def SubmitJobToQueue(
jobid,
datapath,
outpath,
numseq,
numseq_this_user,
email, #{{{
host_ip,
base_www_url):
myfunc.WriteFile("Entering SubmitJobToQueue()\n", g_params['debugfile'],
"a", True)
fafile = "%s/query.fa" % (datapath)
if numseq == -1:
numseq = myfunc.CountFastaSeq(fafile)
if numseq_this_user == -1:
numseq_this_user = numseq
name_software = "boctopus2"
runjob = "%s %s/run_job.py" % (python_exec, rundir)
scriptfile = "%s/runjob;%s;%s;%s;%s;%d.sh" % (
outpath, name_software, jobid, host_ip, email, numseq)
code_str_list = []
code_str_list.append("#!/bin/bash")
code_str_list.append("source %s/bin/activate" % (virt_env_path))
cmdline = "%s %s -outpath %s -tmpdir %s -jobid %s " % (
runjob, fafile, outpath, datapath, jobid)
if email != "":
cmdline += "-email \"%s\" " % (email)
if base_www_url != "":
cmdline += "-baseurl \"%s\" " % (base_www_url)
if g_params['isForceRun']:
cmdline += "-force "
if g_params['isOnlyGetCache']:
cmdline += "-only-get-cache "
code_str_list.append(cmdline)
code = "\n".join(code_str_list)
msg = "Write scriptfile %s" % (scriptfile)
myfunc.WriteFile(msg + "\n", g_params['debugfile'], "a", True)
myfunc.WriteFile(code, scriptfile, mode="w", isFlush=True)
os.chmod(scriptfile, 0o755)
myfunc.WriteFile("Getting priority" + "\n", g_params['debugfile'], "a",
True)
priority = myfunc.GetSuqPriority(numseq_this_user)
if email in vip_user_list:
priority = 999999999.0
myfunc.WriteFile("priority=%d\n" % (priority), g_params['debugfile'], "a",
True)
st1 = webcom.SubmitSlurmJob(datapath, outpath, scriptfile,
g_params['debugfile'])
return st1
def SubmitJobToQueue(
jobid,
datapath,
outpath,
numseq,
numseq_this_user,
email, #{{{
host_ip,
base_www_url):
myfunc.WriteFile("Entering SubmitJobToQueue()\n", g_params['debugfile'],
"a", True)
fafile = "%s/query.fa" % (datapath)
if numseq == -1:
numseq = myfunc.CountFastaSeq(fafile)
if numseq_this_user == -1:
numseq_this_user = numseq
query_parafile = "%s/query.para.txt" % (outpath)
query_para = {}
content = myfunc.ReadFile(query_parafile)
para_str = content
if content != "":
query_para = json.loads(content)
try:
name_software = query_para['name_software']
except KeyError:
name_software = "prodres"
runjob = "%s %s/run_job.py" % (python_exec, rundir)
scriptfile = "%s/runjob,%s,%s,%s,%s,%d.sh" % (
outpath, name_software, jobid, host_ip, email, numseq)
code_str_list = []
code_str_list.append("#!/bin/bash")
code_str_list.append("source %s/bin/activate" % (virt_env_path))
cmdline = "%s %s -outpath %s -tmpdir %s -jobid %s " % (
runjob, fafile, outpath, datapath, jobid)
if email != "":
cmdline += "-email \"%s\" " % (email)
if base_www_url != "":
cmdline += "-baseurl \"%s\" " % (base_www_url)
if g_params['isForceRun']:
cmdline += "-force "
if g_params['isOnlyGetCache']:
cmdline += "-only-get-cache "
code_str_list.append(cmdline)
code = "\n".join(code_str_list)
msg = "Writting scriptfile %s" % (scriptfile)
webcom.loginfo(msg, g_params['debugfile'])
myfunc.WriteFile(code, scriptfile, mode="w", isFlush=True)
os.chmod(scriptfile, 0o755)
webcom.loginfo("Getting priority", g_params['debugfile'])
priority = myfunc.GetSuqPriority(numseq_this_user)
if email in vip_user_list:
priority = 999999999.0
webcom.loginfo("priority=%d" % (priority), g_params['debugfile'])
st1 = webcom.SubmitSlurmJob(datapath, outpath, scriptfile,
g_params['debugfile'])
return st1
def SubmitJobToQueue(
jobid,
datapath,
outpath,
nummodel,
nummodel_this_user,
email, #{{{
host_ip,
base_www_url):
myfunc.WriteFile("Entering SubmitJobToQueue()\n", g_params['debugfile'],
"a")
modelfile = "%s/query.pdb" % (datapath)
seqfile = "%s/query.fa" % (datapath)
if nummodel == -1:
nummodel = myfunc.ReadFile(modelfile).count("\nENDMDL")
if nummodel == 0:
nummodel = 1
if nummodel_this_user == -1:
nummodel_this_user = nummodel
query_parafile = "%s/query.para.txt" % (outpath)
query_para = {}
content = myfunc.ReadFile(query_parafile)
para_str = content
if content != "":
query_para = json.loads(content)
try:
name_software = query_para['name_software']
except KeyError:
name_software = "proq3"
runjob = "%s %s/run_job.py" % (python_exec, rundir)
scriptfile = "%s/runjob,%s,%s,%s,%s,%d.sh" % (
outpath, name_software, jobid, host_ip, email, nummodel)
code_str_list = []
code_str_list.append("#!/bin/bash")
code_str_list.append("source %s/bin/activate" % (virt_env_path))
cmdline = "%s %s -outpath %s -tmpdir %s -jobid %s " % (
runjob, modelfile, outpath, datapath, jobid)
if email != "":
cmdline += "-email \"%s\" " % (email)
if os.path.exists(seqfile):
cmdline += "-fasta \"%s\" " % (seqfile)
if base_www_url != "":
cmdline += "-baseurl \"%s\" " % (base_www_url)
if g_params['isForceRun']:
cmdline += "-force "
code_str_list.append(cmdline)
code = "\n".join(code_str_list)
msg = "Write scriptfile %s" % (scriptfile)
myfunc.WriteFile(msg + "\n", g_params['debugfile'], "a")
myfunc.WriteFile(code, scriptfile)
os.chmod(scriptfile, 0o755)
myfunc.WriteFile("Getting priority" + "\n", g_params['debugfile'], "a")
priority = myfunc.GetSuqPriority(nummodel_this_user)
if email in vip_user_list:
priority = 999999999.0
myfunc.WriteFile("priority=%d\n" % (priority), g_params['debugfile'], "a")
st1 = webcom.SubmitSlurmJob(datapath, outpath, scriptfile,
g_params['debugfile'])
return st1