def run_one(row):
label = row['#Organism/Name']
taxid = str(row['TaxID'])
genbank_id = row['Assembly Accession']
s = [
wdi_core.WDExternalID(genbank_id,
uri_map[PROPS['GenBank Assembly accession']],
references=[create_reference(genbank_id)]),
wdi_core.WDExternalID(taxid,
uri_map[PROPS['NCBI Taxonomy ID']],
references=[create_reference(genbank_id)]),
]
item = localItemEngine(
data=s,
item_name=label,
domain="organism",
fast_run=True,
fast_run_base_filter={uri_map[PROPS['NCBI Taxonomy ID']]: ''})
item.set_label(label)
item.set_description("bug")
wdi_helpers.try_write(
item,
login=login,
record_id=genbank_id,
record_prop=uri_map[PROPS['GenBank Assembly accession']])
def test_fast_run(self):
qid = 'Q27552312'
statements = [
wdi_core.WDExternalID(value='P40095', prop_nr='P352'),
wdi_core.WDExternalID(value='YER158C', prop_nr='P705')
]
frc = wdi_fastrun.FastRunContainer(
base_filter={
'P352': '',
'P703': 'Q27510868'
},
base_data_type=wdi_core.WDBaseDataType,
engine=wdi_core.WDItemEngine)
fast_run_result = frc.write_required(data=statements)
if fast_run_result:
message = 'fastrun failed'
else:
message = 'successful fastrun'
print(fast_run_result, message)
# here, fastrun should succeed, if not, test failed
if fast_run_result:
raise ValueError
def test_ref_equals():
# statements are identical
oldref = [
wdi_core.WDExternalID(value='P58742', prop_nr='P352'),
wdi_core.WDItemID(value='Q24784025', prop_nr='P527'),
wdi_core.WDTime('+2001-12-31T12:01:13Z', prop_nr='P813')
]
olditem = wdi_core.WDItemID("Q123", "P123", references=[oldref])
newitem = copy.deepcopy(olditem)
assert olditem.equals(newitem, include_ref=False)
assert olditem.equals(newitem, include_ref=True)
# dates are a month apart
newitem = copy.deepcopy(olditem)
newitem.references[0][2] = wdi_core.WDTime('+2002-1-31T12:01:13Z',
prop_nr='P813')
assert olditem.equals(newitem, include_ref=False)
assert not olditem.equals(newitem, include_ref=True)
# multiple refs
newitem = copy.deepcopy(olditem)
newitem.references.append(
[wdi_core.WDExternalID(value='99999', prop_nr='P352')])
assert olditem.equals(newitem, include_ref=False)
assert not olditem.equals(newitem, include_ref=True)
olditem.references.append(
[wdi_core.WDExternalID(value='99999', prop_nr='P352')])
assert olditem.equals(newitem, include_ref=True)
def do_pharm_prod(drug_qid, brand_rxnorm, emea, url, brand_name):
# write info on the pharmaceutical product page
ref = create_ref_statement(emea, url)
# has active substance
s = [wdi_core.WDItemID(drug_qid, 'P3781', references=[ref])]
# instance of
s.append(wdi_core.WDItemID('Q28885102', 'P31',
references=[ref])) # pharmaceutical product
s.append(wdi_core.WDItemID('Q169336', 'P31',
references=[ref])) # chemical mixture
# emea
s.append(wdi_core.WDExternalID(emea, 'P3637', references=[ref]))
if not pd.isnull(brand_rxnorm):
s.append(wdi_core.WDExternalID(str(int(brand_rxnorm)), "P3345"))
item = wdi_core.WDItemEngine(item_name=brand_name,
data=s,
domain="drugs",
append_value=['P3781'])
item.set_label(brand_name)
if item.get_description() == '':
item.set_description("pharmaceutical product")
wdi_helpers.try_write(item,
emea,
'P3637',
login,
edit_summary="add 'active ingredient'")
return item.wd_item_id
def create_xref_statements(self):
if not self.reference:
self.create_reference()
self.s_xref = []
self.s_xref.append(
wdi_core.WDExternalID(self.doid,
PROPS['Disease Ontology ID'],
references=[self.reference]))
for xref in self.xrefs:
prefix, code = xref.split(":", 1)
if prefix in DOGraph.xref_prop:
self.s_xref.append(
wdi_core.WDExternalID(code,
DOGraph.xref_prop[prefix],
references=[self.reference]))
def create_xref_statements(self):
if not self.reference:
self.create_reference()
self.s_xref = []
self.s_xref.append(wdi_core.WDExternalID(self.doid, PROPS['Disease Ontology ID'], references=[self.reference]))
for xref in self.xrefs:
if ":" in xref:
prefix, code = xref.split(":", 1)
prefix = prefix.strip()
code = code.strip()
if prefix.upper() in DOGraph.xref_prop:
if prefix.upper() == "OMIM" and code.startswith("PS"):
continue
self.s_xref.append(
wdi_core.WDExternalID(code, DOGraph.xref_prop[prefix.upper()], references=[self.reference]))
def create_relationships(self, login, write=True):
try:
