def __init__(self):
handlers = [
(r"/", MainHandler),
(r"/auth/login/", AuthLoginHandler),
(r"/auth/logout/", AuthLogoutHandler),
(r"/auth/create/", AuthCreateHandler),
(r"/auth/verify/(.*)", AuthVerifyHandler),
(r"/auth/forgot/", ForgotPasswordHandler),
(r"/auth/reset/(.*)", ChangeForgotPasswordHandler),
(r"/profile/", UserProfileHandler),
(r"/user/messages/", UserMessagesHander),
(r"/user/jobs/", UserJobs),
(r"/static/(.*)", tornado.web.StaticFileHandler,
{"path": STATIC_PATH}),
# Analysis handlers
(r"/analysis/list/", ListAnalysesHandler),
(r"/analysis/dflt/sumary/", AnalysisSummaryAJAX),
(r"/analysis/create/", CreateAnalysisHandler),
(r"/analysis/selected/", SelectedSamplesHandler),
(r"/analysis/selected/socket/", SelectedSocketHandler),
(r"/analysis/description/(.*)/graph/", AnalysisGraphHandler),
(r"/analysis/description/(.*)/jobs/", AnalysisJobsHandler),
(r"/analysis/description/(.*)/", AnalysisDescriptionHandler),
(r"/analysis/sharing/", ShareAnalysisAJAX),
(r"/artifact/samples/", ArtifactGetSamples),
(r"/artifact/info/", ArtifactGetInfo),
(r"/consumer/", MessageHandler),
(r"/admin/error/", LogEntryViewerHandler),
(r"/admin/approval/", StudyApprovalList),
(r"/admin/artifact/", ArtifactAdminAJAX),
(r"/admin/software/", SoftwareHandler),
(r"/ebi_submission/(.*)", EBISubmitHandler),
# Study handlers
(r"/study/create/", StudyEditHandler),
(r"/study/edit/(.*)", StudyEditHandler),
(r"/study/list/", ListStudiesHandler),
(r"/study/process/commands/options/", ListOptionsHandler),
(r"/study/process/commands/", ListCommandsHandler),
(r"/study/process/workflow/run/", WorkflowRunHandler),
(r"/study/process/workflow/", WorkflowHandler),
(r"/study/process/job/", JobAJAX),
(r"/study/list/socket/", SelectSamplesHandler),
(r"/study/list_studies/(.*)", ListStudiesAJAX),
(r"/study/new_artifact/", NewArtifactHandler),
(r"/study/files/", StudyFilesAJAX),
(r"/study/sharing/", ShareStudyAJAX),
(r"/study/sharing/autocomplete/", AutocompleteHandler),
(r"/study/new_prep_template/", NewPrepTemplateAjax),
(r"/study/tags/(.*)", StudyTags),
(r"/study/get_tags/", StudyGetTags),
(r"/study/([0-9]+)$", Study),
# Artifact handlers
(r"/artifact/graph/", ArtifactGraphAJAX),
(r"/artifact/(.*)/summary/", ArtifactSummaryAJAX),
(r"/artifact/html_summary/(.*)", ArtifactSummaryHandler,
{"path": qiita_config.base_data_dir}),
(r"/artifact/(.*)/", ArtifactAJAX),
# Prep template handlers
(r"/prep_template/", PrepTemplateHandler),
(r"/prep_template/(.*)/graph/", PrepTemplateGraphHandler),
(r"/prep_template/(.*)/jobs/", PrepTemplateJobHandler),
(r"/ontology/", OntologyHandler),
# ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
# Same reasoning as below. /study/description/(.*) should be last.
(r"/study/description/sample_template/overview/",
SampleTemplateOverviewHandler),
(r"/study/description/sample_template/columns/",
SampleTemplateColumnsHandler),
(r"/study/description/sample_template/", SampleTemplateHandler),
(r"/study/description/sample_summary/", SampleAJAX),
