def insert_all_nodes():
"""
reading and inserting all the nodes line by line
"""
with open(r'projectI_hetionet\nodes.tsv')as tsvfile:
tsvreader = csv.reader(tsvfile, delimiter="\t")
tsv_headings = next(tsvreader)
for line in tsvreader:
aline = aline + 1
if "Anatomy" in line:
createAnatomy_node = f"""CREATE ( Anatomy : Anatomy {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
a_query = f"""insert into hetionet.anatomy1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(a_query)
insert_query(createAnatomy_node)
if "Compound" in line:
createCompound_node = f"""CREATE ( Compound : Compound {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
c_query = f"""insert into hetionet.compound1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(c_query)
insert_query(createCompound_node)
if "Disease" in line:
createDisease_node = f"""CREATE ( Disease : Disease {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
d_query = f"""insert into hetionet.disease1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(d_query)
insert_query(createDisease_node)
if"Gene" in line:
createGene_node = f"""CREATE ( Gene : Gene {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
q_query = f"""insert into hetionet.gene1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(q_query)
insert_query(createGene_node)
print("Numbers of nodes => ", aline, "\nNodes inserted successfully!")
def add_node():
"""
http://127.0.0.1:5000/add_node?id=nodeID&name=nodeName&kind=nodekind
:param: id
:param: name
:param: kind
:return:
"""
id = request.args.get('id')
name = request.args.get('name')
kind = request.args.get('kind')
new_node = f"""CREATE ( new : {kind} {{ id : "{id}", name : "{name}", kind : "{kind}" }})"""
insert_query(new_node)
return json.dumps({"success": True})
def add_edges():
"""
http://127.0.0.1:5000/add_edges?source=nodesource&metaedge=nodemetaedge&target=nodetarget
:param: source
:param: metaedge
:param: target
:return:
"""
source = request.args.get('source')
metaedge = request.args.get('metaedge')
target = request.args.get('target')
new_edge = f"""MATCH(dummy1 : {source}), (dummy2: {source}) WHERE dummy1={source} and dummy2={target}
CREATE (dummy1) - [:{metaedge}] -> (dummy2)
RETURN dummy1, dummy2 """
insert_query(new_edge)
return json.dumps({"success": True})
def insert_all_edges():
with open(r'projectI_hetionet\edges.tsv')as tsvfile:
"""
reading and appending all types of edges in list
"""
tsvreader = csv.reader(tsvfile, delimiter="\t")
tsv_headings = next(tsvreader)
# appending all types of edges to list
#['GiG', 'CrC', 'DdG', 'DlA', 'CtD', 'CbG', 'CuG', 'DrD', 'DaG', 'CpD', 'AdG', 'AuG', 'GcG', 'Gr>G', 'CdG', 'DuG', 'AeG']
# for line in tsvreader:
# list = []
# if line[1] not in list:
# list.append(line[1])
for line in tsvreader:
if "CrC" in line: # 6486
print("Compound resembles Compound")
CrC_realation = f"""MATCH (a:Compound), (b:Compound)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
crc = f"""insert into hetionet.relation_crc(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(crc)
insert_query(CrC_realation)
if "CtD" in line: # 755
print("Compound treat Disease")
CtD_realation = f"""MATCH (a:Compound), (b:Disease)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
ctd = f"""insert into hetionet.relation_ctd(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(ctd)
insert_query(CtD_realation)
if "CpD" in line: # 390
print("Compound palliates Disease")
CpD_realation = f"""MATCH (a:Compound), (b:Disease)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
cpd = f"""insert into hetionet.relation_cpd(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
print(cpd)
cqlsh(cpd)
insert_query(CpD_realation)
if "CuG" in line: # 18756
print("Compound upregulates Gene")
CuG_realation = f"""MATCH (a:Compound), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
cug = f"""insert into hetionet.relation_cug(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(cug)
insert_query(CuG_realation)
if "CbG" in line: # 11571
print("Compound binds Gene")
CbG_realation = f"""MATCH (a:Compound), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
cbg = f"""insert into hetionet.relation_cbg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(cbg)
insert_query(CbG_realation)
if "CdG" in line: # 21102
print("Compound downregulates Gene")
CdG_realation = f"""MATCH (a:Compound), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
cdg = f"""insert into hetionet.relation_cdg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(cdg)
insert_query(CdG_realation)
if "DrD" in line: # 543
print("Disease resembles Disease")
DrD_realation = f"""MATCH (a:Disease), (b:Disease)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
drd = f"""insert into hetionet.relation_drd(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(drd)
insert_query(DrD_realation)
if "DuG" in line: # 7731
