def erratum_check(PMID, comments):
""" Does this PMID have an erratum?
I can't do the erratum formatting automatically.
But I can warn user that there is an erratum.
"""
Entrez.email = app.config['EMAIL']
handle = Entrez.efetch(db="pubmed", id=PMID, rettype="gb", retmode="xml")
records = Entrez.read(handle)
erratum_count = 0
try:
corrections = records['PubmedArticle'][0]['MedlineCitation'][
'CommentsCorrectionsList']
for correction in corrections:
if correction.attributes['RefType'] == 'ErratumIn':
if erratum_count == 0:
comments.append(
"I smell an erratum: " + correction['RefSource'] +
". \nAdd it to the end of your citation: [Erratum in Journal, Issue(Volume): page. DOI: #. Accessed date.]"
)
else: # Is this the second (or later) erratum we're reporting for this article? Then shorten report.
comments.append("There's another erratum! What a mess." +
correction['RefSource'])
erratum_count += 1
except:
pass # No errata? Do nothing.
return comments
def genbank_entries_from_accession(accessions,
read_out=False,
email='*****@*****.**'):
import Entrez
entries = []
Entrez.email = email
request = Entrez.epost('nucleotide', id=','.join(map(str, accessions)))
result = Entrez.read(request)
handle = Entrez.efetch(db='nucleotide',
retmode='xml',
webenv=result['WebEnv'],
query_key=result['QueryKey'])
for r in Entrez.parse(handle):
try:
entry = [x for x in r['GBSeq_other-seqids'] if 'gi' in x][0]
gi = int(entry.split('|')[1])
entries.append(gi)
except ValueError:
gi = None
if read_out is True:
print(">GI {0} {1} {2}\n{3}".format(gi,
r['GBSeq_primary-accession'],
r['GBSeq_definition'],
r['GBSeq_sequence'][:15]))
return entries
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 PMID_to_formatted_citation(PMID, comments):
"""
Take a PMID, retrieve the PubMed data, and format it based on our style guide.
:param PMID: PubMed ID
:return:
"""
Entrez.email = app.config['EMAIL']
try:
handle = Entrez.esummary(db="pubmed", id=PMID)
record = Entrez.read(handle)[0]
except IOError:
comments.append(
"Is there a network problem? Unleash me please!") # Network error
return '', comments
except:
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
author_names = authors.format_authors(record)
try:
year = record['PubDate'][0:4]
except:
comments.append("What year is it?")
year = '20??'
title, comments = article_title.format_title(record, PMID, comments)
journal, comments = journal_name.format_journal(record, comments)
vol_iss, comments = volume_issue.format_volume_issue(record, comments)
pages, comments = page_numbers.format_pages(record, comments)
DOI_value, comments = DOI.format_DOI(record, comments)
accessed = accessed_date.format_accessed_date()
# When there's no author: Title (Year)...
if author_names == '':
if title[-1] == '.':
title = title[0:-1]
citation = title + ' (' + year + '). ' + journal + vol_iss + pages + '. ' + DOI_value + accessed
# Otherwise: Authors (Year). Title...
else:
citation = author_names + ' (' + year + '). ' + title + ' ' + journal + vol_iss + pages + '. ' + DOI_value + accessed
# print(citation)
# print(' ')
comments = errata.erratum_check(PMID, comments)
handle.close()
return citation, comments
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