merge changes

18 files changed, 0 insertions, 2392 deletions

diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
deleted file mode 100644
index ce8e60b8..00000000
--- a/wqflask/base/GeneralObject.py
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-class GeneralObject:
-    """
-    Base class to define an Object.
-    a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
-    a.sort(key = lambda x: x.eggs)
-    """
-
-    def __init__(self, *args, **kw):
-        self.contents = list(args)
-        for name, value in list(kw.items()):
-            setattr(self, name, value)
-
-    def __setitem__(self, key, value):
-        setattr(self, key, value)
-
-    def __getitem__(self, key):
-        return getattr(self, key)
-
-    def __getattr__(self, key):
-        return eval("self.__dict__.%s" % key)
-
-    def __len__(self):
-        return len(self.__dict__) - 1
-
-    def __str__(self):
-        s = ''
-        for key in list(self.__dict__.keys()):
-            if key != 'contents':
-                s += '%s = %s\n' % (key, self.__dict__[key])
-        return s
-
-    def __repr__(self):
-        s = ''
-        for key in list(self.__dict__.keys()):
-            s += '%s = %s\n' % (key, self.__dict__[key])
-        return s
-
-    def __eq__(self, other):
-        return (len(list(self.__dict__.keys()))
-                == len(list(other.__dict__.keys())))
diff --git a/wqflask/base/__init__.py b/wqflask/base/__init__.py
deleted file mode 100644
index e69de29b..00000000
--- a/wqflask/base/__init__.py
+++ /dev/null
diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py
deleted file mode 100644
index 69eaab53..00000000
--- a/wqflask/base/data_set/__init__.py
+++ /dev/null
@@ -1,124 +0,0 @@
-"The data_set package ..."
-
-# builtins imports
-import json
-import pickle as pickle
-
-# 3rd-party imports
-from redis import Redis
-
-# local imports
-from .dataset import DataSet
-from base import webqtlConfig
-from utility.tools import get_setting, USE_REDIS
-from .datasettype import DatasetType
-from .tempdataset import TempDataSet
-from .datasetgroup import DatasetGroup
-from .utils import query_table_timestamp
-from .genotypedataset import GenotypeDataSet
-from .phenotypedataset import PhenotypeDataSet
-from .mrnaassaydataset import MrnaAssayDataSet
-from wqflask.database import database_connection
-
-# Used by create_database to instantiate objects
-# Each subclass will add to this
-
-DS_NAME_MAP = {
-    "Temp": "TempDataSet",
-    "Geno": "GenotypeDataSet",
-    "Publish": "PhenotypeDataSet",
-    "ProbeSet": "MrnaAssayDataSet"
-}
-
-def __dataset_type__(dataset_name):
-    """Get dataset type."""
-    if "Temp" in dataset_name:
-        return "Temp"
-    if "Geno" in dataset_name:
-        return "Geno"
-    if "Publish" in dataset_name:
-        return "Publish"
-    return "ProbeSet"
-
-def create_dataset(dataset_name, dataset_type=None,
-                   get_samplelist=True, group_name=None, redis_conn=Redis()):
-    dataset_type = dataset_type or __dataset_type__(dataset_name)
-
-    dataset_ob = DS_NAME_MAP[dataset_type]
-    dataset_class = globals()[dataset_ob]
-    if dataset_type == "Temp":
-        return dataset_class(dataset_name, get_samplelist, group_name)
-    else:
-        return dataset_class(dataset_name, get_samplelist)
-
-def datasets(group_name, this_group=None, redis_conn=Redis()):
-    key = "group_dataset_menu:v2:" + group_name
-    dataset_menu = []
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        cursor.execute('''
-            (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
-            FROM PublishFreeze,InbredSet
-            WHERE PublishFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name = '%s'
-            ORDER BY PublishFreeze.Id ASC)
-            UNION
-            (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
-            FROM GenoFreeze, InbredSet
-            WHERE GenoFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name = '%s')
-            UNION
-            (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
-            FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
-            WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-                and ProbeFreeze.TissueId = Tissue.Id
-                and ProbeFreeze.InbredSetId = InbredSet.Id
-                and InbredSet.Name like %s
-            ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
-            ''' % (group_name,
-                group_name,
-                "'" + group_name + "'"))
-        the_results = cursor.fetchall()
-
-    sorted_results = sorted(the_results, key=lambda kv: kv[0])
-
-    # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
-    pheno_inserted = False
-    geno_inserted = False
-    for dataset_item in sorted_results:
-        tissue_name = dataset_item[0]
-        dataset = dataset_item[1]
-        dataset_short = dataset_item[2]
-        if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
-            if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
-                dataset_menu.insert(
-                    0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
-                pheno_inserted = True
-            elif pheno_inserted and tissue_name == '#GenoFreeze':
-                dataset_menu.insert(
-                    1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
-                geno_inserted = True
-            else:
-                dataset_menu.append(
-                    dict(tissue=None, datasets=[(dataset, dataset_short)]))
-        else:
-            tissue_already_exists = False
-            for i, tissue_dict in enumerate(dataset_menu):
-                if tissue_dict['tissue'] == tissue_name:
-                    tissue_already_exists = True
-                    break
-
-            if tissue_already_exists:
-                dataset_menu[i]['datasets'].append((dataset, dataset_short))
-            else:
-                dataset_menu.append(dict(tissue=tissue_name,
-                                         datasets=[(dataset, dataset_short)]))
-
-    if USE_REDIS:
-        redis_conn.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
-        redis_conn.expire(key, 60 * 5)
-
-    if this_group != None:
-        this_group._datasets = dataset_menu
-        return this_group._datasets
-    else:
-        return dataset_menu
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py
deleted file mode 100644
index 435d74a9..00000000
--- a/wqflask/base/data_set/dataset.py
+++ /dev/null
@@ -1,305 +0,0 @@
-"Base Dataset class ..."
-
-import math
-import collections
-
-from redis import Redis
-
-from base import species
-from utility import chunks
-from 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 .utils import fetch_cached_results, cache_dataset_results
-
-
-class DataSet:
-    """
-    DataSet class defines a dataset in webqtl, can be either Microarray,
-    Published phenotype, genotype, or user input dataset(temp)
-
-    """
-
-    def __init__(self, name, get_samplelist=True, group_name=None, redis_conn=Redis()):
-
-        assert name, "Need a name"
-        self.name = name
-        self.id = None
-        self.shortname = None
-        self.fullname = None
-        self.type = None
-        self.data_scale = None  # ZS: For example log2
-        self.accession_id = Nothing
-
-        self.setup()
-
-        if self.type == "Temp":  # Need to supply group name as input if temp trait
-            # sets self.group and self.group_id and gets genotype
-            self.group = DatasetGroup(self, name=group_name)
-        else:
-            self.check_confidentiality()
-            self.retrieve_other_names()
-            # sets self.group and self.group_id and gets genotype
-            self.group = DatasetGroup(self)
-            self.accession_id = self.get_accession_id()
-        if get_samplelist == True:
-            self.group.get_samplelist(redis_conn)
-        self.species = species.TheSpecies(dataset=self)
-
-    def as_monadic_dict(self):
-        _result = MonadicDict({
-            'name': self.name,
-            'shortname': self.shortname,
-            'fullname': self.fullname,
-            'type': self.type,
-            'data_scale': self.data_scale,
-            'group': self.group.name
-        })
-        _result["accession_id"] = self.accession_id
-        return _result
-
-    def get_accession_id(self) -> Maybe[str]:
-        """Get the accession_id of this dataset depending on the
-        dataset type."""
-        __query = ""
-        with database_connection(get_setting("SQL_URI")) as conn:
-            if self.type == "Publish":
-                __query = (
-                    "SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
-                    "InfoFiles, PublishFreeze, InbredSet "
-                    "WHERE InbredSet.Name = "
-                    f"'{conn.escape_string(self.group.name).decode()}' "
-                    "AND PublishFreeze.InbredSetId = InbredSet.Id "
-                    "AND InfoFiles.InfoPageName = PublishFreeze.Name "
-                    "AND PublishFreeze.public > 0 AND "
-                    "PublishFreeze.confidentiality < 1 "
-                    "ORDER BY PublishFreeze.CreateTime DESC"
-                )
-            elif self.type == "Geno":
-                __query = (
-                    "SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
-                    "InfoFiles, GenoFreeze, InbredSet WHERE InbredSet.Name = "
-                    f"'{conn.escape_string(self.group.name).decode()}' AND "
-                    "GenoFreeze.InbredSetId = InbredSet.Id "
-                    "AND InfoFiles.InfoPageName = GenoFreeze.ShortName "
-                    "AND GenoFreeze.public > 0 AND "
-                    "GenoFreeze.confidentiality < 1 "
-                    "ORDER BY GenoFreeze.CreateTime DESC"
-                )
-            elif self.type == "ProbeSet":
-                __query = (
-                    "SELECT InfoFiles.GN_AccesionId AS accession_id "
-                    "FROM InfoFiles WHERE InfoFiles.InfoPageName = "
-                    f"'{conn.escape_string(self.name).decode()}'"
-                )
-            else:  # The Value passed is not present
-                raise LookupError
-
-            # Should there be an empty row, query_sql returns a None
-            # value instead of yielding a value; this block
-            # accomodates this non-intuitive edge-case
-            for result in query_sql(conn, __query) or ():
-                return result["accession_id"]
-        return Nothing
-
-    def retrieve_other_names(self):
-        """This method fetches the the dataset names in search_result.
