Example #1
0
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)
Example #2
0
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)
Example #3
0
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)
Example #4
0
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)
Example #5
0
    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)
Example #6
0
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)
Example #7
0
    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
Example #8
0
    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)
Example #9
0
    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
Example #10
0
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()