import atexit
import json
import os
import sys
import traceback
import webapp2
import webapp2_extras.routes
from . import encoder
from . import root
from . import util
from . import config
from .request import SciTranRequest
from .centralclient import CentralClient
from .download import Download
from .handlers.collectionshandler import CollectionsHandler
from .handlers.confighandler import Config, Version
from .handlers.containerhandler import ContainerHandler
from .handlers.devicehandler import DeviceHandler
from .handlers.grouphandler import GroupHandler
from .handlers.listhandler import AnalysesHandler, ListHandler, FileListHandler, NotesListHandler, PermissionsListHandler, TagsListHandler
from .handlers.reporthandler import ReportHandler
from .handlers.resolvehandler import ResolveHandler
from .handlers.schemahandler import SchemaHandler
from .handlers.searchhandler import SearchHandler
from .handlers.userhandler import UserHandler
from .jobs.handlers import JobsHandler, JobHandler, GearsHandler, GearHandler, RulesHandler
from .upload import Upload
log = config.log
try:
import uwsgi
except ImportError:
uwsgi = None
routing_regexes = {
# Group ID: 2-32 characters of form [0-9a-z.@_-]. Start and ends with alphanum.
'gid': '[0-9a-z][0-9a-z.@_-]{0,30}[0-9a-z]',
# Container ID: 24-character hex
'cid': '[0-9a-f]{24}',
# Site ID: <= 24-character alphanum
'sid': '[0-9a-z_]{0,24}',
# User ID: any length, [0-9a-z.@_-]
'uid': '[0-9a-z.@_-]*',
# Container name
'cname': 'projects|sessions|acquisitions|collections',
# Tag name
'tag': '[^/]{1,32}',
# Filename
'fname': '[^/]+',
# Note ID
'nid': '[0-9a-f]{24}',
# Schema path
'schema': r'[^/.]{3,60}/[^/.]{3,60}\.json'
}
def route(path, target, h=None, m=None, name=None):
# https://webapp2.readthedocs.io/en/latest/api/webapp2.html#webapp2.Route
return webapp2.Route(
# re.compile(path)
path.format(**routing_regexes),
target,
handler_method=h,
methods=m,
name=name
)
def prefix(path, routes):
# https://webapp2.readthedocs.io/en/latest/api/webapp2_extras/routes.html#webapp2_extras.routes.PathPrefixRoute
return webapp2_extras.routes.PathPrefixRoute(
path.format(**routing_regexes),
routes
)
endpoints = [
route('/api', root.Root),
prefix('/api', [
# System configuration
route('/config', Config, m=['GET']),
route('/config.js', Config, h='get_js', m=['GET']),
route('/version', Version, m=['GET']),
# General-purpose upload & download
route('/download', Download, h='download', m=['GET', 'POST']),
route('/upload/<strategy:label|uid|uid-match>', Upload, h='upload', m=['POST']),
route('/clean-packfiles', Upload, h='clean_packfile_tokens', m=['POST']),
route('/engine', Upload, h='engine', m=['POST']),
# Top-level endpoints
route('/resolve', ResolveHandler, h='resolve', m=['POST']),
route('/schemas/<schema:{schema}>', SchemaHandler, m=['GET']),
route('/report/<report_type:site|project>', ReportHandler, m=['GET']),
# Search
route('/search', SearchHandler, h='advanced_search', m=['POST']),
route('/search/files', SearchHandler, h='get_datatree', m=['GET']),
route('/search/<cont_name:{cname}>', SearchHandler, m=['GET']),
# Users
route( '/users', UserHandler, 'get_all', m=['GET']),
route( '/users', UserHandler, m=['POST']),
prefix('/users', [
route('/self', UserHandler, h='self', m=['GET']),
route('/self/avatar', UserHandler, h='self_avatar', m=['GET']),
route('/self/key', UserHandler, h='generate_api_key',m=['POST']),
route('/<_id:{uid}>', UserHandler),
route('/<uid:{uid}>/groups', GroupHandler, h='get_all', m=['GET']),
route('/<uid:{uid}>/avatar', UserHandler, h='avatar', m=['GET']),
