def includeme(config):
""" this configuration must be included as the last order
"""
print('genaf_base:', config)
config.add_static_view('genaf_static',
'genaf_base:static/',
cache_max_age=3600)
# override assets here
#config.override_asset('rhombus:templates/base.mako', 'genaf_base:templates/base.mako')
#config.override_asset('rhombus:templates/plainbase.mako', 'genaf_base:templates/plainbase.mako')
# add route and view for home ('/'), /login and /logout
config.add_route('home', '/')
config.add_view('genaf_base.views.home.index', route_name='home')
config.add_route('login', '/login')
config.add_view('genaf_base.views.home.login', route_name='login')
config.add_route('logout', '/logout')
config.add_view('genaf_base.views.home.logout', route_name='logout')
# add additional routes and views here
add_route_view(
config,
'rhombus.views.fso',
'rhombus.fso',
'/fso{path:.*}@@view',
'/fso{path:.*}@@edit',
'/fso{path:.*}@@save',
'/fso{path:.*}@@action',
('/fso{path:.*}', 'index'),
)
add_route_view_class(config, 'genaf_base.views.batch.BatchViewer',
'genaf.batch', '/batch', '/batch/@@action',
'/batch/{id}@@edit', '/batch/{id}@@save',
('/batch/{id}', 'view'))
add_route_view_class(config, 'genaf_base.views.sample.SampleViewer',
'genaf.sample', '/sample', '/sample/@@action',
'/sample/{id}@@edit', '/sample/{id}@@save',
('/sample/{id}', 'view'))
# ANALYSIS PART
config.add_route('analysis-samplesummary', '/analysis/samplesummary')
config.add_view('genaf_base.views.analysis.samplesummary.SampleSummary',
route_name='analysis-samplesummary')
# subscriber
config.add_subscriber(add_genaf_global, BeforeRender)
def includeme(config):
# specific plasmogen_snp configuration
add_route_view(config, 'plasmogen_snp.views.subject',
'plasmogen_snp.subject', '/subject', '/subject/@@action',
'/subject/{id}@@edit', '/subject/{id}@@save',
('/subject/{id}', 'view'))
# set essential pages
config.add_route('home', '/')
config.add_view('plasmogen_snp.views.home.index', route_name='home')
config.add_route('login', '/login')
config.add_view('plasmogen_snp.views.home.login', route_name='login')
config.add_route('logout', '/logout')
config.add_view('plasmogen_snp.views.home.logout', route_name='logout')
add_route_view(
config,
'plasmogen_snp.views.docs',
'plasmogen_snp.docs',
#'/docs{path:.*}@@view',
#'/docs{path:.*}@@edit',
#'/docs{path:.*}@@save',
#'/docs{path:.*}@@action',
('/docs{path:.*}', 'index'),
)
# set other related functions
import genaf_snp.views.sample, plasmogen_snp.views.sample
genaf_snp.views.sample.set_format_sampleinfo(
plasmogen_snp.views.sample.format_sampleinfo)
# include genaf_snp configuration
config.include(genaf_snp_includeme)
config.add_view('plasmogen_snp.views.tools.sample.index',
route_name='tools-sample')
config.override_asset('rhombus:templates/base.mako',
'plasmogen_snp:templates/base.mako')
config.override_asset('rhombus:templates/plainbase.mako',
'plasmogen_snp:templates/plainbase.mako')
return config
def includeme( config ):
# specific PlasmoGen configuration
add_route_view( config, 'plasmogen.views.subject', 'plasmogen.subject',
'/subject',
'/subject/@@action',
'/subject/{id}@@edit',
'/subject/{id}@@save',
('/subject/{id}', 'view')
)
# set essential pages
config.add_route('home', '/')
config.add_view('plasmogen.views.home.index', route_name = 'home')
config.add_route('login', '/login')
config.add_view('plasmogen.views.home.login', route_name = 'login')
config.add_route('logout', '/logout')
config.add_view('plasmogen.views.home.logout', route_name = 'logout')
add_route_view( config, 'plasmogen.views.docs', 'plasmogen.docs',
#'/docs{path:.*}@@view',
#'/docs{path:.*}@@edit',
#'/docs{path:.*}@@save',
#'/docs{path:.*}@@action',
('/docs{path:.*}', 'index'),
)
# include GenAF configuration
config.include( genaf_includeme)
config.add_view('plasmogen.views.tools.sample.index', route_name='tools-sample')
config.override_asset('rhombus:templates/base.mako', 'plasmogen:templates/base.mako')
config.override_asset('rhombus:templates/plainbase.mako', 'plasmogen:templates/plainbase.mako')
return config
def includeme( config ):
# GenAF configuration
#config.add_static_view('genaf_assets', 'genaf:static/assets/')