(r"/study/description/prep_summary/", PrepTemplateSummaryAJAX),
(r"/study/description/prep_template/", PrepTemplateAJAX),
(r"/study/description/baseinfo/", StudyBaseInfoAJAX),
(r"/study/description/data_type_menu/", DataTypesMenuAJAX),
(r"/study/description/(.*)", StudyIndexHandler),
(r"/study/delete/", StudyDeleteAjax),
(r"/study/upload/remote/(.*)", StudyUploadViaRemote),
(r"/study/upload/(.*)", StudyUploadFileHandler),
(r"/upload/", UploadFileHandler),
(r"/check_study/", CreateStudyAJAX),
(r"/stats/", StatsHandler),
(r"/download/(.*)", DownloadHandler),
(r"/download_study_bioms/(.*)", DownloadStudyBIOMSHandler),
(r"/download_raw_data/(.*)", DownloadRawData),
(r"/download_ebi_accessions/samples/(.*)",
DownloadEBISampleAccessions),
(r"/download_ebi_accessions/experiments/(.*)",
DownloadEBIPrepAccessions),
(r"/download_upload/(.*)", DownloadUpload),
(r"/release/download/(.*)", DownloadRelease),
(r"/vamps/(.*)", VAMPSHandler),
(r"/redbiom/(.*)", RedbiomPublicSearch),
(r"/iframe/", IFrame),
# Plugin handlers - the order matters here so do not change
# qiita_db/jobs/(.*) should go after any of the
# qiita_db/jobs/(.*)/XXXX because otherwise it will match the
# regular expression and the qiita_db/jobs/(.*)/XXXX will never
# be hit.
(r"/qiita_db/authenticate/", TokenAuthHandler),
(r"/qiita_db/jobs/(.*)/heartbeat/", HeartbeatHandler),
(r"/qiita_db/jobs/(.*)/step/", ActiveStepHandler),
(r"/qiita_db/jobs/(.*)/complete/", CompleteHandler),
(r"/qiita_db/jobs/(.*)", JobHandler),
(r"/qiita_db/artifacts/types/", ArtifactTypeHandler),
(r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
(r"/qiita_db/users/", UsersListDBHandler),
(r"/qiita_db/user/(.*)/data/", UserInfoDBHandler),
(r"/qiita_db/sample_information/(.*)/data/", SampleInfoDBHandler),
(r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
(r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
(r"/qiita_db/references/(.*)/", ReferenceHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/activate/",
CommandActivateHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/", CommandHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/", CommandListHandler),
(r"/qiita_db/plugins/(.*)/(.*)/", PluginHandler),
(r"/qiita_db/analysis/(.*)/metadata/", APIAnalysisMetadataHandler),
(r"/qiita_db/archive/observations/", APIArchiveObservations)
]
# rest endpoints
handlers.extend(REST_ENDPOINTS)
if qiita_config.portal == "QIITA":
# Add portals editing pages only on main portal
portals = [
(r"/admin/portals/studies/", StudyPortalHandler),
(r"/admin/portals/studiesAJAX/", StudyPortalAJAXHandler)
]
handlers.extend(portals)
if is_test_environment():
# We add the endpoints for testing plugins
test_handlers = [
(r"/apitest/processing_job/", ProcessingJobAPItestHandler),
(r"/apitest/reset/", ResetAPItestHandler),
(r"/apitest/prep_template/", PrepTemplateAPItestHandler),
(r"/apitest/artifact/", ArtifactAPItestHandler),
(r"/apitest/reload_plugins/", ReloadPluginAPItestHandler)
]
handlers.extend(test_handlers)
