def handle_update_claim(self, req_post):
logging.info("Hit 'update_claim'")
claim_id = req_post['claim']
assert claim_id == self.ref_id, "claim_id {0}, ref_id {1}".format(claim_id, self.ref_id)
session = self.session
claim = session.query(Claim).filter_by(ref_id=claim_id).first()
scf = self.set_claim_form_choices(ClaimEdit(req_post))
self.claim_form = scf
if scf.validate():
logging.info("Validated claim form")
claim.publication = expand_curie(scf.publication.data)
if scf.narrative.data == "None":
claim.narrative = None
else:
claim.narrative = expand_curie(scf.narrative.data)
claim.behavior_term = expand_curie(scf.behavior_term.data)
claim.publication_behavior = scf.publication_behavior.data
claim.evidence = expand_curie(scf.evidence.data)
parts, part_links, _ = get_participants(session, claim_id)
participant_id = req_post['participant']
participant = get_participant(session, participant_id)
element_id = req_post['element']
element = get_pelement(session, element_id)
self.set_participant_form(participant, parts)
self.set_element_form(element, element_choices(session, participant))
if part_links:
self.update_graph(claim, parts, part_links)
self.set_hidden_fields(claim_id, participant_id, element_id)
def handle_commit_element(self, part_links, parts, req_post):
logging.info("Hit commit element")
claim_id = req_post['claim']
assert self.ref_id == claim_id, "{0} != {1}".format(repr(self.ref_id), repr(claim_id))
session = self.session
claim = session.query(Claim).filter_by(ref_id=claim_id).first()
e_choice = self.int_post_field('element_choice')
if e_choice:
active_element = get_pelement(session, e_choice)
participant = active_element.participant
else:
participant = self.find_participant_without_elements(claim)
active_element = None # best choice here?
form = ElementCreate(req_post)
form.element_choice.choices = element_choices(session, participant)
form = self.set_element_form_choices(form)
participant_id = participant.ref_id
if self.enforce_element_type_constraints(form):
self.report_bad_fields(form)
logging.info("errors(1): {0}".format(form.errors))
new_element = ParticipantElement(participant_id=participant_id, old_id=0)
expression_type = form.expression_type.data
new_element.expression_type = expression_type
session.add(new_element)
transaction.commit()
element_id = new_element.element_id
logging.info("New element is {0}".format(repr(element_id)))
if expression_type == "individual":
p2i = Pelement2Individual()
p2i.element = element_id
p2i.individual = expand_curie(form.individual.data)
p2i.dummy_id = 0
session.add(p2i)
elif expression_type == 'some_term':
p2t = Pelement2Term()
p2t.element = element_id
p2t.term = expand_curie(form.term.data)
p2t.dummy_id = 0
session.add(p2t)
if active_element:
plink = ParticipantLink()
plink.child = element_id
plink.parent = active_element.element_id
session.add(plink)
else:
self.update_participant_links(participant_id, element_id)
else:
logging.info("errors(2): {0}".format(form.errors))
form.element_choice.choices = [("None", "None")]
form.expression_type.choices = expression_type_choice(session)
form.parent_link_property.choices = property_choice(session)
element_id = NOELEMENT
self.set_claim_form(claim)
participant = get_participant(session, participant_id)
self.set_participant_form(participant, parts)
self.element_form = form
transaction.commit()
self.update_graph(claim, parts, part_links)
self.set_hidden_fields(claim_id, participant_id, element_id)
def test_expand_curie(self):
"""Test the conversion from curie to URI."""