-
-        If the data set name parameter is not found in the 'Name' field of
-        the data set table, check if it is actually the FullName or
-        ShortName instead.
-
-        This is not meant to retrieve the data set info if no name at
-        all is passed.
-
-        """
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            try:
-                if self.type == "ProbeSet":
-                    cursor.execute(
-                        "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
-                        "ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, "
-                        "ProbeSetFreeze.DataScale, Tissue.Name "
-                        "FROM ProbeSetFreeze, ProbeFreeze, Tissue "
-                        "WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
-                        "AND ProbeFreeze.TissueId = Tissue.Id "
-                        "AND (ProbeSetFreeze.Name = %s OR "
-                        "ProbeSetFreeze.FullName = %s "
-                        "OR ProbeSetFreeze.ShortName = %s)",
-                        (self.name,)*3)
-                    (self.id, self.name, self.fullname, self.shortname,
-                    self.data_scale, self.tissue) = cursor.fetchone()
-                else:
-                    self.tissue = "N/A"
-                    cursor.execute(
-                        "SELECT Id, Name, FullName, ShortName "
-                        f"FROM {self.type}Freeze "
-                        "WHERE (Name = %s OR FullName = "
-                        "%s OR ShortName = %s)",
-                        (self.name,)*3)
-                    (self.id, self.name, self.fullname,
-                    self.shortname) = cursor.fetchone()
-            except TypeError:
-                pass
-
-    def chunk_dataset(self, dataset, n):
-
-        results = {}
-        traits_name_dict = ()
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT ProbeSetXRef.DataId,ProbeSet.Name "
-                "FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze "
-                "WHERE ProbeSetFreeze.Name = %s AND "
-                "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
-                "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id",
-                (self.name,))
-            # should cache this
-            traits_name_dict = dict(cursor.fetchall())
-
-        for i in range(0, len(dataset), n):
-            matrix = list(dataset[i:i + n])
-            trait_name = traits_name_dict[matrix[0][0]]
-
-            my_values = [value for (trait_name, strain, value) in matrix]
-            results[trait_name] = my_values
-        return results
-
-    def get_probeset_data(self, sample_list=None, trait_ids=None):
-
-        # improvement of get trait data--->>>
-        if sample_list:
-            self.samplelist = sample_list
-
-        else:
-            self.samplelist = self.group.samplelist
-
-        if self.group.parlist != None and self.group.f1list != None:
-            if (self.group.parlist + self.group.f1list) in self.samplelist:
-                self.samplelist += self.group.parlist + self.group.f1list
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT Strain.Name, Strain.Id FROM "
-                "Strain, Species WHERE Strain.Name IN "
-                f"{create_in_clause(self.samplelist)} "
-                "AND Strain.SpeciesId=Species.Id AND "
-                "Species.name = %s", (self.group.species,)
-            )
-            results = dict(cursor.fetchall())
-            sample_ids = [results[item] for item in self.samplelist]
-
-            sorted_samplelist = [strain_name for strain_name, strain_id in sorted(
-                results.items(), key=lambda item: item[1])]
-
-            cursor.execute(
-                "SELECT * from ProbeSetData WHERE StrainID IN "
-                f"{create_in_clause(sample_ids)} AND id IN "
-                "(SELECT ProbeSetXRef.DataId FROM "
-                "(ProbeSet, ProbeSetXRef, ProbeSetFreeze) "
-                "WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
-                "AND ProbeSetFreeze.Name = %s AND "
-                "ProbeSet.Id = ProbeSetXRef.ProbeSetId)",
-                (self.name,)
-            )
-
-            query_results = list(cursor.fetchall())
-            data_results = self.chunk_dataset(query_results, len(sample_ids))
-            self.samplelist = sorted_samplelist
-            self.trait_data = data_results
-
-    def get_trait_data(self, sample_list=None):
-        if sample_list:
-            self.samplelist = sample_list
-        else:
-            self.samplelist = self.group.samplelist
-
-        if self.group.parlist != None and self.group.f1list != None:
-            if (self.group.parlist + self.group.f1list) in self.samplelist:
-                self.samplelist += self.group.parlist + self.group.f1list
-
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT Strain.Name, Strain.Id FROM Strain, Species "
-                f"WHERE Strain.Name IN {create_in_clause(self.samplelist)} "
-                "AND Strain.SpeciesId=Species.Id "
-                "AND Species.name = %s",
-                (self.group.species,)
-            )
-            results = dict(cursor.fetchall())
-            sample_ids = [
-                sample_id for sample_id in
-                (results.get(item) for item in self.samplelist
-                 if item is not None)
-                if sample_id is not None
-            ]
-
-            # MySQL limits the number of tables that can be used in a join to 61,
-            # so we break the sample ids into smaller chunks
-            # Postgres doesn't have that limit, so we can get rid of this after we transition
-            chunk_size = 50
-            number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-
-            cached_results = fetch_cached_results(self.name, self.type, self.samplelist)
-
-            if cached_results is None:
-                trait_sample_data = []
-                for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
-                    if self.type == "Publish":
-                        dataset_type = "Phenotype"
-                    else:
-                        dataset_type = self.type
-                    temp = ['T%s.value' % item for item in sample_ids_step]
-                    if self.type == "Publish":
-                        query = "SELECT {}XRef.Id".format(escape(self.type))
-                    else:
-                        query = "SELECT {}.Name".format(escape(dataset_type))
-                    data_start_pos = 1
-                    if len(temp) > 0:
-                        query = query + ", " + ', '.join(temp)
-                    query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
-                                                                             self.type,
-                                                                             self.type))
-
-                    for item in sample_ids_step:
-                        query += """
-                                left join {}Data as T{} on T{}.Id = {}XRef.DataId
-                                and T{}.StrainId={}\n
-                                """.format(*mescape(self.type, item, item, self.type, item, item))
-
-                    if self.type == "Publish":
-                        query += """
-                                WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
-                                and {}Freeze.Name = '{}'
-                                and {}.Id = {}XRef.{}Id
-                                order by {}.Id
-                                """.format(*mescape(self.type, self.type, self.type, self.name,
-                                                    dataset_type, self.type, dataset_type, dataset_type))
-                    else:
-                        query += """
-                                WHERE {}XRef.{}FreezeId = {}Freeze.Id
-                                and {}Freeze.Name = '{}'
-                                and {}.Id = {}XRef.{}Id
-                                order by {}.Id
-                                """.format(*mescape(self.type, self.type, self.type, self.type,
-                                                    self.name, dataset_type, self.type, self.type, dataset_type))
-                    cursor.execute(query)
-                    results = cursor.fetchall()
-                    trait_sample_data.append([list(result) for result in results])
-
-                trait_count = len(trait_sample_data[0])
-                self.trait_data = collections.defaultdict(list)
-
-                data_start_pos = 1
-                for trait_counter in range(trait_count):
-                    trait_name = trait_sample_data[0][trait_counter][0]
-                    for chunk_counter in range(int(number_chunks)):
-                        self.trait_data[trait_name] += (
-                            trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
-
-                cache_dataset_results(
-                    self.name, self.type, self.samplelist, self.trait_data)
-            else:
-                self.trait_data = cached_results
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py
deleted file mode 100644
index 95dc976f..00000000
--- a/wqflask/base/data_set/datasetgroup.py
+++ /dev/null
@@ -1,195 +0,0 @@
-"Dataset Group class ..."
-
-import os
-import json
-
-
-from 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 (
-    locate,
-    USE_REDIS,
-    flat_files,
-    get_setting,
-    flat_file_exists,
-    locate_ignore_error)
-
-class DatasetGroup:
-    """
-    Each group has multiple datasets; each species has multiple groups.
-
-    For example, Mouse has multiple groups (BXD, BXA, etc), and each group
-    has multiple datasets associated with it.