# 404 PAGE MUST BE LAST IN THIS LIST!
handlers.append((r".*", NoPageHandler))
settings = {
"template_path": TEMPLATE_PATH,
"debug": DEBUG,
"cookie_secret": qiita_config.cookie_secret,
"login_url": "%s/auth/login/" % qiita_config.portal_dir,
}
tornado.web.Application.__init__(self, handlers, **settings)
def __init__(self):
handlers = [
(r"/", MainHandler),
(r"/auth/login/", AuthLoginHandler),
(r"/auth/logout/", AuthLogoutHandler),
(r"/auth/create/", AuthCreateHandler),
(r"/auth/verify/(.*)", AuthVerifyHandler),
(r"/auth/forgot/", ForgotPasswordHandler),
(r"/auth/reset/(.*)", ChangeForgotPasswordHandler),
(r"/profile/", UserProfileHandler),
(r"/user/messages/", UserMessagesHander),
(r"/user/jobs/", UserJobs),
(r"/static/(.*)", tornado.web.StaticFileHandler, {
"path": STATIC_PATH
}),
# Analysis handlers
(r"/analysis/list/", ListAnalysesHandler),
(r"/analysis/dflt/sumary/", AnalysisSummaryAJAX),
(r"/analysis/create/", CreateAnalysisHandler),
(r"/analysis/selected/", SelectedSamplesHandler),
(r"/analysis/selected/socket/", SelectedSocketHandler),
(r"/analysis/description/(.*)/graph/", AnalysisGraphHandler),
(r"/analysis/description/(.*)/jobs/", AnalysisJobsHandler),
(r"/analysis/description/(.*)/", AnalysisDescriptionHandler),
(r"/analysis/sharing/", ShareAnalysisAJAX),
(r"/artifact/samples/", ArtifactGetSamples),
(r"/artifact/info/", ArtifactGetInfo),
(r"/consumer/", MessageHandler),
(r"/admin/error/", LogEntryViewerHandler),
(r"/admin/approval/", StudyApprovalList),
(r"/admin/artifact/", ArtifactAdminAJAX),
(r"/ebi_submission/(.*)", EBISubmitHandler),
# Study handlers
(r"/study/create/", StudyEditHandler),
(r"/study/edit/(.*)", StudyEditHandler),
(r"/study/list/", ListStudiesHandler),
(r"/study/process/commands/options/", ListOptionsHandler),
(r"/study/process/commands/", ListCommandsHandler),
(r"/study/process/workflow/run/", WorkflowRunHandler),
(r"/study/process/workflow/", WorkflowHandler),
(r"/study/process/job/", JobAJAX),
(r"/study/list/socket/", SelectSamplesHandler),
(r"/study/list_studies/(.*)", ListStudiesAJAX),
(r"/study/new_artifact/", NewArtifactHandler),
(r"/study/files/", StudyFilesAJAX),
(r"/study/sharing/", ShareStudyAJAX),
(r"/study/sharing/autocomplete/", AutocompleteHandler),
(r"/study/new_prep_template/", NewPrepTemplateAjax),
(r"/study/analyses/", AnalysesAjax),
(r"/study/tags/(.*)", StudyTags),
(r"/study/get_tags/", StudyGetTags),
(r"/study/([0-9]+)$", Study),
# Artifact handlers
(r"/artifact/graph/", ArtifactGraphAJAX),
(r"/artifact/(.*)/summary/", ArtifactSummaryAJAX),
(r"/artifact/html_summary/(.*)", ArtifactSummaryHandler, {
"path": qiita_config.base_data_dir
}),
(r"/artifact/(.*)/", ArtifactAJAX),
# Prep template handlers
(r"/prep_template/", PrepTemplateHandler),
(r"/prep_template/(.*)/graph/", PrepTemplateGraphHandler),
(r"/prep_template/(.*)/jobs/", PrepTemplateJobHandler),
(r"/ontology/", OntologyHandler),
# ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
# Same reasoning as below. /study/description/(.*) should be last.
(r"/study/description/sample_template/overview/",
SampleTemplateOverviewHandler),
(r"/study/description/sample_template/columns/",
SampleTemplateColumnsHandler),
(r"/study/description/sample_template/", SampleTemplateHandler),
(r"/study/description/sample_summary/", SampleAJAX),
(r"/study/description/prep_summary/", PrepTemplateSummaryAJAX),
