def load(info):
# set the title of the HTML pages
info['serverRoot'].updateHtmlVars({'title': 'ISIC Archive'})
# add event listeners
events.bind('rest.get.describe/:resource.after', 'onDescribeResource',
onDescribeResource)
events.bind('model.job.save', 'onJobSave', onJobSave)
# add custom model searching
resource.allowedSearchTypes.update({
'image.isic_archive',
'featureset.isic_archive',
'study.isic_archive',
})
# register licenses for template usage
mail_utils.addTemplateDirectory(os.path.join(info['pluginRootDir'],
'server',
'license_templates'),
prepend=True)
registerPluginWebroot(Webroot(), info['name'])
# add static file serving
info['config']['/uda'] = {
'tools.staticdir.on': 'True',
'tools.staticdir.dir': os.path.join(info['pluginRootDir'], 'custom')
}
# add dynamic root routes
# root endpoints -> where a user may go and expect a UI
class Root(object):
pass
legacyWebroot = Root()
legacyWebroot.gallery = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'gallery.html'))
legacyWebroot.segment = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'phase1.html'))
legacyWebroot.annotate = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'phase2.html'))
registerPluginWebroot(legacyWebroot, 'markup')
# create all necessary users, groups, collections, etc
provisionDatabase()
# add api routes
# remove docs for default Girder API, to simplify page
clearRouteDocs()
# TODO: nest these under a "/isic" path?
info['apiRoot'].annotation = api.AnnotationResource()
info['apiRoot'].dataset = api.DatasetResource()
info['apiRoot'].featureset = api.FeaturesetResource()
info['apiRoot'].image = api.ImageResource()
info['apiRoot'].segmentation = api.SegmentationResource()
info['apiRoot'].study = api.StudyResource()
info['apiRoot'].task = api.TaskResource()
api.attachUserApi(info['apiRoot'].user)
def load(info):
# set the title of the HTML pages
info['serverRoot'].updateHtmlVars({'title': 'ISIC Archive'})
# add event listeners
events.bind('rest.get.describe/:resource.after',
'onDescribeResource', onDescribeResource)
events.bind('model.job.save', 'onJobSave', onJobSave)
# add custom model searching
resource.allowedSearchTypes.update({
'image.isic_archive',
'featureset.isic_archive',
'study.isic_archive',
})
# register licenses for template usage
mail_utils.addTemplateDirectory(
os.path.join(info['pluginRootDir'], 'server', 'license_templates'),
prepend=True)
registerPluginWebroot(Webroot(), info['name'])
# add static file serving
info['config']['/uda'] = {
'tools.staticdir.on': 'True',
'tools.staticdir.dir': os.path.join(info['pluginRootDir'], 'custom')
}
# add dynamic root routes
# root endpoints -> where a user may go and expect a UI
class Root(object):
pass
legacyWebroot = Root()
legacyWebroot.gallery = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'gallery.html'))
legacyWebroot.segment = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'phase1.html'))
legacyWebroot.annotate = staticFile(
os.path.join(info['pluginRootDir'], 'custom', 'phase2.html'))
registerPluginWebroot(legacyWebroot, 'markup')
# create all necessary users, groups, collections, etc
provisionDatabase()
# add api routes
# remove docs for default Girder API, to simplify page
clearRouteDocs()
