from zendesk import Zendesk
################################################################
## NEW CONNECTION CLIENT
################################################################
zendesk = Zendesk(
zendesk_url='https://yourcompany.zendesk.com',
zendesk_username='******',
zendesk_password='******',
use_api_token=True,
api_version=2
)
# Are you getting an error such as...
# "SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed"?
zendesk = Zendesk('https://yourcompany.zendesk.com', '*****@*****.**', 'passwd',
client_args={
"disable_ssl_certificate_validation": True
}
)
################################################################
## TICKETS
################################################################
# List
zendesk.list_tickets(view_id=1) # Must have a view defined
# Create
new_ticket = {
import os
from config import ENV
from salesforce import SalesForce
from zendesk import Zendesk
from migration import MigrationItem
from log_helper import get_logger
import helpers
log = get_logger('Main')
if __name__ == "__main__":
migration_plan = json.load(open('migration_plan.json', 'r'))
sf_config = migration_plan['salesforce']
sf = SalesForce(**sf_config)
zd_config = migration_plan['zendesk']
zd = Zendesk(**zd_config)
for item in migration_plan['migration_items']:
if item['skip'] == False:
if item['type'] == 'migration_object':
migration_item = MigrationItem(sf, zd, mode=ENV, **item)
if migration_item.skip == False:
try:
migration_item.migrate()
except Exception as err:
log.critical(err)
raise err
elif item['type'] == 'script':
eval(item['script'], {"helpers": helpers, "env": ENV})
def get_zd_instance():
migration_plan = json.load(open('migration_plan.json', 'r'))
zd_config = migration_plan['zendesk']
return Zendesk(**zd_config)
42730237: 'Tickets/LSM',
42730227: 'Tickets/WSM',
42771018: 'Tickets/Mobile',
42730217: 'Tickets/Insights',
44896573: 'Tickets/Browser',
42771028: 'Tickets/Platform',
42730207: 'Tickets/Other'
}
post_url = "https://platform-api.newrelic.com/platform/v1/metrics"
guid = 'com.NewRelic.ZedScraper'
#update bash_profile on server with this info
zendesk = Zendesk(environ['ZENDESK_URL'],
environ['ZENDESK_USERNAME'],
environ['ZENDESK_APITOKEN'],
use_api_token=True,
api_version=2,
client_args={"disable_ssl_certificate_validation": True})
platform_key = environ['NEW_RELIC_APIKEY']
view_blob = zendesk.count_many_views(ids=view_ids.keys())
counted_views = {}
for view in view_blob['view_counts']:
metric_name = "Component/test2/%s[Tickets]" % view_ids[view['view_id']]
total_tickets = view['value']
data = {
"agent": {
"host": "db.zendesk.newrelic_tickets",
def main(argv=None):
import sys, tempfile, argparse
# Log to stdout
import logging
logging.basicConfig()
# Declare a class for an argparse custom action.
# Handles converting ascii input from argparse that may contain unicode
# to a real unicode string.
class UnicodeStore(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, values.decode('utf-8'))
# Options precedence:
# program state defaults, which are overridden by
# ~/.zdf2pdf.cfg [zdf2pdf] section options, which are overridden by
# command line options, which are overridden by
# -c CONFIG_FILE [zdf2pdf] section options, which are overridden by
# ~/.zdf2pdf.cfg [RUN_SECTION] section options, which are overridden by
# -c CONFIG_FILE [RUN_SECTION] section options
#
# Program state, with defaults
#
state = {
'verbose': False,
'json_file': None,
'categories': None,
'forums': None,
'topics': None,
'run_section': None,
'list_zdf': 'forums',
'style_file': None,
'output_file': 'PCLOADLETTER.pdf',
'title': None,
'title_class': None,
'author': None,
'date': None,
'copyright': None,
'toc': False,
'toc_class': None,
'toc_title': 'Table of Contents',
'pre_width': None,
'strip_empty': False,
'header': None,
'footer': None,
'category_sections': False,
'forum_sections': False,
'topics_heading': None,
'work_dir': tempfile.gettempdir(),
'delete': False,
'url': None,
'mail': None,
'password': '******',
'is_token': False,
}
argp = argparse.ArgumentParser(
description='Make a PDF from Zendesk forums or entries.')
