def efetch(self, db, id):
"""query the efetch endpoint
"""
db = db.lower()
xml = self._qs.efetch({'db': db, 'id': str(id)})
doc = le.XML(xml)
if db in ['gene']:
return EntrezgeneSet(doc)
if db in ['nuccore', 'nucest']:
# TODO: GBSet is misnamed; it should be GBSeq and get the GBSeq XML node as root (see gbset.py)
return GBSet(doc)
if db in ['pubmed']:
return PubmedArticleSet(doc)
if db in ['snp']:
return ExchangeSet(xml)
if db in ['pmc']:
return PubmedCentralArticleSet(doc)
raise EutilsError('database {db} is not currently supported by eutils'.format(db=db))
def efetch(self, db, id=None, webenv=None, query_key=None, **kw):
"""query the efetch endpoint
"""
db = db.lower()
kw.update({'db': db})
if id:
kw.update({'id': id})
else:
kw.update({'webenv': webenv, 'query_key': query_key})
xml = self._qs.efetch(kw)
if db in ['gene']:
return Gene(xml)
if db in ['nuccore']:
# TODO: GBSet is misnamed; it should be GBSeq and get the GBSeq XML node as root (see gbset.py)
return GBSet(xml)
if db in ['pubmed']:
return PubMedArticleSet(xml)
if db in ['snp']:
return ExchangeSet(xml)
raise EutilsError(
'database {db} is not currently supported by eutils'.format(db=db))
@property
def inference(self):
return self._xml_root.xpath(
'GBFeature_quals/GBQualifier[GBQualifier_name/text()="inference"]/GBQualifier_value/text()')[0]
if __name__ == "__main__":
import os
import lxml.etree as le
from eutils.xmlfacades.gbset import GBSet
data_dir = os.path.join(os.path.dirname(__file__), '..', '..', 'tests', 'data')
relpath = 'efetch.fcgi?db=nuccore&id=148536845&retmode=xml.xml'
path = os.path.join(data_dir, relpath)
gbset = GBSet(le.parse(path).getroot())
gbseq = next(iter(gbset))
# <LICENSE>
# Copyright 2015 eutils Committers
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express