def deserialize_institution(data, persistent=False):
"""
Transforms data (as JSON string or a dict) to an institution
"""
if not data:
return None
if not persistent:
pass # TODO if necessary
else:
from repository.models import Institution
from vocabulary.models import CountryCode, InstitutionType
if isinstance(data, basestring):
data = DictKeyAttribute(simplejson.loads(data))
elif isinstance(data, dict):
data = DictKeyAttribute(data)
try:
institution = Institution.objects.get(pk=data.pk)
except Institution.DoesNotExist:
institution = Institution()
institution.id = data.pk
institution.name = data.name
institution.address = data.address
institution.country = deserialize_vocabulary(
data.country, True, CountryCode)
institution.creator = deserialize_user(data.creator, True)
institution.i_type = deserialize_vocabulary(
data.i_type, True, InstitutionType)
institution.save()
return institution
def deserialize_institution(data, persistent=False):
"""
Transforms data (as JSON string or a dict) to an institution
"""
if not data:
return None
if not persistent:
pass # TODO if necessary
else:
from repository.models import Institution
from vocabulary.models import CountryCode, InstitutionType
if isinstance(data, basestring):
data = DictKeyAttribute(simplejson.loads(data))
elif isinstance(data, dict):
data = DictKeyAttribute(data)
try:
institution = Institution.objects.get(pk=data.pk)
except Institution.DoesNotExist:
institution = Institution()
institution.id = data.pk
institution.name = data.name
institution.address = data.address
institution.country = deserialize_vocabulary(data.country, True, CountryCode)
institution.creator = deserialize_user(data.creator, True)
institution.i_type = deserialize_vocabulary(data.i_type, True, InstitutionType)
institution.save()
return institution
def post_save_submission(xml_file_path):
clinical_trial_xpath = {
'trial_id':'',
'date_registration':'',
'scientific_title':'trial_identification/scientific_title',
'scientific_acronym':'trial_identification/scientific_acronym',
'public_title':'trial_identification/public_title',
'acronym':'trial_identification/acronym',
'hc_freetext':'health_conditions/freetext',
'i_freetext':'interventions/freetext',
'inclusion_criteria':'recruitment/inclusion_criteria',
'gender':'recruitment/gender/@value',
'agemin_value':'recruitment/agemin',
'agemin_unit':'recruitment/agemin/@unit',
'agemax_value':'recruitment/agemax',
'agemax_unit':'recruitment/agemax/@unit',
'exclusion_criteria':'recruitment/exclusion_criteria',
'study_design':'study_type/study_design',
'expanded_access_program':'study_type/study_design/@expanded_access_program',
'number_of_arms':'study_type/study_design/@number_of_arms',
'date_enrollment_anticipated':'recruitment/date_enrolment_anticipated',
'date_enrollment_actual':'recruitment/date_enrolment_actual',
'target_sample_size':'recruitment/target_size',
'created':'',
'updated':'',
'exported':'',
'status':'',
'staff_note':''
}
contact_types_map = {
'public_contact':PublicContact,
'scientific_contact':ScientificContact,
'site_contact':SiteContact
}
study_design_map = {
'allocation': StudyAllocation,
'intervention_assignment':InterventionAssigment,
'masking': StudyMasking,
'purpose': StudyPurpose
}
xml = open(xml_file_path)
tree = ElementTree()
root = tree.parse(xml)
ct = ClinicalTrial()
ct.save()
# Non-relational Fields from Clinical Trial
for field,xpath in clinical_trial_xpath.items():
if xpath != '':
resultEl = root.xpath(xpath)
if len(resultEl) > 0:
if hasattr(resultEl[0],'text'):
setattr(ct, field, resultEl[0].text)
else:
setattr(ct, field, resultEl[0])
# Add Sponsors
for sponsorNode in root.xpath('sponsors_and_support/*'):
sponsor = Institution()
sponsor.name = sponsorNode.find('name').text
sponsor.address = sponsorNode.find('address').text
sponsor.country = CountryCode.objects.get(label=sponsorNode.attrib['country_code'])
sponsor.save()
if sponsorNode.tag == 'primary_sponsor':
ct.primary_sponsor = sponsor
elif sponsorNode.tag == 'secondary_sponsor':
TrialSecondarySponsor.objects.create(trial=ct,institution=sponsor)
elif sponsorNode.tag == 'source_support':
TrialSupportSource.objects.create(trial=ct,institution=sponsor)
# Add Contacts
contactList = {}
for personNode in root.xpath('contacts/person'):
contact = Contact()
for attr in ['firstname','middlename','lastname','email','address','city','zip','telephone']:
value = personNode.find(attr)
if value is not None:
setattr(contact, attr, value.text)
contact.country = CountryCode.objects.get(label=sponsorNode.attrib['country_code'])
contact.save()
contactList[ personNode.attrib['pid'] ] = contact
# Assign PublicContact, ScientificContact and SiteContact to the trial
for cType,model in contact_types_map.items():
for typeNode in root.xpath('contacts/'+cType):
pattern = re.compile('p[0-9]+')
for person in pattern.findall(typeNode.attrib['persons']):
model.objects.create(trial=ct,contact=contactList[person])
# Interventions
for icodeNode in root.xpath('interventions/i_code'):
i_code = InterventionCode.objects.get(label=icodeNode.attrib['value'])
if isinstance(i_code,InterventionCode):
ct.i_code.add(i_code)
# Recruitment Country
for rcountryNode in root.xpath('recruitment/recruitment_country'):
ccode = CountryCode.objects.get(label=rcountryNode.attrib['value'])
if isinstance(ccode,CountryCode):
ct.recruitment_country.add(ccode)
# StudyType
study_type_node = StudyType.objects.get(label=root.attrib['type'])
if study_type_node is not None:
ct.study_type = study_type_node
study_design_node = root.find('study_type/study_design')
if study_design_node is not None:
for attr,model in study_design_map.items():
setattr(ct, attr, model.objects.get(label=study_design_node.attrib[attr]))
study_phase_node = root.find('study_type/phase')
if study_phase_node is not None:
ct.phase = StudyPhase.objects.get(label=study_phase_node.attrib['value'])
recruitment_status = RecruitmentStatus.objects.get(label = root.find('recruitment').attrib['study_status'])
if recruitment_status is not None:
ct.status = recruitment_status