# TODO: nest these under a "/isic" path?
info['apiRoot'].annotation = api.AnnotationResource()
info['apiRoot'].dataset = api.DatasetResource()
info['apiRoot'].featureset = api.FeaturesetResource()
info['apiRoot'].image = api.ImageResource()
info['apiRoot'].segmentation = api.SegmentationResource()
info['apiRoot'].study = api.StudyResource()
info['apiRoot'].task = api.TaskResource()
api.attachUserApi(info['apiRoot'].user)
def load(info):
info["serverRoot"], info["serverRoot"].girder = (CustomAppRoot(), info["serverRoot"])
info["serverRoot"].api = info["serverRoot"].girder.api
del info["serverRoot"].girder.api
info["apiRoot"].collection.route("GET", ("unbound", "default", "noargs"), unboundHandlerDefaultNoArgs)
info["apiRoot"].collection.route("GET", ("unbound", "default"), unboundHandlerDefault)
info["apiRoot"].collection.route("GET", ("unbound", "explicit"), unboundHandlerExplicit)
info["apiRoot"].other = Other()
path = os.path.join(globals()["PLUGIN_ROOT_DIR"], "static.txt")
info["serverRoot"].static_route = staticFile(path)
def load(info):
info['serverRoot'], info['serverRoot'].girder = (CustomAppRoot(),
info['serverRoot'])
info['serverRoot'].api = info['serverRoot'].girder.api
del info['serverRoot'].girder.api
info['apiRoot'].collection.route('GET', ('unbound', 'default'),
unboundHandlerDefault)
info['apiRoot'].collection.route('GET', ('unbound', 'explicit'),
unboundHandlerExplicit)
info['apiRoot'].other = Other()
path = os.path.join(globals()['PLUGIN_ROOT_DIR'], 'static.txt')
info['serverRoot'].static_route = staticFile(path)
def load(self, info):
info['serverRoot'], info['serverRoot'].girder = (
CustomAppRoot(), info['serverRoot'])
info['serverRoot'].api = info['serverRoot'].girder.api
del info['serverRoot'].girder.api
info['apiRoot'].collection.route('GET', ('unbound', 'default', 'noargs'),
unboundHandlerDefaultNoArgs)
info['apiRoot'].collection.route('GET', ('unbound', 'default'),
unboundHandlerDefault)
info['apiRoot'].other = Other()
path = os.path.join(os.path.dirname(__file__), 'data', 'static.txt')
info['serverRoot'].static_route = staticFile(path)
def load(info):
info['serverRoot'], info['serverRoot'].girder = (
CustomAppRoot(), info['serverRoot'])
info['serverRoot'].api = info['serverRoot'].girder.api
del info['serverRoot'].girder.api
info['apiRoot'].collection.route('GET', ('unbound', 'default'),
unboundHandlerDefault)
info['apiRoot'].collection.route('GET', ('unbound', 'explicit'),
unboundHandlerExplicit)
info['apiRoot'].other = Other()
path = os.path.join(globals()['PLUGIN_ROOT_DIR'], 'static.txt')
info['serverRoot'].static_route = staticFile(path)
def load(self, info):
getPlugin('worker').load(info)
dist = os.path.join(os.path.dirname(__file__), 'dist')
webroot = staticFile(os.path.join(dist, 'index.html'))
registerPluginWebroot(webroot, 'stroke')
info['config']['/stroke_static'] = {
'tools.staticdir.on': True,
'tools.staticdir.dir': os.path.join(dist, 'stroke_static')
}
info['config']['/itk'] = {
'tools.staticdir.on': True,
'tools.staticdir.dir': os.path.join(dist, 'itk')
}
info['apiRoot'].study = Study()
info['apiRoot'].series = Series()
info['apiRoot'].item.route('GET', (':id', 'dicom_thumbnail', ':uid'),
_getThumbnail)
info['apiRoot'].item.route('POST', (':id', 'dicom_thumbnail'),
_createThumbnail)
Folder().ensureIndex(('isStudy', {'sparse': True}))
Folder().exposeFields(level=AccessType.READ,
fields={
'isStudy', 'nSeries', 'studyDate',
'patientId', 'studyModality'
})
Item().exposeFields(level=AccessType.READ, fields={'isSeries'})
events.bind('model.file.finalizeUpload.after', 'stroke', _handleUpload)
events.bind('model.item.remove', 'stroke.decrement_series_count',
_decrementSeriesCount)
events.bind('model.item.remove', 'stroke.clean_thumbnails',
lambda e: _removeThumbnails(e.info))
# Guest user support
events.bind('model.user.authenticate', 'stroke',
_authenticateGuestUser)
try:
User().createUser(login='******',
password='******',
firstName='Guest',
lastName='User',
email='*****@*****.**')
except ValidationException:
pass
def load(self, info):
info['serverRoot'], info['serverRoot'].girder = (
CustomAppRoot(), info['serverRoot'])
info['serverRoot'].api = info['serverRoot'].girder.api
del info['serverRoot'].girder.api
info['apiRoot'].collection.route('GET', ('unbound', 'default', 'noargs'),
unboundHandlerDefaultNoArgs)
info['apiRoot'].collection.route('GET', ('unbound', 'default'),
