527 files changed, 740 insertions, 748 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index a03ad6ef..2ac83c7f 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -159,18 +159,15 @@ set|grep TMPDIR
 
 # Now handle command parameter -c which runs python
 if [ "$1" = '-c' ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
-    cmd=${2#wqflask/}
     echo PYTHONPATH="${PYTHONPATH}"
-    shift ; shift
-    echo "RUNNING COMMAND ${cmd} ${*}"
-    python $cmd $*
+    shift
+    echo "RUNNING COMMAND python ${*}"
+    python $*
     exit $?
 fi
 
 # Now handle command parameter -cli which runs in bash
 if [ "$1" = "-cli" ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
     cmd=$2
     echo PYTHONPATH="${PYTHONPATH}"
     shift ; shift
@@ -179,7 +176,6 @@ if [ "$1" = "-cli" ] ; then
     exit $?
 fi
 if [ "$1" = '-gunicorn' ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
     cmd=$2
     echo PYTHONPATH="${PYTHONPATH}"
     echo "RUNNING gunicorn ${cmd}"
@@ -187,20 +183,18 @@ if [ "$1" = '-gunicorn' ] ; then
     exit $?
 fi
 if [ "$1" = '-gunicorn-dev' ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
     echo PYTHONPATH="${PYTHONPATH}"
     if [ -z "${SERVER_PORT}" ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
-    cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload run_gunicorn:app"
+    cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload gn2.run_gunicorn:app"
     echo "RUNNING gunicorn ${cmd}"
     gunicorn $cmd
     exit $?
 fi
 if [ "$1" = '-gunicorn-prod' ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
     echo PYTHONPATH="${PYTHONPATH}"
     if [ -z "${SERVER_PORT}" ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     PID=$TMPDIR/gunicorn.$USER.pid
-    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 100 --max-requests-jitter 30 --timeout 1200 wsgi"
+    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 100 --max-requests-jitter 30 --timeout 1200 gn2.wsgi"
     echo "RUNNING gunicorn ${cmd}"
     gunicorn $cmd
     exit $?
@@ -219,16 +213,14 @@ fi
 
 
 if [ "$1" = "--with-pdb" ] ; then
-    cd "${GN2_BASE_DIR}/wqflask"
     cmd=$2
     echo PYTHONPATH="${PYTHONPATH}"
     shift ; shift
-    echo "RUNNING COMMAND python3 -m runserver.py"
+    echo "RUNNING COMMAND python3 -m gn2.runserver.py"
     python3 -m pdb runserver.py
     exit $?
 fi
 
 # Start the flask server running GN2
-cd "${GN2_BASE_DIR}/wqflask"
 echo "Starting with $settings"
-python runserver.py
+python gn2.runserver.py
diff --git a/etc/default_settings.py b/etc/default_settings.py
index bf73a8d5..f54cab7c 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,7 +24,7 @@
 import os
 import sys
 
-with open("../etc/VERSION", "r") as version_file:
+with open("etc/VERSION", "r") as version_file:
     GN_VERSION = version_file.read()
 
 SECRET_KEY = ""
diff --git a/wqflask/.coveragerc b/gn2/.coveragerc
index 939e51b9..939e51b9 100644
--- a/wqflask/.coveragerc
+++ b/gn2/.coveragerc
diff --git a/wqflask/__init__.py b/gn2/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/__init__.py
+++ b/gn2/__init__.py
diff --git a/wqflask/base/GeneralObject.py b/gn2/base/GeneralObject.py
index ce8e60b8..ce8e60b8 100644
--- a/wqflask/base/GeneralObject.py
+++ b/gn2/base/GeneralObject.py
diff --git a/wqflask/base/__init__.py b/gn2/base/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/base/__init__.py
+++ b/gn2/base/__init__.py
diff --git a/wqflask/base/data_set/__init__.py b/gn2/base/data_set/__init__.py
index 69eaab53..40ef1c75 100644
--- a/wqflask/base/data_set/__init__.py
+++ b/gn2/base/data_set/__init__.py
@@ -9,8 +9,8 @@ from redis import Redis
 
 # local imports
 from .dataset import DataSet
-from base import webqtlConfig
-from utility.tools import get_setting, USE_REDIS
+from gn2.base import webqtlConfig
+from gn2.utility.tools import get_setting, USE_REDIS
 from .datasettype import DatasetType
 from .tempdataset import TempDataSet
 from .datasetgroup import DatasetGroup
@@ -18,7 +18,7 @@ from .utils import query_table_timestamp
 from .genotypedataset import GenotypeDataSet
 from .phenotypedataset import PhenotypeDataSet
 from .mrnaassaydataset import MrnaAssayDataSet
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 # Used by create_database to instantiate objects
 # Each subclass will add to this
diff --git a/wqflask/base/data_set/dataset.py b/gn2/base/data_set/dataset.py
index 435d74a9..3a62fbde 100644
--- a/wqflask/base/data_set/dataset.py
+++ b/gn2/base/data_set/dataset.py
@@ -5,14 +5,14 @@ import collections
 
 from redis import Redis
 
-from base import species
-from utility import chunks
-from utility.tools import get_setting
+from gn2.base import species
+from gn2.utility import chunks
+from gn2.utility.tools import get_setting
 from gn3.monads import MonadicDict, query_sql
 from pymonad.maybe import Maybe, Nothing
 from .datasetgroup import DatasetGroup
-from wqflask.database import database_connection
-from utility.db_tools import escape, mescape, create_in_clause
+from gn2.wqflask.database import database_connection
+from gn2.utility.db_tools import escape, mescape, create_in_clause
 from .utils import fetch_cached_results, cache_dataset_results
 
 
diff --git a/wqflask/base/data_set/datasetgroup.py b/gn2/base/data_set/datasetgroup.py
index 95dc976f..d124283f 100644
--- a/wqflask/base/data_set/datasetgroup.py
+++ b/gn2/base/data_set/datasetgroup.py
@@ -4,14 +4,14 @@ import os
 import json
 
 
-from base import webqtlConfig
+from gn2.base import webqtlConfig
 from .markers import Markers, HumanMarkers
-from utility import webqtlUtil
-from utility import gen_geno_ob
-from db import webqtlDatabaseFunction
-from maintenance import get_group_samplelists
-from wqflask.database import database_connection
-from utility.tools import (
+from gn2.utility import webqtlUtil
+from gn2.utility import gen_geno_ob
+from gn2.db import webqtlDatabaseFunction
+from gn2.maintenance import get_group_samplelists
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import (
     locate,
     USE_REDIS,
     flat_files,
diff --git a/wqflask/base/data_set/datasettype.py b/gn2/base/data_set/datasettype.py
index 05f0f564..52d41b41 100644
--- a/wqflask/base/data_set/datasettype.py
+++ b/gn2/base/data_set/datasettype.py
@@ -8,8 +8,8 @@ from typing import Optional, Dict
 from redis import Redis
 
 
-from utility.tools import GN2_BASE_URL
-from wqflask.database import database_connection
+from gn2.utility.tools import GN2_BASE_URL
+from gn2.wqflask.database import database_connection
 
 
 class DatasetType:
diff --git a/wqflask/base/data_set/genotypedataset.py b/gn2/base/data_set/genotypedataset.py
index b903cd72..77af1dad 100644
--- a/wqflask/base/data_set/genotypedataset.py
+++ b/gn2/base/data_set/genotypedataset.py
@@ -1,11 +1,11 @@
 "GenotypeDataSet class ..."
 
 from .dataset import DataSet
-from utility import webqtlUtil
-from utility.tools import get_setting
-from db import webqtlDatabaseFunction
+from gn2.utility import webqtlUtil
+from gn2.utility.tools import get_setting
+from gn2.db import webqtlDatabaseFunction
 from .utils import geno_mrna_confidentiality
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 class GenotypeDataSet(DataSet):
 
diff --git a/wqflask/base/data_set/markers.py b/gn2/base/data_set/markers.py
index 6f56445e..68503577 100644
--- a/wqflask/base/data_set/markers.py
+++ b/gn2/base/data_set/markers.py
@@ -2,7 +2,7 @@
 
 import math
 
-from utility.tools import locate, flat_files
+from gn2.utility.tools import locate, flat_files
 
 class Markers:
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
diff --git a/wqflask/base/data_set/mrnaassaydataset.py b/gn2/base/data_set/mrnaassaydataset.py
index 4eb998b5..f641de27 100644
--- a/wqflask/base/data_set/mrnaassaydataset.py
+++ b/gn2/base/data_set/mrnaassaydataset.py
@@ -5,8 +5,8 @@ import codecs
 
 from .dataset import DataSet
 from .utils import geno_mrna_confidentiality
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 class MrnaAssayDataSet(DataSet):
     '''
diff --git a/wqflask/base/data_set/phenotypedataset.py b/gn2/base/data_set/phenotypedataset.py
index 5a39418a..b14556fe 100644
--- a/wqflask/base/data_set/phenotypedataset.py
+++ b/gn2/base/data_set/phenotypedataset.py
@@ -1,9 +1,9 @@
 "PhenotypeDataSet class ..."
 
 from .dataset import DataSet
-from base import webqtlConfig
-from utility.tools import get_setting
-from wqflask.database import database_connection
+from gn2.base import webqtlConfig
+from gn2.utility.tools import get_setting
+from gn2.wqflask.database import database_connection
 
 class PhenotypeDataSet(DataSet):
 
diff --git a/wqflask/base/data_set/probably_unused.py b/gn2/base/data_set/probably_unused.py
index abd3ad07..12be05a7 100644
--- a/wqflask/base/data_set/probably_unused.py
+++ b/gn2/base/data_set/probably_unused.py
@@ -2,8 +2,8 @@
 
 import pickle as pickle
 
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 def create_datasets_list():
     if USE_REDIS:
diff --git a/wqflask/base/data_set/tempdataset.py b/gn2/base/data_set/tempdataset.py
index b1c26a3b..b1c26a3b 100644
--- a/wqflask/base/data_set/tempdataset.py
+++ b/gn2/base/data_set/tempdataset.py
diff --git a/wqflask/base/data_set/utils.py b/gn2/base/data_set/utils.py
index d18180c4..fc17026e 100644
--- a/wqflask/base/data_set/utils.py
+++ b/gn2/base/data_set/utils.py
@@ -7,9 +7,9 @@ import hashlib
 from typing import List
 
 
-from utility.tools import get_setting, SQL_URI
-from base.webqtlConfig import TMPDIR
-from wqflask.database import parse_db_url, database_connection
+from gn2.utility.tools import get_setting, SQL_URI
+from gn2.base.webqtlConfig import TMPDIR
+from gn2.wqflask.database import parse_db_url, database_connection
 
 def geno_mrna_confidentiality(ob):
     with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/gn2/base/mrna_assay_tissue_data.py
index a78182e3..7b7914aa 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/gn2/base/mrna_assay_tissue_data.py
@@ -1,6 +1,6 @@
 import collections
 
-from utility import Bunch
+from gn2.utility import Bunch
 
 
 class MrnaAssayTissueData:
diff --git a/wqflask/base/species.py b/gn2/base/species.py
index 0844fada..0844fada 100644
--- a/wqflask/base/species.py
+++ b/gn2/base/species.py
diff --git a/wqflask/base/trait.py b/gn2/base/trait.py
index 103ff0c0..701958d7 100644
--- a/wqflask/base/trait.py
+++ b/gn2/base/trait.py
@@ -1,18 +1,18 @@
 import requests
 import simplejson as json
-from wqflask import app
+from gn2.wqflask import app
 
-import utility.hmac as hmac
-from base import webqtlConfig
-from base.webqtlCaseData import webqtlCaseData
-from base.data_set import create_dataset
-from utility.authentication_tools import check_resource_availability
-from utility.tools import get_setting, GN2_BASE_URL
-from utility.redis_tools import get_redis_conn, get_resource_id
+import gn2.utility.hmac as hmac
+from gn2.base import webqtlConfig
+from gn2.base.webqtlCaseData import webqtlCaseData
+from gn2.base.data_set import create_dataset
+from gn2.utility.authentication_tools import check_resource_availability
+from gn2.utility.tools import get_setting, GN2_BASE_URL
+from gn2.utility.redis_tools import get_redis_conn, get_resource_id
 
 from flask import g, request, url_for
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 
 Redis = get_redis_conn()
diff --git a/wqflask/base/webqtlCaseData.py b/gn2/base/webqtlCaseData.py
index dd6fad04..b4717b4b 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/gn2/base/webqtlCaseData.py
@@ -21,9 +21,9 @@
 # Created by GeneNetwork Core Team 2010/08/10
 
 
-import utility.tools
+import gn2.utility.tools
 
-utility.tools.show_settings()
+gn2.utility.tools.show_settings()
 
 
 class webqtlCaseData:
diff --git a/wqflask/base/webqtlConfig.py b/gn2/base/webqtlConfig.py
index a7dbed3d..998c0efc 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/gn2/base/webqtlConfig.py
@@ -8,7 +8,7 @@
 #
 #########################################
 import os
-from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
+from gn2.utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
 
 # Debug Level
 # 1 for debug, mod python will reload import each time
diff --git a/wqflask/db/__init__.py b/gn2/db/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/db/__init__.py
+++ b/gn2/db/__init__.py
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/gn2/db/webqtlDatabaseFunction.py
index b09cf377..9438c474 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/gn2/db/webqtlDatabaseFunction.py
@@ -20,9 +20,9 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
-from utility.tools import get_setting
+from gn2.utility.tools import get_setting
 
 
 def retrieve_species(group):
diff --git a/gn2/gn2_main.py b/gn2/gn2_main.py
new file mode 100644
index 00000000..38444620
--- /dev/null
+++ b/gn2/gn2_main.py
@@ -0,0 +1,19 @@
+"""Main application entry point."""
+
+from gn2.wqflask import app
+
+
+from gn2.wqflask import docs
+from gn2.wqflask import gsearch
+from gn2.wqflask import db_info
+from gn2.wqflask import user_login
+from gn2.wqflask.api import router
+from gn2.wqflask import user_session
+from gn2.wqflask import group_manager
+from gn2.wqflask import export_traits
+from gn2.wqflask import search_results
+from gn2.wqflask import resource_manager
+from gn2.wqflask import update_search_results
+
+import gn2.wqflask.views
+import gn2.wqflask.partial_correlations_views
diff --git a/wqflask/jobs/__init__.py b/gn2/jobs/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/jobs/__init__.py
+++ b/gn2/jobs/__init__.py
diff --git a/wqflask/jobs/jobs.py b/gn2/jobs/jobs.py
index f796fa9a..f796fa9a 100644
--- a/wqflask/jobs/jobs.py
+++ b/gn2/jobs/jobs.py
diff --git a/wqflask/maintenance/README.md b/gn2/maintenance/README.md
index 873eaa32..873eaa32 100644
--- a/wqflask/maintenance/README.md
+++ b/gn2/maintenance/README.md
diff --git a/wqflask/maintenance/__init__.py b/gn2/maintenance/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/maintenance/__init__.py
+++ b/gn2/maintenance/__init__.py
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/gn2/maintenance/convert_dryad_to_bimbam.py
index 18fbb8a1..18fbb8a1 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/gn2/maintenance/convert_dryad_to_bimbam.py
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/gn2/maintenance/convert_geno_to_bimbam.py
index 078be529..078be529 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/gn2/maintenance/convert_geno_to_bimbam.py
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/gn2/maintenance/gen_ind_genofiles.py
index b755c648..b755c648 100644
--- a/wqflask/maintenance/gen_ind_genofiles.py
+++ b/gn2/maintenance/gen_ind_genofiles.py
diff --git a/wqflask/maintenance/gen_select_dataset.py b/gn2/maintenance/gen_select_dataset.py
index 01b2fc15..5f41da29 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/gn2/maintenance/gen_select_dataset.py
@@ -35,9 +35,9 @@ import sys
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
 sys.path.insert(0, './')
 # NEW: import app to avoid a circular dependency on utility.tools
-from wqflask import app
+from gn2.wqflask import app
 
-from utility.tools import get_setting
+from gn2.utility.tools import get_setting
 
 import simplejson as json
 import urllib.parse
@@ -45,7 +45,7 @@ import urllib.parse
 
 from pprint import pformat as pf
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 
 def get_species(cursor):
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/gn2/maintenance/generate_kinship_from_bimbam.py
index 9f01d094..9f01d094 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/gn2/maintenance/generate_kinship_from_bimbam.py
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/gn2/maintenance/generate_probesetfreeze_file.py
index 2f917c71..00c2cddf 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/gn2/maintenance/generate_probesetfreeze_file.py
@@ -8,12 +8,12 @@ import os
 import collections
 import csv
 
-from base import webqtlConfig
+from gn2.base import webqtlConfig
 
 from pprint import pformat as pf
 
-from utility.tools import get_setting
-from wqflask.database import database_connection
+from gn2.utility.tools import get_setting
+from gn2.wqflask.database import database_connection
 
 
 def show_progress(process, counter):
diff --git a/wqflask/maintenance/geno_to_json.py b/gn2/maintenance/geno_to_json.py
index 32e0e34b..7be2ed83 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/gn2/maintenance/geno_to_json.py
@@ -23,7 +23,7 @@ import simplejson as json
 
 from pprint import pformat as pf
 
-#from utility.tools import flat_files
+#from gn2.utility.tools import flat_files
 
 
 class EmptyConfigurations(Exception):
diff --git a/wqflask/maintenance/get_group_samplelists.py b/gn2/maintenance/get_group_samplelists.py
index 0a450d3f..6af637ea 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/gn2/maintenance/get_group_samplelists.py
@@ -2,7 +2,7 @@ import os
 import glob
 import gzip
 
-from base import webqtlConfig
+from gn2.base import webqtlConfig
 
 
 def get_samplelist(file_type, geno_file):
diff --git a/wqflask/maintenance/print_benchmark.py b/gn2/maintenance/print_benchmark.py
index 9d12da8a..9d12da8a 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/gn2/maintenance/print_benchmark.py
diff --git a/wqflask/maintenance/quantile_normalize.py b/gn2/maintenance/quantile_normalize.py
index 36049a82..5620b552 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/gn2/maintenance/quantile_normalize.py
@@ -7,9 +7,9 @@ import pandas as pd
 
 from flask import Flask, g, request
 
-from wqflask import app
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask import app
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 
 def create_dataframe(input_file):
diff --git a/wqflask/maintenance/set_resource_defaults.py b/gn2/maintenance/set_resource_defaults.py
index cebe33c0..f9e5494a 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/gn2/maintenance/set_resource_defaults.py
@@ -23,16 +23,16 @@ import json
 sys.path.insert(0, './')
 
 # NEW: import app to avoid a circular dependency on utility.tools
-from wqflask import app
+from gn2.wqflask import app
 
-from utility import hmac
-from utility.tools import get_setting
-from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
+from gn2.utility import hmac
+from gn2.utility.tools import get_setting
+from gn2.utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
 Redis = get_redis_conn()
 
 import urllib.parse
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 
 def insert_probeset_resources(cursor, default_owner_id):
diff --git a/wqflask/run_gunicorn.py b/gn2/run_gunicorn.py
index af117466..6de470fe 100644
--- a/wqflask/run_gunicorn.py
+++ b/gn2/run_gunicorn.py
@@ -9,8 +9,8 @@
 
 print("===> Starting up Gunicorn process")
 
-from gn2_main import app
-from utility.startup_config import app_config
+from gn2.gn2_main import app
+from gn2.utility.startup_config import app_config
 
 app_config()
 
diff --git a/wqflask/runserver.py b/gn2/runserver.py
index 0ec4846a..45a51385 100644
--- a/wqflask/runserver.py
+++ b/gn2/runserver.py
@@ -8,8 +8,8 @@
 # /sbin/iptables -A INPUT -p tcp -i eth0 -s ! 71.236.239.43 --dport 5003 -j DROP
 
 from gn2_main import app
-from utility.startup_config import app_config
-from utility.tools import WEBSERVER_MODE, SERVER_PORT
+from gn2.utility.startup_config import app_config
+from gn2.utility.tools import WEBSERVER_MODE, SERVER_PORT
 
 import logging
 
diff --git a/wqflask/scripts/__init__.py b/gn2/scripts/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/scripts/__init__.py
+++ b/gn2/scripts/__init__.py
diff --git a/wqflask/scripts/corr_compute.py b/gn2/scripts/corr_compute.py
index 34c3ad54..44dcac68 100644
--- a/wqflask/scripts/corr_compute.py
+++ b/gn2/scripts/corr_compute.py
@@ -8,10 +8,10 @@ import datetime
 
 from flask import g
 
-from wqflask import app
-from wqflask.user_session import UserSession
-from wqflask.correlation.show_corr_results import set_template_vars
-from wqflask.correlation.correlation_gn3_api import compute_correlation
+from gn2.wqflask import app
+from gn2.wqflask.user_session import UserSession
+from gn2.wqflask.correlation.show_corr_results import set_template_vars
+from gn2.wqflask.correlation.correlation_gn3_api import compute_correlation
 
 class UserSessionSimulator():
 
diff --git a/wqflask/scripts/parse_corr_html_results_to_csv.py b/gn2/scripts/parse_corr_html_results_to_csv.py
index 464eb2ca..464eb2ca 100644
--- a/wqflask/scripts/parse_corr_html_results_to_csv.py
+++ b/gn2/scripts/parse_corr_html_results_to_csv.py
diff --git a/wqflask/scripts/profile_corrs.py b/gn2/scripts/profile_corrs.py
index a42e2935..5f9a06da 100644
--- a/wqflask/scripts/profile_corrs.py
+++ b/gn2/scripts/profile_corrs.py
@@ -5,11 +5,11 @@ import cProfile
 
 from flask import g, request
 
-from utility.startup_config import app_config
+from gn2.utility.startup_config import app_config
 
