From ad389e2557611b2fed1d163527d948a3b1f89898 Mon Sep 17 00:00:00 2001
From: Carlos Vega <carlos.vega@uni.lu>
Date: Wed, 20 Nov 2019 10:50:42 +0100
Subject: [PATCH] retrieve publication details from solr repository using solr
ids from biokb virtuoso triple store
---
biokb/textminingservice_biokb/biokb.py | 28 ++++++++++++++++++++------
1 file changed, 22 insertions(+), 6 deletions(-)
diff --git a/biokb/textminingservice_biokb/biokb.py b/biokb/textminingservice_biokb/biokb.py
index 02ebb8e..84d7534 100644
--- a/biokb/textminingservice_biokb/biokb.py
+++ b/biokb/textminingservice_biokb/biokb.py
@@ -51,19 +51,35 @@ class BioKBService(TextMiningService):
query = """
select ?publication str(?solrId) as ?solrId where {{
- {}
+ {}
?publication <http://lcsb.uni.lu/biokb#solrId> ?solrId .
}} LIMIT {}
""".format(entity_subquery, limit)
results = self._run_sparql_query(query)
- values = []
+ solr_ids = set()
for result in results['results']['bindings']:
solr_id = result['solrId']['value']
- pub = Publication(other_id=solr_id)
- values.append(pub)
-
- return values
+ solr_ids.add(solr_id)
+ # pub = Publication(other_id=solr_id)
+ # solr_ids[solr_id] = pub
+
+ # translate ids
+ response = requests.get(BioKBService.SOLR_TRANSLATOR_URL,
+ data={'solrIds': solr_ids})
+ assert response.ok
+ data = json.loads(response.content.decode().strip())
+ publications = []
+ for pub in data['publications']:
+ p = Publication(title=pub.get('title', None),
+ journal_title=pub.get('journal_title', None),
+ doi=pub.get('doi', None),
+ pm_id=pub.get('pubmed_id', None),
+ pmc_id=pub.get('pmc_id', None),
+ other_id=pub['id'],
+ year=pub.get('year', None))
+ publications.append(p)
+ return publications
def get_co_occurrences(self, entity: str, limit: int = 20, types: List[str] = None) -> List[CoOccurrence]:
--
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