def test_bad_values_fail():
for i, s in [(4, "target_path = /wasdfkshdf"),
(6, "inbox_path = /dfsdfhljfwe/wefsdfh")]:
new_lines = copy.copy(conf_lines)
new_lines[i] = s
h = cStringIO.StringIO('\n'.join(new_lines))
with pytest.raises(ValueError):
config.read_configuration(h)
def test_bad_values_fail():
for i,s in [(4,"target_path = /wasdfkshdf"),
(6,"inbox_path = /dfsdfhljfwe/wefsdfh")]:
new_lines = copy.copy(conf_lines)
new_lines[i] = s
h = cStringIO.StringIO('\n'.join(new_lines))
with pytest.raises(ValueError):
config.read_configuration(h)
def action(self):
omit_blast = self.omit_blast
with open(self.config_path) as h:
config = cf.read_configuration(h)
monitor_path = config['target_path']
syslog.syslog(syslog.LOG_NOTICE, "sequencereportd monitoring %s for runs to process." % monitor_path)
class Handler(pyinotify.ProcessEvent):
def process_IN_UNMOUNT(self, event):
syslog.syslog(syslog.LOG_NOTICE, "Backing filesystem of %s was unmounted. Exiting." % \
(event.path,))
exit(0)
def process_default(self, event):
syslog.syslog(syslog.LOG_NOTICE, "Event on %s in monitored share." % (event.pathname,))
if event.name != 'workup.json' and \
not event.name.endswith('.ab1'):
syslog.syslog(syslog.LOG_NOTICE, "Ignoring event on %s." % (event.pathname,))
return
wrote, result = try_report(event.path, omit_blast)
if not wrote:
syslog.syslog(syslog.LOG_NOTICE, "No action in %s: %s" % \
(event.path,result))
else:
syslog.syslog(syslog.LOG_NOTICE, "Wrote report in %s." % (result,))
wm = pyinotify.WatchManager()
notifier = pyinotify.Notifier(wm, Handler())
wm.add_watch(monitor_path,
pyinotify.IN_CREATE |
pyinotify.IN_DELETE |
pyinotify.IN_MOVED_TO |
pyinotify.IN_ATTRIB |
pyinotify.IN_MODIFY,
rec=True)
notifier.loop()
def action(self):
with open(self.config_path) as h:
config = cf.read_configuration(h)
monitor_path = config['target_path']
syslog.syslog(syslog.LOG_NOTICE, "dailysummaryd monitoring %s for reports to summarize." % monitor_path)
class Handler(pyinotify.ProcessEvent):
def process_IN_UNMOUNT(self, event):
syslog.syslog(syslog.LOG_NOTICE, "Backing filesystem of %s was unmounted. Exiting." % \
(event.path,))
exit(0)
def process_default(self, event):
syslog.syslog(syslog.LOG_NOTICE, "Event on %s in monitored share." % (event.pathname,))
if not event.name.endswith('report.html'):
syslog.syslog(syslog.LOG_NOTICE, "Ignoring event on %s." % (event.pathname,))
return
wrote, result = summarize(os.path.dirname(event.path))
if not wrote:
syslog.syslog(syslog.LOG_NOTICE, "No action in %s: %s" % \
(event.path,result))
else:
syslog.syslog(syslog.LOG_NOTICE, "Wrote summary in %s." % (result,))
wm = pyinotify.WatchManager()
notifier = pyinotify.Notifier(wm, Handler())
wm.add_watch(monitor_path,
pyinotify.IN_CREATE |
pyinotify.IN_DELETE |
pyinotify.IN_MOVED_TO |
pyinotify.IN_ATTRIB |
pyinotify.IN_MODIFY,
rec=True)
notifier.loop()
def test_good_config_works():
good_config = cStringIO.StringIO('\n'.join(conf_lines))
assert config.read_configuration(good_config) == \
{'target_path': '/var',
'inbox_path': '/usr/bin',
'db_port': 5432, 'db_name': 'mdx',
'db_server': 'localhost', 'db_username': '******',
'db_credentials': 'data/dbcredential', 'db_password': '******'}
def test_good_config_works():
good_config = cStringIO.StringIO('\n'.join(conf_lines))
assert config.read_configuration(good_config) == \
{'target_path': '/var',
'inbox_path': '/usr/bin',
'db_port': 5432, 'db_name': 'mdx',
'db_server': 'localhost', 'db_username': '******',
'db_credentials': 'data/dbcredential', 'db_password': '******'}
def action(self):
with open(self.config_path) as h:
config = cf.read_configuration(h)
db = oursql.connect(host=config['db_server'],
user=config['db_username'],
passwd=config['db_password'],
db=config['db_name'],
port=config['db_port'])
syslog.syslog(syslog.LOG_NOTICE, "Placed monitoring %s for incoming files." % (config['inbox_path'],))
class Handler(pyinotify.ProcessEvent):
def process_IN_UNMOUNT(self, event):
syslog.syslog(syslog.LOG_NOTICE, "Backing filesystem of %s was unmounted. Exiting." % event.path)
exit(0)
def process_default(self, event):
syslog.syslog(syslog.LOG_NOTICE, "File %s created...processing." % (event.pathname,))
seqlab.place.placewrapper(db, event.pathname, config['target_path'])
wm = pyinotify.WatchManager()
notifier = pyinotify.Notifier(wm, Handler())
wm.add_watch(config['inbox_path'], pyinotify.IN_CREATE, rec=True)
notifier.loop()
