__init__.py

"""
Everything that needs to be set up to get flask running is initialized in this file.

  * set up and configure the app
  * start the database (db)
  * load LoginManager (for user system)
  * start Flask Debug Toolbar
  * load all (!) models used (essential to create the database using db_create)
  * load all (!) controllers and register their blueprints to a subdomain
  * add admin panel

  * set up global things like the search form and custom 403/404 error messages
"""
from flask import Flask, render_template, g
from flask_admin import Admin
from flask_admin.menu import MenuLink
from flask_cache import Cache
from flask_compress import Compress
from flask_debugtoolbar import DebugToolbarExtension
from flask_htmlmin import HTMLMIN
from flask_login import LoginManager
from flask_sqlalchemy import SQLAlchemy

from .flask_blast import BlastThread

db = SQLAlchemy()
login_manager = LoginManager()
toolbar = DebugToolbarExtension()
cache = Cache()
htmlmin = HTMLMIN()
blast_thread = BlastThread()
compress = Compress()


def create_app(config):
    # Set up app, database and login manager before importing models and controllers
    # Important for db_create script

    app = Flask(__name__)

    app.config.from_object(config)

    configure_extensions(app)

    # Import all models here
    from planet.models.users import User
    from planet.models.species import Species
    from planet.models.sequences import Sequence
    from planet.models.go import GO
    from planet.models.interpro import Interpro
    from planet.models.gene_families import GeneFamilyMethod, GeneFamily
    from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod, CoexpressionCluster
    from planet.models.expression.profiles import ExpressionProfile
    from planet.models.expression.networks import ExpressionNetworkMethod, ExpressionNetwork
    from planet.models.expression.specificity import ExpressionSpecificityMethod, ExpressionSpecificity
    from planet.models.condition_tissue import ConditionTissue
    from planet.models.clades import Clade
    from planet.models.xrefs import XRef
    from planet.models.news import News

    # Import all relationships (tables for many-to-many relationships)
    import planet.models.relationships
    from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation
    from planet.models.relationships.cluster_similarity import CoexpressionClusterSimilarity
    from planet.models.relationships.cluster_go import ClusterGOEnrichment
    from planet.models.relationships.sequence_go import SequenceGOAssociation
    from planet.models.relationships.sequence_interpro import SequenceInterproAssociation
    from planet.models.relationships.sequence_family import SequenceFamilyAssociation
    from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation
    from planet.models.relationships.sequence_xref import SequenceXRefAssociation
    from planet.models.relationships.family_xref import FamilyXRefAssociation

    configure_blueprints(app)

    # Admin panel
    LOGIN_ENABLED = app.config['LOGIN_ENABLED']
    if LOGIN_ENABLED:
        from planet.controllers.admin.views import MyAdminIndexView
        from planet.controllers.admin.views import SpeciesAdminView, GeneFamilyMethodAdminView, ExpressionNetworkMethodAdminView, \
            CoexpressionClusteringMethodAdminView, CladesAdminView, ExpressionSpecificityMethodAdminView, \
            ConditionTissueAdminView, ControlsView, AddSpeciesView, AddFunctionalDataView, AddXRefsView, \
            AddXRefsFamiliesView, AddFamiliesView, AddExpressionProfilesView, AddCoexpressionClustersView, \
            AddCoexpressionNetworkView, AddGOView, AddInterProView, AddCladesView, AddSpecificityView, \
            AddSequenceDescriptionsView, NewsAdminView, BuildCoexpressionClustersView

        admin = Admin(app, index_view=MyAdminIndexView(template='admin/home.html'), template_mode='bootstrap3')

        # Add views used to build the database

        admin.add_view(AddSpeciesView(name='Species', endpoint='admin.add.species', url='add/species/', category='Add'))
        admin.add_view(AddSequenceDescriptionsView(name='Sequence Descriptions',
                                                   endpoint='admin.add.sequence_descriptions',
                                                   url='add/sequence_descriptions/', category='Add'))

        admin.add_menu_item(MenuLink("------------", class_name="divider", url='#'), target_category='Add')
        admin.add_menu_item(MenuLink("Functional Annotation", class_name="disabled", url="#"), target_category='Add')

        admin.add_view(AddFunctionalDataView(name='GO and InterPro definitions',
                                             endpoint='admin.add.functional_data',
                                             url='add/functional_data/', category='Add'))

        admin.add_view(AddGOView(name='GO Genes',
                                 endpoint='admin.add.go_sequences',
                                 url='add/go/', category='Add'))