-from wqflask import app
-from wqflask.user_session import UserSession
-from wqflask.correlation.correlation_gn3_api import compute_correlation
+from gn2.wqflask import app
+from gn2.wqflask.user_session import UserSession
+from gn2.wqflask.correlation.correlation_gn3_api import compute_correlation
 
 def sample_vals():
     return '{"C57BL/6J":"10.835","DBA/2J":"11.142","B6D2F1":"11.126","D2B6F1":"11.143","BXD1":"10.811","BXD2":"11.503","BXD5":"10.766","BXD6":"10.986","BXD8":"11.050","BXD9":"10.822","BXD11":"10.670","BXD12":"10.946","BXD13":"10.890","BXD14":"x","BXD15":"10.884","BXD16":"11.222","BXD18":"x","BXD19":"10.968","BXD20":"10.962","BXD21":"10.906","BXD22":"11.080","BXD23":"11.046","BXD24":"11.146","BXD24a":"x","BXD25":"x","BXD27":"11.078","BXD28":"11.034","BXD29":"10.808","BXD30":"x","BXD31":"11.087","BXD32":"11.029","BXD33":"10.662","BXD34":"11.482","BXD35":"x","BXD36":"x","BXD37":"x","BXD38":"10.836","BXD39":"10.926","BXD40":"10.638","BXD41":"x","BXD42":"10.974","BXD43":"10.828","BXD44":"10.900","BXD45":"11.358","BXD48":"11.042","BXD48a":"10.975","BXD49":"x","BXD50":"11.228","BXD51":"11.126","BXD52":"x","BXD53":"x","BXD54":"x","BXD55":"11.580","BXD56":"x","BXD59":"x","BXD60":"10.829","BXD61":"11.152","BXD62":"11.156","BXD63":"10.942","BXD64":"10.506","BXD65":"11.126","BXD65a":"11.272","BXD65b":"11.157","BXD66":"11.071","BXD67":"11.080","BXD68":"10.997","BXD69":"11.096","BXD70":"11.152","BXD71":"x","BXD72":"x","BXD73":"11.262","BXD73a":"11.444","BXD73b":"x","BXD74":"10.974","BXD75":"11.150","BXD76":"10.920","BXD77":"10.928","BXD78":"x","BXD79":"11.371","BXD81":"x","BXD83":"10.946","BXD84":"11.181","BXD85":"10.992","BXD86":"10.770","BXD87":"11.200","BXD88":"x","BXD89":"10.930","BXD90":"11.183","BXD91":"x","BXD93":"11.056","BXD94":"10.737","BXD95":"x","BXD98":"10.986","BXD99":"10.892","BXD100":"x","BXD101":"x","BXD102":"x","BXD104":"x","BXD105":"x","BXD106":"x","BXD107":"x","BXD108":"x","BXD109":"x","BXD110":"x","BXD111":"x","BXD112":"x","BXD113":"x","BXD114":"x","BXD115":"x","BXD116":"x","BXD117":"x","BXD119":"x","BXD120":"x","BXD121":"x","BXD122":"x","BXD123":"x","BXD124":"x","BXD125":"x","BXD126":"x","BXD127":"x","BXD128":"x","BXD128a":"x","BXD130":"x","BXD131":"x","BXD132":"x","BXD133":"x","BXD134":"x","BXD135":"x","BXD136":"x","BXD137":"x","BXD138":"x","BXD139":"x","BXD141":"x","BXD142":"x","BXD144":"x","BXD145":"x","BXD146":"x","BXD147":"x","BXD148":"x","BXD149":"x","BXD150":"x","BXD151":"x","BXD152":"x","BXD153":"x","BXD154":"x","BXD155":"x","BXD156":"x","BXD157":"x","BXD160":"x","BXD161":"x","BXD162":"x","BXD165":"x","BXD168":"x","BXD169":"x","BXD170":"x","BXD171":"x","BXD172":"x","BXD173":"x","BXD174":"x","BXD175":"x","BXD176":"x","BXD177":"x","BXD178":"x","BXD180":"x","BXD181":"x","BXD183":"x","BXD184":"x","BXD186":"x","BXD187":"x","BXD188":"x","BXD189":"x","BXD190":"x","BXD191":"x","BXD192":"x","BXD193":"x","BXD194":"x","BXD195":"x","BXD196":"x","BXD197":"x","BXD198":"x","BXD199":"x","BXD200":"x","BXD201":"x","BXD202":"x","BXD203":"x","BXD204":"x","BXD205":"x","BXD206":"x","BXD207":"x","BXD208":"x","BXD209":"x","BXD210":"x","BXD211":"x","BXD212":"x","BXD213":"x","BXD214":"x","BXD215":"x","BXD216":"x","BXD217":"x","BXD218":"x","BXD219":"x","BXD220":"x"}'
diff --git a/wqflask/scripts/run_external.py b/gn2/scripts/run_external.py
index b44a6db7..297d17a1 100644
--- a/wqflask/scripts/run_external.py
+++ b/gn2/scripts/run_external.py
@@ -17,7 +17,7 @@ from tempfile import TemporaryDirectory
 # import psutil
 from redis import Redis
 
-import jobs.jobs as jobs
+import gn2.jobs.jobs as jobs
 
 def print_help(args, parser):
     print(parser.format_help())
diff --git a/wqflask/tests/__init__.py b/gn2/tests/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/__init__.py
+++ b/gn2/tests/__init__.py
diff --git a/wqflask/tests/integration/__init__.py b/gn2/tests/integration/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/integration/__init__.py
+++ b/gn2/tests/integration/__init__.py
diff --git a/wqflask/tests/integration/wqflask/__init__.py b/gn2/tests/integration/wqflask/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/integration/wqflask/__init__.py
+++ b/gn2/tests/integration/wqflask/__init__.py
diff --git a/wqflask/tests/unit/__init__.py b/gn2/tests/unit/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/__init__.py
+++ b/gn2/tests/unit/__init__.py
diff --git a/wqflask/tests/unit/base/__init__.py b/gn2/tests/unit/base/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/base/__init__.py
+++ b/gn2/tests/unit/base/__init__.py
diff --git a/wqflask/tests/unit/base/test_data_set.py b/gn2/tests/unit/base/test_data_set.py
index 744c8a94..9f9fb132 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/gn2/tests/unit/base/test_data_set.py
@@ -5,9 +5,9 @@ from unittest import mock
 from dataclasses import dataclass
 from gn3.monads import MonadicDict
 
-from wqflask import app
-from base.data_set import DatasetType
-from base.data_set.dataset import DataSet
+from gn2.wqflask import app
+from gn2.base.data_set import DatasetType
+from gn2.base.data_set.dataset import DataSet
 
 GEN_MENU_JSON = """
 {
@@ -173,7 +173,7 @@ class TestDataSetTypes(unittest.TestCase):
                              ("All Phenotypes", redis_mock, cursor_mock), "Publish")
             redis_mock.get.assert_called_once_with("dataset_structure")
 
-    @mock.patch('base.data_set.datasettype.requests.get')
+    @mock.patch('gn2.base.data_set.datasettype.requests.get')
     def test_data_set_type_with_empty_redis(self, request_mock):
         """Test that DatasetType returns correctly if the Redis Instance is empty and
         the name variable exists in the dictionary
@@ -204,8 +204,8 @@ class TestDataSetTypes(unittest.TestCase):
 class TestDatasetAccessionId(unittest.TestCase):
     """Tests for the DataSetType class"""
 
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
+    @mock.patch("gn2.base.data_set.dataset.query_sql")
+    @mock.patch("gn2.base.data_set.dataset.DatasetGroup")
     def test_get_accession_id(self, mock_dataset_group, mock_query_sql):
         def mock_fn():
             yield MonadicDict({"accession_id": 7})
@@ -221,8 +221,8 @@ class TestDatasetAccessionId(unittest.TestCase):
             .accession_id\
             .bind(lambda x: self.assertEqual(7, x))
 
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
+    @mock.patch("gn2.base.data_set.dataset.query_sql")
+    @mock.patch("gn2.base.data_set.dataset.DatasetGroup")
     def test_get_accession_id_empty_return(self, mock_dataset_group,
                                            mock_query_sql):
         mock_dataset_group.return_value = MockGroup()
diff --git a/wqflask/tests/unit/base/test_general_object.py b/gn2/tests/unit/base/test_general_object.py
index 00fd3c72..1301f18b 100644
--- a/wqflask/tests/unit/base/test_general_object.py
+++ b/gn2/tests/unit/base/test_general_object.py
@@ -1,6 +1,6 @@
 import unittest
 
-from base.GeneralObject import GeneralObject
+from gn2.base.GeneralObject import GeneralObject
 
 
 class TestGeneralObjectTests(unittest.TestCase):
diff --git a/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py b/gn2/tests/unit/base/test_mrna_assay_tissue_data.py
index c43fb4b6..5bc28ffa 100644
--- a/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py
+++ b/gn2/tests/unit/base/test_mrna_assay_tissue_data.py
@@ -1,5 +1,5 @@
 import pytest
-from base.mrna_assay_tissue_data import MrnaAssayTissueData
+from gn2.base.mrna_assay_tissue_data import MrnaAssayTissueData
 
 
 @pytest.mark.parametrize(
diff --git a/wqflask/tests/unit/base/test_species.py b/gn2/tests/unit/base/test_species.py
index f12bde6d..d2845b25 100644
--- a/wqflask/tests/unit/base/test_species.py
+++ b/gn2/tests/unit/base/test_species.py
@@ -1,8 +1,8 @@
 """Tests wqflask/base/species.py"""
 import pytest
-from base.species import TheSpecies
-from base.species import IndChromosome
-from base.species import Chromosomes
+from gn2.base.species import TheSpecies
+from gn2.base.species import IndChromosome
+from gn2.base.species import Chromosomes
 from collections import OrderedDict
 from dataclasses import dataclass
 
@@ -30,7 +30,7 @@ class MockDataset:
      (None, "Random Dataset", None, 1)))
 def test_species(mocker, species_name, dataset,
                  expected_name, chromosome_param):
-    _c = mocker.patch("base.species.Chromosomes",
+    _c = mocker.patch("gn2.base.species.Chromosomes",
                       return_value=chromosome_param)
     test_species = TheSpecies(dataset=dataset,
                               species_name=species_name)
diff --git a/wqflask/tests/unit/base/test_trait.py b/gn2/tests/unit/base/test_trait.py
index 5a27e243..2adb1fdf 100644
--- a/wqflask/tests/unit/base/test_trait.py
+++ b/gn2/tests/unit/base/test_trait.py
@@ -3,8 +3,8 @@
 import unittest
 from unittest import mock
 
-from base.trait import GeneralTrait
-from base.trait import retrieve_trait_info
+from gn2.base.trait import GeneralTrait
+from gn2.base.trait import retrieve_trait_info
 
 
 class TestResponse:
@@ -31,7 +31,7 @@ class MockTrait(GeneralTrait):
 
 class TestRetrieveTraitInfo(unittest.TestCase):
     """Tests for 'retrieve_trait_info'"""
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_empty_dataset(self, mock_db):
         """Test that an exception is raised when dataset is empty"""
         conn = mock.MagicMock()
@@ -40,9 +40,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
             retrieve_trait_info(trait=mock.MagicMock(),
                                 dataset={})
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_empty_trait_info(self,
                                                        mock_db,
                                                        requests_mock):
@@ -57,9 +57,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
             retrieve_trait_info(trait=mock.MagicMock(),
                                 dataset=mock.MagicMock())
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_non_empty_trait_info(self,
                                                            mock_db,
                                                            requests_mock):
@@ -80,9 +80,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         self.assertEqual(test_trait.c, 3)
         self.assertEqual(test_trait.d, 4)
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_utf8_parsing(self,
                                               mock_db,
                                               requests_mock):
@@ -120,9 +120,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
 
 
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.database_connection')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.database_connection')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_non_empty_lrs(self,
                                                     resource_id_mock,
                                                     mock_db,
@@ -169,9 +169,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                              "2.4")
 
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_empty_lrs_field(self,
                                                       resource_id_mock,
                                                       g_mock,
@@ -215,9 +215,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                          "Chr2: 3.000000")
         
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_empty_chr_field(self,
                                                       resource_id_mock,
                                                       g_mock,
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/gn2/tests/unit/base/test_webqtl_case_data.py
index e1555cb4..250b8358 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/gn2/tests/unit/base/test_webqtl_case_data.py
@@ -1,8 +1,8 @@
 """Tests for wqflask/base/webqtlCaseData.py"""
 import unittest
 
-from wqflask import app  # Required because of utility.tools in webqtlCaseData.py
-from base.webqtlCaseData import webqtlCaseData
+from gn2.wqflask import app  # Required because of utility.tools in webqtlCaseData.py
+from gn2.base.webqtlCaseData import webqtlCaseData
 
 
 class TestWebqtlCaseData(unittest.TestCase):
diff --git a/wqflask/tests/unit/utility/__init__.py b/gn2/tests/unit/utility/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/utility/__init__.py
+++ b/gn2/tests/unit/utility/__init__.py
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/gn2/tests/unit/utility/test_authentication_tools.py
index fb8de292..90945b0f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/gn2/tests/unit/utility/test_authentication_tools.py
@@ -2,8 +2,8 @@
 import unittest
 from unittest import mock
 
-from utility.authentication_tools import check_resource_availability
-from utility.authentication_tools import add_new_resource
+from gn2.utility.authentication_tools import check_resource_availability
+from gn2.utility.authentication_tools import add_new_resource
 
 
 class TestResponse:
@@ -38,10 +38,10 @@ def mock_add_resource(resource_ob, update=False):
 
 class TestCheckResourceAvailability(unittest.TestCase):
     """Test methods related to checking the resource availability"""
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_default_mask(
             self,
             resource_id_mock,
@@ -56,11 +56,11 @@ class TestCheckResourceAvailability(unittest.TestCase):
         add_new_resource_mock.return_value = {"default_mask": 2}
         self.assertEqual(check_resource_availability(test_dataset, user_id), 2)
 
-    @mock.patch('utility.authentication_tools.requests.get')
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.requests.get')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_non_default_mask(
             self,
             resource_id_mock,
@@ -77,13 +77,13 @@ class TestCheckResourceAvailability(unittest.TestCase):
         self.assertEqual(check_resource_availability(test_dataset, user_id),
                          ['foo'])
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
                 "SUPERUSER")
-    @mock.patch('utility.authentication_tools.requests.get')
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.requests.get')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_of_super_user(
             self,
             resource_id_mock,
@@ -100,14 +100,14 @@ class TestCheckResourceAvailability(unittest.TestCase):
         self.assertEqual(check_resource_availability(test_dataset, user_id),
                          "SUPERUSER")
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
     def test_check_resource_availability_string_dataset(self):
         """Test the resource availability if the dataset is a string"""
         self.assertEqual(check_resource_availability("Test", user_id),
                          "John Doe")
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
     def test_check_resource_availability_temp(self):
         """Test the resource availability if the dataset is a string"""
@@ -119,10 +119,10 @@ class TestCheckResourceAvailability(unittest.TestCase):
 
 class TestAddNewResource(unittest.TestCase):
     """Test cases for add_new_resource method"""
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_publish_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is 'publish'"""
         group_code_mock.return_value = "Test"
@@ -143,10 +143,10 @@ class TestAddNewResource(unittest.TestCase):
         self.assertEqual(add_new_resource(test_dataset),
                          expected_value)
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_geno_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is 'geno'"""
         group_code_mock.return_value = "Test"
@@ -167,10 +167,10 @@ class TestAddNewResource(unittest.TestCase):
         self.assertEqual(add_new_resource(test_dataset),
                          expected_value)
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_other_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
         group_code_mock.return_value = "Test"
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/gn2/tests/unit/utility/test_chunks.py
index 1d349193..1b5a9413 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/gn2/tests/unit/utility/test_chunks.py
@@ -2,7 +2,7 @@
 
 import unittest
 
-from utility.chunks import divide_into_chunks
+from gn2.utility.chunks import divide_into_chunks
 
 
 class TestChunks(unittest.TestCase):
diff --git a/wqflask/tests/unit/utility/test_corestats.py b/gn2/tests/unit/utility/test_corestats.py
index cf91a248..c0eaf566 100644
--- a/wqflask/tests/unit/utility/test_corestats.py
+++ b/gn2/tests/unit/utility/test_corestats.py
@@ -2,7 +2,7 @@
 
 import unittest
 
-from utility.corestats import Stats
+from gn2.utility.corestats import Stats
 
 
 class TestChunks(unittest.TestCase):
diff --git a/wqflask/tests/unit/utility/test_corr_result_helpers.py b/gn2/tests/unit/utility/test_corr_result_helpers.py
index e196fbdf..59260ba6 100644
--- a/wqflask/tests/unit/utility/test_corr_result_helpers.py
+++ b/gn2/tests/unit/utility/test_corr_result_helpers.py
@@ -1,7 +1,7 @@
 """ Test correlation helper methods """
 
 import unittest
-from utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples
+from gn2.utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples
 
 
 class TestCorrelationHelpers(unittest.TestCase):
diff --git a/wqflask/tests/unit/utility/test_formatting.py b/gn2/tests/unit/utility/test_formatting.py
index 9d3033d1..aad9735d 100644
--- a/wqflask/tests/unit/utility/test_formatting.py
+++ b/gn2/tests/unit/utility/test_formatting.py
@@ -1,5 +1,5 @@
 import unittest
-from utility.formatting import numify, commify
+from gn2.utility.formatting import numify, commify
 
 
 class TestFormatting(unittest.TestCase):
diff --git a/wqflask/tests/unit/utility/test_hmac.py b/gn2/tests/unit/utility/test_hmac.py
index 13d6261d..f148ea5b 100644
--- a/wqflask/tests/unit/utility/test_hmac.py
+++ b/gn2/tests/unit/utility/test_hmac.py
@@ -3,20 +3,20 @@
 import unittest
 from unittest import mock
 
-from utility.hmac import data_hmac
-from utility.hmac import url_for_hmac
-from utility.hmac import hmac_creation
+from gn2.utility.hmac import data_hmac
+from gn2.utility.hmac import url_for_hmac
+from gn2.utility.hmac import hmac_creation
 
 
 class TestHmacUtil(unittest.TestCase):
     """Test Utility method for hmac creation"""
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_hmac_creation(self):
         """Test hmac creation with a utf-8 string"""
         self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
 
-    @mock.patch("utility.hmac.app.config",
+    @mock.patch("gn2.utility.hmac.app.config",
                 {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
                                       '\xd9\\H@\\\x9f`\x98d^'
                                       '\xb4a;\xc6OM\x946a\xbc'
@@ -29,21 +29,21 @@ class TestHmacUtil(unittest.TestCase):
             hmac_creation(uuid_),
             "af4fcf5eace9e7c864ce")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_data_hmac(self):
         """Test data_hmac fn with a utf-8 string"""
         self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
-    @mock.patch("utility.hmac.url_for")
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.url_for")
     def test_url_for_hmac_with_plain_url(self, mock_url):
         """Test url_for_hmac without params"""
         mock_url.return_value = "https://mock_url.com/ファイ/"
         self.assertEqual(url_for_hmac("ファイ"),
                          "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
-    @mock.patch("utility.hmac.url_for")
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.url_for")
     def test_url_for_hmac_with_param_in_url(self, mock_url):
         """Test url_for_hmac with params"""
         mock_url.return_value = "https://mock_url.com/?ファイ=1"
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/gn2/tests/unit/utility/test_type_checking.py
index 48d110c7..e7b8e953 100644
--- a/wqflask/tests/unit/utility/test_type_checking.py
+++ b/gn2/tests/unit/utility/test_type_checking.py
@@ -1,10 +1,10 @@
 import unittest
-from utility.type_checking import is_float
-from utility.type_checking import is_int
-from utility.type_checking import is_str
-from utility.type_checking import get_float
-from utility.type_checking import get_int
-from utility.type_checking import get_string
+from gn2.utility.type_checking import is_float
+from gn2.utility.type_checking import is_int
+from gn2.utility.type_checking import is_str
+from gn2.utility.type_checking import get_float
+from gn2.utility.type_checking import get_int
+from gn2.utility.type_checking import get_string
 
 
 class TestTypeChecking(unittest.TestCase):
diff --git a/wqflask/tests/unit/wqflask/__init__.py b/gn2/tests/unit/wqflask/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/__init__.py
+++ b/gn2/tests/unit/wqflask/__init__.py
diff --git a/wqflask/tests/unit/wqflask/api/__init__.py b/gn2/tests/unit/wqflask/api/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/api/__init__.py
+++ b/gn2/tests/unit/wqflask/api/__init__.py
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/gn2/tests/unit/wqflask/api/test_correlation.py
index 53e1b9a2..2a1907af 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/gn2/tests/unit/wqflask/api/test_correlation.py
@@ -1,12 +1,12 @@
 import unittest
 from unittest import mock
-from wqflask import app
+from gn2.wqflask import app
 from collections import OrderedDict
-from wqflask.api.correlation import init_corr_params
-from wqflask.api.correlation import convert_to_mouse_gene_id
-from wqflask.api.correlation import do_literature_correlation_for_all_traits
-from wqflask.api.correlation import get_sample_r_and_p_values
-from wqflask.api.correlation import calculate_results
+from gn2.wqflask.api.correlation import init_corr_params
+from gn2.wqflask.api.correlation import convert_to_mouse_gene_id
+from gn2.wqflask.api.correlation import do_literature_correlation_for_all_traits
+from gn2.wqflask.api.correlation import get_sample_r_and_p_values
+from gn2.wqflask.api.correlation import calculate_results
 
 
 class AttributeSetter:
@@ -39,7 +39,7 @@ class TestCorrelations(unittest.TestCase):
 
         self.assertEqual(corr_params_results, expected_results)
 
-    @mock.patch("wqflask.api.correlation.database_connection")
+    @mock.patch("gn2.wqflask.api.correlation.database_connection")
     def test_convert_to_mouse_gene_id(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
@@ -59,8 +59,8 @@ class TestCorrelations(unittest.TestCase):
                 convert_to_mouse_gene_id(species="human", gene_id="H1"), "MG-2"
             )
 
-    @mock.patch("wqflask.api.correlation.database_connection")
-    @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
+    @mock.patch("gn2.wqflask.api.correlation.database_connection")
+    @mock.patch("gn2.wqflask.api.correlation.convert_to_mouse_gene_id")
     def test_do_literature_correlation_for_all_traits(
         self, mock_convert_to_mouse_geneid, mock_db
     ):
@@ -88,7 +88,7 @@ class TestCorrelations(unittest.TestCase):
             }
             self.assertEqual(results, expected_results)
 
-    @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
+    @mock.patch("gn2.wqflask.api.correlation.corr_result_helpers.normalize_values")
     def test_get_sample_r_and_p_values(self, mock_normalize):
 
         group = AttributeSetter(
@@ -146,7 +146,7 @@ class TestCorrelations(unittest.TestCase):
             self.assertAlmostEqual(val, results_spearmanr[i], 4)
         self.assertEqual(results_num_overlap, None)
 
-    @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
+    @mock.patch("gn2.wqflask.api.correlation.do_literature_correlation_for_all_traits")
     def test_calculate_results(self, literature_correlation):
 
         literature_correlation.return_value = {
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/gn2/tests/unit/wqflask/api/test_gen_menu.py
index 7e477da2..2416b3f6 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/gn2/tests/unit/wqflask/api/test_gen_menu.py
@@ -2,14 +2,14 @@
 import unittest
 from unittest import mock
 
