def create_item(self, login):
statements = [
PBB_Core.WDExternalID(value=self.id,
prop_nr=INTERPRO,
references=[self.reference]),
PBB_Core.WDItemID(value=self.type_wdid,
prop_nr="P279",
references=[self.reference])
]
wd_item = PBB_Core.WDItemEngine(
item_name=self.name,
domain='interpro',
data=statements,
append_value=["P279"],
fast_run=True,
fast_run_base_filter=IPRTerm.fast_run_base_filter)
wd_item.set_label(self.name, lang='en')
for lang, description in self.lang_descr.items():
wd_item.set_description(description, lang=lang)
wd_item.set_aliases([self.short_name, self.id])
PBB_Helpers.try_write(wd_item, self.id, INTERPRO, login)
return wd_item
def create_relationships(self, ipr_wd):
# ipr_wd is a dict ipr ID to wikidata ID mapping
statements = [
PBB_Core.WDExternalID(value=self.id,
prop_nr=INTERPRO,
references=[self.reference])
]
if self.parent:
statements.append(
PBB_Core.WDItemID(value=ipr_wd[self.parent],
prop_nr='P279',
references=[self.reference])) # subclass of
if self.contains:
for c in self.contains:
statements.append(
PBB_Core.WDItemID(value=ipr_wd[c],
prop_nr='P527',
references=[self.reference])) # has part
if self.found_in:
for f in self.found_in:
statements.append(
PBB_Core.WDItemID(value=ipr_wd[f],
prop_nr='P361',
references=[self.reference])) # part of
if len(statements) == 1:
return
# write data
item = PBB_Core.WDItemEngine(item_name=self.name,
domain='interpro',
data=statements,
server=SERVER,
append_value=["P279", "P527", "P361"])
try:
item.write(self.login)
except WDApiError as e:
print(e)
PBB_Core.WDItemEngine.log(
'ERROR',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'
.format(main_data_id=self.id,
exception_type=type(e),
message=e.__str__(),
wd_id=self.wd_item_id,
duration=datetime.now()))
return
PBB_Core.WDItemEngine.log(
'INFO',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'
.format(main_data_id=self.id,
exception_type='',
message='created interpro relationships: {}'.format([
(x.prop_nr, x.value) for x in statements
]),
wd_id=item.wd_item_id,
duration=datetime.now()))
def create_relationships(self, login):
try:
# endpoint may not get updated in time?
self.do_wdid_lookup()
except KeyError as e:
PBB_Core.WDItemEngine.log(
"ERROR", format_msg(self.id, INTERPRO, None, str(e), type(e)))
return
statements = [
PBB_Core.WDExternalID(value=self.id,
prop_nr=INTERPRO,
references=[self.reference])
]
if self.parent:
# subclass of
statements.append(
PBB_Core.WDItemID(value=self.parent_wdid,
prop_nr='P279',
references=[self.reference]))
if self.contains:
for c in self.contains_wdid:
statements.append(
PBB_Core.WDItemID(value=c,
prop_nr='P527',
references=[self.reference])) # has part
if self.found_in:
for f in self.found_in_wdid:
statements.append(
PBB_Core.WDItemID(value=f,
prop_nr='P361',
references=[self.reference])) # part of
if len(statements) == 1:
return
wd_item = PBB_Core.WDItemEngine(
wd_item_id=self.wdid,
domain='interpro',
data=statements,
append_value=['P279', 'P527', 'P361'],
fast_run=True,
fast_run_base_filter=IPRTerm.fast_run_base_filter)
PBB_Helpers.try_write(
wd_item,
self.id,
INTERPRO,
login,
edit_summary="create/update subclass/has part/part of")
def do_umls_statement(self, doid, umls_list, dry_run=False):
statements = []
for umls in umls_list:
statements.append(PBB_Core.WDExternalID(value=umls, prop_nr=self.UMLS_PROP, references=[self.reference]))
wd_item = PBB_Core.WDItemEngine(wd_item_id=self.DOID2WD[doid], domain='disease', data=statements,
append_value=[self.UMLS_PROP], fast_run=True,
fast_run_base_filter=self.fast_run_base_filter)
# no item creation should be done
if wd_item.create_new_item:
raise ValueError("something bad happpened")
if dry_run:
if wd_item.require_write:
info_logger.info(" ".join(["item_updated", doid, wd_item.wd_item_id]))
if wd_item.require_write and not dry_run:
self.try_write(wd_item, doid)
def create_item(self):
statements = [
PBB_Core.WDExternalID(value=self.id,
prop_nr=INTERPRO,
references=[self.reference]),
PBB_Core.WDItemID(value=IPRItem.type2subclass[self.type],
prop_nr="P279",
references=[self.reference])
]
item = PBB_Core.WDItemEngine(item_name=self.name,
domain='interpro',
data=statements,
server=SERVER)
item.set_label(self.name)
for lang, description in self.description.items():
item.set_description(description, lang=lang)
item.set_aliases([self.short_name, self.id])
try:
item.write(login=self.login)
except WDApiError as e:
print(e)
PBB_Core.WDItemEngine.log(
'ERROR',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'
.format(main_data_id=self.id,
exception_type=type(e),
message=e.__str__(),
wd_id=self.wd_item_id,
duration=datetime.now()))
return
self.wd_item_id = item.wd_item_id
PBB_Core.WDItemEngine.log(
'INFO',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'
.format(main_data_id=self.id,
exception_type='',
message='created/updated interpro item',
wd_id=item.wd_item_id,
duration=datetime.now()))