route('/<uid:{uid}>/<cont_name:{cname}>', ContainerHandler, h='get_all_for_user', m=['GET']),
]),
# Jobs & gears
route( '/jobs', JobsHandler),
prefix('/jobs', [
route('/next', JobsHandler, h='next', m=['GET']),
route('/stats', JobsHandler, h='stats', m=['GET']),
route('/reap', JobsHandler, h='reap_stale', m=['POST']),
route('/add', JobsHandler, h='add', m=['POST']),
route('/<:[^/]+>', JobHandler),
route('/<:[^/]+>/config.json', JobHandler, h='get_config'),
route('/<:[^/]+>/retry', JobHandler, h='retry', m=['POST']),
]),
route('/gears', GearsHandler),
prefix('/gears', [
route('/<:[^/]+>', GearHandler),
route('/<:[^/]+>/invocation', GearHandler, h='get_invocation'),
route('/<:[^/]+>/suggest/<:[^/]+>/<:[^/]+>', GearHandler, h='suggest'),
]),
route('/rules', RulesHandler),
# Devices
route( '/devices', DeviceHandler, h='get_all', m=['GET']),
route( '/devices', DeviceHandler, m=['POST']),
prefix('/devices', [
route('/status', DeviceHandler, h='get_status', m=['GET']),
route('/self', DeviceHandler, h='get_self', m=['GET']),
route('/<device_id:[^/]+>', DeviceHandler, m=['GET']),
]),
# Groups
route('/groups', GroupHandler, h='get_all', m=['GET']),
route('/groups', GroupHandler, m=['POST']),
route('/groups/<_id:{gid}>', GroupHandler, m=['GET', 'DELETE', 'PUT']),
prefix('/<cont_name:groups>', [
route('/<cid:{gid}>/<list_name:roles>', ListHandler, m=['POST']),
route('/<cid:{gid}>/<list_name:roles>/<site:{sid}>/<_id:{uid}>', ListHandler, m=['GET', 'PUT', 'DELETE']),
route('/<cid:{gid}>/<list_name:tags>', TagsListHandler, m=['POST']),
route('/<cid:{gid}>/<list_name:tags>/<value:{tag}>', TagsListHandler, m=['GET', 'PUT', 'DELETE']),
]),
# Projects
prefix('/projects', [
route('/groups', ContainerHandler, h='get_groups_with_project', m=['GET']),
route('/recalc', ContainerHandler, h='calculate_project_compliance', m=['POST']),
route('/<cid:{cid}>/template', ContainerHandler, h='set_project_template', m=['POST']),
route('/<cid:{cid}>/template', ContainerHandler, h='delete_project_template', m=['DELETE']),
route('/<cid:{cid}>/recalc', ContainerHandler, h='calculate_project_compliance', m=['POST']),
]),
# Sessions
route('/sessions/<cid:{cid}>/jobs', ContainerHandler, h='get_jobs', m=['GET']),
# Collections
route( '/collections', CollectionsHandler, h='get_all', m=['GET']),
route( '/collections', CollectionsHandler, m=['POST']),
prefix('/collections', [
route('/curators', CollectionsHandler, h='curators', m=['GET']),
route('/<cid:{cid}>', CollectionsHandler, m=['GET', 'PUT', 'DELETE']),
route('/<cid:{cid}>/sessions', CollectionsHandler, h='get_sessions', m=['GET']),
route('/<cid:{cid}>/acquisitions', CollectionsHandler, h='get_acquisitions', m=['GET']),
]),
# Collections / Projects
prefix('/<cont_name:collections|projects>', [
prefix('/<cid:{cid}>', [
route('/<list_name:permissions>', PermissionsListHandler, m=['POST']),
route('/<list_name:permissions>/<site:{sid}>/<_id:{uid}>', PermissionsListHandler, m=['GET', 'PUT', 'DELETE']),
]),
]),
# Containers
route('/<cont_name:{cname}>', ContainerHandler, name='cont_list', h='get_all', m=['GET']),
route('/<cont_name:{cname}>', ContainerHandler, m=['POST']),
prefix('/<cont_name:{cname}>', [
route('/<cid:{cid}>', ContainerHandler, m=['GET','PUT','DELETE']),
prefix('/<cid:{cid}>', [
route('/<list_name:tags>', TagsListHandler, m=['POST']),
route('/<list_name:tags>/<value:{tag}>', TagsListHandler, m=['GET', 'PUT', 'DELETE']),
route('/packfile-start', FileListHandler, h='packfile_start', m=['POST']),