(r"/study/description/prep_template/", PrepTemplateAJAX),
(r"/study/description/baseinfo/", StudyBaseInfoAJAX),
(r"/study/description/data_type_menu/", DataTypesMenuAJAX),
(r"/study/description/(.*)", StudyIndexHandler),
(r"/study/delete/", StudyDeleteAjax),
(r"/study/upload/remote/(.*)", StudyUploadViaRemote),
(r"/study/upload/(.*)", StudyUploadFileHandler),
(r"/upload/", UploadFileHandler),
(r"/check_study/", CreateStudyAJAX),
(r"/stats/", StatsHandler),
(r"/software/", SoftwareHandler),
(r"/workflows/", WorkflowsHandler),
(r"/download/(.*)", DownloadHandler),
(r"/download_study_bioms/(.*)", DownloadStudyBIOMSHandler),
(r"/download_raw_data/(.*)", DownloadRawData),
(r"/download_ebi_accessions/samples/(.*)",
DownloadEBISampleAccessions),
(r"/download_sample_info_per_prep/(.*)",
DownloadSampleInfoPerPrep),
(r"/download_ebi_accessions/experiments/(.*)",
DownloadEBIPrepAccessions),
(r"/download_upload/(.*)", DownloadUpload),
(r"/release/download/(.*)", DownloadRelease),
(r"/public_download/", DownloadPublicHandler),
(r"/public_artifact_download/", DownloadPublicArtifactHandler),
(r"/private_download/(.*)", DownloadPrivateArtifactHandler),
(r"/public/", PublicHandler),
(r"/vamps/(.*)", VAMPSHandler),
(r"/redbiom/(.*)", RedbiomPublicSearch),
(r"/iframe/", IFrame),
# Plugin handlers - the order matters here so do not change
# qiita_db/jobs/(.*) should go after any of the
# qiita_db/jobs/(.*)/XXXX because otherwise it will match the
# regular expression and the qiita_db/jobs/(.*)/XXXX will never
# be hit.
(r"/qiita_db/authenticate/", TokenAuthHandler),
(r"/qiita_db/jobs/(.*)/heartbeat/", HeartbeatHandler),
(r"/qiita_db/jobs/(.*)/step/", ActiveStepHandler),
(r"/qiita_db/jobs/(.*)/complete/", CompleteHandler),
(r"/qiita_db/jobs/(.*)", JobHandler),
(r"/qiita_db/artifacts/types/", ArtifactTypeHandler),
(r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
(r"/qiita_db/artifact/", APIArtifactHandler),
(r"/qiita_db/users/", UsersListDBHandler),
(r"/qiita_db/user/(.*)/data/", UserInfoDBHandler),
(r"/qiita_db/sample_information/(.*)/data/", SampleInfoDBHandler),
(r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
(r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
(r"/qiita_db/references/(.*)/", ReferenceHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/activate/",
CommandActivateHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/", CommandHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/", CommandListHandler),
(r"/qiita_db/plugins/(.*)/(.*)/", PluginHandler),
(r"/qiita_db/analysis/(.*)/metadata/", APIAnalysisMetadataHandler),
(r"/qiita_db/archive/observations/", APIArchiveObservations)
]
# rest endpoints
handlers.extend(REST_ENDPOINTS)
if qiita_config.portal == "QIITA":
# Add portals editing pages only on main portal
portals = [(r"/admin/portals/studies/", StudyPortalHandler),
(r"/admin/portals/studiesAJAX/", StudyPortalAJAXHandler)
]
handlers.extend(portals)
if is_test_environment():
# We add the endpoints for testing plugins
test_handlers = [
(r"/apitest/processing_job/", ProcessingJobAPItestHandler),
(r"/apitest/reset/", ResetAPItestHandler),
(r"/apitest/prep_template/", PrepTemplateAPItestHandler),
(r"/apitest/artifact/", ArtifactAPItestHandler),
(r"/apitest/reload_plugins/", ReloadPluginAPItestHandler)
]
handlers.extend(test_handlers)
