diff --git a/planet/__init__.py b/conekt/__init__.py similarity index 100% rename from planet/__init__.py rename to conekt/__init__.py diff --git a/planet/app.py b/conekt/app.py similarity index 79% rename from planet/app.py rename to conekt/app.py index 4457a9f..ec3a1bb 100644 --- a/planet/app.py +++ b/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'] diff --git a/planet/controllers/__init__.py b/conekt/controllers/__init__.py similarity index 100% rename from planet/controllers/__init__.py rename to conekt/controllers/__init__.py diff --git a/planet/controllers/admin/__init__.py b/conekt/controllers/admin/__init__.py similarity index 100% rename from planet/controllers/admin/__init__.py rename to conekt/controllers/admin/__init__.py diff --git a/planet/controllers/admin/controls/__init__.py b/conekt/controllers/admin/controls/__init__.py similarity index 100% rename from planet/controllers/admin/controls/__init__.py rename to conekt/controllers/admin/controls/__init__.py diff --git a/planet/controllers/admin/controls/blast.py b/conekt/controllers/admin/controls/blast.py similarity index 73% rename from planet/controllers/admin/controls/blast.py rename to conekt/controllers/admin/controls/blast.py index 24e1939..6c04d54 100644 --- a/planet/controllers/admin/controls/blast.py +++ b/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') diff --git a/planet/controllers/admin/controls/blueprint.py b/conekt/controllers/admin/controls/blueprint.py similarity index 100% rename from planet/controllers/admin/controls/blueprint.py rename to conekt/controllers/admin/controls/blueprint.py diff --git a/planet/controllers/admin/controls/cache.py b/conekt/controllers/admin/controls/cache.py similarity index 71% rename from planet/controllers/admin/controls/cache.py rename to conekt/controllers/admin/controls/cache.py index 24eb486..1a51858 100644 --- a/planet/controllers/admin/controls/cache.py +++ b/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') diff --git a/planet/controllers/admin/controls/clades.py b/conekt/controllers/admin/controls/clades.py similarity index 87% rename from planet/controllers/admin/controls/clades.py rename to conekt/controllers/admin/controls/clades.py index 3b706df..f1d732b 100644 --- a/planet/controllers/admin/controls/clades.py +++ b/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') diff --git a/planet/controllers/admin/controls/counts.py b/conekt/controllers/admin/controls/counts.py similarity index 79% rename from planet/controllers/admin/controls/counts.py rename to conekt/controllers/admin/controls/counts.py index 4ab80c3..c5bd34d 100644 --- a/planet/controllers/admin/controls/counts.py +++ b/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') diff --git a/planet/controllers/admin/controls/ecc.py b/conekt/controllers/admin/controls/ecc.py similarity index 64% rename from planet/controllers/admin/controls/ecc.py rename to conekt/controllers/admin/controls/ecc.py index c68b78d..f823a55 100644 --- a/planet/controllers/admin/controls/ecc.py +++ b/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/') diff --git a/planet/controllers/admin/controls/expression_clusters.py b/conekt/controllers/admin/controls/expression_clusters.py similarity index 90% rename from planet/controllers/admin/controls/expression_clusters.py rename to conekt/controllers/admin/controls/expression_clusters.py index ee44b01..e21e835 100644 --- a/planet/controllers/admin/controls/expression_clusters.py +++ b/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']) diff --git a/planet/controllers/admin/controls/expression_networks.py b/conekt/controllers/admin/controls/expression_networks.py similarity index 87% rename from planet/controllers/admin/controls/expression_networks.py rename to conekt/controllers/admin/controls/expression_networks.py index fb88005..19b0d70 100644 --- a/planet/controllers/admin/controls/expression_networks.py +++ b/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']) diff --git a/planet/controllers/admin/controls/expression_profiles.py b/conekt/controllers/admin/controls/expression_profiles.py similarity index 90% rename from planet/controllers/admin/controls/expression_profiles.py rename to conekt/controllers/admin/controls/expression_profiles.py index a46fffa..b4fa58f 100644 --- a/planet/controllers/admin/controls/expression_profiles.py +++ b/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']) diff --git a/planet/controllers/admin/controls/expression_specificity.py b/conekt/controllers/admin/controls/expression_specificity.py similarity index 90% rename from planet/controllers/admin/controls/expression_specificity.py rename to conekt/controllers/admin/controls/expression_specificity.py index 55c5d0d..a75211f 100644 --- a/planet/controllers/admin/controls/expression_specificity.py +++ b/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']) diff --git a/planet/controllers/admin/controls/families.py b/conekt/controllers/admin/controls/families.py similarity index 91% rename from planet/controllers/admin/controls/families.py rename to conekt/controllers/admin/controls/families.py index 77419ac..1bfda4a 100644 --- a/planet/controllers/admin/controls/families.py +++ b/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']) diff --git a/planet/controllers/admin/controls/ftp.py b/conekt/controllers/admin/controls/ftp.py similarity index 82% rename from planet/controllers/admin/controls/ftp.py rename to conekt/controllers/admin/controls/ftp.py index 0543bbc..d4589ce 100644 --- a/planet/controllers/admin/controls/ftp.py +++ b/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 diff --git a/planet/controllers/admin/controls/go_interpro.py b/conekt/controllers/admin/controls/go_interpro.py similarity index 92% rename from planet/controllers/admin/controls/go_interpro.py rename to conekt/controllers/admin/controls/go_interpro.py index ea461aa..94f24e2 100644 --- a/planet/controllers/admin/controls/go_interpro.py +++ b/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']) diff --git a/planet/controllers/admin/controls/sequences.py b/conekt/controllers/admin/controls/sequences.py similarity index 83% rename from planet/controllers/admin/controls/sequences.py rename to conekt/controllers/admin/controls/sequences.py index 4217589..c735c19 100644 --- a/planet/controllers/admin/controls/sequences.py +++ b/conekt/controllers/admin/controls/sequences.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_sequence_descriptions import AddSequenceDescriptionsForm -from planet.models.sequences import Sequence +from conekt.controllers.admin.controls import admin_controls +from conekt.forms.admin.add_sequence_descriptions import AddSequenceDescriptionsForm +from conekt.models.sequences import Sequence @admin_controls.route('/add/sequence_descriptions', methods=['POST']) diff --git a/planet/controllers/admin/controls/species.py b/conekt/controllers/admin/controls/species.py similarity index 88% rename from planet/controllers/admin/controls/species.py rename to conekt/controllers/admin/controls/species.py index 07ef2c9..623e967 100644 --- a/planet/controllers/admin/controls/species.py +++ b/conekt/controllers/admin/controls/species.py @@ -2,14 +2,14 @@ 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_species import AddSpeciesForm -from planet.models.sequences import Sequence -from planet.models.species import Species +from conekt.controllers.admin.controls import admin_controls +from conekt.forms.admin.add_species import AddSpeciesForm +from conekt.models.sequences import Sequence +from conekt.models.species import Species @admin_controls.route('/add/species', methods=['POST']) diff --git a/planet/controllers/admin/controls/trees.py b/conekt/controllers/admin/controls/trees.py similarity index 92% rename from planet/controllers/admin/controls/trees.py rename to conekt/controllers/admin/controls/trees.py index 1e5fd86..c352ebe 100644 --- a/planet/controllers/admin/controls/trees.py +++ b/conekt/controllers/admin/controls/trees.py @@ -3,20 +3,20 @@ 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 import newick -from planet import db +from conekt import db -from planet.controllers.admin.controls import admin_controls -from planet.forms.admin.add_trees import AddTreesForm -from planet.forms.admin.reconcile_trees import ReconcileTreesForm -from planet.models.trees import TreeMethod -from planet.models.trees import Tree -from planet.models.gene_families import GeneFamily +from conekt.controllers.admin.controls import admin_controls +from conekt.forms.admin.add_trees import AddTreesForm +from conekt.forms.admin.reconcile_trees import ReconcileTreesForm +from conekt.models.trees import TreeMethod +from conekt.models.trees import Tree +from conekt.models.gene_families import GeneFamily def __read_sequence_ids(data): diff --git a/planet/controllers/admin/controls/whooshee.py b/conekt/controllers/admin/controls/whooshee.py similarity index 70% rename from planet/controllers/admin/controls/whooshee.py rename to conekt/controllers/admin/controls/whooshee.py index 056651c..30bd603 100644 --- a/planet/controllers/admin/controls/whooshee.py +++ b/conekt/controllers/admin/controls/whooshee.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 whooshee -from planet.controllers.admin.controls import admin_controls +from conekt import whooshee +from conekt.controllers.admin.controls import admin_controls @admin_controls.route('/reindex/whooshee') diff --git a/planet/controllers/admin/controls/xrefs.py b/conekt/controllers/admin/controls/xrefs.py similarity index 93% rename from planet/controllers/admin/controls/xrefs.py rename to conekt/controllers/admin/controls/xrefs.py index 7492e77..72590fe 100644 --- a/planet/controllers/admin/controls/xrefs.py +++ b/conekt/controllers/admin/controls/xrefs.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_xrefs import AddXRefsForm, AddXRefsFamiliesForm -from planet.models.xrefs import XRef +from conekt.controllers.admin.controls import admin_controls +from conekt.forms.admin.add_xrefs import AddXRefsForm, AddXRefsFamiliesForm +from conekt.models.xrefs import XRef @admin_controls.route('/add/xrefs', methods=['POST']) diff --git a/planet/controllers/admin/views/__init__.py b/conekt/controllers/admin/views/__init__.py similarity index 100% rename from planet/controllers/admin/views/__init__.py rename to conekt/controllers/admin/views/__init__.py diff --git a/planet/controllers/admin/views/clades.py b/conekt/controllers/admin/views/clades.py similarity index 71% rename from planet/controllers/admin/views/clades.py rename to conekt/controllers/admin/views/clades.py index 3373685..40d9eec 100644 --- a/planet/controllers/admin/views/clades.py +++ b/conekt/controllers/admin/views/clades.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView, AdminBaseView -from planet.forms.admin.add_clades import AddCladesForm +from conekt.controllers.admin.views import MyModelView, AdminBaseView +from conekt.forms.admin.add_clades import AddCladesForm class CladesAdminView(MyModelView): diff --git a/planet/controllers/admin/views/controls.py b/conekt/controllers/admin/views/controls.py similarity index 87% rename from planet/controllers/admin/views/controls.py rename to conekt/controllers/admin/views/controls.py index ec6fe7f..b16352f 100644 --- a/planet/controllers/admin/views/controls.py +++ b/conekt/controllers/admin/views/controls.py @@ -2,8 +2,8 @@ from flask_admin import expose from markupsafe import Markup -from planet.controllers.admin.views import AdminBaseView -from planet.models.gene_families import GeneFamilyMethod +from conekt.controllers.admin.views import AdminBaseView +from conekt.models.gene_families import GeneFamilyMethod class ControlsView(AdminBaseView): diff --git a/planet/controllers/admin/views/ecc.py b/conekt/controllers/admin/views/ecc.py similarity index 82% rename from planet/controllers/admin/views/ecc.py rename to conekt/controllers/admin/views/ecc.py index e925a88..fbea806 100644 --- a/planet/controllers/admin/views/ecc.py +++ b/conekt/controllers/admin/views/ecc.py @@ -2,8 +2,8 @@ from flask_admin import expose from markupsafe import Markup -from planet.controllers.admin.views import AdminBaseView -from planet.models.gene_families import GeneFamilyMethod +from conekt.controllers.admin.views import AdminBaseView +from conekt.models.gene_families import GeneFamilyMethod class ECCView(AdminBaseView): diff --git a/planet/controllers/admin/views/expression_clusters.py b/conekt/controllers/admin/views/expression_clusters.py similarity index 86% rename from planet/controllers/admin/views/expression_clusters.py rename to conekt/controllers/admin/views/expression_clusters.py index 590af25..5c0a4a9 100644 --- a/planet/controllers/admin/views/expression_clusters.py +++ b/conekt/controllers/admin/views/expression_clusters.py @@ -2,11 +2,11 @@ from flask_admin import expose from markupsafe import Markup -from planet.controllers.admin.views import MyModelView, AdminBaseView -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.gene_families import GeneFamilyMethod +from conekt.controllers.admin.views import MyModelView, AdminBaseView +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.gene_families import GeneFamilyMethod class CoexpressionClusteringMethodAdminView(MyModelView): diff --git a/planet/controllers/admin/views/expression_networks.py b/conekt/controllers/admin/views/expression_networks.py similarity index 84% rename from planet/controllers/admin/views/expression_networks.py rename to conekt/controllers/admin/views/expression_networks.py index 6263fcd..566fa1e 100644 --- a/planet/controllers/admin/views/expression_networks.py +++ b/conekt/controllers/admin/views/expression_networks.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView, AdminBaseView -from planet.forms.admin.add_coexpression_network import AddCoexpressionNetworkForm +from conekt.controllers.admin.views import MyModelView, AdminBaseView +from conekt.forms.admin.add_coexpression_network import AddCoexpressionNetworkForm class ExpressionNetworkMethodAdminView(MyModelView): diff --git a/planet/controllers/admin/views/expression_profiles.py b/conekt/controllers/admin/views/expression_profiles.py similarity index 73% rename from planet/controllers/admin/views/expression_profiles.py rename to conekt/controllers/admin/views/expression_profiles.py index f5a3b28..e655646 100644 --- a/planet/controllers/admin/views/expression_profiles.py +++ b/conekt/controllers/admin/views/expression_profiles.