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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. #
# #
#############################################################
"""
Mobyle.Index
This module manages the list of available programs to:
- search them (using search fields)
- classify them (building the categories tree)
- cache this information (on disk as a JSON file)
"""
from logging import getLogger
r_log =getLogger(__name__)
from Mobyle import IndexBase
queries = {
'title': '/*/head/doc/description/text/text()',
'name': '/*/head/name/text()',
'parameter': './/parameter[name]',
'parameter_isinput': '(not(@isout) and not(@isstdout) and not(@ishidden))',
'parameter_name': 'name/text()',
'parameter_prompt': 'prompt/text()',
'parameter_type': 'type',
'parameter_biotype': 'biotype/text()',
'parameter_datatype': 'datatype',
'parameter_class': 'class/text()',
'parameter_superclass': 'superclass/text()',
'parameter_cardinality': 'card/text()',
'parameter_dataformats': './/dataFormat/text()',
}
nifdt = [None,
'',
'Boolean',
'Integer',
'Float',
'String',
'Choice',
'MultipleChoice',
'FileNameDataType',
'StructureDataType',
'PropertiesDataType']
class DataInputsIndex(IndexBase.Index):
indexFileName = 'inputs.dat'
def getList(self):
inputs_list = {}
for key, entry in self.index.items():
for item in entry:
inputs_list['%s|%s' % (key, item['name'])] = item
return inputs_list
@classmethod
def getIndexEntry(cls, doc, program):
"""
Return an description index entry value
@return: the index entry: value
@rtype: object
"""
inputParameters=[]
programName = IndexBase._XPathQuery(doc, queries['name'])
programPID = programName
if program.server.name != 'local':
programName += '@'+program.server.name
programPID = program.server.name + '.' + programPID
programTitle = IndexBase._XPathQuery(doc, queries['title'])
pars = IndexBase._XPathQuery(doc, queries['parameter'], 'rawResult')
for p in pars:
parameter = {}
parameter['isInput'] = str(IndexBase._XPathQuery(p, \
queries['parameter_isinput'],\
'rawResult'))
parameter['name'] = IndexBase._XPathQuery(p, queries['parameter_name'])
parameter['programName'] = programName
parameter['programPID'] = programPID
parameter['programTitle'] = programTitle
parameter['prompt'] = IndexBase._XPathQuery(p, queries['parameter_prompt'])
parType = IndexBase._XPathQuery(p, \
queries['parameter_type'],
'rawResult')[0]
parameter['bioTypes'] = IndexBase._XPathQuery(parType, \
queries['parameter_biotype'],"valueList")
parDataType = IndexBase._XPathQuery(parType, \
queries['parameter_datatype'],\
'rawResult')[0]
parameter['dataTypeClass'] = IndexBase._XPathQuery(parDataType, \
queries['parameter_class'])
parameter['dataTypeSuperClass'] = IndexBase._XPathQuery(parDataType, \
queries['parameter_superclass'])
parameter['dataTypeFormats'] = IndexBase._XPathQuery(parType, \
queries['parameter_dataformats'],"valueList")
card = IndexBase._XPathQuery(parType, queries['parameter_cardinality'])
mincard = 1
maxcard = 1
if card != '':
card = card.split(',')
mincard = card[0]
if len(card) > 1:
maxcard = card[1]
else:
maxcard = card[0]
parameter['minCard'] = mincard
parameter['maxCard'] = maxcard
#parameter['id']=program.url+'|'+parameter['name']
for key, value in parameter.items():
if value == '':
parameter[key]=None
if parameter['isInput']=='True' and parameter['dataTypeClass'] not in nifdt:
inputParameters.append(parameter)
return inputParameters
|