-from wqflask.api.gen_menu import gen_dropdown_json
-from wqflask.api.gen_menu import get_groups
-from wqflask.api.gen_menu import get_types
-from wqflask.api.gen_menu import get_datasets
-from wqflask.api.gen_menu import phenotypes_exist
-from wqflask.api.gen_menu import genotypes_exist
-from wqflask.api.gen_menu import build_datasets
-from wqflask.api.gen_menu import build_types
+from gn2.wqflask.api.gen_menu import gen_dropdown_json
+from gn2.wqflask.api.gen_menu import get_groups
+from gn2.wqflask.api.gen_menu import get_types
+from gn2.wqflask.api.gen_menu import get_datasets
+from gn2.wqflask.api.gen_menu import phenotypes_exist
+from gn2.wqflask.api.gen_menu import genotypes_exist
+from gn2.wqflask.api.gen_menu import build_datasets
+from gn2.wqflask.api.gen_menu import build_types
 
 
 class TestGenMenu(unittest.TestCase):
@@ -258,7 +258,7 @@ class TestGenMenu(unittest.TestCase):
                 "ORDER BY -ProbeSetFreeze.OrderList DESC, "
                 "ProbeSetFreeze.CreateTime DESC")
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_build_types(self, datasets_mock):
         """Test that correct tissue metadata is returned"""
         db_mock = mock.MagicMock()
@@ -286,9 +286,9 @@ class TestGenMenu(unittest.TestCase):
                 "ORDER BY Tissue.Name"
             )
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_existing_genotype_and_phenotypes(
             self,
             phenotypes_exist_mock,
@@ -310,9 +310,9 @@ class TestGenMenu(unittest.TestCase):
                                    mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes(
             self,
             phenotypes_exist_mock,
@@ -329,9 +329,9 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_types(self.test_group, mock.MagicMock()),
                          {'mouse': {}, 'human': {}})
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype(
             self,
             phenotypes_exist_mock,
@@ -357,7 +357,7 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_types(self.test_group, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_get_datasets_with_existent_datasets(self,
                                                  build_datasets_mock):
         """Test correct dataset is returned with existent build_datasets"""
@@ -379,7 +379,7 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_get_datasets_with_non_existent_datasets(self,
                                                      build_datasets_mock):
         """Test correct dataset is returned with non-existent build_datasets"""
@@ -393,10 +393,10 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.get_datasets')
-    @mock.patch('wqflask.api.gen_menu.get_types')
-    @mock.patch('wqflask.api.gen_menu.get_groups')
-    @mock.patch('wqflask.api.gen_menu.get_all_species')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_groups')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_all_species')
     def test_gen_dropdown_json(self,
                                species_mock,
                                groups_mock,
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/gn2/tests/unit/wqflask/api/test_mapping.py
index 006e9826..226e2a9b 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/gn2/tests/unit/wqflask/api/test_mapping.py
@@ -1,7 +1,7 @@
 import unittest
 from unittest import mock
-from wqflask.api.mapping import initialize_parameters
-from wqflask.api.mapping import do_mapping_for_api
+from gn2.wqflask.api.mapping import initialize_parameters
+from gn2.wqflask.api.mapping import do_mapping_for_api
 
 
 class AttributeSetter:
@@ -63,12 +63,12 @@ class TestMapping(unittest.TestCase):
 
         self.assertEqual(results_2, expected_results)
 
-    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl")
-    @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
-    @mock.patch("wqflask.api.mapping.initialize_parameters")
-    @mock.patch("wqflask.api.mapping.retrieve_sample_data")
-    @mock.patch("wqflask.api.mapping.create_trait")
-    @mock.patch("wqflask.api.mapping.data_set.create_dataset")
+    @mock.patch("gn2.wqflask.api.mapping.rqtl_mapping.run_rqtl")
+    @mock.patch("gn2.wqflask.api.mapping.gemma_mapping.run_gemma")
+    @mock.patch("gn2.wqflask.api.mapping.initialize_parameters")
+    @mock.patch("gn2.wqflask.api.mapping.retrieve_sample_data")
+    @mock.patch("gn2.wqflask.api.mapping.create_trait")
+    @mock.patch("gn2.wqflask.api.mapping.data_set.create_dataset")
     def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
         start_vars = {
             "db": "Temp",
diff --git a/wqflask/tests/unit/wqflask/api/test_markdown_routes.py b/gn2/tests/unit/wqflask/api/test_markdown_routes.py
index 4f575c4c..ecf64a81 100644
--- a/wqflask/tests/unit/wqflask/api/test_markdown_routes.py
+++ b/gn2/tests/unit/wqflask/api/test_markdown_routes.py
@@ -4,7 +4,7 @@ import unittest
 from unittest import mock
 
 from dataclasses import dataclass
-from wqflask.api.markdown import render_markdown
+from gn2.wqflask.api.markdown import render_markdown
 
 
 @dataclass
@@ -26,7 +26,7 @@ This is another sub-heading"""
 class TestMarkdownRoutesFunctions(unittest.TestCase):
     """Test cases for functions in markdown"""
 
-    @mock.patch('wqflask.api.markdown.requests.get')
+    @mock.patch('gn2.wqflask.api.markdown.requests.get')
     def test_render_markdown_when_fetching_locally(self, requests_mock):
         requests_mock.return_value = MockRequests404()
         markdown_content = render_markdown("general/glossary/glossary.md")
@@ -38,7 +38,7 @@ class TestMarkdownRoutesFunctions(unittest.TestCase):
         self.assertRegex(markdown_content,
                          "Content for general/glossary/glossary.md not available.")
 
-    @mock.patch('wqflask.api.markdown.requests.get')
+    @mock.patch('gn2.wqflask.api.markdown.requests.get')
     def test_render_markdown_when_fetching_remotely(self, requests_mock):
         requests_mock.return_value = MockRequests200()
         markdown_content = render_markdown("general/glossary/glossary.md")
diff --git a/wqflask/tests/unit/wqflask/correlation/__init__.py b/gn2/tests/unit/wqflask/correlation/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/correlation/__init__.py
+++ b/gn2/tests/unit/wqflask/correlation/__init__.py
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py
index bb07d41e..f76ef57e 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -3,15 +3,15 @@
 import unittest
 from unittest import mock
 
-from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
-from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+from gn2.wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
+from gn2.wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
 
 
 def test_tissue_corr_computation(mocker):
     """Test for cal_zero_order_corr_for_tiss"""
     primary_values = [9.288, 9.313, 8.988, 9.660, 8.21]
     target_values = [9.586, 8.498, 9.362, 8.820, 8.786]
-    _m = mocker.patch(("wqflask.correlation.correlation_functions."
+    _m = mocker.patch(("gn2.wqflask.correlation.correlation_functions."
                        "compute_corr_coeff_p_value"),
                       return_value=(0.51, 0.7))
     results = cal_zero_order_corr_for_tiss(primary_values, target_values)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py b/gn2/tests/unit/wqflask/correlation/test_correlation_gn3.py
index e1bd6d86..432dbc95 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
+++ b/gn2/tests/unit/wqflask/correlation/test_correlation_gn3.py
@@ -1,6 +1,6 @@
 """this module contains tests for code used in integrating to gn3 api"""
 from unittest import TestCase
-from base.data_set import create_dataset
+from gn2.base.data_set import create_dataset
 
 class TestCorrelation(TestCase):
 
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/gn2/tests/unit/wqflask/correlation/test_show_corr_results.py
index e29b18ca..b1459dd9 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
+++ b/gn2/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -1,6 +1,6 @@
 import unittest
 from unittest import mock
-from wqflask.correlation.show_corr_results import get_header_fields
+from gn2.wqflask.correlation.show_corr_results import get_header_fields
 
 
 class AttributeSetter:
diff --git a/wqflask/tests/unit/wqflask/marker_regression/__init__.py b/gn2/tests/unit/wqflask/marker_regression/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/__init__.py
+++ b/gn2/tests/unit/wqflask/marker_regression/__init__.py
diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
+++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
diff --git a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
+++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index f4869c45..580d79cf 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -1,7 +1,7 @@
 import unittest
 
 import htmlgen as HT
-from wqflask.marker_regression.display_mapping_results import (
+from gn2.wqflask.marker_regression.display_mapping_results import (
     DisplayMappingResults,
     HtmlGenWrapper
 )
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 9d988597..b4d80ad7 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -3,10 +3,10 @@ import os
 import unittest
 import random
 from unittest import mock
-from wqflask.marker_regression.gemma_mapping import run_gemma
-from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
-from wqflask.marker_regression.gemma_mapping import gen_covariates_file
-from wqflask.marker_regression.gemma_mapping import parse_loco_output
+from gn2.wqflask.marker_regression.gemma_mapping import run_gemma
+from gn2.wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
+from gn2.wqflask.marker_regression.gemma_mapping import gen_covariates_file
+from gn2.wqflask.marker_regression.gemma_mapping import parse_loco_output
 
 
 class AttributeSetter:
@@ -22,7 +22,7 @@ class MockGroup(AttributeSetter):
 
 class TestGemmaMapping(unittest.TestCase):
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output")
     def test_run_gemma_firstrun_set_false(self, mock_parse_loco):
         """add tests for gemma function where  first run is set to false"""
         dataset = AttributeSetter(
@@ -38,17 +38,17 @@ class TestGemmaMapping(unittest.TestCase):
         expected_results = ([], "file1")
         self.assertEqual(expected_results, result)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR",
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR",
                 os.path.join(os.path.dirname(__file__), "user/data"))
-    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
-    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.gen_covariates_file")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
     def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco):
         """add tests for run_gemma where first run is set to true"""
         this_chromosomes = {}
@@ -78,7 +78,7 @@ class TestGemmaMapping(unittest.TestCase):
             ('/home/user/imgfile_output.assoc.txt'))
         self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
     def test_gen_pheno_txt_file(self):
         """add tests for generating pheno txt file"""
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -95,9 +95,9 @@ class TestGemmaMapping(unittest.TestCase):
 
             filehandler.write.assert_has_calls(write_calls)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_trait")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_dataset")
     def test_gen_covariates_file(self, create_dataset, create_trait, flat_files):
         """add tests for generating covariates files"""
         covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2"
@@ -140,9 +140,9 @@ class TestGemmaMapping(unittest.TestCase):
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.json")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.json")
     def test_parse_loco_outputfile_found(self, mock_json, mock_os):
         """add tests for parse loco output file found"""
         mock_json.load.return_value = {
@@ -174,8 +174,8 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
                 {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -10.55, 'lod_score': 0.22184874961635637}]
             self.assertEqual(expected_results, results)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
     def test_parse_loco_outputfile_not_found(self, mock_os):
         """add tests for parse loco output where  output file not found"""
 
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index fd21a825..7542e15a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -1,11 +1,11 @@
 # test for wqflask/marker_regression/plink_mapping.py
 import unittest
 from unittest import mock
-from wqflask.marker_regression.plink_mapping import build_line_list
-from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file
-from wqflask.marker_regression.plink_mapping import flat_files
-from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink
-from wqflask.marker_regression.plink_mapping import parse_plink_output
+from gn2.wqflask.marker_regression.plink_mapping import build_line_list
+from gn2.wqflask.marker_regression.plink_mapping import get_samples_from_ped_file
+from gn2.wqflask.marker_regression.plink_mapping import flat_files
+from gn2.wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink
+from gn2.wqflask.marker_regression.plink_mapping import parse_plink_output
 
 
 class AttributeSetter:
@@ -27,7 +27,7 @@ class TestPlinkMapping(unittest.TestCase):
         self.assertEqual([], build_line_list())
         self.assertEqual(["this", "is", "an,", "irregular", "line"], results)
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.flat_files")
     def test_get_samples_from_ped_file(self, mock_flat_files):
         """test for getting samples from ped file"""
         dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
@@ -42,8 +42,8 @@ Expected_2\there
             self.assertEqual(
                 ["Expected_1", "Expected_2", "Expected_3"], results)
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
-    @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
     def test_gen_pheno_txt_file_plink(self, mock_samples):
         """test for getting gen_pheno txt file"""
         mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"]
@@ -64,8 +64,8 @@ Expected_2\there
 
             filehandler.close.assert_called_once()
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
-    @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.build_line_list")
     def test_parse_plink_output(self, mock_line_list):
         """test for parsing plink output"""
         chromosomes = [0, 34, 110, 89, 123, 23, 2]
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 8b4337ec..c2753141 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -1,13 +1,13 @@
 import unittest
 from unittest import mock
-from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+from gn2.wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
 
 # issues some methods in genofile object are not defined
 # modify samples should equal to vals
 
 
 class TestQtlReaperMapping(unittest.TestCase):
-    @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+    @mock.patch("gn2.wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
     def test_gen_pheno_txt_file(self):
         vals = ["V1", "x", "V4", "V3", "x"]
         samples = ["S1", "S2", "S3", "S4", "S5"]
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index b4423d8f..9f646fb0 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -2,7 +2,7 @@ import unittest
 from unittest import mock
 from dataclasses import dataclass
 
-from wqflask.marker_regression.rqtl_mapping import run_rqtl
+from gn2.wqflask.marker_regression.rqtl_mapping import run_rqtl
 
 @dataclass
 class MockGroup:
@@ -15,9 +15,9 @@ class MockDataset:
 
 class TestRqtlMapping(unittest.TestCase):
     """Tests for functions in rqtl_mapping.py"""
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.requests.post")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.locate")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
     def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
         """Test for run_rqtl with permutations > 0"""
         dataset_group = MockGroup("GP1", "file_geno")
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 2e1b5810..817bf2b9 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -2,13 +2,13 @@ import unittest
 import datetime
 from unittest import mock
 
-from wqflask.marker_regression.run_mapping import get_genofile_samplelist
-from wqflask.marker_regression.run_mapping import geno_db_exists
-from wqflask.marker_regression.run_mapping import write_input_for_browser
-from wqflask.marker_regression.run_mapping import export_mapping_results
-from wqflask.marker_regression.run_mapping import trim_markers_for_figure
-from wqflask.marker_regression.run_mapping import get_perm_strata
-from wqflask.marker_regression.run_mapping import get_chr_lengths
+from gn2.wqflask.marker_regression.run_mapping import get_genofile_samplelist
+from gn2.wqflask.marker_regression.run_mapping import geno_db_exists
+from gn2.wqflask.marker_regression.run_mapping import write_input_for_browser
+from gn2.wqflask.marker_regression.run_mapping import export_mapping_results
+from gn2.wqflask.marker_regression.run_mapping import trim_markers_for_figure
+from gn2.wqflask.marker_regression.run_mapping import get_perm_strata
+from gn2.wqflask.marker_regression.run_mapping import get_chr_lengths
 
 
 class AttributeSetter:
@@ -61,7 +61,7 @@ class TestRunMapping(unittest.TestCase):
         result_2 = get_genofile_samplelist(self.dataset)
         self.assertEqual(result_2, [])
 
-    @mock.patch("wqflask.marker_regression.run_mapping.data_set")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.data_set")
     def test_if_geno_db_exists(self, mock_data_set):
         mock_data_set.create_dataset.side_effect = [
             AttributeSetter({}), Exception()]
@@ -178,7 +178,7 @@ class TestRunMapping(unittest.TestCase):
 
         with mock.patch("builtins.open", mock.mock_open()) as mock_open:
 
-            with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+            with mock.patch("gn2.wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
                                        results_path="~/results", mapping_method="gemma", mapping_scale="physic",
                                        score_type="-logP", transform="qnorm",
@@ -215,7 +215,7 @@ class TestRunMapping(unittest.TestCase):
                 filehandler = mock_open()
                 filehandler.write.assert_has_calls(write_calls)
 
-    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice")
     def test_write_input_for_browser(self, mock_choice):
         """test for writing input for browser"""
         mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"]
diff --git a/wqflask/tests/unit/wqflask/show_trait/__init__.py b/gn2/tests/unit/wqflask/show_trait/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/show_trait/__init__.py
+++ b/gn2/tests/unit/wqflask/show_trait/__init__.py
diff --git a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
index 8aa3ffd5..1ecf394b 100644
--- a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
+++ b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -1,10 +1,10 @@
 import datetime
 import unittest
 from unittest import mock
-from wqflask.show_trait.export_trait_data import dict_to_sorted_list
-from wqflask.show_trait.export_trait_data import cmp_samples
-from wqflask.show_trait.export_trait_data import export_sample_table
-from wqflask.show_trait.export_trait_data import get_export_metadata
+from gn2.wqflask.show_trait.export_trait_data import dict_to_sorted_list
+from gn2.wqflask.show_trait.export_trait_data import cmp_samples
+from gn2.wqflask.show_trait.export_trait_data import export_sample_table
+from gn2.wqflask.show_trait.export_trait_data import get_export_metadata
 
 
 class AttributesSetter:
@@ -16,9 +16,9 @@ class AttributesSetter:
 class TestExportTraits(unittest.TestCase):
     """Test methods for exporting traits and metadata"""
 
-    @mock.patch("wqflask.show_trait.export_trait_data.datetime")
-    @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
-    @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.datetime")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.create_trait")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.data_set")
     def test_get_export_metadata(self, data_mock, trait_mock, date_mock):
         """test for exporting metadata with dataset.type=Publish"""
         mock_dataset = AttributesSetter({"type": "Publish",
diff --git a/wqflask/tests/unit/wqflask/show_trait/test_get_max_digits.py b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py
index da10b13c..45484f17 100644
--- a/wqflask/tests/unit/wqflask/show_trait/test_get_max_digits.py
+++ b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py
@@ -1,7 +1,7 @@
 import pytest
 import unittest
 
-from wqflask.show_trait.show_trait import get_max_digits
+from gn2.wqflask.show_trait.show_trait import get_max_digits
 
 @unittest.skip("Too complicated")
 @pytest.mark.parametrize(
diff --git a/wqflask/tests/unit/wqflask/snp_browser/__init__.py b/gn2/tests/unit/wqflask/snp_browser/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/__init__.py
+++ b/gn2/tests/unit/wqflask/snp_browser/__init__.py
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py
index a09d1538..bf0421c0 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -1,11 +1,11 @@
 import unittest
 from unittest import mock
-from wqflask import app
-from wqflask.snp_browser.snp_browser import get_gene_id
-from wqflask.snp_browser.snp_browser import get_gene_id_name_dict
-from wqflask.snp_browser.snp_browser import check_if_in_gene
-from wqflask.snp_browser.snp_browser import get_browser_sample_lists
-from wqflask.snp_browser.snp_browser import get_header_list
+from gn2.wqflask import app
+from gn2.wqflask.snp_browser.snp_browser import get_gene_id
+from gn2.wqflask.snp_browser.snp_browser import get_gene_id_name_dict
+from gn2.wqflask.snp_browser.snp_browser import check_if_in_gene
+from gn2.wqflask.snp_browser.snp_browser import get_browser_sample_lists
+from gn2.wqflask.snp_browser.snp_browser import get_header_list
 
 
 class TestSnpBrowser(unittest.TestCase):
@@ -102,7 +102,7 @@ class TestSnpBrowser(unittest.TestCase):
         self.assertEqual(expected_results, results_with_snp)
         self.assertEqual(expected_results_with_indel, results_with_indel)
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_get_gene_id(self, mock_db):
         db_query_value = (
             "SELECT geneId FROM GeneList WHERE " "SpeciesId = %s AND geneSymbol = %s"
@@ -122,7 +122,7 @@ class TestSnpBrowser(unittest.TestCase):
             )
             self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_gene_id_name_dict(self, mock_db):
         no_gene_names = []
         conn = mock.MagicMock()
@@ -164,7 +164,7 @@ class TestSnpBrowser(unittest.TestCase):
             self.assertEqual(results_found, expected_found)
             self.assertEqual(no_results, {})
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_check_if_in_gene(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
@@ -196,7 +196,7 @@ class TestSnpBrowser(unittest.TestCase):
             )
             self.assertEqual(gene_not_found, "")
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_get_browser_sample_lists(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/gn2/tests/unit/wqflask/test_collect.py
index 4e99de7f..6c1bafa5 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/gn2/tests/unit/wqflask/test_collect.py
@@ -4,7 +4,7 @@ import unittest
 from unittest import mock
 
 from flask import Flask
-from wqflask.collect import process_traits
+from gn2.wqflask.collect import process_traits
 
 app = Flask(__name__)
 
@@ -42,7 +42,7 @@ class TestCollect(unittest.TestCase):
     def tearDown(self):
         self.app_context.pop()
 
-    @mock.patch("wqflask.collect.g", MockFlaskG())
+    @mock.patch("gn2.wqflask.collect.g", MockFlaskG())
     def test_process_traits_with_bytestring(self):
         """
         Test that the correct traits are returned when the user is logged
@@ -58,7 +58,7 @@ class TestCollect(unittest.TestCase):
                  '1452447_at:HC_M2_0606_P',
                  '1452452_at:HC_M2_0606_P']))
 
-    @mock.patch("wqflask.collect.g", MockFlaskG())
+    @mock.patch("gn2.wqflask.collect.g", MockFlaskG())
     def test_process_traits_with_normal_string(self):
         """
         Test that the correct traits are returned when the user is logged
diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/gn2/tests/unit/wqflask/test_pbkdf2.py
index 7ad6c83e..ed4eff4f 100644
--- a/wqflask/tests/unit/wqflask/test_pbkdf2.py
+++ b/gn2/tests/unit/wqflask/test_pbkdf2.py
@@ -1,7 +1,7 @@
 """Test cases pbkdf2"""
 
 import unittest
-from wqflask.pbkdf2 import pbkdf2_hex
+from gn2.wqflask.pbkdf2 import pbkdf2_hex
 
 
 class TestPbkdf2(unittest.TestCase):
diff --git a/wqflask/tests/unit/wqflask/test_resource_manager.py b/gn2/tests/unit/wqflask/test_resource_manager.py
index f4335425..a4b3a0ee 100644
--- a/wqflask/tests/unit/wqflask/test_resource_manager.py
+++ b/gn2/tests/unit/wqflask/test_resource_manager.py
@@ -58,7 +58,7 @@ class TestGetUserMembership(unittest.TestCase):
 class TestCheckUserAccessRole(unittest.TestCase):
     """Test cases for `get_highest_user_access_role`"""
 
-    @mock.patch("wqflask.resource_manager.requests.get")
+    @mock.patch("gn2.wqflask.resource_manager.requests.get")
     def test_edit_access(self, requests_mock):
         """Test that the right access roles are set"""
         response = mock.PropertyMock(return_value=json.dumps(
@@ -76,7 +76,7 @@ class TestCheckUserAccessRole(unittest.TestCase):
              "metadata": DataRole.EDIT,
              "admin": AdminRole.EDIT_ACCESS})
 
-    @mock.patch("wqflask.resource_manager.requests.get")
+    @mock.patch("gn2.wqflask.resource_manager.requests.get")
     def test_no_access(self, requests_mock):
         response = mock.PropertyMock(return_value=json.dumps(
             {
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/gn2/tests/unit/wqflask/test_server_side.py
index be7ca2df..b3e90eb9 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/gn2/tests/unit/wqflask/test_server_side.py
@@ -1,6 +1,6 @@
 import unittest
 