-
-    """
-
-    def __init__(self, dataset, name=None):
-        """This sets self.group and self.group_id"""
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            if not name:
-                cursor.execute(dataset.query_for_group,
-                               (dataset.name,))
-            else:
-                cursor.execute(
-                    "SELECT InbredSet.Name, "
-                    "InbredSet.Id, "
-                    "InbredSet.GeneticType, "
-                    "InbredSet.InbredSetCode "
-                    "FROM InbredSet WHERE Name = %s",
-                    (name,))
-            results = cursor.fetchone()
-            if results:
-                (self.name, self.id, self.genetic_type, self.code) = results
-            else:
-                self.name = name or dataset.name
-        if self.name == 'BXD300':
-            self.name = "BXD"
-
-        self.f1list = None
-        self.parlist = None
-        self.get_f1_parent_strains()
-
-        self.mapping_id, self.mapping_names = self.get_mapping_methods()
-
-        self.species = webqtlDatabaseFunction.retrieve_species(self.name)
-
-        self.incparentsf1 = False
-        self.allsamples = None
-        self._datasets = None
-        self.genofile = None
-
-    def get_mapping_methods(self):
-        mapping_id = ()
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT MappingMethodId FROM "
-                "InbredSet WHERE Name= %s",
-                (self.name,))
-            results = cursor.fetchone()
-            if results and results[0]:
-                mapping_id = results[0]
-        if mapping_id == "1":
-            mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
-        elif mapping_id == "2":
-            mapping_names = ["GEMMA"]
-        elif mapping_id == "3":
-            mapping_names = ["R/qtl"]
-        elif mapping_id == "4":
-            mapping_names = ["GEMMA", "PLINK"]
-        else:
-            mapping_names = []
-
-        return mapping_id, mapping_names
-
-    def get_markers(self):
-        def check_plink_gemma():
-            if flat_file_exists("mapping"):
-                MAPPING_PATH = flat_files("mapping") + "/"
-                if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
-                    return True
-            return False
-
-        if check_plink_gemma():
-            marker_class = HumanMarkers
-        else:
-            marker_class = Markers
-
-        if self.genofile:
-            self.markers = marker_class(self.genofile[:-5])
-        else:
-            self.markers = marker_class(self.name)
-
-    def get_f1_parent_strains(self):
-        try:
-            # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
-        except KeyError:
-            f1 = f12 = maternal = paternal = None
-
-        if f1 and f12:
-            self.f1list = [f1, f12]
-        if maternal and paternal:
-            self.parlist = [maternal, paternal]
-
-    def get_study_samplelists(self):
-        study_sample_file = locate_ignore_error(
-            self.name + ".json", 'study_sample_lists')
-        try:
-            f = open(study_sample_file)
-        except:
-            return []
-        study_samples = json.load(f)
-        return study_samples
-
-    def get_genofiles(self):
-        jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
-        try:
-            f = open(jsonfile)
-        except:
-            return None
-        jsondata = json.load(f)
-        return jsondata['genofile']
-
-    def get_samplelist(self, redis_conn):
-        result = None
-        key = "samplelist:v3:" + self.name
-        if USE_REDIS:
-            result = redis_conn.get(key)
-
-        if result is not None:
-            self.samplelist = json.loads(result)
-        else:
-            genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
-            if genotype_fn:
-                self.samplelist = get_group_samplelists.get_samplelist(
-                    "geno", genotype_fn)
-            else:
-                self.samplelist = None
-
-            if USE_REDIS:
-                redis_conn.set(key, json.dumps(self.samplelist))
-                redis_conn.expire(key, 60 * 5)
-
-    def all_samples_ordered(self):
-        result = []
-        lists = (self.parlist, self.f1list, self.samplelist)
-        [result.extend(l) for l in lists if l]
-        return result
-
-    def read_genotype_file(self, use_reaper=False):
-        '''Read genotype from .geno file instead of database'''
-        # genotype_1 is Dataset Object without parents and f1
-        # genotype_2 is Dataset Object with parents and f1 (not for intercross)
-
-        # reaper barfs on unicode filenames, so here we ensure it's a string
-        if self.genofile:
-            if "RData" in self.genofile:  # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
-                full_filename = str(
-                    locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
-            else:
-                full_filename = str(locate(self.genofile, 'genotype'))
-        else:
-            full_filename = str(locate(self.name + '.geno', 'genotype'))
-        genotype_1 = gen_geno_ob.genotype(full_filename)
-
-        if genotype_1.type == "group" and self.parlist:
-            genotype_2 = genotype_1.add(
-                Mat=self.parlist[0], Pat=self.parlist[1])  # , F1=_f1)
-        else:
-            genotype_2 = genotype_1
-
-        # determine default genotype object
-        if self.incparentsf1 and genotype_1.type != "intercross":
-            genotype = genotype_2
-        else:
-            self.incparentsf1 = 0
-            genotype = genotype_1
-
-        self.samplelist = list(genotype.prgy)
-
-        return genotype
diff --git a/wqflask/base/data_set/datasettype.py b/wqflask/base/data_set/datasettype.py
deleted file mode 100644
index 05f0f564..00000000
--- a/wqflask/base/data_set/datasettype.py
+++ /dev/null
@@ -1,117 +0,0 @@
-"DatasetType class ..."
-
-import json
-import requests
-from typing import Optional, Dict
-
-
-from redis import Redis
-
-
-from utility.tools import GN2_BASE_URL
-from wqflask.database import database_connection
-
-
-class DatasetType:
-    """Create a dictionary of samples where the value is set to Geno,
-    Publish or ProbeSet. E.g.
-
-        {'AD-cases-controls-MyersGeno': 'Geno',
-         'AD-cases-controls-MyersPublish': 'Publish',
-         'AKXDGeno': 'Geno',
-         'AXBXAGeno': 'Geno',
-         'AXBXAPublish': 'Publish',
-         'Aging-Brain-UCIPublish': 'Publish',
-         'All Phenotypes': 'Publish',
-         'B139_K_1206_M': 'ProbeSet',
-         'B139_K_1206_R': 'ProbeSet' ...
-        }
-        """
-
-    def __init__(self, redis_conn):
-        "Initialise the object"
-        self.datasets = {}
-        self.data = {}
-        # self.redis_instance = redis_instance
-        data = redis_conn.get("dataset_structure")
-        if data:
-            self.datasets = json.loads(data)
-        else:
-            # ZS: I don't think this should ever run unless Redis is
-            # emptied
-            try:
-                data = json.loads(requests.get(
-                    GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
-                    timeout=5).content)
-                for _species in data['datasets']:
-                    for group in data['datasets'][_species]:
-                        for dataset_type in data['datasets'][_species][group]:
-                            for dataset in data['datasets'][_species][group][dataset_type]:
-                                short_dataset_name = dataset[1]
-                                if dataset_type == "Phenotypes":
-                                    new_type = "Publish"
-                                elif dataset_type == "Genotypes":
-                                    new_type = "Geno"
-                                else:
-                                    new_type = "ProbeSet"
-                                self.datasets[short_dataset_name] = new_type
-            except Exception:  # Do nothing
-                pass
-
-            redis_conn.set("dataset_structure", json.dumps(self.datasets))
-        self.data = data
-
-    def set_dataset_key(self, t, name, redis_conn, db_cursor):
-        """If name is not in the object's dataset dictionary, set it, and
-        update dataset_structure in Redis
-        args:
-          t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
-             'other_pheno', 'geno'
-          name: The name of the key to inserted in the datasets dictionary
-
-        """
-        sql_query_mapping = {
-            'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
-                          "ProbeSetFreeze WHERE "
-                          "ProbeSetFreeze.Name = %s "),
-            'pheno': ("SELECT InfoFiles.GN_AccesionId "
-                      "FROM InfoFiles, PublishFreeze, InbredSet "
-                      "WHERE InbredSet.Name = %s AND "
-                      "PublishFreeze.InbredSetId = InbredSet.Id AND "
-                      "InfoFiles.InfoPageName = PublishFreeze.Name"),
-            'other_pheno': ("SELECT PublishFreeze.Name "
-                            "FROM PublishFreeze, InbredSet "
-                            "WHERE InbredSet.Name = %s AND "
-                            "PublishFreeze.InbredSetId = InbredSet.Id"),
-            'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
-                     "GenoFreeze.Name = %s ")
-        }
-
-        dataset_name_mapping = {
-            "mrna_expr": "ProbeSet",
-            "pheno": "Publish",
-            "other_pheno": "Publish",
-            "geno": "Geno",
-        }
-
-        group_name = name
-        if t in ['pheno', 'other_pheno']:
-            group_name = name.replace("Publish", "")
-
-        db_cursor.execute(sql_query_mapping[t], (group_name,))
-        if db_cursor.fetchone():
-            self.datasets[name] = dataset_name_mapping[t]
-            redis_conn.set(
-                "dataset_structure", json.dumps(self.datasets))
-            return True
-
-
-    def __call__(self, name, redis_conn, db_cursor):
-        if name not in self.datasets:
-            for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
-                # This has side-effects, with the end result being a
-                # truth-y value
-                if(self.set_dataset_key(t, name, redis_conn, db_cursor)):
-                    break
-        # Return None if name has not been set
-        return self.datasets.get(name, None)
diff --git a/wqflask/base/data_set/genotypedataset.py b/wqflask/base/data_set/genotypedataset.py
deleted file mode 100644
index b903cd72..00000000
--- a/wqflask/base/data_set/genotypedataset.py
+++ /dev/null
@@ -1,76 +0,0 @@
-"GenotypeDataSet class ..."
