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########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
from lxml import etree,html #@UnresolvedImport
import logging
from Mobyle.Classes.DataType import DataTypeFactory
from Mobyle.Service import MobyleType
log = logging.getLogger('Mobyle')
parser = etree.XMLParser(remove_blank_text=True)
def xbool(s):
if s in ['False', 'false', '','0']:
return False
else:
return True
def boolx(s):
if s==False:
return 'false'
else:
return 'true'
class MobyleElement(etree.ElementBase):
el_props = {} # properties stored as unique elements
text_props = {} # properties stored as text value of an element
list_props = {} # properties stored as lists of elements
att_props = {} # properties stored as attributes
PARSER=parser
# the parser used will be wired to the MobyleLookup class defined below
# so that the results of xpath queries are the Mobyle custom classes
# instead of generic lxml classes
def _init(self):
self.tag=self.mtag
def __getattr__(self, name):
if self.text_props.get(name):
return self._get_text(name)
elif self.att_props.get(name):
return self._get_att(name)
elif self.list_props.get(name):
return self._get_list(name)
elif self.el_props.get(name):
return self._get_el(name)
else:
raise AttributeError("Attribute '%s' does not exist in '%s' object" % (name, self.__class__.__name__))
def _get_text(self, name):
return ''.join(self.xpath(self.text_props[name]+'/text()'))
def _get_att(self, name):
r = self.get(self.att_props[name][0])
if r is not None:
return self.att_props[name][1](r)
def _get_list(self, name):
return self.xpath(self.list_props[name])
def _get_el(self, name):
r = self.xpath(self.el_props[name])
if len(r)==1:
return r[0]
else:
return None
def __setattr__(self, name, value):
if self.text_props.get(name):
self._build_path(self.text_props[name])
self._set_text(name, value)
self.xpath(self.text_props[name])[0].text = value
elif self.att_props.get(name):
self._set_att(name, value)
elif self.list_props.get(name):
self._build_path(self.list_props[name])
self._set_list(name, value)
elif self.el_props.get(name):
self._build_path(self.el_props[name])
self._set_el(name, value)
else:
etree.ElementBase.__setattr__(self, name, value)
def _build_path(self, path):
if not(self.xpath(path)):
p = self
for tag in path.replace('//','/').split('/'):
if not(p.xpath(tag)):
parser = Parser()
p = etree.SubElement(p,tag)
else:
p = p.xpath(tag)[0]
def _set_text(self, name, value):
self.xpath(self.text_props[name])[0].text = value
def _set_att(self, name, value):
self.set(self.att_props[name][0], self.att_props[name][2](value))
def _set_list(self, name, value):
l = self.xpath(self.list_props[name])
parser = Parser()
p = l[0].getparent()
for i in l:
p.remove(i)
for i in list(value):
p.append(i)
def _set_el(self, name, value):
l = self.xpath(self.el_props[name])
p = l[0].getparent()
for i in l:
p.remove(i)
p.append(value)
class Text(MobyleElement):
mtag = 'text'
class Workflow(MobyleElement):
mtag = 'workflow'
el_props = {
'description':'head/doc/description/text',
'comment':'head/doc/comment/text'
}
text_props = {
'name':'head/name',
'version':'head/version',
'title':'head/doc/title',
'authors':'head/doc/authors'
}
list_props = {
'parameters':'parameters//parameter', # WARNING: we do not handle nested paragraph/parameter structures
'paragraphs':'parameters/paragraph', # direct child paragraphs
'tasks':'flow/task',
'links':'flow/link'
}
att_props = {
'id':('id',str,str)
}
owner = None # owner name is added to the workflow name in order to get a meaningfull directory in the Mobyle server jobs folder
def __repr__(self):
return "workflow[%s] %s" % (self.id, self.name)
def getName(self): # added for Service class compatibility (called from Job)
if self.owner is not None: # owner name is added to the workflow name in order to get a meaningfull directory in the Mobyle server jobs folder
return str(self.owner.getKey()) + "_" + str(self.id) # name= session key + workflow number
return self.name
def getUrl(self): # added for Service class compatibility (called from Job)
if not(self.url):
return self.name
else:
return self.url
def isService(self): # added for Service class compatibility (called from Job)
return False # cheating Job.py ;)
def getUserInputParameterByArgpos(self): # added for Service class compatibility (called from JobFacade)
return [p.name for p in self.parameters if not p.isout and not p.isstdout]
def getParameter(self, name): # added for Service class compatibility (called from JobFacade)
return [p for p in self.parameters if p.name==name][0]
def getVdef(self, name): # added for Service class compatibility (called from JobFacade)
return [p for p in self.parameters if p.name==name][0].getVdef()
def getDataType(self,name): # added for Service class compatibility (called from JobFacade)
df = DataTypeFactory()
p = [p for p in self.parameters if p.name==name][0]
datatype_class = p.type.datatype.class_name
datatype_superclass = p.type.datatype.superclass_name
if (datatype_superclass in [None,""] ):
dt = df.newDataType(datatype_class)
else:
dt = df.newDataType(datatype_superclass, datatype_class)
return dt
class Paragraph(MobyleElement):
mtag = 'paragraph'
att_props = {
}
list_props = {
'parameters':'parameters//parameter', # WARNING: we do not handle nested paragraph/parameter structures
'paragraphs':'parameters/paragraph' # direct child paragraphs
}
text_props = {
'name':'name',
'prompt':'prompt'
}