-from wqflask.server_side import ServerSideTable
+from gn2.wqflask.server_side import ServerSideTable
 
 
 class TestServerSideTableTests(unittest.TestCase):
diff --git a/wqflask/tests/unit/wqflask/test_user_login.py b/gn2/tests/unit/wqflask/test_user_login.py
index 61cd9ab9..84e25d45 100644
--- a/wqflask/tests/unit/wqflask/test_user_login.py
+++ b/gn2/tests/unit/wqflask/test_user_login.py
@@ -1,7 +1,7 @@
 """Test cases for some methods in login.py"""
 
 import unittest
-from wqflask.user_login import encode_password
+from gn2.wqflask.user_login import encode_password
 
 
 class TestUserLogin(unittest.TestCase):
diff --git a/wqflask/tests/unit/wqflask/test_user_session.py b/gn2/tests/unit/wqflask/test_user_session.py
index ebb0334a..944e5b6a 100644
--- a/wqflask/tests/unit/wqflask/test_user_session.py
+++ b/gn2/tests/unit/wqflask/test_user_session.py
@@ -1,7 +1,7 @@
 """Test cases for some methods in user_session.py"""
 
 import unittest
-from wqflask.user_session import verify_cookie
+from gn2.wqflask.user_session import verify_cookie
 
 
 class TestUserSession(unittest.TestCase):
diff --git a/wqflask/tests/unit/wqflask/wgcna/__init__.py b/gn2/tests/unit/wqflask/wgcna/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/unit/wqflask/wgcna/__init__.py
+++ b/gn2/tests/unit/wqflask/wgcna/__init__.py
diff --git a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py b/gn2/tests/unit/wqflask/wgcna/test_wgcna.py
index 8e947e2f..2ed5e08f 100644
--- a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py
+++ b/gn2/tests/unit/wqflask/wgcna/test_wgcna.py
@@ -2,7 +2,7 @@
 """module contains for processing gn3 wgcna data"""
 from unittest import TestCase
 
-from wqflask.wgcna.gn3_wgcna import process_wgcna_data
+from gn2.wqflask.wgcna.gn3_wgcna import process_wgcna_data
 
 
 class DataProcessingTests(TestCase):
diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/gn2/tests/wqflask/show_trait/testSampleList.py
index 305586ce..1c5478bb 100644
--- a/wqflask/tests/wqflask/show_trait/testSampleList.py
+++ b/gn2/tests/wqflask/show_trait/testSampleList.py
@@ -1,7 +1,7 @@
 import unittest
 import re
 from unittest import mock
-from wqflask.show_trait.SampleList import natural_sort
+from gn2.wqflask.show_trait.SampleList import natural_sort
 
 
 class TestSampleList(unittest.TestCase):
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/gn2/tests/wqflask/show_trait/test_show_trait.py
index 1291037f..51b0c82c 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/gn2/tests/wqflask/show_trait/test_show_trait.py
@@ -2,15 +2,15 @@
 import unittest
 import pytest
 from unittest import mock
-from wqflask.show_trait.show_trait import check_if_attr_exists
-from wqflask.show_trait.show_trait import get_ncbi_summary
-from wqflask.show_trait.show_trait import has_num_cases
-from wqflask.show_trait.show_trait import get_table_widths
-from wqflask.show_trait.show_trait import get_categorical_variables
-from wqflask.show_trait.show_trait import get_trait_units
-from wqflask.show_trait.show_trait import get_nearest_marker
-from wqflask.show_trait.show_trait import get_genotype_scales
-from wqflask.show_trait.show_trait import get_scales_from_genofile
+from gn2.wqflask.show_trait.show_trait import check_if_attr_exists
+from gn2.wqflask.show_trait.show_trait import get_ncbi_summary
+from gn2.wqflask.show_trait.show_trait import has_num_cases
+from gn2.wqflask.show_trait.show_trait import get_table_widths
+from gn2.wqflask.show_trait.show_trait import get_categorical_variables
+from gn2.wqflask.show_trait.show_trait import get_trait_units
+from gn2.wqflask.show_trait.show_trait import get_nearest_marker
+from gn2.wqflask.show_trait.show_trait import get_genotype_scales
+from gn2.wqflask.show_trait.show_trait import get_scales_from_genofile
 
 
 class TraitObject:
@@ -39,10 +39,10 @@ def test_check_if_attr_exists(trait, id_type, expected):
 
 def test_get_ncbi_summary_request(mocker):
     trait = TraitObject({"geneid": "id"})
-    mocker.patch("wqflask.show_trait.show_trait.check_if_attr_exists",
+    mocker.patch("gn2.wqflask.show_trait.show_trait.check_if_attr_exists",
                  return_value=True)
     mock_get = mocker.patch(
-        "wqflask.show_trait.show_trait.requests.get",
+        "gn2.wqflask.show_trait.show_trait.requests.get",
         return_value=TraitObject({"content": """{
           "result":{
             "id":{
@@ -143,7 +143,7 @@ class TestTraits(unittest.TestCase):
         self.assertEqual(results, "this is a descriptionN/A")
         self.assertEqual(results_no_unit, "value")
 
-    @mock.patch("wqflask.show_trait.show_trait.database_connection")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.database_connection")
     def test_get_nearest_marker(self, mock_db):
         """test for getting nearest marker with non-empty db"""
         conn = mock.MagicMock()
@@ -170,7 +170,7 @@ class TestTraits(unittest.TestCase):
 
             self.assertEqual(results_with_item_db, "Geno1")
 
-    @mock.patch("wqflask.show_trait.show_trait.database_connection")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.database_connection")
     def test_get_nearest_marker_empty_db(self, mock_db):
         """test for getting nearest marker with empty db"""
         conn = mock.MagicMock()
@@ -187,7 +187,7 @@ class TestTraits(unittest.TestCase):
             cursor.execute.assert_called_once()
             self.assertEqual(results_empty_db, "")
 
-    @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.get_scales_from_genofile")
     def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):
         """test for getting genotype scales with genofile as list """
         # where genofile is instance of list
@@ -211,7 +211,7 @@ class TestTraits(unittest.TestCase):
         mock_get_scales.assert_has_calls(multiple_calls)
         self.assertEqual(results, expected_results)
 
-    @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.get_scales_from_genofile")
     def test_genotype_scales_with_genofile_other(self, mock_get_scales):
         """test for getting genotype scales with genofile as a string"""
         file_location = "~/another_file_location"
@@ -220,7 +220,7 @@ class TestTraits(unittest.TestCase):
         self.assertEqual(get_genotype_scales(file_location), expected_results)
         mock_get_scales.assert_called_once_with(file_location)
 
-    @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.locate_ignore_error")
     def test_get_scales_from_genofile_found(self, mock_ignore_location):
         """"add test for get scales from genofile where file is found"""
         mock_ignore_location.return_value = True
@@ -245,7 +245,7 @@ class TestTraits(unittest.TestCase):
             result2 = get_scales_from_genofile(file_location)
             self.assertEqual([['morgan', 'cM']], result2)
 
-    @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+    @mock.patch("gn2.wqflask.show_trait.show_trait.locate_ignore_error")
     def test_get_scales_from_genofile_not_found(self, mock_location_ignore):
         mock_location_ignore.return_value = False
 
diff --git a/wqflask/utility/Plot.py b/gn2/utility/Plot.py
index df7156b4..ace954e4 100644
--- a/wqflask/utility/Plot.py
+++ b/gn2/utility/Plot.py
@@ -30,9 +30,9 @@ from PIL import ImageFont
 
 from math import *
 
-import utility.corestats as corestats
-from base import webqtlConfig
-from utility.pillow_utils import draw_rotated_text
+import gn2.utility.corestats as corestats
+from gn2.base import webqtlConfig
+from gn2.utility.pillow_utils import draw_rotated_text
 
 
 # ---- Define common colours ---- #
diff --git a/wqflask/utility/TDCell.py b/gn2/utility/TDCell.py
index 4b0f4b1d..4b0f4b1d 100644
--- a/wqflask/utility/TDCell.py
+++ b/gn2/utility/TDCell.py
diff --git a/wqflask/utility/THCell.py b/gn2/utility/THCell.py
index f533dcb8..f533dcb8 100644
--- a/wqflask/utility/THCell.py
+++ b/gn2/utility/THCell.py
diff --git a/wqflask/utility/__init__.py b/gn2/utility/__init__.py
index 25273fa0..25273fa0 100644
--- a/wqflask/utility/__init__.py
+++ b/gn2/utility/__init__.py
diff --git a/wqflask/utility/after.py b/gn2/utility/after.py
index 2b560e48..5f802d35 100644
--- a/wqflask/utility/after.py
+++ b/gn2/utility/after.py
@@ -5,7 +5,7 @@ See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks
 
 from flask import g
 
-from wqflask import app
+from gn2.wqflask import app
 
 
 def after_this_request(f):
diff --git a/wqflask/utility/authentication_tools.py b/gn2/utility/authentication_tools.py
index 5d00d600..935f629e 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/gn2/utility/authentication_tools.py
@@ -2,14 +2,14 @@ import json
 import requests
 
 from flask import g
-from wqflask.database import database_connection
-from base import webqtlConfig
+from gn2.wqflask.database import database_connection
+from gn2.base import webqtlConfig
 
-from utility.redis_tools import (get_redis_conn,
+from gn2.utility.redis_tools import (get_redis_conn,
                                  get_resource_info,
                                  get_resource_id,
                                  add_resource)
-from utility.tools import get_setting, GN_PROXY_URL
+from gn2.utility.tools import get_setting, GN_PROXY_URL
 
 Redis = get_redis_conn()
 
diff --git a/wqflask/utility/chunks.py b/gn2/utility/chunks.py
index f6e88cbe..f6e88cbe 100644
--- a/wqflask/utility/chunks.py
+++ b/gn2/utility/chunks.py
diff --git a/wqflask/utility/corestats.py b/gn2/utility/corestats.py
index da0a21db..da0a21db 100644
--- a/wqflask/utility/corestats.py
+++ b/gn2/utility/corestats.py
diff --git a/wqflask/utility/corr_result_helpers.py b/gn2/utility/corr_result_helpers.py
index ea3ababf..ea3ababf 100644
--- a/wqflask/utility/corr_result_helpers.py
+++ b/gn2/utility/corr_result_helpers.py
diff --git a/wqflask/utility/db_tools.py b/gn2/utility/db_tools.py
index 98da33f2..07a6d9ec 100644
--- a/wqflask/utility/db_tools.py
+++ b/gn2/utility/db_tools.py
@@ -1,5 +1,5 @@
-from utility.tools import get_setting
-from wqflask.database import database_connection
+from gn2.utility.tools import get_setting
+from gn2.wqflask.database import database_connection
 
 
 def escape_(string):
diff --git a/wqflask/utility/external.py b/gn2/utility/external.py
index 805d2ffe..805d2ffe 100644
--- a/wqflask/utility/external.py
+++ b/gn2/utility/external.py
diff --git a/wqflask/utility/formatting.py b/gn2/utility/formatting.py
index 1da3e9b7..1da3e9b7 100644
--- a/wqflask/utility/formatting.py
+++ b/gn2/utility/formatting.py
diff --git a/wqflask/utility/gen_geno_ob.py b/gn2/utility/gen_geno_ob.py
index c7a1ea59..c7a1ea59 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/gn2/utility/gen_geno_ob.py
diff --git a/wqflask/utility/genofile_parser.py b/gn2/utility/genofile_parser.py
index 86d9823e..86d9823e 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/gn2/utility/genofile_parser.py
diff --git a/wqflask/utility/helper_functions.py b/gn2/utility/helper_functions.py
index 8b20bd74..fc101959 100644
--- a/wqflask/utility/helper_functions.py
+++ b/gn2/utility/helper_functions.py
@@ -1,11 +1,11 @@
-from base import data_set
-from base.trait import create_trait
-from base.species import TheSpecies
+from gn2.base import data_set
+from gn2.base.trait import create_trait
+from gn2.base.species import TheSpecies
 
-from utility import hmac
-from utility.tools import get_setting
+from gn2.utility import hmac
+from gn2.utility.tools import get_setting
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 
 def get_species_dataset_trait(self, start_vars):
diff --git a/wqflask/utility/hmac.py b/gn2/utility/hmac.py
index 29891677..d7c43f73 100644
--- a/wqflask/utility/hmac.py
+++ b/gn2/utility/hmac.py
@@ -3,7 +3,7 @@ import hashlib
 
 from flask import url_for
 
-from wqflask import app
+from gn2.wqflask import app
 
 
 def hmac_creation(stringy):
diff --git a/wqflask/utility/json/__init__.py b/gn2/utility/json/__init__.py
index b1141a34..b1141a34 100644
--- a/wqflask/utility/json/__init__.py
+++ b/gn2/utility/json/__init__.py
diff --git a/wqflask/utility/json/encoders.py b/gn2/utility/json/encoders.py
index 7c5839ac..7c5839ac 100644
--- a/wqflask/utility/json/encoders.py
+++ b/gn2/utility/json/encoders.py
diff --git a/wqflask/utility/monads.py b/gn2/utility/monads.py
index 2d708261..2d708261 100644
--- a/wqflask/utility/monads.py
+++ b/gn2/utility/monads.py
diff --git a/wqflask/utility/pillow_utils.py b/gn2/utility/pillow_utils.py
index e302df18..6e7b976d 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/gn2/utility/pillow_utils.py
@@ -1,6 +1,6 @@
 from PIL import Image, ImageColor, ImageDraw, ImageFont
 
-from utility.tools import TEMPDIR
+from gn2.utility.tools import TEMPDIR
 
 BLACK = ImageColor.getrgb("black")
 WHITE = ImageColor.getrgb("white")
diff --git a/wqflask/utility/redis_tools.py b/gn2/utility/redis_tools.py
index 945efbbd..b3d197a9 100644
--- a/wqflask/utility/redis_tools.py
+++ b/gn2/utility/redis_tools.py
@@ -4,7 +4,7 @@ import datetime
 
 import redis  # used for collections
 
-from utility.hmac import hmac_creation
+from gn2.utility.hmac import hmac_creation
 
 
 def get_redis_conn():
diff --git a/wqflask/utility/startup_config.py b/gn2/utility/startup_config.py
index 69cac124..4f9c392a 100644
--- a/wqflask/utility/startup_config.py
+++ b/gn2/utility/startup_config.py
@@ -1,11 +1,11 @@
 
-from wqflask import app
+from gn2.wqflask import app
 
-from utility.tools import WEBSERVER_MODE
-from utility.tools import show_settings
-from utility.tools import get_setting_int
-from utility.tools import get_setting
-from utility.tools import get_setting_bool
+from gn2.utility.tools import WEBSERVER_MODE
+from gn2.utility.tools import show_settings
+from gn2.utility.tools import get_setting_int
+from gn2.utility.tools import get_setting
+from gn2.utility.tools import get_setting_bool
 
 
 BLUE = '\033[94m'
diff --git a/wqflask/utility/svg.py b/gn2/utility/svg.py
index 912cd04c..912cd04c 100644
--- a/wqflask/utility/svg.py
+++ b/gn2/utility/svg.py
diff --git a/wqflask/utility/temp_data.py b/gn2/utility/temp_data.py
index 07c5a318..07c5a318 100644
--- a/wqflask/utility/temp_data.py
+++ b/gn2/utility/temp_data.py
diff --git a/wqflask/utility/tools.py b/gn2/utility/tools.py
index 283b0408..7adf8e8f 100644
--- a/wqflask/utility/tools.py
+++ b/gn2/utility/tools.py
@@ -7,7 +7,7 @@ import json
 import socket
 from pathlib import Path
 
-from wqflask import app
+from gn2.wqflask import app
 
 # Use the standard logger here to avoid a circular dependency
 import logging
@@ -235,7 +235,7 @@ ENDC = '\033[0m'
 
 
 def show_settings():
-    from utility.tools import LOG_LEVEL
+    from gn2.utility.tools import LOG_LEVEL
 
     print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC),
           file=sys.stderr)
diff --git a/wqflask/utility/type_checking.py b/gn2/utility/type_checking.py
index 5e98f4ae..5e98f4ae 100644
--- a/wqflask/utility/type_checking.py
+++ b/gn2/utility/type_checking.py
diff --git a/wqflask/utility/webqtlUtil.py b/gn2/utility/webqtlUtil.py
index 0cb71567..74a6ce4b 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/gn2/utility/webqtlUtil.py
@@ -30,7 +30,7 @@ import re
 import math
 from math import *
 
-from base import webqtlConfig
+from gn2.base import webqtlConfig
 
 # NL, 07/27/2010. moved from webqtlForm.py
 # Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
diff --git a/wqflask/wqflask/.DS_Store b/gn2/wqflask/.DS_Store
index a119e235..a119e235 100644
--- a/wqflask/wqflask/.DS_Store
+++ b/gn2/wqflask/.DS_Store
diff --git a/wqflask/wqflask/__init__.py b/gn2/wqflask/__init__.py
index 6de02bfc..9b714868 100644
--- a/wqflask/wqflask/__init__.py
+++ b/gn2/wqflask/__init__.py
@@ -14,31 +14,31 @@ from authlib.integrations.requests_client import OAuth2Session
 from flask import g, Flask, flash, session, url_for, redirect, current_app
 
 
-from utility import formatting
+from gn2.utility import formatting
 
 from gn3.authentication import DataRole, AdminRole
 
-from wqflask.group_manager import group_management
-from wqflask.resource_manager import resource_management
-from wqflask.metadata_edits import metadata_edit
-
-from wqflask.api.markdown import glossary_blueprint
-from wqflask.api.markdown import references_blueprint
-from wqflask.api.markdown import links_blueprint
-from wqflask.api.markdown import policies_blueprint
-from wqflask.api.markdown import environments_blueprint
-from wqflask.api.markdown import facilities_blueprint
-from wqflask.api.markdown import blogs_blueprint
-from wqflask.api.markdown import news_blueprint
-from wqflask.api.jobs import jobs as jobs_bp
-from wqflask.oauth2.routes import oauth2
-from wqflask.oauth2.checks import user_logged_in
-from wqflask.oauth2.collections import num_collections
-from wqflask.oauth2.request_utils import user_details, authserver_authorise_uri
-
-from wqflask.jupyter_notebooks import jupyter_notebooks
-
-from wqflask.startup import (
+from gn2.wqflask.group_manager import group_management
+from gn2.wqflask.resource_manager import resource_management
+from gn2.wqflask.metadata_edits import metadata_edit
+
+from gn2.wqflask.api.markdown import glossary_blueprint
+from gn2.wqflask.api.markdown import references_blueprint
+from gn2.wqflask.api.markdown import links_blueprint
+from gn2.wqflask.api.markdown import policies_blueprint
+from gn2.wqflask.api.markdown import environments_blueprint
+from gn2.wqflask.api.markdown import facilities_blueprint
+from gn2.wqflask.api.markdown import blogs_blueprint
+from gn2.wqflask.api.markdown import news_blueprint
+from gn2.wqflask.api.jobs import jobs as jobs_bp
+from gn2.wqflask.oauth2.routes import oauth2
+from gn2.wqflask.oauth2.checks import user_logged_in
+from gn2.wqflask.oauth2.collections import num_collections
+from gn2.wqflask.oauth2.request_utils import user_details, authserver_authorise_uri
+
+from gn2.wqflask.jupyter_notebooks import jupyter_notebooks
+
+from gn2.wqflask.startup import (
     StartupError,
     startup_errors,
     check_mandatory_configs)
@@ -88,7 +88,7 @@ app.register_blueprint(group_management, url_prefix="/group-management")
 app.register_blueprint(jobs_bp, url_prefix="/jobs")
 app.register_blueprint(oauth2, url_prefix="/oauth2")
 
-from wqflask.app_errors import register_error_handlers
+from gn2.wqflask.app_errors import register_error_handlers
 register_error_handlers(app)
 
 try:
diff --git a/wqflask/wqflask/api/__init__.py b/gn2/wqflask/api/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/api/__init__.py
+++ b/gn2/wqflask/api/__init__.py
diff --git a/wqflask/wqflask/api/correlation.py b/gn2/wqflask/api/correlation.py
index f3910340..090d13ac 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/gn2/wqflask/api/correlation.py
@@ -2,12 +2,12 @@ import collections
 import scipy
 import numpy
 
-from base import data_set
-from base.trait import create_trait, retrieve_sample_data
-from utility import corr_result_helpers
-from utility.tools import get_setting
-from wqflask.correlation import correlation_functions
-from wqflask.database import database_connection
+from gn2.base import data_set
+from gn2.base.trait import create_trait, retrieve_sample_data
+from gn2.utility import corr_result_helpers
+from gn2.utility.tools import get_setting
+from gn2.wqflask.correlation import correlation_functions
+from gn2.wqflask.database import database_connection
 
 def do_correlation(start_vars):
     if 'db' not in start_vars:
diff --git a/wqflask/wqflask/api/gen_menu.py b/gn2/wqflask/api/gen_menu.py
index 45d5739e..45d5739e 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/gn2/wqflask/api/gen_menu.py
diff --git a/wqflask/wqflask/api/jobs.py b/gn2/wqflask/api/jobs.py
index 3f18de77..7a948e1a 100644
--- a/wqflask/wqflask/api/jobs.py
+++ b/gn2/wqflask/api/jobs.py
@@ -5,14 +5,14 @@ from redis import Redis
 from pymonad.io import IO
 from flask import Blueprint, render_template
 
-from jobs.jobs import job
+from gn2.jobs.jobs import job
 
 jobs = Blueprint("jobs", __name__)
 
 @jobs.route("/debug/<uuid:job_id>")
 def debug_job(job_id: uuid.UUID):
     """Display job data to assist in debugging."""
-    from utility.tools import REDIS_URL # Avoids circular import error
+    from gn2.utility.tools import REDIS_URL # Avoids circular import error
 
     def __stream_to_lines__(stream):
         removables = (
diff --git a/wqflask/wqflask/api/mapping.py b/gn2/wqflask/api/mapping.py
index 5eacc83a..1e330963 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/gn2/wqflask/api/mapping.py
@@ -1,8 +1,8 @@
-from base import data_set
-from base.trait import create_trait, retrieve_sample_data
+from gn2.base import data_set
+from gn2.base.trait import create_trait, retrieve_sample_data
 
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping
-from wqflask.show_trait.show_trait import normf
+from gn2.wqflask.marker_regression import gemma_mapping, rqtl_mapping
+from gn2.wqflask.show_trait.show_trait import normf
 
 def do_mapping_for_api(start_vars):
     if ('db' not in start_vars) or ("trait_id" not in start_vars):
diff --git a/wqflask/wqflask/api/markdown.py b/gn2/wqflask/api/markdown.py
index 580b9ac0..580b9ac0 100644
--- a/wqflask/wqflask/api/markdown.py
+++ b/gn2/wqflask/api/markdown.py
diff --git a/wqflask/wqflask/api/router.py b/gn2/wqflask/api/router.py
index a90277c5..bcd08e8d 100644
--- a/wqflask/wqflask/api/router.py
+++ b/gn2/wqflask/api/router.py
@@ -12,18 +12,18 @@ from zipfile import ZipFile, ZIP_DEFLATED
 
 import flask
 from flask import current_app
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 from flask import request
 from flask import make_response
 from flask import send_file
 
