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changed package name
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proost committed Oct 27, 2017
1 parent db6cbb0 commit 170b476
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File renamed without changes.
138 changes: 69 additions & 69 deletions planet/app.py → conekt/app.py
Expand Up @@ -18,7 +18,7 @@
from flask_login import current_user from flask_login import current_user
from flask_admin import Admin from flask_admin import Admin


from planet.extensions import toolbar, db, login_manager, cache, htmlmin, blast_thread, compress, whooshee, migrate from conekt.extensions import toolbar, db, login_manager, cache, htmlmin, blast_thread, compress, whooshee, migrate




def create_app(config): def create_app(config):
Expand Down Expand Up @@ -68,7 +68,7 @@ def configure_extensions(app):
if BLAST_ENABLED: if BLAST_ENABLED:
blast_thread.init_app(app) blast_thread.init_app(app)


from planet.models.users import User from conekt.models.users import User


@login_manager.user_loader @login_manager.user_loader
def load_user(user_id): def load_user(user_id):
Expand All @@ -81,28 +81,28 @@ def unauthorized():


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


LOGIN_ENABLED = app.config['LOGIN_ENABLED'] LOGIN_ENABLED = app.config['LOGIN_ENABLED']
BLAST_ENABLED = app.config['BLAST_ENABLED'] BLAST_ENABLED = app.config['BLAST_ENABLED']
Expand Down Expand Up @@ -142,50 +142,50 @@ def configure_admin_panel(app):
# Admin panel # Admin panel
LOGIN_ENABLED = app.config['LOGIN_ENABLED'] LOGIN_ENABLED = app.config['LOGIN_ENABLED']
if LOGIN_ENABLED: if LOGIN_ENABLED:
from planet.controllers.admin.views import MyAdminIndexView from conekt.controllers.admin.views import MyAdminIndexView


from planet.controllers.admin.views.ecc import ECCView from conekt.controllers.admin.views.ecc import ECCView
from planet.controllers.admin.views.sequences import AddSequenceDescriptionsView from conekt.controllers.admin.views.sequences import AddSequenceDescriptionsView
from planet.controllers.admin.views.expression_profiles import AddExpressionProfilesView from conekt.controllers.admin.views.expression_profiles import AddExpressionProfilesView
from planet.controllers.admin.views.expression_networks import AddCoexpressionNetworkView from conekt.controllers.admin.views.expression_networks import AddCoexpressionNetworkView
from planet.controllers.admin.views.expression_networks import ExpressionNetworkMethodAdminView from conekt.controllers.admin.views.expression_networks import ExpressionNetworkMethodAdminView
from planet.controllers.admin.views.expression_specificity import AddSpecificityView from conekt.controllers.admin.views.expression_specificity import AddSpecificityView
from planet.controllers.admin.views.expression_specificity import ConditionTissueAdminView from conekt.controllers.admin.views.expression_specificity import ConditionTissueAdminView
from planet.controllers.admin.views.expression_specificity import ExpressionSpecificityMethodAdminView from conekt.controllers.admin.views.expression_specificity import ExpressionSpecificityMethodAdminView
from planet.controllers.admin.views.go_interpro import AddInterProView from conekt.controllers.admin.views.go_interpro import AddInterProView
from planet.controllers.admin.views.go_interpro import AddGOView from conekt.controllers.admin.views.go_interpro import AddGOView
from planet.controllers.admin.views.go_interpro import AddFunctionalDataView from conekt.controllers.admin.views.go_interpro import AddFunctionalDataView
from planet.controllers.admin.views.go_interpro import GOEnrichmentView from conekt.controllers.admin.views.go_interpro import GOEnrichmentView
from planet.controllers.admin.views.go_interpro import PredictGOView from conekt.controllers.admin.views.go_interpro import PredictGOView
from planet.controllers.admin.views.families import AddFamiliesView, AddFamilyAnnotationView from conekt.controllers.admin.views.families import AddFamiliesView, AddFamilyAnnotationView
from planet.controllers.admin.views.families import GeneFamilyMethodAdminView from conekt.controllers.admin.views.families import GeneFamilyMethodAdminView
from planet.controllers.admin.views.species import AddSpeciesView from conekt.controllers.admin.views.species import AddSpeciesView
from planet.controllers.admin.views.species import SpeciesAdminView from conekt.controllers.admin.views.species import SpeciesAdminView
from planet.controllers.admin.views.trees import AddTreesView from conekt.controllers.admin.views.trees import AddTreesView
from planet.controllers.admin.views.expression_clusters import BuildNeighorhoodToClustersView from conekt.controllers.admin.views.expression_clusters import BuildNeighorhoodToClustersView
from planet.controllers.admin.views.expression_clusters import BuildCoexpressionClustersView from conekt.controllers.admin.views.expression_clusters import BuildCoexpressionClustersView
from planet.controllers.admin.views.expression_clusters import AddCoexpressionClustersView from conekt.controllers.admin.views.expression_clusters import AddCoexpressionClustersView
from planet.controllers.admin.views.expression_clusters import ClusterSimilaritiesView from conekt.controllers.admin.views.expression_clusters import ClusterSimilaritiesView
from planet.controllers.admin.views.expression_clusters import CoexpressionClusteringMethodAdminView from conekt.controllers.admin.views.expression_clusters import CoexpressionClusteringMethodAdminView
from planet.controllers.admin.views.clades import AddCladesView from conekt.controllers.admin.views.clades import AddCladesView
from planet.controllers.admin.views.clades import CladesAdminView from conekt.controllers.admin.views.clades import CladesAdminView
from planet.controllers.admin.views.xrefs import AddXRefsFamiliesView from conekt.controllers.admin.views.xrefs import AddXRefsFamiliesView
from planet.controllers.admin.views.xrefs import AddXRefsView from conekt.controllers.admin.views.xrefs import AddXRefsView
from planet.controllers.admin.views.controls import ControlsView from conekt.controllers.admin.views.controls import ControlsView
from planet.controllers.admin.views.news import NewsAdminView from conekt.controllers.admin.views.news import NewsAdminView
from planet.controllers.admin.views.trees import TreeMethodAdminView from conekt.controllers.admin.views.trees import TreeMethodAdminView
from planet.controllers.admin.views.trees import ReconcileTreesView from conekt.controllers.admin.views.trees import ReconcileTreesView