route('/packfile', FileListHandler, h='packfile', m=['POST']),
route('/packfile-end', FileListHandler, h='packfile_end'),
route('/<list_name:files>', FileListHandler, m=['POST']),
route('/<list_name:files>/<name:{fname}>', FileListHandler, m=['GET', 'DELETE']),
route('/<list_name:analyses>', AnalysesHandler, m=['POST']),
# Could be in a prefix. Had weird syntax highlighting issues so leaving for another day
route('/<list_name:analyses>/<_id:{cid}>', AnalysesHandler, m=['GET', 'DELETE']),
route('/<list_name:analyses>/<_id:{cid}>/files', AnalysesHandler, h='download', m=['GET']),
route('/<list_name:analyses>/<_id:{cid}>/files/<name:{fname}>', AnalysesHandler, h='download', m=['GET']),
route('/<list_name:analyses>/<_id:{cid}>/notes', AnalysesHandler, h='add_note', m=['POST']),
route('/<list_name:analyses>/<_id:{cid}>/notes/<note_id:{cid}>', AnalysesHandler, h='delete_note', m=['DELETE']),
route('/<list_name:notes>', NotesListHandler, m=['POST']),
route('/<list_name:notes>/<_id:{nid}>', NotesListHandler, name='notes', m=['GET', 'PUT', 'DELETE']),
])
]),
# Misc (to be cleaned up later)
route('/<par_cont_name:groups>/<par_id:{gid}>/<cont_name:projects>', ContainerHandler, h='get_all', m=['GET']),
route('/<par_cont_name:{cname}>/<par_id:{cid}>/<cont_name:{cname}>', ContainerHandler, h='get_all', m=['GET']),
# Multi - site
route('/sites', CentralClient, h='sites', m=['GET']),
route('/register', CentralClient, h='register', m=['POST']),
]),
]
def dispatcher(router, request, response):
try:
if uwsgi is not None:
uwsgi.set_logvar('request_id', request.id)
except: # pylint: disable=bare-except
request.logger.error("Error setting request_id log var", exc_info=True)
try:
rv = router.default_dispatcher(request, response)
if rv is not None:
response.write(json.dumps(rv, default=encoder.custom_json_serializer))
response.headers['Content-Type'] = 'application/json; charset=utf-8'
except webapp2.HTTPException as e:
util.send_json_http_exception(response, str(e), e.code)
except Exception as e: # pylint: disable=broad-except
request.logger.error("Error dispatching request", exc_info=True)
if config.get_item('core', 'debug'):
message = traceback.format_exc()
else:
message = 'Internal Server Error'
util.send_json_http_exception(response, message, 500)
def app_factory(*_, **__):
# pylint: disable=protected-access,unused-argument
# don't use config.get_item() as we don't want to require the database at startup
application = webapp2.WSGIApplication(endpoints, debug=config.__config['core']['debug'])
application.router.set_dispatcher(dispatcher)
application.request_class = SciTranRequest
if os.environ.get("SCITRAN_RUNTIME_COVERAGE") == "true":
start_coverage()
# configure new relic
if config.__config['core']['newrelic']:
try:
import newrelic.agent, newrelic.api.exceptions
newrelic.agent.initialize(config.__config['core']['newrelic'])
application = newrelic.agent.WSGIApplicationWrapper(application)
log.info('New Relic detected and loaded. Monitoring enabled.')
except ImportError:
log.critical('New Relic libraries not found.')
sys.exit(1)
except newrelic.api.exceptions.ConfigurationError:
log.critical('New Relic detected, but configuration invalid.')
sys.exit(1)
return application
# Functions to enable code coverage when API is started for testing
def start_coverage():
import coverage
config.log.info("Enabling code coverage")
cov = coverage.coverage(source=["api"], data_suffix="integration-tests")
cov.start()
atexit.register(save_coverage, cov)
def save_coverage(cov):
config.log.info("Saving coverage")
cov.stop()
cov.save()