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###############################################################################
#
# This file is part of the Utopia Documents application.
# Copyright (c) 2008-2014 Lost Island Labs
# <info@utopiadocs.com>
#
# Utopia Documents is free software: you can redistribute it and/or modify
# it under the terms of the GNU GENERAL PUBLIC LICENSE VERSION 3 as
# published by the Free Software Foundation.
#
# Utopia Documents is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# In addition, as a special exception, the copyright holders give
# permission to link the code of portions of this program with the OpenSSL
# library under certain conditions as described in each individual source
# file, and distribute linked combinations including the two.
#
# You must obey the GNU General Public License in all respects for all of
# the code used other than OpenSSL. If you modify file(s) with this
# exception, you may extend this exception to your version of the file(s),
# but you are not obligated to do so. If you do not wish to do so, delete
# this exception statement from your version.
#
# You should have received a copy of the GNU General Public License
# along with Utopia Documents. If not, see <http://www.gnu.org/licenses/>
#
###############################################################################
import common.eutils
import common.pubmed
import datetime
import utopia.library
from lxml import etree
class TestRemoteQuery(utopia.library.RemoteQuery):
"""Test remote query"""
def parse(self, article):
#print etree.tostring(article, pretty_print=True, encoding='utf8')
info = common.pubmed.parse_PubmedArticle(article)
if len(info) > 0:
# For PubMed entries, the uid is the PubMed ID
unique_id = info.get('identifiers', {}).get('pubmed')
if unique_id is not None:
info['__id__'] = 'pubmed:{0}'.format(unique_id)
return info
def fetch(self, query, offset, limit):
# Get the date range to search in
last_searched = self.get_property('last_searched', '1970/01/01')
today = datetime.date.today().strftime('%Y/%m/%d')
# Get previous search metadata
webEnv = self.get_property('WebEnv')
queryKey = self.get_property('QueryKey')
count = int(self.get_property('Count', 0))
last_id = self.get_property('last_id')
#print webEnv, queryKey, count, last_id
# Known domains
domain_map = {
'title': 'Title',
'authors': 'Author',
'abstract': 'Title/Abstract',
}
# Unpack the search term(s)
domain = domain_map.get(query.get('domain'), '')
term = query.get('query')
if term is not None:
# Remove hashtags
term = ' '.join((t for t in term.split() if not t.startswith('#')))
if term is not None and len(term) > 0:
# Remove hashtags
term = ' '.join((t for t in term.split() if not t.startswith('#')))
# List to hold the results
results = []
# If no previous search exists, search now
if webEnv is None:
# Fetch from PubMed any matching documents
searchresult = common.eutils.esearch(**{
'db': 'pubmed',
'retmax': limit,
'term': term,
'field': domain,
'datetype': 'pdat',
'mindate': last_searched,
'maxdate': today,
})
root = etree.fromstring(searchresult)
#print etree.tostring(root, pretty_print=True, encoding='utf8')
# Store history information
webEnv = root.findtext('WebEnv')
queryKey = root.findtext('QueryKey')
count = int(root.findtext('Count'))
self.set_property('WebEnv', webEnv)
self.set_property('QueryKey', queryKey)
self.set_property('Count', count)
else:
# If previous search exists, then get everything from then until now
searchresult = common.eutils.esearch(**{
'db': 'pubmed',
'retmax': limit,
'term': term,
'field': domain,
'datetype': 'pdat',
'mindate': last_searched,
'maxdate': today,
})
root = etree.fromstring(searchresult)
#print etree.tostring(root, pretty_print=True, encoding='utf8')
newWebEnv = root.findtext('WebEnv')
newQueryKey = root.findtext('QueryKey')
newCount = int(root.findtext('Count'))
exhausted = False
for newOffset in xrange(0, newCount, limit):
if exhausted:
break
# Fetch the next set of new results
#print "-- fetching", newOffset, limit, newWebEnv, newQueryKey
searchresult = common.eutils.efetch(**{
'db': 'pubmed',
'retmax': limit,
'WebEnv': newWebEnv,
'query_key': newQueryKey,
'retstart': newOffset,
})
#print searchresult
root = etree.fromstring(searchresult)
#print etree.tostring(root, pretty_print=True, encoding='utf8')
#print etree.tostring(root.find('PubmedArticle'), pretty_print=True, encoding='utf8')
for article in root.findall("PubmedArticle"):
info = self.parse(article)
if info.get('__id__') == last_id:
exhausted = True
break
if len(info) > 0:
info['flags'] = ['unread']
#print info
results.append(info)
if len(results) > 0:
if '__id__' in results[0]:
last_id = results[0]['__id__']
# Fetch the next set of results
#print "-- fetching", offset, limit, webEnv, queryKey
searchresult = common.eutils.efetch(**{
'db': 'pubmed',
'retmax': limit,
'WebEnv': webEnv,
'query_key': queryKey,
'retstart': offset,
})
#print searchresult
root = etree.fromstring(searchresult)
#print etree.tostring(root, pretty_print=True, encoding='utf8')
#print etree.tostring(root.find('PubmedArticle'), pretty_print=True, encoding='utf8')
if root.find('ERROR') is None:
for article in root.findall("PubmedArticle"):
info = self.parse(article)
if len(info) > 0:
#print info
results.append(info)
if last_id is None and len(results) > 0:
if '__id__' in results[0]:
last_id = results[0]['__id__']
self.set_property('last_id', last_id)
# Reset last searched date to today
self.set_property('last_searched', today)
#print (offset, limit, count, results)
return (offset, limit, count, results)
else:
print etree.tostring(root, pretty_print=True, encoding='utf8')
# Default
return (0, 0, 0, [])
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