# -----------------------------------------------------------------------------

# Copyright (c) 2014--, The Qiita Development Team.

#

# Distributed under the terms of the BSD 3-clause License.

#

# The full license is in the file LICENSE, distributed with this software.

# -----------------------------------------------------------------------------

# login code modified from https://gist.github.com/guillaumevincent/4771570

import tornado.auth

import tornado.escape

import tornado.web

import tornado.websocket

from os.path import dirname, join

from base64 import b64encode

from uuid import uuid4

from qiita_core.qiita_settings import qiita_config

from qiita_core.util import is_test_environment

from qiita_pet.handlers.base_handlers import (

    MainHandler, NoPageHandler, IFrame)

from qiita_pet.handlers.auth_handlers import (

    AuthCreateHandler, AuthLoginHandler, AuthLogoutHandler, AuthVerifyHandler)

from qiita_pet.handlers.user_handlers import (

    ChangeForgotPasswordHandler, ForgotPasswordHandler, UserProfileHandler,

    UserMessagesHander, UserJobs, PurgeUsersAJAXHandler, PurgeUsersHandler)

from qiita_pet.handlers.admin_processing_job import (

    AdminProcessingJob, AJAXAdminProcessingJobListing, SampleValidation)

from qiita_pet.handlers.analysis_handlers import (

    ListAnalysesHandler, AnalysisSummaryAJAX, SelectedSamplesHandler,

    AnalysisHandler, AnalysisGraphHandler, CreateAnalysisHandler,

    AnalysisJobsHandler, ShareAnalysisAJAX)

from qiita_pet.handlers.study_handlers import (

    StudyIndexHandler, StudyBaseInfoAJAX, SampleTemplateHandler,

    SampleTemplateOverviewHandler, SampleTemplateColumnsHandler,

    StudyEditHandler, ListStudiesHandler, ListStudiesAJAX, EBISubmitHandler,

    CreateStudyAJAX, ShareStudyAJAX, StudyApprovalList, ArtifactGraphAJAX,

    VAMPSHandler, Study, StudyTags, StudyGetTags,

    ListCommandsHandler, ListOptionsHandler, PrepTemplateSummaryAJAX,

    PrepTemplateAJAX, NewArtifactHandler, SampleAJAX, StudyDeleteAjax,

    ArtifactAdminAJAX, NewPrepTemplateAjax, DataTypesMenuAJAX, StudyFilesAJAX,

    ArtifactGetSamples, ArtifactGetInfo, WorkflowHandler, AnalysesAjax,

    WorkflowRunHandler, AddDefaultWorkflowHandler, JobAJAX,

    AutocompleteHandler)

from qiita_pet.handlers.artifact_handlers import (

    ArtifactSummaryAJAX, ArtifactAJAX, ArtifactSummaryHandler)

from qiita_pet.handlers.websocket_handlers import (

    MessageHandler, SelectedSocketHandler, SelectSamplesHandler)

from qiita_pet.handlers.logger_handlers import LogEntryViewerHandler

from qiita_pet.handlers.upload import (

    UploadFileHandler, StudyUploadFileHandler, StudyUploadViaRemote)

from qiita_pet.handlers.stats import StatsHandler

from qiita_pet.handlers.resources import ResourcesHandler

from qiita_pet.handlers.download import (

    DownloadHandler, DownloadStudyBIOMSHandler, DownloadRelease,

    DownloadRawData, DownloadEBISampleAccessions, DownloadEBIPrepAccessions,

    DownloadUpload, DownloadPublicHandler, DownloadPublicArtifactHandler,

    DownloadSampleInfoPerPrep, DownloadPrivateArtifactHandler,

    DownloadDataReleaseFromPrep)

from qiita_pet.handlers.prep_template import (

    PrepTemplateHandler, PrepTemplateGraphHandler, PrepTemplateJobHandler)

from qiita_pet.handlers.ontology import OntologyHandler

from qiita_pet.handlers.software import SoftwareHandler, WorkflowsHandler

from qiita_db.handlers.processing_job import (

    JobHandler, HeartbeatHandler, ActiveStepHandler, CompleteHandler,

    ProcessingJobAPItestHandler)

from qiita_db.handlers.artifact import (

    ArtifactHandler, ArtifactAPItestHandler, ArtifactTypeHandler,

    APIArtifactHandler)

from qiita_db.handlers.sample_information import SampleInfoDBHandler

from qiita_db.handlers.user import UserInfoDBHandler, UsersListDBHandler

from qiita_db.handlers.prep_template import (

    PrepTemplateDataHandler, PrepTemplateAPItestHandler,

    PrepTemplateAPIHandler, PrepTemplateDBHandler)

from qiita_db.handlers.oauth2 import TokenAuthHandler

from qiita_db.handlers.reference import ReferenceHandler

from qiita_db.handlers.core import ResetAPItestHandler

from qiita_db.handlers.plugin import (

    PluginHandler, CommandHandler, CommandListHandler, CommandActivateHandler,

    ReloadPluginAPItestHandler)

from qiita_db.handlers.analysis import APIAnalysisMetadataHandler

from qiita_db.handlers.archive import APIArchiveObservations

from qiita_db.handlers.studies import APIStudiesListing

from qiita_db.util import get_mountpoint

from qiita_pet.handlers.rest import ENDPOINTS as REST_ENDPOINTS

from qiita_pet.handlers.qiita_redbiom import RedbiomPublicSearch

from qiita_pet.handlers.public import PublicHandler

if qiita_config.portal == "QIITA":

    from qiita_pet.handlers.portal import (

        StudyPortalHandler, StudyPortalAJAXHandler)

DIRNAME = dirname(__file__)

STATIC_PATH = join(DIRNAME, "static")

TEMPLATE_PATH = join(DIRNAME, "templates")  # base folder for webpages

_, RES_PATH = get_mountpoint('job')[0]

COOKIE_SECRET = b64encode(uuid4().bytes + uuid4().bytes)

DEBUG = qiita_config.test_environment

_vendor_js = join(STATIC_PATH, 'vendor', 'js')

class Application(tornado.web.Application):

    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/(.*)/", AnalysisHandler),

            (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/processing_jobs/", AdminProcessingJob),

            (r"/admin/processing_jobs/list", AJAXAdminProcessingJobListing),

            (r"/admin/sample_validation/", SampleValidation),

            (r"/admin/purge_users/", PurgeUsersHandler),

            (r"/admin/purge_usersAjax/", PurgeUsersAJAXHandler),

            (r"/admin/resources/", ResourcesHandler),

            (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/default/", AddDefaultWorkflowHandler),

            (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_data_release_from_prep/(.*)",

                DownloadDataReleaseFromPrep),

            (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/prep_template/", PrepTemplateAPIHandler),

            (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),

            (r"/qiita_db/studies/(.*)", APIStudiesListing)

        ]

        # 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)