From 8c21b407244693bb767a71eca4c534b9add130ab Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 26 Oct 2012 13:00:02 +0000
Subject: [PATCH] Mutalyzer instance monitor script
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@623 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/monitor/mutalyzer-monitor.py | 98 +++++++++++++++++++++++++++++
1 file changed, 98 insertions(+)
create mode 100755 extras/monitor/mutalyzer-monitor.py
diff --git a/extras/monitor/mutalyzer-monitor.py b/extras/monitor/mutalyzer-monitor.py
new file mode 100755
index 00000000..c46cb21b
--- /dev/null
+++ b/extras/monitor/mutalyzer-monitor.py
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+"""
+Monitor a Mutalyzer server by some basic uptime checks.
+
+Run with no arguments for usage info. The script returns a 0 exit status
+on success, 1 on failure. It writes nothing to standard output/error.
+
+Currently implemented checks:
+- Website homepage exists.
+- Name checker SOAP web service can be called.
+- Batch name checker can be called.
+"""
+
+
+import argparse
+import logging
+import sys
+import time
+import urllib2
+
+from suds import WebFault
+from suds.client import Client
+
+
+DEFAULT_MUTALYZER_URL = 'https://mutalyzer.nl'
+BATCH_MAX_POLL = 25
+BATCH_POLL_WAIT = 5
+
+
+logging.getLogger('suds.client').setLevel(logging.CRITICAL)
+
+
+def main(mutalyzer_url):
+ """
+ Run all checks.
+ """
+ checks = check_website, check_soap, check_batch
+ try:
+ [check(mutalyzer_url) for check in checks]
+ except:
+ sys.exit(1)
+
+
+def check_website(mutalyzer_url):
+ """
+ Check if website homepage exists.
+ """
+ response = urllib2.urlopen(mutalyzer_url)
+ html = response.read()
+ assert 'Welcome to the Mutalyzer web site' in html
+
+
+def check_soap(mutalyzer_url):
+ """
+ Check if the name checker SOAP web service can be called.
+ """
+ wsdl_url = mutalyzer_url + '/services/?wsdl'
+ service = Client(wsdl_url, cache=None).service
+
+ result = service.runMutalyzer('AB026906.1:c.274G>T')
+ assert result.genomicDescription == 'AB026906.1:g.7872G>T'
+
+
+def check_batch(mutalyzer_url):
+ """
+ Check if the batch name checker can be called.
+ """
+ wsdl_url = mutalyzer_url + '/services/?wsdl'
+ service = Client(wsdl_url, cache=None).service
+
+ variants = ['AB026906.1(SDHD):g.7872G>T',
+ 'NM_003002.1:c.3_4insG',
+ 'AL449423.14(CDKN2A_v002):c.5_400del']
+ data = '\n'.join(variants).encode('base64')
+ result = service.submitBatchJob(data, 'NameChecker')
+
+ job_id = int(result)
+
+ for _ in range(BATCH_MAX_POLL):
+ try:
+ result = service.getBatchJob(job_id)
+ break
+ except WebFault:
+ time.sleep(BATCH_POLL_WAIT)
+ else:
+ sys.exit(1)
+
+ response = result.decode('base64')
+ assert len([_ for line in response.split('\n') if line.strip()]) - 1 == len(variants)
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description=__doc__.split('\n\n')[0])
+ parser.add_argument('mutalyzer_url', metavar='MUTALYZER_URL',
+ default=DEFAULT_MUTALYZER_URL, nargs='?',
+ help='Mutalyzer instance URL (default: %(default)s')
+ args = parser.parse_args()
+ main(args.mutalyzer_url)
--
GitLab