argp.add_argument('-v',
'--verbose',
action='store_true',
help='Verbose output')
argp.add_argument('--json-file',
action=UnicodeStore,
dest='json_file',
help='Zendesk entries JSON file to convert to PDF')
argp.add_argument(
'--categories',
action=UnicodeStore,
dest='categories',
help='Comma separated Category IDs to download and convert to PDF')
argp.add_argument(
'--forums',
action=UnicodeStore,
dest='forums',
help='Comma separated Forum IDs to download and convert to PDF')
argp.add_argument(
'--topics',
action=UnicodeStore,
dest='topics',
help='Comma separated Topic (Entry) IDs to download and convert to PDF'
)
argp.add_argument('-r',
action=UnicodeStore,
dest='run_section',
help='Run pre-configured section in configuration file')
argp.add_argument(
'-l',
action=UnicodeStore,
dest='list_zdf',
help="""List a forum's entries by ID and title. If no forum ID is
supplied, list forums by ID and title organized by category""",
nargs='?',
const=state['list_zdf'],
metavar='FORUM_TO_LIST')
argp.add_argument('-c',
action=UnicodeStore,
dest='config_file',
help='Configuration file (overrides ~/.zdf2pdf.cfg)')
argp.add_argument('-s',
action=UnicodeStore,
dest='style_file',
help='Style file (CSS) to <link>')
argp.add_argument('-o',
action=UnicodeStore,
dest='output_file',
help='Output filename (default: PCLOADLETTER.pdf)',
default=state['output_file'])
argp.add_argument('-t',
action=UnicodeStore,
dest='title',
help='Title to be added to the beginning of the PDF')
argp.add_argument(
'-a',
action=UnicodeStore,
dest='author',
help='Author line to be added to the beginning of the PDF')
argp.add_argument('--date',
action=UnicodeStore,
dest='date',
help='Date line to be added to the beginning of the PDF')
argp.add_argument(
'--copyright',
action=UnicodeStore,
dest='copyright',
help='Copyright line to be added to the beginning of the PDF')
argp.add_argument('--title-class',
action=UnicodeStore,
dest='title_class',
help='CSS class to be added to title page div')
argp.add_argument('--toc',
action='store_true',
dest='toc',
help="Generate a Table of Contents (default: false)")
argp.add_argument('--toc-title',
action=UnicodeStore,
dest='toc_title',
help="ToC title (default: Table of Contents)")
argp.add_argument('--toc-class',
action=UnicodeStore,
dest='toc_class',
help='CSS class to be added to ToC div')
argp.add_argument('--pre-width',
action=UnicodeStore,
dest='pre_width',
help='Width to wrap contents of <pre></pre> tags.')
argp.add_argument('--strip-empty',
action='store_true',
dest='strip_empty',
help='Strip empty tags. (default: false)')
argp.add_argument('--header',
action=UnicodeStore,
dest='header',
help='HTML header to add to the PDF (see docs)')
argp.add_argument('--footer',
action=UnicodeStore,
dest='footer',
help='HTML footer to add to the PDF (see docs)')
argp.add_argument('--category-sections',
action='store_true',
dest='category_sections',
help='Make categories sections (default: false)')
argp.add_argument('--forum-sections',
action='store_true',
dest='category_sections',
help='Make categories sections (default: false)')
argp.add_argument(
'--topics-heading',
action=UnicodeStore,
dest='topics_heading',
help='Heading to put at start of topics retrieved individually')
argp.add_argument(
'-w',
action=UnicodeStore,
dest='work_dir',
help="""Working directory in which to store JSON output and images
(default: temp dir)""")
argp.add_argument('-d',
'--delete',
action='store_true',
dest='delete',
help="""Delete working directory at program exit
(default: do not delete)""")
argp.add_argument('-u',
action=UnicodeStore,
dest='url',
help='URL of Zendesk (e.g. https://example.zendesk.com)')
argp.add_argument('-m',
action=UnicodeStore,
dest='mail',
help='E-Mail address for Zendesk login')
argp.add_argument('-p',
action=UnicodeStore,
dest='password',
help='Password for Zendesk login',
nargs='?',
const=state['password'])
argp.add_argument(
'-i',
'--is-token',
action='store_true',
dest='is_token',
help='Is token? Specify if password supplied a Zendesk token')
# Set argparse defaults with program defaults.
# Skip password and list_zdf as they are argparse const, not argparse default
argp.set_defaults(**dict((k, v) for k, v in state.iteritems()
if k != 'password' and k != 'list_zdf'))
# Read ~/.zdf2pdf.cfg [zdf2pdf] section and update argparse defaults
try:
config_state(
os.path.expanduser('~') + '/.zdf2pdf.cfg', 'zdf2pdf', state)
# Skip list_zdf because it is not a config file value, not an argparse
# const value, and we don't want to lose it by overwriting it with None.
# Password is OK now, because we either have one from the config file or
# it is still None.
argp.set_defaults(**dict(
(k, v) for k, v in state.iteritems() if k != 'list_zdf'))
except configparser.NoSectionError:
# -c CONFIG_FILE did not have a [zdf2pdf] section. Skip it.
pass
# Parse the command line options
if argv is None:
argv = sys.argv
args = argp.parse_args()
# Update the program state with command line options
for k in state.keys():
state[k] = getattr(args, k)
# -c CONFIG_FILE given on command line read args.config_file [zdf2pdf], update state
if args.config_file:
if state['verbose']:
print('Reading config file {}'.format(args.config_file))
try:
config_state(args.config_file, 'zdf2pdf', state)
except configparser.NoSectionError:
# -c CONFIG_FILE did not have a [zdf2pdf] section. Skip it.
pass
# -r RUN_SECTION given
if args.run_section:
if state['verbose']:
print('Searching for {} in ~/.zdf2pdf'.format(args.run_section))
section_found = False
try:
config_state(
os.path.expanduser('~') + '/.zdf2pdf.cfg', args.run_section,
state)
section_found = True
if state['verbose']:
print('Found {} in ~/.zdf2pdf'.format(args.run_section))
except configparser.NoSectionError:
# ~/.zdf2pdf.cfg did not have this section. Hope it's found later.
pass
# -c CONFIG_FILE and -r RUN_SECTION given
if args.config_file:
if state['verbose']:
print('Searching for {} in {}'.format(args.run_section,
args.config_file))
try:
config_state(args.config_file, args.run_section, state)
section_found = True
if state['verbose']:
print('Found {} in {}'.format(args.run_section,
args.config_file))
except configparser.NoSectionError:
