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