def load(info):
girderRoot = info['serverRoot']
histomicsRoot = WebrootHistomicsTK(_template)
histomicsRoot.updateHtmlVars(girderRoot.vars)
ImageBrowseResource(info['apiRoot'])
# The interface is always available under histomicstk and also available
# under the specified path.
info['serverRoot'].histomicstk = histomicsRoot
webrootPath = Setting().get(PluginSettings.HISTOMICSTK_WEBROOT_PATH)
setattr(info['serverRoot'], webrootPath, histomicsRoot)
info['serverRoot'].girder = girderRoot
pluginName = 'HistomicsTK'
# create root resource for all REST end points of HistomicsTK
resource = HistomicsTKResource(pluginName)
setattr(info['apiRoot'], resource.resourceName, resource)
# load docker images from cache
dockerImageModel = ModelImporter.model('docker_image_model',
'slicer_cli_web')
dockerCache = dockerImageModel.loadAllImages()
# generate REST end points for slicer CLIs of each docker image
genRESTEndPointsForSlicerCLIsInDockerCache(resource, dockerCache)
# auto-ingest annotations into database when a .anot file is uploaded
events.bind('data.process', pluginName, process_annotations)
events.bind('jobs.job.update.after', resource.resourceName,
resource.AddRestEndpoints)
events.bind('model.job.save', pluginName, _saveJob)
def updateWebroot(event):
"""
If the webroot path setting is changed, bind the new path to the
histomicstk webroot resource.
"""
if event.info.get('key') == PluginSettings.HISTOMICSTK_WEBROOT_PATH:
setattr(info['serverRoot'], event.info['value'], histomicsRoot)
events.bind('model.setting.save.after', 'histomicstk', updateWebroot)
curConfig = config.getConfig().get('histomicstk', {})
if curConfig.get('restrict_downloads'):
# Change some endpoints to require token access
endpoints = [
('collection', 'GET', (':id', 'download')),
('file', 'GET', (':id', 'download')),
('file', 'GET', (':id', 'download', ':name')),
('folder', 'GET', (':id', 'download')),
('item', 'GET', (':id', 'download')),
('resource', 'GET', ('download', )),
('resource', 'POST', ('download', )),
('item', 'GET', (':itemId', 'tiles', 'images', ':image')),
]
for resource, method, route in endpoints:
cls = getattr(info['apiRoot'], resource)
func = cls.getRouteHandler(method, route)
if func.accessLevel == 'public':
func = access.token(func)
cls.removeRoute(method, route)
cls.route(method, route, func)
def load(self, info):
plugin.getPlugin('jobs').load(info)
plugin.getPlugin('slicer_cli_web').load(info)
plugin.getPlugin('large_image_annotation').load(info)
# Python's http cookie parser fails for all cookies when there are some
# invalid cookies. Work around some of that.
patchCookieParsing()
ModelImporter.registerModel('aperio', Aperio, 'histomicsui')
ModelImporter.registerModel('case', Case, 'histomicsui')
ModelImporter.registerModel('cohort', Cohort, 'histomicsui')
ModelImporter.registerModel('image', Image, 'histomicsui')
ModelImporter.registerModel('pathology', Pathology, 'histomicsui')
ModelImporter.registerModel('slide', Slide, 'histomicsui')
rest.addEndpoints(info['apiRoot'])
info['serverRoot'].updateHtmlVars(
{'brandName': Setting().get(SettingKey.BRAND_NAME)})
global originalChildItems
if not getattr(Folder, '_childItemsBeforeHUI', None):
Folder._childItemsBeforeHUI = Folder.childItems
Folder.childItems = childItems
girderRoot = info['serverRoot']
huiRoot = WebrootHistomicsUI(_template)
huiRoot.updateHtmlVars(girderRoot.vars)
# The interface is always available under hui and also available
# under the specified path.
info['serverRoot'].hui = huiRoot
webrootPath = Setting().get(PluginSettings.HUI_WEBROOT_PATH)
alternateWebrootPath = Setting().get(
PluginSettings.HUI_ALTERNATE_WEBROOT_PATH)
setattr(info['serverRoot'], webrootPath, huiRoot)
if alternateWebrootPath:
for alt_webroot_path in alternateWebrootPath.split(','):
if alt_webroot_path:
setattr(info['serverRoot'], alt_webroot_path, huiRoot)
info['serverRoot'].girder = girderRoot
# auto-ingest annotations into database when a .anot file is uploaded
events.bind('data.process', 'histomicsui', process_annotations)
events.bind('model.job.save', 'histomicsui', _saveJob)
def updateWebroot(event):
"""
If the webroot path setting is changed, bind the new path to the
hui webroot resource. Note that a change to the alternate webroot
requires a restart.
"""
if event.info.get('key') == PluginSettings.HUI_WEBROOT_PATH:
setattr(info['serverRoot'], event.info['value'], huiRoot)
events.bind('model.setting.save.after', 'histomicsui', updateWebroot)
curConfig = config.getConfig().get('histomicsui', {})
if curConfig.get('restrict_downloads'):
# Change some endpoints to require token access
endpoints = [
('collection', 'GET', (':id', 'download')),
('file', 'GET', (':id', 'download')),
('file', 'GET', (':id', 'download', ':name')),
('folder', 'GET', (':id', 'download')),
('item', 'GET', (':id', 'download')),
('resource', 'GET', ('download', )),
('resource', 'POST', ('download', )),
('item', 'GET', (':itemId', 'tiles', 'images', ':image')),
]
for resource, method, route in endpoints:
cls = getattr(info['apiRoot'], resource)
func = cls.getRouteHandler(method, route)
if func.accessLevel == 'public':
func = access.token(func)
cls.removeRoute(method, route)
cls.route(method, route, func)