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import AdminBaseView -from planet.forms.admin.add_expression_profiles import AddExpressionProfilesForm +from conekt.controllers.admin.views import AdminBaseView +from conekt.forms.admin.add_expression_profiles import AddExpressionProfilesForm class AddExpressionProfilesView(AdminBaseView): diff --git a/planet/controllers/admin/views/expression_specificity.py b/conekt/controllers/admin/views/expression_specificity.py similarity index 86% rename from planet/controllers/admin/views/expression_specificity.py rename to conekt/controllers/admin/views/expression_specificity.py index 00c254c..7bedacb 100644 --- a/planet/controllers/admin/views/expression_specificity.py +++ b/conekt/controllers/admin/views/expression_specificity.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView, AdminBaseView -from planet.forms.admin.add_expression_specificity import AddConditionSpecificityForm, AddTissueSpecificityForm +from conekt.controllers.admin.views import MyModelView, AdminBaseView +from conekt.forms.admin.add_expression_specificity import AddConditionSpecificityForm, AddTissueSpecificityForm class ExpressionSpecificityMethodAdminView(MyModelView): diff --git a/planet/controllers/admin/views/families.py b/conekt/controllers/admin/views/families.py similarity index 82% rename from planet/controllers/admin/views/families.py rename to conekt/controllers/admin/views/families.py index b5f5a59..1663611 100644 --- a/planet/controllers/admin/views/families.py +++ b/conekt/controllers/admin/views/families.py @@ -1,8 +1,8 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView, AdminBaseView -from planet.models.gene_families import GeneFamilyMethod -from planet.forms.admin.add_family import AddFamiliesForm +from conekt.controllers.admin.views import MyModelView, AdminBaseView +from conekt.models.gene_families import GeneFamilyMethod +from conekt.forms.admin.add_family import AddFamiliesForm class GeneFamilyMethodAdminView(MyModelView): diff --git a/planet/controllers/admin/views/go_interpro.py b/conekt/controllers/admin/views/go_interpro.py similarity index 85% rename from planet/controllers/admin/views/go_interpro.py rename to conekt/controllers/admin/views/go_interpro.py index 24f9e10..0ed63be 100644 --- a/planet/controllers/admin/views/go_interpro.py +++ b/conekt/controllers/admin/views/go_interpro.py @@ -2,11 +2,11 @@ from flask_admin import expose from markupsafe import Markup -from planet.controllers.admin.views import AdminBaseView -from planet.forms.admin.add_go_interpro import AddFunctionalDataForm -from planet.forms.admin.add_go_sequences import AddGOForm -from planet.forms.admin.predict_go import PredictGOForm -from planet.forms.admin.add_interpro_sequences import AddInterProForm +from conekt.controllers.admin.views import AdminBaseView +from conekt.forms.admin.add_go_interpro import AddFunctionalDataForm +from conekt.forms.admin.add_go_sequences import AddGOForm +from conekt.forms.admin.predict_go import PredictGOForm +from conekt.forms.admin.add_interpro_sequences import AddInterProForm class GOEnrichmentView(AdminBaseView): diff --git a/planet/controllers/admin/views/news.py b/conekt/controllers/admin/views/news.py similarity index 77% rename from planet/controllers/admin/views/news.py rename to conekt/controllers/admin/views/news.py index 580ffb0..7aceabb 100644 --- a/planet/controllers/admin/views/news.py +++ b/conekt/controllers/admin/views/news.py @@ -1,4 +1,4 @@ -from planet.controllers.admin.views import MyModelView +from conekt.controllers.admin.views import MyModelView class NewsAdminView(MyModelView): diff --git a/planet/controllers/admin/views/sequences.py b/conekt/controllers/admin/views/sequences.py similarity index 72% rename from planet/controllers/admin/views/sequences.py rename to conekt/controllers/admin/views/sequences.py index 90fd6b5..5526468 100644 --- a/planet/controllers/admin/views/sequences.py +++ b/conekt/controllers/admin/views/sequences.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import AdminBaseView -from planet.forms.admin.add_sequence_descriptions import AddSequenceDescriptionsForm +from conekt.controllers.admin.views import AdminBaseView +from conekt.forms.admin.add_sequence_descriptions import AddSequenceDescriptionsForm class AddSequenceDescriptionsView(AdminBaseView): diff --git a/planet/controllers/admin/views/species.py b/conekt/controllers/admin/views/species.py similarity index 84% rename from planet/controllers/admin/views/species.py rename to conekt/controllers/admin/views/species.py index 09e79f0..0bcbfc6 100644 --- a/planet/controllers/admin/views/species.py +++ b/conekt/controllers/admin/views/species.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView, AdminBaseView -from planet.forms.admin.add_species import AddSpeciesForm +from conekt.controllers.admin.views import MyModelView, AdminBaseView +from conekt.forms.admin.add_species import AddSpeciesForm class SpeciesAdminView(MyModelView): diff --git a/planet/controllers/admin/views/trees.py b/conekt/controllers/admin/views/trees.py similarity index 82% rename from planet/controllers/admin/views/trees.py rename to conekt/controllers/admin/views/trees.py index 8d7a5f6..95f5967 100644 --- a/planet/controllers/admin/views/trees.py +++ b/conekt/controllers/admin/views/trees.py @@ -1,8 +1,8 @@ from flask_admin import expose -from planet.controllers.admin.views import MyModelView,AdminBaseView -from planet.forms.admin.add_trees import AddTreesForm -from planet.forms.admin.reconcile_trees import ReconcileTreesForm +from conekt.controllers.admin.views import MyModelView,AdminBaseView +from conekt.forms.admin.add_trees import AddTreesForm +from conekt.forms.admin.reconcile_trees import ReconcileTreesForm class TreeMethodAdminView(MyModelView): diff --git a/planet/controllers/admin/views/xrefs.py b/conekt/controllers/admin/views/xrefs.py similarity index 82% rename from planet/controllers/admin/views/xrefs.py rename to conekt/controllers/admin/views/xrefs.py index 0038f37..6e94253 100644 --- a/planet/controllers/admin/views/xrefs.py +++ b/conekt/controllers/admin/views/xrefs.py @@ -1,7 +1,7 @@ from flask_admin import expose -from planet.controllers.admin.views import AdminBaseView -from planet.forms.admin.add_xrefs import AddXRefsForm, AddXRefsFamiliesForm +from conekt.controllers.admin.views import AdminBaseView +from conekt.forms.admin.add_xrefs import AddXRefsForm, AddXRefsFamiliesForm class AddXRefsView(AdminBaseView): diff --git a/planet/controllers/auth.py b/conekt/controllers/auth.py similarity index 94% rename from planet/controllers/auth.py rename to conekt/controllers/auth.py index 93aaac1..bf0c75b 100644 --- a/planet/controllers/auth.py +++ b/conekt/controllers/auth.py @@ -1,12 +1,12 @@ from flask import g, Blueprint, flash, redirect, url_for, render_template, request from flask_login import current_user, login_user, logout_user, login_required -from planet import login_manager, db -from planet.helpers.url import is_safe_url -from planet.models.users import User -from planet.forms.login import LoginForm -from planet.forms.registration import RegistrationForm -from planet import db +from conekt import login_manager, db +from conekt.helpers.url import is_safe_url +from conekt.models.users import User +from conekt.forms.login import LoginForm +from conekt.forms.registration import RegistrationForm +from conekt import db from datetime import datetime diff --git a/planet/controllers/blast.py b/conekt/controllers/blast.py similarity index 96% rename from planet/controllers/blast.py rename to conekt/controllers/blast.py index 3bbd6db..75463a0 100644 --- a/planet/controllers/blast.py +++ b/conekt/controllers/blast.py @@ -1,9 +1,9 @@ from flask import Blueprint, current_app, Response, redirect, url_for, request, render_template, flash from sqlalchemy.sql.expression import func -from planet import blast_thread -from planet.models.sequences import Sequence -from planet.forms.blast import BlastForm +from conekt import blast_thread +from conekt.models.sequences import Sequence +from conekt.forms.blast import BlastForm import os import json diff --git a/planet/controllers/clade.py b/conekt/controllers/clade.py similarity index 94% rename from planet/controllers/clade.py rename to conekt/controllers/clade.py index 80fd209..1b74e2b 100644 --- a/planet/controllers/clade.py +++ b/conekt/controllers/clade.py @@ -1,10 +1,10 @@ from flask import Blueprint, redirect, url_for, render_template, g, Response -from planet import cache -from planet.models.clades import Clade -from planet.models.species import Species -from planet.models.gene_families import GeneFamily -from planet.models.interpro import Interpro +from conekt import cache +from conekt.models.clades import Clade +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamily +from conekt.models.interpro import Interpro import json diff --git a/planet/controllers/custom_network.py b/conekt/controllers/custom_network.py similarity index 95% rename from planet/controllers/custom_network.py rename to conekt/controllers/custom_network.py index e46d32d..4a603a9 100644 --- a/planet/controllers/custom_network.py +++ b/conekt/controllers/custom_network.py @@ -2,10 +2,10 @@ from flask import Blueprint, request, render_template, Response, Markup -from planet.forms.custom_network import CustomNetworkForm -from planet.helpers.cytoscape import CytoscapeHelper -from planet.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod -from planet.models.sequences import Sequence +from conekt.forms.custom_network import CustomNetworkForm +from conekt.helpers.cytoscape import CytoscapeHelper +from conekt.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod +from conekt.models.sequences import Sequence custom_network = Blueprint('custom_network', __name__) diff --git a/planet/controllers/ecc.py b/conekt/controllers/ecc.py similarity index 95% rename from planet/controllers/ecc.py rename to conekt/controllers/ecc.py index d43fd32..e974801 100644 --- a/planet/controllers/ecc.py +++ b/conekt/controllers/ecc.py @@ -1,10 +1,10 @@ from flask import Blueprint, redirect, url_for, render_template from sqlalchemy import and_ -from planet.models.sequences import Sequence -from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation +from conekt.models.sequences import Sequence +from conekt.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation -from planet.helpers.cytoscape import CytoscapeHelper +from conekt.helpers.cytoscape import CytoscapeHelper import json diff --git a/planet/controllers/expression_cluster.py b/conekt/controllers/expression_cluster.py similarity index 94% rename from planet/controllers/expression_cluster.py rename to conekt/controllers/expression_cluster.py index 63137ae..18c627b 100644 --- a/planet/controllers/expression_cluster.py +++ b/conekt/controllers/expression_cluster.py @@ -3,15 +3,15 @@ from flask import Blueprint, render_template, g, Response from sqlalchemy import or_ -from planet import cache -from planet.helpers.cytoscape import CytoscapeHelper -from planet.models.expression.coexpression_clusters import CoexpressionCluster, CoexpressionClusteringMethod -from planet.models.relationships.cluster_similarity import CoexpressionClusterSimilarity -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.sequences import Sequence -from planet.models.gene_families import GeneFamilyMethod - -from planet.helpers.chartjs import prepare_avg_profiles +from conekt import cache +from conekt.helpers.cytoscape import CytoscapeHelper +from conekt.models.expression.coexpression_clusters import CoexpressionCluster, CoexpressionClusteringMethod +from conekt.models.relationships.cluster_similarity import CoexpressionClusterSimilarity +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.sequences import Sequence +from conekt.models.gene_families import GeneFamilyMethod + +from conekt.helpers.chartjs import prepare_avg_profiles expression_cluster = Blueprint('expression_cluster', __name__) diff --git a/planet/controllers/expression_network.py b/conekt/controllers/expression_network.py similarity index 95% rename from planet/controllers/expression_network.py rename to conekt/controllers/expression_network.py index 8774345..3799afa 100644 --- a/planet/controllers/expression_network.py +++ b/conekt/controllers/expression_network.py @@ -2,11 +2,11 @@ from flask import Blueprint, url_for, render_template, flash, redirect, Response -from planet import cache -from planet.helpers.cytoscape import CytoscapeHelper -from planet.models.expression.networks import ExpressionNetworkMethod, ExpressionNetwork -from planet.models.species import Species -from planet.models.gene_families import GeneFamilyMethod +from conekt import cache +from conekt.helpers.cytoscape import CytoscapeHelper +from conekt.models.expression.networks import ExpressionNetworkMethod, ExpressionNetwork +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamilyMethod from utils.benchmark import benchmark diff --git a/planet/controllers/expression_profile.py b/conekt/controllers/expression_profile.py similarity index 96% rename from planet/controllers/expression_profile.py rename to conekt/controllers/expression_profile.py index 007a0ac..43eea57 100644 --- a/planet/controllers/expression_profile.py +++ b/conekt/controllers/expression_profile.py @@ -6,14 +6,14 @@ from statistics import mean import sys -from planet import cache -from planet.helpers.chartjs import prepare_expression_profile, prepare_profile_comparison -from planet.models.expression.cross_species_profile import CrossSpeciesExpressionProfile -from planet.models.condition_tissue import ConditionTissue -from planet.models.expression.profiles import ExpressionProfile -from planet.models.expression.networks import ExpressionNetwork -from planet.models.expression.specificity import ExpressionSpecificityMethod -from planet.forms.export_condition import ExportConditionForm +from conekt import cache +from conekt.helpers.chartjs import prepare_expression_profile, prepare_profile_comparison +from conekt.models.expression.cross_species_profile import CrossSpeciesExpressionProfile +from conekt.models.condition_tissue import ConditionTissue +from conekt.models.expression.profiles import ExpressionProfile +from conekt.models.expression.networks import ExpressionNetwork +from conekt.models.expression.specificity import ExpressionSpecificityMethod +from conekt.forms.export_condition import ExportConditionForm expression_profile = Blueprint('expression_profile', __name__) diff --git a/planet/controllers/family.py b/conekt/controllers/family.py similarity index 96% rename from planet/controllers/family.py rename to conekt/controllers/family.py index 88141e8..d61b524 100644 --- a/planet/controllers/family.py +++ b/conekt/controllers/family.py @@ -1,10 +1,10 @@ from flask import Blueprint, redirect, url_for, render_template, Response, g from sqlalchemy.orm import joinedload -from planet import cache -from planet.helpers.chartjs import prepare_doughnut -from planet.models.gene_families import GeneFamily -from planet.models.sequences import Sequence +from conekt import cache +from conekt.helpers.chartjs import prepare_doughnut +from conekt.models.gene_families import GeneFamily +from conekt.models.sequences import Sequence import json import time diff --git a/planet/controllers/go.py b/conekt/controllers/go.py similarity index 96% rename from planet/controllers/go.py rename to conekt/controllers/go.py index 1226039..bc084c8 100644 --- a/planet/controllers/go.py +++ b/conekt/controllers/go.py @@ -1,10 +1,10 @@ from flask import Blueprint, redirect, url_for, render_template, Response, g from sqlalchemy.orm import joinedload -from planet import cache -from planet.helpers.chartjs import prepare_doughnut -from planet.models.go import GO -from planet.models.sequences import Sequence +from conekt import cache +from conekt.helpers.chartjs import prepare_doughnut +from conekt.models.go import GO +from conekt.models.sequences import Sequence import json diff --git a/planet/controllers/graph_comparison.py b/conekt/controllers/graph_comparison.py similarity index 93% rename from planet/controllers/graph_comparison.py rename to conekt/controllers/graph_comparison.py index f10d6b9..3c7bb40 100644 --- a/planet/controllers/graph_comparison.py +++ b/conekt/controllers/graph_comparison.py @@ -2,10 +2,10 @@ from flask import Blueprint, render_template, Response -from planet import cache -from planet.helpers.cytoscape import CytoscapeHelper -from planet.models.expression.coexpression_clusters import CoexpressionCluster -from planet.models.gene_families import GeneFamilyMethod +from conekt import cache +from conekt.helpers.cytoscape import CytoscapeHelper +from conekt.models.expression.coexpression_clusters import CoexpressionCluster +from conekt.models.gene_families import GeneFamilyMethod graph_comparison = Blueprint('graph_comparison', __name__) diff --git a/planet/controllers/heatmap.py b/conekt/controllers/heatmap.py similarity index 93% rename from planet/controllers/heatmap.py rename to conekt/controllers/heatmap.py index d54e8df..989fd15 100644 --- a/planet/controllers/heatmap.py +++ b/conekt/controllers/heatmap.py @@ -2,12 +2,12 @@ import json -from planet import cache -from planet.forms.heatmap import HeatmapForm -from planet.models.expression.coexpression_clusters import CoexpressionCluster -from planet.models.expression.profiles import ExpressionProfile -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.sequences import Sequence +from conekt import cache +from conekt.forms.heatmap import HeatmapForm +from conekt.models.expression.coexpression_clusters import CoexpressionCluster +from conekt.models.expression.profiles import ExpressionProfile +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.sequences import Sequence heatmap = Blueprint('heatmap', __name__) diff --git a/planet/controllers/help.py b/conekt/controllers/help.py similarity index 98% rename from planet/controllers/help.py rename to conekt/controllers/help.py index 8b93977..24ccdc5 100644 --- a/planet/controllers/help.py +++ b/conekt/controllers/help.py @@ -1,6 +1,6 @@ from flask import Blueprint, render_template, abort -from planet import cache +from conekt import cache # Dict containing all keywords and the template with the information __TOPICS = {"gene_family": "modals/help/gene_family.html", diff --git a/planet/controllers/interpro.py b/conekt/controllers/interpro.py similarity index 96% rename from planet/controllers/interpro.py rename to conekt/controllers/interpro.py index 8c37801..07d7934 100644 --- a/planet/controllers/interpro.py +++ b/conekt/controllers/interpro.py @@ -1,10 +1,10 @@ from flask import Blueprint, redirect, url_for, render_template, Response, g from sqlalchemy.orm import joinedload, noload -from planet import cache -from planet.helpers.chartjs import prepare_doughnut -from planet.models.interpro import Interpro -from planet.models.sequences import Sequence +from conekt import cache +from conekt.helpers.chartjs import prepare_doughnut +from conekt.models.interpro import Interpro +from conekt.models.sequences import Sequence import json diff --git a/planet/controllers/main.py b/conekt/controllers/main.py similarity index 97% rename from planet/controllers/main.py rename to conekt/controllers/main.py index aa8f489..c97d3a3 100644 --- a/planet/controllers/main.py +++ b/conekt/controllers/main.py @@ -1,6 +1,6 @@ from flask import Blueprint, render_template, current_app, redirect, g, flash, url_for -from planet.models.news import News +from conekt.models.news import News main = Blueprint('main', __name__) diff --git a/planet/controllers/profile_comparison.py b/conekt/controllers/profile_comparison.py similarity index 92% rename from planet/controllers/profile_comparison.py rename to conekt/controllers/profile_comparison.py index 9b90dd9..cd11f63 100644 --- a/planet/controllers/profile_comparison.py +++ b/conekt/controllers/profile_comparison.py @@ -4,13 +4,13 @@ from flask import Blueprint, request, render_template, flash, Markup, url_for from sqlalchemy.orm import noload -from planet import cache -from planet.forms.profile_comparison import ProfileComparisonForm -from planet.helpers.chartjs import prepare_profiles, prepare_profiles_download -from planet.models.expression.coexpression_clusters import CoexpressionCluster -from planet.models.expression.profiles import ExpressionProfile -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.sequences import Sequence +from conekt import cache +from conekt.forms.profile_comparison import ProfileComparisonForm +from conekt.helpers.chartjs import prepare_profiles, prepare_profiles_download +from conekt.models.expression.coexpression_clusters import CoexpressionCluster +from conekt.models.expression.profiles import ExpressionProfile +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.sequences import Sequence profile_comparison = Blueprint('profile_comparison', __name__) diff --git a/planet/controllers/search.py b/conekt/controllers/search.py similarity index 96% rename from planet/controllers/search.py rename to conekt/controllers/search.py index 5756c27..babaa27 100644 --- a/planet/controllers/search.py +++ b/conekt/controllers/search.py @@ -5,18 +5,18 @@ from sqlalchemy.sql import or_, and_ from sqlalchemy.orm import joinedload -from planet import cache -from planet.forms.search_enriched_clusters import SearchEnrichedClustersForm -from planet.forms.search_specific_profiles import SearchSpecificProfilesForm -from planet.forms.advanced_search import AdvancedSequenceSearchForm -from planet.models.expression.specificity import ExpressionSpecificityMethod, ExpressionSpecificity -from planet.models.relationships.cluster_go import ClusterGOEnrichment -from planet.models.interpro import Interpro -from planet.models.go import GO -from planet.models.search import Search -from planet.models.species import Species -from planet.models.sequences import Sequence -from planet.models.xrefs import XRef +from conekt import cache +from conekt.forms.search_enriched_clusters import SearchEnrichedClustersForm +from conekt.forms.search_specific_profiles import SearchSpecificProfilesForm +from conekt.forms.advanced_search import AdvancedSequenceSearchForm +from conekt.models.expression.specificity import ExpressionSpecificityMethod, ExpressionSpecificity +from conekt.models.relationships.cluster_go import ClusterGOEnrichment +from conekt.models.interpro import Interpro +from conekt.models.go import GO +from conekt.models.search import Search +from conekt.models.species import Species +from conekt.models.sequences import Sequence +from conekt.models.xrefs import XRef from utils.benchmark import benchmark import logging diff --git a/planet/controllers/sequence.py b/conekt/controllers/sequence.py similarity index 98% rename from planet/controllers/sequence.py rename to conekt/controllers/sequence.py index 163123a..b349c60 100644 --- a/planet/controllers/sequence.py +++ b/conekt/controllers/sequence.py @@ -1,7 +1,7 @@ from flask import Blueprint, redirect, url_for, render_template, make_response -from planet import cache -from planet.models.sequences import Sequence +from conekt import cache +from conekt.models.sequences import Sequence from sqlalchemy.orm import undefer, noload sequence = Blueprint('sequence', __name__) diff --git a/planet/controllers/species.py b/conekt/controllers/species.py similarity index 97% rename from planet/controllers/species.py rename to conekt/controllers/species.py index c5ef3ea..f8e0d26 100644 --- a/planet/controllers/species.py +++ b/conekt/controllers/species.py @@ -1,10 +1,10 @@ from flask import Blueprint, render_template, g, make_response, Response, Markup, flash from markdown import markdown -from planet import db, cache -from planet.models.species import Species -from planet.models.sequences import Sequence -from planet.models.clades import Clade +from conekt import db, cache +from conekt.models.species import Species +from conekt.models.sequences import Sequence +from conekt.models.clades import Clade from sqlalchemy.orm import undefer, noload from sqlalchemy import desc diff --git a/planet/controllers/specificity_comparison.py b/conekt/controllers/specificity_comparison.py similarity index 95% rename from planet/controllers/specificity_comparison.py rename to conekt/controllers/specificity_comparison.py index 14add1e..f9f2f81 100644 --- a/planet/controllers/specificity_comparison.py +++ b/conekt/controllers/specificity_comparison.py @@ -2,11 +2,11 @@ from flask import Blueprint, request, render_template -from planet.forms.compare_specificity import CompareSpecificityForm -from planet.models.expression.specificity import ExpressionSpecificityMethod, ExpressionSpecificity -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_interpro import SequenceInterproAssociation -from planet.models.species import Species +from conekt.forms.compare_specificity import CompareSpecificityForm +from conekt.models.expression.specificity import ExpressionSpecificityMethod, ExpressionSpecificity +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_interpro import SequenceInterproAssociation +from conekt.models.species import Species specificity_comparison = Blueprint('specificity_comparison', __name__) diff --git a/planet/controllers/tree.py b/conekt/controllers/tree.py similarity index 95% rename from planet/controllers/tree.py rename to conekt/controllers/tree.py index 30d5b65..4a874a5 100644 --- a/planet/controllers/tree.py +++ b/conekt/controllers/tree.py @@ -1,9 +1,9 @@ from flask import Blueprint, render_template, g, make_response, Response, Markup -from planet import db, cache -from planet.models.trees import TreeMethod, Tree -from planet.models.sequences import Sequence -from planet.models.relationships.sequence_sequence_clade import SequenceSequenceCladeAssociation +from conekt import db, cache +from conekt.models.trees import TreeMethod, Tree +from conekt.models.sequences import Sequence +from conekt.models.relationships.sequence_sequence_clade import SequenceSequenceCladeAssociation from sqlalchemy.orm import joinedload diff --git a/planet/extensions.py b/conekt/extensions.py similarity index 97% rename from planet/extensions.py rename to conekt/extensions.py index 3b0f58e..22bf463 100644 --- a/planet/extensions.py +++ b/conekt/extensions.py @@ -13,7 +13,7 @@ from sqlalchemy import event from sqlite3 import Connection as SQLite3Connection -from planet.flask_blast import BlastThread +from conekt.flask_blast import BlastThread __all__ = ['db', 'login_manager', 'cache', 'htmlmin', 'blast_thread', 'compress', 'whooshee', 'migrate'] diff --git a/planet/flask_blast/__init__.py b/conekt/flask_blast/__init__.py similarity index 100% rename from planet/flask_blast/__init__.py rename to conekt/flask_blast/__init__.py diff --git a/planet/flask_blast/blast.py b/conekt/flask_blast/blast.py similarity index 100% rename from planet/flask_blast/blast.py rename to conekt/flask_blast/blast.py diff --git a/planet/forms/admin/add_clades.py b/conekt/forms/admin/add_clades.py similarity index 100% rename from planet/forms/admin/add_clades.py rename to conekt/forms/admin/add_clades.py diff --git a/planet/forms/admin/add_coexpression_clusters.py b/conekt/forms/admin/add_coexpression_clusters.py similarity index 90% rename from planet/forms/admin/add_coexpression_clusters.py rename to conekt/forms/admin/add_coexpression_clusters.py index d8892c4..8261c4a 100644 --- a/planet/forms/admin/add_coexpression_clusters.py +++ b/conekt/forms/admin/add_coexpression_clusters.py @@ -3,7 +3,7 @@ from wtforms.validators import InputRequired from wtforms import StringField, SelectField -from planet.models.expression.networks import ExpressionNetworkMethod +from conekt.models.expression.networks import ExpressionNetworkMethod class AddCoexpressionClustersForm(FlaskForm): diff --git a/planet/forms/admin/add_coexpression_network.py b/conekt/forms/admin/add_coexpression_network.py similarity index 95% rename from planet/forms/admin/add_coexpression_network.py rename to conekt/forms/admin/add_coexpression_network.py index ab76114..35c4b52 100644 --- a/planet/forms/admin/add_coexpression_network.py +++ b/conekt/forms/admin/add_coexpression_network.py @@ -3,7 +3,7 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class AddCoexpressionNetworkForm(FlaskForm): diff --git a/planet/forms/admin/add_expression_profiles.py b/conekt/forms/admin/add_expression_profiles.py similarity index 92% rename from planet/forms/admin/add_expression_profiles.py rename to conekt/forms/admin/add_expression_profiles.py index bfb9242..0306a4a 100644 --- a/planet/forms/admin/add_expression_profiles.py +++ b/conekt/forms/admin/add_expression_profiles.py @@ -2,7 +2,7 @@ from wtforms import StringField, RadioField, SelectField from flask_wtf.file import FileRequired, FileField -from planet.models.species import Species +from conekt.models.species import Species class AddExpressionProfilesForm(FlaskForm): diff --git a/planet/forms/admin/add_expression_specificity.py b/conekt/forms/admin/add_expression_specificity.py similarity index 94% rename from planet/forms/admin/add_expression_specificity.py rename to conekt/forms/admin/add_expression_specificity.py index 1d899be..b9b5dc1 100644 --- a/planet/forms/admin/add_expression_specificity.py +++ b/conekt/forms/admin/add_expression_specificity.py @@ -3,7 +3,7 