from planet.models.users import User from conekt.models.users import User
from planet.models.species import Species from conekt.models.species import Species
from planet.models.gene_families import GeneFamilyMethod from conekt.models.gene_families import GeneFamilyMethod
from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod
from planet.models.expression.networks import ExpressionNetworkMethod from conekt.models.expression.networks import ExpressionNetworkMethod
from planet.models.expression.specificity import ExpressionSpecificityMethod from conekt.models.expression.specificity import ExpressionSpecificityMethod
from planet.models.condition_tissue import ConditionTissue from conekt.models.condition_tissue import ConditionTissue
from planet.models.clades import Clade from conekt.models.clades import Clade
from planet.models.news import News from conekt.models.news import News
from planet.models.trees import TreeMethod from conekt.models.trees import TreeMethod


admin = Admin(template_mode='bootstrap3', base_template='admin/my_base.html') admin = Admin(template_mode='bootstrap3', base_template='admin/my_base.html')


Expand Down Expand Up @@ -344,7 +344,7 @@ def access_denied(e):


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


LOGIN_ENABLED = app.config['LOGIN_ENABLED'] LOGIN_ENABLED = app.config['LOGIN_ENABLED']
BLAST_ENABLED = app.config['BLAST_ENABLED'] BLAST_ENABLED = app.config['BLAST_ENABLED']
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File renamed without changes.
File renamed without changes.
@@ -1,9 +1,9 @@
from flask import flash, url_for from flask import flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.models.blast_db import BlastDB from conekt.models.blast_db import BlastDB




@admin_controls.route('/build_blast_db') @admin_controls.route('/build_blast_db')
Expand Down
@@ -1,9 +1,9 @@
from flask import flash, url_for from flask import flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet import cache from conekt import cache
from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls




@admin_controls.route('/clear/cache') @admin_controls.route('/clear/cache')
Expand Down
@@ -1,13 +1,13 @@
import json import json


from flask import flash, url_for, request from flask import flash, url_for, request
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_clades import AddCladesForm from conekt.forms.admin.add_clades import AddCladesForm
from planet.models.clades import Clade from conekt.models.clades import Clade




@admin_controls.route('/update/clades') @admin_controls.route('/update/clades')
Expand Down
@@ -1,13 +1,13 @@
from flask import flash, url_for from flask import flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod
from planet.models.expression.networks import ExpressionNetworkMethod from conekt.models.expression.networks import ExpressionNetworkMethod
from planet.models.gene_families import GeneFamilyMethod from conekt.models.gene_families import GeneFamilyMethod
from planet.models.go import GO from conekt.models.go import GO
from planet.models.species import Species from conekt.models.species import Species




@admin_controls.route('/update/counts') @admin_controls.route('/update/counts')
Expand Down
@@ -1,9 +1,9 @@
from flask import flash, url_for from flask import flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.models.expression.networks import ExpressionNetworkMethod from conekt.models.expression.networks import ExpressionNetworkMethod