# endpoint may not get updated in time?
self.do_wdid_lookup()
except KeyError as e:
wdi_core.WDItemEngine.log("ERROR", format_msg(self.id, INTERPRO, None, str(e), type(e)))
return
statements = [wdi_core.WDExternalID(value=self.id, prop_nr=INTERPRO, references=[self.reference])]
if self.parent:
# subclass of
statements.append(wdi_core.WDItemID(value=self.parent_wdid, prop_nr='P279', references=[self.reference]))
if self.contains:
for c in self.contains_wdid:
statements.append(wdi_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(wdi_core.WDItemID(value=f, prop_nr='P361', references=[self.reference])) # part of
if len(statements) == 1:
return
wd_item = wdi_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)
wdi_helpers.try_write(wd_item, self.id, INTERPRO, login, edit_summary="create/update subclass/has part/part of",
write=write)
def create_item(self, login=None, fast_run=True, write=True):
# if no login given, write will not be attempted
statements = [wdi_core.WDExternalID(value=self.id, prop_nr=INTERPRO, references=[self.reference]),
wdi_core.WDItemID(value=self.type_wdid, prop_nr=INSTANCE_OF,
references=[self.reference])]
try:
wd_item = wdi_core.WDItemEngine(item_name=self.name, domain='interpro', data=statements,
append_value=["P279", "P31"],
fast_run=fast_run, fast_run_base_filter=IPRTerm.fast_run_base_filter)
except JSONDecodeError as e:
wdi_core.WDItemEngine.log("ERROR",
wdi_helpers.format_msg(self.id, INTERPRO, None, str(e), msg_type=type(e)))
return None
wd_item.set_label(self.name, lang='en')
for lang, description in self.lang_descr.items():
if wd_item.get_description(lang=lang) == "":
wd_item.set_description(description, lang=lang)
wd_item.set_aliases([self.short_name, self.id])
if login:
wdi_helpers.try_write(wd_item, self.id, INTERPRO, login, write=write)
return wd_item
def set_taxon(taxid):
ncbiTaxon = json.loads(
requests.get(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&id={}&format=json"
.format(taxid)).text)
taxonitemStatements = []
ncbiTaxref = createNCBITaxReference(taxid, retrieved)
## instance of
taxonitemStatements.append(
wdi_core.WDItemID(value="Q16521",
prop_nr="P31",
references=[copy.deepcopy(ncbiTaxref)]))
## NCBI tax id
taxonitemStatements.append(
wdi_core.WDExternalID(value=taxid,
prop_nr="P685",
references=[copy.deepcopy(ncbiTaxref)]))
## scientificname
scientificName = ncbiTaxon["result"][taxid]['scientificname']
taxonitemStatements.append(
wdi_core.WDString(scientificName,
prop_nr="P225",
references=[copy.deepcopy(ncbiTaxref)]))
item = wdi_core.WDItemEngine(data=taxonitemStatements)
if item.get_label() == "":
item.set_label(label=scientificName, lang="en")
if item.get_label() != scientificName:
item.set_aliases(aliases=[scientificName])
if item.get_description(lang="en") == "":
item.set_description(description="strain of virus", lang="en")
return item
def run_one(taxid, genbank_id):
# get the QID
taxid = str(taxid)
if taxid not in tax_qid_map:
msg = wdi_helpers.format_msg(
genbank_id, PROPS['GenBank Assembly accession'], "",
"organism with taxid {} not found or skipped".format(taxid))
wdi_core.WDItemEngine.log("WARNING", msg)
return None
qid = tax_qid_map[taxid]
reference = create_reference(genbank_id)
genbank_statement = wdi_core.WDExternalID(
genbank_id,
PROPS['GenBank Assembly accession'],
references=[reference])
# create the item object, specifying the qid
item = wdi_core.WDItemEngine(
data=[genbank_statement],
wd_item_id=qid,
fast_run=True,
fast_run_base_filter={PROPS['GenBank Assembly accession']: ''},
global_ref_mode='CUSTOM',
fast_run_use_refs=True,
ref_handler=update_retrieved_if_new)
wdi_helpers.try_write(item,
record_id=genbank_id,
record_prop=PROPS['GenBank Assembly accession'],
login=login,
edit_summary="update GenBank Assembly accession")
def make_ref(nui):
refs = [[
wdi_core.WDItemID(value='Q21008030', prop_nr='P248', is_reference=True), # stated in ndfrt
wdi_core.WDExternalID(value=nui, prop_nr='P2115', is_reference=True), # NDF-RT ID
