Merge branch 'master' into search_page

Author: haohangyan

indra/databases/chebi_client.py

@@ -1,7 +1,6 @@
 import os
 import logging
 import requests
-from lxml import etree
 from functools import lru_cache, cmp_to_key
 from indra.util import read_unicode_csv
 from indra.databases.obo_client import OboClient
@@ -10,10 +9,6 @@
 
 logger = logging.getLogger(__name__)
 
-# Namespaces used in the XML
-chebi_xml_ns = {'n': 'http://schemas.xmlsoap.org/soap/envelope/',
-                'c': 'https://www.ebi.ac.uk/webservices/chebi'}
-
 
 def _add_prefix(chid):
     if chid and not chid.startswith('CHEBI:'):
@@ -162,29 +157,17 @@ def get_chebi_entry_from_web(chebi_id):
 
     Returns
     -------
-    xml.etree.ElementTree.Element
-        An ElementTree element representing the ChEBI entry.
+    dict
+        A dictionary containing the ChEBI entry data. If the lookup
+        fails, None is returned.
     """
-    url_base = 'http://www.ebi.ac.uk/webservices/chebi/2.0/test/'
-    url_fmt = url_base + 'getCompleteEntity?chebiId=%s'
+    url_fmt = 'https://www.ebi.ac.uk/chebi/backend/api/public/compound/%s/'
     resp = requests.get(url_fmt % chebi_id)
     if resp.status_code != 200:
         logger.warning("Got bad code form CHEBI client: %s" % resp.status_code)
         return None
-    tree = etree.fromstring(resp.content)
-    path = 'n:Body/c:getCompleteEntityResponse/c:return'
-    elem = tree.find(path, namespaces=chebi_xml_ns)
-    return elem
-
-
-def _get_chebi_value_from_entry(entry, key):
-    if entry is None:
-        return None
-    path = 'c:%s' % key
-    elem = entry.find(path, namespaces=chebi_xml_ns)
-    if elem is not None:
-        return elem.text
-    return None
+    data = resp.json()
+    return data
 
 
 def get_chebi_name_from_id_web(chebi_id):
@@ -201,8 +184,8 @@ def get_chebi_name_from_id_web(chebi_id):
         The name corresponding to the given ChEBI ID. If the lookup
         fails, None is returned.
     """
-    entry = get_chebi_entry_from_web(chebi_id)
-    return _get_chebi_value_from_entry(entry, 'chebiAsciiName')
+    json_data = get_chebi_entry_from_web(chebi_id)
+    return json_data.get('name') if json_data else None
 
 
 def get_inchi_key(chebi_id):
@@ -219,8 +202,11 @@ def get_inchi_key(chebi_id):
         The InChIKey corresponding to the given ChEBI ID. If the lookup
         fails, None is returned.
     """
-    entry = get_chebi_entry_from_web(chebi_id)
-    return _get_chebi_value_from_entry(entry, 'inchiKey')
+    json_data = get_chebi_entry_from_web(chebi_id)
+    if not json_data:
+        return None
+    structure_data = json_data.get('default_structure')
+    return structure_data.get('standard_inchi_key') if structure_data else None
 
 
 def get_primary_id(chebi_id):

indra/resources/grounding/misgrounding_map.csv

@@ -305,3 +305,4 @@ Sn,HGNC,11127
 CIs,HGNC,7701
 autosomal dominant,HGNC,7106
 DIO,CHEBI,CHEBI:52032
+HS,HGNC,6853

indra/tests/test_indranet_assembler.py

@@ -337,3 +337,9 @@ def test_stmt_to_rows():
     assert len(rows) == 1
     assert rows[0] == ['a', 'b', 'HGNC', '1', 'TEXT', 'b', None, None,
                        'Activation', 1, 8197018847132618, 1, {None: 1}, None]
+
+    source_count = {-25125767941752990: {'db1': 1}}
+    rows = statement_to_rows(st2, source_counts=source_count)
+    assert rows[0] == ['a', 'c', 'HGNC', '1', 'TEXT', 'c', None, None,
+                       'Inhibition', 1, -25125767941752990, 0.76, {'db1': 1}, None]
+