def main(global_config, **local_config):
""" This function returns a Pyramid WSGI application.
"""
settings = global_config
settings.update(local_config)
# TODO - these need to be set for dummy app
# settings['snovault.jsonld.namespaces'] = json_asset('snovault:schemas/namespaces.json')
# settings['snovault.jsonld.terms_namespace'] = 'https://www.encodeproject.org/terms/'
settings['snovault.jsonld.terms_prefix'] = 'snovault'
settings['snovault.elasticsearch.index'] = 'snovault'
config = Configurator(settings=settings)
from snovault.elasticsearch import APP_FACTORY
config.registry[APP_FACTORY] = main # used by mp_indexer
config.include(app_version)
config.include(
'pyramid_multiauth') # must be before calling set_authorization_policy
from pyramid_localroles import LocalRolesAuthorizationPolicy
# Override default authz policy set by pyramid_multiauth
config.set_authorization_policy(LocalRolesAuthorizationPolicy())
config.include(session)
config.include(configure_dbsession)
config.include('snovault')
config.commit() # commit so search can override listing
# Render an HTML page to browsers and a JSON document for API clients
config.include('snowflakes.renderers')
# these two should be application specific
config.include('.authentication')
config.include('snowflakes.root')
if 'elasticsearch.server' in config.registry.settings:
config.include('snovault.elasticsearch')
config.include('snowflakes.search_views')
config.include(static_resources)
config.include(changelogs)
# TODO This is optional AWS only - possibly move to a plug-in
aws_ip_ranges = json_from_path(settings.get('aws_ip_ranges_path'),
{'prefixes': []})
config.registry['aws_ipset'] = netaddr.IPSet(
record['ip_prefix'] for record in aws_ip_ranges['prefixes']
if record['service'] == 'AMAZON')
if asbool(settings.get('testing', False)):
config.include('.tests.testing_views')
# Load upgrades last so that all views (including testing views) are
# registered.
# TODO we would need a generic upgrade audit PACKAGE (__init__)
# config.include('.audit)
# config.include('.upgrade')
app = config.make_wsgi_app()
return app
def main(global_config, **local_config):
""" This function returns a Pyramid WSGI application.
"""
settings = global_config
settings.update(local_config)
settings['snovault.jsonld.namespaces'] = json_asset('snowflakes:schemas/namespaces.json')
settings['snovault.jsonld.terms_namespace'] = 'https://www.encodeproject.org/terms/'
settings['snovault.jsonld.terms_prefix'] = 'snowflake'
settings['snovault.elasticsearch.index'] = 'snovault'
hostname_command = settings.get('hostname_command', '').strip()
if hostname_command:
hostname = subprocess.check_output(hostname_command, shell=True).strip()
config = Configurator(settings=settings)
from snovault.elasticsearch import APP_FACTORY
config.registry[APP_FACTORY] = main # used by mp_indexer
config.include(app_version)
config.include('pyramid_multiauth') # must be before calling set_authorization_policy
from pyramid_localroles import LocalRolesAuthorizationPolicy
# Override default authz policy set by pyramid_multiauth
config.set_authorization_policy(LocalRolesAuthorizationPolicy())
config.include(session)
config.include(configure_dbsession)
config.include('snovault')
config.commit() # commit so search can override listing
# Render an HTML page to browsers and a JSON document for API clients
config.include('.renderers')
config.include('snovault.authentication')
config.include('.server_defaults')
config.include('.types')
config.include('.root')
if 'elasticsearch.server' in config.registry.settings:
config.include('snovault.elasticsearch')
config.include('snowflakes.viewconfigs.views')
config.include(static_resources)
config.include(changelogs)
aws_ip_ranges = json_from_path(settings.get('aws_ip_ranges_path'), {'prefixes': []})
config.registry['aws_ipset'] = netaddr.IPSet(
record['ip_prefix'] for record in aws_ip_ranges['prefixes'] if record['service'] == 'AMAZON')
if asbool(settings.get('testing', False)):
config.include('snovault.tests.testing_views')
# Load upgrades last so that all views (including testing views) are
# registered.
config.include('.upgrade')
config.include('.audit')
app = config.make_wsgi_app()
return app
def main(global_config, **local_config):
""" This function returns a Pyramid WSGI application.
"""
settings = global_config
settings.update(local_config)
settings['snovault.jsonld.namespaces'] = json_asset('encoded:schemas/namespaces.json')
settings['snovault.jsonld.terms_namespace'] = 'https://www.encodeproject.org/terms/'
settings['snovault.jsonld.terms_prefix'] = 'encode'
settings['snovault.elasticsearch.index'] = 'snovault'
config = Configurator(settings=settings)
from snovault.elasticsearch import APP_FACTORY
config.registry[APP_FACTORY] = main # used by mp_indexer
config.include(app_version)
config.include('pyramid_multiauth') # must be before calling set_authorization_policy
from pyramid_localroles import LocalRolesAuthorizationPolicy
# Override default authz policy set by pyramid_multiauth
config.set_authorization_policy(LocalRolesAuthorizationPolicy())
config.include(session)
config.include('.auth0')
config.include(configure_dbsession)
config.include('snovault')
config.commit() # commit so search can override listing
# Render an HTML page to browsers and a JSON document for API clients
config.include('.renderers')
config.include('.authentication')
config.include('.server_defaults')
config.include('.types')
config.include('.root')
config.include('.batch_download')
config.include('.visualization')
if 'elasticsearch.server' in config.registry.settings:
config.include('snovault.elasticsearch')
config.include('.search')
if 'snp_search.server' in config.registry.settings:
addresses = aslist(config.registry.settings['snp_search.server'])
config.registry['snp_search'] = Elasticsearch(
addresses,
serializer=PyramidJSONSerializer(json_renderer),
connection_class=TimedUrllib3HttpConnection,
retry_on_timeout=True,
timeout=60,
maxsize=50
)
config.include('.region_search')
config.include('.peak_indexer')
config.include(static_resources)
config.include(changelogs)
config.registry['ontology'] = json_from_path(settings.get('ontology_path'), {})
aws_ip_ranges = json_from_path(settings.get('aws_ip_ranges_path'), {'prefixes': []})
config.registry['aws_ipset'] = netaddr.IPSet(
record['ip_prefix'] for record in aws_ip_ranges['prefixes'] if record['service'] == 'AMAZON')
if asbool(settings.get('testing', False)):
config.include('.tests.testing_views')
