".join(param._dependants)
param.htmlCondParams = ",".join(param._conditionParams)
else:
# OTHER PARAM
param = PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar)
context = {
"projectName": project.getName(),
"package_logo": logoPath,
"protocol": protocol,
"protRunIdViewer": protRunIdViewer,
"definition": protocol._definition,
"visualize": visualize,
"paramProt": paramProt,
"favicon": getResourceIcon("favicon"),
"comment": getResourceIcon("edit_toolbar"),
"jquery_ui_css": getResourceCss("jquery_ui"),
"wizard": getResourceIcon("wizard"),
"protocol_form_utils": getResourceJs("protocol_form_utils"),
"hosts": hosts,
"comment": parseText(protocol.getObjComment()),
"showHost": True,
"showParallel": True,
}
# Update the context dictionary with the special params
for paramName in SPECIAL_PARAMS:
context[paramName] = protocol.getAttributeValue(paramName, "")
# Cross Site Request Forgery protection is need it
context.update(csrf(request))
context = base_form(request, context)
return context
def PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar):
try:
# MULTI POINTER
if isinstance(param, MultiPointerParam):
htmlValueList = []
htmlIdValueList = []
for pointer in protVar:
htmlValue, htmlIdValue = getPointerHtml(pointer)
htmlValueList.append(htmlValue)
htmlIdValueList.append(htmlIdValue)
param.htmlValueIdZip = zip(htmlValueList, htmlIdValueList)
# POINTER
elif isinstance(param, PointerParam):
param.htmlValue, param.htmlIdValue = getPointerHtml(protVar)
# RELATION PARAM
elif isinstance(param, RelationParam):
param.htmlValue, param.htmlIdValue = getPointerHtml(protVar)
param.relationName = param.getName()
param.attributeName = param.getAttributeName()
param.direction = param.getDirection()
else:
param.htmlValue = protVar.get(param.default.get(""))
if isinstance(protVar, Boolean):
if param.htmlValue:
param.htmlValue = "true"
else:
param.htmlValue = "false"
if paramName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[paramName].__name__
# print "param: ", paramName, " has wizard", " view: "
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
# print "param: ", paramName, " has viewer"
param.htmlCond = param.condition.get()
param.htmlDepend = ",".join(param._dependants)
param.htmlCondParams = ",".join(param._conditionParams)
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
# param.htmlExpertLevel = param.expertLevel.get()
""" Workflow Addon """
valueURL = request.GET.get(paramName, None)
if valueURL is not None:
if valueURL is not param.htmlValue:
param.htmlValue = valueURL
return param
except Exception, ex:
print "ERROR with param: ", paramName
raise ex
# Method to launch a protocol #
def protocol(request):
project, protocol = loadProtocolProject(request)
updateProtocolParams(request, protocol, project)
errors = protocol.validate()
if len(errors) == 0:
# No errors, launch the protocol
try:
project.launchProtocol(protocol)
except Exception, ex:
errors = [parseText(str(ex))]
jsonStr = json.dumps({"errors": parseText(errors)}, ensure_ascii=False)
return HttpResponse(jsonStr, mimetype="application/javascript")
def updateProtocolParams(request, protocol, project):
""" Update the protocol values from the Web-form.
This function will be used from save_protocol and execute_protocol.
"""
# PARAMS
for paramName, _ in protocol.iterDefinitionAttributes():
updateParam(request, project, protocol, paramName)
# SPECIAL_PARAMS
for paramName in SPECIAL_PARAMS:
updateParam(request, project, protocol, paramName)