# CONFIG_FILE did not have this section.
pass
# If the section wasn't found, print an error and exit
if not section_found:
print('Error: Run section {} was not found'.format(
args.run_section))
return 1
if state['categories'] or state['topics'] or state['forums'] or state[
'list_zdf']:
from zendesk import Zendesk
if state['url'] and state['mail'] and state['password']:
if state['verbose']:
print(
'Configuring Zendesk with:\n'
'url: {}\n'
'mail: {}\n'
'password: (hidden)\n'
'is_token: {}\n'.format(state['url'], state['mail'],
repr(state['is_token'])))
zd = Zendesk(state['url'],
zendesk_username=state['mail'],
zendesk_password=state['password'],
use_api_token=state['is_token'])
else:
msg = textwrap.dedent("""\
Error: Need Zendesk config for requested operation. Use -u, -m,
-p options or a config file to provide the information.
Config file (e.g. ~/.zdf2pdf.cfg) should be something like:
[zdf2pdf]
url = https://example.zendesk.com
mail = [email protected]
password = dneib393fwEF3ifbsEXAMPLEdhb93dw343
is_token = 1
""")
print(msg)
return 1
# All config options are in, state is set.
# Handle any last minute type checking or setting
if state['pre_width']:
try:
state['pre_width'] = int(state['pre_width'])
except TypeError:
print('Could not convert pre_width {} to integer'.format(
repr(state['pre_width'])))
return 1
# Log the state
if state['verbose']:
print('Running with program state:')
for k, v in state.iteritems():
print('{} {}'.format(k, repr(v)))
if state['list_zdf'] == 'forums':
# List available zendesk forums with their IDs and titles and exit.
# Listing is formatted like for following:
# 12345 Category 1 name
# 09876 Forum 1 name
# 54321 Forum 2 name
# 67890 Category 2 name
if state['verbose']: print('Listing all forums')
categories = zd.list_categories()
for cat in categories['categories']:
print('{} {}'.format(cat['id'], cat['name']))
forums = zd.list_category_forums(category_id=cat['id'])['forums']
for forum in forums:
print(' {} {}'.format(forum['id'], forum['name']))
return 0
elif state['list_zdf']:
if state['verbose']:
print('Listing all entries in forum {}'.format(state['list_zdf']))
# List a zendesk forum's entries with their IDs and titles and exit
try:
forum_id = int(state['list_zdf'])
except ValueError:
print('Error: Could not convert to integer: {}'.format(
state['list_zdf']))
return 1
entries = zd.list_topics(forum_id=state['list_zdf'])
for entry in entries['topics']:
print('{} {}'.format(entry['id'], entry['title']))
return 0
# Use an entries file on disk
if state['json_file']:
if state['verbose']:
print('Reading entries from {}'.format(state['json_file']))
# Get the entries off disk
with open(state['json_file'], 'r') as infile:
entries = json.loads(infile.read())
else:
entries = []
# Get the entries from one or more zendesk categories
if state['categories']:
try:
cat_ids = [int(i) for i in state['categories'].split(',')]
except ValueError:
print('Error: Could not convert to integers: {}'.format(
state['forums']))
return 1
for cat_id in cat_ids:
if state['verbose']:
print('Obtaining entries from category {}'.format(cat_id))
cat_entries = []
forums = zd.list_category_forums(category_id=cat_id)['forums']
for forum in forums:
if state['verbose']:
print('Obtaining entries from forum {}'.format(
forum['id']))
# topics = [{entry}, {entry}, ..., {entry}]
topics = zd.list_topics(forum_id=forum['id'])['topics']
if state['forum_sections']:
cat_entries.append({
'section': forum['name'],
'id': forum['id'],
'body': forum['description'],
'topics': topics
})
# result:
# cat_entries = [
# <previous forums,>
# {
# 'section':'FORUM TITLE',
# 'topics':
# [
# {entry},
# ...
# {entry}
# ]
# }
# ]
else:
cat_entries += topics
# result:
# cat_entries = [
# {entry},
# ...
# {entry}
# ]
if state['category_sections']:
cat = zd.show_category(category_id=cat_id)
entries.append({
'section': cat['name'],
'id': cat_id,
'body': cat['description'],
'topics': cat_entries
})
