def new_submission(request):
if request.method == 'POST':
initial_form = InitialTrialForm(request.POST,request.FILES)
sponsor_form = PrimarySponsorForm(request.POST)
if initial_form.is_valid() and sponsor_form.is_valid():
trial = ClinicalTrial()
su = Submission(creator=request.user)
su.language = initial_form.cleaned_data['language']
su.title = initial_form.cleaned_data['scientific_title']
if su.language == 'en':
trial.scientific_title = su.title
else:
trial.save()
ctt = ClinicalTrialTranslation()
ctt.language = su.language
ctt.scientific_title = su.title
trial.translations.add(ctt)
trial.save()
su.save()
sponsor = sponsor_form.save(commit=False)
sponsor.creator = request.user
sponsor.save()
trial.primary_sponsor = su.primary_sponsor = sponsor
trial.recruitment_country = [CountryCode.objects.get(pk=id) for id in initial_form.cleaned_data['recruitment_country']]
su.trial = trial
trial.save()
su.save()
# sets the initial status of the fields
fields_status = {}
FIELDS = {
TRIAL_FORMS[0]: MISSING, TRIAL_FORMS[1]: PARTIAL, TRIAL_FORMS[2]: MISSING,
TRIAL_FORMS[3]: MISSING, TRIAL_FORMS[4]: MISSING, TRIAL_FORMS[5]: MISSING,
TRIAL_FORMS[6]: MISSING, TRIAL_FORMS[7]: MISSING, TRIAL_FORMS[8]: PARTIAL
}
for lang in su.get_mandatory_languages():
lang = lang.lower()
fields_status.update({lang: dict(FIELDS)})
if lang == su.language.lower():
fields_status[lang].update({TRIAL_FORMS[0]: PARTIAL})
su.fields_status = pickle.dumps(fields_status)
su.save()
return HttpResponseRedirect(reverse('repository.edittrial',args=[trial.id]))
else:
initial_form = InitialTrialForm(user=request.user)
sponsor_form = PrimarySponsorForm()
forms = [initial_form, sponsor_form]
return render_to_response('reviewapp/new_submission.html', {
'forms': forms },
context_instance=RequestContext(request))
def new_submission(request):
if request.method == 'POST':
initial_form = InitialTrialForm(request.POST,request.FILES)
sponsor_form = PrimarySponsorForm(request.POST)
if initial_form.is_valid() and sponsor_form.is_valid():
trial = ClinicalTrial()
su = Submission(creator=request.user)
trial.scientific_title = su.title = initial_form.cleaned_data['scientific_title']
trial.save()
su.save()
trial.primary_sponsor = su.primary_sponsor = sponsor_form.save()
trial.recruitment_country = [CountryCode.objects.get(pk=id) for id in initial_form.cleaned_data['recruitment_country']]
su.trial = trial
trial.save()
su.save()
return HttpResponseRedirect(reverse('repository.edittrial',args=[trial.id]))
else:
initial_form = InitialTrialForm()
sponsor_form = PrimarySponsorForm()
forms = [initial_form, sponsor_form]
return render_to_response('reviewapp/new_submission.html', {
'forms': forms,
'username':request.user.username,
})
def new_submission(request):
if request.method == 'POST':
initial_form = InitialTrialForm(request.POST, request.FILES, user=request.user)
if initial_form.is_valid():
trial = ClinicalTrial()
su = Submission(creator=request.user)
su.language = initial_form.cleaned_data['language']
su.title = initial_form.cleaned_data['scientific_title']
su.primary_sponsor = initial_form.cleaned_data['primary_sponsor']
trial.utrn_number = initial_form.cleaned_data['utrn_number']
trial.language = settings.DEFAULT_SUBMISSION_LANGUAGE
trial.primary_sponsor = su.primary_sponsor
if su.language == settings.DEFAULT_SUBMISSION_LANGUAGE:
trial.scientific_title = su.title
else:
trial.save()
ctt = ClinicalTrialTranslation.objects.get_translation_for_object(
su.language, trial, create_if_not_exist=True
)
ctt.scientific_title = su.title
ctt.save()
trial.save()
for country in initial_form.cleaned_data['recruitment_country']:
trial.recruitment_country.add(country) # What about the removed ones? FIXME
su.trial = trial
trial.save()
su.save()
# sets the initial status of the fields
su.init_fields_status()
return HttpResponseRedirect(reverse('repository.edittrial',args=[trial.id]))
else:
initial_form = InitialTrialForm(user=request.user, display_language=request.trials_language)
forms = [initial_form]
return render_to_response('reviewapp/new_submission.html', {
'forms': forms,},
context_instance=RequestContext(request))
def import_parsed(self, if_exists=UPDATE_IF_EXISTS):
"""
Imports from parsed trials, stored in the attribute '_parsed_trials'. They
should be collected using the method 'parse_opentrials'.