def __repr__(self):
return "paragraph (%s)" % (self.name)
def getName(self): # added for Service.Parameter class compatibility (called from JobFacade)
return self.name
def promptHas_lang(self, lang): # added for UserValueError class compatibility (called from WorkflowJob)
return True
def getPrompt(self, lang):
return self.prompt
class Parameter(MobyleElement):
mtag = 'parameter'
att_props = {
'id':('id',str,str),
'ismaininput':('ismaininput',xbool,boolx),
'ismandatory':('ismandatory',xbool,boolx),
'ishidden':('ishidden',xbool,boolx),
'issimple':('issimple',xbool,boolx),
'isout':('isout',xbool,boolx),
'isstdout':('isstdout',xbool,boolx)
}
text_props = {
'name':'name',
'prompt':'prompt',
'example':'example'
}
list_props = {
'vdef':'vdef/value'
}
el_props = {
'type':'type',
'vlist':'vlist'
}
def __repr__(self):
return "parameter[%s] (%s)" % (self.id, self.name)
def getName(self): # added for Service.Parameter class compatibility (called from JobFacade)
return self.name
def promptHas_lang(self, lang): # added for UserValueError class compatibility (called from WorkflowJob)
return True
def getPrompt(self, lang):
return self.prompt
def isInfile(self): # added for Service.Parameter class compatibility (called from JobFacade)
mt = self.getType()
return (not(self.isout) and mt.isFile())
def getDataType( self ) :
mt = self.getType()
return mt.getDataType()
def getType(self): # added for Service.Parameter
try:
return self._mobyleType
except AttributeError:
df = DataTypeFactory()
datatype_class = self.type.datatype.class_name
datatype_superclass = self.type.datatype.superclass_name
if (datatype_superclass in [None,""] ):
dt = df.newDataType(datatype_class)
else:
dt = df.newDataType(datatype_superclass, datatype_class)
self._mobyleType = MobyleType(dt)
return self._mobyleType
def getVdef(self):
"""
WARNING: returns the vdef as currently processed by Mobyle, i.e. a one value list is one value, and a multiple values list is a list
this should change with the merge of the "mobyle-multiple branch", which will allow to test if the parameter datatype is a list (or not)
"""
if len( self.vdef ) == 1 :
if self.vdef[0].reference in ["",None]:
return self.vdef[0].value
else:
return {'src':self.vdef[0].reference,'srcFileName':self.vdef[0].safe_name}
else:
return [value.value for value in self.vdef]
class Type(MobyleElement):
mtag = 'type'
list_props = {
'biotypes':'biotype',
}
el_props = {
'datatype':'datatype',
}
def __repr__(self):
return "type %s::%s" % (self.biotypes, self.datatype)
class Biotype(MobyleElement):
mtag = 'biotype'
class Datatype(MobyleElement):
mtag = 'datatype'
text_props = {
'class_name':'class',
'superclass_name':'superclass'
}
def __repr__(self):
return "datatype %s::%s" % (self.class_name, self.superclass_name)
class Task(MobyleElement):
mtag = 'task'
att_props = {
'id':('id',str,str),
'service':('service',str,str),
'service_url':('service_url',str,str),
'server':('server',str,str),
'suspend':('suspend',xbool,boolx)
}
list_props = {
'input_values':'inputValue',
}
text_props = {
'description':'description',
}
def __repr__(self):
return self.id
#return "task[%s] (%s)" % (self.id, self.service)
class InputValue(MobyleElement):
mtag = 'inputValue'
att_props = {
'name':('name',str,str),
'reference':('reference',str,str),
'user_name':('userName',str,str),
'safe_name':('safeName',str,str)
}
text_props = {
'value':'.',
}
def __repr__(self):
return "inputValue[%s]" % (self.name)
class Value(MobyleElement):
mtag = 'value'
att_props = {
'reference':('reference',str,str),
'user_name':('userName',str,str),
'safe_name':('safeName',str,str)
}
text_props = {
'value':'.',
}
def __repr__(self):
return "value[%s]" % (self.value)
class Vlist(MobyleElement):
mtag = 'vlist'
list_props = {
'velems':'velem',
}
def __repr__(self):
return "vlist[%s]" % (self.value)
class VElem(MobyleElement):
mtag = 'velem'
text_props = {
'value':'value',
'label':'label',
}
def __repr__(self):
return "velem[%s(%s)]" % (self.label,self.value)
class Link(MobyleElement):
mtag = 'link'
att_props = {
'id':('id',str,str),
'from_task':('fromTask',str,str),
'to_task':('toTask',str,str),
'from_parameter':('fromParameter',str,str),
'to_parameter':('toParameter',str,str)
}
def __repr__(self):
return "link[%s] %s:%s->%s:%s" % (self.id, self.from_task, self.from_parameter, self.to_task, self.to_parameter)
import inspect, sys
clsmembers = inspect.getmembers(sys.modules[__name__], inspect.isclass)
tagDict = {}
for i in clsmembers:
if hasattr(i[1],'mtag'):
tagDict[i[1].mtag] = i[1]
class MobyleLookup(etree.PythonElementClassLookup):
def lookup(self, document, element):
name = element.tag
return tagDict.get(name,None)
parser.set_element_class_lookup(MobyleLookup())
class Parser(object):
def __init__(self):
self.parser = parser
def parse(self, url):
""" parse from a URL """
o = etree.parse(url,self.parser)
return o.getroot()
def XML(self, str):
""" parse from a string """
o = etree.XML(str,self.parser)
return o
def tostring(self, xml,pretty_print=True):
return etree.tostring(xml, xml_declaration=True , encoding='UTF-8', pretty_print=pretty_print)
def parseTextOrHTML(str):
frags = html.fragments_fromstring(str)
if len(frags)==1 and isinstance(frags[0],basestring):
return Text(frags[0])
else:
if len(frags)==1:
wrapper = frags[0]
else:
wrapper = html.fragment_fromstring('<div xmlns="http://www.w3.org/1999/xhtml">%s</div>' % str)
return wrapper
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