# modules in this package
import cas_auth
import genshi_render
import drocnotice
import stats
import perf_reports
from admin_lib import medcenter
from admin_lib import heron_policy
from admin_lib import redcap_connect
from admin_lib import rtconfig
from admin_lib.rtconfig import Options, TestTimeOptions
from admin_lib import disclaimer
from admin_lib.ocap_file import WebReadable, Token, Path
import traincheck
KAppSettings = injector.Key('AppSettings')
KI2B2Address = injector.Key('I2B2Address')
KErrorOptions = injector.Key('ErrorOptions')
log = logging.getLogger(__name__)
def test_home_page_redirects_to_cas():
'''A plain request for the homepage redirects us to the CAS login page:
>>> t, r1 = test_home_page_redirects_to_cas()
>>> dict(r1.headers)['Location']
'https://example/cas/login?service=http%3A%2F%2Fheron-service%2F'
'''
from paste.fixture import TestApp
import injector
from injector import inject, provides, singleton
import rtconfig
import ldaplib
import sealing
from notary import makeNotary
from ocap_file import WebReadable, Path
log = logging.getLogger(__name__)
TRAINING_SECTION = 'training'
# Injector keys are not shareable, so...
KTrainingFunction = (type(lambda: 1), TRAINING_SECTION)
KExecutives = injector.Key('Executives')
KTestingFaculty = injector.Key('TestingFaculty')
KStudyTeamLookup = injector.Key('StudyTeamLookup')
PERM_BROWSER = __name__ + '.browse'
PERM_BADGE = __name__ + '.badge'
@singleton
class Browser(object):
''''Search the directory and study teams without conferring authority.
>>> (m, ) = Mock.make([Browser])
>>> hits = m.search(10, 'john.smith', '', '')
>>> hits
[John Smith <*****@*****.**>]
'''
import logging
import injector
from injector import inject, provides, singleton
from sqlalchemy import text, orm, Table, MetaData
import jndi_util
import rtconfig
import ocap_file
log = logging.getLogger(__name__)
CONFIG_SECTION_MD = 'i2b2md'
Ki2b2meta_schema = injector.Key('i2b2meta_schema')
class I2B2Metadata(ocap_file.Token):
@inject(metadatasm=(orm.session.Session, CONFIG_SECTION_MD),
i2b2meta_schema=Ki2b2meta_schema)
def __init__(self, metadatasm, i2b2meta_schema):
'''
:param metadatasm: a function that returns an sqlalchemy session
'''
self._mdsm = metadatasm
self.i2b2meta_schema = i2b2meta_schema
def project_terms(self, i2b2_pid, rc_pids, rct_table='REDCAP_TERMS'):
'''Create heron_terms view in the chosen i2b2 project.
'''
import injector
from injector import inject, provides, singleton
from sqlalchemy import Column, ForeignKey, and_
from sqlalchemy import func, orm
from sqlalchemy.types import String, DateTime, Enum
from sqlalchemy.ext.declarative import declarative_base
import rtconfig
import jndi_util
import ocap_file
import i2b2metadata
from sqlite_mem import _test_engine
CONFIG_SECTION = 'i2b2pm'
KUUIDGen = injector.Key('UUIDGen')
KIdentifiedData = injector.Key('IdentifiedData')
DEFAULT_PID = 'BlueHeron'
Base = declarative_base()
log = logging.getLogger(__name__)
class I2B2PM(ocap_file.Token):
@inject(datasrc=(orm.session.Session, CONFIG_SECTION),
i2b2md=i2b2metadata.I2B2Metadata,
identified_data=KIdentifiedData,
uuidgen=KUUIDGen)
def __init__(self, datasrc, i2b2md, identified_data, uuidgen):
'''
from injector import inject, provides
from pyramid.response import Response
from pyramid_mailer.mailer import Mailer, DummyMailer
from pyramid_mailer.message import Message
import sqlalchemy
from sqlalchemy.sql import func
import genshi_render
from admin_lib import heron_policy
from admin_lib.noticelog import DecisionRecords
from admin_lib import noticelog
from admin_lib import redcapdb
from admin_lib import rtconfig
from admin_lib.ocap_file import Token
KMailSettings = injector.Key('MailSettings')
log = logging.getLogger(__name__)
class DROCNotice(Token):