@admin_controls.route('/calculate_ecc/<int:gf_method_id>') @admin_controls.route('/calculate_ecc/<int:gf_method_id>')
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Expand Up @@ -2,16 +2,16 @@
from tempfile import mkstemp from tempfile import mkstemp


from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_coexpression_clusters import AddCoexpressionClustersForm from conekt.forms.admin.add_coexpression_clusters import AddCoexpressionClustersForm
from planet.forms.admin.build_coexpression_clusters import BuildCoexpressionClustersForm from conekt.forms.admin.build_coexpression_clusters import BuildCoexpressionClustersForm
from planet.forms.admin.neighborhood_to_clusters import NeighborhoodToClustersForm from conekt.forms.admin.neighborhood_to_clusters import NeighborhoodToClustersForm
from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod, CoexpressionCluster from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod, CoexpressionCluster
from planet.models.relationships.cluster_similarity import CoexpressionClusterSimilarity from conekt.models.relationships.cluster_similarity import CoexpressionClusterSimilarity




@admin_controls.route('/build/neighborhoods_to_clusters', methods=['POST']) @admin_controls.route('/build/neighborhoods_to_clusters', methods=['POST'])
Expand Down
Expand Up @@ -2,13 +2,13 @@
from tempfile import mkstemp from tempfile import mkstemp


from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_coexpression_network import AddCoexpressionNetworkForm from conekt.forms.admin.add_coexpression_network import AddCoexpressionNetworkForm
from planet.models.expression.networks import ExpressionNetwork from conekt.models.expression.networks import ExpressionNetwork




@admin_controls.route('/add/coexpression_network', methods=['POST']) @admin_controls.route('/add/coexpression_network', methods=['POST'])
Expand Down
Expand Up @@ -2,13 +2,13 @@
from tempfile import mkstemp from tempfile import mkstemp


from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_expression_profiles import AddExpressionProfilesForm from conekt.forms.admin.add_expression_profiles import AddExpressionProfilesForm
from planet.models.expression.profiles import ExpressionProfile from conekt.models.expression.profiles import ExpressionProfile




@admin_controls.route('/add/expression_profile', methods=['POST']) @admin_controls.route('/add/expression_profile', methods=['POST'])
Expand Down
@@ -1,12 +1,12 @@
from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_expression_specificity import AddConditionSpecificityForm, AddTissueSpecificityForm from conekt.forms.admin.add_expression_specificity import AddConditionSpecificityForm, AddTissueSpecificityForm
from planet.models.condition_tissue import ConditionTissue from conekt.models.condition_tissue import ConditionTissue
from planet.models.expression.specificity import ExpressionSpecificityMethod from conekt.models.expression.specificity import ExpressionSpecificityMethod




@admin_controls.route('/add/condition_specificity', methods=['POST']) @admin_controls.route('/add/condition_specificity', methods=['POST'])
Expand Down
Expand Up @@ -2,13 +2,13 @@
from tempfile import mkstemp from tempfile import mkstemp


from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_family import AddFamiliesForm from conekt.forms.admin.add_family import AddFamiliesForm
from planet.models.gene_families import GeneFamily, GeneFamilyMethod from conekt.models.gene_families import GeneFamily, GeneFamilyMethod




@admin_controls.route('/add/family', methods=['POST']) @admin_controls.route('/add/family', methods=['POST'])
Expand Down
@@ -1,11 +1,11 @@
import os import os


from flask import current_app, flash, url_for from flask import current_app, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.ftp import export_coding_sequences, export_protein_sequences, export_go_annotation, \ from conekt.ftp import export_coding_sequences, export_protein_sequences, export_go_annotation, \
export_interpro_annotation, export_families, export_coexpression_clusters, export_expression_networks export_interpro_annotation, export_families, export_coexpression_clusters, export_expression_networks




Expand Down
Expand Up @@ -2,19 +2,19 @@
from tempfile import mkstemp from tempfile import mkstemp


from flask import request, flash, url_for from flask import request, flash, url_for
from planet.extensions import admin_required from conekt.extensions import admin_required
from markupsafe import Markup from markupsafe import Markup
from werkzeug.exceptions import abort from werkzeug.exceptions import abort
from werkzeug.utils import redirect from werkzeug.utils import redirect


from planet.controllers.admin.controls import admin_controls from conekt.controllers.admin.controls import admin_controls
from planet.forms.admin.add_go_interpro import AddFunctionalDataForm from conekt.forms.admin.add_go_interpro import AddFunctionalDataForm
from planet.forms.admin.predict_go import PredictGOForm from conekt.forms.admin.predict_go import PredictGOForm
from planet.forms.admin.add_go_sequences import AddGOForm from conekt.forms.admin.add_go_sequences import AddGOForm
from planet.forms.admin.add_interpro_sequences import AddInterProForm from conekt.forms.admin.add_interpro_sequences import AddInterProForm
from planet.models.expression.coexpression_clusters import CoexpressionCluster from conekt.models.expression.coexpression_clusters import CoexpressionCluster
from planet.models.go import GO from conekt.models.go import GO
from planet.models.interpro import Interpro from conekt.models.interpro import Interpro




@admin_controls.route('/add/functional_data', methods=['POST']) @admin_controls.route('/add/functional_data', methods=['POST'])
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