-
-from .dataset import DataSet
-from utility import webqtlUtil
-from utility.tools import get_setting
-from db import webqtlDatabaseFunction
-from .utils import geno_mrna_confidentiality
-from wqflask.database import database_connection
-
-class GenotypeDataSet(DataSet):
-
-    def setup(self):
-        # Fields in the database table
-        self.search_fields = ['Name',
-                              'Chr']
-
-        # Find out what display_fields is
-        self.display_fields = ['name',
-                               'chr',
-                               'mb',
-                               'source2',
-                               'sequence']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'ID',
-                              'Location']
-
-        # Todo: Obsolete or rename this field
-        self.type = 'Geno'
-        self.query_for_group = """
-SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
-FROM InbredSet, GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id AND
-GenoFreeze.Name = %s"""
-
-    def check_confidentiality(self):
-        return geno_mrna_confidentiality(self)
-
-    def get_trait_info(self, trait_list, species=None):
-        for this_trait in trait_list:
-            if not this_trait.haveinfo:
-                this_trait.retrieveInfo()
-
-            if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (
-                    this_trait.chr, float(this_trait.mb))
-
-    def retrieve_sample_data(self, trait):
-        results = []
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT Strain.Name, GenoData.value, "
-                "GenoSE.error, 'N/A', Strain.Name2 "
-                "FROM (GenoData, GenoFreeze, Strain, Geno, "
-                "GenoXRef) LEFT JOIN GenoSE ON "
-                "(GenoSE.DataId = GenoData.Id AND "
-                "GenoSE.StrainId = GenoData.StrainId) "
-                "WHERE Geno.SpeciesId = %s AND "
-                "Geno.Name = %s AND GenoXRef.GenoId = Geno.Id "
-                "AND GenoXRef.GenoFreezeId = GenoFreeze.Id "
-                "AND GenoFreeze.Name = %s AND "
-                "GenoXRef.DataId = GenoData.Id "
-                "AND GenoData.StrainId = Strain.Id "
-                "ORDER BY Strain.Name",
-                (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
-                 trait, self.name,))
-            results = list(cursor.fetchall())
-
-        if self.group.name in webqtlUtil.ParInfo:
-            f1_1, f1_2, ref, nonref = webqtlUtil.ParInfo[self.group.name]
-            results.append([f1_1, 0, None, "N/A", f1_1])
-            results.append([f1_2, 0, None, "N/A", f1_2])
-            results.append([ref, -1, None, "N/A", ref])
-            results.append([nonref, 1, None, "N/A", nonref])
-
-        return results
diff --git a/wqflask/base/data_set/markers.py b/wqflask/base/data_set/markers.py
deleted file mode 100644
index 6f56445e..00000000
--- a/wqflask/base/data_set/markers.py
+++ /dev/null
@@ -1,96 +0,0 @@
-"Base Class: Markers - "
-
-import math
-
-from utility.tools import locate, flat_files
-
-class Markers:
-    """Todo: Build in cacheing so it saves us reading the same file more than once"""
-
-    def __init__(self, name):
-        json_data_fh = open(locate(name + ".json", 'genotype/json'))
-
-        markers = []
-        with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
-            if len(bimbam_fh.readline().split(", ")) > 2:
-                delimiter = ", "
-            elif len(bimbam_fh.readline().split(",")) > 2:
-                delimiter = ","
-            elif len(bimbam_fh.readline().split("\t")) > 2:
-                delimiter = "\t"
-            else:
-                delimiter = " "
-            for line in bimbam_fh:
-                marker = {}
-                marker['name'] = line.split(delimiter)[0].rstrip()
-                marker['Mb'] = float(line.split(delimiter)[
-                                     1].rstrip()) / 1000000
-                marker['chr'] = line.split(delimiter)[2].rstrip()
-                markers.append(marker)
-
-        for marker in markers:
-            if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"):
-                marker['chr'] = int(marker['chr'])
-            marker['Mb'] = float(marker['Mb'])
-
-        self.markers = markers
-
-    def add_pvalues(self, p_values):
-        if isinstance(p_values, list):
-            # THIS IS only needed for the case when we are limiting the number of p-values calculated
-            # if len(self.markers) > len(p_values):
-            #    self.markers = self.markers[:len(p_values)]
-
-            for marker, p_value in zip(self.markers, p_values):
-                if not p_value:
-                    continue
-                marker['p_value'] = float(p_value)
-                if math.isnan(marker['p_value']) or marker['p_value'] <= 0:
-                    marker['lod_score'] = 0
-                    marker['lrs_value'] = 0
-                else:
-                    marker['lod_score'] = -math.log10(marker['p_value'])
-                    # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                    marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif isinstance(p_values, dict):
-            filtered_markers = []
-            for marker in self.markers:
-                if marker['name'] in p_values:
-                    marker['p_value'] = p_values[marker['name']]
-                    if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
-                        marker['lod_score'] = 0
-                        marker['lrs_value'] = 0
-                    else:
-                        marker['lod_score'] = -math.log10(marker['p_value'])
-                        # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                        marker['lrs_value'] = - \
-                            math.log10(marker['p_value']) * 4.61
-                    filtered_markers.append(marker)
-            self.markers = filtered_markers
-
-
-class HumanMarkers(Markers):
-    "Markers for humans ..."
-
-    def __init__(self, name, specified_markers=[]):
-        marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
-        self.markers = []
-        for line in marker_data_fh:
-            splat = line.strip().split()
-            if len(specified_markers) > 0:
-                if splat[1] in specified_markers:
-                    marker = {}
-                    marker['chr'] = int(splat[0])
-                    marker['name'] = splat[1]
-                    marker['Mb'] = float(splat[3]) / 1000000
-                else:
-                    continue
-            else:
-                marker = {}
-                marker['chr'] = int(splat[0])
-                marker['name'] = splat[1]
-                marker['Mb'] = float(splat[3]) / 1000000
-            self.markers.append(marker)
-
-    def add_pvalues(self, p_values):
-        super(HumanMarkers, self).add_pvalues(p_values)
diff --git a/wqflask/base/data_set/mrnaassaydataset.py b/wqflask/base/data_set/mrnaassaydataset.py
deleted file mode 100644
index 4eb998b5..00000000
--- a/wqflask/base/data_set/mrnaassaydataset.py
+++ /dev/null
@@ -1,179 +0,0 @@
-"MrnaAssayDataSet class ..."
-
-import codecs
-
-
-from .dataset import DataSet
-from .utils import geno_mrna_confidentiality
-from wqflask.database import database_connection
-from utility.tools import get_setting
-
-class MrnaAssayDataSet(DataSet):
-    '''
-    An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait
-
-    This used to be called ProbeSet, but that term only refers specifically to the Affymetrix
-    platform and is far too specific.
-
-    '''
-
-    def setup(self):
-        # Fields in the database table
-        self.search_fields = ['Name',
-                              'Description',
-                              'Probe_Target_Description',
-                              'Symbol',
-                              'Alias',
-                              'GenbankId',
-                              'UniGeneId',
-                              'RefSeq_TranscriptId']
-
-        # Find out what display_fields is
-        self.display_fields = ['name', 'symbol',
-                               'description', 'probe_target_description',
-                               'chr', 'mb',
-                               'alias', 'geneid',
-                               'genbankid', 'unigeneid',
-                               'omim', 'refseq_transcriptid',
-                               'blatseq', 'targetseq',
-                               'chipid', 'comments',
-                               'strand_probe', 'strand_gene',
-                               'proteinid', 'uniprotid',
-                               'probe_set_target_region',
-                               'probe_set_specificity',
-                               'probe_set_blat_score',
-                               'probe_set_blat_mb_start',
-                               'probe_set_blat_mb_end',
-                               'probe_set_strand',
-                               'probe_set_note_by_rw',
-                               'flag']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'Record',
-                              'Symbol',
-                              'Description',
-                              'Location',
-                              'Mean',
-                              'Max LRS',
-                              'Max LRS Location',
-                              'Additive Effect']
-
-        # Todo: Obsolete or rename this field
-        self.type = 'ProbeSet'
-        self.query_for_group = """
-SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
-FROM InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id AND
-ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s"""
-
-    def check_confidentiality(self):
-        return geno_mrna_confidentiality(self)
-
-    def get_trait_info(self, trait_list=None, species=''):
-
-        #  Note: setting trait_list to [] is probably not a great idea.
