Commit 0c90ba78 authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

Fix code refactoring + except on all errors for run job

parent a303cf89
......@@ -111,9 +111,9 @@ def parse_started_jobs():
with Job.connect():
jobs_started = [] # Only local jobs
cluster_jobs_started = [] # Only cluster jobs
jobs = Job.select().where((Job.status == "started") | (Job.status == "starting") | (Job.status == "merging") |
(Job.status == "scheduled-cluster") | (Job.status == "prepare-scheduled") |
(Job.status == "prepare-cluster"))
jobs = Job.select().where((Job.status == "started") | (Job.status == "starting") | (Job.status == "succeed") |
(Job.status == "merging") | (Job.status == "scheduled-cluster") |
(Job.status == "prepare-scheduled") | (Job.status == "prepare-cluster"))
for job in jobs:
pid = job.id_process
if job.batch_type == "local":
......
......@@ -126,7 +126,7 @@ class JobManager:
def check_job_success(self):
if os.path.exists(self.paf_raw):
if os.path.getsize(self.paf_raw) > 0:
return "success"
return "succeed"
else:
return "no-match"
return "fail"
......@@ -262,7 +262,7 @@ class JobManager:
job.save()
else:
self.set_status_standalone(status)
return status == "success"
return status == "succeed"
self.error = self.search_error()
status = "fail"
if MODE == "webserver":
......@@ -404,7 +404,7 @@ class JobManager:
# db.commit()
self.update_job_status(status)
s.deleteJobTemplate(jt)
return status == "success" or status == "prepared"
return status == "succeed" or status == "prepared"
self.update_job_status("fail")
s.deleteJobTemplate(jt)
return False
......@@ -846,7 +846,8 @@ class JobManager:
return False
ptime.write(str(round(time.time())) + "\n")
self.set_job_status("prepared")
self.run_job("local")
if MODE != "webserver":
self.run_job("local")
def _end_of_prepare_dotplot(self):
# Parse alignment file:
......@@ -970,83 +971,88 @@ class JobManager:
self.prepare_dotplot_local()
def run_job(self, batch_system_type):
success = False
if batch_system_type == "local":
success = self.__launch_local()
elif batch_system_type in ["slurm", "sge"]:
success = self.__launch_drmaa(batch_system_type)
if success:
with Job.connect():
if MODE == "webserver":
job = Job.get(Job.id_job == self.id_job)
with open(self.logs) as logs:
measures = logs.readlines()[-1].strip("\n").split(" ")
map_elapsed = round(float(measures[0]))
job.mem_peak = int(measures[1])
with open(self.preptime_file) as ptime:
lines = ptime.readlines()
start = int(lines[0].strip("\n"))
end = int(lines[1].strip("\n"))
prep_elapsed = end - start
job.time_elapsed = prep_elapsed + map_elapsed
else:
job = None
status = "merging"
if MODE == "webserver":
job.status = "merging"
job.save()
else:
self.set_status_standalone(status)
if self.tool.split_before and self.query is not None:
start = time.time()
paf_raw = self.paf_raw + ".split"
os.remove(self.get_query_split())
merger = Merger(self.paf_raw, paf_raw, self.query_index_split,
self.idx_q, debug=DEBUG)
merger.merge()
os.remove(self.paf_raw)
os.remove(self.query_index_split)
self.paf_raw = paf_raw
end = time.time()
if MODE == "webserver":
job.time_elapsed += end - start
elif self.query is None:
shutil.copyfile(self.idx_t, self.idx_q)
Path(os.path.join(self.output_dir, ".all-vs-all")).touch()
if self.tool.parser is not None:
paf_raw = self.paf_raw + ".parsed"
getattr(parsers, self.tool.parser)(self.paf_raw, paf_raw)
os.remove(self.paf_raw)
self.paf_raw = paf_raw
sorter = Sorter(self.paf_raw, self.paf)
sorter.sort()
os.remove(self.paf_raw)
if self.target is not None and os.path.exists(self.target.get_path()):
os.remove(self.target.get_path())
if os.path.isfile(os.path.join(self.output_dir, ".do-sort")):
paf = Paf(paf=self.paf,
idx_q=self.idx_q,
idx_t=self.idx_t,
auto_parse=False)
paf.sort()
if not paf.parsed:
success = False
status = "fail"
error = "Error while sorting query. Please contact us to report the bug"
if MODE == "webserver":
job = Job.get(Job.id_job == self.id_job)
job.status = status
job.error = error
else:
self.set_status_standalone(status, error)
if success:
status = "success"
try:
success = False
if batch_system_type == "local":
success = self.__launch_local()
elif batch_system_type in ["slurm", "sge"]:
success = self.__launch_drmaa(batch_system_type)
if success:
with Job.connect():
if MODE == "webserver":