# Load upgrades last so that all views (including testing views) are
# registered.
config.include('.upgrade')
config.include('.audit')
app = config.make_wsgi_app()
workbook_filename = settings.get('load_workbook', '')
load_test_only = asbool(settings.get('load_test_only', False))
docsdir = settings.get('load_docsdir', None)
if docsdir is not None:
docsdir = [path.strip() for path in docsdir.strip().split('\n')]
if workbook_filename:
load_workbook(app, workbook_filename, docsdir, test=load_test_only)
return app
def main(global_config, **local_config):
""" This function returns a Pyramid WSGI application.
"""
settings = global_config
settings.update(local_config)
settings['contentbase.jsonld.namespaces'] = json_asset('clincoded:schemas/namespaces.json')
settings['contentbase.jsonld.terms_namespace'] = 'https://www.encodeproject.org/terms/'
settings['contentbase.jsonld.terms_prefix'] = 'encode'
settings['contentbase.elasticsearch.index'] = 'clincoded'
config = Configurator(settings=settings)
config.registry['app_factory'] = main # used by mp_indexer
config.include('pyramid_multiauth') # must be before calling set_authorization_policy
from pyramid_localroles import LocalRolesAuthorizationPolicy
# Override default authz policy set by pyramid_multiauth
config.set_authorization_policy(LocalRolesAuthorizationPolicy())
config.include(session)
config.include('.auth0')
configure_engine(settings)
config.include('contentbase')
config.commit() # commit so search can override listing
# Render an HTML page to browsers and a JSON document for API clients
config.include('.renderers')
config.include('.authentication')
config.include('.server_defaults')
config.include('.types')
config.include('.root')
config.include('.batch_download')
config.include('.visualization')
config.include('.ldh')
# config.include('.messaging')
if 'elasticsearch.server' in config.registry.settings:
config.include('contentbase.elasticsearch')
config.include('.search')
config.include(static_resources)
config.include(changelogs)
config.registry['ontology'] = json_from_path(settings.get('ontology_path'), {})
if asbool(settings.get('testing', False)):
config.include('.tests.testing_views')
# Load upgrades last so that all views (including testing views) are
# registered.
config.include('.upgrade')
config.include('.audit')
app = config.make_wsgi_app()
workbook_filename = settings.get('load_workbook', '')
load_test_only = asbool(settings.get('load_test_only', False))
docsdir = settings.get('load_docsdir', None)
if docsdir is not None:
docsdir = [path.strip() for path in docsdir.strip().split('\n')]
if workbook_filename:
load_workbook(app, workbook_filename, docsdir, test=load_test_only)
return app
def main(global_config, **local_config):
""" This function returns a Pyramid WSGI application.
"""
settings = global_config
settings.update(local_config)
config = Configurator(settings=settings)
config.include(session)
config.include('pyramid_tm')
configure_engine(settings)
# Render an HTML page to browsers and a JSON document for API clients
config.include('.calculated')
config.include('.embedding')
config.include('.renderers')
config.include('.authentication')
config.include('.validation')
config.include('.predicates')
config.include('.contentbase')
config.include('.indexing')
config.include('.server_defaults')
config.include('.types')
config.include('.views')
config.include('.migrator')
config.include('.auditor')
settings = config.registry.settings
hostname_command = settings.get('hostname_command', '').strip()
if hostname_command:
hostname = subprocess.check_output(hostname_command,
shell=True).strip()
settings.setdefault('persona.audiences', '')
settings['persona.audiences'] += '\nhttp://%s' % hostname
settings['persona.audiences'] += '\nhttp://%s:6543' % hostname
config.include('.persona')
config.include('pyramid_multiauth')
from pyramid_localroles import LocalRolesAuthorizationPolicy
config.set_authorization_policy(LocalRolesAuthorizationPolicy())
config.include(static_resources)
config.include(load_ontology)
if asbool(settings.get('testing', False)):
config.include('.tests.testing_views')
# Load upgrades last so that all views (including testing views) are
# registered.
config.include('.upgrade')
config.include('.audit')
app = config.make_wsgi_app()
if asbool(settings.get('load_sample_data', False)):
load_sample_data(app)
workbook_filename = settings.get('load_workbook', '')
load_test_only = asbool(settings.get('load_test_only', False))
docsdir = settings.get('load_docsdir', None)
if docsdir is not None:
docsdir = [path.strip() for path in docsdir.strip().split('\n')]
if workbook_filename:
load_workbook(app, workbook_filename, docsdir, test=load_test_only)
return app