wdi_core.WDTime(time=time.strftime('+%Y-%m-%dT00:00:00Z'), prop_nr='P813', is_reference=True) # retrieved
]]
return refs
def create(self, label: str, rxcui: str, ingredient_qids: list):
rxcui = str(rxcui)
# check to make sure it doesn't exist
if rxcui in self.rxnorm_qid:
raise ValueError("rxcui {} already exists: {}".format(rxcui, self.rxnorm_qid[rxcui]))
# check by ingredients
qid = self.get_mixture_qid(ingredient_qids)
if qid:
raise ValueError("mixture already exists: {}".format(qid))
# has part
s = [wdi_core.WDItemID(x, 'P527', references=make_ref(rxcui)) for x in ingredient_qids]
# instance of
s.append(wdi_core.WDItemID('Q12140', 'P31', references=make_ref(rxcui))) # drug
s.append(wdi_core.WDItemID('Q79529', 'P31', references=make_ref(rxcui))) # chemical substance
s.append(wdi_core.WDItemID('Q169336', 'P31', references=make_ref(rxcui))) # mixture
# rxnorm
s.append(wdi_core.WDExternalID(rxcui, "P3345", references=make_ref(rxcui)))
item = wdi_core.WDItemEngine(item_name=label, data=s, domain="drugs")
if item.create_new_item:
item.set_label(label)
item.set_label(label)
if not item.get_description():
item.set_description("combination drug")
item.write(self.login)
qid = item.wd_item_id
# update cache
self.components_mixture[frozenset(ingredient_qids)] = qid
self.mixture_components[qid] = ingredient_qids
self.rxnorm_qid[rxcui] = qid
return qid
def make_ref(rxnorm):
refs = [[
wdi_core.WDItemID(value='Q7383767', prop_nr='P248', is_reference=True), # stated in rxnorm
wdi_core.WDExternalID(value=rxnorm, prop_nr='P3345', is_reference=True), # rxcui
wdi_core.WDTime(time=time.strftime('+%Y-%m-%dT00:00:00Z'), prop_nr='P813', is_reference=True) # retrieved
]]
return refs
def to_wikidata(self):
refs = [[
wdi_core.WDItemID(value='Q278487',
prop_nr='P248',
is_reference=True), # stated in
wdi_core.WDExternalID(value=self.cid,
prop_nr='P662',
is_reference=True), # source element
wdi_core.WDTime(time=time.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True) # retrieved
]]
elements = {'P662': self.cid[3:]}
data = []
for k, v in elements.items():
if not v:
continue
print('{}:'.format(k), v)
if isinstance(v, list) or isinstance(v, set):
for x in v:
data.append(
wdi_core.WDString(prop_nr=k, value=x, references=refs))
else:
data.append(
wdi_core.WDString(prop_nr=k, value=v, references=refs))
return data
def test_fastrun_label(self):
# tests fastrun label, description and aliases, and label in another language
data = [wdi_core.WDExternalID('/m/02j71', 'P646')]
fast_run_base_filter = {'P361': 'Q18589965'}
item = wdi_core.WDItemEngine(wd_item_id="Q2",
data=data,
fast_run=True,
fast_run_base_filter=fast_run_base_filter)
frc = wdi_core.WDItemEngine.fast_run_store[0]
frc.debug = True
assert item.get_label('en') == "Earth"
descr = item.get_description('en')
assert len(descr) > 3
aliases = item.get_aliases()
assert "Terra" in aliases
assert list(
item.fast_run_container.get_language_data("Q2", 'en',
'label'))[0] == "Earth"
assert item.fast_run_container.check_language_data(
"Q2", ['not the Earth'], 'en', 'label')
assert "Terra" in item.get_aliases()
assert "planet" in item.get_description()
assert item.get_label("es") == "Tierra"
item.set_description(descr)
item.set_description("fghjkl")
assert item.wd_json_representation['descriptions']['en'] == {
'language': 'en',
'value': 'fghjkl'
}
item.set_label("Earth")
item.set_label("xfgfdsg")
assert item.wd_json_representation['labels']['en'] == {
'language': 'en',
'value': 'xfgfdsg'
}
item.set_aliases(["fake alias"], append=True)
assert {
'language': 'en',
'value': 'fake alias'
} in item.wd_json_representation['aliases']['en']
# something thats empty (for now.., can change, so this just makes sure no exception is thrown)
frc.check_language_data("Q2", ['Ewiase'], 'ak', 'label')
frc.check_language_data("Q2", ['not Ewiase'], 'ak', 'label')
frc.check_language_data("Q2", [''], 'ak', 'description')
frc.check_language_data("Q2", [], 'ak', 'aliases')