job = Job.get(Job.id_job == self.id_job)
job.status = "success"
with open(self.logs) as logs:
measures = logs.readlines()[-1].strip("\n").split(" ")
map_elapsed = round(float(measures[0]))
job.mem_peak = int(measures[1])
with open(self.preptime_file) as ptime:
lines = ptime.readlines()
start = int(lines[0].strip("\n"))
end = int(lines[1].strip("\n"))
prep_elapsed = end - start
job.time_elapsed = prep_elapsed + map_elapsed
else:
job = None
status = "merging"
if MODE == "webserver":
job.status = "merging"
job.save()
else:
self.set_status_standalone(status)
if self.tool.split_before and self.query is not None:
start = time.time()
paf_raw = self.paf_raw + ".split"
os.remove(self.get_query_split())
merger = Merger(self.paf_raw, paf_raw, self.query_index_split,
self.idx_q, debug=DEBUG)
merger.merge()
os.remove(self.paf_raw)
os.remove(self.query_index_split)
self.paf_raw = paf_raw
end = time.time()
if MODE == "webserver":
job.time_elapsed += end - start
elif self.query is None:
shutil.copyfile(self.idx_t, self.idx_q)
Path(os.path.join(self.output_dir, ".all-vs-all")).touch()
if self.tool.parser is not None:
paf_raw = self.paf_raw + ".parsed"
getattr(parsers, self.tool.parser)(self.paf_raw, paf_raw)
os.remove(self.paf_raw)
self.paf_raw = paf_raw
sorter = Sorter(self.paf_raw, self.paf)
sorter.sort()
os.remove(self.paf_raw)
if self.target is not None and os.path.exists(self.target.get_path()):
os.remove(self.target.get_path())
if os.path.isfile(os.path.join(self.output_dir, ".do-sort")):
paf = Paf(paf=self.paf,
idx_q=self.idx_q,
idx_t=self.idx_t,
auto_parse=False)
paf.sort()
if not paf.parsed:
success = False
status = "fail"
error = "Error while sorting query. Please contact us to report the bug"
if MODE == "webserver":
job = Job.get(Job.id_job == self.id_job)
job.status = status
job.error = error
else:
self.set_status_standalone(status, error)
if success:
status = "success"
if MODE == "webserver":
job = Job.get(Job.id_job == self.id_job)
job.status = "success"
job.save()
else:
self.set_status_standalone(status)
except Exception as e:
traceback.print_exc()
self.set_job_status("fail", "Your job has failed for an unexpected reason. Please contact the support if"
"the problem persists.")
if MODE == "webserver" and self.config.send_mail_status:
self.send_mail_post()
......
......@@ -692,6 +692,10 @@ h2.status {
width: 80.4%;
}
.progress-status-bar.succeed {
width: 75.0%;
}
.progress-status-bar.success, .progress-status-bar.fail, .progress-status-bar.no-match {
width: 100%;
}
......
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\ No newline at end of file
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25px;border-top-left-radius:10px;border-top-right-radius:10px;cursor:pointer}#tabs .tab.active{background-color:#eee;font-weight:bold}#tabs .tab:hover{background-color:#f7f7f7}div.buttons{margin-top:20px}div.footnotes{margin-top:25px}.notifyjs-corner{top:50px!important}div.top-forms{position:relative;width:810px}form#select-zone{margin-bottom:5px;margin-left:40px}div.top-forms select,div.top-forms input{height:28px}form#select-zone div.chosen-widget,form#select-zone input[type=button]{display:inline-block;vertical-align:middle}form#select-zone input[type=button]{line-height:100%}div.chosen-container{width:200px!important}a.chosen-single{height:30px!important;line-height:30px!important;font-size:11pt!important}a.chosen-single div b{background-position-y:4px!important}form#form-parameters{margin-top:20px;margin-left:15px}form#export{position:absolute;top:0;right:0}span.tip{position:absolute;z-index:2;display:none;font-size:12pt;height:auto;padding:10px;border-radius:3px;box-shadow:0 1px 2px #666;background:#ededed}table.drawtooltip td.tt-label{padding-right:5px;vertical-align:middle;font-weight:bold}#body-container{max-width:100%!important}div.navbar{background-image:linear-gradient(to bottom,#2B3044 0,#141a30 100%)}div.submit-form table td{padding-bottom:8px;vertical-align:bottom}div.submit-form table td label{padding-right:20px}div.submit-form table input#id_job,div.submit-form table input#email{width:410px}.input-group{display:inline-block}.input-group .input-group-btn,.input-group input{display:inline-block!important;position:relative!important;float:none!important}.input-group