        admin.add_view(AddInterProView(name='InterPro Genes',
                                       endpoint='admin.add.interpro_sequences',
                                       url='add/interpro/', category='Add'))

        admin.add_menu_item(MenuLink("------------", class_name="divider", url='#'), target_category='Add')
        admin.add_menu_item(MenuLink("Expression", class_name="disabled", url="#"), target_category='Add')

        admin.add_view(AddExpressionProfilesView(name='Expression profiles',
                                                 endpoint='admin.add.expression_profiles',
                                                 url='add/expression_profiles/', category='Add'))

        admin.add_view(AddCoexpressionNetworkView(name='Coexpression network',
                                                  endpoint='admin.add.coexpression_network',
                                                  url='add/coexpression_network/', category='Add'))

        admin.add_view(AddCoexpressionClustersView(name='Coexpression clusters',
                                                   endpoint='admin.add.coexpression_clusters',
                                                   url='add/coexpression_clusters/', category='Add'))

        admin.add_view(AddSpecificityView(name='Expression Specificity',
                                          endpoint='admin.add.expression_specificity',
                                          url='add/expression_specificity/', category='Add'))

        admin.add_menu_item(MenuLink("------------", class_name="divider", url='#'), target_category='Add')
        admin.add_menu_item(MenuLink("Comparative Genomics", class_name="disabled", url="#"), target_category='Add')

        admin.add_view(AddFamiliesView(name='Gene Families',
                                       endpoint='admin.add.families',
                                       url='add/families/', category='Add'))

        admin.add_view(AddCladesView(name='Clades',
                                     endpoint='admin.add.clades',
                                     url='add/clades/', category='Add'))

        admin.add_menu_item(MenuLink("------------", class_name="divider", url='#'), target_category='Add')
        admin.add_menu_item(MenuLink("Misc.", class_name="disabled", url="#"), target_category='Add')

        admin.add_view(AddXRefsView(name='XRefs Genes',
                                    endpoint='admin.add.xrefs',
                                    url='add/xrefs/', category='Add'))

        admin.add_view(AddXRefsFamiliesView(name='XRefs Families',
                                            endpoint='admin.add.xrefs_families',
                                            url='add/xrefs_families/', category='Add'))

        # Build Menu
        admin.add_view(BuildCoexpressionClustersView(name='HCCA Clusters',
                                                     endpoint='admin.build.hcca_clusters',
                                                     url='build/hcca_clusters/', category='Build'))

        # Control panel
        admin.add_view(ControlsView(name='Controls', endpoint='admin.controls', url='controls/'))

        # CRUD for various database tables
        admin.add_view(NewsAdminView(News, db.session,
                                     endpoint='admin.news',
                                     url='news/', category='Browse'))
        admin.add_view(SpeciesAdminView(Species, db.session, url='species/', category='Browse'))
        admin.add_view(CladesAdminView(Clade, db.session, url='clades/', category='Browse', name='Clades'))
        admin.add_view(ConditionTissueAdminView(ConditionTissue, db.session, url='condition_tissue/',
                                                category="Browse", name='Condition to Tissue'))

        admin.add_menu_item(MenuLink("------------", class_name="divider", url='#'), target_category='Browse')
        admin.add_menu_item(MenuLink("Methods", class_name="disabled", url="#"), target_category='Browse')

        admin.add_view(GeneFamilyMethodAdminView(GeneFamilyMethod, db.session, url='families/', category="Browse", name='Gene Families'))
        admin.add_view(ExpressionNetworkMethodAdminView(ExpressionNetworkMethod, db.session, url='networks/',
                                                        category="Browse", name='Expression Networks'))
        admin.add_view(CoexpressionClusteringMethodAdminView(CoexpressionClusteringMethod, db.session, url='clusters/',
                                                             category="Browse", name='Coexpression Clustering'))
        admin.add_view(ExpressionSpecificityMethodAdminView(ExpressionSpecificityMethod, db.session, url='specificity/',
                                                            category="Browse", name='Expression Specificity'))

    configure_error_handlers(app)

    configure_hooks(app)

    return app


def configure_extensions(app):
    db.app = app
    db.init_app(app)

    # Enable login manager

    login_manager.init_app(app)
    login_manager.login_view = 'auth.login'

    # Enable cach
    cache.init_app(app)

    # Enable Compress
    compress.init_app(app)

    # Enable HTMLMIN
    htmlmin.init_app(app)

    # Enable DebugToolBar
    toolbar.init_app(app)

    BLAST_ENABLED = app.config['BLAST_ENABLED']

