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changed package name

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proost committed Oct 27, 2017
1 parent db6cbb0 commit 170b47692bdbe2133e8ca9b99f8cc40742dc1d44
Showing 321 changed files with 496 additions and 496 deletions.
File renamed without changes.
@@ -18,7 +18,7 @@
from flask_login import current_user
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):
@@ -68,7 +68,7 @@ def configure_extensions(app):
if BLAST_ENABLED:
blast_thread.init_app(app)

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

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

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
from planet.controllers.tree import tree
from conekt.controllers.main import main
from conekt.controllers.auth import auth, no_login
from conekt.controllers.blast import blast
from conekt.controllers.sequence import sequence
from conekt.controllers.species import species
from conekt.controllers.go import go
from conekt.controllers.interpro import interpro
from conekt.controllers.family import family
from conekt.controllers.expression_cluster import expression_cluster
from conekt.controllers.expression_profile import expression_profile
from conekt.controllers.expression_network import expression_network
from conekt.controllers.search import search
from conekt.controllers.help import help
from conekt.controllers.heatmap import heatmap
from conekt.controllers.profile_comparison import profile_comparison
from conekt.controllers.custom_network import custom_network
from conekt.controllers.graph_comparison import graph_comparison
from conekt.controllers.clade import clade
from conekt.controllers.ecc import ecc
from conekt.controllers.specificity_comparison import specificity_comparison
from conekt.controllers.admin.controls import admin_controls
from conekt.controllers.tree import tree

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

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

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

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

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

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

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

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
from conekt.forms.search import BasicSearchForm

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

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


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

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


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

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.utils import redirect

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


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

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


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

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


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

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.utils import redirect

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


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

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.utils import redirect

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


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

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.utils import redirect

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


@admin_controls.route('/add/expression_profile', methods=['POST'])
@@ -1,12 +1,12 @@
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.utils import redirect

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


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

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.utils import redirect

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


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

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


@@ -2,19 +2,19 @@
from tempfile import mkstemp

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

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


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

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