#od[zd.show_category(category_id=cat_id)['name']] =
#entries.append([zd.show_category(category_id=cat_id)['name']] =
# result if forum sections:
# entries = [
# <previous categories,>
# {
# 'section': 'CATEGORY TITLE',
# 'id': 'CATEGORY ID',
# 'body': 'CATEGORY DESCRIPTION',
# 'topics':
# [
# {
# 'section':'FORUM TITLE',
# 'topics':
# [
# {entry},
# ...
# {entry}
# ]
# }
# ]
# }
# ]
#
# result if not forum sections:
# entries = [
# <previous categories,>
# {
# 'section':'CATEGORY TITLE',
# 'topics':
# [
# {entry},
# ...
# {entry}
# ]
# }
# ]
else:
entries += cat_entries
# result: whatever cat_entries was (forums as sections or not)
# is concatenated onto the end of entries
# Get the entries from one or more zendesk forums
if state['forums']:
try:
forum_ids = [int(i) for i in state['forums'].split(',')]
for forum_id in forum_ids:
if state['verbose']:
print('Obtaining entries from forum {}'.format(forum_id))
topics = zd.list_topics(forum_id=forum_id)['topics']
# see above for description of what entries looks like
if state['forum_sections']:
forum = zd.show_forum(forum_id=forum_id)['forum']
entries.append({
'section': forum['name'],
'id': forum['id'],
'body': forum['description'],
'topics': topics
})
else:
entries += topics
except ValueError:
print('Error: Could not convert to integers: {}'.format(
state['forums']))
return 1
# Get individual entries from zendesk
if state['topics']:
topic_ids = state['topics'].replace(' ', '')
topics = zd.show_multiple_topics(topic_ids)['topics']
if state['entries_heading']:
entries.append({
'section': state['entries_heading'],
'topics': topics
})
else:
entries += topics
if len(entries) == 0:
# Didn't get entries from any inputs.
print("Error: Did not receive any entries.")
return 1
zdf2pdf(entries, state)
if state['delete']:
shutil.rmtree(state['work_dir'])
return 0
def main():
arguments = docopt(__doc__)
logger.setLevel(arguments['--level'])
logger.debug(arguments)
global cfg
global run_open
global open_cmd
global zendesk
# read in YAML configuration file
if "~" in arguments['--config']:
pattern = re.compile('~')
arguments['--config'] = pattern.sub(os.path.expanduser("~"), arguments['--config'])
if not os.path.exists(arguments['--config']):
logger.error("Specified configuration file does not exist!")
exit(1)
with open(arguments['--config'], 'r') as ymlfile:
cfg = yaml.load(ymlfile)
# determine if run_open is defined and enabled
try:
run_open = cfg['downloader']['run_open']
if str(run_open).lower() == "true" or run_open == 1:
run_open = True
else:
run_open = False
except:
run_open = False
# determine if open_command is defined
try:
open_cmd = cfg['downloader']['open_command']
except:
if run_open:
logger.warning("'run_open' is set, but 'open_command' doesn't exist - disabling auto open. Please configure 'open_cmd' in .zendesk.yml.")
run_open = False
# check directory for downloads, expand '~' and append '/' if necessary
if "~" in cfg['downloader']['directory']:
pattern = re.compile('~')
cfg['downloader']['directory'] = pattern.sub(os.path.expanduser("~"), cfg['downloader']['directory'])
if not cfg['downloader']['directory'].endswith('/'):
cfg['downloader']['directory'] += '/'
logger.debug("download directory: {}".format(cfg['downloader']['directory']))
options = {}
if 'extensions' in cfg['downloader']:
options['extensions'] = cfg['downloader']['extensions']
if 'exclude' in cfg['downloader']:
options['exclude'] = cfg['downloader']['exclude']
if 'rm_after_extract' in cfg['downloader']:
options['rm_after_extract'] = cfg['downloader']['rm_after_extract']
zendesk = Zendesk(cfg['credentials']['username'], cfg['credentials']['password'], cfg['credentials']['url'], options=options)
if '{0}'.format(arguments['--case']) == 'None':
logger.info("No case specified, downloading attachments for all cases with updates in the last {0} hours".format(arguments['--recent']))
start_time = datetime.datetime.now() - datetime.timedelta(hours=int(arguments['--recent']))
updated_tickets = zendesk.getUpdatedTickets(start_time)
logger.debug(updated_tickets)
if not "error" in updated_tickets:
for ticket in updated_tickets['ids']:
processTicket(ticket)
else:
logger.error(updated_tickets['error'])
else:
ticket = arguments['--case']
processTicket(ticket)
from zendesk import Zendesk
################################################################
## NEW CONNECTION CLIENT
################################################################
zendesk = Zendesk('https://yourcompany.zendesk.com', '*****@*****.**', 'passwd')