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class AddConditionSpecificityForm(FlaskForm): diff --git a/planet/forms/admin/add_family.py b/conekt/forms/admin/add_family.py similarity index 100% rename from planet/forms/admin/add_family.py rename to conekt/forms/admin/add_family.py diff --git a/planet/forms/admin/add_go_interpro.py b/conekt/forms/admin/add_go_interpro.py similarity index 100% rename from planet/forms/admin/add_go_interpro.py rename to conekt/forms/admin/add_go_interpro.py diff --git a/planet/forms/admin/add_go_sequences.py b/conekt/forms/admin/add_go_sequences.py similarity index 91% rename from planet/forms/admin/add_go_sequences.py rename to conekt/forms/admin/add_go_sequences.py index 05ec658..45d134b 100644 --- a/planet/forms/admin/add_go_sequences.py +++ b/conekt/forms/admin/add_go_sequences.py @@ -3,7 +3,7 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class AddGOForm(FlaskForm): diff --git a/planet/forms/admin/add_interpro_sequences.py b/conekt/forms/admin/add_interpro_sequences.py similarity index 91% rename from planet/forms/admin/add_interpro_sequences.py rename to conekt/forms/admin/add_interpro_sequences.py index 10475fa..372dcab 100644 --- a/planet/forms/admin/add_interpro_sequences.py +++ b/conekt/forms/admin/add_interpro_sequences.py @@ -3,7 +3,7 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class AddInterProForm(FlaskForm): diff --git a/planet/forms/admin/add_sequence_descriptions.py b/conekt/forms/admin/add_sequence_descriptions.py similarity index 91% rename from planet/forms/admin/add_sequence_descriptions.py rename to conekt/forms/admin/add_sequence_descriptions.py index 1954a52..6a10fd4 100644 --- a/planet/forms/admin/add_sequence_descriptions.py +++ b/conekt/forms/admin/add_sequence_descriptions.py @@ -3,7 +3,7 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class AddSequenceDescriptionsForm(FlaskForm): diff --git a/planet/forms/admin/add_species.py b/conekt/forms/admin/add_species.py similarity index 100% rename from planet/forms/admin/add_species.py rename to conekt/forms/admin/add_species.py diff --git a/planet/forms/admin/add_trees.py b/conekt/forms/admin/add_trees.py similarity index 90% rename from planet/forms/admin/add_trees.py rename to conekt/forms/admin/add_trees.py index defa45b..20b50aa 100644 --- a/planet/forms/admin/add_trees.py +++ b/conekt/forms/admin/add_trees.py @@ -2,7 +2,7 @@ from wtforms import TextAreaField, FileField, SelectField from wtforms.validators import InputRequired -from planet.models.gene_families import GeneFamilyMethod +from conekt.models.gene_families import GeneFamilyMethod class AddTreesForm(FlaskForm): diff --git a/planet/forms/admin/add_xrefs.py b/conekt/forms/admin/add_xrefs.py similarity index 86% rename from planet/forms/admin/add_xrefs.py rename to conekt/forms/admin/add_xrefs.py index ae868d1..4b43233 100644 --- a/planet/forms/admin/add_xrefs.py +++ b/conekt/forms/admin/add_xrefs.py @@ -3,8 +3,8 @@ from flask_wtf.file import FileRequired, FileField from wtforms.validators import InputRequired, DataRequired -from planet.models.species import Species -from planet.models.gene_families import GeneFamilyMethod +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamilyMethod class AddXRefsForm(FlaskForm): diff --git a/planet/forms/admin/build_coexpression_clusters.py b/conekt/forms/admin/build_coexpression_clusters.py similarity index 87% rename from planet/forms/admin/build_coexpression_clusters.py rename to conekt/forms/admin/build_coexpression_clusters.py index 7791a95..9377c8a 100644 --- a/planet/forms/admin/build_coexpression_clusters.py +++ b/conekt/forms/admin/build_coexpression_clusters.py @@ -2,7 +2,7 @@ from wtforms.validators import InputRequired from wtforms import StringField, SelectField -from planet.models.expression.networks import ExpressionNetworkMethod +from conekt.models.expression.networks import ExpressionNetworkMethod class BuildCoexpressionClustersForm(FlaskForm): diff --git a/planet/forms/admin/neighborhood_to_clusters.py b/conekt/forms/admin/neighborhood_to_clusters.py similarity index 87% rename from planet/forms/admin/neighborhood_to_clusters.py rename to conekt/forms/admin/neighborhood_to_clusters.py index a0b2a2a..1db3daf 100644 --- a/planet/forms/admin/neighborhood_to_clusters.py +++ b/conekt/forms/admin/neighborhood_to_clusters.py @@ -2,7 +2,7 @@ from wtforms.validators import InputRequired from wtforms import StringField, SelectField -from planet.models.expression.networks import ExpressionNetworkMethod +from conekt.models.expression.networks import ExpressionNetworkMethod class NeighborhoodToClustersForm(FlaskForm): diff --git a/planet/forms/admin/predict_go.py b/conekt/forms/admin/predict_go.py similarity index 89% rename from planet/forms/admin/predict_go.py rename to conekt/forms/admin/predict_go.py index 5ad4c5a..838eb22 100644 --- a/planet/forms/admin/predict_go.py +++ b/conekt/forms/admin/predict_go.py @@ -2,7 +2,7 @@ from wtforms.validators import InputRequired from wtforms import StringField, SelectField -from planet.models.expression.networks import ExpressionNetworkMethod +from conekt.models.expression.networks import ExpressionNetworkMethod class PredictGOForm(FlaskForm): diff --git a/planet/forms/admin/reconcile_trees.py b/conekt/forms/admin/reconcile_trees.py similarity index 87% rename from planet/forms/admin/reconcile_trees.py rename to conekt/forms/admin/reconcile_trees.py index 3d5caa0..022ce34 100644 --- a/planet/forms/admin/reconcile_trees.py +++ b/conekt/forms/admin/reconcile_trees.py @@ -1,7 +1,7 @@ from flask_wtf import FlaskForm from wtforms import SelectField -from planet.models.trees import TreeMethod +from conekt.models.trees import TreeMethod class ReconcileTreesForm(FlaskForm): diff --git a/planet/forms/advanced_search.py b/conekt/forms/advanced_search.py similarity index 92% rename from planet/forms/advanced_search.py rename to conekt/forms/advanced_search.py index f5b1028..11772f0 100644 --- a/planet/forms/advanced_search.py +++ b/conekt/forms/advanced_search.py @@ -1,5 +1,5 @@ -from planet.models.species import Species -from planet.models.gene_families import GeneFamilyMethod +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamilyMethod from flask_wtf import FlaskForm from wtforms import Form, FormField, FieldList,StringField, SelectField, RadioField, TextAreaField, BooleanField diff --git a/planet/forms/blast.py b/conekt/forms/blast.py similarity index 100% rename from planet/forms/blast.py rename to conekt/forms/blast.py diff --git a/planet/forms/compare_specificity.py b/conekt/forms/compare_specificity.py similarity index 92% rename from planet/forms/compare_specificity.py rename to conekt/forms/compare_specificity.py index 279ce1d..301232d 100644 --- a/planet/forms/compare_specificity.py +++ b/conekt/forms/compare_specificity.py @@ -2,8 +2,8 @@ from wtforms import StringField, SelectField, FloatField, BooleanField from wtforms.validators import InputRequired -from planet.models.species import Species -from planet.models.gene_families import GeneFamilyMethod +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamilyMethod class CompareSpecificityForm(FlaskForm): diff --git a/planet/forms/custom_network.py b/conekt/forms/custom_network.py similarity index 76% rename from planet/forms/custom_network.py rename to conekt/forms/custom_network.py index 4254dd5..b2082e1 100644 --- a/planet/forms/custom_network.py +++ b/conekt/forms/custom_network.py @@ -2,10 +2,10 @@ from wtforms import TextAreaField, SelectField from wtforms.validators import InputRequired -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.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.gene_families import GeneFamilyMethod class CustomNetworkForm(FlaskForm): diff --git a/planet/forms/export_condition.py b/conekt/forms/export_condition.py similarity index 92% rename from planet/forms/export_condition.py rename to conekt/forms/export_condition.py index d05e02d..e4a0d41 100644 --- a/planet/forms/export_condition.py +++ b/conekt/forms/export_condition.py @@ -1,7 +1,7 @@ from flask_wtf import FlaskForm from wtforms import SelectField -from planet.models.species import Species +from conekt.models.species import Species class ExportConditionForm(FlaskForm): diff --git a/planet/forms/heatmap.py b/conekt/forms/heatmap.py similarity index 93% rename from planet/forms/heatmap.py rename to conekt/forms/heatmap.py index 0247f60..4d20d3f 100644 --- a/planet/forms/heatmap.py +++ b/conekt/forms/heatmap.py @@ -2,7 +2,7 @@ from wtforms import TextAreaField, SelectField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class HeatmapForm(FlaskForm): diff --git a/planet/forms/login.py b/conekt/forms/login.py similarity index 100% rename from planet/forms/login.py rename to conekt/forms/login.py diff --git a/planet/forms/profile_comparison.py b/conekt/forms/profile_comparison.py similarity index 91% rename from planet/forms/profile_comparison.py rename to conekt/forms/profile_comparison.py index 5dc29a2..2c2f52e 100644 --- a/planet/forms/profile_comparison.py +++ b/conekt/forms/profile_comparison.py @@ -2,7 +2,7 @@ from wtforms import TextAreaField, SelectField, BooleanField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class ProfileComparisonForm(FlaskForm): diff --git a/planet/forms/registration.py b/conekt/forms/registration.py similarity index 100% rename from planet/forms/registration.py rename to conekt/forms/registration.py diff --git a/planet/forms/search.py b/conekt/forms/search.py similarity index 100% rename from planet/forms/search.py rename to conekt/forms/search.py diff --git a/planet/forms/search_enriched_clusters.py b/conekt/forms/search_enriched_clusters.py similarity index 93% rename from planet/forms/search_enriched_clusters.py rename to conekt/forms/search_enriched_clusters.py index 91fbb94..a7b3588 100644 --- a/planet/forms/search_enriched_clusters.py +++ b/conekt/forms/search_enriched_clusters.py @@ -2,7 +2,7 @@ from wtforms import StringField, SelectField, FloatField, BooleanField from wtforms.validators import InputRequired -from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod +from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod class SearchEnrichedClustersForm(FlaskForm): diff --git a/planet/forms/search_specific_profiles.py b/conekt/forms/search_specific_profiles.py similarity index 93% rename from planet/forms/search_specific_profiles.py rename to conekt/forms/search_specific_profiles.py index 3677ec0..78f76b3 100644 --- a/planet/forms/search_specific_profiles.py +++ b/conekt/forms/search_specific_profiles.py @@ -2,7 +2,7 @@ from wtforms import StringField, SelectField, FloatField, BooleanField from wtforms.validators import InputRequired -from planet.models.species import Species +from conekt.models.species import Species class SearchSpecificProfilesForm(FlaskForm): diff --git a/planet/ftp.py b/conekt/ftp.py similarity index 94% rename from planet/ftp.py rename to conekt/ftp.py index 1e7f494..789b577 100644 --- a/planet/ftp.py +++ b/conekt/ftp.py @@ -8,15 +8,15 @@ from flask import current_app from sqlalchemy.orm import joinedload, noload -from planet import create_app, db -from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod -from planet.models.expression.networks import ExpressionNetworkMethod, ExpressionNetwork -from planet.models.gene_families import GeneFamilyMethod -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_go import SequenceGOAssociation -from planet.models.sequences import Sequence -from planet.models.species import Species +from conekt import create_app, db +from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod +from conekt.models.expression.networks import ExpressionNetworkMethod, ExpressionNetwork +from conekt.models.gene_families import GeneFamilyMethod +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_go import SequenceGOAssociation +from conekt.models.sequences import Sequence +from conekt.models.species import Species from utils.sequence import translate diff --git a/planet/helpers/chartjs.py b/conekt/helpers/chartjs.py similarity index 100% rename from planet/helpers/chartjs.py rename to conekt/helpers/chartjs.py diff --git a/planet/helpers/cytoscape.py b/conekt/helpers/cytoscape.py similarity index 97% rename from planet/helpers/cytoscape.py rename to conekt/helpers/cytoscape.py index ef7aa5f..3cc30ca 100644 --- a/planet/helpers/cytoscape.py +++ b/conekt/helpers/cytoscape.py @@ -3,14 +3,14 @@ from flask import url_for from sqlalchemy.orm import joinedload -from planet.models.expression.specificity import ExpressionSpecificity -from planet.models.expression.profiles import ExpressionProfile -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_interpro import SequenceInterproAssociation -from planet.models.sequences import Sequence -from planet.models.species import Species -from planet.models.clades import Clade +from conekt.models.expression.specificity import ExpressionSpecificity +from conekt.models.expression.profiles import ExpressionProfile +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_interpro import SequenceInterproAssociation +from conekt.models.sequences import Sequence +from conekt.models.species import Species +from conekt.models.clades import Clade from utils.color import family_to_shape_and_color, index_to_shape_and_color diff --git a/planet/helpers/url.py b/conekt/helpers/url.py similarity index 100% rename from planet/helpers/url.py rename to conekt/helpers/url.py diff --git a/planet/models/__init__.py b/conekt/models/__init__.py similarity index 100% rename from planet/models/__init__.py rename to conekt/models/__init__.py diff --git a/planet/models/blast_db.py b/conekt/models/blast_db.py similarity index 94% rename from planet/models/blast_db.py rename to conekt/models/blast_db.py index bd5102e..d2bb14d 100644 --- a/planet/models/blast_db.py +++ b/conekt/models/blast_db.py @@ -1,6 +1,6 @@ from flask import current_app -from planet.models.sequences import Sequence +from conekt.models.sequences import Sequence import subprocess import shlex diff --git a/planet/models/clades.py b/conekt/models/clades.py similarity index 95% rename from planet/models/clades.py rename to conekt/models/clades.py index e44a8ea..66a760e 100644 --- a/planet/models/clades.py +++ b/conekt/models/clades.py @@ -1,7 +1,7 @@ -from planet import db -from planet.models.species import Species -from planet.models.gene_families import GeneFamily -from planet.models.interpro import Interpro +from conekt import db +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamily +from conekt.models.interpro import Interpro from utils.phylo import get_clade diff --git a/planet/models/condition_tissue.py b/conekt/models/condition_tissue.py similarity index 98% rename from planet/models/condition_tissue.py rename to conekt/models/condition_tissue.py index 13c34bc..29f0459 100644 --- a/planet/models/condition_tissue.py +++ b/conekt/models/condition_tissue.