-from wqflask import app
+from gn2.wqflask import app
 
-from wqflask.api import correlation, mapping, gen_menu
+from gn2.wqflask.api import correlation, mapping, gen_menu
 
-from utility.tools import flat_files, get_setting
+from gn2.utility.tools import flat_files, get_setting
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 
 version = "pre1"
diff --git a/wqflask/wqflask/app_errors.py b/gn2/wqflask/app_errors.py
index 8847ad2e..c6081e08 100644
--- a/wqflask/wqflask/app_errors.py
+++ b/gn2/wqflask/app_errors.py
@@ -2,8 +2,8 @@
 from flask import flash, redirect, current_app, render_template
 from authlib.integrations.base_client.errors import InvalidTokenError
 
-from wqflask.oauth2 import session
-from wqflask.decorators import AuthorisationError
+from gn2.wqflask.oauth2 import session
+from gn2.wqflask.decorators import AuthorisationError
 
 def handle_authorisation_error(exc: AuthorisationError):
     """Handle AuthorisationError if not handled anywhere else."""
diff --git a/wqflask/wqflask/collect.py b/gn2/wqflask/collect.py
index f7b33a59..21168908 100644
--- a/wqflask/wqflask/collect.py
+++ b/gn2/wqflask/collect.py
@@ -13,24 +13,24 @@ from flask import redirect
 from flask import flash
 from flask import current_app
 
-from wqflask import app
-from utility import hmac
-from utility.formatting import numify
-from utility.tools import GN_SERVER_URL, TEMPDIR
-from utility.redis_tools import get_redis_conn
-
-from base.trait import create_trait
-from base.trait import retrieve_trait_info
-from base.trait import jsonable
-from base.data_set import create_dataset
-
-from wqflask.oauth2 import client
-from wqflask.oauth2 import session
-from wqflask.oauth2.session import session_info
-from wqflask.oauth2.checks import user_logged_in
-from wqflask.oauth2.request_utils import (
+from gn2.wqflask import app
+from gn2.utility import hmac
+from gn2.utility.formatting import numify
+from gn2.utility.tools import GN_SERVER_URL, TEMPDIR
+from gn2.utility.redis_tools import get_redis_conn
+
+from gn2.base.trait import create_trait
+from gn2.base.trait import retrieve_trait_info
+from gn2.base.trait import jsonable
+from gn2.base.data_set import create_dataset
+
+from gn2.wqflask.oauth2 import client
+from gn2.wqflask.oauth2 import session
+from gn2.wqflask.oauth2.session import session_info
+from gn2.wqflask.oauth2.checks import user_logged_in
+from gn2.wqflask.oauth2.request_utils import (
     process_error, with_flash_error, with_flash_success)
-from wqflask.oauth2.client import (
+from gn2.wqflask.oauth2.client import (
     oauth2_get, oauth2_post, no_token_get, no_token_post)
 
 
diff --git a/wqflask/wqflask/comparison_bar_chart/__init__.py b/gn2/wqflask/comparison_bar_chart/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/comparison_bar_chart/__init__.py
+++ b/gn2/wqflask/comparison_bar_chart/__init__.py
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 438d2276..3fb3cb40 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -20,11 +20,11 @@
 
 from pprint import pformat as pf
 
-from base.trait import create_trait
-from base import data_set
-from utility import webqtlUtil, helper_functions, corr_result_helpers
-import utility.webqtlUtil  # this is for parallel computing only.
-from wqflask.correlation import correlation_functions
+from gn2.base.trait import create_trait
+from gn2.base import data_set
+from gn2.utility import webqtlUtil, helper_functions, corr_result_helpers
+import gn2.utility.webqtlUtil  # this is for parallel computing only.
+from gn2.wqflask.correlation import correlation_functions
 
 from flask import Flask, g
 
diff --git a/wqflask/wqflask/correlation/__init__.py b/gn2/wqflask/correlation/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/correlation/__init__.py
+++ b/gn2/wqflask/correlation/__init__.py
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/gn2/wqflask/correlation/corr_scatter_plot.py
index 16e36f9d..59e9ac4a 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/gn2/wqflask/correlation/corr_scatter_plot.py
@@ -4,10 +4,10 @@ import math
 from redis import Redis
 Redis = Redis()
 
-from base.trait import create_trait, retrieve_sample_data
-from base import data_set, webqtlCaseData
-from utility import corr_result_helpers
-from wqflask.oauth2.collections import num_collections
+from gn2.base.trait import create_trait, retrieve_sample_data
+from gn2.base import data_set, webqtlCaseData
+from gn2.utility import corr_result_helpers
+from gn2.wqflask.oauth2.collections import num_collections
 
 from scipy import stats
 import numpy as np
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/gn2/wqflask/correlation/correlation_functions.py
index 75399256..911f6dc8 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/gn2/wqflask/correlation/correlation_functions.py
@@ -23,10 +23,10 @@
 # Created by GeneNetwork Core Team 2010/08/10
 
 
-from base.mrna_assay_tissue_data import MrnaAssayTissueData
+from gn2.base.mrna_assay_tissue_data import MrnaAssayTissueData
 from gn3.computations.correlations import compute_corr_coeff_p_value
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 #####################################################################################
 # Input: primaryValue(list): one list of expression values of one probeSet,
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/gn2/wqflask/correlation/correlation_gn3_api.py
index 64a17548..76c75ec3 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/gn2/wqflask/correlation/correlation_gn3_api.py
@@ -3,13 +3,13 @@ import json
 import time
 from functools import wraps
 
-from utility.tools import SQL_URI
+from gn2.utility.tools import SQL_URI
 
-from wqflask.correlation import correlation_functions
-from base import data_set
+from gn2.wqflask.correlation import correlation_functions
+from gn2.base import data_set
 
-from base.trait import create_trait
-from base.trait import retrieve_sample_data
+from gn2.base.trait import create_trait
+from gn2.base.trait import retrieve_sample_data
 
 from gn3.db_utils import database_connection
 from gn3.commands import run_sample_corr_cmd
@@ -189,7 +189,7 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
     method -- Correlation method to be used (pearson, spearman, or bicor)
     compute_all -- Include sample, tissue, and literature correlations (when applicable)
     """
-    from wqflask.correlation.rust_correlation import compute_correlation_rust
+    from gn2.wqflask.correlation.rust_correlation import compute_correlation_rust
 
     corr_type = start_vars['corr_type']
     method = start_vars['corr_sample_method']
diff --git a/wqflask/wqflask/correlation/exceptions.py b/gn2/wqflask/correlation/exceptions.py
index f4e2b72b..f4e2b72b 100644
--- a/wqflask/wqflask/correlation/exceptions.py
+++ b/gn2/wqflask/correlation/exceptions.py
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/gn2/wqflask/correlation/pre_computes.py
index 2831bd39..4bd888ad 100644
--- a/wqflask/wqflask/correlation/pre_computes.py
+++ b/gn2/wqflask/correlation/pre_computes.py
@@ -8,9 +8,9 @@ import lmdb
 import pickle
 from pathlib import Path
 
-from base.data_set import query_table_timestamp
-from base.webqtlConfig import TEXTDIR
-from base.webqtlConfig import TMPDIR
+from gn2.base.data_set import query_table_timestamp
+from gn2.base.webqtlConfig import TEXTDIR
+from gn2.base.webqtlConfig import TMPDIR
 
 from json.decoder import JSONDecodeError
 
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/gn2/wqflask/correlation/rust_correlation.py
index 41dd77a1..a0dcbcb4 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/gn2/wqflask/correlation/rust_correlation.py
@@ -2,26 +2,26 @@
 import json
 from functools import reduce
 
-from utility.tools import SQL_URI
-from utility.db_tools import mescape
-from utility.db_tools import create_in_clause
-from wqflask.correlation.correlation_functions\
+from gn2.utility.tools import SQL_URI
+from gn2.utility.db_tools import mescape
+from gn2.utility.db_tools import create_in_clause
+from gn2.wqflask.correlation.correlation_functions\
     import get_trait_symbol_and_tissue_values
-from wqflask.correlation.correlation_gn3_api import create_target_this_trait
-from wqflask.correlation.correlation_gn3_api import lit_for_trait_list
-from wqflask.correlation.correlation_gn3_api import do_lit_correlation
-from wqflask.correlation.pre_computes import fetch_text_file
-from wqflask.correlation.pre_computes import read_text_file
-from wqflask.correlation.pre_computes import write_db_to_textfile
-from wqflask.correlation.pre_computes import read_trait_metadata
-from wqflask.correlation.pre_computes import cache_trait_metadata
+from gn2.wqflask.correlation.correlation_gn3_api import create_target_this_trait
+from gn2.wqflask.correlation.correlation_gn3_api import lit_for_trait_list
+from gn2.wqflask.correlation.correlation_gn3_api import do_lit_correlation
+from gn2.wqflask.correlation.pre_computes import fetch_text_file
+from gn2.wqflask.correlation.pre_computes import read_text_file
+from gn2.wqflask.correlation.pre_computes import write_db_to_textfile
+from gn2.wqflask.correlation.pre_computes import read_trait_metadata
+from gn2.wqflask.correlation.pre_computes import cache_trait_metadata
 from gn3.computations.correlations import compute_all_lit_correlation
 from gn3.computations.rust_correlation import run_correlation
 from gn3.computations.rust_correlation import get_sample_corr_data
 from gn3.computations.rust_correlation import parse_tissue_corr_data
 from gn3.db_utils import database_connection
 
-from wqflask.correlation.exceptions import WrongCorrelationType
+from gn2.wqflask.correlation.exceptions import WrongCorrelationType
 
 
 def query_probes_metadata(dataset, trait_list):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/gn2/wqflask/correlation/show_corr_results.py
index 35cb50b8..c8625222 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/gn2/wqflask/correlation/show_corr_results.py
@@ -22,12 +22,12 @@ import hashlib
 import html
 import json
 
-from base.trait import create_trait, jsonable
-from base.data_set import create_dataset
+from gn2.base.trait import create_trait, jsonable
+from gn2.base.data_set import create_dataset
 
-from utility import hmac
-from utility.type_checking import get_float, get_int, get_string
-from utility.redis_tools import get_redis_conn
+from gn2.utility import hmac
+from gn2.utility.type_checking import get_float, get_int, get_string
+from gn2.utility.redis_tools import get_redis_conn
 Redis = get_redis_conn()
 
 def set_template_vars(start_vars, correlation_data):
diff --git a/wqflask/wqflask/correlation_matrix/__init__.py b/gn2/wqflask/correlation_matrix/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/correlation_matrix/__init__.py
+++ b/gn2/wqflask/correlation_matrix/__init__.py
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/gn2/wqflask/correlation_matrix/show_corr_matrix.py
index 617f5c2e..f7eb0b4c 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/gn2/wqflask/correlation_matrix/show_corr_matrix.py
@@ -24,13 +24,13 @@ import string
 import numpy as np
 import scipy
 
-from base.data_set import create_dataset
-from base.webqtlConfig import GENERATED_TEXT_DIR
+from gn2.base.data_set import create_dataset
+from gn2.base.webqtlConfig import GENERATED_TEXT_DIR
 
 
-from utility.helper_functions import get_trait_db_obs
-from utility.corr_result_helpers import normalize_values
-from utility.redis_tools import get_redis_conn
+from gn2.utility.helper_functions import get_trait_db_obs
+from gn2.utility.corr_result_helpers import normalize_values
+from gn2.utility.redis_tools import get_redis_conn
 
 
 from gn3.computations.pca import compute_pca
diff --git a/wqflask/wqflask/ctl/__init__.py b/gn2/wqflask/ctl/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/ctl/__init__.py
+++ b/gn2/wqflask/ctl/__init__.py
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/gn2/wqflask/ctl/ctl_analysis.py
index 96a47eb8..513c1b1c 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/gn2/wqflask/ctl/ctl_analysis.py
@@ -7,20 +7,20 @@ import rpy2.rinterface as ri
 
 import simplejson as json
 
-from base.webqtlConfig import GENERATED_IMAGE_DIR
-from utility import webqtlUtil                # Random number for the image
-from utility import genofile_parser           # genofile_parser
+from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
+from gn2.utility import webqtlUtil                # Random number for the image
+from gn2.utility import genofile_parser           # genofile_parser
 
 import base64
 import array
 import csv
 import itertools
 
-from base import data_set
-from base.trait import create_trait, retrieve_sample_data
+from gn2.base import data_set
+from gn2.base.trait import create_trait, retrieve_sample_data
 
-from utility import helper_functions
-from utility.tools import locate, GN2_BRANCH_URL
+from gn2.utility import helper_functions
+from gn2.utility.tools import locate, GN2_BRANCH_URL
 
 from rpy2.robjects.packages import importr
 
diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/gn2/wqflask/ctl/gn3_ctl_analysis.py
index 8f790597..64c2ff0d 100644
--- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py
+++ b/gn2/wqflask/ctl/gn3_ctl_analysis.py
@@ -1,13 +1,13 @@
 import requests
 import itertools
 
-from utility import genofile_parser
-from utility.tools import GN3_LOCAL_URL
-from utility.tools import locate
+from gn2.utility import genofile_parser
+from gn2.utility.tools import GN3_LOCAL_URL
+from gn2.utility.tools import locate
 
-from base.trait import create_trait
-from base.trait import retrieve_sample_data
-from base import data_set
+from gn2.base.trait import create_trait
+from gn2.base.trait import retrieve_sample_data
+from gn2.base import data_set
 
 
 def process_significance_data(dataset):
diff --git a/wqflask/wqflask/database.py b/gn2/wqflask/database.py
index 331ad380..331ad380 100644
--- a/wqflask/wqflask/database.py
+++ b/gn2/wqflask/database.py
diff --git a/wqflask/wqflask/db_info.py b/gn2/wqflask/db_info.py
index 7eae86e7..f6b94dde 100644
--- a/wqflask/wqflask/db_info.py
+++ b/gn2/wqflask/db_info.py
@@ -4,8 +4,8 @@ import urllib.parse
 import re
 
 from MySQLdb.cursors import DictCursor
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 
 class InfoPage:
diff --git a/wqflask/wqflask/decorators.py b/gn2/wqflask/decorators.py
index 88535187..4fe865c9 100644
--- a/wqflask/wqflask/decorators.py
+++ b/gn2/wqflask/decorators.py
@@ -11,10 +11,10 @@ from flask import g, flash, request, url_for, redirect, current_app
 from gn3.authentication import AdminRole
 from gn3.authentication import DataRole
 
-from wqflask.oauth2 import client
-from wqflask.oauth2.session import session_info
-from wqflask.oauth2.checks import user_logged_in
-from wqflask.oauth2.request_utils import process_error
+from gn2.wqflask.oauth2 import client
+from gn2.wqflask.oauth2.session import session_info
+from gn2.wqflask.oauth2.checks import user_logged_in
+from gn2.wqflask.oauth2.request_utils import process_error
 
 
 def login_required(pagename: str = ""):
diff --git a/wqflask/wqflask/do_search.py b/gn2/wqflask/do_search.py
index b6f540fa..3c81783d 100644
--- a/wqflask/wqflask/do_search.py
+++ b/gn2/wqflask/do_search.py
@@ -3,12 +3,12 @@ import re
 import requests
 import string
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
 import sys
 
-from db import webqtlDatabaseFunction
-from utility.tools import get_setting, GN2_BASE_URL
+from gn2.db import webqtlDatabaseFunction
+from gn2.utility.tools import get_setting, GN2_BASE_URL
 
 
 class DoSearch:
@@ -47,14 +47,14 @@ class DoSearch:
 
     def sescape(self, item):
         """Single escape"""
-        from utility.tools import get_setting
+        from gn2.utility.tools import get_setting
         with database_connection(get_setting("SQL_URI")) as conn:
             escaped = conn.escape_string(str(item)).decode()
         return escaped
 
     def mescape(self, *items):
         """Multiple escape"""
-        from utility.tools import get_setting
+        from gn2.utility.tools import get_setting
         escaped = []
         with database_connection(get_setting("SQL_URI")) as conn:
             escaped = [conn.escape_string(str(item)).decode() for item in items]
@@ -950,12 +950,12 @@ if __name__ == "__main__":
     # And it runs the code below
     import sys
 
-    from base import webqtlConfig
-    from base.data_set import create_dataset
-    from utility import webqtlUtil
-    from db import webqtlDatabaseFunction
+    from gn2.base import webqtlConfig
+    from gn2.base.data_set import create_dataset
+    from gn2.utility import webqtlUtil
+    from gn2.db import webqtlDatabaseFunction
 
-    from wqflask.database import database_connection
+    from gn2.wqflask.database import database_connection
 
     with database_connection(get_setting("SQL_URI")) as db_conn:
         with db_conn.cursor() as cursor:
diff --git a/wqflask/wqflask/docs.py b/gn2/wqflask/docs.py
index 5d20ce4d..3453a3c1 100644
--- a/wqflask/wqflask/docs.py
+++ b/gn2/wqflask/docs.py
@@ -1,8 +1,8 @@
 import codecs
 
 from flask import g
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 class Docs:
 
diff --git a/wqflask/wqflask/export_traits.py b/gn2/wqflask/export_traits.py
index 534822e9..2d2a40cc 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/gn2/wqflask/export_traits.py
@@ -12,7 +12,7 @@ import simplejson as json
 
 from gn3.computations.gemma import generate_hash_of_string
 
-from base.trait import create_trait, retrieve_trait_info
+from gn2.base.trait import create_trait, retrieve_trait_info
 
 
 def export_traits(targs, export_type):
diff --git a/wqflask/wqflask/external_tools/__init__.py b/gn2/wqflask/external_tools/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/external_tools/__init__.py
+++ b/gn2/wqflask/external_tools/__init__.py
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/gn2/wqflask/external_tools/send_to_bnw.py
index dfb59c63..fdbc0d93 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/gn2/wqflask/external_tools/send_to_bnw.py
@@ -18,8 +18,8 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from base.trait import GeneralTrait
-from utility import helper_functions, corr_result_helpers
+from gn2.base.trait import GeneralTrait
+from gn2.utility import helper_functions, corr_result_helpers
 
 
 class SendToBNW:
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/gn2/wqflask/external_tools/send_to_geneweaver.py
index 94407ae8..76ff7302 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/gn2/wqflask/external_tools/send_to_geneweaver.py
@@ -17,9 +17,9 @@
 #
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
-from wqflask.database import database_connection
-from utility import helper_functions
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility import helper_functions
+from gn2.utility.tools import get_setting
 
 
 class SendToGeneWeaver:
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/gn2/wqflask/external_tools/send_to_webgestalt.py
index 4b972642..9633e560 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/gn2/wqflask/external_tools/send_to_webgestalt.py
@@ -18,11 +18,11 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
-from base.trait import retrieve_trait_info
-from utility import helper_functions
-from utility.tools import get_setting
+from gn2.base.trait import retrieve_trait_info
+from gn2.utility import helper_functions
+from gn2.utility.tools import get_setting
 
 
 class SendToWebGestalt:
diff --git a/wqflask/wqflask/group_manager.py b/gn2/wqflask/group_manager.py
index 71ced4dd..b589acb6 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/gn2/wqflask/group_manager.py
@@ -12,7 +12,7 @@ from flask import url_for
 from gn3.authentication import get_groups_by_user_uid
 from gn3.authentication import get_user_info_by_key
 from gn3.authentication import create_group
-from wqflask.decorators import login_required
+from gn2.wqflask.decorators import login_required
 
 group_management = Blueprint("group_management", __name__)
 
diff --git a/wqflask/wqflask/gsearch.py b/gn2/wqflask/gsearch.py
index 72c55153..cad6db94 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/gn2/wqflask/gsearch.py
@@ -5,9 +5,9 @@ from pymonad.tools import curry
 import requests
 
 from gn3.monads import MonadicDict
-from utility.hmac import hmac_creation
-from utility.tools import GN3_LOCAL_URL
-from base import webqtlConfig
+from gn2.utility.hmac import hmac_creation
+from gn2.utility.tools import GN3_LOCAL_URL
+from gn2.base import webqtlConfig
 
 # KLUDGE: Due to the lack of pagination, we hard-limit the maximum
 # number of search results.
diff --git a/wqflask/wqflask/heatmap/__init__.py b/gn2/wqflask/heatmap/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/heatmap/__init__.py
+++ b/gn2/wqflask/heatmap/__init__.py
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/gn2/wqflask/heatmap/heatmap.py
index 43ea4a4d..c2dd55bd 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/gn2/wqflask/heatmap/heatmap.py
@@ -1,16 +1,16 @@
 import string
 import os
 import random
-from base import species
-from base import webqtlConfig
-from utility import helper_functions
+from gn2.base import species
+from gn2.base import webqtlConfig
+from gn2.utility import helper_functions
 
-from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
+from gn2.utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 from redis import Redis
 from flask import Flask, g
 
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 Redis = Redis()
 
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/gn2/wqflask/interval_analyst/GeneUtil.py
index 72bd8bae..d3b00e31 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/gn2/wqflask/interval_analyst/GeneUtil.py
@@ -1,8 +1,8 @@
 import string
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
-from utility.tools import flat_files, get_setting
+from gn2.utility.tools import flat_files, get_setting
 
 def load_homology(chr_name, start_mb, end_mb, source_file):
     homology_list = []
diff --git a/wqflask/wqflask/interval_analyst/__init__.py b/gn2/wqflask/interval_analyst/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/interval_analyst/__init__.py
+++ b/gn2/wqflask/interval_analyst/__init__.py
diff --git a/wqflask/wqflask/jupyter_notebooks.py b/gn2/wqflask/jupyter_notebooks.py
index a6d06af0..a6d06af0 100644
--- a/wqflask/wqflask/jupyter_notebooks.py
+++ b/gn2/wqflask/jupyter_notebooks.py
diff --git a/wqflask/wqflask/marker_regression/__init__.py b/gn2/wqflask/marker_regression/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/marker_regression/__init__.py
+++ b/gn2/wqflask/marker_regression/__init__.py
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/gn2/wqflask/marker_regression/display_mapping_results.py
index 7d6d3ad4..b3bf3bc3 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/gn2/wqflask/marker_regression/display_mapping_results.py
@@ -36,15 +36,15 @@ import json
 
 import htmlgen as HT
 
-from base import webqtlConfig
-from base.GeneralObject import GeneralObject
-from utility import webqtlUtil
-from utility import Plot
-from utility.tools import get_setting
-from wqflask.interval_analyst import GeneUtil
-from base.webqtlConfig import GENERATED_IMAGE_DIR
-from utility.pillow_utils import draw_rotated_text, draw_open_polygon
-from wqflask.database import database_connection
+from gn2.base import webqtlConfig
+from gn2.base.GeneralObject import GeneralObject
+from gn2.utility import webqtlUtil
+from gn2.utility import Plot
+from gn2.utility.tools import get_setting
+from gn2.wqflask.interval_analyst import GeneUtil
+from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
+from gn2.utility.pillow_utils import draw_rotated_text, draw_open_polygon
+from gn2.wqflask.database import database_connection
 
 try:  # Only import this for Python3
     from functools import reduce
@@ -81,11 +81,11 @@ COLOR_CODES = ["#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF",
 DISTINCT_COLOR_LIST = [ImageColor.getrgb(color) for color in COLOR_CODES]
 