from arachcurator.views.curie_utils import expand_curie
curie1 = "arachb:ARACHB_000000322"
url1 = expand_curie(curie1)
self.assertEqual("http://arachb.org/arachb/ARACHB_000000322", url1)
curie2 = "obo:BFO_0000050"
url2 = expand_curie(curie2)
self.assertEqual("http://purl.obolibrary.org/obo/BFO_0000050", url2)
url3 = "OWL:TransitiveProperty"
curie3 = expand_curie(url3)
self.assertEqual(url3, curie3)
url4 = ""
curie4 = expand_curie(url4)
self.assertEqual(url4, curie4)
def handle_commit_participant(self, req_post):
logging.info("Hit 'commit_participant'")
ref_id = self.ref_id
session = self.session
assert req_post['claim'] == ref_id
claim = session.query(Claim).filter_by(ref_id=ref_id).first()
claim_id = claim.ref_id
self.set_claim_form(claim)
form = ParticipantCreate(req_post)
self.set_participant_form_no_navigator_choices(form)
form.participant_choice.data = "None"
form.participant_choice.choices = [("None", "None")]
form.validate()
if form.errors:
logging.warning("Participant Create Errors: {0}".format(repr(form.errors)))
self.participant_form = form
self.element_form = InactiveElementEdit(None)
self.set_hidden_fields(claim_id, req_post['participant'], NOELEMENT)
else:
form = ParticipantEdit(self.request.POST)
participant = Participant()
new_ref_id = request_uid(self.session)
transaction.commit() # maybe not needed
participant.ref_id = new_ref_id
participant.type = form.type.data
participant.label = form.label.data
participant.publication_taxon = form.publication_taxon.data
participant.publication_anatomy = form.publication_anatomy.data
participant.publication_substrate = form.publication_substrate.data
participant.publication_text = form.publication_text.data
participant.participation_property = expand_curie(form.participation_property.data)
participant.claim_id = ref_id
parts, part_links, _ = get_participants(self.session, ref_id)
parts[participant.ref_id] = participant
self.participant_form = form
property_key = expand_curie(form.participation_property.data)
property_term = session.query(Property).filter_by(ref_id=property_key).one()
part_links[participant.ref_id] = property_term
self.set_participant_form(participant, parts)
self.set_participant_form(participant, parts)
self.element_form = ElementCreateOnly()
self.element_form.expression_type.data = "None"
self.element_form.expression_type.choices = expression_type_choice(session)
session.add(participant)
transaction.commit()
self.update_graph(claim, parts, part_links)
self.set_hidden_fields(claim_id, new_ref_id, NOELEMENT)
logging.info("Exiting commit participant")
def test_c_form_commit_claim_success_redirect(self):
"""Test committing a claim form with valid data."""
from pyramid.httpexceptions import HTTPFound
from arachcurator.models.models import Claim
from arachcurator.views.curie_utils import expand_curie
request = self.__make_request_no_param__(post_fields=CLAIM_COMMIT_DATA2)
response = self._callFUT(request)
self.assertTrue(isinstance(response, HTTPFound))
self.assertEqual('302 Found', response.status)
redirect = get_redirect(response)
where = redirect.find('ref_id=') + len('ref_id=')
claim_id = redirect[where:]
target = self.session.query(Claim).filter(Claim.ref_id == claim_id).one()
self.assertEqual(expand_curie(TEST_PUBLICATION_CURIE), target.publication)
self.assertEqual(expand_curie(TEST_BEHAVIOR_TERM_CURIE), target.behavior_term)
self.assertEqual(expand_curie(NON_TRACABLE_AUTHOR_STATEMENT_CURIE), target.evidence)
def handle_update_participant(self, req_post):
logging.info("Hit 'update_participant'")
claim_id = req_post['claim']
assert claim_id == self.ref_id, "claim_id {0}, ref_id {1}".format(claim_id, self.ref_id)
session = self.session
claim = session.query(Claim).filter_by(ref_id=claim_id).one()
self.set_claim_form(claim)
participant_id = req_post['participant_choice']
participant = get_participant(session, participant_id)
parts, part_links, _ = get_participants(session, claim_id)
form = ParticipantEdit(req_post)
form.ref_id = participant_id
form = self.finish_participant_form(form, parts)
form.validate()
if form.errors:
active_element = get_head_element(session, participant)
self.choose_element_form(req_post,
active_element,