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db import json diff --git a/planet/models/expression/__init__.py b/conekt/models/expression/__init__.py similarity index 100% rename from planet/models/expression/__init__.py rename to conekt/models/expression/__init__.py diff --git a/planet/models/expression/coexpression_clusters.py b/conekt/models/expression/coexpression_clusters.py similarity index 97% rename from planet/models/expression/coexpression_clusters.py rename to conekt/models/expression/coexpression_clusters.py index acf7f4c..304b596 100644 --- a/planet/models/expression/coexpression_clusters.py +++ b/conekt/models/expression/coexpression_clusters.py @@ -6,18 +6,18 @@ from sqlalchemy import join from sqlalchemy.orm import joinedload, load_only, undefer -from planet import db -from planet.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod -from planet.models.gene_families import GeneFamily -from planet.models.interpro import Interpro -from planet.models.go import GO -from planet.models.relationships.cluster_similarity import CoexpressionClusterSimilarity -from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_go import SequenceGOAssociation -from planet.models.relationships.cluster_go import ClusterGOEnrichment -from planet.models.sequences import Sequence -from planet.models.expression.profiles import ExpressionProfile +from conekt import db +from conekt.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod +from conekt.models.gene_families import GeneFamily +from conekt.models.interpro import Interpro +from conekt.models.go import GO +from conekt.models.relationships.cluster_similarity import CoexpressionClusterSimilarity +from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_go import SequenceGOAssociation +from conekt.models.relationships.cluster_go import ClusterGOEnrichment +from conekt.models.sequences import Sequence +from conekt.models.expression.profiles import ExpressionProfile from utils.benchmark import benchmark from utils.enrichment import hypergeo_sf, fdr_correction diff --git a/planet/models/expression/cross_species_profile.py b/conekt/models/expression/cross_species_profile.py similarity index 95% rename from planet/models/expression/cross_species_profile.py rename to conekt/models/expression/cross_species_profile.py index 0aaaa6c..5bb96a7 100644 --- a/planet/models/expression/cross_species_profile.py +++ b/conekt/models/expression/cross_species_profile.py @@ -1,5 +1,5 @@ -from planet.models.condition_tissue import ConditionTissue -from planet.models.expression.profiles import ExpressionProfile +from conekt.models.condition_tissue import ConditionTissue +from conekt.models.expression.profiles import ExpressionProfile import json from statistics import mean diff --git a/planet/models/expression/networks.py b/conekt/models/expression/networks.py similarity index 99% rename from planet/models/expression/networks.py rename to conekt/models/expression/networks.py index df6c867..25efdae 100644 --- a/planet/models/expression/networks.py +++ b/conekt/models/expression/networks.py @@ -1,10 +1,10 @@ from flask import url_for -from planet import db +from conekt import db -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation -from planet.models.gene_families import GeneFamily -from planet.models.sequences import Sequence +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation +from conekt.models.gene_families import GeneFamily +from conekt.models.sequences import Sequence from utils.jaccard import jaccard from utils.benchmark import benchmark diff --git a/planet/models/expression/profiles.py b/conekt/models/expression/profiles.py similarity index 98% rename from planet/models/expression/profiles.py rename to conekt/models/expression/profiles.py index 3045ead..271c6ee 100644 --- a/planet/models/expression/profiles.py +++ b/conekt/models/expression/profiles.py @@ -1,7 +1,7 @@ -from planet import db -from planet.models.species import Species -from planet.models.sequences import Sequence -from planet.models.condition_tissue import ConditionTissue +from conekt import db +from conekt.models.species import Species +from conekt.models.sequences import Sequence +from conekt.models.condition_tissue import ConditionTissue import json from collections import defaultdict diff --git a/planet/models/expression/specificity.py b/conekt/models/expression/specificity.py similarity index 98% rename from planet/models/expression/specificity.py rename to conekt/models/expression/specificity.py index e79b168..ff63644 100644 --- a/planet/models/expression/specificity.py +++ b/conekt/models/expression/specificity.py @@ -1,8 +1,8 @@ import json from statistics import mean -from planet import db, whooshee -from planet.models.expression.profiles import ExpressionProfile +from conekt import db, whooshee +from conekt.models.expression.profiles import ExpressionProfile from utils.entropy import entropy_from_values from utils.expression import expression_specificity from utils.tau import tau diff --git a/planet/models/gene_families.py b/conekt/models/gene_families.py similarity index 96% rename from planet/models/gene_families.py rename to conekt/models/gene_families.py index c7544c1..31521f9 100644 --- a/planet/models/gene_families.py +++ b/conekt/models/gene_families.py @@ -1,12 +1,12 @@ -from planet import db -from planet.models.relationships import sequence_family, family_xref, family_interpro -from planet.models.relationships.sequence_family import SequenceFamilyAssociation -from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation -from planet.models.relationships.family_interpro import FamilyInterproAssociation -from planet.models.relationships.family_go import FamilyGOAssociation -from planet.models.sequences import Sequence -from planet.models.interpro import Interpro -from planet.models.go import GO +from conekt import db +from conekt.models.relationships import sequence_family, family_xref, family_interpro +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation +from conekt.models.relationships.family_interpro import FamilyInterproAssociation +from conekt.models.relationships.family_go import FamilyGOAssociation +from conekt.models.sequences import Sequence +from conekt.models.interpro import Interpro +from conekt.models.go import GO import re import json @@ -69,7 +69,7 @@ def get_interpro_annotation(self): db.engine.execute(FamilyInterproAssociation.__table__.insert(), relations) def get_go_annotation(self): - from planet.models.relationships.sequence_go import SequenceGOAssociation + from conekt.models.relationships.sequence_go import SequenceGOAssociation families = self.families.all() relations = [] diff --git a/planet/models/go.py b/conekt/models/go.py similarity index 98% rename from planet/models/go.py rename to conekt/models/go.py index 15b7b9a..db62dab 100644 --- a/planet/models/go.py +++ b/conekt/models/go.py @@ -1,7 +1,7 @@ -from planet import db, whooshee -from planet.models.relationships import sequence_go -from planet.models.relationships.sequence_go import SequenceGOAssociation -from planet.models.sequences import Sequence +from conekt import db, whooshee +from conekt.models.relationships import sequence_go +from conekt.models.relationships.sequence_go import SequenceGOAssociation +from conekt.models.sequences import Sequence from utils.parser.obo import Parser as OBOParser from utils.parser.plaza.go import Parser as GOParser @@ -84,7 +84,7 @@ def parent_count(self): @property def interpro_stats(self): - from planet.models.interpro import Interpro + from conekt.models.interpro import Interpro return Interpro.sequence_stats_subquery(self.sequences) @@ -94,7 +94,7 @@ def go_stats(self): @property def family_stats(self): - from planet.models.gene_families import GeneFamily + from conekt.models.gene_families import GeneFamily return GeneFamily.sequence_stats_subquery(self.sequences) @@ -420,7 +420,7 @@ def predict_from_network(expression_network_method_id, threshold=5, source="PlaN :param threshold: number of neighboring genes that should have the label to allow transfor :param source: Value for the source field """ - from planet.models.expression.networks import ExpressionNetworkMethod + from conekt.models.expression.networks import ExpressionNetworkMethod expression_network_method = ExpressionNetworkMethod.query.get(expression_network_method_id) @@ -491,7 +491,7 @@ def predict_from_network(expression_network_method_id, threshold=5, source="PlaN @staticmethod def predict_from_network_enrichment(expression_network_method_id, cutoff=0.05, source="PlaNet Prediction"): - from planet.models.expression.networks import ExpressionNetworkMethod + from conekt.models.expression.networks import ExpressionNetworkMethod expression_network_method = ExpressionNetworkMethod.query.get(expression_network_method_id) diff --git a/planet/models/interpro.py b/conekt/models/interpro.py similarity index 96% rename from planet/models/interpro.py rename to conekt/models/interpro.py index fc9a890..65ca7ed 100644 --- a/planet/models/interpro.py +++ b/conekt/models/interpro.py @@ -1,7 +1,7 @@ -from planet import db, whooshee -from planet.models.relationships import sequence_interpro -from planet.models.relationships.sequence_interpro import SequenceInterproAssociation -from planet.models.sequences import Sequence +from conekt import db, whooshee +from conekt.models.relationships import sequence_interpro +from conekt.models.relationships.sequence_interpro import SequenceInterproAssociation +from conekt.models.sequences import Sequence from utils.parser.interpro import Parser as InterproParser from utils.parser.interpro import DomainParser as InterproDomainParser @@ -118,13 +118,13 @@ def interpro_stats(self): @property def go_stats(self): - from planet.models.go import GO + from conekt.models.go import GO return GO.sequence_stats_subquery(self.sequences) @property def family_stats(self): - from planet.models.gene_families import GeneFamily + from conekt.models.gene_families import GeneFamily return GeneFamily.sequence_stats_subquery(self.sequences) diff --git a/planet/models/news.py b/conekt/models/news.py similarity index 95% rename from planet/models/news.py rename to conekt/models/news.py index c88b834..76448c3 100644 --- a/planet/models/news.py +++ b/conekt/models/news.py @@ -1,4 +1,4 @@ -from planet import db, whooshee +from conekt import db, whooshee from flask import Markup from markdown import markdown diff --git a/planet/models/relationships/__init__.py b/conekt/models/relationships/__init__.py similarity index 99% rename from planet/models/relationships/__init__.py rename to conekt/models/relationships/__init__.py index 1d92516..fbfbe03 100644 --- a/planet/models/relationships/__init__.py +++ b/conekt/models/relationships/__init__.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db sequence_go = db.Table('sequence_go', db.Column('id', db.Integer, primary_key=True), diff --git a/planet/models/relationships/cluster_clade.py b/conekt/models/relationships/cluster_clade.py similarity index 98% rename from planet/models/relationships/cluster_clade.py rename to conekt/models/relationships/cluster_clade.py index 7df2a11..91fff47 100644 --- a/planet/models/relationships/cluster_clade.py +++ b/conekt/models/relationships/cluster_clade.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class ClusterCladeEnrichment(db.Model): diff --git a/planet/models/relationships/cluster_go.py b/conekt/models/relationships/cluster_go.py similarity index 96% rename from planet/models/relationships/cluster_go.py rename to conekt/models/relationships/cluster_go.py index b8ff8db..4774795 100644 --- a/planet/models/relationships/cluster_go.py +++ b/conekt/models/relationships/cluster_go.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class ClusterGOEnrichment(db.Model): diff --git a/planet/models/relationships/cluster_similarity.py b/conekt/models/relationships/cluster_similarity.py similarity index 98% rename from planet/models/relationships/cluster_similarity.py rename to conekt/models/relationships/cluster_similarity.py index 3c749ed..d9f71e1 100644 --- a/planet/models/relationships/cluster_similarity.py +++ b/conekt/models/relationships/cluster_similarity.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class CoexpressionClusterSimilarity(db.Model): diff --git a/planet/models/relationships/family_go.py b/conekt/models/relationships/family_go.py similarity index 97% rename from planet/models/relationships/family_go.py rename to conekt/models/relationships/family_go.py index 3ad752a..5517183 100644 --- a/planet/models/relationships/family_go.py +++ b/conekt/models/relationships/family_go.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class FamilyGOAssociation(db.Model): diff --git a/planet/models/relationships/family_interpro.py b/conekt/models/relationships/family_interpro.py similarity index 97% rename from planet/models/relationships/family_interpro.py rename to conekt/models/relationships/family_interpro.py index d5a3aea..04bd12b 100644 --- a/planet/models/relationships/family_interpro.py +++ b/conekt/models/relationships/family_interpro.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class FamilyInterproAssociation(db.Model): diff --git a/planet/models/relationships/family_xref.py b/conekt/models/relationships/family_xref.py similarity index 94% rename from planet/models/relationships/family_xref.py rename to conekt/models/relationships/family_xref.py index 5c1b67a..9af22a8 100644 --- a/planet/models/relationships/family_xref.py +++ b/conekt/models/relationships/family_xref.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class FamilyXRefAssociation(db.Model): diff --git a/planet/models/relationships/sequence_cluster.py b/conekt/models/relationships/sequence_cluster.py similarity index 93% rename from planet/models/relationships/sequence_cluster.py rename to conekt/models/relationships/sequence_cluster.py index b5ed924..7689d82 100644 --- a/planet/models/relationships/sequence_cluster.py +++ b/conekt/models/relationships/sequence_cluster.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class SequenceCoexpressionClusterAssociation(db.Model): diff --git a/planet/models/relationships/sequence_family.py b/conekt/models/relationships/sequence_family.py similarity index 97% rename from planet/models/relationships/sequence_family.py rename to conekt/models/relationships/sequence_family.py index 226e7fd..83a12df 100644 --- a/planet/models/relationships/sequence_family.py +++ b/conekt/models/relationships/sequence_family.