Case "if_exists" ==
- UPDATE_IF_EXISTS: will keep the trials exactly as they are, just updating their fields.
This means that existing child objects will keep as they are, just updating.
- REPLACE_IF_EXISTS: will empty the current trial and fill its fields again with imported field values.
This means that existing child objects will be deleted to have only the imported ones.
- SKIP_IF_EXISTS: will not import anything for existing trials
"""
if not hasattr(self, '_parsed_trials'):
raise Exception(_("To import parsed trials it's necessary to call method 'parse_opentrials' before."))
imported_trials = []
for fields, ct in self._parsed_trials:
# Loads the trial from database and clear it or just create a new instance in memory
if not ct:
try:
ct = ClinicalTrial.objects.get(trial_id=fields['trial_id'])
except ClinicalTrial.DoesNotExist:
ct = None
if ct:
if if_exists == SKIP_IF_EXISTS:
continue
elif if_exists == REPLACE_IF_EXISTS:
self.clear_fields(ct)
else:
ct = ClinicalTrial()
# Sets the field values and clean them
self.set_trial_fields(ct, fields)
# Children objects
self.set_trial_children(ct, fields)
# Set translations
self.set_trial_translations(ct, fields)
# TODO: call validation
# Set the status as draft
ct.status = 'draft'
ct.language = fields.get('language', settings.DEFAULT_SUBMISSION_LANGUAGE)
ct.save()
imported_trials.append(ct)
#Creating submission
submission = Submission(creator=self.creator)
submission.title = ct.public_title
submission.language = ct.language
submission.trial = ct
submission.save()
submission.init_fields_status()
ct.save()
return imported_trials
def new_submission(request):
if request.method == 'POST':
initial_form = InitialTrialForm(request.POST,
request.FILES,
user=request.user)
if initial_form.is_valid():
trial = ClinicalTrial()
su = Submission(creator=request.user)
su.language = initial_form.cleaned_data['language']
su.title = initial_form.cleaned_data['scientific_title']
su.primary_sponsor = initial_form.cleaned_data['primary_sponsor']
trial.utrn_number = initial_form.cleaned_data['utrn_number']
trial.language = settings.DEFAULT_SUBMISSION_LANGUAGE
trial.primary_sponsor = su.primary_sponsor
if su.language == settings.DEFAULT_SUBMISSION_LANGUAGE:
trial.scientific_title = su.title
else:
trial.save()
ctt = ClinicalTrialTranslation.objects.get_translation_for_object(
su.language, trial, create_if_not_exist=True)
ctt.scientific_title = su.title
ctt.save()
trial.save()
for country in initial_form.cleaned_data['recruitment_country']:
trial.recruitment_country.add(
country) # What about the removed ones? FIXME
su.trial = trial
trial.save()
su.save()
# sets the initial status of the fields
su.init_fields_status()
return HttpResponseRedirect(
reverse('repository.edittrial', args=[trial.id]))
else:
initial_form = InitialTrialForm(
user=request.user, display_language=request.trials_language)
forms = [initial_form]
return render_to_response('reviewapp/new_submission.html', {
'forms': forms,
},
context_instance=RequestContext(request))
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