frc.check_language_data("Q2", ['sdf', 'sdd'], 'ak', 'aliases')
item.get_label("ak")
item.get_description("ak")
item.get_aliases("ak")
item.set_label("label", lang="ak")
item.set_description("d", lang="ak")
item.set_aliases(["a"], lang="ak", append=True)
def create_ref_statement(emea_id, url):
ref_url = wdi_core.WDUrl(url, prop_nr='P854', is_reference=True)
ref_emea = wdi_core.WDExternalID(emea_id, 'P3637', is_reference=True)
ref_retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()),
prop_nr='P813',
is_reference=True)
reference = [ref_emea, ref_url, ref_retrieved]
return reference
def create_ref_statement(self, doid):
if not self.release:
self.create_release()
stated_in = wdi_core.WDItemID(value=self.release, prop_nr='P248', is_reference=True)
ref_doid = wdi_core.WDExternalID(value=doid, prop_nr='P699', is_reference=True)
ref_retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()), prop_nr='P813', is_reference=True)
do_reference = [stated_in, ref_retrieved, ref_doid]
return do_reference
def append_cellosaurus_id(cellosaurus_cell_line_id,
information_to_insert_on_wikidata, reference):
# P3289 : Cellosaurus ID
information_to_insert_on_wikidata.append(
wdi_core.WDExternalID(value=cellosaurus_cell_line_id,
prop_nr="P3289",
references=reference))
return information_to_insert_on_wikidata
def createMONDOReference(id):
statedin = wdi_core.WDItemID("Q2", prop_nr="P6", is_reference=True)
retrieved = datetime.now()
timeStringNow = retrieved.strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow,
prop_nr="P7",
is_reference=True)
mondoid = wdi_core.WDExternalID(id, prop_nr="P5", is_reference=True)
return [statedin, refRetrieved, mondoid]
async def add_topic(self,
topic_id: str,
categories: [str],
fid=None) -> str:
data = [
wdi_core.WDExternalID(value=topic_id, prop_nr=self.PROP_TOPIC),
wdi_core.WDItemID('Q887', prop_nr=self.PROP_POST_TYPE)
]
for c in categories:
data.append(
wdi_core.WDExternalID(value=c, prop_nr=self.PROP_CATEGORY))
if fid:
data.append(wdi_core.WDExternalID(value=fid,
prop_nr=self.PROP_FID))
cur_id = await get_qid_from_property(12, topic_id)
wd_item = wdi_core.WDItemEngine(wd_item_id=cur_id,
data=data,
mediawiki_api_url=self.MW_URL)
return wd_item.write(self.get_login())
def update_song(entity, song_obj, artist_wikidata_id, artist_name):
existing_instanceOf_ids = get_wikidata_property_values(
entity, INSTANCE_OF_ID)
song_name = get_song_name(song_obj)
data = entity.statements
song_mb_id = get_musicbrainz_song_id(song_obj)
# Set to be musician if not already
if SONG_ID not in existing_instanceOf_ids:
# Add occupation musician relation
data.append(wdi_core.WDItemID(value=SONG_ID, prop_nr=INSTANCE_OF_ID))
# Set MusicBrainzID if not already set
if MUSIC_BRAINZ_SONG_PROP_ID not in entity.wd_json_representation[
'claims']:
data.append(
wdi_core.WDExternalID(value=get_musicbrainz_song_id(song_obj),
prop_nr=MUSIC_BRAINZ_SONG_PROP_ID))
elif song_mb_id not in get_wikidata_property_values(
entity, MUSIC_BRAINZ_SONG_PROP_ID):
data.append(
wdi_core.WDExternalID(value=get_musicbrainz_song_id(song_obj),
prop_nr=MUSIC_BRAINZ_SONG_PROP_ID))
# Set performer to be the artist if no performer set or performer is not artist
if PERFORMER_ID not in entity.wd_json_representation['claims']:
data.append(
wdi_core.WDItemID(value=artist_wikidata_id, prop_nr=PERFORMER_ID))
elif artist_wikidata_id not in get_wikidata_property_values(
entity, PERFORMER_ID):
data.append(
wdi_core.WDItemID(value=artist_wikidata_id, prop_nr=PERFORMER_ID))
# Set performer to be the artist if no performer set or performer is not artist
# Set song name property
if TITLE_ID not in entity.wd_json_representation['claims']:
data.append(
wdi_core.WDMonolingualText(value=song_name, prop_nr=TITLE_ID))
if get_description(entity) == '':
entity.set_description(f"Song performed by {artist_name}")
write_to_wikidata(entity, data)
print(
f"Song {song_name} by {artist_name} has been updated on WikiData server."
