[在my previous question中更改代码以构建密码交易而不是在Py2neo中创建节点和关系之后，它似乎可以成功运行，但是交易在大约90秒后停止，没有错误消息。该脚本继续运行，但是迭代停止，并且不再进行任何事务，并查看日志，它似乎停止了与数据库的所有交互。谁能帮我理解为什么会这样吗？正在从Jupyter执行以下代码。
import pandas as pd
import csv
import math
import allel
import zarr
from py2neo import Graph, Node, Relationship, NodeMatcher
zarr_path = '/media/user/Seagate Backup Plus Drive/uk_twin_cohort/exome/chroms.zarr'
callset = zarr.open_group(zarr_path, mode='r')
graph = Graph(user="neo4j", password="password")
chrom_list = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,'X']
matcher = NodeMatcher(graph)
for chrom in chrom_list:
chrom_label = "Chromosome_" + str(chrom)
samples = callset[chrom]['samples']
variants = allel.VariantChunkedTable(callset[chrom]['variants'], names=['AC','AF_AFR', 'AF_AMR', 'AF_ASN', 'AF_EUR', 'AF_MAX', 'CGT', 'CLR', 'CSQ', 'DP', 'DP4', 'ESP_MAF', 'FILTER_LowQual', 'FILTER_MinHWE', 'FILTER_MinVQSLOD', 'FILTER_PASS', 'HWE', 'ICF', 'ID', 'IS', 'PC2', 'PCHI2', 'POS', 'PR', 'QCHI2', 'QUAL', 'REF', 'ALT', 'INDEL', 'SHAPEIT', 'SNP_ID', 'TYPE', 'UGT', 'VQSLOD', 'dbSNPmismatch', 'is_snp', 'numalt'], index='POS')
pos = variants['POS'][:]
pos = pos.tolist()
ref = variants['REF'][:]
alt = variants['ALT'][:]
dpz = callset[chrom]['calldata/DP']
dp = dpz[:, 0]
psz = callset[chrom]['calldata/PS']
plz = callset[chrom]['calldata/PL']
gpz = callset[chrom]['calldata/GP']
calldata = callset[chrom]['calldata']
gt = allel.GenotypeDaskArray(calldata['GT'])
hap = gt.to_haplotypes()
hap = gt.to_haplotypes()
hap1 = hap[:, ::2]
hap2 = hap[:, 1::2]
list_h1 = hap1[:, 0].compute()
list_h1 = list_h1.tolist()
list_h2 = hap2[:, 0].compute()
for i in range(len(samples)):
subject = samples[i]
dp = dpz[:, i]
ps = psz[:, i]
pl = plz[:, i]
gp = gpz[:, i]
list_h1 = hap1[:, i].compute()
list_h2 = hap2[:, i].compute()
bp1 = []
bp2 = []
hpt = []
n1 = []
n2 = []
g = Graph()
print(subject)
print("Subject " + str(i) + " of " + str(len(samples)))
s = matcher.match("Subject", subject_id= subject).first()
print(s)
if s is None:
continue
j = 0
nodes = []
for j in range(len(pos)):
h1 = int(list_h1[j])
h2 = int(list_h2[j])
k = int(pos[j])
l = str(ref[j])
m = str(alt[j][h1-1])
o = str(alt[j][h2-1])
if h1 == 0 and h2 == 0:
a = matcher.match(chrom_label, pos=k, bp=l).first()
nodes.append(a)
nodes.append(a)
elif h1 == 0 and h2 > 0:
a = matcher.match(chrom_label, pos=k, bp=l).first()
nodes.append(a)
a = matcher.match(chrom_label, pos=k, bp=o).first()
nodes.append(a)
elif h1 > 0 and h2 == 0:
a = matcher.match(chrom_label, pos=k, bp=m).first()
nodes.append(a)
a = matcher.match(chrom_label, pos=k, bp=l).first()
nodes.append(a)
elif h1 == h2 and h1 > 0:
a = matcher.match(chrom_label, pos=k, bp=m).first()
nodes.append(a)
nodes.append(a)
else:
a = matcher.match(chrom_label, pos=k, bp=m).first()
nodes.append(a)
a = matcher.match(chrom_label, pos=k, bp=o).first()
nodes.append(a)
if j % 10000 == 0:
print(str(j) + " rows complete.")
print(subject + " matching complete.")
print(len(nodes))
j=0
tx = g.begin()
for j in range(len(pos)):
read_depth = int(dp[j])
ps1 = int(ps[j])
PL0 = int(pl[j][0])
PL1 = int(pl[j][1])
PL2 = int(pl[j][2])
genotype = str(h1) + '|' + str(h2)
GP0 = float(gp[j][0])
GP1 = float(gp[j][1])
GP2 = float(gp[j][2])
h1 = int(list_h1[j])
h2 = int(list_h2[j])
k = int(pos[j])
l = str(ref[j])
m = str(alt[j][h1-1])
o = str(alt[j][h2-1])
if h1 == 0 and h2 == 0:
x = (2*j)
a = nodes[x]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {A} MERGE (s)-[r:HOMOZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "A":a.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
elif h1 == 0 and h2 > 0:
x = (2*j)
a = nodes[x]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {A} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "A":a.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
y = (2*j)+1
b = nodes[y]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {B} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "B":b.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
elif h1 > 0 and h2 == 0:
x = (2*j)
a = nodes[j]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {A} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "A":a.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
y = (2*j)+1
b = nodes[y]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {B} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "B":b.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
elif h1 == h2 and h1 > 0:
x = (2*j)
a = nodes[j]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {A} MERGE (s)-[r:HOMOZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "A":a.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
else:
x = (2*j)
a = nodes[j]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {A} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "A":a.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
y = (2*j)+1
b = nodes[y]
tx.run("MATCH (s) WHERE id(s) = {S} MATCH (a) WHERE id(a) = {B} MERGE (s)-[r:HETEROZYGOUS {HTA:{H1}, HTB:{H2}, GT:{GT}, dp:{DP}, phase_set:{PS1}, PL0:{PL0}, PL1:{PL1}, PL2:{PL2}, GP0:{GP0}, GP1:{GP1}, GP2:{GP2}}]->(a)", {"S":s.identity, "B":b.identity, "H1":h1, "H2":h2, "GT":genotype, "DP":read_depth, "PS1":ps1, "PL0":PL0, "PL1":PL1, "PL2":PL2, "GP0":GP0, "GP1":GP1, "GP2":GP2 })
if j % 1000 == 0:
print(str(j) + " rows added to database.")
tx.commit()
tx = g.begin()
print(chrom_label + " completed.")
仅在tx.commit()测试成功时才呼叫j % 1000 == 0。您需要确保在退出tx.commit() for循环后必要时调用j，否则将丢弃最后一批操作。
顺便说一下，您当前是第一次通过循环调用tx.commit()（因为0 % 1000 == 0）。您可能想避免这种情况。