# 404 PAGE MUST BE LAST IN THIS LIST!
handlers.append((r".*", NoPageHandler))
settings = {
"template_path": TEMPLATE_PATH,
"debug": DEBUG,
"cookie_secret": qiita_config.cookie_secret,
"login_url": "%s/auth/login/" % qiita_config.portal_dir,
}
tornado.web.Application.__init__(self, handlers, **settings)
def test_is_test_environment(self):
self.assertTrue(is_test_environment())
def __init__(self):
handlers = [
(r"/", MainHandler),
(r"/auth/login/", AuthLoginHandler),
(r"/auth/logout/", AuthLogoutHandler),
(r"/auth/create/", AuthCreateHandler),
(r"/auth/verify/(.*)", AuthVerifyHandler),
(r"/auth/forgot/", ForgotPasswordHandler),
(r"/auth/reset/(.*)", ChangeForgotPasswordHandler),
(r"/profile/", UserProfileHandler),
(r"/user/messages/", UserMessagesHander),
(r"/results/(.*)", ResultsHandler,
{"path": RES_PATH}),
(r"/static/(.*)", tornado.web.StaticFileHandler,
{"path": STATIC_PATH}),
(r"/analysis/3", SelectCommandsHandler),
(r"/analysis/wait/(.*)", AnalysisWaitHandler),
(r"/analysis/results/(.*)", AnalysisResultsHandler),
(r"/analysis/show/", ShowAnalysesHandler),
(r"/analysis/dflt/sumary/", AnalysisSummaryAJAX),
(r"/analysis/selected/", SelectedSamplesHandler),
(r"/analysis/selected/socket/", SelectedSocketHandler),
(r"/analysis/sharing/", ShareAnalysisAJAX),
(r"/moi-ws/", MOIMessageHandler),
(r"/consumer/", MessageHandler),
(r"/admin/error/", LogEntryViewerHandler),
(r"/admin/approval/", StudyApprovalList),
(r"/admin/artifact/", ArtifactAdminAJAX),
(r"/ebi_submission/(.*)", EBISubmitHandler),
(r"/study/create/", StudyEditHandler),
(r"/study/edit/(.*)", StudyEditHandler),
(r"/study/list/", ListStudiesHandler),
(r"/study/process/commands/options/", ListOptionsHandler),
(r"/study/process/commands/", ListCommandsHandler),
(r"/study/process/workflow/run/", WorkflowRunHandler),
(r"/study/process/workflow/", WorkflowHandler),
(r"/study/process/job/", JobAJAX),
(r"/study/process/", ProcessArtifactHandler),
(r"/study/list/socket/", SelectSamplesHandler),
(r"/study/search/(.*)", SearchStudiesAJAX),
(r"/study/new_artifact/", NewArtifactHandler),
(r"/study/files/", StudyFilesAJAX),
(r"/study/sharing/", ShareStudyAJAX),
(r"/study/sharing/autocomplete/", AutocompleteHandler),
(r"/study/new_prep_template/", NewPrepTemplateAjax),
(r"/prep/graph/", PrepTemplateGraphAJAX),
(r"/artifact/", ArtifactAJAX),
(r"/artifact/graph/", ArtifactGraphAJAX),
(r"/prep_template/", PrepTemplateHandler),
(r"/ontology/", OntologyHandler),
# ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
# Same reasoning as below. /study/description/(.*) should be last.
(r"/study/description/sample_template/", SampleTemplateAJAX),
(r"/study/description/sample_summary/", SampleAJAX),
(r"/study/description/prep_summary/", PrepTemplateSummaryAJAX),
(r"/study/description/prep_template/", PrepTemplateAJAX),
(r"/study/description/artifact_summary/", ArtifactSummaryAJAX),
(r"/study/description/baseinfo/", StudyBaseInfoAJAX),
(r"/study/description/data_type_menu/", DataTypesMenuAJAX),
(r"/study/description/(.*)", StudyIndexHandler),
(r"/study/delete/", StudyDeleteAjax),
(r"/study/upload/(.*)", StudyUploadFileHandler),
(r"/upload/", UploadFileHandler),
(r"/check_study/", CreateStudyAJAX),
(r"/stats/", StatsHandler),
(r"/download/(.*)", DownloadHandler),
(r"/vamps/(.*)", VAMPSHandler),
# Plugin handlers - the order matters here so do not change
# qiita_db/jobs/(.*) should go after any of the
# qiita_db/jobs/(.*)/XXXX because otherwise it will match the
# regular expression and the qiita_db/jobs/(.*)/XXXX will never
# be hit.
(r"/qiita_db/authenticate/", TokenAuthHandler),
(r"/qiita_db/jobs/(.*)/heartbeat/", HeartbeatHandler),
(r"/qiita_db/jobs/(.*)/step/", ActiveStepHandler),
(r"/qiita_db/jobs/(.*)/complete/", CompleteHandler),
(r"/qiita_db/jobs/(.*)", JobHandler),
(r"/qiita_db/artifacts/types/", ArtifactTypeHandler),
(r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
(r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
(r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
(r"/qiita_db/references/(.*)/", ReferenceHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/activate/",
CommandActivateHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/(.*)/", CommandHandler),
(r"/qiita_db/plugins/(.*)/(.*)/commands/", CommandListHandler),
(r"/qiita_db/plugins/(.*)/(.*)/", PluginHandler)
]
if qiita_config.portal == "QIITA":
# Add portals editing pages only on main portal
portals = [
(r"/admin/portals/studies/", StudyPortalHandler),
(r"/admin/portals/studiesAJAX/", StudyPortalAJAXHandler)
]
handlers.extend(portals)
if is_test_environment():
# We add the endpoints for testing plugins
test_handlers = [
(r"/apitest/processing_job/", ProcessingJobAPItestHandler),
(r"/apitest/reset/", ResetAPItestHandler),
(r"/apitest/prep_template/", PrepTemplateAPItestHandler),
(r"/apitest/artifact/", ArtifactAPItestHandler),
(r"/apitest/reload_plugins/", ReloadPluginAPItestHandler)
]
handlers.extend(test_handlers)
# 404 PAGE MUST BE LAST IN THIS LIST!
handlers.append((r".*", NoPageHandler))
settings = {
"template_path": TEMPLATE_PATH,
"debug": DEBUG,
"cookie_secret": qiita_config.cookie_secret,
"login_url": "%s/auth/login/" % qiita_config.portal_dir,
"ui_modules": uimodules,
}
tornado.web.Application.__init__(self, handlers, **settings)
def test_is_test_environment(self):
self.assertTrue(is_test_environment())
def __init__(self):