button{padding-top:0}div.input-group{padding-left:15px!important}.upload-btn-wrapper{position:relative;height:30px;width:42px;overflow:hidden;display:inline-block}button.btn-file{height:30px;width:42px}div.in-label{position:relative;display:inline-block;width:300px;height:30px;vertical-align:middle}div.progress{width:300px;height:30px;position:absolute;top:0;left:0;z-index:5!important;background:white;margin-bottom:0!important;box-shadow:none}div.progress .bar{height:100%;background:#33b234;z-index:5!important}select.select-type-input,.input-group button,.input-group input{height:30px;line-height:30px}input.show-file{padding-left:2px;padding-right:2px;width:auto;z-index:10!important;background:none!important;color:black}div.hidden-input-files{display:none}label.error{color:red}div.loading-file{display:inline-block;vertical-align:middle;width:30px;height:30px;background:url(images/loading1.gif) no-repeat 0 0;background-size:30px 30px}div.upload-success{display:inline-block;vertical-align:middle;width:30px;height:30px;background:url(images/success.svg) no-repeat 0 0;background-size:30px 30px}div.file-size{display:inline-block;vertical-align:middle;margin-left:10px}div#uploading-loading{height:30px;line-height:30px;width:200px;font-size:14pt;font-weight:bold;text-align:center;color:black}div.progress,input.show-file{width:100%!important}div.in-label{width:300px}div.in-label.grp2{width:365px}div.submit-form table input[type=text],div.submit-form table input[type=email]{border:1px solid #A9A9A9;border-image:none}div.submit-form table input,div.submit-form button,div.submit-form select{border-radius:5px!important;-moz-border-radius:5px!important;-webkit-border-radius:5px!important;height:30px;outline:none!important}div.submit-form select:hover{border-radius:5px 5px 0 0!important;-moz-border-radius:5px 5px 0 0!important;-webkit-border-radius:5px 5px 0 0!important;outline:none!important}.beta-warning{height:30px;line-height:30px;text-align:center;color:white;background-color:#6e0000}.beta-warning a{color:white;font-weight:bold}h2.status{font-size:18pt;margin-bottom:15px;margin-top:10px}.status-body{margin-top:25px;margin-bottom:30px}.progress-status{position:relative;width:500px;height:30px;border:solid 1px black;margin-left:55px;margin-bottom:100px}.progress-status-bar .inner{background:linear-gradient(90deg,rgb(255,254,80) 0%,rgba(16,128,6,1) 100%);width:500px;height:100%}.progress-status-bar{position:absolute;width:0;height:28px;top:0;left:0;overflow:hidden}.progress-status-bar.getfiles,.progress-status-bar.getfiles-waiting{width:3.7%}.progress-status-bar.waiting{width:7%}.progress-status-bar.preparing,.progress-status-bar.prepare-scheduled,.progress-status-bar.preparing-cluster{width:10.7%}.progress-status-bar.prepared{width:20.4%}.progress-status-bar.scheduled{width:30.3%}.progress-status-bar.starting,.progress-status-bar.scheduled-cluster{width:35.2%}.progress-status-bar.started{width:40.3%}.progress-status-bar.merging{width:80.4%}.progress-status-bar.succeed{width:75.0%}.progress-status-bar.success,.progress-status-bar.fail,.progress-status-bar.no-match{width:100%}.progress-status-bar.fail .inner{background:rgb(195,16,18)}.progress-status .tick{position:absolute;top:29px;width:1px;height:10px;border:solid 1px black}.progress-status .tick p{transform:rotate(-45deg);margin-left:-70px;margin-top:35px;text-align:right;display:block;width:80px;overflow:hidden}.progress-status .tick.submitted{left:-1px}.progress-status .tick.prepared{left:20%}.progress-status .tick.scheduled{left:30%}.progress-status .tick.started{left:40%}.progress-status .tick.merging{left:80%}.progress-status .tick.success{right:-1px}h2.status,div.status-body{margin-left:55px}div#sidebar{position:relative}div#sidebar p.bottom{position:absolute;bottom:0;right:0;width:100px}div#sidebar p.bottom input#delete-job{background:#ffbba8!important}ul.nav ul.dropdown-menu{max-height:300px;overflow-y:auto}
\ No newline at end of file
......@@ -14,7 +14,7 @@
{% block content %}
<h2 class="status">Job name: {{ id_job }}</h2>
<div class="status-body">
{% if status == "started" %}
{% if status == "started" or status == "succeed" %}
<p>Your job has started.<br/>
{% elif status == "starting" %}
<p>Your job is starting...<br/>
......
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