print("Disease upregulates Gene")
DuG_realation = f"""MATCH (a:Disease), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
dug = f"""insert into hetionet.relation_dug(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(dug)
insert_query(DuG_realation)
if "DaG" in line: # 12623
print("Disease associates Gene")
DaG_realation = f"""MATCH (a:Disease), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
dag = f"""insert into hetionet.relation_dag(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(dag)
insert_query(DaG_realation)
if "DdG" in line: # 7623
print("Disease downregulates Gene")
DdG_realation = f"""MATCH (a:Disease), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
ddg = f"""insert into hetionet.relation_ddg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(ddg)
insert_query(DdG_realation)
if "DlA" in line: # 3602
print("disease localizes Anatomy")
DlA_realation = f"""MATCH (a:Disease), (b:Anatomy)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
dla = f"""insert into hetionet.relation_dla(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(dla)
insert_query(DlA_realation)
if "AuG" in line: # 97848
print("Anatomy upregulates Gene")
AuG_realation = f"""MATCH (a:Anatomy), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
aug = f"""insert into hetionet.relation_aug(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(aug)
insert_query(AuG_realation)
if "AeG" in line: # 526407
print("Anatomy express Gene")
AeG_realation = f"""MATCH (a:Anatomy), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
aeg = f"""insert into hetionet.relation_aeg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(aeg)
insert_query(AeG_realation)
if "AdG" in line: # 102240
# print("Anatomy downregulates Gene")
AdG_realation = f"""MATCH (a:Anatomy), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
adg = f"""insert into hetionet.relation_adg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(adg)
insert_query(AdG_realation)
if "GiG" in line: # 147164
print("Gene interacts Gene")
GiG_realation = f"""MATCH (a:Gene), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
gig = f"""insert into hetionet.relation_gig(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(gig)
insert_query(GiG_realation)
if "GcG" in line: # 61690
print("Gene covaries Gene")
GcG_realation = f"""MATCH (a:Gene), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: {line[1]}]-> (b)
RETURN a, b"""
gcg = f"""insert into hetionet.relation_gcg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(gcg)
insert_query(GcG_realation)
if "Gr>G" in line: # 265672
print("Gene regulates Gene")
Gr_G_realation = f"""MATCH (a:Gene), (b:Gene)where a.id="{line[0]}" and b.id="{line[2]}"
CREATE (a)-[r: Gr_G]-> (b)
RETURN a, b"""
grg = f"""insert into hetionet.relation_grg(source, metaedge, target) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(grg)
insert_query(Gr_G_realation)
import csv
from Cassandra.CQLsh import cqlsh
from Neo4j.query import insert_query
"""Creating dummy relationship: "KNOWS" to check DB connection"""
dummy_edge = """MATCH (dummy1: dummy), (dummy2: dummy) where dummy1.name="dummy" and dummy2.name="dummy"
CREATE (dummy1) - [KNOWS : KNOWS ] -> (dummy2)
RETURN dummy1, dummy2"""
insert_query(dummy_edge)
def insert_all_edges():
with open(r'projectI_hetionet\edges.tsv')as tsvfile:
"""
reading and appending all types of edges in list
"""
tsvreader = csv.reader(tsvfile, delimiter="\t")
tsv_headings = next(tsvreader)
# appending all types of edges to list
#['GiG', 'CrC', 'DdG', 'DlA', 'CtD', 'CbG', 'CuG', 'DrD', 'DaG', 'CpD', 'AdG', 'AuG', 'GcG', 'Gr>G', 'CdG', 'DuG', 'AeG']
# for line in tsvreader:
# list = []
# if line[1] not in list:
# list.append(line[1])
for line in tsvreader:
if "CrC" in line: # 6486
print("Compound resembles Compound")
import csv
from Cassandra.CQLsh import cqlsh
from Neo4j.query import insert_query
"""Dummy insertion to check DB connection"""
dummy_node = """CREATE (dummy_node: dummy{name: "dummy"})"""
insert_query(dummy_node)
aline = 0 # line counter
def insert_all_nodes():
"""
reading and inserting all the nodes line by line
"""
with open(r'projectI_hetionet\nodes.tsv')as tsvfile:
tsvreader = csv.reader(tsvfile, delimiter="\t")
tsv_headings = next(tsvreader)
for line in tsvreader:
aline = aline + 1
if "Anatomy" in line:
createAnatomy_node = f"""CREATE ( Anatomy : Anatomy {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
a_query = f"""insert into hetionet.anatomy1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(a_query)
insert_query(createAnatomy_node)
if "Compound" in line:
createCompound_node = f"""CREATE ( Compound : Compound {{ id : "{line[0]}", name : "{line[1]}", kind : "{line[2]}" }})"""
c_query = f"""insert into hetionet.compound1(id, kind, name) values( '{line[0]}' , '{line[1]}' , '{line[2]}');"""
cqlsh(c_query)