handlers = [
(r"/", MainHandler),
(r"/auth/login/", AuthLoginHandler),
(r"/auth/logout/", AuthLogoutHandler),
(r"/auth/create/", AuthCreateHandler),
(r"/auth/verify/(.*)", AuthVerifyHandler),
(r"/auth/forgot/", ForgotPasswordHandler),
(r"/auth/reset/(.*)", ChangeForgotPasswordHandler),
(r"/profile/", UserProfileHandler),
(r"/user/messages/", UserMessagesHander),
(r"/results/(.*)", ResultsHandler, {
"path": RES_PATH
}),
(r"/static/(.*)", tornado.web.StaticFileHandler, {
"path": STATIC_PATH
}),
(r"/analysis/3", SelectCommandsHandler),
(r"/analysis/wait/(.*)", AnalysisWaitHandler),
(r"/analysis/results/(.*)", AnalysisResultsHandler),
(r"/analysis/show/", ShowAnalysesHandler),
(r"/analysis/dflt/sumary/", AnalysisSummaryAJAX),
(r"/analysis/selected/", SelectedSamplesHandler),
(r"/analysis/selected/socket/", SelectedSocketHandler),
(r"/analysis/sharing/", ShareAnalysisAJAX),
(r"/moi-ws/", MOIMessageHandler),
(r"/consumer/", MessageHandler),
(r"/admin/error/", LogEntryViewerHandler),
(r"/admin/approval/", StudyApprovalList),
(r"/admin/artifact/", ArtifactAdminAJAX),
(r"/ebi_submission/(.*)", EBISubmitHandler),
(r"/study/create/", StudyEditHandler),
(r"/study/edit/(.*)", StudyEditHandler),
(r"/study/list/", ListStudiesHandler),
(r"/study/process/commands/options/", ListOptionsHandler),
(r"/study/process/commands/", ListCommandsHandler),
(r"/study/process/workflow/run/", WorkflowRunHandler),
(r"/study/process/workflow/", WorkflowHandler),
(r"/study/process/job/", JobAJAX),
(r"/study/process/", ProcessArtifactHandler),
(r"/study/list/socket/", SelectSamplesHandler),
(r"/study/search/(.*)", SearchStudiesAJAX),
(r"/study/new_artifact/", NewArtifactHandler),
(r"/study/files/", StudyFilesAJAX),
(r"/study/sharing/", ShareStudyAJAX),
(r"/study/sharing/autocomplete/", AutocompleteHandler),
(r"/study/new_prep_template/", NewPrepTemplateAjax),
(r"/prep/graph/", PrepTemplateGraphAJAX),
(r"/artifact/", ArtifactAJAX),
(r"/artifact/graph/", ArtifactGraphAJAX),
(r"/prep_template/", PrepTemplateHandler),
(r"/ontology/", OntologyHandler),
# ORDER FOR /study/description/ SUBPAGES HERE MATTERS.
# Same reasoning as below. /study/description/(.*) should be last.
(r"/study/description/sample_template/", SampleTemplateAJAX),
(r"/study/description/sample_summary/", SampleAJAX),
(r"/study/description/prep_summary/", PrepTemplateSummaryAJAX),
(r"/study/description/prep_template/", PrepTemplateAJAX),
(r"/study/description/artifact_summary/", ArtifactSummaryAJAX),
(r"/study/description/baseinfo/", StudyBaseInfoAJAX),
(r"/study/description/data_type_menu/", DataTypesMenuAJAX),
(r"/study/description/(.*)", StudyIndexHandler),
(r"/study/delete/", StudyDeleteAjax),