# Are you getting an error such as...
# "SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed"?
zendesk = Zendesk('https://yourcompany.zendesk.com', '*****@*****.**', 'passwd',
client_args={
"disable_ssl_certificate_validation": True
}
)
################################################################
## TICKETS
################################################################
# List
zendesk.list_tickets(view_id=1) # Must have a view defined
# Create
new_ticket = {
'ticket': { _
'requester_name': 'Howard Schultz',
'requester_email': '*****@*****.**',
'subject':'My Starbucks coffee is cold!',
'description': 'please reheat my coffee',
'set_tags': 'coffee drinks',
import re
from zendesk import Zendesk
def get_id_from_url(url):
match = re.match(r".*/(?P<identifier>\d+)\.xml", url)
if match and match.group('identifier'):
return match.group('identifier')
################################################################
## NEW CONNECTION CLIENT
################################################################
zendesk = Zendesk('https://yourcompany.zendesk.com', '*****@*****.**',
'passwd')
################################################################
## TICKETS
################################################################
# List
zendesk.list_tickets(view_id=1) # Must have a view defined
# Create
new_ticket = {
'ticket': {
'requester-name': 'Howard Schultz',
'requester-email': '*****@*****.**',
'subject': 'My Starbucks coffee is cold!',
'description': 'please reheat my coffee',
'set-tags': 'coffee drinks',
def __init__(self, settings):
# Set up a set of globals to pass to every template
self.gs_globals = {}
# GENOMICS STATUS MAJOR VERSION NUMBER
# Bump this with any change that requires an update to documentation
self.gs_globals['gs_version'] = '1.0';
# Get the latest git commit hash
# This acts as a minor version number for small updates
# It also forces javascript / CSS updates and solves caching problems
try:
self.gs_globals['git_commit'] = subprocess.check_output(['git', 'rev-parse', '--short=7', 'HEAD']).strip()
self.gs_globals['git_commit_full'] = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip()
except:
self.gs_globals['git_commit'] = 'unknown'
self.gs_globals['git_commit_full'] = 'unknown'
handlers = [
("/", MainHandler),
("/login", LoginHandler),
("/logout", LogoutHandler),
("/unauthorized", UnAuthorizedHandler),
("/api/v1", DataHandler),
("/api/v1/applications", ApplicationsDataHandler),
("/api/v1/application/([^/]*)$", ApplicationDataHandler),
("/api/v1/bioinfo_analysis", BioinfoAnalysisHandler),
("/api/v1/bioinfo_analysis/([^/]*)$", BioinfoAnalysisHandler),
("/api/v1/expected", BarcodeVsExpectedDataHandler),
tornado.web.URLSpec("/api/v1/caliper_image/(?P<project>[^/]+)/(?P<sample>[^/]+)/(?P<step>[^/]+)", CaliperImageHandler, name="CaliperImageHandler"),
("/api/v1/charon_summary/([^/]*)$",CharonProjectHandler ),
("/api/v1/delivered_monthly", DeliveredMonthlyDataHandler),
("/api/v1/delivered_monthly.png", DeliveredMonthlyPlotHandler),
("/api/v1/delivered_quarterly", DeliveredQuarterlyDataHandler),
("/api/v1/delivered_quarterly.png", DeliveredQuarterlyPlotHandler),
("/api/v1/flowcells", FlowcellsDataHandler),
("/api/v1/flowcell_count/", FlowcellCountApiHandler),
("/api/v1/flowcell_info2/([^/]*)$", FlowcellsInfoDataHandler),
("/api/v1/flowcell_info/([^/]*)$", OldFlowcellsInfoDataHandler),
("/api/v1/flowcell_qc/([^/]*)$", FlowcellQCHandler),
("/api/v1/flowcell_demultiplex/([^/]*)$",
FlowcellDemultiplexHandler),
("/api/v1/flowcell_q30/([^/]*)$", FlowcellQ30Handler),
# ("/api/v1/flowcells/([^/]*)$", FlowcellDataHandler),
("/api/v1/flowcell_notes/([^/]*)$", FlowcellNotesDataHandler),
("/api/v1/flowcell_links/([^/]*)$", FlowcellLinksDataHandler),
("/api/v1/flowcell_search/([^/]*)$", FlowcellSearchHandler),
("/api/v1/flowcell_yield/([^/]*)$", DataFlowcellYieldHandler),
("/api/v1/generate_workset", GenerateWorksetHandler),
("/api/v1/instrument_cluster_density",
InstrumentClusterDensityDataHandler),
("/api/v1/instrument_cluster_density.png",
InstrumentClusterDensityPlotHandler),
("/api/v1/instrument_error_rates", InstrumentErrorrateDataHandler),
("/api/v1/instrument_error_rates.png",
InstrumentErrorratePlotHandler),
("/api/v1/instrument_logs", DataInstrumentLogsHandler),
("/api/v1/instrument_logs/([^/]*)$", DataInstrumentLogsHandler),
("/api/v1/instrument_names",InstrumentNamesHandler ),
("/api/v1/instrument_unmatched", InstrumentUnmatchedDataHandler),
("/api/v1/instrument_unmatched.png", InstrumentUnmatchedPlotHandler),
("/api/v1/instrument_yield", InstrumentYieldDataHandler),
("/api/v1/instrument_yield.png", InstrumentYieldPlotHandler),
("/api/v1/internal_costs/([^/]*)", ProjectInternalCostsHandler),
("/api/v1/last_updated", UpdatedDocumentsDatahandler),
("/api/v1/last_psul", LastPSULRunHandler),
("/api/v1/load_workset_samples", WorksetSampleLoadHandler),
("/api/v1/plot/q30.png", Q30PlotHandler),
("/api/v1/plot/samples_per_lane.png",
SamplesPerLanePlotHandler),
("/api/v1/plot/reads_per_lane.png", ReadsPerLanePlotHandler),
("/api/v1/plot/clusters_per_lane.png", ClustersPerLanePlotHandler),
("/api/v1/plot/barcodes_vs_expected([^/]*)$", BarcodeVsExpectedPlotHandler),
("/api/v1/samples_per_lane", SamplesPerLaneDataHandler),
("/api/v1/produced_monthly", ProducedMonthlyDataHandler),
("/api/v1/produced_monthly.png", ProducedMonthlyPlotHandler),