unboundHandlerDefault)
info['apiRoot'].collection.route('GET', ('unbound', 'explicit'),
unboundHandlerExplicit)
info['apiRoot'].other = Other()
path = os.path.join(os.path.dirname(__file__), 'data', 'static.txt')
info['serverRoot'].static_route = staticFile(path)
def load(self, info):
getPlugin('worker').load(info)
addTemplateDirectory(os.path.join(os.path.dirname(__file__)),
'mail_templates')
dist = os.path.join(os.path.dirname(__file__), 'dist')
webroot = staticFile(os.path.join(dist, 'index.html'))
registerPluginWebroot(webroot, 'demo_site')
info['config']['/stroke_ct_static'] = {
'tools.staticdir.on': True,
'tools.staticdir.dir': os.path.join(dist, 'stroke_ct_static')
}
info['config']['/itk'] = {
'tools.staticdir.on': True,
'tools.staticdir.dir': os.path.join(dist, 'itk')
}
info['apiRoot'].study = Study()
info['apiRoot'].series = Series()
info['apiRoot'].photomorph = Photomorph()
info['apiRoot'].inpainting = Inpainting()
Folder().ensureIndex(('isStudy', {'sparse': True}))
Folder().ensureIndex(('isPhotomorph', {'sparse': True}))
Folder().ensureIndex(('photomorphExampleFolder', {'sparse': True}))
Folder().ensureIndex(('inpaintingExampleFolder', {'sparse': True}))
Folder().exposeFields(level=AccessType.READ,
fields={
'isStudy', 'nSeries', 'studyDate',
'patientId', 'studyModality',
'photomorphJobId', 'isPhotomorph',
'photomorphInputFolderId',
'photomorphOutputItems',
'photomorphJobStatus', 'photomorphMaskRect'
})
Item().exposeFields(level=AccessType.READ,
fields={
'isSeries', 'isPhotomorph', 'originalName',
'photomorphTakenDate'
})
Job().exposeFields(level=AccessType.READ,
fields={
'photomorphId', 'inpaintingImageId',
'inpaintingMaskId', 'inpaintingImageResultId',
'inpaintingFolderId'
})
events.bind('model.file.finalizeUpload.after', 'demo_site',
_handleUpload)
events.bind('model.item.remove', 'demo_site', _itemDeleted)
events.bind('jobs.job.update', 'demo_site', _jobUpdated)
# Guest user support
events.bind('model.user.authenticate', 'demo_site',
_authenticateGuestUser)
try:
User().createUser(login='******',
password='******',
firstName='Guest',
lastName='User',
email='*****@*****.**')
except ValidationException:
pass
def load(info):
# set the title of the HTML pages
info['serverRoot'].updateHtmlVars({'title': 'ISIC Archive'})
# add event listeners
# note, 'model.setting.validate' must be bound before initialSetup is called
events.bind('model.setting.validate', 'isic', validateSettings)
events.bind('model.user.save.created', 'onUserCreated', onUserCreated)
events.bind('rest.get.item/:id.after', 'onGetItem', onGetItem)
ModelImporter.model('setting').set(SettingKey.USER_DEFAULT_FOLDERS, 'none')
# add custom model searching
resource.allowedSearchTypes.update({
'image.isic_archive',
'featureset.isic_archive',
'study.isic_archive',
})
# create all necessary users, groups, collections, etc
initialSetup(info)
# add static file serving
app_base = os.path.join(os.curdir, os.pardir)
app_path = os.path.join(app_base, 'girder', 'plugins', 'isic_archive', 'custom')
info['config']['/uda'] = {
'tools.staticdir.on': 'True',
'tools.staticdir.dir': app_path
}
# add dynamic root routes
# root endpoints -> where a user may go and expect a UI
class Root(object):
pass
info['serverRoot'].uda = Root()
# "/uda/gallery" -> returns a single page gallery
info['serverRoot'].uda.gallery = staticFile(os.path.join(info['pluginRootDir'], 'custom', 'gallery.html'))
# "/uda/task" -> redirects to appropriate task view for the user
info['serverRoot'].uda.task = TaskHandler(info['pluginRootDir'])
# "/uda/annotator/:id" -> the reconfigurable image annotator
info['serverRoot'].uda.annotate = staticFile(os.path.join(info['pluginRootDir'], 'custom', 'phase1.html'))
# "/uda/map/:id"
info['serverRoot'].uda.map = staticFile(os.path.join(info['pluginRootDir'], 'custom', 'phase2.html'))
# add api routes
# remove docs for default Girder API, to simplify page
clearRouteDocs()
info['apiRoot'].uda = UDAResource(info['pluginRootDir'])
# TODO: nest these under a "/isic" path
info['apiRoot'].annotation = api.AnnotationResource(info['pluginRootDir'])
info['apiRoot'].dataset = api.DatasetResource()
info['apiRoot'].featureset = api.FeaturesetResource()
info['apiRoot'].image = api.ImageResource()
info['apiRoot'].segmentation = api.SegmentationResource()
info['apiRoot'].study = api.StudyResource()
# Serve isic app from /isic
info['serverRoot'].isic = Webroot()