def __init__(self):
self.abs_path = realpath('%s/../' % dirname(__file__))
self.app_name = 'gorIV'
self.app_path = 'gorIV'
self.app_title = basename(__file__).replace('_bx_WS.py', '')
self.wsdl = '%s/wsdl/GorIV_bx.wsdl' % self.abs_path
CommonService.__init__(self)
GorIV.__init__(self)
def soap_submitGorIV(self, ps, **kw):
request, response = GorIV.soap_submitGorIV(self, ps, **kw)
self.job_id = str(uuid1())
self.initJob()
self.app_args = ['-prd', self.input_file, '-seq', '/usr/share/gorIV/DATABASE/New_KS.267.seq',
'-obs', '/usr/share/gorIV/DATABASE/New_KS.267.obs', '-pro', self.output_file, '>', self.log_file]
self.submit()
save_sequence = SequenceRecord()
save_sequence.sequence = str(request.get_element_sequence())
save_sequence.customName = str(request.get_element_customName())
save_sequence.customNote = str(request.get_element_customNote())
formalReference = request.get_element_formalReference()
if formalReference is not None:
save_sequence.formalReference_accession = str(formalReference.get_element_accession())
sequenceFile = '>1 %s %s\n%s\n' % (save_sequence.formalReference_accession or '<None',
save_sequence.customName, save_sequence.sequence)
# TODO: Return SOAP fault
if not s3uploadContents(self.job_id, 'sequence.pick', dumps(save_sequence)):
response.set_element_jobId('error')
elif not s3uploadContents(self.job_id, self.input_file, sequenceFile):
response.set_element_jobId('error')
else:
response.set_element_jobId(self.job_id)
return request, response
def soap_getResultsGorIV(self, ps, **kw):
request, response = GorIV.soap_getResultsGorIV(self, ps, **kw)
self.job_id = request.get_element_jobId()
if check_jobid(self.job_id) == 1:
# Return a soap fault!
return request, response
if self.check_status() != 'done':
# Return a soap fault!
return request, response
self.initIOFile()
secondaryStructure = response.new_secondaryStructure()
# Sequence record
seqDump = s3retrieveContents(self.job_id, 'sequence.pick')
# TODO: Return SOAP fault if seqDump == ''
sequence = loads(seqDump)
sequenceRecord = secondaryStructure.new_sequenceRecord()
sequenceRecord.set_element_sequence(sequence.sequence)
if sequence.customName != 'None':
sequenceRecord.set_element_customName(sequence.customName)
if sequence.customNote != 'None':
sequenceRecord.set_element_customNote(sequence.customNote)
## FormalReference
if sequence.formalReference_accession != 'None':
formalReference = sequenceRecord.new_formalReference()
formalReference.set_element_accession(sequence.formalReference_accession)
sequenceRecord.set_element_formalReference(formalReference)
secondaryStructure.set_element_sequenceRecord(sequenceRecord)
# Method
method = secondaryStructure.new_method()
method.set_attribute_localId('%s%s' % (datetime.now().strftime('%Y-%m-%d'), self.app_title))
method.set_element_name(self.app_title)
method.set_element_uri('%s%s/' % (SITE_URL, self.app_title))
method.set_element_version('0.2')
method.set_element_date(time())
## WebservicReference
webserviceReference = method.new_webserviceReference()
webserviceReference.set_element_wsdl('%s%s/wsdl/' % (SITE_URL, self.app_title))
method.set_element_webserviceReference(webserviceReference)
secondaryStructure.set_element_method([method])
# Anotation
idx = 0
previous_prd = None
annotation = None
occurence_list = []
annotation_list = []
gorIVoutfile = s3retrieveContents(self.job_id, self.output_file)
lines = gorIVoutfile.split('\n')
for i in lines[5:]:
if len(i) == 0:
continue
_, seq, _, _, prd, _, h, e, c = i.split(' ')
idx+=1
if prd != previous_prd:
previous_prd = prd
if len(occurence_list) > 0:
annotation.set_element_occurence(occurence_list)
occurence_list = []
annotation_list.append(annotation)
annotation = secondaryStructure.new_annotation()
## Feature
feature = annotation.new_feature()
feature.set_element_name(prd)
annotation.set_element_feature(feature)
## Occurence
occurence = annotation.new_occurence()
### Position
position = occurence.new_position()
position.set_element_point(idx)
occurence.set_element_position(position)
### Evidence
evidence = occurence.new_evidence()
#### Predicted
predicted = evidence.new_predicted()
score_list = []
predicted.set_element_methodId('%s%s' % (datetime.now().strftime('%Y-%m-%d'), self.app_title))
for t, v in (('H', h), ('E', e), ('C', c)):
score = predicted.new_score()
score.set_element_type(t)
score.set_element_value(float(v))
score_list.append(score)
predicted.set_element_score(score_list)
if h > e and h > c:
verdict = 'H'
elif e > h and e > c:
verdict = 'E'
else:
verdict = 'C'
predicted.set_element_verdict(verdict)
evidence.set_element_predicted(predicted)
occurence.set_element_evidence([evidence,])
occurence_list.append(occurence)
secondaryStructure.set_element_annotation(annotation_list)
response.set_element_secondaryStructure(secondaryStructure)
response.set_element_logout(s3retrieveContents(self.job_id, self.log_file))
return request, response
def soap_cancelGorIV(self, ps, **kw):
request, response = GorIV.soap_cancelGorIV(self, ps, **kw)
self.job_id = request.get_element_jobId()
response.set_element_status(self.cancel())
return request, response