 # ---- FONT FILES ---- #
-VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf"
-VERDANA_BOLD_FILE = "./wqflask/static/fonts/verdanab.ttf"
-TREBUC_FILE = "./wqflask/static/fonts/trebucbd.ttf"
-FNT_BS_FILE = "./wqflask/static/fonts/fnt_bs.ttf"
-ARIAL_FILE = "./wqflask/static/fonts/arial.ttf"
+VERDANA_FILE = "./gn2/wqflask/static/fonts/verdana.ttf"
+VERDANA_BOLD_FILE = "./gn2/wqflask/static/fonts/verdanab.ttf"
+TREBUC_FILE = "./gn2/wqflask/static/fonts/trebucbd.ttf"
+FNT_BS_FILE = "./gn2/wqflask/static/fonts/fnt_bs.ttf"
+ARIAL_FILE = "./gn2/wqflask/static/fonts/arial.ttf"
 
 assert(os.path.isfile(VERDANA_FILE))
 
diff --git a/wqflask/wqflask/marker_regression/exceptions.py b/gn2/wqflask/marker_regression/exceptions.py
index 8c7e822b..8c7e822b 100644
--- a/wqflask/wqflask/marker_regression/exceptions.py
+++ b/gn2/wqflask/marker_regression/exceptions.py
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/gn2/wqflask/marker_regression/gemma_mapping.py
index 47ad5638..d8851486 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/gn2/wqflask/marker_regression/gemma_mapping.py
@@ -4,16 +4,16 @@ import string
 import random
 import json
 
-from base import webqtlConfig
-from base.trait import create_trait
-from base.data_set import create_dataset
-from utility.redis_tools import get_redis_conn
-from utility.tools import flat_files, assert_file
-from utility.tools import GEMMA_WRAPPER_COMMAND
-from utility.tools import TEMPDIR
-from utility.tools import WEBSERVER_MODE
-from utility.tools import get_setting
-from wqflask.database import database_connection
+from gn2.base import webqtlConfig
+from gn2.base.trait import create_trait
+from gn2.base.data_set import create_dataset
+from gn2.utility.redis_tools import get_redis_conn
+from gn2.utility.tools import flat_files, assert_file
+from gn2.utility.tools import GEMMA_WRAPPER_COMMAND
+from gn2.utility.tools import TEMPDIR
+from gn2.utility.tools import WEBSERVER_MODE
+from gn2.utility.tools import get_setting
+from gn2.wqflask.database import database_connection
 from gn3.computations.gemma import generate_hash_of_string
 
 
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/gn2/wqflask/marker_regression/plink_mapping.py
index 75ee189e..7427717a 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/gn2/wqflask/marker_regression/plink_mapping.py
@@ -1,9 +1,9 @@
 import string
 import os
 
-from base.webqtlConfig import TMPDIR
-from utility import webqtlUtil
-from utility.tools import flat_files, PLINK_COMMAND
+from gn2.base.webqtlConfig import TMPDIR
+from gn2.utility import webqtlUtil
+from gn2.utility.tools import flat_files, PLINK_COMMAND
 
 
 def run_plink(this_trait, dataset, species, vals, maf):
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/gn2/wqflask/marker_regression/qtlreaper_mapping.py
index 4d5db2ee..2c9ca1b2 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/gn2/wqflask/marker_regression/qtlreaper_mapping.py
@@ -5,10 +5,10 @@ import random
 import json
 import re
 
-from base import webqtlConfig
-from base.trait import GeneralTrait
-from base.data_set import create_dataset
-from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
+from gn2.base import webqtlConfig
+from gn2.base.trait import GeneralTrait
+from gn2.base.data_set import create_dataset
+from gn2.utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 
 
 def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/gn2/wqflask/marker_regression/rqtl_mapping.py
index f6ef2e9a..b7739228 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/gn2/wqflask/marker_regression/rqtl_mapping.py
@@ -11,11 +11,11 @@ from typing import TextIO
 
 import numpy as np
 
-from base.webqtlConfig import TMPDIR
-from base.trait import create_trait
-from utility.redis_tools import get_redis_conn
-from utility.tools import locate, get_setting, GN3_LOCAL_URL
-from wqflask.database import database_connection
+from gn2.base.webqtlConfig import TMPDIR
+from gn2.base.trait import create_trait
+from gn2.utility.redis_tools import get_redis_conn
+from gn2.utility.tools import locate, get_setting, GN3_LOCAL_URL
+from gn2.wqflask.database import database_connection
 
 
 def run_rqtl(trait_name, vals, samples, dataset, pair_scan, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors):
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/gn2/wqflask/marker_regression/run_mapping.py
index 98a97d8d..7d2d40f7 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/gn2/wqflask/marker_regression/run_mapping.py
@@ -1,5 +1,5 @@
-from base.trait import GeneralTrait
-from base import data_set  # import create_dataset
+from gn2.base.trait import GeneralTrait
+from gn2.base import data_set  # import create_dataset
 
 from pprint import pformat as pf
 
@@ -25,19 +25,19 @@ Redis = Redis()
 
 from flask import Flask, g
 
-from base.trait import GeneralTrait
-from base import data_set
-from base import species
-from base import webqtlConfig
-from utility import webqtlUtil, helper_functions, hmac, Plot, Bunch, temp_data
-from utility.redis_tools import get_redis_conn
-from wqflask.database import database_connection
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
-from wqflask.show_trait.SampleList import SampleList
-
-from utility.tools import locate, get_setting, locate_ignore_error, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
-from utility.external import shell
-from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
+from gn2.base.trait import GeneralTrait
+from gn2.base import data_set
+from gn2.base import species
+from gn2.base import webqtlConfig
+from gn2.utility import webqtlUtil, helper_functions, hmac, Plot, Bunch, temp_data
+from gn2.utility.redis_tools import get_redis_conn
+from gn2.wqflask.database import database_connection
+from gn2.wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
+from gn2.wqflask.show_trait.SampleList import SampleList
+
+from gn2.utility.tools import locate, get_setting, locate_ignore_error, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
+from gn2.utility.external import shell
+from gn2.base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
 Redis = get_redis_conn()
 
diff --git a/wqflask/wqflask/metadata_edits.py b/gn2/wqflask/metadata_edits.py
index 2798e4b4..b9514b35 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/gn2/wqflask/metadata_edits.py
@@ -22,16 +22,16 @@ from flask import render_template
 from flask import request
 from flask import url_for
 
-from utility.json import CustomJSONEncoder
+from gn2.utility.json import CustomJSONEncoder
 
-from wqflask.database import database_connection
-from wqflask.decorators import login_required
-from wqflask.decorators import required_access
-from wqflask.decorators import edit_admins_access_required
+from gn2.wqflask.database import database_connection
+from gn2.wqflask.decorators import login_required
+from gn2.wqflask.decorators import required_access
+from gn2.wqflask.decorators import edit_admins_access_required
 
-from wqflask.oauth2 import client
-from wqflask.oauth2 import session
-from wqflask.oauth2.request_utils import flash_error, process_error
+from gn2.wqflask.oauth2 import client
+from gn2.wqflask.oauth2 import session
+from gn2.wqflask.oauth2.request_utils import flash_error, process_error
 
 from gn3.authentication import AdminRole
 from gn3.authentication import get_highest_user_access_role
@@ -114,7 +114,7 @@ def edit_phenotype(conn, name, dataset_id):
 @required_access(
     ("group:resource:view-resource", "group:resource:edit-resource"))
 def display_phenotype_metadata(dataset_id: str, name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     with database_connection(get_setting("SQL_URI")) as conn:
         _d = edit_phenotype(conn=conn, name=name, dataset_id=dataset_id)
 
@@ -142,7 +142,7 @@ def display_phenotype_metadata(dataset_id: str, name: str):
 @required_access(
     ("group:resource:view-resource", "group:resource:edit-resource"))
 def display_probeset_metadata(name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     with database_connection(get_setting("SQL_URI")) as conn:
         _d = {"probeset": fetch_probeset_metadata_by_name(conn, name)}
 
@@ -170,7 +170,7 @@ def display_probeset_metadata(name: str):
 @required_access(
     ("group:resource:view-resource", "group:resource:edit-resource"))
 def update_phenotype(dataset_id: str, name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     data_ = request.form.to_dict()
     TMPDIR = current_app.config.get("TMPDIR")
     author = session.session_info()["user"]["user_id"]
@@ -389,7 +389,7 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success")
     ("group:resource:view-resource", "group:resource:edit-resource"),
     dataset_key="dataset_id", trait_key="name")
 def update_probeset(name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     data_ = request.form.to_dict()
     TMPDIR = current_app.config.get("TMPDIR")
     author = session.session_info()["user"]["user_id"]
@@ -584,7 +584,7 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success")
 @metadata_edit.route("/pheno/<name>/group/<group_id>/csv")
 @login_required()
 def get_pheno_sample_data_as_csv(name: int, group_id: int):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     with database_connection(get_setting("SQL_URI")) as conn:
         group_name = retrieve_phenotype_group_name(conn, group_id)
         return Response(
@@ -604,7 +604,7 @@ filename=sample-data-{group_name}-{name}.csv"
 @metadata_edit.route("/mrna/<probeset_id>/dataset/<dataset_name>/csv")
 @login_required()
 def get_mrna_sample_data_as_csv(probeset_id: int, dataset_name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
 
     with database_connection(get_setting("SQL_URI")) as conn:
         csv_data = get_mrna_csv_sample_data(
@@ -716,7 +716,7 @@ def show_diff(name):
 @metadata_edit.route("/<dataset_id>/traits/<name>/history")
 @metadata_edit.route("/probeset/<name>")
 def show_history(dataset_id: str = "", name: str = ""):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     diff_data_ = None
     with database_connection(get_setting("SQL_URI")) as conn:
         json_data = None
@@ -819,7 +819,7 @@ def reject_data(resource_id: str, file_name: str):
     ("group:resource:view-resource", "group:resource:edit-resource"),
     trait_key="trait_name")
 def approve_data(resource_id: str, file_name: str):
-    from utility.tools import get_setting
+    from gn2.utility.tools import get_setting
     sample_data = {file_name: str}
     TMPDIR = current_app.config.get("TMPDIR")
     diffpath = Path(TMPDIR, "sample-data/diffs", file_name)
diff --git a/wqflask/wqflask/network_graph/__init__.py b/gn2/wqflask/network_graph/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/network_graph/__init__.py
+++ b/gn2/wqflask/network_graph/__init__.py
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/gn2/wqflask/network_graph/network_graph.py
index 9b70f03d..d60d50ff 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/gn2/wqflask/network_graph/network_graph.py
@@ -21,11 +21,11 @@
 import scipy
 import simplejson as json
 
-from base.trait import create_trait
-from base import data_set
-from utility import helper_functions
-from utility import corr_result_helpers
-from utility.tools import GN2_BRANCH_URL
+from gn2.base.trait import create_trait
+from gn2.base import data_set
+from gn2.utility import helper_functions
+from gn2.utility import corr_result_helpers
+from gn2.utility.tools import GN2_BRANCH_URL
 
 
 class NetworkGraph:
diff --git a/wqflask/wqflask/oauth2/__init__.py b/gn2/wqflask/oauth2/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/oauth2/__init__.py
+++ b/gn2/wqflask/oauth2/__init__.py
diff --git a/wqflask/wqflask/oauth2/checks.py b/gn2/wqflask/oauth2/checks.py
index 4ef1ab3e..5d90f986 100644
--- a/wqflask/wqflask/oauth2/checks.py
+++ b/gn2/wqflask/oauth2/checks.py
@@ -32,7 +32,7 @@ def require_oauth2(func):
             return redirect("/")
 
         def __with_token__(token):
-            from utility.tools import (
+            from gn2.utility.tools import (
                 AUTH_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET)
             client = OAuth2Session(
                 OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET, token=token)
diff --git a/wqflask/wqflask/oauth2/client.py b/gn2/wqflask/oauth2/client.py
index af6a1876..c6a3110b 100644
--- a/wqflask/wqflask/oauth2/client.py
+++ b/gn2/wqflask/oauth2/client.py
@@ -9,15 +9,15 @@ from pymonad.maybe import Just, Maybe, Nothing
 from pymonad.either import Left, Right, Either
 from authlib.integrations.requests_client import OAuth2Session
 
-from wqflask.oauth2 import session
-from wqflask.oauth2.checks import user_logged_in
+from gn2.wqflask.oauth2 import session
+from gn2.wqflask.oauth2.checks import user_logged_in
 
 SCOPE = ("profile group role resource register-client user masquerade "
          "introspect migrate-data")
 
 def oauth2_client():
     def __client__(token) -> OAuth2Session:
-        from utility.tools import (
+        from gn2.utility.tools import (
             AUTH_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET)
         return OAuth2Session(
             OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET,
@@ -39,7 +39,7 @@ def __no_token__(_err) -> Left:
 
 def oauth2_get(uri_path: str, data: dict = {}, **kwargs) -> Either:
     def __get__(token) -> Either:
-        from utility.tools import (
+        from gn2.utility.tools import (
             AUTH_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET)
         client = OAuth2Session(
             OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET,
@@ -59,7 +59,7 @@ def oauth2_post(
         uri_path: str, data: Optional[dict] = None, json: Optional[dict] = None,
         **kwargs) -> Either:
     def __post__(token) -> Either:
-        from utility.tools import (
+        from gn2.utility.tools import (
             AUTH_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET)
         client = OAuth2Session(
             OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET,
@@ -75,14 +75,14 @@ def oauth2_post(
     return session.user_token().either(__no_token__, __post__)
 
 def no_token_get(uri_path: str, **kwargs) -> Either:
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     resp = requests.get(urljoin(AUTH_SERVER_URL, uri_path), **kwargs)
     if resp.status_code == 200:
         return Right(resp.json())
     return Left(resp)
 
 def no_token_post(uri_path: str, **kwargs) -> Either:
-    from utility.tools import (
+    from gn2.utility.tools import (
         AUTH_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET)
     data = kwargs.get("data", {})
     the_json = kwargs.get("json", {})
diff --git a/wqflask/wqflask/oauth2/collections.py b/gn2/wqflask/oauth2/collections.py
index 63bf206e..63bf206e 100644
--- a/wqflask/wqflask/oauth2/collections.py
+++ b/gn2/wqflask/oauth2/collections.py
diff --git a/wqflask/wqflask/oauth2/data.py b/gn2/wqflask/oauth2/data.py
index 2e05bcd5..a1dfdf95 100644
--- a/wqflask/wqflask/oauth2/data.py
+++ b/gn2/wqflask/oauth2/data.py
@@ -10,9 +10,9 @@ from flask import (
     flash, request, jsonify, url_for, redirect, Response, Blueprint,
     current_app as app)
 
-from wqflask.oauth2.request_utils import with_flash_error
+from gn2.wqflask.oauth2.request_utils import with_flash_error
 
-from jobs import jobs
+from gn2.jobs import jobs
 from .ui import render_ui
 from .request_utils import process_error
 from .client import oauth2_get, oauth2_post
@@ -20,7 +20,7 @@ from .client import oauth2_get, oauth2_post
 data = Blueprint("data", __name__)
 
 def __search_mrna__(query, template, **kwargs):
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     species_name = kwargs["species_name"]
     search_uri = urljoin(AUTH_SERVER_URL, "auth/data/search")
     datasets = oauth2_get(
@@ -45,7 +45,7 @@ def __selected_datasets__():
                             request.form.get("selected", []))
 
 def __search_genotypes__(query, template, **kwargs):
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     species_name = kwargs["species_name"]
     search_uri = urljoin(AUTH_SERVER_URL, "auth/data/search")
     datasets = oauth2_get(
@@ -61,7 +61,7 @@ def __search_genotypes__(query, template, **kwargs):
     return render_ui(template, search_uri=search_uri, **datasets, **kwargs)
 
 def __search_phenotypes__(query, template, **kwargs):
-    from utility.tools import GN_SERVER_URL, AUTH_SERVER_URL
+    from gn2.utility.tools import GN_SERVER_URL, AUTH_SERVER_URL
     page = int(request.args.get("page", 1))
     per_page = int(request.args.get("per_page", 50))
     selected_traits = request.form.getlist("selected_traits")
@@ -124,7 +124,7 @@ def json_search_mrna() -> Response:
 @data.route("/phenotype/search", methods=["POST"])
 def json_search_phenotypes() -> Response:
     """Search for phenotypes."""
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     form = request.json
     def __handle_error__(err):
         error = process_error(err)
diff --git a/wqflask/wqflask/oauth2/groups.py b/gn2/wqflask/oauth2/groups.py
index fd5ab7eb..fd5ab7eb 100644
--- a/wqflask/wqflask/oauth2/groups.py
+++ b/gn2/wqflask/oauth2/groups.py
diff --git a/wqflask/wqflask/oauth2/request_utils.py b/gn2/wqflask/oauth2/request_utils.py
index 4c5b970a..ade0923b 100644
--- a/wqflask/wqflask/oauth2/request_utils.py
+++ b/gn2/wqflask/oauth2/request_utils.py
@@ -10,7 +10,7 @@ from flask import (
 from .client import SCOPE, oauth2_get
 
 def authserver_authorise_uri():
-    from utility.tools import AUTH_SERVER_URL, OAUTH2_CLIENT_ID
+    from gn2.utility.tools import AUTH_SERVER_URL, OAUTH2_CLIENT_ID
     req_baseurl = urlparse(request.base_url, scheme=request.scheme)
     host_uri = f"{req_baseurl.scheme}://{req_baseurl.netloc}/"
     return urljoin(
diff --git a/wqflask/wqflask/oauth2/resources.py b/gn2/wqflask/oauth2/resources.py
index 7d20b859..7d20b859 100644
--- a/wqflask/wqflask/oauth2/resources.py
+++ b/gn2/wqflask/oauth2/resources.py
diff --git a/wqflask/wqflask/oauth2/roles.py b/gn2/wqflask/oauth2/roles.py
index 2fe35f9b..2fe35f9b 100644
--- a/wqflask/wqflask/oauth2/roles.py
+++ b/gn2/wqflask/oauth2/roles.py
diff --git a/wqflask/wqflask/oauth2/routes.py b/gn2/wqflask/oauth2/routes.py
index 4c4b877b..4c4b877b 100644
--- a/wqflask/wqflask/oauth2/routes.py
+++ b/gn2/wqflask/oauth2/routes.py
diff --git a/wqflask/wqflask/oauth2/session.py b/gn2/wqflask/oauth2/session.py
index 2ef534e2..2ef534e2 100644
--- a/wqflask/wqflask/oauth2/session.py
+++ b/gn2/wqflask/oauth2/session.py
diff --git a/wqflask/wqflask/oauth2/toplevel.py b/gn2/wqflask/oauth2/toplevel.py
index 65f60067..65f60067 100644
--- a/wqflask/wqflask/oauth2/toplevel.py
+++ b/gn2/wqflask/oauth2/toplevel.py
diff --git a/wqflask/wqflask/oauth2/ui.py b/gn2/wqflask/oauth2/ui.py
index b706cdd9..b706cdd9 100644
--- a/wqflask/wqflask/oauth2/ui.py
+++ b/gn2/wqflask/oauth2/ui.py
diff --git a/wqflask/wqflask/oauth2/users.py b/gn2/wqflask/oauth2/users.py
index 76ae56cb..12d07d0c 100644
--- a/wqflask/wqflask/oauth2/users.py
+++ b/gn2/wqflask/oauth2/users.py
@@ -65,7 +65,7 @@ def request_add_to_group() -> Response:
 @users.route("/login", methods=["GET", "POST"])
 def login():
     """Route to allow users to sign up."""
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     next_endpoint=request.args.get("next", False)
 
     if request.method == "POST":
@@ -101,7 +101,7 @@ def login():
 
 @users.route("/logout", methods=["GET", "POST"])
 def logout():
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     if user_logged_in():
         resp = oauth2_client().revoke_token(
             urljoin(AUTH_SERVER_URL, "auth/revoke"))
@@ -124,7 +124,7 @@ def logout():
 
 @users.route("/register", methods=["GET", "POST"])
 def register_user():
-    from utility.tools import AUTH_SERVER_URL
+    from gn2.utility.tools import AUTH_SERVER_URL
     if user_logged_in():
         next_endpoint=request.args.get("next", "/")
         flash(("You cannot register a new user while logged in. "
diff --git a/wqflask/wqflask/parser.py b/gn2/wqflask/parser.py
index ddf48d90..ddf48d90 100644
--- a/wqflask/wqflask/parser.py
+++ b/gn2/wqflask/parser.py
diff --git a/wqflask/wqflask/partial_correlations_views.py b/gn2/wqflask/partial_correlations_views.py
index c680d913..44b0fba1 100644
--- a/wqflask/wqflask/partial_correlations_views.py
+++ b/gn2/wqflask/partial_correlations_views.py
@@ -13,9 +13,9 @@ from flask import (
     current_app,
     render_template)
 
-from wqflask import app
-from utility.tools import get_setting, GN_SERVER_URL
-from wqflask.database import database_connection
+from gn2.wqflask import app
+from gn2.utility.tools import get_setting, GN_SERVER_URL
+from gn2.wqflask.database import database_connection
 from gn3.db.partial_correlations import traits_info
 
 def publish_target_databases(conn, groups, threshold):
diff --git a/wqflask/wqflask/pbkdf2.py b/gn2/wqflask/pbkdf2.py
index 1a965fc5..1a965fc5 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/gn2/wqflask/pbkdf2.py
diff --git a/wqflask/wqflask/requests.py b/gn2/wqflask/requests.py
index 43c8001f..43c8001f 100644
--- a/wqflask/wqflask/requests.py
+++ b/gn2/wqflask/requests.py
diff --git a/wqflask/wqflask/resource_manager.py b/gn2/wqflask/resource_manager.py
index 375e3d64..b0da6d6f 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/gn2/wqflask/resource_manager.py
@@ -20,9 +20,9 @@ from typing import Dict, Tuple
 from urllib.parse import urljoin
 
