From aedac6b640e40ae181eaa88da9714ea687dcc7d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 22 Mar 2017 09:47:49 +0100
Subject: [PATCH] correct uniprot web service and add taxonomy web service
---
ippisite/ippidb/ws.py | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 422a5219..de60b857 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -36,10 +36,18 @@ def get_epo_info(patent_number):
'authors_list': authors}
def get_uniprot_info(uniprot_id):
- uniprot_client = Uniprot()
+ uniprot_client = UniProt()
resp = uniprot_client.retrieve(uniprot_id)
- recommended_name = res.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}protein/{http://uniprot.org/uniprot}recommendedName/{http://uniprot.org/uniprot}fullName')[0].text
- organism = res.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}organism/{http://uniprot.org/uniprot}dbReference[@type="NCBI Taxonomy"]/@id')
+ recommended_name = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}protein/{http://uniprot.org/uniprot}recommendedName/{http://uniprot.org/uniprot}fullName')[0].text
+ organism = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}organism/{http://uniprot.org/uniprot}dbReference[@type="NCBI Taxonomy"]')[0].attrib['id']
+ gene = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}gene/{http://uniprot.org/uniprot}name[@type="primary"]')[0].text
return {'recommended_name': recommended_name,
- 'organism': organism
- }
+ 'organism': int(organism),
+ 'gene': gene
+ }
+
+def get_taxonomy_info(taxonomy_id):
+ eu = EUtils()
+ r = eu.EFetch('taxonomy', taxonomy_id, retmode='dict')
+ scientific_name = r['TaxaSet']['Taxon']['ScientificName']
+ return {'scientific_name': scientific_name}
--
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