def get_common_ancestors(id1, id2):
e1 = ssm.get_id(id1.replace(":", "_"))
e2 = ssm.get_id(id2.replace(":", "_"))
#print(id1, id2, e1, e2)
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
return a
def get_common_ancestors(id1, id2):
"""
:param id1:
:param id2:
:return:
"""
if id1.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if id1.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if id1.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if id1.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e1 = ssm.get_id(id1.replace(':', '_'))
if id2.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if id2.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if id2.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if id2.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e2 = ssm.get_id(id2.replace(':', '_'))
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
return a
def get_common_ancestors(id1, id2):
global chebi_cache
if (id1, id2) in chebi_cache:
#logging.info("using chebi cache")
return chebi_cache[(id1, id2)]
else:
e1 = ssm.get_id(id1.replace(":", "_"))
e2 = ssm.get_id(id2.replace(":", "_"))
#print(id1, id2, e1, e2)
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
chebi_cache[(id1, id2)] = a
return a
def get_dist_direct(cid1, cid2, max_dist=100):
global ssm_cache
#print("getting dist between", cid1, cid2)
if (cid1, cid2) in ssm_cache:
#print("cached")
return ssm_cache[(cid1, cid2)]
#else:
#print("newdist")
#rows = ssm.connection.execute("""
# SELECT MAX(distance)
# FROM transitive t, entry e1, entry e2
# WHERE ((t.entry1=e1.id and t.entry2=e2.id) or
# (t.entry1=e2.id and t.entry2=e1.id))
# and e1.name = ? and e2.name = ?
# """, (cid1, cid2,)).fetchone()
#if rows[0] is None:
# dist = 0
#else:
# dist = rows[0]
#if dist > 0:
# print(cid1, cid2, dist)
e1 = ssm.get_id(cid1.replace(":", "_"))
e2 = ssm.get_id(cid2.replace(":", "_"))
#ca = ssm.common_ancestors(e1, e2)
# print(e1, e2, ca)
d1 = ssm.connection.execute("""
SELECT distance
FROM transitive t, entry e1, entry e2
WHERE t.distance < ? and ((t.entry1=e1.id and t.entry2=e2.id) or
(t.entry1=e2.id and t.entry2=e1.id))
and e1.id = ? and e2.id = ?
""", (max_dist,e1, e2,)).fetchone()
#d2 = ssm.connection.execute("""
# SELECT distance
# FROM transitive t, entry e1, entry e2
# WHERE ((t.entry1=e1.id and t.entry2=e2.id) or
# (t.entry1=e2.id and t.entry2=e1.id))
# and e1.name = ? and e2.id = ?
# """, (cid2, ca[0],)).fetchone()
#d1 = len(ssm.common_ancestors(e1, e1)) - len(ca)
#d2 = len(ssm.common_ancestors(e2, e2)) - len(ca)
if d1 is None:
ssm_cache[(cid1, cid2)] = -1
return -1
else:
ssm_cache[(cid1, cid2)] = d1[0]
return d1[0]
def get_path_to_root(id1):
global chebi_cache
if id1 in chebi_cache:
#logging.info("using chebi cache")
return chebi_cache[id1]
else:
e1 = ssm.get_id(id1.replace(":", "_"))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
chebi_cache[id1] = a
return a
def get_path_to_root(entity_id):
"""
:param entity_id:
:return:
"""
if entity_id.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if entity_id.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if entity_id.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if entity_id.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e1 = ssm.get_id(entity_id.replace(':', '_'))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
return a
def get_path_to_root(id1):
e1 = ssm.get_id(id1.replace(":", "_"))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
return a