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class SequenceFamilyAssociation(db.Model): diff --git a/planet/models/relationships/sequence_go.py b/conekt/models/relationships/sequence_go.py similarity index 98% rename from planet/models/relationships/sequence_go.py rename to conekt/models/relationships/sequence_go.py index 041a037..92cf85c 100644 --- a/planet/models/relationships/sequence_go.py +++ b/conekt/models/relationships/sequence_go.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db import json diff --git a/planet/models/relationships/sequence_interpro.py b/conekt/models/relationships/sequence_interpro.py similarity index 97% rename from planet/models/relationships/sequence_interpro.py rename to conekt/models/relationships/sequence_interpro.py index 2a6661d..0c5c511 100644 --- a/planet/models/relationships/sequence_interpro.py +++ b/conekt/models/relationships/sequence_interpro.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class SequenceInterproAssociation(db.Model): diff --git a/planet/models/relationships/sequence_sequence_clade.py b/conekt/models/relationships/sequence_sequence_clade.py similarity index 96% rename from planet/models/relationships/sequence_sequence_clade.py rename to conekt/models/relationships/sequence_sequence_clade.py index 1a42f0a..d32cdd9 100644 --- a/planet/models/relationships/sequence_sequence_clade.py +++ b/conekt/models/relationships/sequence_sequence_clade.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class SequenceSequenceCladeAssociation(db.Model): diff --git a/planet/models/relationships/sequence_sequence_ecc.py b/conekt/models/relationships/sequence_sequence_ecc.py similarity index 99% rename from planet/models/relationships/sequence_sequence_ecc.py rename to conekt/models/relationships/sequence_sequence_ecc.py index 08fe8e3..7363aa6 100644 --- a/planet/models/relationships/sequence_sequence_ecc.py +++ b/conekt/models/relationships/sequence_sequence_ecc.py @@ -2,8 +2,8 @@ from sqlalchemy import and_ -from planet import db -from planet.models.relationships.sequence_family import SequenceFamilyAssociation +from conekt import db +from conekt.models.relationships.sequence_family import SequenceFamilyAssociation class SequenceSequenceECCAssociation(db.Model): diff --git a/planet/models/relationships/sequence_xref.py b/conekt/models/relationships/sequence_xref.py similarity index 94% rename from planet/models/relationships/sequence_xref.py rename to conekt/models/relationships/sequence_xref.py index 3c823b3..c2af3f5 100644 --- a/planet/models/relationships/sequence_xref.py +++ b/conekt/models/relationships/sequence_xref.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db class SequenceXRefAssociation(db.Model): diff --git a/planet/models/search.py b/conekt/models/search.py similarity index 96% rename from planet/models/search.py rename to conekt/models/search.py index 8efa8e5..0984c53 100644 --- a/planet/models/search.py +++ b/conekt/models/search.py @@ -1,14 +1,14 @@ from sqlalchemy import func from sqlalchemy.sql import or_, and_ -from planet.models.expression.profiles import ExpressionProfile -from planet.models.gene_families import GeneFamily -from planet.models.go import GO -from planet.models.interpro import Interpro -from planet.models.relationships.cluster_go import ClusterGOEnrichment -from planet.models.sequences import Sequence -from planet.models.xrefs import XRef -from planet.models.species import Species +from conekt.models.expression.profiles import ExpressionProfile +from conekt.models.gene_families import GeneFamily +from conekt.models.go import GO +from conekt.models.interpro import Interpro +from conekt.models.relationships.cluster_go import ClusterGOEnrichment +from conekt.models.sequences import Sequence +from conekt.models.xrefs import XRef +from conekt.models.species import Species import re import whoosh diff --git a/planet/models/sequences.py b/conekt/models/sequences.py similarity index 98% rename from planet/models/sequences.py rename to conekt/models/sequences.py index 6d3a8ec..231f618 100644 --- a/planet/models/sequences.py +++ b/conekt/models/sequences.py @@ -1,7 +1,7 @@ -from planet import db, whooshee +from conekt import db, whooshee -from planet.models.relationships import sequence_go, sequence_interpro, sequence_family, sequence_coexpression_cluster -from planet.models.relationships import sequence_xref, sequence_sequence_ecc +from conekt.models.relationships import sequence_go, sequence_interpro, sequence_family, sequence_coexpression_cluster +from conekt.models.relationships import sequence_xref, sequence_sequence_ecc from utils.sequence import translate from utils.parser.fasta import Fasta diff --git a/planet/models/species.py b/conekt/models/species.py similarity index 93% rename from planet/models/species.py rename to conekt/models/species.py index 8d51739..8a08a7d 100644 --- a/planet/models/species.py +++ b/conekt/models/species.py @@ -1,4 +1,4 @@ -from planet import db +from conekt import db SQL_COLLATION = 'NOCASE' if db.engine.name == 'sqlite' else '' @@ -39,8 +39,8 @@ def __repr__(self): @property def has_interpro(self): - from planet.models.sequences import Sequence - from planet.models.relationships.sequence_interpro import SequenceInterproAssociation + from conekt.models.sequences import Sequence + from conekt.models.relationships.sequence_interpro import SequenceInterproAssociation domain = SequenceInterproAssociation.query.join(Sequence, Sequence.id == SequenceInterproAssociation.sequence_id).filter(Sequence.species_id == self.id).first() @@ -51,8 +51,8 @@ def has_interpro(self): @property def has_go(self): - from planet.models.sequences import Sequence - from planet.models.relationships.sequence_go import SequenceGOAssociation + from conekt.models.sequences import Sequence + from conekt.models.relationships.sequence_go import SequenceGOAssociation go = SequenceGOAssociation.query.join(Sequence, Sequence.id == SequenceGOAssociation.sequence_id).filter(Sequence.species_id == self.id).first() diff --git a/planet/models/trees.py b/conekt/models/trees.py similarity index 97% rename from planet/models/trees.py rename to conekt/models/trees.py index a81b7d4..1033cf6 100644 --- a/planet/models/trees.py +++ b/conekt/models/trees.py @@ -1,9 +1,9 @@ -from planet import db -from planet.models.sequences import Sequence -from planet.models.clades import Clade -from planet.models.relationships.sequence_sequence_clade import SequenceSequenceCladeAssociation +from conekt import db +from conekt.models.sequences import Sequence +from conekt.models.clades import Clade +from conekt.models.relationships.sequence_sequence_clade import SequenceSequenceCladeAssociation -from planet.models.expression.cross_species_profile import CrossSpeciesExpressionProfile +from conekt.models.expression.cross_species_profile import CrossSpeciesExpressionProfile import utils.phylo as phylo diff --git a/planet/models/users.py b/conekt/models/users.py similarity index 98% rename from planet/models/users.py rename to conekt/models/users.py index 4ab911b..e7a3a37 100644 --- a/planet/models/users.py +++ b/conekt/models/users.py @@ -1,5 +1,5 @@ from werkzeug.security import generate_password_hash, check_password_hash -from planet import db +from conekt import db from datetime import datetime diff --git a/planet/models/xrefs.py b/conekt/models/xrefs.py similarity index 96% rename from planet/models/xrefs.py rename to conekt/models/xrefs.py index 255c8ae..bda6ed4 100644 --- a/planet/models/xrefs.py +++ b/conekt/models/xrefs.py @@ -1,6 +1,6 @@ -from planet import db, whooshee -from planet.models.species import Species -from planet.models.gene_families import GeneFamilyMethod +from conekt import db, whooshee +from conekt.models.species import Species +from conekt.models.gene_families import GeneFamilyMethod SQL_COLLATION = 'NOCASE' if db.engine.name == 'sqlite' else '' diff --git a/planet/static/css/bootstrap-slider.css b/conekt/static/css/bootstrap-slider.css similarity index 100% rename from planet/static/css/bootstrap-slider.css rename to conekt/static/css/bootstrap-slider.css diff --git a/planet/static/css/bootstrap-slider.min.css b/conekt/static/css/bootstrap-slider.min.css similarity index 100% rename from planet/static/css/bootstrap-slider.min.css rename to conekt/static/css/bootstrap-slider.min.css diff --git a/planet/static/css/bootstrap.min.css b/conekt/static/css/bootstrap.min.css similarity index 100% rename from planet/static/css/bootstrap.min.css rename to conekt/static/css/bootstrap.min.css diff --git a/planet/static/css/cookieconsent.min.css b/conekt/static/css/cookieconsent.min.css similarity index 100% rename from planet/static/css/cookieconsent.min.css rename to conekt/static/css/cookieconsent.min.css diff --git a/planet/static/css/font-awesome.css b/conekt/static/css/font-awesome.css similarity index 100% rename from planet/static/css/font-awesome.css rename to conekt/static/css/font-awesome.css diff --git a/planet/static/css/font-awesome.min.css b/conekt/static/css/font-awesome.min.css similarity index 100% rename from planet/static/css/font-awesome.min.css rename to conekt/static/css/font-awesome.min.css diff --git a/planet/static/css/jquery.qtip.min.css b/conekt/static/css/jquery.qtip.min.css similarity index 100% rename from planet/static/css/jquery.qtip.min.css rename to conekt/static/css/jquery.qtip.min.css diff --git a/planet/static/css/main.css b/conekt/static/css/main.css similarity index 100% rename from planet/static/css/main.css rename to conekt/static/css/main.css diff --git a/planet/static/css/phyd3.css b/conekt/static/css/phyd3.css similarity index 100% rename from planet/static/css/phyd3.css rename to conekt/static/css/phyd3.css diff --git a/planet/static/css/phyd3.min.css b/conekt/static/css/phyd3.min.css similarity index 100% rename from planet/static/css/phyd3.min.css rename to conekt/static/css/phyd3.min.css diff --git a/planet/static/css/tabbed_panel.css b/conekt/static/css/tabbed_panel.css similarity index 100% rename from planet/static/css/tabbed_panel.css rename to conekt/static/css/tabbed_panel.css diff --git a/planet/static/css/typeahead.css b/conekt/static/css/typeahead.css similarity index 100% rename from planet/static/css/typeahead.css rename to conekt/static/css/typeahead.css diff --git a/planet/static/css/uploader.css b/conekt/static/css/uploader.css similarity index 100% rename from planet/static/css/uploader.css rename to conekt/static/css/uploader.css diff --git a/planet/static/favicon.ico b/conekt/static/favicon.ico similarity index 100% rename from planet/static/favicon.ico rename to conekt/static/favicon.ico diff --git a/planet/static/fonts/FontAwesome.otf b/conekt/static/fonts/FontAwesome.otf similarity index 100% rename from planet/static/fonts/FontAwesome.otf rename to conekt/static/fonts/FontAwesome.otf diff --git a/planet/static/fonts/fontawesome-webfont.eot b/conekt/static/fonts/fontawesome-webfont.eot similarity index 100% rename from planet/static/fonts/fontawesome-webfont.eot rename to conekt/static/fonts/fontawesome-webfont.eot diff --git a/planet/static/fonts/fontawesome-webfont.svg b/conekt/static/fonts/fontawesome-webfont.svg similarity index 100% rename from planet/static/fonts/fontawesome-webfont.svg rename to conekt/static/fonts/fontawesome-webfont.svg diff --git a/planet/static/fonts/fontawesome-webfont.ttf b/conekt/static/fonts/fontawesome-webfont.ttf similarity index 100% rename from planet/static/fonts/fontawesome-webfont.ttf rename to 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planet/templates/admin/add/go.html rename to conekt/templates/admin/add/go.html diff --git a/planet/templates/admin/add/interpro.html b/conekt/templates/admin/add/interpro.html similarity index 100% rename from planet/templates/admin/add/interpro.html rename to conekt/templates/admin/add/interpro.html diff --git a/planet/templates/admin/add/sequence_descriptions.html b/conekt/templates/admin/add/sequence_descriptions.html similarity index 100% rename from planet/templates/admin/add/sequence_descriptions.html rename to conekt/templates/admin/add/sequence_descriptions.html diff --git a/planet/templates/admin/add/species.html b/conekt/templates/admin/add/species.html similarity index 100% rename from planet/templates/admin/add/species.html rename to conekt/templates/admin/add/species.html diff --git a/planet/templates/admin/add/trees.html b/conekt/templates/admin/add/trees.html similarity index 100% rename from planet/templates/admin/add/trees.html rename to conekt/templates/admin/add/trees.html diff --git a/planet/templates/admin/add/xrefs.html b/conekt/templates/admin/add/xrefs.html similarity index 100% rename from planet/templates/admin/add/xrefs.html rename to conekt/templates/admin/add/xrefs.html diff --git a/planet/templates/admin/add/xrefs_families.html b/conekt/templates/admin/add/xrefs_families.html similarity index 100% rename from planet/templates/admin/add/xrefs_families.html rename to conekt/templates/admin/add/xrefs_families.html diff --git a/planet/templates/admin/build/cluster_similarities.html b/conekt/templates/admin/build/cluster_similarities.html similarity index 100% rename from planet/templates/admin/build/cluster_similarities.html rename to conekt/templates/admin/build/cluster_similarities.html diff --git a/planet/templates/admin/build/coexpression_clusters.html b/conekt/templates/admin/build/coexpression_clusters.html similarity index 100% rename from planet/templates/admin/build/coexpression_clusters.html rename to conekt/templates/admin/build/coexpression_clusters.html diff --git a/planet/templates/admin/build/ecc.html b/conekt/templates/admin/build/ecc.html similarity index 100% rename from planet/templates/admin/build/ecc.html rename to conekt/templates/admin/build/ecc.html diff --git a/planet/templates/admin/build/go_enrichment.html b/conekt/templates/admin/build/go_enrichment.html similarity index 100% rename from planet/templates/admin/build/go_enrichment.html rename to conekt/templates/admin/build/go_enrichment.html diff --git a/planet/templates/admin/build/neighborhood_to_clusters.html b/conekt/templates/admin/build/neighborhood_to_clusters.html similarity index 100% rename from planet/templates/admin/build/neighborhood_to_clusters.html rename to conekt/templates/admin/build/neighborhood_to_clusters.html diff --git a/planet/templates/admin/build/reconcile_trees.html b/conekt/templates/admin/build/reconcile_trees.html