changed package name

planet/app.py → conekt/app.py

@@ -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']

planet/controllers/admin/controls/blast.py → conekt/controllers/admin/controls/blast.py

@@ -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')

planet/controllers/admin/controls/cache.py → conekt/controllers/admin/controls/cache.py

@@ -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')

planet/controllers/admin/controls/clades.py → conekt/controllers/admin/controls/clades.py

@@ -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')

planet/controllers/admin/controls/counts.py → conekt/controllers/admin/controls/counts.py

@@ -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')

planet/controllers/admin/controls/ecc.py → conekt/controllers/admin/controls/ecc.py

@@ -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>')

planet/controllers/admin/controls/expression_clusters.py → conekt/controllers/admin/controls/expression_clusters.py

@@ -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'])

planet/controllers/admin/controls/expression_networks.py → conekt/controllers/admin/controls/expression_networks.py

@@ -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'])

planet/controllers/admin/controls/expression_profiles.py → conekt/controllers/admin/controls/expression_profiles.py

@@ -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'])

planet/controllers/admin/controls/expression_specificity.py → conekt/controllers/admin/controls/expression_specificity.py

@@ -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'])

planet/controllers/admin/controls/families.py → conekt/controllers/admin/controls/families.py

@@ -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'])

planet/controllers/admin/controls/ftp.py → conekt/controllers/admin/controls/ftp.py

@@ -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
 
 

planet/controllers/admin/controls/go_interpro.py → conekt/controllers/admin/controls/go_interpro.py

@@ -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'])