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

+#!/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)