 
-from wqflask.decorators import edit_access_required
-from wqflask.decorators import edit_admins_access_required
-from wqflask.decorators import login_required
+from gn2.wqflask.decorators import edit_access_required
+from gn2.wqflask.decorators import edit_admins_access_required
+from gn2.wqflask.decorators import login_required
 
 
 resource_management = Blueprint('resource_management', __name__)
diff --git a/wqflask/wqflask/search_results.py b/gn2/wqflask/search_results.py
index f661aba7..b0f08463 100644
--- a/wqflask/wqflask/search_results.py
+++ b/gn2/wqflask/search_results.py
@@ -8,17 +8,17 @@ import json
 
 from flask import g
 
-from base.data_set import create_dataset
-from base.webqtlConfig import PUBMEDLINK_URL
-from wqflask import parser
-from wqflask import do_search
+from gn2.base.data_set import create_dataset
+from gn2.base.webqtlConfig import PUBMEDLINK_URL
+from gn2.wqflask import parser
+from gn2.wqflask import do_search
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
-from utility import hmac
-from utility.authentication_tools import check_resource_availability
-from utility.tools import get_setting, GN2_BASE_URL
-from utility.type_checking import is_str
+from gn2.utility import hmac
+from gn2.utility.authentication_tools import check_resource_availability
+from gn2.utility.tools import get_setting, GN2_BASE_URL
+from gn2.utility.type_checking import is_str
 
 
 class SearchResultPage:
diff --git a/wqflask/wqflask/send_mail.py b/gn2/wqflask/send_mail.py
index 299c866a..299c866a 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/gn2/wqflask/send_mail.py
diff --git a/wqflask/wqflask/server_side.py b/gn2/wqflask/server_side.py
index e661c407..e661c407 100644
--- a/wqflask/wqflask/server_side.py
+++ b/gn2/wqflask/server_side.py
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/gn2/wqflask/show_trait/SampleList.py
index b5110dcd..64fc8fe6 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/gn2/wqflask/show_trait/SampleList.py
@@ -1,13 +1,13 @@
 import re
 import itertools
 
-from wqflask.database import database_connection
-from base import webqtlCaseData, webqtlConfig
+from gn2.wqflask.database import database_connection
+from gn2.base import webqtlCaseData, webqtlConfig
 from pprint import pformat as pf
 
-from utility import Plot
-from utility import Bunch
-from utility.tools import get_setting
+from gn2.utility import Plot
+from gn2.utility import Bunch
+from gn2.utility.tools import get_setting
 
 class SampleList:
     def __init__(self,
diff --git a/wqflask/wqflask/show_trait/__init__.py b/gn2/wqflask/show_trait/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/show_trait/__init__.py
+++ b/gn2/wqflask/show_trait/__init__.py
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/gn2/wqflask/show_trait/export_trait_data.py
index e8e34a26..06c1c502 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/gn2/wqflask/show_trait/export_trait_data.py
@@ -3,8 +3,8 @@ import simplejson as json
 
 from pprint import pformat as pf
 from functools import cmp_to_key
-from base.trait import create_trait
-from base import data_set
+from gn2.base.trait import create_trait
+from gn2.base import data_set
 
 
 def export_sample_table(targs):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/gn2/wqflask/show_trait/show_trait.py
index fc4df4b7..64d9be3b 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/gn2/wqflask/show_trait/show_trait.py
@@ -11,16 +11,16 @@ from collections import OrderedDict
 import numpy as np
 import scipy.stats as ss
 
-from wqflask.database import database_connection
-
-from base import webqtlConfig
-from wqflask.show_trait.SampleList import SampleList
-from base.trait import create_trait
-from base import data_set
-from utility import helper_functions
-from utility.tools import get_setting, locate_ignore_error
-from utility.tools import GN_PROXY_URL
-from utility.redis_tools import get_redis_conn, get_resource_id
+from gn2.wqflask.database import database_connection
+
+from gn2.base import webqtlConfig
+from gn2.wqflask.show_trait.SampleList import SampleList
+from gn2.base.trait import create_trait
+from gn2.base import data_set
+from gn2.utility import helper_functions
+from gn2.utility.tools import get_setting, locate_ignore_error
+from gn2.utility.tools import GN_PROXY_URL
+from gn2.utility.redis_tools import get_redis_conn, get_resource_id
 
 from gn3.authentication import get_highest_user_access_role
 
diff --git a/wqflask/wqflask/snp_browser/__init__.py b/gn2/wqflask/snp_browser/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/snp_browser/__init__.py
+++ b/gn2/wqflask/snp_browser/__init__.py
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/gn2/wqflask/snp_browser/snp_browser.py
index 59a4dccf..2d17f82b 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/gn2/wqflask/snp_browser/snp_browser.py
@@ -1,12 +1,12 @@
 import string
 from PIL import (Image)
 
-from base import species
-from base import webqtlConfig
+from gn2.base import species
+from gn2.base import webqtlConfig
 
-from wqflask.database import database_connection
+from gn2.wqflask.database import database_connection
 
-from utility.tools import get_setting
+from gn2.utility.tools import get_setting
 
 
 class SnpBrowser:
diff --git a/wqflask/wqflask/startup.py b/gn2/wqflask/startup.py
index 069755fe..069755fe 100644
--- a/wqflask/wqflask/startup.py
+++ b/gn2/wqflask/startup.py
diff --git a/wqflask/wqflask/static/Congenic.png b/gn2/wqflask/static/Congenic.png
index 8cd489a4..8cd489a4 100644
--- a/wqflask/wqflask/static/Congenic.png
+++ b/gn2/wqflask/static/Congenic.png
diff --git a/wqflask/wqflask/static/fonts/README b/gn2/wqflask/static/fonts/README
index 75a3e444..75a3e444 100644
--- a/wqflask/wqflask/static/fonts/README
+++ b/gn2/wqflask/static/fonts/README
diff --git a/wqflask/wqflask/static/fonts/arial.ttf b/gn2/wqflask/static/fonts/arial.ttf
index bf0d4a95..bf0d4a95 100644
--- a/wqflask/wqflask/static/fonts/arial.ttf
+++ b/gn2/wqflask/static/fonts/arial.ttf
diff --git a/wqflask/wqflask/static/fonts/courbd.ttf b/gn2/wqflask/static/fonts/courbd.ttf
index c8081467..c8081467 100644
--- a/wqflask/wqflask/static/fonts/courbd.ttf
+++ b/gn2/wqflask/static/fonts/courbd.ttf
diff --git a/wqflask/wqflask/static/fonts/fnt_bs.ttf b/gn2/wqflask/static/fonts/fnt_bs.ttf
index 712c38cf..712c38cf 100644
--- a/wqflask/wqflask/static/fonts/fnt_bs.ttf
+++ b/gn2/wqflask/static/fonts/fnt_bs.ttf
diff --git a/wqflask/wqflask/static/fonts/tahoma.ttf b/gn2/wqflask/static/fonts/tahoma.ttf
index bb314be3..bb314be3 100644
--- a/wqflask/wqflask/static/fonts/tahoma.ttf
+++ b/gn2/wqflask/static/fonts/tahoma.ttf
diff --git a/wqflask/wqflask/static/fonts/trebucbd.ttf b/gn2/wqflask/static/fonts/trebucbd.ttf
index 1ab1ae0a..1ab1ae0a 100644
--- a/wqflask/wqflask/static/fonts/trebucbd.ttf
+++ b/gn2/wqflask/static/fonts/trebucbd.ttf
diff --git a/wqflask/wqflask/static/fonts/verdana.ttf b/gn2/wqflask/static/fonts/verdana.ttf
index 754a9b7b..754a9b7b 100644
--- a/wqflask/wqflask/static/fonts/verdana.ttf
+++ b/gn2/wqflask/static/fonts/verdana.ttf
diff --git a/wqflask/wqflask/static/fonts/verdanab.ttf b/gn2/wqflask/static/fonts/verdanab.ttf
index 1a99258f..1a99258f 100644
--- a/wqflask/wqflask/static/fonts/verdanab.ttf
+++ b/gn2/wqflask/static/fonts/verdanab.ttf
diff --git a/wqflask/wqflask/static/gif/89.gif b/gn2/wqflask/static/gif/89.gif
index e9b3279d..e9b3279d 100644
--- a/wqflask/wqflask/static/gif/89.gif
+++ b/gn2/wqflask/static/gif/89.gif
diff --git a/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif b/gn2/wqflask/static/gif/error/Wild-Type-Mouse.gif
index 2c68b5ee..2c68b5ee 100644
--- a/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif b/gn2/wqflask/static/gif/error/animated-gifs-aliens-29.gif
index e9d38277..e9d38277 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif b/gn2/wqflask/static/gif/error/animated-gifs-angels-04.gif
index 94e11847..94e11847 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif
+++ b/gn2/wqflask/static/gif/error/animated-gifs-angels-04.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif b/gn2/wqflask/static/gif/error/animated-gifs-cats-016.gif
index 7e6ec9a3..7e6ec9a3 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif b/gn2/wqflask/static/gif/error/animated-gifs-cats-031.gif
index af7ef655..af7ef655 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif b/gn2/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
index 89c79ddf..89c79ddf 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
+++ b/gn2/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif b/gn2/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
index 7530d180..7530d180 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
+++ b/gn2/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-13.gif
index afb05c62..afb05c62 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-28.gif
index f5b4a563..f5b4a563 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-32.gif
index 7258e594..7258e594 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-42.gif
index ed1f8722..ed1f8722 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-60.gif
index f58d69f1..f58d69f1 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-64.gif
index 5d5b4fdf..5d5b4fdf 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif b/gn2/wqflask/static/gif/error/animated-gifs-computers-65.gif
index b4b10845..b4b10845 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif
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index e60cb4fe..e60cb4fe 100644
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index bd7b72f3..bd7b72f3 100644
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index 916d6b33..916d6b33 100644
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index 0ec782c4..0ec782c4 100644
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index 9515c18a..9515c18a 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif
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index f1e2e1f5..f1e2e1f5 100644
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index 572849d5..572849d5 100644
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index d808c9ee..d808c9ee 100644
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index 9865ee45..9865ee45 100644
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif b/gn2/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif
index ee9c113d..ee9c113d 100644
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index 5ca2ee5c..5ca2ee5c 100644
--- a/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif b/gn2/wqflask/static/gif/error/animated-gifs-mice-09.gif
index 7cb361e4..7cb361e4 100644
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index 96a26450..96a26450 100644
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif b/gn2/wqflask/static/gif/error/animated-gifs-smileys-063.gif
index 62de166c..62de166c 100644
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index 3550e978..3550e978 100644
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index 954ab614..954ab614 100644
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index 596174d7..596174d7 100644
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index 5aba636b..5aba636b 100644
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index 7896ff1f..7896ff1f 100644
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index 89da6441..89da6441 100644
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index b7887630..b7887630 100644
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index f6697d02..f6697d02 100644
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index 2b2496a4..2b2496a4 100644
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index f2188656..f2188656 100644
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index aa8f7bd3..aa8f7bd3 100644
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index 473212e4..473212e4 100644
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index 81c8ba26..81c8ba26 100644
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index 7232c58b..7232c58b 100644
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index 2384ceb6..2384ceb6 100644
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index d77c708d..d77c708d 100644
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index 1b2de7ec..1b2de7ec 100644
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index f354a4cc..f354a4cc 100644
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index ba2eeb37..ba2eeb37 100644
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index 4cdec5cb..4cdec5cb 100644
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index 164220e7..164220e7 100644
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index c2146b77..c2146b77 100644
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index 50aff7f2..50aff7f2 100644
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index 46305fa1..46305fa1 100644
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index 881a08e8..881a08e8 100644
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index 8cd489a4..8cd489a4 100644
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index dc239f8e..dc239f8e 100644
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index 5b4b2c70..5b4b2c70 100644
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index 5b91d991..5b91d991 100644
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index f3a65f29..f3a65f29 100644
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diff --git a/wqflask/wqflask/static/images/Winsorize3.png b/gn2/wqflask/static/images/Winsorize3.png
index a9ed95d6..a9ed95d6 100644
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index 571b08cd..571b08cd 100644
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index 1501e280..1501e280 100644
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diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/gn2/wqflask/static/new/javascript/group_manager.js
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diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/gn2/wqflask/static/new/javascript/histogram.js
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diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/gn2/wqflask/static/new/javascript/init_genome_browser.js
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--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
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diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js
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diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js b/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js
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diff --git a/wqflask/wqflask/static/new/javascript/loadings_plot.js b/gn2/wqflask/static/new/javascript/loadings_plot.js
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diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/gn2/wqflask/static/new/javascript/lod_chart.js
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--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
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diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/gn2/wqflask/static/new/javascript/lodheatmap.js
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diff --git a/wqflask/wqflask/static/new/javascript/login.js b/gn2/wqflask/static/new/javascript/login.js
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diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/gn2/wqflask/static/new/javascript/network_graph.js
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diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/gn2/wqflask/static/new/javascript/panelutil.js
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diff --git a/wqflask/wqflask/static/new/javascript/partial_correlations.js b/gn2/wqflask/static/new/javascript/partial_correlations.js
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diff --git a/wqflask/wqflask/static/new/javascript/password_strength.js b/gn2/wqflask/static/new/javascript/password_strength.js
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diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/gn2/wqflask/static/new/javascript/plotly_probability_plot.js
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diff --git a/wqflask/wqflask/static/new/javascript/scatter-matrix.js b/gn2/wqflask/static/new/javascript/scatter-matrix.js
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diff --git a/wqflask/wqflask/static/new/javascript/scatterplot.js b/gn2/wqflask/static/new/javascript/scatterplot.js
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diff --git a/wqflask/wqflask/static/new/javascript/search_autocomplete.js b/gn2/wqflask/static/new/javascript/search_autocomplete.js
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diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js
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diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/gn2/wqflask/static/new/javascript/stats.js
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diff --git a/wqflask/wqflask/templates/admin/change_resource_owner.html b/gn2/wqflask/templates/admin/change_resource_owner.html
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--- a/wqflask/wqflask/templates/geneweaver_page.html
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diff --git a/wqflask/wqflask/templates/genotype.html b/gn2/wqflask/templates/genotype.html
index fc5b1ad7..fc5b1ad7 100644
--- a/wqflask/wqflask/templates/genotype.html
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diff --git a/wqflask/wqflask/templates/glossary.html b/gn2/wqflask/templates/glossary.html
index aaee7c5a..aaee7c5a 100644
--- a/wqflask/wqflask/templates/glossary.html
+++ b/gn2/wqflask/templates/glossary.html
diff --git a/wqflask/wqflask/templates/gn3_ctl_results.html b/gn2/wqflask/templates/gn3_ctl_results.html
index c42707f6..c42707f6 100644
--- a/wqflask/wqflask/templates/gn3_ctl_results.html
+++ b/gn2/wqflask/templates/gn3_ctl_results.html
diff --git a/wqflask/wqflask/templates/gn3_wgcna_results.html b/gn2/wqflask/templates/gn3_wgcna_results.html
index 8a31bf28..8a31bf28 100644
--- a/wqflask/wqflask/templates/gn3_wgcna_results.html
+++ b/gn2/wqflask/templates/gn3_wgcna_results.html
diff --git a/wqflask/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html
index 46cc1e90..46cc1e90 100644
--- a/wqflask/wqflask/templates/gnqa.html
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diff --git a/wqflask/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html
index 99242b29..99242b29 100644
--- a/wqflask/wqflask/templates/gnqa_answer.html
+++ b/gn2/wqflask/templates/gnqa_answer.html
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html
index 6bc92377..6bc92377 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/gn2/wqflask/templates/gsearch_gene.html
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/gn2/wqflask/templates/gsearch_pheno.html
index a1fef2c8..a1fef2c8 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/gn2/wqflask/templates/gsearch_pheno.html
diff --git a/wqflask/wqflask/templates/heatmap.html b/gn2/wqflask/templates/heatmap.html
index 92754266..92754266 100644
--- a/wqflask/wqflask/templates/heatmap.html
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diff --git a/wqflask/wqflask/templates/index_page.html b/gn2/wqflask/templates/index_page.html
index 7b5a1d16..7b5a1d16 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/gn2/wqflask/templates/index_page.html
diff --git a/wqflask/wqflask/templates/info_page.html b/gn2/wqflask/templates/info_page.html
index 91d34573..91d34573 100644
--- a/wqflask/wqflask/templates/info_page.html
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diff --git a/wqflask/wqflask/templates/jobs/debug.html b/gn2/wqflask/templates/jobs/debug.html
index 828ab1cc..828ab1cc 100644
--- a/wqflask/wqflask/templates/jobs/debug.html
+++ b/gn2/wqflask/templates/jobs/debug.html
diff --git a/wqflask/wqflask/templates/jobs/no-such-job.html b/gn2/wqflask/templates/jobs/no-such-job.html
index 6fe7d014..6fe7d014 100644
--- a/wqflask/wqflask/templates/jobs/no-such-job.html
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diff --git a/wqflask/wqflask/templates/jupyter_notebooks.html b/gn2/wqflask/templates/jupyter_notebooks.html
index afc95a15..afc95a15 100644
--- a/wqflask/wqflask/templates/jupyter_notebooks.html
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diff --git a/wqflask/wqflask/templates/links.html b/gn2/wqflask/templates/links.html
index 6e91adae..6e91adae 100644
--- a/wqflask/wqflask/templates/links.html
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index f5c7482f..f5c7482f 100644
--- a/wqflask/wqflask/templates/list_case_attribute_diffs.html
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diff --git a/wqflask/wqflask/templates/list_case_attribute_diffs_error.html b/gn2/wqflask/templates/list_case_attribute_diffs_error.html
index 6ca70984..6ca70984 100644
--- a/wqflask/wqflask/templates/list_case_attribute_diffs_error.html
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diff --git a/wqflask/wqflask/templates/loading.html b/gn2/wqflask/templates/loading.html
index a6d9ae5e..a6d9ae5e 100644
--- a/wqflask/wqflask/templates/loading.html
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diff --git a/wqflask/wqflask/templates/loading_corrs.html b/gn2/wqflask/templates/loading_corrs.html
index 8abd5464..8abd5464 100644
--- a/wqflask/wqflask/templates/loading_corrs.html
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diff --git a/wqflask/wqflask/templates/mapping_error.html b/gn2/wqflask/templates/mapping_error.html
index 8364af3c..8364af3c 100644
--- a/wqflask/wqflask/templates/mapping_error.html
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diff --git a/wqflask/wqflask/templates/mapping_results.html b/gn2/wqflask/templates/mapping_results.html
index 0e084ba7..0e084ba7 100644
--- a/wqflask/wqflask/templates/mapping_results.html
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diff --git a/wqflask/wqflask/templates/marker_regression.html b/gn2/wqflask/templates/marker_regression.html
index b633f815..b633f815 100644
--- a/wqflask/wqflask/templates/marker_regression.html
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diff --git a/wqflask/wqflask/templates/metadata/dataset.html b/gn2/wqflask/templates/metadata/dataset.html
index 06df6a68..06df6a68 100644
--- a/wqflask/wqflask/templates/metadata/dataset.html
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diff --git a/wqflask/wqflask/templates/network_graph.html b/gn2/wqflask/templates/network_graph.html
index cff69ac8..cff69ac8 100644
--- a/wqflask/wqflask/templates/network_graph.html
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diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/gn2/wqflask/templates/new_security/forgot_password.html
index 60a221da..60a221da 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password.html
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diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/gn2/wqflask/templates/new_security/forgot_password_step2.html
index 1835fd4c..1835fd4c 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html
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diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/gn2/wqflask/templates/new_security/login_user.html
index b8cdf6ef..b8cdf6ef 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
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diff --git a/wqflask/wqflask/templates/new_security/not_authenticated.html b/gn2/wqflask/templates/new_security/not_authenticated.html
index ea688346..ea688346 100644
--- a/wqflask/wqflask/templates/new_security/not_authenticated.html
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diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/gn2/wqflask/templates/new_security/password_reset.html
index e21f075c..e21f075c 100644
--- a/wqflask/wqflask/templates/new_security/password_reset.html
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diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/gn2/wqflask/templates/new_security/register_user.html
index c2895517..c2895517 100644
--- a/wqflask/wqflask/templates/new_security/register_user.html
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diff --git a/wqflask/wqflask/templates/new_security/registered.html b/gn2/wqflask/templates/new_security/registered.html
index 29889a97..29889a97 100644
--- a/wqflask/wqflask/templates/new_security/registered.html
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diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/gn2/wqflask/templates/new_security/thank_you.html
index d4f5e574..d4f5e574 100644
--- a/wqflask/wqflask/templates/new_security/thank_you.html
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diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/gn2/wqflask/templates/new_security/verification_still_needed.html
index 1f91fd8d..1f91fd8d 100644
--- a/wqflask/wqflask/templates/new_security/verification_still_needed.html
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diff --git a/wqflask/wqflask/templates/news.html b/gn2/wqflask/templates/news.html
index a615564b..a615564b 100644
--- a/wqflask/wqflask/templates/news.html
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diff --git a/wqflask/wqflask/templates/oauth2/create-resource.html b/gn2/wqflask/templates/oauth2/create-resource.html
index 479f4152..479f4152 100644
--- a/wqflask/wqflask/templates/oauth2/create-resource.html
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diff --git a/wqflask/wqflask/templates/oauth2/create-role.html b/gn2/wqflask/templates/oauth2/create-role.html
index f2bff7b4..f2bff7b4 100644
--- a/wqflask/wqflask/templates/oauth2/create-role.html
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diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/gn2/wqflask/templates/oauth2/data-list-genotype.html
index c780a583..c780a583 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html
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diff --git a/wqflask/wqflask/templates/oauth2/data-list-mrna.html b/gn2/wqflask/templates/oauth2/data-list-mrna.html
index 0e163235..0e163235 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-mrna.html
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diff --git a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html b/gn2/wqflask/templates/oauth2/data-list-phenotype.html
index 8c79c0d6..8c79c0d6 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html
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diff --git a/wqflask/wqflask/templates/oauth2/data-list.html b/gn2/wqflask/templates/oauth2/data-list.html
index 8a8f6694..8a8f6694 100644
--- a/wqflask/wqflask/templates/oauth2/data-list.html
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diff --git a/wqflask/wqflask/templates/oauth2/display_error.html b/gn2/wqflask/templates/oauth2/display_error.html
index 9abe02c4..9abe02c4 100644
--- a/wqflask/wqflask/templates/oauth2/display_error.html
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diff --git a/wqflask/wqflask/templates/oauth2/group.html b/gn2/wqflask/templates/oauth2/group.html
index f4c29d18..f4c29d18 100644
--- a/wqflask/wqflask/templates/oauth2/group.html
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diff --git a/wqflask/wqflask/templates/oauth2/group_join_or_create.html b/gn2/wqflask/templates/oauth2/group_join_or_create.html
index 8255d2f8..8255d2f8 100644
--- a/wqflask/wqflask/templates/oauth2/group_join_or_create.html
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diff --git a/wqflask/wqflask/templates/oauth2/join-requests.html b/gn2/wqflask/templates/oauth2/join-requests.html
index 833b4e93..833b4e93 100644
--- a/wqflask/wqflask/templates/oauth2/join-requests.html
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diff --git a/wqflask/wqflask/templates/oauth2/list_roles.html b/gn2/wqflask/templates/oauth2/list_roles.html
index a4061fca..a4061fca 100644
--- a/wqflask/wqflask/templates/oauth2/list_roles.html
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index eaa1a192..eaa1a192 100644
--- a/wqflask/wqflask/templates/oauth2/login.html
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index 48ec6cee..48ec6cee 100644
--- a/wqflask/wqflask/templates/oauth2/masquerade.html
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diff --git a/wqflask/wqflask/templates/oauth2/profile_nav.html b/gn2/wqflask/templates/oauth2/profile_nav.html
index aa752905..aa752905 100644
--- a/wqflask/wqflask/templates/oauth2/profile_nav.html
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diff --git a/wqflask/wqflask/templates/oauth2/register_user.html b/gn2/wqflask/templates/oauth2/register_user.html
index 27ccbd30..27ccbd30 100644
--- a/wqflask/wqflask/templates/oauth2/register_user.html
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index e6ed5fff..e6ed5fff 100644
--- a/wqflask/wqflask/templates/oauth2/request_error.html
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index c52043db..c52043db 100644
--- a/wqflask/wqflask/templates/oauth2/resources.html
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diff --git a/wqflask/wqflask/templates/oauth2/role.html b/gn2/wqflask/templates/oauth2/role.html
index c33c93ee..c33c93ee 100644
--- a/wqflask/wqflask/templates/oauth2/role.html
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diff --git a/wqflask/wqflask/templates/oauth2/view-group-role.html b/gn2/wqflask/templates/oauth2/view-group-role.html
index 5da023bf..5da023bf 100644
--- a/wqflask/wqflask/templates/oauth2/view-group-role.html
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diff --git a/wqflask/wqflask/templates/oauth2/view-resource.html b/gn2/wqflask/templates/oauth2/view-resource.html
index 275fcb24..275fcb24 100644
--- a/wqflask/wqflask/templates/oauth2/view-resource.html
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diff --git a/wqflask/wqflask/templates/oauth2/view-user.html b/gn2/wqflask/templates/oauth2/view-user.html
index 34526b14..34526b14 100644
--- a/wqflask/wqflask/templates/oauth2/view-user.html
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diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/gn2/wqflask/templates/pair_scan_results.html
index dbd90bc7..dbd90bc7 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
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diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_error.html b/gn2/wqflask/templates/partial_correlations/pcorrs_error.html
index 8d6c4bbe..8d6c4bbe 100644
--- a/wqflask/wqflask/templates/partial_correlations/pcorrs_error.html
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diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_poll_results.html b/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html
index 38577c32..38577c32 100644
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diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_results_presentation.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html
index dac02397..dac02397 100644
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diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
index c1ef6001..c1ef6001 100644
--- a/wqflask/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html
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diff --git a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html b/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html
index fe7f8cd4..fe7f8cd4 100644
--- a/wqflask/wqflask/templates/partial_correlations/pcorrs_select_operations.html
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diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/gn2/wqflask/templates/pca_scree_plot.html
index 74eb2c15..74eb2c15 100644
--- a/wqflask/wqflask/templates/pca_scree_plot.html
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diff --git a/wqflask/wqflask/templates/phenotype.html b/gn2/wqflask/templates/phenotype.html
index 4f4fba6e..4f4fba6e 100644
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index e36c9e08..e36c9e08 100644
--- a/wqflask/wqflask/templates/policies.html
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diff --git a/wqflask/wqflask/templates/publication.html b/gn2/wqflask/templates/publication.html
index 556d184f..556d184f 100644
--- a/wqflask/wqflask/templates/publication.html
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index 04e60361..04e60361 100644
--- a/wqflask/wqflask/templates/references.html
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index b8d0514e..b8d0514e 100644
--- a/wqflask/wqflask/templates/search_autocomplete.html
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diff --git a/wqflask/wqflask/templates/search_error.html b/gn2/wqflask/templates/search_error.html
index df8d9dff..df8d9dff 100644
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diff --git a/wqflask/wqflask/templates/search_history.html b/gn2/wqflask/templates/search_history.html
index 11586c0a..11586c0a 100644
--- a/wqflask/wqflask/templates/search_history.html
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diff --git a/wqflask/wqflask/templates/search_result_page.html b/gn2/wqflask/templates/search_result_page.html
index cade198a..cade198a 100644
--- a/wqflask/wqflask/templates/search_result_page.html
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diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/gn2/wqflask/templates/set_group_privileges.html
index a0a53292..a0a53292 100644
--- a/wqflask/wqflask/templates/set_group_privileges.html
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diff --git a/wqflask/wqflask/templates/show_image.html b/gn2/wqflask/templates/show_image.html
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--- a/wqflask/wqflask/templates/show_image.html
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diff --git a/wqflask/wqflask/templates/show_trait.html b/gn2/wqflask/templates/show_trait.html
index dd054ffc..dd054ffc 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/gn2/wqflask/templates/show_trait.html
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/gn2/wqflask/templates/show_trait_calculate_correlations.html
index 22fe6142..22fe6142 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/gn2/wqflask/templates/show_trait_calculate_correlations.html
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/gn2/wqflask/templates/show_trait_details.html
index 9c12393d..9c12393d 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/gn2/wqflask/templates/show_trait_details.html
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/gn2/wqflask/templates/show_trait_edit_data.html
index 91cbdb6e..91cbdb6e 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/gn2/wqflask/templates/show_trait_edit_data.html
diff --git a/wqflask/wqflask/templates/show_trait_error.html b/gn2/wqflask/templates/show_trait_error.html
index c924d1f1..c924d1f1 100644
--- a/wqflask/wqflask/templates/show_trait_error.html
+++ b/gn2/wqflask/templates/show_trait_error.html
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/gn2/wqflask/templates/show_trait_mapping_tools.html
index f1ed8922..f1ed8922 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/gn2/wqflask/templates/show_trait_mapping_tools.html
diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/gn2/wqflask/templates/show_trait_progress_bar.html
index f9a34070..f9a34070 100644
--- a/wqflask/wqflask/templates/show_trait_progress_bar.html
+++ b/gn2/wqflask/templates/show_trait_progress_bar.html
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/gn2/wqflask/templates/show_trait_statistics.html
index 9ee0de5c..9ee0de5c 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/gn2/wqflask/templates/show_trait_statistics.html
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/gn2/wqflask/templates/show_trait_transform_and_filter.html
index 0706f64d..0706f64d 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/gn2/wqflask/templates/show_trait_transform_and_filter.html
diff --git a/wqflask/wqflask/templates/snp_browser.html b/gn2/wqflask/templates/snp_browser.html
index b9aea570..b9aea570 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/gn2/wqflask/templates/snp_browser.html
diff --git a/wqflask/wqflask/templates/startup_errors.html b/gn2/wqflask/templates/startup_errors.html
index 82d85572..82d85572 100644
--- a/wqflask/wqflask/templates/startup_errors.html
+++ b/gn2/wqflask/templates/startup_errors.html
diff --git a/wqflask/wqflask/templates/submit_trait.html b/gn2/wqflask/templates/submit_trait.html
index 10ddf69f..10ddf69f 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/gn2/wqflask/templates/submit_trait.html
diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/gn2/wqflask/templates/test_correlation_page.html
index 991773a2..991773a2 100644
--- a/wqflask/wqflask/templates/test_correlation_page.html
+++ b/gn2/wqflask/templates/test_correlation_page.html
diff --git a/wqflask/wqflask/templates/tool_buttons.html b/gn2/wqflask/templates/tool_buttons.html
index c6d1476c..c6d1476c 100644
--- a/wqflask/wqflask/templates/tool_buttons.html
+++ b/gn2/wqflask/templates/tool_buttons.html
diff --git a/wqflask/wqflask/templates/tutorials.html b/gn2/wqflask/templates/tutorials.html
index 74c84726..74c84726 100644
--- a/wqflask/wqflask/templates/tutorials.html
+++ b/gn2/wqflask/templates/tutorials.html
diff --git a/wqflask/wqflask/templates/view_case_attribute_diff.html b/gn2/wqflask/templates/view_case_attribute_diff.html
index 0b5c95f1..0b5c95f1 100644
--- a/wqflask/wqflask/templates/view_case_attribute_diff.html
+++ b/gn2/wqflask/templates/view_case_attribute_diff.html
diff --git a/wqflask/wqflask/templates/view_case_attribute_diff_error.html b/gn2/wqflask/templates/view_case_attribute_diff_error.html
index a10f7ab9..a10f7ab9 100644
--- a/wqflask/wqflask/templates/view_case_attribute_diff_error.html
+++ b/gn2/wqflask/templates/view_case_attribute_diff_error.html
diff --git a/wqflask/wqflask/templates/webgestalt_page.html b/gn2/wqflask/templates/webgestalt_page.html
index 759e0251..759e0251 100644
--- a/wqflask/wqflask/templates/webgestalt_page.html
+++ b/gn2/wqflask/templates/webgestalt_page.html
diff --git a/wqflask/wqflask/templates/wgcna_results.html b/gn2/wqflask/templates/wgcna_results.html
index 0dc030b1..0dc030b1 100644
--- a/wqflask/wqflask/templates/wgcna_results.html
+++ b/gn2/wqflask/templates/wgcna_results.html
diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/gn2/wqflask/templates/wgcna_setup.html
index d7acd5f2..d7acd5f2 100644
--- a/wqflask/wqflask/templates/wgcna_setup.html
+++ b/gn2/wqflask/templates/wgcna_setup.html
diff --git a/wqflask/wqflask/templates/with-trait-items.html b/gn2/wqflask/templates/with-trait-items.html
index 66d6fd22..66d6fd22 100644
--- a/wqflask/wqflask/templates/with-trait-items.html
+++ b/gn2/wqflask/templates/with-trait-items.html
diff --git a/wqflask/wqflask/update_search_results.py b/gn2/wqflask/update_search_results.py
index 8789c903..e6d2b0ca 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/gn2/wqflask/update_search_results.py
@@ -1,10 +1,10 @@
 import json
 
