1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3c4696f6af0d/ changeset: 3c4696f6af0d user: natefoo date: 2012-11-27 21:57:05 summary: Fix check_galaxy for recent framework changes. affected #: 1 file
diff -r 51ffca8538ff769f54f379d6e070494fc2c14833 -r 3c4696f6af0d9c6c7885568c1fee02df53849322 contrib/nagios/check_galaxy.py --- a/contrib/nagios/check_galaxy.py +++ b/contrib/nagios/check_galaxy.py @@ -4,7 +4,7 @@ via the check_galaxy.sh script in Galaxy's cron/ directory. """
-import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt +import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt, json from user import home
import warnings @@ -63,13 +63,6 @@ username = args[1] password = args[2]
-if server.endswith(".g2.bx.psu.edu"): - if debug: - print "Checking a PSU Galaxy server, using maint file" - maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0] -else: - maint = None - new_history = False for o, a in opts: if o == "-n": @@ -95,13 +88,12 @@
def __init__(self): self.server = server - self.maint = maint self.tool = None self.tool_opts = None - self.id = None - self.status = None + self._hda_id = None + self._hda_state = None + self._history_id = None self.check_file = None - self.hid = None self.cookie_jar = os.path.join( var_dir, "cookie_jar" ) dprint("cookie jar path: %s" % self.cookie_jar) if not os.access(self.cookie_jar, os.R_OK): @@ -116,19 +108,14 @@ def reset(self): self.tool = None self.tool_opts = None - self.id = None - self.status = None + self._hda_id = None + self._hda_state = None + self._history_id = None self.check_file = None - self.delete_datasets() - self.get("/root/history") - p = didParser() - p.feed(tc.browser.get_html()) - if len(p.dids) > 0: - print "Remaining datasets ids:", " ".join( p.dids ) - raise Exception, "History still contains datasets after attempting to delete them" if new_history: self.get("/history/delete_current") tc.save_cookies(self.cookie_jar) + self.delete_datasets()
def check_redir(self, url): try: @@ -143,25 +130,9 @@ dprint( "%s is not returning redirect (302): %s" % (url, e) ) code = tc.browser.get_code() if code == 502: - is_maint = self.check_maint() - if is_maint: - dprint( "Galaxy is down, but a maint file was found, so not sending alert" ) - sys.exit(0) - else: - print "Galaxy is down (code 502)" - sys.exit(1) - return(False) - - # checks for a maint file - def check_maint(self): - if self.maint is None: - #dprint( "Warning: unable to check maint file for %s" % self.server ) - return(False) - try: - self.get(self.maint) - return(True) - except twill.errors.TwillAssertionError, e: - return(False) + print "Galaxy is down (code 502)" + sys.exit(1) + return False
def login(self, user, pw): self.get("/user/login") @@ -210,15 +181,64 @@ tc.submit("runtool_btn") tc.code(200)
+ @property + def history_id(self): + if self._history_id is None: + self.get('/api/histories') + self._history_id = json.loads(tc.browser.get_html())[0]['id'] + return self._history_id + + @property + def history_contents(self): + self.get('/api/histories/%s/contents' % self.history_id) + return json.loads(tc.browser.get_html()) + + @property + def hda_id(self): + if self._hda_id is None: + self.set_top_hda() + return self._hda_id + + @property + def hda_state(self): + if self._hda_state is None: + self.set_top_hda() + return self._hda_state + + def set_top_hda(self): + self.get(self.history_contents[-1]['url']) + hda = json.loads(tc.browser.get_html()) + self._hda_id = hda['id'] + self._hda_state = hda['state'] + + @property + def undeleted_hdas(self): + rval = [] + for item in self.history_contents: + self.get(item['url']) + hda = json.loads(tc.browser.get_html()) + if hda['deleted'] == False: + rval.append(hda) + return rval + + @property + def history_state(self): + self.get('/api/histories/%s' % self.history_id) + return json.loads(tc.browser.get_html())['state'] + + @property + def history_state_terminal(self): + if self.history_state not in ['queued', 'running', 'paused']: + return True + return False + def wait(self): sleep_amount = 1 count = 0 maxiter = 16 while count < maxiter: count += 1 - self.get("/root/history") - page = tc.browser.get_html() - if page.find( '<!-- running: do not change this comment, used by TwillTestCase.wait -->' ) > -1: + if not self.history_state_terminal: time.sleep( sleep_amount ) sleep_amount += 1 else: @@ -226,20 +246,14 @@ if count == maxiter: raise Exception, "Tool never finished"
- def check_status(self): - self.get("/root/history") - p = historyParser() - p.feed(tc.browser.get_html()) - if p.status != "ok": - self.get("/datasets/%s/stderr" % p.id) + def check_state(self): + if self.hda_state != "ok": + self.get("/datasets/%s/stderr" % self.hda_id) print tc.browser.get_html() - raise Exception, "HDA %s NOT OK: %s" % (p.id, p.status) - self.id = p.id - self.status = p.status - #return((p.id, p.status)) + raise Exception, "HDA %s NOT OK: %s" % (self.hda_id, self.hda_state)
def diff(self): - self.get("/datasets/%s/display?to_ext=%s" % (self.id, self.tool_opts.get('out_format', 'fasta'))) + self.get("/datasets/%s/display?to_ext=%s" % (self.hda_id, self.tool_opts.get('out_format', 'fasta'))) data = tc.browser.get_html() tmp = tempfile.mkstemp() dprint("tmp file: %s" % tmp[1]) @@ -256,12 +270,12 @@ os.remove(tmp[1])
def delete_datasets(self): - self.get("/root/history") - p = didParser() - p.feed(tc.browser.get_html()) - dids = p.dids - for did in dids: - self.get("/datasets/%s/delete" % did) + for hda in self.undeleted_hdas: + self.get('/datasets/%s/delete' % hda['id']) + hdas = [hda['id'] for hda in self.undeleted_hdas] + if hdas: + print "Remaining datasets ids:", " ".join(hdas) + raise Exception, "History still contains datasets after attempting to delete them"
def check_if_logged_in(self): self.get("/user?cntrller=user") @@ -294,33 +308,6 @@ elif data == "User with that email already exists": self.already_exists = True
-class historyParser(htmllib.HTMLParser): - def __init__(self): - htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) - self.status = None - self.id = None - def start_div(self, attrs): - # find the top history item - for i in attrs: - if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"): - self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1] - dprint("status: %s" % self.status) - if i[0] == "id" and i[1].startswith("historyItem-"): - self.id = i[1].rsplit("historyItem-", 1)[1] - dprint("id: %s" % self.id) - if self.status is not None: - self.reset() - -class didParser(htmllib.HTMLParser): - def __init__(self): - htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) - self.dids = [] - def start_div(self, attrs): - for i in attrs: - if i[0] == "id" and i[1].startswith("historyItemContainer-"): - self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] ) - dprint("got a dataset id: %s" % self.dids[-1]) - class loggedinParser(htmllib.HTMLParser): def __init__(self): htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) @@ -379,15 +366,9 @@
b.runtool() b.wait() - b.check_status() + b.check_state() b.diff() b.delete_datasets()
- # by this point, everything else has succeeded. there should be no maint. - is_maint = b.check_maint() - if is_maint: - print "Galaxy is up and fully functional, but a maint file is in place." - sys.exit(1) - print "OK" sys.exit(0)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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