("/api/v1/produced_quarterly", ProducedQuarterlyDataHandler),
("/api/v1/produced_quarterly.png", ProducedQuarterlyPlotHandler),
("/api/v1/projects", ProjectsDataHandler),
("/api/v1/project/([^/]*)$", ProjectSamplesDataHandler),
("/api/v1/project/([^/]*)/tickets", ProjectTicketsDataHandler),
("/api/v1/projects_fields", ProjectsFieldsDataHandler),
("/api/v1/project_summary/([^/]*)$", ProjectDataHandler),
("/api/v1/project_summary_update/([^/]*)/([^/]*)$", ProjectSummaryUpdateHandler),
("/api/v1/project_search/([^/]*)$", ProjectsSearchHandler),
("/api/v1/presets", PresetsHandler),
("/api/v1/qc/([^/]*)$", SampleQCDataHandler),
("/api/v1/projectqc/([^/]*)$", ProjectQCDataHandler),
("/api/v1/reads_vs_quality", ReadsVsQDataHandler),
("/api/v1/rna_report/([^/]*$)", ProjectRNAMetaDataHandler),
("/api/v1/running_notes/([^/]*)$", RunningNotesDataHandler),
("/api/v1/links/([^/]*)$", LinksDataHandler),
("/api/v1/sample_info/([^/]*)$", SampleInfoDataHandler),
("/api/v1/sample_readcount/(\w+)?", SampleReadCountDataHandler),
("/api/v1/sample_run_counts/(\w+)?",
SampleRunReadCountDataHandler),
("/api/v1/sample_alignment/([^/]*)$",
SampleQCAlignmentDataHandler),
("/api/v1/sample_coverage/([^/]*)$", SampleQCCoverageDataHandler),
("/api/v1/sample_summary/([^/]*)$", SampleQCSummaryDataHandler),
("/api/v1/sample_insert_sizes/([^/]*)$",
SampleQCInsertSizesDataHandler),
("/api/v1/samples/start/([^/]*)$", PagedQCDataHandler),
("/api/v1/samples/([^/]*)$", SampleRunDataHandler),
("/api/v1/stats",StatsAggregationHandler),
("/api/v1/stats/application_open_projects",ApplicationOpenProjectsHandler),
("/api/v1/stats/application_open_samples",ApplicationOpenSamplesHandler),
("/api/v1/stats/week_instr_yield",WeekInstrumentTypeYieldHandler),
("/api/v1/stats/year_application",YearApplicationsProjectHandler),
("/api/v1/stats/year_application_samples",YearApplicationsSamplesHandler),
("/api/v1/stats/year_affiliation_projects",YearAffiliationProjectsHandler),
("/api/v1/stats/year_deliverytime_projects",YearDeliverytimeProjectsHandler),
("/api/v1/stats/year_deliverytime_application",YearDeliverytimeApplicationHandler),
("/api/v1/deliveries/set_bioinfo_responsible$", DeliveriesPageHandler),
("/api/v1/suggestions", SuggestionBoxDataHandler),
("/api/v1/test/(\w+)?", TestDataHandler),
("/api/v1/phix_err_rate", PhixErrorRateDataHandler),
("/api/v1/worksets", WorksetsDataHandler),
("/api/v1/workset/([^/]*)$", WorksetDataHandler),
("/api/v1/workset_search/([^/]*)$", WorksetSearchHandler),
("/api/v1/workset_notes/([^/]*)$", WorksetNotesDataHandler),
("/api/v1/workset_links/([^/]*)$", WorksetLinksHandler),
("/api/v1/ws_pl_to_lims", WorksetPlacementSavingHandler),
("/applications", ApplicationsHandler),
("/application/([^/]*)$", ApplicationHandler),
("/barcode_vs_expected", ExpectedHandler),
("/bioinfo/(P[^/]*)$", BioinfoAnalysisHandler),
("/deliveries", DeliveriesPageHandler),
("/clusters_per_lane", ClustersPerLaneHandler),
("/flowcells", FlowcellsHandler),
("/flowcells/([^/]*)$", FlowcellHandler),
("/flowcells_plot", FlowcellPlotHandler),
("/flowcell_count_plot", FlowcellCountPlotHandler),
("/instrument_logs",InstrumentLogsHandler),
("/instrument_logs/([^/]*)$", InstrumentLogsHandler),
("/multiqc_report/([^/]*)$", MultiQCReportHandler),
("/nas_quotas", NASQuotasHandler),
("/q30", Q30Handler),
("/qc/([^/]*)$", SampleQCSummaryHandler),
(r"/qc_reports/(.*)", SafeStaticFileHandler, {"path": 'qc_reports'}),
("/quotas", QuotasHandler),
("/phix_err_rate", PhixErrorRateHandler),
("/production", ProductionHandler),
("/production/cronjobs", ProductionCronjobsHandler),
("/project/([^/]*)$", ProjectSamplesHandler),
("/project/(P[^/]*)/([^/]*)$", ProjectSamplesHandler),
("/project_summary/([^/]*)$", ProjectSummaryHandler),
("/projects/([^/]*)$", ProjectsHandler),
("/proj_meta", ProjMetaCompareHandler),
("/reads_total/([^/]*)$", ReadsTotalHandler),
("/reads_vs_qv", ReadsVsQvhandler),
("/reads_per_lane", ReadsPerLaneHandler),
("/rec_ctrl_view/([^/]*)$", RecCtrlDataHandler),
("/samples_per_lane", SamplesPerLaneHandler),
("/samples/([^/]*)$", SampleRunHandler),
("/sequencing", SequencingStatsHandler),
("/suggestion_box", SuggestionBoxHandler),
("/worksets", WorksetsHandler),
("/workset/([^/]*)$", WorksetHandler),
("/workset_placement",WorksetPlacementHandler),
(r'.*', BaseHandler)
]
self.declared_handlers = handlers
# Load templates
self.loader = template.Loader("design")
# Global connection to the database
couch = Server(settings.get("couch_server", None))
if couch:
self.analysis_db= couch["analysis"]
self.application_categories_db = couch["application_categories"]
self.bioinfo_db = couch["bioinfo_analysis"]
self.cronjobs_db = couch["cronjobs"]
self.flowcells_db = couch["flowcells"]
self.gs_users_db = couch["gs_users"]
self.instruments_db= couch["instruments"]
self.instrument_logs_db = couch["instrument_logs"]
self.projects_db = couch["projects"]
self.samples_db = couch["samples"]
self.server_status_db = couch['server_status']
self.suggestions_db = couch["suggestion_box"]
self.worksets_db = couch["worksets"]
self.x_flowcells_db = couch["x_flowcells"]
else:
print settings.get("couch_server", None)
raise IOError("Cannot connect to couchdb");
# Load columns and presets from genstat-defaults user in StatusDB
genstat_id = ''
for u in self.gs_users_db.view('authorized/users'):
if u.get('key') == 'genstat-defaults':
genstat_id = u.get('value')