)
def add_extra_statements(self):
if self.url:
is_download_url = wdi_core.WDItemID('Q7126717',
'P642',
is_qualifier=True)
self.statements.append(
wdi_core.WDUrl(self.url, 'P2699',
qualifiers=[is_download_url]))
if self.doi:
self.statements.append(wdi_core.WDExternalID(self.doi, 'P356'))
def create_ref_statement(self):
assert self.graph.release_qid, "create the release first (on the graph class)"
stated_in = wdi_core.WDItemID(value=self.graph.release_qid, prop_nr=self.helper.get_pid('P248'),
is_reference=True)
ref_extid = wdi_core.WDExternalID(value=self.id_value, prop_nr=self.id_pid, is_reference=True)
ref_retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()),
prop_nr=self.helper.get_pid('P813'), is_reference=True)
reference = [stated_in, ref_retrieved, ref_extid]
return reference
def create_xref_statements(self):
"""
These are string only and do not rely on any other items existing
:return:
"""
if not self.reference:
self.create_reference()
s = [
wdi_core.WDExternalID(self.id_colon,
self.primary_ext_prop_qid,
references=[self.reference])
]
for xref in self.xrefs:
prefix, code = xref.split(":", 1)
if prefix in self.graph.xref_props:
s.append(
wdi_core.WDExternalID(code,
self.graph.xref_props[prefix],
references=[self.reference]))
return s
def append_mesh_id(cell_line_object, data_to_add_to_wikidata):
# P486 : MeSH ID
cell_line_mesh = cell_line_object.cell_line_dump["MeSH"]
reference = cell_line_object.references_in_wdi_format
if cell_line_mesh != "NULL":
data_to_add_to_wikidata.append(
wdi_core.WDExternalID(
value=cell_line_object.cell_line_dump["MeSH"],
prop_nr="P486",
references=reference))
return data_to_add_to_wikidata
def buildRefs(refseq):
refs = [
wdi_core.WDItemID(value="Q7307074", prop_nr='P248', is_reference=True)
]
refs.append(
wdi_core.WDTime("+2018-09-12T00:00:00Z",
prop_nr='P813',
is_reference=True))
refs.append(
wdi_core.WDExternalID(value=refseq, prop_nr='P2249',
is_reference=True))
return refs
def create_xref_statement(self, xref):
ref = self.create_ref_statement()
if xref.split(":")[0] not in cu.curie_map:
# log this curie prefix not being found
m = wdi_helpers.format_msg(self.id_curie, self.id_pid, self.qid,
"curie prefix not found: {}".format(xref.split(":")[0]))
wdi_core.WDItemEngine.log("WARNING", m)
return None
pid, ext_id = cu.parse_curie(xref)
pid = self.helper.get_pid(pid)
self.pids.add(pid)
return wdi_core.WDExternalID(ext_id, pid, references=[ref])
def append_hpscreg_id(cell_line_object, data_to_add_to_wikidata):
# P9554 : hPSCreg cell line ID
cell_line_hpscreg = cell_line_object.cell_line_dump["hPSCreg"]
reference = cell_line_object.references_in_wdi_format
if cell_line_hpscreg != "NULL":
data_to_add_to_wikidata.append(
wdi_core.WDExternalID(
value=cell_line_object.cell_line_dump["hPSCreg"],
prop_nr="P9554",
references=reference,
))
return data_to_add_to_wikidata
def create_ref_statement(release_qid, external_prop_id, external_id):
stated_in = wdi_core.WDItemID(value=release_qid,
prop_nr='P248',
is_reference=True)
ref_external_id = wdi_core.WDExternalID(value=external_id,
prop_nr=external_prop_id,
is_reference=True)
ref_retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z",
gmtime()),
prop_nr='P813',
is_reference=True)
do_reference = [stated_in, ref_retrieved, ref_external_id]
return do_reference
def make_ref(mesh_id):
refs = [[
wdi_core.WDItemID(value=ITEMS['Medical Subject Headings'],
prop_nr='P248',
is_reference=True), # stated in mesh
wdi_core.WDExternalID(value=mesh_id,
prop_nr=PROPS['MeSH ID'],
is_reference=True), # mesh id
wdi_core.WDTime(time=time.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True) # retrieved
]]
return refs