config.add_static_view(name='genaf_static', path="genaf:static/")
add_route_view( config, 'genaf.views.marker', 'genaf.marker',
'/marker',
'/marker/@@action',
'/marker/{id}@@edit',
'/marker/{id}@@save',
('/marker/{id}', 'view')
)
add_route_view( config, 'genaf.views.panel', 'genaf.panel',
'/panel',
'/panel/@@action',
'/panel/{id}@@edit',
'/panel/{id}@@save',
('/panel/{id}', 'view')
)
add_route_view( config, 'genaf.views.batch', 'genaf.batch',
'/batch',
'/batch/@@action',
'/batch/{id}@@edit',
'/batch/{id}@@save',
('/batch/{id}', 'view')
)
add_route_view( config, 'genaf.views.sample', 'genaf.sample',
'/sample',
'/sample/@@action',
'/sample/{id}@@edit',
'/sample/{id}@@save',
('/sample/{id}', 'view')
)
add_route_view( config, 'genaf.views.location', 'genaf.location',
'/location',
'/location/@@action',
'/location/{id}@@edit',
'/location/{id}@@save',
('/location/{id}', 'view')
)
add_route_view( config, 'genaf.views.assay', 'genaf.assay',
'/assay',
'/assay/@@action',
'/assay/{id}@@drawchannels',
'/assay/{id}@@edit',
'/assay/{id}@@save',
('/assay/{id}', 'view')
)
add_route_view( config, 'genaf.views.channel', 'genaf.channel',
'/channel/@@action',
('/channel/{id}', 'view'),
)
add_route_view( config, 'genaf.views.uploadmgr', 'genaf.uploadmgr',
'/uploadmgr',
'/uploadmgr/@@action',
'/uploadmgr/{id}@@edit',
'/uploadmgr/{id}@@save',
('/uploadmgr/{id}@@mainpanel', 'mainpanel', 'json'),
('/uploadmgr/{id}@@rpc', 'rpc', 'json'),
('/uploadmgr/{id}@@uploaddata', 'uploaddata', 'json'),
('/uploadmgr/{id}@@uploadinfo', 'uploadinfo', 'json'),
'/uploadmgr/{id}@@template',
('/uploadmgr/{id}', 'view')
)
add_route_view( config, 'genaf.views.famgr', 'genaf.famgr',
'/famgr',
'/famgr/{id}@@process',
('/famgr/{id}', 'view')
)
add_route_view( config, 'genaf.views.task', 'genaf.task',
'/task',
('/task/{id}', 'view'),
)
add_route_view( config, 'rhombus.views.fso', 'rhombus.fso',
'/fso{path:.*}@@view',
'/fso{path:.*}@@edit',
'/fso{path:.*}@@save',
'/fso{path:.*}@@action',
('/fso{path:.*}', 'index'),
)
# tools and analysis
config.add_route('tools-help', '/tools/help')
config.add_view('genaf.views.tools.help.index', route_name='tools-help')
config.add_route('tools-allele', '/tools/allele')
config.add_view('genaf.views.tools.allele.index', route_name='tools-allele')
config.add_route('tools-he', '/tools/he')
config.add_view('genaf.views.tools.he.index', route_name='tools-he')
config.add_route('tools-genotype', '/tools/genotype')
config.add_view('genaf.views.tools.genotype.index', route_name='tools-genotype')
config.add_route('tools-moi', '/tools/moi')
config.add_view('genaf.views.tools.moi.index', route_name='tools-moi')
config.add_route('tools-pcoa', '/tools/pcoa')
config.add_view('genaf.views.tools.pcoa.index', route_name='tools-pcoa')
config.add_route('tools-mca', '/tools/mca')
config.add_view('genaf.views.tools.mca.index', route_name='tools-mca')
config.add_route('tools-export', '/tools/export')
config.add_view('genaf.views.tools.export.index', route_name='tools-export')
config.add_route('tools-fst', '/tools/fst')
config.add_view('genaf.views.tools.fst.index', route_name='tools-fst')
config.add_route('tools-ld', '/tools/ld')
config.add_view('genaf.views.tools.ld.index', route_name='tools-ld')
config.add_route('tools-nj', '/tools/nj')
config.add_view('genaf.views.tools.nj.index', route_name='tools-nj')
config.add_route('tools-sample', '/tools/sample')
config.add_view('genaf.views.tools.sample.index', route_name='tools-sample')
config.add_route('tools-djost', '/tools/djost')
config.add_view('genaf.views.tools.djost.index', route_name='tools-djost')
# utilities
config.add_route('utils-export', '/utils/export')
config.add_view('genaf.views.utils.export.index', route_name='utils-export')
config.add_route('utils-plot', '/utils/plot')
config.add_view('genaf.views.utils.plot.index', route_name='utils-plot')
def msaf_config( config, prefix='', default_module='msaf', module_map = {} ):
config.add_route('explore', '/explore')
config.add_view('msaf.views.explore.index', route_name='explore')
module_name = module_for_view('marker', default_module, module_map)
add_route_view( config, module_name, '%s.views.marker' % module_name, prefix,