-        if not trait_list:
-            trait_list = []
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            for this_trait in trait_list:
-
-                if not this_trait.haveinfo:
-                    this_trait.retrieveInfo(QTL=1)
-
-                if not this_trait.symbol:
-                    this_trait.symbol = "N/A"
-
-                # XZ, 12/08/2008: description
-                # XZ, 06/05/2009: Rob asked to add probe target description
-                description_string = str(
-                    str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-                target_string = str(
-                    str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
-                if len(description_string) > 1 and description_string != 'None':
-                    description_display = description_string
-                else:
-                    description_display = this_trait.symbol
-
-                if (len(description_display) > 1 and description_display != 'N/A'
-                        and len(target_string) > 1 and target_string != 'None'):
-                    description_display = description_display + '; ' + target_string.strip()
-
-                # Save it for the jinja2 template
-                this_trait.description_display = description_display
-
-                if this_trait.chr and this_trait.mb:
-                    this_trait.location_repr = 'Chr%s: %.6f' % (
-                        this_trait.chr, float(this_trait.mb))
-
-                # Get mean expression value
-                cursor.execute(
-                    "SELECT ProbeSetXRef.mean FROM "
-                    "ProbeSetXRef, ProbeSet WHERE "
-                    "ProbeSetXRef.ProbeSetFreezeId = %s "
-                    "AND ProbeSet.Id = ProbeSetXRef.ProbeSetId "
-                    "AND ProbeSet.Name = %s",
-                    (str(this_trait.dataset.id), this_trait.name,)
-                )
-                result = cursor.fetchone()
-
-                mean = result[0] if result else 0
-
-                if mean:
-                    this_trait.mean = "%2.3f" % mean
-
-                # LRS and its location
-                this_trait.LRS_score_repr = 'N/A'
-                this_trait.LRS_location_repr = 'N/A'
-
-                # Max LRS and its Locus location
-                if this_trait.lrs and this_trait.locus:
-                    cursor.execute(
-                        "SELECT Geno.Chr, Geno.Mb FROM "
-                        "Geno, Species WHERE "
-                        "Species.Name = %s AND "
-                        "Geno.Name = %s AND "
-                        "Geno.SpeciesId = Species.Id",
-                        (species, this_trait.locus,)
-                    )
-                    if result := cursor.fetchone():
-                        lrs_chr, lrs_mb = result
-                        this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
-                        this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
-                            lrs_chr, float(lrs_mb))
-
-        return trait_list
-
-    def retrieve_sample_data(self, trait):
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                "SELECT Strain.Name, ProbeSetData.value, "
-                "ProbeSetSE.error, NStrain.count, "
-                "Strain.Name2 FROM (ProbeSetData, "
-                "ProbeSetFreeze, Strain, ProbeSet, "
-                "ProbeSetXRef) LEFT JOIN ProbeSetSE ON "
-                "(ProbeSetSE.DataId = ProbeSetData.Id AND "
-                "ProbeSetSE.StrainId = ProbeSetData.StrainId) "
-                "LEFT JOIN NStrain ON "
-                "(NStrain.DataId = ProbeSetData.Id AND "
-                "NStrain.StrainId = ProbeSetData.StrainId) "
-                "WHERE ProbeSet.Name = %s AND "
-                "ProbeSetXRef.ProbeSetId = ProbeSet.Id "
-                "AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
-                "AND ProbeSetFreeze.Name = %s AND "
-                "ProbeSetXRef.DataId = ProbeSetData.Id "
-                "AND ProbeSetData.StrainId = Strain.Id "
-                "ORDER BY Strain.Name",
-                (trait, self.name,)
-            )
-            return cursor.fetchall()
-
-    def retrieve_genes(self, column_name):
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-                f"SELECT ProbeSet.Name, ProbeSet.{column_name} "
-                "FROM ProbeSet,ProbeSetXRef WHERE "
-                "ProbeSetXRef.ProbeSetFreezeId = %s "
-                "AND ProbeSetXRef.ProbeSetId=ProbeSet.Id",
-                (str(self.id),))
-            return dict(cursor.fetchall())
diff --git a/wqflask/base/data_set/phenotypedataset.py b/wqflask/base/data_set/phenotypedataset.py
deleted file mode 100644
index 5a39418a..00000000
--- a/wqflask/base/data_set/phenotypedataset.py
+++ /dev/null
@@ -1,134 +0,0 @@
-"PhenotypeDataSet class ..."
-
-from .dataset import DataSet
-from base import webqtlConfig
-from utility.tools import get_setting
-from wqflask.database import database_connection
-
-class PhenotypeDataSet(DataSet):
-
-    def setup(self):
-        # Fields in the database table
-        self.search_fields = ['Phenotype.Post_publication_description',
-                              'Phenotype.Pre_publication_description',
-                              'Phenotype.Pre_publication_abbreviation',
-                              'Phenotype.Post_publication_abbreviation',
-                              'PublishXRef.mean',
-                              'Phenotype.Lab_code',
-                              'Publication.PubMed_ID',
-                              'Publication.Abstract',
-                              'Publication.Title',
-                              'Publication.Authors',
-                              'PublishXRef.Id']
-
-        # Figure out what display_fields is
-        self.display_fields = ['name', 'group_code',
-                               'pubmed_id',
-                               'pre_publication_description',
-                               'post_publication_description',
-                               'original_description',
-                               'pre_publication_abbreviation',
-                               'post_publication_abbreviation',
-                               'mean',
-                               'lab_code',
-                               'submitter', 'owner',
-                               'authorized_users',
-                               'authors', 'title',
-                               'abstract', 'journal',
-                               'volume', 'pages',
-                               'month', 'year',
-                               'sequence', 'units', 'comments']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'Record',
-                              'Description',
-                              'Authors',
-                              'Year',
-                              'Max LRS',
-                              'Max LRS Location',
-                              'Additive Effect']
-
-        self.type = 'Publish'
-        self.query_for_group = """
-SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id AND PublishFreeze.Name = %s"""
-
-    def check_confidentiality(self):
-        # (Urgently?) Need to write this
-        pass
-
-    def get_trait_info(self, trait_list, species=''):
-        for this_trait in trait_list:
-
-            if not this_trait.haveinfo:
-                this_trait.retrieve_info(get_qtl_info=True)
-
-            description = this_trait.post_publication_description
-
-            # If the dataset is confidential and the user has access to confidential
-            # phenotype traits, then display the pre-publication description instead
-            # of the post-publication description
-            if this_trait.confidential:
-                this_trait.description_display = ""
-                continue   # for now, because no authorization features
-
-                if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
-                        privilege=self.privilege,
-                        userName=self.userName,
-                        authorized_users=this_trait.authorized_users):
-
-                    description = this_trait.pre_publication_description
-
-            if len(description) > 0:
-                this_trait.description_display = description.strip()
-            else:
-                this_trait.description_display = ""
-
-            if not this_trait.year.isdigit():
-                this_trait.pubmed_text = "N/A"
-            else:
-                this_trait.pubmed_text = this_trait.year
-
-            if this_trait.pubmed_id:
-                this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
-
-            # LRS and its location
-            this_trait.LRS_score_repr = "N/A"
-            this_trait.LRS_location_repr = "N/A"
-
-            if this_trait.lrs:
-                with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-                    cursor.execute(
-                        "SELECT Geno.Chr, Geno.Mb FROM "
-                        "Geno, Species WHERE "
-                        "Species.Name = %s AND "
-                        "Geno.Name = %s AND "
-                        "Geno.SpeciesId = Species.Id",
-                        (species, this_trait.locus,)
-                    )
-                    if result := cursor.fetchone():
-                        if result[0] and result[1]:
-                            LRS_Chr, LRS_Mb = result[0], result[1]
-                            this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
-                            this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
-                                LRS_Chr, float(LRS_Mb))
-
-    def retrieve_sample_data(self, trait):
-        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-            cursor.execute(
-            "SELECT Strain.Name, PublishData.value, "
-                "PublishSE.error, NStrain.count, "
-                "Strain.Name2 FROM (PublishData, Strain, "
-                "PublishXRef, PublishFreeze) LEFT JOIN "
-                "PublishSE ON "
-                "(PublishSE.DataId = PublishData.Id "
-                "AND PublishSE.StrainId = PublishData.StrainId) "
-                "LEFT JOIN NStrain ON "
-                "(NStrain.DataId = PublishData.Id AND "
-                "NStrain.StrainId = PublishData.StrainId) "
-                "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
-                "AND PublishData.Id = PublishXRef.DataId AND "
-                "PublishXRef.Id = %s AND PublishFreeze.Id = %s "
-                "AND PublishData.StrainId = Strain.Id "
-                "ORDER BY Strain.Name", (trait, self.id))
-            return cursor.fetchall()
diff --git a/wqflask/base/data_set/probably_unused.py b/wqflask/base/data_set/probably_unused.py
deleted file mode 100644
index abd3ad07..00000000
--- a/wqflask/base/data_set/probably_unused.py
+++ /dev/null
@@ -1,35 +0,0 @@
-"Functions that are probably unused in the code"
-
-import pickle as pickle
-
-from wqflask.database import database_connection
-from utility.tools import get_setting
-
-def create_datasets_list():
-    if USE_REDIS:
-        key = "all_datasets"
-        result = redis_conn.get(key)
-
-        if result:
-            datasets = pickle.loads(result)
-
-    if result is None:
-        datasets = list()
-        type_dict = {'Publish': 'PublishFreeze',
-                     'ProbeSet': 'ProbeSetFreeze',
-                     'Geno': 'GenoFreeze'}
-
-        for dataset_type in type_dict:
-            with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-                cursor.execute("SELECT Name FROM %s",
-                               (type_dict[dataset_type],))
-                results = cursor.fetchall(query)
-                if results:
-                    for result in results:
-                        datasets.append(
-                            create_dataset(result.Name, dataset_type))
-        if USE_REDIS:
-            redis_conn.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
-            redis_conn.expire(key, 60 * 60)
-
-    return datasets
diff --git a/wqflask/base/data_set/tempdataset.py b/wqflask/base/data_set/tempdataset.py
deleted file mode 100644
index b1c26a3b..00000000
--- a/wqflask/base/data_set/tempdataset.py
+++ /dev/null
@@ -1,23 +0,0 @@
-"TempDataSet class ..."
