def ncbi_search(self, database, term):
"""
Submit search to NCBI and return the records.
"""
self.handle = Entrez.esearch(db=database, term=term, usehistory="y",
retmax=100000000)
self.record = Entrez.read(self.handle)
self.handle.close()
return self.record
def ncbi_search(self, database, term):
"""
Submit search to NCBI and return the records.
"""
self.handle = Entrez.esearch(db=database, term=term, usehistory="y",
retmax=10, idtype="acc")
self.record = Entrez.read(self.handle)
self.handle.close()
return self.record
def validate_and_convert_DOI_or_PMID_to_PMID(lookupID, comments):
"""
Look up a DOI -- or PMID -- and return a PMID.
:param lookupID: either a DOI or a PMID.
:return a PMID
"""
# Format as string and strip any leading white spaces. Do now so we can reach DOI/PMIDs.
lookupID = str(lookupID).lstrip()
# Remove any prefacing text that might've come through. Only if it's at the start of the lookupID.
preface_tags = ['DOI:', 'doi:', 'PMID:', 'pmid:']
for tag in preface_tags:
if lookupID.startswith(tag):
lookupID = re.sub(tag, '', lookupID)
# Drop any white spaces that remain.
lookupID = lookupID.replace(" ", "")
try:
Entrez.email = app.config['EMAIL']
handle = Entrez.esearch(db="pubmed", retmax=10, term=lookupID)
record = Entrez.read(handle)
handle.close()
if int(record['Count']) == 0:
comments.append("I can't fetch an article with that ID."
) # DOI not on PubMed? Or Bad PMID?
comments.append(
"Try looking up the article on www.pubmed.gov. (Note: PubMed may not have the DOI.) If the article is there, copy its PMID and bring it to me. If the article isn't on PubMed, I can't fetch a citation for you. Sorry. :( "
)
return '', comments
elif int(record['Count']) > 1:
comments.append(
'I found more than one article. Are there characters missing from the ID?'
)
return '', comments
else: # Only 1 result, perfect!
return (record['IdList'][0]), comments
except IOError: # Network error
comments.append(
"Is there a network problem? Unleash me please!") # Network error
return '', comments
except:
comments.append("I can't fetch an article with ID " + lookupID +
'. Can you double check it?') # Bad PMID?
comments.append(
"Try looking up the article on www.pubmed.gov. (Note: PubMed may not have the DOI.) If the article is there, copy its PMID and bring it to me. If the article isn't on PubMed, I can't fetch a citation for you. Sorry. :( "
)
return '', comments