# It's important to check that this user exists!
if not genstat_id:
raise RuntimeError("genstat-defaults user not found on {}, please " \
"make sure that the user is abailable with the " \
"corresponding defaults information.".format(settings.get("couch_server", None)))
# We need to get this database as OrderedDict, so the pv_columns doesn't
# mess up
user = settings.get("username", None)
password = settings.get("password", None)
headers = {"Accept": "application/json",
"Authorization": "Basic " + "{}:{}".format(user, password).encode('base64')[:-1]}
decoder = json.JSONDecoder(object_pairs_hook=OrderedDict)
user_url = "{}/gs_users/{}".format(settings.get("couch_server"), genstat_id)
json_user = requests.get(user_url, headers=headers).content.rstrip()
self.genstat_defaults = decoder.decode(json_user)
# Load private instrument listing
self.instrument_list = settings.get("instruments")
# If settings states mode, no authentication is used
self.test_mode = settings["Testing mode"]
# google oauth key
self.oauth_key = settings["google_oauth"]["key"]
# ZenDesk
self.zendesk_url = settings["zendesk"]["url"]
self.zendesk_user = settings["zendesk"]["username"]
self.zendesk_token = settings["zendesk"]["token"]
self.zendesk = Zendesk(self.zendesk_url, use_api_token=True, zendesk_username=self.zendesk_user,
zendesk_password=self.zendesk_token, api_version=2)
# Trello
self.trello_api_key = settings['trello']['api_key']
self.trello_api_secret = settings['trello']['api_secret']
self.trello_token = settings['trello']['token']
# Load password seed
self.password_seed = settings.get("password_seed")
# load logins for the genologics sftp
self.genologics_login=settings['sftp']['login']
self.genologics_pw=settings['sftp']['password']
# Location of the psul log
self.psul_log=settings.get("psul_log")
# index page - to display quotas of uppmax projects
self.uppmax_projects = settings.get('uppmax_projects')
# to display instruments in the server status
self.server_status = settings.get('server_status')
# project summary - multiqc tab
self.multiqc_path = settings.get('multiqc_path')
# Setup the Tornado Application
cookie_secret = base64.b64encode(uuid.uuid4().bytes + uuid.uuid4().bytes)
settings["debug"]= True
settings["static_path"]= "static"
settings["cookie_secret"]= cookie_secret
settings["login_url"]= "/login"
if options['develop']:
tornado.autoreload.watch("design/application.html")
tornado.autoreload.watch("design/applications.html")
tornado.autoreload.watch("design/barcode_vs_expected.html")
tornado.autoreload.watch("design/base.html")
tornado.autoreload.watch("design/bioinfo_tab.html")
tornado.autoreload.watch("design/bioinfo_tab/run_lane_sample_view.html")
tornado.autoreload.watch("design/bioinfo_tab/sample_run_lane_view.html")
tornado.autoreload.watch("design/clusters_per_lane.html")
tornado.autoreload.watch("design/cronjobs.html")
tornado.autoreload.watch("design/deliveries.html")
tornado.autoreload.watch("design/error_page.html")
tornado.autoreload.watch("design/flowcell.html")
tornado.autoreload.watch("design/flowcell_error.html")
tornado.autoreload.watch("design/flowcell_samples.html")
tornado.autoreload.watch("design/flowcells.html")
tornado.autoreload.watch("design/index.html")
tornado.autoreload.watch("design/instrument_logs.html")
tornado.autoreload.watch("design/link_tab.html")
tornado.autoreload.watch("design/nas_quotas.html")
tornado.autoreload.watch("design/phix_err_rate.html")
tornado.autoreload.watch("design/production.html")
tornado.autoreload.watch("design/proj_meta_compare.html")
tornado.autoreload.watch("design/project_samples.html")
tornado.autoreload.watch("design/project_summary.html")
tornado.autoreload.watch("design/projects.html")
tornado.autoreload.watch("design/q30.html")
tornado.autoreload.watch("design/reads_per_lane.html")
tornado.autoreload.watch("design/reads_total.html")
tornado.autoreload.watch("design/reads_vs_qv.html")
tornado.autoreload.watch("design/rec_ctrl_view.html")
tornado.autoreload.watch("design/running_notes_help.html")
tornado.autoreload.watch("design/running_notes_tab.html")
tornado.autoreload.watch("design/samples_per_lane.html")
tornado.autoreload.watch("design/sequencing_stats.html")
tornado.autoreload.watch("design/suggestion_box.html")
tornado.autoreload.watch("design/unauthorized.html")
tornado.autoreload.watch("design/uppmax_quotas.html")
tornado.autoreload.watch("design/workset_placement.html")
tornado.autoreload.watch("design/workset_samples.html")
tornado.autoreload.watch("design/worksets.html")
tornado.autoreload.watch("design/yield_plot.html")
tornado.web.Application.__init__(self, handlers, **settings)
def config(argv=None):