    # Enable BLAST
    if BLAST_ENABLED:
        blast_thread.init_app(app)

    from planet.models.users import User

    @login_manager.user_loader
    def load_user(user_id):
        return User.get(user_id)

    @login_manager.unauthorized_handler
    def unauthorized():
        return render_template('error/403.html'), 403


def configure_blueprints(app):
    # Import controllers and register as blueprint
    from planet.controllers.main import main
    from planet.controllers.auth import auth, no_login
    from planet.controllers.blast import blast
    from planet.controllers.sequence import sequence
    from planet.controllers.species import species
    from planet.controllers.go import go
    from planet.controllers.interpro import interpro
    from planet.controllers.family import family
    from planet.controllers.expression_cluster import expression_cluster
    from planet.controllers.expression_profile import expression_profile
    from planet.controllers.expression_network import expression_network
    from planet.controllers.search import search
    from planet.controllers.help import help
    from planet.controllers.heatmap import heatmap
    from planet.controllers.profile_comparison import profile_comparison
    from planet.controllers.custom_network import custom_network
    from planet.controllers.graph_comparison import graph_comparison
    from planet.controllers.clade import clade
    from planet.controllers.ecc import ecc
    from planet.controllers.specificity_comparison import specificity_comparison
    from planet.controllers.admin.controls import admin_controls

    LOGIN_ENABLED = app.config['LOGIN_ENABLED']
    BLAST_ENABLED = app.config['LOGIN_ENABLED']

    app.register_blueprint(main)
    if LOGIN_ENABLED:
        app.register_blueprint(auth, url_prefix='/auth')
        app.register_blueprint(admin_controls, url_prefix='/admin_controls')
    else:
        app.register_blueprint(no_login, url_prefix='/auth')
        app.register_blueprint(no_login, url_prefix='/admin_controls')

    if BLAST_ENABLED:
        app.register_blueprint(blast, url_prefix='/blast')

    app.register_blueprint(sequence, url_prefix='/sequence')
    app.register_blueprint(species, url_prefix='/species')
    app.register_blueprint(go, url_prefix='/go')
    app.register_blueprint(interpro, url_prefix='/interpro')
    app.register_blueprint(family, url_prefix='/family')
    app.register_blueprint(expression_cluster, url_prefix='/cluster')
    app.register_blueprint(expression_profile, url_prefix='/profile')
    app.register_blueprint(expression_network, url_prefix='/network')
    app.register_blueprint(search, url_prefix='/search')
    app.register_blueprint(help, url_prefix='/help')
    app.register_blueprint(heatmap, url_prefix='/heatmap')
    app.register_blueprint(profile_comparison, url_prefix='/profile_comparison')
    app.register_blueprint(custom_network, url_prefix='/custom_network')
    app.register_blueprint(graph_comparison, url_prefix='/graph_comparison')
    app.register_blueprint(clade, url_prefix='/clade')
    app.register_blueprint(ecc, url_prefix='/ecc')
    app.register_blueprint(specificity_comparison, url_prefix='/specificity_comparison')

def configure_error_handlers(app):
    # Custom error handler for 404 errors

    @app.errorhandler(405)
    def method_not_allowed(e):
        return render_template('error/405.html'), 405

    @app.errorhandler(404)
    def page_not_found(e):
        return render_template('error/404.html'), 404

    @app.errorhandler(403)
    def access_denied(e):
        return render_template('error/403.html'), 403


def configure_hooks(app):
    # Register form for basic searches, needs to be done here as it is included on every page!
    from planet.forms.search import BasicSearchForm

    LOGIN_ENABLED = app.config['LOGIN_ENABLED']
    BLAST_ENABLED = app.config['BLAST_ENABLED']
    TWITTER_HANDLE = app.config['TWITTER_HANDLE'] if 'TWITTER_HANDLE' in app.config.keys() else None

    @app.before_request
    def before_request():
        g.login_enabled = LOGIN_ENABLED
        g.blast_enabled = BLAST_ENABLED
        g.search_form = BasicSearchForm()
        g.twitter_handle = TWITTER_HANDLE
        g.page_items = 30

        g.debug = app.config['DEBUG'] if 'DEBUG' in app.config else False

        if 'GLOB_MSG' in app.config and app.config['GLOB_MSG'] is not None:
            g.msg = app.config['GLOB_MSG']
            g.msg_title = app.config['GLOB_MSG_TITLE'] if 'GLOB_MSG_TITLE' in app.config else 'info'
        else:
            g.msg = None