similarity index 100% rename from planet/templates/admin/build/reconcile_trees.html rename to conekt/templates/admin/build/reconcile_trees.html diff --git a/planet/templates/admin/controls.html b/conekt/templates/admin/controls.html similarity index 100% rename from planet/templates/admin/controls.html rename to conekt/templates/admin/controls.html diff --git a/planet/templates/admin/home.html b/conekt/templates/admin/home.html similarity index 100% rename from planet/templates/admin/home.html rename to conekt/templates/admin/home.html diff --git a/planet/templates/admin/my_base.html b/conekt/templates/admin/my_base.html similarity index 100% rename from planet/templates/admin/my_base.html rename to conekt/templates/admin/my_base.html diff --git a/planet/templates/admin/predict/go.html b/conekt/templates/admin/predict/go.html similarity index 100% rename from planet/templates/admin/predict/go.html rename to conekt/templates/admin/predict/go.html diff --git a/planet/templates/async/family_stats.html b/conekt/templates/async/family_stats.html similarity index 100% rename from planet/templates/async/family_stats.html rename to conekt/templates/async/family_stats.html diff --git a/planet/templates/async/go_stats.html b/conekt/templates/async/go_stats.html similarity index 100% rename from planet/templates/async/go_stats.html rename to conekt/templates/async/go_stats.html diff --git a/planet/templates/async/interpro_stats.html b/conekt/templates/async/interpro_stats.html similarity index 100% rename from planet/templates/async/interpro_stats.html rename to conekt/templates/async/interpro_stats.html diff --git a/planet/templates/base.html b/conekt/templates/base.html similarity index 100% rename from planet/templates/base.html rename to conekt/templates/base.html diff --git a/planet/templates/blast.html b/conekt/templates/blast.html similarity index 100% rename from planet/templates/blast.html rename to conekt/templates/blast.html diff --git a/planet/templates/clade.html b/conekt/templates/clade.html similarity index 100% rename from planet/templates/clade.html rename to conekt/templates/clade.html diff --git a/planet/templates/compare_profiles.html b/conekt/templates/compare_profiles.html similarity index 100% rename from planet/templates/compare_profiles.html rename to conekt/templates/compare_profiles.html diff --git a/planet/templates/compare_specificity.html b/conekt/templates/compare_specificity.html similarity index 100% rename from planet/templates/compare_specificity.html rename to conekt/templates/compare_specificity.html diff --git a/planet/templates/custom_network.html b/conekt/templates/custom_network.html similarity index 100% rename from planet/templates/custom_network.html rename to conekt/templates/custom_network.html diff --git a/planet/templates/error/403.html b/conekt/templates/error/403.html similarity index 100% rename from planet/templates/error/403.html rename to conekt/templates/error/403.html diff --git a/planet/templates/error/404.html b/conekt/templates/error/404.html similarity index 100% rename from planet/templates/error/404.html rename to conekt/templates/error/404.html diff --git a/planet/templates/error/405.html b/conekt/templates/error/405.html similarity index 100% rename from planet/templates/error/405.html rename to conekt/templates/error/405.html diff --git a/planet/templates/export_condition.html b/conekt/templates/export_condition.html similarity index 100% rename from planet/templates/export_condition.html rename to conekt/templates/export_condition.html diff --git a/planet/templates/expression_cluster.html b/conekt/templates/expression_cluster.html similarity index 100% rename from planet/templates/expression_cluster.html rename to conekt/templates/expression_cluster.html diff --git a/planet/templates/expression_graph.html b/conekt/templates/expression_graph.html similarity index 100% rename from planet/templates/expression_graph.html rename to conekt/templates/expression_graph.html diff --git a/planet/templates/expression_heatmap.html b/conekt/templates/expression_heatmap.html similarity index 100% rename from planet/templates/expression_heatmap.html rename to conekt/templates/expression_heatmap.html diff --git a/planet/templates/expression_network.html b/conekt/templates/expression_network.html similarity index 100% rename from planet/templates/expression_network.html rename to conekt/templates/expression_network.html diff --git a/planet/templates/expression_profile.html b/conekt/templates/expression_profile.html similarity index 100% rename from planet/templates/expression_profile.html rename to conekt/templates/expression_profile.html diff --git a/planet/templates/expression_profile_comparison.html b/conekt/templates/expression_profile_comparison.html similarity index 100% rename from planet/templates/expression_profile_comparison.html rename to conekt/templates/expression_profile_comparison.html diff --git a/planet/templates/family.html b/conekt/templates/family.html similarity index 100% rename from planet/templates/family.html rename to conekt/templates/family.html diff --git a/planet/templates/find_enriched_clusters.html b/conekt/templates/find_enriched_clusters.html similarity index 100% rename from planet/templates/find_enriched_clusters.html rename to conekt/templates/find_enriched_clusters.html diff --git a/planet/templates/find_specific_profiles.html b/conekt/templates/find_specific_profiles.html similarity index 100% rename from planet/templates/find_specific_profiles.html rename to conekt/templates/find_specific_profiles.html diff --git a/planet/templates/go.html b/conekt/templates/go.html similarity index 100% rename from planet/templates/go.html rename to conekt/templates/go.html diff --git a/planet/templates/inchlib_heatmap.html b/conekt/templates/inchlib_heatmap.html similarity index 100% rename from planet/templates/inchlib_heatmap.html rename to conekt/templates/inchlib_heatmap.html diff --git a/planet/templates/interpro.html b/conekt/templates/interpro.html similarity index 100% rename from planet/templates/interpro.html rename to conekt/templates/interpro.html diff --git a/planet/templates/login.html b/conekt/templates/login.html similarity index 100% rename from planet/templates/login.html rename to conekt/templates/login.html diff --git a/planet/templates/macros/ajax_table.html b/conekt/templates/macros/ajax_table.html similarity index 100% rename from planet/templates/macros/ajax_table.html rename to conekt/templates/macros/ajax_table.html diff --git a/planet/templates/macros/chartjs.html b/conekt/templates/macros/chartjs.html similarity index 100% rename from planet/templates/macros/chartjs.html rename to conekt/templates/macros/chartjs.html diff --git a/planet/templates/macros/cluster_actions.html b/conekt/templates/macros/cluster_actions.html similarity index 100% rename from planet/templates/macros/cluster_actions.html rename to conekt/templates/macros/cluster_actions.html diff --git a/planet/templates/macros/neighborhood_actions.html b/conekt/templates/macros/neighborhood_actions.html similarity index 100% rename from planet/templates/macros/neighborhood_actions.html rename to conekt/templates/macros/neighborhood_actions.html diff --git a/planet/templates/macros/pagination.html b/conekt/templates/macros/pagination.html similarity index 100% rename from planet/templates/macros/pagination.html rename to conekt/templates/macros/pagination.html diff --git a/planet/templates/modals/expression_profile.html b/conekt/templates/modals/expression_profile.html similarity index 100% rename from planet/templates/modals/expression_profile.html rename to conekt/templates/modals/expression_profile.html diff --git a/planet/templates/modals/help/blast.html b/conekt/templates/modals/help/blast.html similarity index 100% rename from planet/templates/modals/help/blast.html rename to conekt/templates/modals/help/blast.html diff --git a/planet/templates/modals/help/cluster.html b/conekt/templates/modals/help/cluster.html similarity index 100% rename from planet/templates/modals/help/cluster.html rename to conekt/templates/modals/help/cluster.html diff --git a/planet/templates/modals/help/ecc.html b/conekt/templates/modals/help/ecc.html similarity index 100% rename from planet/templates/modals/help/ecc.html rename to conekt/templates/modals/help/ecc.html diff --git a/planet/templates/modals/help/entropy.html b/conekt/templates/modals/help/entropy.html similarity index 100% rename from planet/templates/modals/help/entropy.html rename to conekt/templates/modals/help/entropy.html diff --git a/planet/templates/modals/help/fdr.html b/conekt/templates/modals/help/fdr.html similarity index 100% rename from planet/templates/modals/help/fdr.html rename to conekt/templates/modals/help/fdr.html diff --git a/planet/templates/modals/help/gene_family.html b/conekt/templates/modals/help/gene_family.html similarity index 100% rename from planet/templates/modals/help/gene_family.html rename to conekt/templates/modals/help/gene_family.html diff --git a/planet/templates/modals/help/go.html b/conekt/templates/modals/help/go.html similarity index 100% rename from planet/templates/modals/help/go.html rename to conekt/templates/modals/help/go.html diff --git a/planet/templates/modals/help/hrr.html b/conekt/templates/modals/help/hrr.html similarity index 100% rename from planet/templates/modals/help/hrr.html rename to conekt/templates/modals/help/hrr.html diff --git a/planet/templates/modals/help/interpro_domain.html b/conekt/templates/modals/help/interpro_domain.html similarity index 100% rename from planet/templates/modals/help/interpro_domain.html rename to conekt/templates/modals/help/interpro_domain.html diff --git a/planet/templates/modals/help/low_abundance.html b/conekt/templates/modals/help/low_abundance.html similarity index 100% rename from planet/templates/modals/help/low_abundance.html rename to conekt/templates/modals/help/low_abundance.html diff --git a/planet/templates/modals/help/neighborhood.html b/conekt/templates/modals/help/neighborhood.html similarity index 100% rename from planet/templates/modals/help/neighborhood.html rename to conekt/templates/modals/help/neighborhood.html diff --git a/planet/templates/modals/help/pcc.html b/conekt/templates/modals/help/pcc.html similarity index 100% rename from planet/templates/modals/help/pcc.html rename to conekt/templates/modals/help/pcc.html diff --git a/planet/templates/modals/help/spm.html b/conekt/templates/modals/help/spm.html similarity index 100% rename from planet/templates/modals/help/spm.html rename to conekt/templates/modals/help/spm.html diff --git a/planet/templates/modals/help/tau.html b/conekt/templates/modals/help/tau.html similarity index 100% rename from planet/templates/modals/help/tau.html rename to conekt/templates/modals/help/tau.html diff --git a/planet/templates/modals/sequence.html b/conekt/templates/modals/sequence.html similarity index 100% rename from planet/templates/modals/sequence.html rename to conekt/templates/modals/sequence.html diff --git a/planet/templates/pagination/clade_relations.html b/conekt/templates/pagination/clade_relations.html similarity index 100% rename from planet/templates/pagination/clade_relations.html rename to conekt/templates/pagination/clade_relations.html diff --git a/planet/templates/pagination/cluster_probes.html b/conekt/templates/pagination/cluster_probes.html similarity index 100% rename from planet/templates/pagination/cluster_probes.html rename to conekt/templates/pagination/cluster_probes.html diff --git a/planet/templates/pagination/ecc_relations.html b/conekt/templates/pagination/ecc_relations.html similarity index 100% rename from planet/templates/pagination/ecc_relations.html rename to conekt/templates/pagination/ecc_relations.html diff --git a/planet/templates/pagination/families.html b/conekt/templates/pagination/families.html similarity index 100% rename from planet/templates/pagination/families.html rename to conekt/templates/pagination/families.html diff --git a/planet/templates/pagination/interpro.html b/conekt/templates/pagination/interpro.html similarity index 100% rename from planet/templates/pagination/interpro.html rename to conekt/templates/pagination/interpro.html diff --git a/planet/templates/pagination/sequences.html b/conekt/templates/pagination/sequences.html similarity index 100% rename from planet/templates/pagination/sequences.html rename to conekt/templates/pagination/sequences.html diff --git a/planet/templates/register.html b/conekt/templates/register.html similarity index 100% rename from planet/templates/register.html rename to conekt/templates/register.html diff --git a/planet/templates/search_advanced.html b/conekt/templates/search_advanced.html similarity index 100% rename from planet/templates/search_advanced.html rename to conekt/templates/search_advanced.html diff --git a/planet/templates/search_results.html b/conekt/templates/search_results.html similarity index 100% rename from planet/templates/search_results.html rename to conekt/templates/search_results.html diff --git a/planet/templates/sequence.html b/conekt/templates/sequence.html similarity index 100% rename from planet/templates/sequence.html rename to conekt/templates/sequence.html diff --git a/planet/templates/species.html b/conekt/templates/species.html similarity index 100% rename from planet/templates/species.html rename to conekt/templates/species.html diff --git a/planet/templates/static_pages/about.html b/conekt/templates/static_pages/about.html similarity index 100% rename from planet/templates/static_pages/about.html rename to conekt/templates/static_pages/about.html diff --git a/planet/templates/static_pages/contact.html b/conekt/templates/static_pages/contact.html similarity index 100% rename from planet/templates/static_pages/contact.html rename to conekt/templates/static_pages/contact.html diff --git a/planet/templates/static_pages/disclaimer.html b/conekt/templates/static_pages/disclaimer.html similarity index 100% rename from planet/templates/static_pages/disclaimer.html rename to conekt/templates/static_pages/disclaimer.html diff --git a/planet/templates/static_pages/features.html b/conekt/templates/static_pages/features.html similarity index 100% rename from planet/templates/static_pages/features.html rename to conekt/templates/static_pages/features.html diff --git a/planet/templates/static_pages/main.html b/conekt/templates/static_pages/main.html similarity index 100% rename from planet/templates/static_pages/main.html rename to conekt/templates/static_pages/main.html diff --git