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 create_reference(spl_url,source_type):
timeStringNow = datetime.now().strftime("+%Y-%m-%dT00:00:00Z")
archived_date = datetime.strptime('9/29/2015','%m/%d/%Y').strftime("+%Y-%m-%dT00:00:00Z")
refStatedIn = wdi_core.WDItemID(value="Q73670648", prop_nr="P248", is_reference=True)
refRetrieved = wdi_core.WDTime(timeStringNow, prop_nr="P813", is_reference=True)
refRetrieved2 = wdi_core.WDTime(archived_date, prop_nr="P2960", is_reference=True)
refURL = wdi_core.WDUrl(value=spl_url, prop_nr="P854", is_reference=True)
reftype = wdi_core.WDString(value=source_type, prop_nr="P958", is_reference=True)
return [refStatedIn, refRetrieved, refRetrieved2, refURL, reftype]
def create_reference():
refStatedIn = wdi_core.WDItemID(value="Q70116865",
prop_nr="P248",
is_reference=True)
timeStringNow = datetime.now().strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow,
prop_nr="P813",
is_reference=True)
refStatedIn2 = wdi_core.WDItemID(value="Q21008030",
prop_nr="P248",
is_reference=True)
refRetrieved2 = wdi_core.WDTime(timeStringNow,
prop_nr="P813",
is_reference=True)
return [refStatedIn, refRetrieved, refStatedIn2, refRetrieved2]
def task_processor(self, task, n):
ref = [[
wdi_core.WDItemID(value=self.source,
prop_nr='P248',
is_reference=True),
wdi_core.WDUrl(value=self.url_pattern +
urllib.parse.quote_plus(str(task[1])),
prop_nr='P854',
is_reference=True),
wdi_core.WDTime(task[2], prop_nr='P813', is_reference=True)
]]
data = []
for cited_item in task[3]:
data.append(
wdi_core.WDItemID(value='Q' + str(cited_item),
prop_nr='P2860',
references=ref))
itemengine = self.integrator[n]['core'].WDItemEngine(
wd_item_id='Q' + str(task[0]),
data=data,
append_value=self.append_value,
good_refs=self.good_refs,
keep_good_ref_statements=True)
print(
itemengine.write(self.integrator[n]['login'],
edit_summary=self.edit_summary))
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 createNCBITaxReference(ncbiTaxId, retrieved):
refStatedIn = wdi_core.WDItemID(value="Q13711410", prop_nr="P248", is_reference=True)
timeStringNow = retrieved.strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow, prop_nr="P813", is_reference=True)
refNcbiTaxID = wdi_core.WDString(value=ncbiTaxId, prop_nr="P685", is_reference=True)
ncbi_reference = [refStatedIn, refRetrieved, refNcbiTaxID]
return ncbi_reference
def create_reference(unii: str, url=None):
"""
Reference is:
retrieved: date
stated in: links to pmid items
optional reference URL
"""
#
ref = [
wdi_core.WDItemID(ITEMS['Inxight: Drugs Database'],
PROPS['stated in'],
is_reference=True)
]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
ref.append(
wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
if unii:
ref_url = "https://drugs.ncats.io/drug/{}".format(unii)
ref.append(
wdi_core.WDUrl(ref_url,
PROPS['reference URL'],
is_reference=True))
if url:
for u in url:
try:
ref.append(
wdi_core.WDUrl(u,
PROPS['reference URL'],
is_reference=True))
except Exception as e:
print(e)
print(u)
return ref
def create_references(self, gdr):
references = []
# Reference URL for phenocarta
references.append(
wdi_core.WDUrl(value=gdr.phenocarta_url,
prop_nr=PROPS['reference URL'],
is_reference=True))
# Reference URL for genome.gov
references.append(
wdi_core.WDUrl(value=gdr.link,
prop_nr=PROPS['reference URL'],
is_reference=True))
# Stated in Phenocarta
references.append(
wdi_core.WDItemID(value='Q22330995',
prop_nr=PROPS['stated in'],
is_reference=True))
# Stated in PubMed
references.append(
wdi_core.WDItemID(value=self.pmid_qid_map[gdr.pmid],
prop_nr=PROPS['stated in'],
is_reference=True))
# Date retrieved
references.append(
wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()),