-
-from .dataset import DataSet
-
-class TempDataSet(DataSet):
-    """Temporary user-generated data set"""
-
-    def setup(self):
-        self.search_fields = ['name',
-                              'description']
-
-        self.display_fields = ['name',
-                               'description']
-
-        self.header_fields = ['Name',
-                              'Description']
-
-        self.type = 'Temp'
-
-        # Need to double check later how these are used
-        self.id = 1
-        self.fullname = 'Temporary Storage'
-        self.shortname = 'Temp'
diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
deleted file mode 100644
index d18180c4..00000000
--- a/wqflask/base/data_set/utils.py
+++ /dev/null
@@ -1,80 +0,0 @@
-"data_set package utilities"
-
-import datetime
-import os
-import json
-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
-
-def geno_mrna_confidentiality(ob):
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        cursor.execute(
-            "SELECT confidentiality, "
-            f"AuthorisedUsers FROM {ob.type}Freeze WHERE Name = %s",
-            (ob.name,)
-        )
-        result = cursor.fetchall()
-        if len(result) > 0 and result[0]:
-            return True
-
-def query_table_timestamp(dataset_type: str):
-    """function to query the update timestamp of a given dataset_type"""
-
-    # computation data and actions
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        fetch_db_name = parse_db_url(SQL_URI)
-        cursor.execute(
-            "SELECT UPDATE_TIME FROM "
-            "information_schema.tables "
-            f"WHERE TABLE_SCHEMA = '{fetch_db_name[3]}' "
-            f"AND TABLE_NAME = '{dataset_type}Data'")
-        date_time_obj = cursor.fetchone()[0]
-        if not date_time_obj:
-            date_time_obj = datetime.datetime.now()
-        return date_time_obj.strftime("%Y-%m-%d %H:%M:%S")
-
-
-def generate_hash_file(dataset_name: str, dataset_type: str, dataset_timestamp: str, samplelist: str):
-    """given the trait_name generate a unique name for this"""
-    string_unicode = f"{dataset_name}{dataset_timestamp}{samplelist}".encode()
-    md5hash = hashlib.md5(string_unicode)
-    return md5hash.hexdigest()
-
-
-def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List, query_results: List):
-    """function to cache dataset query results to file
-    input dataset_name and type query_results(already processed in default dict format)
-    """
-    # data computations actions
-    # store the file path on redis
-
-    table_timestamp = query_table_timestamp(dataset_type)
-    samplelist_as_str = ",".join(samplelist)
-
-    file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
-    file_path = os.path.join(TMPDIR, f"{file_name}.json")
-
-    with open(file_path, "w") as file_handler:
-        json.dump(query_results, file_handler)
-
-
-def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List):
-    """function to fetch the cached results"""
-
-    table_timestamp = query_table_timestamp(dataset_type)
-    samplelist_as_str = ",".join(samplelist)
-
-    file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
-    file_path = os.path.join(TMPDIR, f"{file_name}.json")
-    try:
-        with open(file_path, "r") as file_handler:
-
-            return json.load(file_handler)
-
-    except Exception:
-        pass
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
deleted file mode 100644
index a78182e3..00000000
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ /dev/null
@@ -1,102 +0,0 @@
-import collections
-
-from utility import Bunch
-
-
-class MrnaAssayTissueData:
-
-    def __init__(self, conn, gene_symbols=None):
-        self.gene_symbols = gene_symbols
-        self.conn = conn
-        if self.gene_symbols is None:
-            self.gene_symbols = []
-
-        self.data = collections.defaultdict(Bunch)
-        results = ()
-        # Note that inner join is necessary in this query to get
-        # distinct record in one symbol group with highest mean value
-        # Due to the limit size of TissueProbeSetFreezeId table in DB,
-        # performance of inner join is
-        # acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
-        with conn.cursor() as cursor:
-            if len(self.gene_symbols) == 0:
-                cursor.execute(
-                    "SELECT t.Symbol, t.GeneId, t.DataId, "
-                    "t.Chr, t.Mb, t.description, "
-                    "t.Probe_Target_Description FROM (SELECT Symbol, "
-                    "max(Mean) AS maxmean "
-                    "FROM TissueProbeSetXRef WHERE "
-                    "TissueProbeSetFreezeId=1 AND "
-                    "Symbol != '' AND Symbol IS NOT "
-                    "Null GROUP BY Symbol) "
-                    "AS x INNER JOIN "
-                    "TissueProbeSetXRef AS t ON "
-                    "t.Symbol = x.Symbol "
-                    "AND t.Mean = x.maxmean")
-            else:
-                cursor.execute(
-                    "SELECT t.Symbol, t.GeneId, t.DataId, "
-                    "t.Chr, t.Mb, t.description, "
-                    "t.Probe_Target_Description FROM (SELECT Symbol, "
-                    "max(Mean) AS maxmean "
-                    "FROM TissueProbeSetXRef WHERE "
-                    "TissueProbeSetFreezeId=1 AND "
-                    "Symbol IN "
-                    f"({', '.join(['%s'] * len(self.gene_symbols))}) "
-                    "GROUP BY Symbol) AS x INNER JOIN "
-                    "TissueProbeSetXRef AS t ON t.Symbol = x.Symbol "
-                    "AND t.Mean = x.maxmean",
-                    tuple(self.gene_symbols))
-            results = list(cursor.fetchall())
-        lower_symbols = {}
-        for gene_symbol in self.gene_symbols:
-            if gene_symbol is not None:
-                lower_symbols[gene_symbol.lower()] = True
-
-        for result in results:
-            (symbol, gene_id, data_id, _chr, _mb,
-             descr, probeset_target_descr) = result
-            if symbol is not None and lower_symbols.get(symbol.lower()):
-                symbol = symbol.lower()
-                self.data[symbol].gene_id = gene_id
-                self.data[symbol].data_id = data_id
-                self.data[symbol].chr = _chr
-                self.data[symbol].mb = _mb
-                self.data[symbol].description = descr
-                (self.data[symbol]
-                 .probe_target_description) = probeset_target_descr
-
-
-    def get_symbol_values_pairs(self):
-        """Get one dictionary whose key is gene symbol and value is
-        tissue expression data (list type).  All keys are lower case.
-
-        The output is a symbolValuepairDict (dictionary): one
-        dictionary of Symbol and Value Pair; key is symbol, value is
-        one list of expression values of one probeSet;
-
-        """
-        id_list = [self.data[symbol].data_id for symbol in self.data]
-
-        symbol_values_dict = {}
-
-        if len(id_list) > 0:
-            results = []
-            with self.conn.cursor() as cursor:
-
-                cursor.execute(
-                    "SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value "
-                    "FROM TissueProbeSetXRef, TissueProbeSetData"
-                    f" WHERE TissueProbeSetData.Id IN ({', '.join(['%s'] * len(id_list))})"
-                    " AND TissueProbeSetXRef.DataId = TissueProbeSetData.Id"
-                    ,tuple(id_list))
-
-                results = cursor.fetchall()
-                for result in results:
-                    (symbol, value) = result
-                    if symbol.lower() not in symbol_values_dict:
-                        symbol_values_dict[symbol.lower()] = [value]
-                    else:
-                        symbol_values_dict[symbol.lower()].append(
-                            value)
-        return symbol_values_dict
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
deleted file mode 100644
index 0844fada..00000000
--- a/wqflask/base/species.py
+++ /dev/null
@@ -1,59 +0,0 @@
-from dataclasses import dataclass
-from typing import Optional, Union
-from collections import OrderedDict
-
-
-class TheSpecies:
-    """Data related to species."""