-from base.data_set import create_dataset
-from base.trait import GeneralTrait
-from db import webqtlDatabaseFunction
-from wqflask.database import database_connection
-from utility.tools import get_setting
+from gn2.base.data_set import create_dataset
+from gn2.base.trait import GeneralTrait
+from gn2.db import webqtlDatabaseFunction
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
 
 
 class GSearch:
diff --git a/wqflask/wqflask/user_login.py b/gn2/wqflask/user_login.py
index ae61edb0..55af2081 100644
--- a/wqflask/wqflask/user_login.py
+++ b/gn2/wqflask/user_login.py
@@ -12,16 +12,16 @@ import simplejson as json
 from flask import (Flask, g, render_template, url_for, request, make_response,
                    redirect, flash, abort)
 
-from wqflask import app
-from wqflask import pbkdf2
-from wqflask.user_session import UserSession
+from gn2.wqflask import app
+from gn2.wqflask import pbkdf2
+from gn2.wqflask.user_session import UserSession
 
-from utility import hmac
-from utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
+from gn2.utility import hmac
+from gn2.utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
 Redis = get_redis_conn()
 
 from smtplib import SMTP
-from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
+from gn2.utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
 
 THREE_DAYS = 60 * 60 * 24 * 3
 
@@ -173,7 +173,7 @@ def verify_email():
 def login():
     params = request.form if request.form else request.args
     if not params:  # ZS: If coming to page for first time
-        from utility.tools import GITHUB_AUTH_URL, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID
+        from gn2.utility.tools import GITHUB_AUTH_URL, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID
         external_login = {}
         if GITHUB_AUTH_URL and GITHUB_CLIENT_ID != 'UNKNOWN':
             external_login["github"] = GITHUB_AUTH_URL
@@ -251,7 +251,7 @@ def login():
 
 @app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
 def github_oauth2():
-    from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
+    from gn2.utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
     code = request.args.get("code")
     data = {
         "client_id": GITHUB_CLIENT_ID,
@@ -285,7 +285,7 @@ def github_oauth2():
 
 
 def get_github_user_details(access_token):
-    from utility.tools import GITHUB_API_URL
+    from gn2.utility.tools import GITHUB_API_URL
     result = requests.get(GITHUB_API_URL, headers={
                           'Authorization': 'token ' + access_token}).content
 
@@ -295,7 +295,7 @@ def get_github_user_details(access_token):
 @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
 def orcid_oauth2():
     from uuid import uuid4
-    from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
+    from gn2.utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
     code = request.args.get("code")
     error = request.args.get("error")
     url = "/n/login"
@@ -332,7 +332,7 @@ def orcid_oauth2():
 
 
 def get_github_user_details(access_token):
-    from utility.tools import GITHUB_API_URL
+    from gn2.utility.tools import GITHUB_API_URL
     result = requests.get(GITHUB_API_URL, headers={
                           'Authorization': 'token ' + access_token}).content
 
diff --git a/wqflask/wqflask/user_session.py b/gn2/wqflask/user_session.py
index 39b2aec1..af4e8cb4 100644
--- a/wqflask/wqflask/user_session.py
+++ b/gn2/wqflask/user_session.py
@@ -7,10 +7,10 @@ import simplejson as json
 from flask import (Flask, g, render_template, url_for, request, make_response,
                    redirect, flash, abort)
 
-from wqflask import app
-from utility import hmac
+from gn2.wqflask import app
+from gn2.utility import hmac
 
-from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
+from gn2.utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
 Redis = get_redis_conn()
 
 
diff --git a/wqflask/wqflask/views.py b/gn2/wqflask/views.py
index a10d613e..4f636ebc 100644
--- a/wqflask/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -27,7 +27,7 @@ from uuid import UUID
 
 from urllib.parse import urljoin
 
-from wqflask import app
+from gn2.wqflask import app
 
 from gn3.computations.gemma import generate_hash_of_string
 from flask import current_app
@@ -45,70 +45,70 @@ from flask import session
 
 # Some of these (like collect) might contain endpoints, so they're still used.
 # Blueprints should probably be used instead.
-from wqflask import collect
-from wqflask import search_results
-from wqflask import server_side
-from base.data_set import create_dataset  # Used by YAML in marker_regression
-from wqflask.show_trait import show_trait
-from wqflask.show_trait import export_trait_data
-from wqflask.show_trait.show_trait import get_diff_of_vals
-from wqflask.heatmap import heatmap
-from wqflask.external_tools import send_to_bnw
-from wqflask.external_tools import send_to_webgestalt
-from wqflask.external_tools import send_to_geneweaver
-from wqflask.comparison_bar_chart import comparison_bar_chart
-from wqflask.marker_regression import run_mapping
-from wqflask.marker_regression.exceptions import NoMappingResultsError
-from wqflask.marker_regression import display_mapping_results
-from wqflask.network_graph import network_graph
-from wqflask.correlation.show_corr_results import set_template_vars
-from wqflask.correlation.correlation_gn3_api import compute_correlation
-from wqflask.correlation.rust_correlation import compute_correlation_rust
-from wqflask.correlation_matrix import show_corr_matrix
-from wqflask.correlation import corr_scatter_plot
-from wqflask.correlation.exceptions import WrongCorrelationType
-from wqflask.ctl.gn3_ctl_analysis import run_ctl
-
-from wqflask.wgcna.gn3_wgcna import run_wgcna
-from wqflask.snp_browser import snp_browser
-from wqflask.search_results import SearchResultPage
-from wqflask.export_traits import export_traits
-from wqflask.gsearch import GSearch
-from wqflask.update_search_results import GSearch as UpdateGSearch
-from wqflask.docs import Docs, update_text
-from wqflask.decorators import edit_access_required
-from wqflask.db_info import InfoPage
-
-from wqflask.oauth2 import client
-from wqflask.oauth2.client import no_token_get
-from wqflask.oauth2.request_utils import with_flash_error, with_flash_success
-
-from utility import temp_data
-from utility.tools import get_setting
-from utility.tools import TEMPDIR
-from utility.tools import USE_REDIS
-from utility.tools import REDIS_URL
-from utility.tools import GN_SERVER_URL
-from utility.tools import GN3_LOCAL_URL
-from utility.tools import GN_VERSION
-from utility.tools import JS_TWITTER_POST_FETCHER_PATH
-from utility.tools import JS_GUIX_PATH
-from utility.helper_functions import get_species_groups
-from utility.redis_tools import get_redis_conn
-
-import utility.hmac as hmac
-
-from base.webqtlConfig import TMPDIR
-from base.webqtlConfig import GENERATED_IMAGE_DIR
-
-from wqflask.database import database_connection
-
-import jobs.jobs as jobs
-
-from wqflask.oauth2.session import session_info
-from wqflask.oauth2.checks import user_logged_in
-
-from wqflask import requests as monad_requests
+from gn2.wqflask import collect
+from gn2.wqflask import search_results
+from gn2.wqflask import server_side
+from gn2.base.data_set import create_dataset  # Used by YAML in marker_regression
+from gn2.wqflask.show_trait import show_trait
+from gn2.wqflask.show_trait import export_trait_data
+from gn2.wqflask.show_trait.show_trait import get_diff_of_vals
+from gn2.wqflask.heatmap import heatmap
+from gn2.wqflask.external_tools import send_to_bnw
+from gn2.wqflask.external_tools import send_to_webgestalt
+from gn2.wqflask.external_tools import send_to_geneweaver
+from gn2.wqflask.comparison_bar_chart import comparison_bar_chart
+from gn2.wqflask.marker_regression import run_mapping
+from gn2.wqflask.marker_regression.exceptions import NoMappingResultsError
+from gn2.wqflask.marker_regression import display_mapping_results
+from gn2.wqflask.network_graph import network_graph
+from gn2.wqflask.correlation.show_corr_results import set_template_vars
+from gn2.wqflask.correlation.correlation_gn3_api import compute_correlation
+from gn2.wqflask.correlation.rust_correlation import compute_correlation_rust
+from gn2.wqflask.correlation_matrix import show_corr_matrix
+from gn2.wqflask.correlation import corr_scatter_plot
+from gn2.wqflask.correlation.exceptions import WrongCorrelationType
+from gn2.wqflask.ctl.gn3_ctl_analysis import run_ctl
+
+from gn2.wqflask.wgcna.gn3_wgcna import run_wgcna
+from gn2.wqflask.snp_browser import snp_browser
+from gn2.wqflask.search_results import SearchResultPage
+from gn2.wqflask.export_traits import export_traits
+from gn2.wqflask.gsearch import GSearch
+from gn2.wqflask.update_search_results import GSearch as UpdateGSearch
+from gn2.wqflask.docs import Docs, update_text
+from gn2.wqflask.decorators import edit_access_required
+from gn2.wqflask.db_info import InfoPage
+
+from gn2.wqflask.oauth2 import client
+from gn2.wqflask.oauth2.client import no_token_get
+from gn2.wqflask.oauth2.request_utils import with_flash_error, with_flash_success
+
+from gn2.utility import temp_data
+from gn2.utility.tools import get_setting
+from gn2.utility.tools import TEMPDIR
+from gn2.utility.tools import USE_REDIS
+from gn2.utility.tools import REDIS_URL
+from gn2.utility.tools import GN_SERVER_URL
+from gn2.utility.tools import GN3_LOCAL_URL
+from gn2.utility.tools import GN_VERSION
+from gn2.utility.tools import JS_TWITTER_POST_FETCHER_PATH
+from gn2.utility.tools import JS_GUIX_PATH
+from gn2.utility.helper_functions import get_species_groups
+from gn2.utility.redis_tools import get_redis_conn
+
+import gn2.utility.hmac as hmac
+
+from gn2.base.webqtlConfig import TMPDIR
+from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
+
+from gn2.wqflask.database import database_connection
+
+import gn2.jobs.jobs as jobs
+
+from gn2.wqflask.oauth2.session import session_info
+from gn2.wqflask.oauth2.checks import user_logged_in
+
+from gn2.wqflask import requests as monad_requests
 
 Redis = get_redis_conn()
 
diff --git a/wqflask/wqflask/wgcna/__init__.py b/gn2/wqflask/wgcna/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/wqflask/wgcna/__init__.py
+++ b/gn2/wqflask/wgcna/__init__.py
diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/gn2/wqflask/wgcna/gn3_wgcna.py
index ab7fe46c..2cae4f18 100644
--- a/wqflask/wqflask/wgcna/gn3_wgcna.py
+++ b/gn2/wqflask/wgcna/gn3_wgcna.py
@@ -5,8 +5,8 @@ and process data to be rendered by datatables
 import requests
 from types import SimpleNamespace
 
-from utility.helper_functions import get_trait_db_obs
-from utility.tools import GN3_LOCAL_URL
+from gn2.utility.helper_functions import get_trait_db_obs
+from gn2.utility.tools import GN3_LOCAL_URL
 
 
 def fetch_trait_data(requestform):
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/gn2/wqflask/wgcna/wgcna_analysis.py
index f96892a0..f982c021 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/gn2/wqflask/wgcna/wgcna_analysis.py
@@ -10,11 +10,11 @@ import rpy2.rinterface as ri
 
 from array import array as arr
 from numpy import *
-from base.webqtlConfig import GENERATED_IMAGE_DIR
+from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
 from rpy2.robjects.packages import importr
 
-from utility import webqtlUtil                # Random number for the image
-from utility import helper_functions
+from gn2.utility import webqtlUtil                # Random number for the image
+from gn2.utility import helper_functions
 
 utils = importr("utils")
 
diff --git a/gn2/wsgi.py b/gn2/wsgi.py
new file mode 100644
index 00000000..94cc605d
--- /dev/null
+++ b/gn2/wsgi.py
@@ -0,0 +1,4 @@
+from gn2.run_gunicorn import app as application  # expect application as a name
+
+if __name__ == "__main__":
+    application.run()
diff --git a/setup.py b/setup.py
index 8436dcd3..e192ea61 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@ setup(name='genenetwork2',
       url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md",
       description = 'Website and tools for genetics.',
       include_package_data=True,
-      packages=['wqflask', 'etc'],
+      packages=find_packages(),
       scripts=['bin/genenetwork2'],
       # package_data = {
       #   'etc': ['*.py']
diff --git a/wqflask/gn2_main.py b/wqflask/gn2_main.py
deleted file mode 100644
index 11f24d3b..00000000
--- a/wqflask/gn2_main.py
+++ /dev/null
@@ -1,19 +0,0 @@
-"""Main application entry point."""
-
-from wqflask import app
-
-
-from wqflask import docs
-from wqflask import gsearch
-from wqflask import db_info
-from wqflask import user_login
-from wqflask.api import router
-from wqflask import user_session
-from wqflask import group_manager
-from wqflask import export_traits
-from wqflask import search_results
-from wqflask import resource_manager
-from wqflask import update_search_results
-
-import wqflask.views
-import wqflask.partial_correlations_views
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
deleted file mode 100644
index 755da333..00000000
--- a/wqflask/wsgi.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from run_gunicorn import app as application  # expect application as a name
-
-if __name__ == "__main__":
-    application.run()