a/planet/templates/static_pages/privacy_policy.html b/conekt/templates/static_pages/privacy_policy.html similarity index 100% rename from planet/templates/static_pages/privacy_policy.html rename to conekt/templates/static_pages/privacy_policy.html diff --git a/planet/templates/tables/clade_associations.csv b/conekt/templates/tables/clade_associations.csv similarity index 100% rename from planet/templates/tables/clade_associations.csv rename to conekt/templates/tables/clade_associations.csv diff --git a/planet/templates/tables/families.csv b/conekt/templates/tables/families.csv similarity index 100% rename from planet/templates/tables/families.csv rename to conekt/templates/tables/families.csv diff --git a/planet/templates/tables/interpro.csv b/conekt/templates/tables/interpro.csv similarity index 100% rename from planet/templates/tables/interpro.csv rename to conekt/templates/tables/interpro.csv diff --git a/planet/templates/tables/sequences.csv b/conekt/templates/tables/sequences.csv similarity index 100% rename from planet/templates/tables/sequences.csv rename to conekt/templates/tables/sequences.csv diff --git a/planet/templates/tooltips/cluster.html b/conekt/templates/tooltips/cluster.html similarity index 100% rename from planet/templates/tooltips/cluster.html rename to conekt/templates/tooltips/cluster.html diff --git a/planet/templates/tooltips/family.html b/conekt/templates/tooltips/family.html similarity index 100% rename from planet/templates/tooltips/family.html rename to conekt/templates/tooltips/family.html diff --git a/planet/templates/tooltips/interpro.html b/conekt/templates/tooltips/interpro.html similarity index 100% rename from planet/templates/tooltips/interpro.html rename to conekt/templates/tooltips/interpro.html diff --git a/planet/templates/tooltips/low_abundance.html b/conekt/templates/tooltips/low_abundance.html similarity index 100% rename from planet/templates/tooltips/low_abundance.html rename to conekt/templates/tooltips/low_abundance.html diff --git a/planet/templates/tooltips/sequence.html b/conekt/templates/tooltips/sequence.html similarity index 100% rename from planet/templates/tooltips/sequence.html rename to conekt/templates/tooltips/sequence.html diff --git a/planet/templates/tree.html b/conekt/templates/tree.html similarity index 100% rename from planet/templates/tree.html rename to conekt/templates/tree.html diff --git a/master_build.template.py b/master_build.template.py index a8316ba..210f8f2 100644 --- a/master_build.template.py +++ b/master_build.template.py @@ -1,4 +1,4 @@ -from planet import create_app +from conekt import create_app def check_sanity_species_data(data, name=''): @@ -241,15 +241,15 @@ def check_sanity_species_data(data, name=''): # from build.db.expression import parse_expression_network # from build.db.coexpression_clusters import add_planet_coexpression_clusters - 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.species import Species - from planet.models.sequences import Sequence - from planet.models.clades import Clade - from planet.models.go import GO - from planet.models.interpro import Interpro - from planet.models.expression.specificity import ExpressionSpecificityMethod + 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.species import Species + from conekt.models.sequences import Sequence + from conekt.models.clades import Clade + from conekt.models.go import GO + from conekt.models.interpro import Interpro + from conekt.models.expression.specificity import ExpressionSpecificityMethod print("Checking input") print("==============") diff --git a/planet.template.wsgi b/planet.template.wsgi index a01b91e..8dfe21d 100644 --- a/planet.template.wsgi +++ b/planet.template.wsgi @@ -16,6 +16,6 @@ with open(activator) as f: exec(f.read(), {'__file__': activator}) # import the app. Note that it should not run by itself ! -from planet import create_app +from conekt import create_app application = create_app('config') diff --git a/run.py b/run.py index 91ef9fd..9694c54 100644 --- a/run.py +++ b/run.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 import click -from planet import create_app, db -from planet.models.users import User +from conekt import create_app, db +from conekt.models.users import User app = create_app('config') diff --git a/tests/admin.py b/tests/admin.py index a093d9d..5318cbe 100644 --- a/tests/admin.py +++ b/tests/admin.py @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -from planet import create_app, db +from conekt import create_app, db from flask import url_for from flask_testing import TestCase @@ -43,7 +43,7 @@ def setUp(self): """ Creates a database and fills it with sufficient dummy data to run the tests. """ - from planet.models.users import User + from conekt.models.users import User db.create_all() test_admin = User('admin', 'admin', '', is_admin=True) test_user = User('user', 'user', '', is_admin=False) diff --git a/tests/build.py b/tests/build.py index 84589d9..88914f1 100644 --- a/tests/build.py +++ b/tests/build.py @@ -3,7 +3,7 @@ from flask_testing import TestCase -from planet import create_app, db +from conekt import create_app, db class BuildTest(TestCase): @@ -29,18 +29,18 @@ def setUp(self): """ db.create_all() - from planet.models.species import Species - from planet.models.sequences import Sequence + from conekt.models.species import Species + from conekt.models.sequences import Sequence - from planet.models.xrefs import XRef - from planet.models.go import GO - from planet.models.interpro import Interpro - from planet.models.expression.profiles import ExpressionProfile - from planet.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod - from planet.models.expression.coexpression_clusters import CoexpressionClusteringMethod - from planet.models.expression.specificity import ExpressionSpecificityMethod - from planet.models.gene_families import GeneFamily, GeneFamilyMethod - from planet.models.clades import Clade + from conekt.models.xrefs import XRef + from conekt.models.go import GO + from conekt.models.interpro import Interpro + from conekt.models.expression.profiles import ExpressionProfile + from conekt.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod + from conekt.models.expression.coexpression_clusters import CoexpressionClusteringMethod + from conekt.models.expression.specificity import ExpressionSpecificityMethod + from conekt.models.gene_families import GeneFamily, GeneFamilyMethod + from conekt.models.clades import Clade Species.add('mmu', 'Marek mutwiliana') s = Species.query.first() @@ -89,8 +89,8 @@ def tearDown(self): db.drop_all() def test_build(self): - from planet.models.sequences import Sequence - from planet.models.species import Species + from conekt.models.sequences import Sequence + from conekt.models.species import Species s = Species.query.first() diff --git a/tests/website.py b/tests/website.py index 474e9c4..e4809c4 100644 --- a/tests/website.py +++ b/tests/website.py @@ -4,8 +4,8 @@ from flask_testing import TestCase -from planet import create_app, db -from planet.controllers.help import __TOPICS as topics +from conekt import create_app, db +from conekt.controllers.help import __TOPICS as topics from .config import LOGIN_ENABLED, BLAST_ENABLED @@ -30,19 +30,19 @@ def setUp(self): """ Creates a database and fills it with sufficient dummy data to run the tests. """ - from planet.models.users import User - from planet.models.expression.profiles import ExpressionProfile - from planet.models.sequences import Sequence - from planet.models.species import Species - from planet.models.interpro import Interpro - from planet.models.go import GO - from planet.models.gene_families import GeneFamily, GeneFamilyMethod - from planet.models.expression.coexpression_clusters import CoexpressionCluster, CoexpressionClusteringMethod - from planet.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod - from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation - from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation - from planet.models.expression.specificity import ExpressionSpecificityMethod - from planet.models.clades import Clade + from conekt.models.users import User + from conekt.models.expression.profiles import ExpressionProfile + from conekt.models.sequences import Sequence + from conekt.models.species import Species + from conekt.models.interpro import Interpro + from conekt.models.go import GO + from conekt.models.gene_families import GeneFamily, GeneFamilyMethod + from conekt.models.expression.coexpression_clusters import CoexpressionCluster, CoexpressionClusteringMethod + from conekt.models.expression.networks import ExpressionNetwork, ExpressionNetworkMethod + from conekt.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation + from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation + from conekt.models.expression.specificity import ExpressionSpecificityMethod + from conekt.models.clades import Clade db.create_all() @@ -249,7 +249,7 @@ def test_sequence(self): """ Test for routes associated with a Sequence """ - from planet.models.sequences import Sequence + from conekt.models.sequences import Sequence sequence = Sequence.query.first() @@ -297,7 +297,7 @@ def test_species(self): """ Test for routes associated with a Species """ - from planet.models.species import Species + from conekt.models.species import Species # Should have a main page response = self.client.get("/species/") @@ -356,7 +356,7 @@ def test_interpro(self): """ Test for routes associated with an InterPro domain """ - from planet.models.interpro import Interpro + from conekt.models.interpro import Interpro # Should redirect to main page as there is no overview response = self.client.get('/interpro/') @@ -400,7 +400,7 @@ def test_go(self): """ Test for routes associated with a GO label """ - from planet.models.go import GO + from conekt.models.go import GO response = self.client.get('/go/') self.assertRedirects(response, "/") @@ -449,7 +449,7 @@ def test_family(self): """ Test for routes associated with a GeneFamily """ - from planet.models.gene_families import GeneFamily + from conekt.models.gene_families import GeneFamily response = self.client.get('/family/') self.assertRedirects(response, "/") @@ -487,7 +487,7 @@ def test_profile(self): """ Test for routes associated with an ExpressionProfile """ - from planet.models.expression.profiles import ExpressionProfile + from conekt.models.expression.profiles import ExpressionProfile response = self.client.get('/profile/') self.assertRedirects(response, "/") @@ -558,11 +558,11 @@ def test_search(self): """ Test different components of the search function """ - from planet.models.sequences import Sequence - from planet.models.interpro import Interpro - from planet.models.go import GO - from planet.models.gene_families import GeneFamily - from planet.models.expression.profiles import ExpressionProfile + from conekt.models.sequences import Sequence + from conekt.models.interpro import Interpro + from conekt.models.go import GO + from conekt.models.gene_families import GeneFamily + from conekt.models.expression.profiles import ExpressionProfile sequence = Sequence.query.first() interpro = Interpro.query.first() @@ -693,8 +693,8 @@ def test_blast(self): self.assertTrue('status' in data) def test_heatmap(self): - from planet.models.expression.profiles import ExpressionProfile - from planet.models.expression.coexpression_clusters import CoexpressionCluster + from conekt.models.expression.profiles import ExpressionProfile + from conekt.models.expression.coexpression_clusters import CoexpressionCluster profile = ExpressionProfile.query.first() cluster = CoexpressionCluster.query.first() @@ -724,8 +724,8 @@ def test_heatmap(self): self.assert200(response) def test_profile_comparison(self): - from planet.models.expression.profiles import ExpressionProfile - from planet.models.expression.coexpression_clusters import CoexpressionCluster + from conekt.models.expression.profiles import ExpressionProfile + from conekt.models.expression.coexpression_clusters import CoexpressionCluster profile = ExpressionProfile.query.first() cluster = CoexpressionCluster.query.first() @@ -751,8 +751,8 @@ def test_profile_comparison(self): self.assert200(response) def test_expression_network(self): - from planet.models.species import Species - from planet.models.expression.networks import ExpressionNetwork + from conekt.models.species import Species + from conekt.models.expression.networks import ExpressionNetwork species = Species.query.first() expression_network = ExpressionNetwork.query.first() @@ -778,8 +778,8 @@ def test_expression_network(self): def test_coexpression_cluster(self): # from planet.models.species import Species - from planet.models.expression.coexpression_clusters import CoexpressionCluster - from planet.models.gene_families import GeneFamilyMethod + from conekt.models.expression.coexpression_clusters import CoexpressionCluster + from conekt.models.gene_families import GeneFamilyMethod # species = Species.query.first() cluster = CoexpressionCluster.query.first() @@ -815,8 +815,8 @@ def test_coexpression_cluster(self): self.assertCytoscapeJson(data) def test_graph_comparison(self): - from planet.models.expression.coexpression_clusters import CoexpressionCluster - from planet.models.gene_families import GeneFamilyMethod + from conekt.models.expression.coexpression_clusters import CoexpressionCluster + from conekt.models.gene_families import GeneFamilyMethod cluster = CoexpressionCluster.query.first() gf_method = GeneFamilyMethod.query.first() @@ -832,9 +832,9 @@ def test_graph_comparison(self): self.assertCytoscapeJson(data) def test_clades(self): - from planet.models.clades import Clade - from planet.models.gene_families import GeneFamily - from planet.models.interpro import Interpro + from conekt.models.clades import Clade + from conekt.models.gene_families import GeneFamily + from conekt.models.interpro import Interpro clade = Clade.query.first() family = GeneFamily.query.first() @@ -866,7 +866,7 @@ def test_clades(self): self.assertTrue(interpro.label in response.data.decode('utf-8')) def test_ecc(self): - from planet.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation + from conekt.models.relationships.sequence_sequence_ecc import SequenceSequenceECCAssociation ecc = SequenceSequenceECCAssociation.query.first() @@ -884,7 +884,7 @@ def test_ecc(self): self.assertCytoscapeJson(data, ecc_graph=True) def test_specificity_search(self): - from planet.models.sequences import Sequence + from conekt.models.sequences import Sequence response = self.client.get('/search/specific/profiles') self.assert200(response)