-
-    def __init__(self, dataset=None, species_name=None) -> None:
-        "Initialise the Species object"
-        self.dataset = dataset
-        self.name = self.species_name = species_name
-        self.chromosomes = Chromosomes(species=species_name,
-                                       dataset=dataset)
-
-
-@dataclass
-class IndChromosome:
-    """Data related to IndChromosome"""
-    name: str
-    length: int
-
-    @property
-    def mb_length(self) -> Union[int, float]:
-        """Chromosome length in mega-bases"""
-        return self.length / 1000000
-
-
-@dataclass
-class Chromosomes:
-    """Data related to a chromosome"""
-
-    def __init__(self, dataset, species: Optional[str]) -> None:
-        "initialise the Chromosome object"
-        self.species = species
-        if species is None:
-            self.dataset = dataset
-
-    def chromosomes(self, db_cursor) -> OrderedDict:
-        """Lazily fetch the chromosomes"""
-        chromosomes = OrderedDict()
-        if self.species is not None:
-            db_cursor.execute(
-                "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
-                "FROM Chr_Length, Species WHERE "
-                "Chr_Length.SpeciesId = Species.SpeciesId AND "
-                "Species.Name = %s "
-                "ORDER BY OrderId", (self.species.capitalize(),))
-        else:
-            db_cursor.execute(
-                "SELECT Chr_Length.Name, Chr_Length.OrderId, "
-                "Length FROM Chr_Length, InbredSet WHERE "
-                "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
-                "InbredSet.Name = "
-                "%s ORDER BY OrderId", (self.dataset.group.name,))
-        for name, _, length in db_cursor.fetchall():
-            chromosomes[name] = IndChromosome(
-                name=name, length=length)
-        return chromosomes
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
deleted file mode 100644
index 103ff0c0..00000000
--- a/wqflask/base/trait.py
+++ /dev/null
@@ -1,613 +0,0 @@
-import requests
-import simplejson as json
-from 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
-
-from flask import g, request, url_for
-
-from wqflask.database import database_connection
-
-
-Redis = get_redis_conn()
-
-
-def create_trait(**kw):
-    assert bool(kw.get('dataset')) != bool(
-        kw.get('dataset_name')), "Needs dataset ob. or name"
-
-    assert bool(kw.get('name')), "Needs trait name"
-
-
-    if bool(kw.get('dataset')):
-        dataset = kw.get('dataset')
-
-
-    else:
-        if kw.get('dataset_name') != "Temp":
-
-
-            dataset = create_dataset(kw.get('dataset_name'))
-        else:
-
-            dataset = create_dataset(
-                    dataset_name="Temp",
-                    dataset_type="Temp",
-                    group_name= kw.get('name').split("_")[2])
-
-
-    if dataset.type == 'Publish':
-        permissions = check_resource_availability(
-            dataset, g.user_session.user_id, kw.get('name'))
-    else:
-        permissions = check_resource_availability(
-            dataset, g.user_session.user_id)
-
-
-    if permissions['data'] != "no-access":
-        
-        the_trait = GeneralTrait(**dict(kw,dataset=dataset))
-        if the_trait.dataset.type != "Temp":
-            the_trait = retrieve_trait_info(
-                the_trait,
-                the_trait.dataset,
-                get_qtl_info=kw.get('get_qtl_info'))
-        return the_trait
-    else:
-        return None
-
-
-class GeneralTrait:
-    """
-    Trait class defines a trait in webqtl, can be either Microarray,
-    Published phenotype, genotype, or user input trait
-
-    """
-
-    def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
-        # xor assertion
-        assert kw.get("dataset"), "Dataset obj is needed as a kwarg"
-
-        # Trait ID, ProbeSet ID, Published ID, etc.
-        self.name = kw.get('name')
-        self.dataset = kw.get("dataset")
-        self.cellid = kw.get('cellid')
-        self.identification = kw.get('identification', 'un-named trait')
-        self.haveinfo = kw.get('haveinfo', False)
-        # Blat sequence, available for ProbeSet
-        self.sequence = kw.get('sequence')
-        self.data = kw.get('data', {})
-        self.view = True
-
-        # Sets defaults
-        self.locus = None
-        self.lrs = None
-        self.pvalue = None
-        self.mean = None
-        self.additive = None
-        self.num_overlap = None
-        self.strand_probe = None
-        self.symbol = None
-        self.abbreviation = None
-        self.display_name = self.name
-
-        self.LRS_score_repr = "N/A"
-        self.LRS_location_repr = "N/A"
-        self.chr = self.mb = self.locus_chr = self.locus_mb = ""
-
-        if kw.get('fullname'):
-            name2 = value.split("::")
-            if len(name2) == 2:
-                self.dataset, self.name = name2
-                # self.cellid is set to None above
-            elif len(name2) == 3:
-                self.dataset, self.name, self.cellid = name2
-
-        # Todo: These two lines are necessary most of the time, but
-        # perhaps not all of the time So we could add a simple if
-        # statement to short-circuit this if necessary
-        if get_sample_info is not False:
-            self = retrieve_sample_data(self, self.dataset)
-
-    def export_informative(self, include_variance=0):
-        """
-        export informative sample
-        mostly used in qtl regression
-
-        """
-        samples = []
-        vals = []
-        the_vars = []
-        sample_aliases = []
-        for sample_name, sample_data in list(self.data.items()):
-            if sample_data.value is not None:
-                if not include_variance or sample_data.variance is not None:
-                    samples.append(sample_name)
-                    vals.append(sample_data.value)
-                    the_vars.append(sample_data.variance)
-                    sample_aliases.append(sample_data.name2)
-        return samples, vals, the_vars, sample_aliases
-
-    @property
-    def description_fmt(self):
-        """Return a text formated description"""
-        if self.dataset.type == 'ProbeSet':
-            if self.description:
-                formatted = self.description
-                if self.probe_target_description:
-                    formatted += "; " + self.probe_target_description
-            else:
-                formatted = "Not available"
-        elif self.dataset.type == 'Publish':
-            if self.confidential:
-                formatted = self.pre_publication_description
-            else:
-                formatted = self.post_publication_description
-        else:
-            formatted = "Not available"
-        if isinstance(formatted, bytes):
-            formatted = formatted.decode("utf-8")
-        return formatted
-
-    @property
-    def alias_fmt(self):
-        """Return a text formatted alias"""
-
-        alias = 'Not available'
-        if getattr(self, "alias", None):
-            alias = self.alias.replace(";", " ")
-            alias = ", ".join(alias.split())
-
-        return alias
-
-    @property
-    def wikidata_alias_fmt(self):
-        """Return a text formatted alias"""
-
-        alias = 'Not available'
-        if self.symbol:
-            human_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
-            mouse_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
-            other_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
-
-            if human_response and mouse_response and other_response:
-                alias_list = json.loads(human_response.content) + json.loads(
-                    mouse_response.content) + \
-                    json.loads(other_response.content)
-
-                filtered_aliases = []
-                seen = set()
-                for item in alias_list:
-                    if item in seen:
-                        continue
-                    else:
-                        filtered_aliases.append(item)
-                        seen.add(item)
-                alias = "; ".join(filtered_aliases)
-
-        return alias
-
-    @property
-    def location_fmt(self):
-        """Return a text formatted location
-
-        While we're at it we set self.location in case we need it
-        later (do we?)