prop_nr=PROPS['retrieved'],
is_reference=True))
return references
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_reference(omim, pmid, login=None):
"""
Reference is:
retrieved: date
stated in: links to pmid items
optional reference URL
"""
#
ref = [
wdi_core.WDItemID(ITEMS['MitoDB'],
PROPS['curator'],
is_reference=True)
]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
ref.append(
wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
pmid_qid, _, success = PublicationHelper(
ext_id=pmid, id_type='pmid',
source="europepmc").get_or_create(login)
if success is True:
ref.append(
wdi_core.WDItemID(pmid_qid,
PROPS['stated in'],
is_reference=True))
ref_url = "http://mitodb.com/symptoms.php?oid={}&symptoms=Show"
ref.append(
wdi_core.WDUrl(ref_url.format(omim),
PROPS['reference URL'],
is_reference=True))
return ref
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 create_reference(source_str, evidence_level, login):
"""
Reference is:
curator: Cancer Biomarkers database
retrieved: date
stated in: links to pmid items
no reference URL
"""
reference = [
wdi_core.WDItemID(ITEMS['Cancer Biomarkers database'],
PROPS['curator'],
is_reference=True)
]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
reference.append(
wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
for source in source_str.split(";"):
if source.startswith("PMID:"):
qid, _, success = wdi_helpers.PublicationHelper(
source.replace("PMID:", ""),
id_type="pmid",
source="europepmc").get_or_create(login)
if success:
reference.append(
wdi_core.WDItemID(qid,
PROPS['stated in'],
is_reference=True))
elif source in source_map:
reference.append(
wdi_core.WDItemID(source_map[source],
PROPS['stated in'],
is_reference=True))
else:
print("unknown source: {}".format(source))
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 createNCBIGeneReference(ncbiGeneId, retrieved):
refStatedIn = wdi_core.WDItemID(value="Q20641742", prop_nr="P248", is_reference=True)
timeStringNow = retrieved.strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow, prop_nr="P813", is_reference=True)
refNcbiGeneID = wdi_core.WDString(value=ncbiGeneId, prop_nr="P351", is_reference=True)
ncbi_reference = [refStatedIn, refRetrieved, refNcbiGeneID]
return ncbi_reference
def createUniprotReference(uniprotId, retrieved):
refStatedIn = wdi_core.WDItemID(value="Q905695", prop_nr="P248", is_reference=True)
timeStringNow = retrieved.strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow, prop_nr="P813", is_reference=True)
refUniprotID = wdi_core.WDString(value=uniprotId, prop_nr="P352", is_reference=True)
reference = [refStatedIn, refRetrieved, refUniprotID]
return reference
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 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]
def create_qualifiers(date: datetime) -> List[Any]:
ref_time_str = f'+{date.isoformat()}Z'
point_in_time = wdi_core.WDTime(time=ref_time_str,
prop_nr='P585',
is_qualifier=True)
determination_method = wdi_core.WDItemID(value='Q90878157',
prop_nr="P459",
is_qualifier=True)
return [point_in_time, determination_method]
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_reference(genbank_id):
stated_in = wdi_core.WDItemID(ITEMS['GenBank'],
PROPS['stated in'],
is_reference=True)
retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()),
PROPS['retrieved'],
is_reference=True)
url = "https://www.ncbi.nlm.nih.gov/genome/?term={}".format(genbank_id)
ref_url = wdi_core.WDUrl(url, PROPS['reference URL'], is_reference=True)
return [stated_in, retrieved, ref_url]
def make_go_ref(curator,
pmid_map,
external_id,
uniprot_id,
evidence_wdid,
retrieved,
pmid=None):
# initialize this reference for this evidence code with retrieved
reference = [