# We send notice only on final decisions, not defer.
FINAL_DECISIONS = (DecisionRecords.YES, DecisionRecords.NO)
'''Route to HERON home page. '''
home = 'heron_home' # oops... should be passed in from heron_srv
@inject(dr=DecisionRecords,
smaker=(sqlalchemy.orm.session.Session, redcapdb.CONFIG_SECTION),
mailer=Mailer)
def __init__(self, dr, smaker, mailer):
self._dr = dr
import injector
from injector import inject, provides, singleton
from sqlalchemy import Column, ForeignKey, and_
from sqlalchemy import func, orm
from sqlalchemy.types import String, DateTime, Enum
from sqlalchemy.ext.declarative import declarative_base
import rtconfig
import jndi_util
import ocap_file
import i2b2metadata
from sqlite_mem import _test_engine
CONFIG_SECTION = 'i2b2pm'
KUUIDGen = injector.Key('UUIDGen')
KIdentifiedData = injector.Key('IdentifiedData')
Ki2b2crc_schema = injector.Key('i2b2crc_schema')
Ki2b2pm_schema = injector.Key('i2b2pm_schema')
DEFAULT_PID = 'BlueHeron'
Base = declarative_base()
log = logging.getLogger(__name__)
class I2B2PM(ocap_file.Token):
@inject(datasrc=(orm.session.Session, CONFIG_SECTION),
i2b2md=i2b2metadata.I2B2Metadata,
identified_data=KIdentifiedData,
uuidgen=KUUIDGen)
import pyramid
from pyramid import security
from pyramid.httpexceptions import HTTPForbidden, HTTPFound, HTTPSeeOther
from pyramid.authentication import AuthTktAuthenticationPolicy
from pyramid.session import UnencryptedCookieSessionFactoryConfig
from admin_lib.rtconfig import (Options, TestTimeOptions, IniModule)
from admin_lib.rtconfig import MockMixin
from admin_lib.ocap_file import edef, Token, Path
from admin_lib.ocap_file import WebReadable
log = logging.getLogger(__name__)
CONFIG_SECTION = 'cas'
KServiceUrl = injector.Key('ServiceUrl')
class Issuer(Token):
'''Issuer of capabilities based on CAS login credentials.
See MockIssuer for an example.
'''
permissions = ()
def __repr__(self):
return self.__class__.__name__ + '()'
def authenticated(self, uid, req):
'''Mark a request's context as authenticated.
import pkg_resources as pkg
# from this package
from ddict import DataDict
from notary import makeNotary
from ocap_file import WebReadable, WebPostable, Token, Path
from redcapdb import add_mock_eav
import medcenter
import redcap_api
import rtconfig
import redcapdb
DISCLAIMERS_SECTION = 'disclaimers'
ACKNOWLEGEMENTS_SECTION = 'disclaimer_acknowledgements'
KNotary = injector.Key('Notary')
KBadgeInspector = injector.Key('BadgeInspector')
log = logging.getLogger(__name__)
class Disclaimer(redcapdb.REDCapRecord):
fields = ('disclaimer_id', 'url', 'current')
def content(self, rdcap):
r'''
>>> d = Disclaimer()
>>> d.url = 'http://example/'
>>> d.content(_MockTracBlog())
... # doctest: +ELLIPSIS
('<div id="blog-main">\n<h1 class="blog-title">...', 'headline')
from sqlalchemy.types import Integer, VARCHAR, TIMESTAMP
from sqlalchemy.schema import ForeignKey
from sqlalchemy import orm
from sqlalchemy.sql import select, func, and_
import pkg_resources as pkg
import rtconfig
import redcapdb
from redcap_connect import _test_settings as rc_test_settings
from ddict import DataDict
import medcenter
from ocap_file import Token, Path
log = logging.getLogger(__name__)
OVERSIGHT_CONFIG_SECTION = 'oversight_survey'
KProjectId = injector.Key('ProjectId')
KNoticeLogSchema = injector.Key('NoticeLogSchema')
notice_log = Table('notice_log', redcapdb.Base.metadata,
Column('id', Integer, primary_key=True),
Column('record', VARCHAR(100),
ForeignKey('redcap_data.record')),
Column('timestamp', TIMESTAMP()),
mysql_engine='InnoDB',
mysql_collate='utf8_unicode_ci')
class DecisionRecords(Token):
'''
.. note:: At test time, let's check consistency with the data
dictionary.