element_choices(session, participant))
else:
logging.info("participant_choice: {0}".format(participant_id))
participant.type = form.type.data
participant.label = form.label.data
participant.publication_taxon = form.publication_taxon.data
participant.publication_anatomy = form.publication_anatomy.data
participant.publication_substrate = form.publication_substrate.data
participant.publication_text = form.publication_text.data
participant.participation_property = expand_curie(form.participation_property.data)
self.participant_form = form
element_id = req_post['element']
element = get_pelement(session, element_id)
self.set_element_form(element, element_choices(session, participant))
self.update_graph(claim, parts, part_links)
self.set_hidden_fields(claim_id, participant_id, element_id)
def handle_commit_claim(self, req_post):
logging.info("Hit 'commit_claim'")
scf = ClaimCreate(req_post)
self.set_claim_form_choices(scf)
if scf.validate():
scf = ClaimEdit(req_post)
self.set_claim_form_choices(scf)
claim = Claim()
new_ref_id = request_uid(self.session)
claim.ref_id = new_ref_id
claim.publication = expand_curie(scf.publication.data)
if scf.narrative.data == "None":
claim.narrative = None
else:
claim.narrative = expand_curie(scf.narrative.data)
claim.behavior_term = expand_curie(scf.behavior_term.data)
claim.publication_behavior = scf.publication_behavior.data
claim.evidence = expand_curie(scf.evidence.data)
transaction.commit() # make sure the ref_id is committed first
self.session.add(claim)
# commit so HTTPFound 'exception' doesn't drop transaction (TODO - is there a better way)
transaction.commit()
logging.info("About to redirect to {0}".format(generate_route_id(self.request, 'claim_edit', new_ref_id)))
# TODO - can this setup forms and return normally?
# self.set_hidden_fields("test claim", "test participant", "test element")
return HTTPFound(location=generate_route_id(self.request, 'claim_edit', new_ref_id))
else:
session = self.session
old_claim_id = req_post['claim']
old_participant_id = req_post['participant']
old_element_id = req_post['element']
parts, part_links, _ = get_participants(session, old_claim_id)
self.claim_form = scf
participant = parts[old_participant_id]
self.set_participant_form(participant, parts)
element = session.query(ParticipantElement).filter_by(element_id=old_element_id).one()
self.set_element_form(element, element_choices(session, participant))
self.set_hidden_fields(old_claim_id, old_participant_id, old_element_id)
return self.render()
def __check_update_participant__(self, response):
from arachcurator.models.models import Participant
from arachcurator.views.curie_utils import expand_curie
from arachcurator.views.forms.ParticipantForm import ParticipantEdit
update_data = PARTICIPANT_UPDATE_DATA
self.assertIsInstance(response['p_form'], ParticipantEdit)
p_form = response['p_form']
self.assertIsNotNone(p_form.ref_id)
self.assertEqual({}, p_form.errors)
updated_participant = self.session.query(Participant).filter(Participant.ref_id == p_form.ref_id).one()
for field in PARTICIPANT_EDIT_FIELDS:
with self.subTest(field=field):
field_value = updated_participant.__getattribute__(field)
self.assertIsNotNone(field_value)
if field_value.startswith('http:'):
self.assertEqual(expand_curie(update_data[field]), field_value)
else:
self.assertEqual(update_data[field], field_value)
import transaction
from pyramid import testing
from pyramid.i18n import TranslationStringFactory
from webob.multidict import MultiDict
from arachcurator.views.curie_utils import expand_curie
from arachcurator.views.claim_edit import NOELEMENT
_ = TranslationStringFactory('arachcurator')
POSTGRES_SPEC = "postgresql+psycopg2://arachcurator:''@localhost:5432/testadmin"
TEST_CLAIM_REF_ID2 = 'arachb:ARACHB_0000343'
TEST_CLAIM_REF_URL2 = expand_curie(TEST_CLAIM_REF_ID2)
TEST_CLAIM_URI3 = 'http://arachb.org/arachb/ARACHB_0000412'
TEST_PUBLICATION_CURIE = 'arachb:ARACHB_0000099'
TEST_PUBLICATION_CURIE2 = 'arachb:ARACHB_0000311'
TEST_PUBLICATION_URI2 = expand_curie(TEST_PUBLICATION_CURIE2)
TEST_BEHAVIOR_TERM_CURIE = 'obo:NBO_0000001'
TEST_BEHAVIOR_TERM_CURIE2 = 'obo:NBO_0000002'
ACTIVELY_PARTICIPATES_IN_CURIE = 'obo:RO_0002217'