wdi_core.WDTime(retrieved.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True)
]
# stated in pmid
if pmid:
if pmid in pmid_map:
reference.append(
wdi_core.WDItemID(pmid_map[pmid], 'P248', is_reference=True))
else:
raise ValueError(
"article item for pmid {} not found. skipping item".format(
pmid))
# stated in uniprot-GOA Q28018111
reference.append(wdi_core.WDItemID('Q28018111', 'P248', is_reference=True))
# curator
if curator in curators_wdids:
reference.append(
wdi_core.WDItemID(curators_wdids[curator],
'P1640',
is_reference=True))
# curator-specific reference URLs
# If curator is SGD, add external ID to ref
if curator in curator_ref and curator_ref[curator] in external_id:
reference.append(
wdi_core.WDString(external_id[curator_ref[curator]],
PROPS[curator_ref[curator]],
is_reference=True))
else:
raise ValueError("curator not found: {}".format(curator))
# reference URL
# ref_url = "http://www.ebi.ac.uk/QuickGO/GAnnotation?protein={}".format(uniprot_id)
ref_url = "http://www.ebi.ac.uk/QuickGO/annotations?protein={}&geneProductId=UniProtKB:{}".format(
uniprot_id, uniprot_id)
reference.append(wdi_core.WDString(ref_url, 'P854', is_reference=True))
# ref determination method
reference.append(
wdi_core.WDItemID(evidence_wdid, 'P459', is_reference=True))
return reference
def create_reference(ghr_url):
refStatedIn = wdi_core.WDItemID(value="Q62606821",
prop_nr="P248",
is_reference=True)
timeStringNow = datetime.now().strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow,
prop_nr="P813",
is_reference=True)
refURL = wdi_core.WDUrl(value=ghr_url, prop_nr="P854", is_reference=True)
return [refStatedIn, refRetrieved, refURL]
def create_reference():
refStatedIn = wdi_core.WDItemID(value="Q64403342",
prop_nr="P248",
is_reference=True)
timeStringNow = datetime.now().strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow,
prop_nr="P813",
is_reference=True)
refURL = wdi_core.WDUrl((df.loc[index, 'Report Reference URL']),
prop_nr="P854",
is_reference=True)
return [refStatedIn, refRetrieved, refURL]
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_reference():
"""Create references for an item."""
stated_in = wdi_core.WDItemID(ITEMS['Schools Portal'],
PROPS['stated in'],
is_reference=True)
retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()),
PROPS['retrieved'],
is_reference=True)
url = "http://dati.istruzione.it/opendata/opendata/catalogo/elements1/?area=Scuole"
ref_url = wdi_core.WDUrl(url, PROPS['reference URL'], is_reference=True)
return [stated_in, retrieved, ref_url]
def create_reference(self):
"""
Reference is:
retrieved: date
stated in: links to pmid items
no reference URL
"""
# Drug Indications Extracted from FAERS (Q56863002)
ref = [wdi_core.WDItemID("Q56863002", PROPS['stated in'], is_reference=True)]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
ref.append(wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
self.refs = [ref]
def create_qualifier(start_time: datetime):
q = []
if start_time:
q.append(
wdi_core.WDTime(start_time.strftime('+%Y-%m-%dT00:00:00Z'),
PROPS['start time'],
is_qualifier=True))
q.append(
wdi_core.WDItemID(ITEMS['Food and Drug Administration'],
PROPS['approved by'],
is_qualifier=True))
return q
def create_reference(dbsnp_id):
refStatedIn = wdi_core.WDItemID(value="Q5243761",
prop_nr="P248",
is_reference=True)
retrieved = datetime.datetime.now()
timeStringNow = retrieved.strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow,
prop_nr="P813",
is_reference=True)
refDbSNP = wdi_core.WDString(value=dbsnp_id,
prop_nr="P6861",
is_reference=True)
return [refStatedIn, refRetrieved, refDbSNP]
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
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