import os, sys, argparse
# Declare a class for an argparse custom action.
# Handles converting ascii input from argparse that may contain unicode
# to a real unicode string.
class UnicodeStore(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, values.decode('utf-8'))
# Options precedence:
# program state defaults, which are overridden by
# ~/.zd.cfg [zdgrab] section options, which are overridden by
# command line options, which are overridden by
# -c CONFIG_FILE [zdgrab] section options, which are overridden by
# ~/.zd.cfg [RUN_SECTION] section options, which are overridden by
# -c CONFIG_FILE [RUN_SECTION] section options
#
# Program state, with defaults
#
state = {
'verbose': False,
'tickets': None,
'work_dir': os.path.join(os.path.expanduser('~'), 'zdgrab'),
'agent': 'me',
'url': None,
'mail': None,
'password': '******',
'is_token': False,
}
argp = argparse.ArgumentParser(
description='Download attachments from Zendesk tickets.')
argp.add_argument('-v',
'--verbose',
action='store_true',
help='Verbose output')
argp.add_argument(
'-t',
action=UnicodeStore,
dest='tickets',
help='Ticket(s) to grab attachments (default: all of your open tickets)'
)
argp.add_argument('-c',
action=UnicodeStore,
dest='config_file',
help='Configuration file (overrides ~/.zd.cfg)')
argp.add_argument('-w',
action=UnicodeStore,
dest='work_dir',
help="""Working directory in which to store attachments.
(default: ~/zdgrab/)""")
argp.add_argument('-a',
action=UnicodeStore,
dest='agent',
help='Agent whose open tickets to search (default: me)')
argp.add_argument('-u',
action=UnicodeStore,
dest='url',
help='URL of Zendesk (e.g. https://example.zendesk.com)')
argp.add_argument('-m',
action=UnicodeStore,
dest='mail',
help='E-Mail address for Zendesk login')
argp.add_argument('-p',
action=UnicodeStore,
dest='password',
help='Password for Zendesk login',
nargs='?',
const=state['password'])
argp.add_argument(
'-i',
'--is-token',
action='store_true',
dest='is_token',
help='Is token? Specify if password supplied a Zendesk token')
# Set argparse defaults with program defaults.
# Skip password as it is argparse const, not argparse default
argp.set_defaults(**dict(
(k, v) for k, v in state.iteritems() if k != 'password'))
# Read ~/.zd.cfg [zdgrab] section and update argparse defaults
try:
config_state(os.path.join(os.path.expanduser('~'), '.zd.cfg'), 'zd',
state)
# Password is OK now, because we either have one from the config file or
# it is still None.
argp.set_defaults(**dict((k, v) for k, v in state.iteritems()))
except configparser.NoSectionError:
# -c CONFIG_FILE did not have a [zdgrab] section. Skip it.
pass
# Parse the command line options
if argv is None:
argv = sys.argv
args = argp.parse_args()
# Update the program state with command line options
for k in state.keys():
state[k] = getattr(args, k)
# -c CONFIG_FILE given on command line read args.config_file [zdgrab], update state
if args.config_file:
if state['verbose']:
print('Reading config file {}'.format(args.config_file))
try:
config_state(args.config_file, 'zd', state)
except configparser.NoSectionError:
# -c CONFIG_FILE did not have a [zdgrab] section. Skip it.
pass
from zendesk import Zendesk
if state['url'] and state['mail'] and state['password']:
if state['verbose']:
print(
'Configuring Zendesk with:\n'
' url: {}\n'
' mail: {}\n'
' is_token: {}\n'
' password: (hidden)\n'.format(state['url'], state['mail'],
repr(state['is_token'])))
zd = Zendesk(state['url'],
zendesk_username=state['mail'],
zendesk_password=state['password'],
use_api_token=state['is_token'],
api_version=2)
else:
msg = textwrap.dedent("""\
Error: Need Zendesk config to continue. Use -u, -m, -p options
or a config file to provide the information.
Config file (e.g. ~/.zd.cfg) should be something like:
[zd]
url = https://example.zendesk.com
mail = [email protected]
password = dneib393fwEF3ifbsEXAMPLEdhb93dw343
is_token = 1
agent = [email protected]
""")
print(msg)
return 1
# Log the state
if state['verbose']:
print('Running with program state:')
# Let's go around our ass to get to our elbow to hide the password here.
for (k, v) in [(k, v) for k, v in state.iteritems()
if k != 'password']:
print(' {}: {}'.format(k, repr(v)))
print(' password: (hidden)\n')
# tickets=None means default to getting all of the attachments for this
# user's open tickets. If tickets is given, try to split it into ints
if state['tickets']:
# User gave a list of tickets
try:
state['tickets'] = [int(i) for i in state['tickets'].split(',')]
except ValueError:
print('Error: Could not convert to integers: {}'.format(
state['tickets']))
return 1
return zd, state