('marker', '/marker'),
('marker-action', '/marker/@@action'),
('marker-edit', '/marker/{id}@@edit'),
('marker-save', '/marker/{id}@@save'),
('marker-view', '/marker/{id}', 'view')
)
add_route_view( config, 'msaf', 'msaf.views.batch', prefix,
('batch', '/batch'),
('batch-action', '/batch/@@action'),
('batch-edit', '/batch/{id}@@edit'),
('batch-save', '/batch/{id}@@save'),
('batch-view', '/batch/{id}', 'view')
)
module_name = module_for_view('location', default_module, module_map)
add_route_view( config, module_name, '%s.views.location' % module_name, prefix,
('location', '/location'),
('location-action', '/location/@@action'),
('location-lookup', '/location/@@lookup', 'lookup', 'json'),
('location-edit', '/location/{id}@@edit'),
('location-save', '/location/{id}@@save'),
('location-view', '/location/{id}', 'view')
)
module_name = module_for_view('sample', default_module, module_map)
add_route_view( config, module_name, '%s.views.sample' % module_name, prefix,
('sample', '/sample'),
('sample-action', '/sample/@@action'),
('sample-edit', '/sample/{id}@@edit'),
('sample-save', '/sample/{id}@@save'),
('sample-view', '/sample/{id}', 'view'),
)
add_route_view( config, 'msaf', 'msaf.views.assay', prefix,
('assay', '/assay'),
('assay-action', '/assay/@@action'),
('assay-edit', '/assay/{id}@@edit'),
('assay-save', '/assay/{id}@@save'),
('assay-drawchannels', '/assay/{id}@@drawchannels'),
('assay-view', '/assay/{id}', 'view'),
)
add_route_view( config, 'msaf', 'msaf.views.channel', prefix,
('channel', '/channel'),
('channel-action', '/channel/@@action'),
('channel-edit', '/channel/{id}@@edit'),
('channel-save', '/channel/{id}@@save'),
('channel-view', '/channel/{id}', 'view'),
)
config.add_route('not-implemented', '/not_implemented')
config.add_view('msaf.views.home.not_implemented', route_name='not-implemented')
config.add_route('upload', '/upload')
config.add_view('msaf.views.upload.index', route_name='upload')
config.add_route('upload-verify', '/upload/verify')
config.add_view('msaf.views.upload.verify', route_name='upload-verify')
config.add_route('upload-commit', '/upload/commit')
config.add_view('msaf.views.upload.commit', route_name='upload-commit')
config.add_route('queryset', '/queryset')
config.add_view('msaf.views.queryset.index', route_name='queryset')
config.add_route('analysis-allele', '/analysis/allele')
config.add_view('msaf.views.analysis.allele.index', route_name='analysis-allele')
config.add_route('analysis-moi', '/analysis/moi')
config.add_view('msaf.views.analysis.moi.index', route_name='analysis-moi')
config.add_route('tools-moi', '/tools/moi')
config.add_view('msaf.views.tools.moi.index', route_name='tools-moi')
config.add_route('tools-he', '/tools/he')
config.add_view('msaf.views.tools.he.index', route_name='tools-he')
config.add_route('tools-genotype', '/tools/genotype')
config.add_view('msaf.views.tools.genotype.index', route_name='tools-genotype')
config.add_route('tools-haplotype', '/tools/haplotype')
config.add_view('msaf.views.tools.haplotype.index', route_name='tools-haplotype')
config.add_route('tools-allele', '/tools/allele')
config.add_view('msaf.views.tools.allele.index', route_name='tools-allele')
config.add_route('analysis-predefined', '/analysis/predefined')
config.add_view('msaf.views.analysis.predefined.index', route_name='analysis-predefined')
config.add_route('tools-report', '/tools/report')
config.add_view('msaf.views.tools.report.index', route_name='tools-report')
config.add_route('tools-export', '/tools/export')
config.add_view('msaf.views.tools.export.index', route_name='tools-export')
config.add_route('tools-lian', '/tools/lian')
config.add_view('msaf.views.tools.lian.index', route_name='tools-lian')
config.add_route('tools-pca', '/tools/pca')
config.add_view('msaf.views.tools.pca.index', route_name='tools-pca')
config.add_route('tools-nj', '/tools/nj')
config.add_view('msaf.views.tools.nj.index', route_name='tools-nj')
config.add_route('tools-structure', '/tools/structure')
config.add_view('msaf.views.tools.structure.index', route_name='tools-structure')
config.add_subscriber( add_global, BeforeRender )