(r"/study/upload/(.*)", StudyUploadFileHandler),
(r"/upload/", UploadFileHandler),
(r"/check_study/", CreateStudyAJAX),
(r"/stats/", StatsHandler),
(r"/download/(.*)", DownloadHandler),
(r"/vamps/(.*)", VAMPSHandler),
# Plugin handlers - the order matters here so do not change
# qiita_db/jobs/(.*) should go after any of the
# qiita_db/jobs/(.*)/XXXX because otherwise it will match the
# regular expression and the qiita_db/jobs/(.*)/XXXX will never
# be hit.
(r"/qiita_db/authenticate/", TokenAuthHandler),
(r"/qiita_db/jobs/(.*)/heartbeat/", HeartbeatHandler),
(r"/qiita_db/jobs/(.*)/step/", ActiveStepHandler),
(r"/qiita_db/jobs/(.*)/complete/", CompleteHandler),
(r"/qiita_db/jobs/(.*)", JobHandler),
(r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
(r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
(r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
(r"/qiita_db/references/(.*)/", ReferenceHandler)
]
if qiita_config.portal == "QIITA":
# Add portals editing pages only on main portal
portals = [(r"/admin/portals/studies/", StudyPortalHandler),
(r"/admin/portals/studiesAJAX/", StudyPortalAJAXHandler)
]
handlers.extend(portals)
if is_test_environment():
# We add the endpoints for testing plugins
test_handlers = [
(r"/apitest/processing_job/", ProcessingJobAPItestHandler),
(r"/apitest/reset/", ResetAPItestHandler),
(r"/apitest/prep_template/", PrepTemplateAPItestHandler),
(r"/apitest/artifact/", ArtifactAPItestHandler)
]
handlers.extend(test_handlers)
# 404 PAGE MUST BE LAST IN THIS LIST!
handlers.append((r".*", NoPageHandler))
settings = {
"template_path": TEMPLATE_PATH,
"debug": DEBUG,
"cookie_secret": qiita_config.cookie_secret,
"login_url": "%s/auth/login/" % qiita_config.portal_dir,
"ui_modules": uimodules,
}
tornado.web.Application.__init__(self, handlers, **settings)
(r"/qiita_db/archive/observations/", APIArchiveObservations)
]
# rest endpoints
handlers.extend(REST_ENDPOINTS)
if qiita_config.portal == "QIITA":
# Add portals editing pages only on main portal
portals = [
(r"/admin/portals/studies/", StudyPortalHandler),
(r"/admin/portals/studiesAJAX/", StudyPortalAJAXHandler)
]
handlers.extend(portals)
if is_test_environment():
# We add the endpoints for testing plugins
test_handlers = [
(r"/apitest/processing_job/", ProcessingJobAPItestHandler),
(r"/apitest/reset/", ResetAPItestHandler),
(r"/apitest/prep_template/", PrepTemplateAPItestHandler),
(r"/apitest/artifact/", ArtifactAPItestHandler),
(r"/apitest/reload_plugins/", ReloadPluginAPItestHandler)
]
handlers.extend(test_handlers)
# 404 PAGE MUST BE LAST IN THIS LIST!
handlers.append((r".*", NoPageHandler))
settings = {
"template_path": TEMPLATE_PATH,