-
-        """
-
-        if self.chr == "Un":
-            return 'Not available'
-
-        if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
-        elif self.chr:
-            self.location = 'Chr %s @ Unknown position' % (self.chr)
-        else:
-            self.location = 'Not available'
-
-        fmt = self.location
-        # XZ: deal with direction
-        if self.strand_probe == '+':
-            fmt += (' on the plus strand ')
-        elif self.strand_probe == '-':
-            fmt += (' on the minus strand ')
-
-        return fmt
-
-
-def retrieve_sample_data(trait, dataset, samplelist=None):
-    if samplelist is None:
-        samplelist = []
-
-    if dataset.type == "Temp":
-        results = Redis.get(trait.name).split()
-    else:
-        results = dataset.retrieve_sample_data(trait.name)
-    # Todo: is this necessary? If not remove
-    trait.data.clear()
-
-    if results:
-        if dataset.type == "Temp":
-            all_samples_ordered = dataset.group.all_samples_ordered()
-            for i, item in enumerate(results):
-                try:
-                    trait.data[all_samples_ordered[i]] = webqtlCaseData(
-                        all_samples_ordered[i], float(item))
-                except:
-                    pass
-        else:
-            for item in results:
-                name, value, variance, num_cases, name2 = item
-                if not samplelist or (samplelist and name in samplelist):
-                    # name, value, variance, num_cases)
-                    trait.data[name] = webqtlCaseData(*item)
-    return trait
-
-
-@app.route("/trait/get_sample_data")
-def get_sample_data():
-    params = request.args
-    trait = params['trait']
-    dataset = params['dataset']
-
-    trait_ob = create_trait(name=trait, dataset_name=dataset)
-    if trait_ob:
-        trait_dict = {}
-        trait_dict['name'] = trait
-        trait_dict['db'] = dataset
-        trait_dict['type'] = trait_ob.dataset.type
-        trait_dict['group'] = trait_ob.dataset.group.name
-        trait_dict['tissue'] = trait_ob.dataset.tissue
-        trait_dict['species'] = trait_ob.dataset.group.species
-        trait_dict['url'] = url_for(
-            'show_trait_page', trait_id=trait, dataset=dataset)
-        if trait_ob.dataset.type == "ProbeSet":
-            trait_dict['symbol'] = trait_ob.symbol
-            trait_dict['location'] = trait_ob.location_repr
-            trait_dict['description'] = trait_ob.description_display
-        elif trait_ob.dataset.type == "Publish":
-            trait_dict['description'] = trait_ob.description_display
-            if trait_ob.pubmed_id:
-                trait_dict['pubmed_link'] = trait_ob.pubmed_link
-            trait_dict['pubmed_text'] = trait_ob.pubmed_text
-        else:
-            trait_dict['location'] = trait_ob.location_repr
-
-        return json.dumps([trait_dict, {key: value.value for
-                                        key, value in list(
-                                            trait_ob.data.items())}])
-    else:
-        return None
-
-
-def jsonable(trait, dataset=None):
-    """Return a dict suitable for using as json
-
-    Actual turning into json doesn't happen here though"""
-
-    if not dataset:
-        dataset = create_dataset(dataset_name=trait.dataset.name,
-                                dataset_type=trait.dataset.type,
-                                group_name=trait.dataset.group.name)
-
-
-    trait_symbol = "N/A"
-    trait_mean = "N/A"
-    if trait.symbol:
-        trait_symbol = trait.symbol
-    if trait.mean:
-        trait_mean = trait.mean
-
-    if dataset.type == "ProbeSet":
-        return dict(name=trait.name,
-                    display_name=trait.display_name,
-                    hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
-                    view=str(trait.view),
-                    symbol=trait_symbol,
-                    dataset=dataset.name,
-                    dataset_name=dataset.shortname,
-                    description=trait.description_display,
-                    mean=trait_mean,
-                    location=trait.location_repr,
-                    chr=trait.chr,
-                    mb=trait.mb,
-                    lrs_score=trait.LRS_score_repr,
-                    lrs_location=trait.LRS_location_repr,
-                    lrs_chr=trait.locus_chr,
-                    lrs_mb=trait.locus_mb,
-                    additive=trait.additive
-                    )
-    elif dataset.type == "Publish":
-        if trait.pubmed_id:
-            return dict(name=trait.name,
-                        display_name=trait.display_name,
-                        hmac=hmac.data_hmac('{}:{}'.format(trait.name, dataset.name)),
-                        view=str(trait.view),
-                        symbol=trait.abbreviation,
-                        dataset=dataset.name,
-                        dataset_name=dataset.shortname,
-                        description=trait.description_display,
-                        abbreviation=trait.abbreviation,
-                        authors=trait.authors,
-                        pubmed_id=trait.pubmed_id,
-                        pubmed_text=trait.pubmed_text,
-                        pubmed_link=trait.pubmed_link,
-                        mean=trait_mean,
-                        lrs_score=trait.LRS_score_repr,
-                        lrs_location=trait.LRS_location_repr,
-                        lrs_chr=trait.locus_chr,
-                        lrs_mb=trait.locus_mb,
-                        additive=trait.additive
-                        )
-        else:
-            return dict(name=trait.name,
-                        display_name=trait.display_name,
-                        hmac=hmac.data_hmac('{}:{}'.format(trait.name, dataset.name)),
-                        view=str(trait.view),
-                        symbol=trait.abbreviation,
-                        dataset=dataset.name,
-                        dataset_name=dataset.shortname,
-                        description=trait.description_display,
-                        abbreviation=trait.abbreviation,
-                        authors=trait.authors,
-                        pubmed_text=trait.pubmed_text,
-                        mean=trait_mean,
-                        lrs_score=trait.LRS_score_repr,
-                        lrs_location=trait.LRS_location_repr,
-                        lrs_chr=trait.locus_chr,
-                        lrs_mb=trait.locus_mb,
-                        additive=trait.additive
-                        )
-    elif dataset.type == "Geno":
-        return dict(name=trait.name,
-                    display_name=trait.display_name,
-                    hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
-                    view=str(trait.view),
-                    dataset=dataset.name,
-                    dataset_name=dataset.shortname,
-                    location=trait.location_repr,
-                    chr=trait.chr,
-                    mb=trait.mb
-                    )
-    elif dataset.name == "Temp":
-        return dict(name=trait.name,
-                    display_name=trait.display_name,
-                    hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
-                    view=str(trait.view),
-                    dataset="Temp",
-                    dataset_name="Temp")
-    else:
-        return dict()
-
-
-def retrieve_trait_info(trait, dataset, get_qtl_info=False):
-    if not dataset:
-        raise ValueError("Dataset doesn't exist")
-
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        trait_info = ()
-        if dataset.type == 'Publish':
-            cursor.execute(
-                "SELECT PublishXRef.Id, InbredSet.InbredSetCode, "
-                "Publication.PubMed_ID, "
-                "CAST(Phenotype.Pre_publication_description AS BINARY), "
-                "CAST(Phenotype.Post_publication_description AS BINARY), "
-                "CAST(Phenotype.Original_description AS BINARY), "
-                "CAST(Phenotype.Pre_publication_abbreviation AS BINARY), "
-                "CAST(Phenotype.Post_publication_abbreviation AS BINARY), "
-                "PublishXRef.mean, Phenotype.Lab_code, "
-                "Phenotype.Submitter, Phenotype.Owner, "
-                "Phenotype.Authorized_Users, "
-                "CAST(Publication.Authors AS BINARY), "
-                "CAST(Publication.Title AS BINARY), "
-                "CAST(Publication.Abstract AS BINARY), "
-                "CAST(Publication.Journal AS BINARY), "
-                "Publication.Volume, Publication.Pages, "
-                "Publication.Month, Publication.Year, "
-                "PublishXRef.Sequence, Phenotype.Units, "
-                "PublishXRef.comments FROM PublishXRef, Publication, "
-                "Phenotype, PublishFreeze, InbredSet WHERE "
-                "PublishXRef.Id = %s AND "
-                "Phenotype.Id = PublishXRef.PhenotypeId "
-                "AND Publication.Id = PublishXRef.PublicationId "
-                "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
-                "AND PublishXRef.InbredSetId = InbredSet.Id AND "
-                "PublishFreeze.Id = %s",
-                (trait.name, dataset.id,)
-            )
-            trait_info = cursor.fetchone()
-
-        # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-        # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-        elif dataset.type == 'ProbeSet':
-            display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
-            display_fields_string = f'ProbeSet.{display_fields_string}'
-            cursor.execute(
-                f"SELECT {display_fields_string} FROM ProbeSet, ProbeSetFreeze, "
-                "ProbeSetXRef WHERE "
-                "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
-                "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
-                "ProbeSetFreeze.Name = %s AND "
-                "ProbeSet.Name = %s",
-                (dataset.name, str(trait.name),)
-            )
-            trait_info = cursor.fetchone()
-        # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
-        # to avoid the problem of same marker name from different species.
-        elif dataset.type == 'Geno':
-            display_fields_string = ',Geno.'.join(dataset.display_fields)
-            display_fields_string = f'Geno.{display_fields_string}'
-            cursor.execute(
-                f"SELECT {display_fields_string} FROM Geno, GenoFreeze, "
-                "GenoXRef WHERE "
-                "GenoXRef.GenoFreezeId = GenoFreeze.Id "
-                "AND GenoXRef.GenoId = Geno.Id "
-                "AND GenoFreeze.Name = %s "
-                "AND Geno.Name = %s",
-                (dataset.name, trait.name)
-            )
-            trait_info = cursor.fetchone()
-        else:  # Temp type
-            cursor.execute(
-                f"SELECT {','.join(dataset.display_fields)} "
-                f"FROM {dataset.type} WHERE Name = %s",
-                (trait.name,)
-            )
-            trait_info = cursor.fetchone()
-
-        if trait_info:
-            trait.haveinfo = True
-            for i, field in enumerate(dataset.display_fields):
-                holder = trait_info[i]
-                if isinstance(holder, bytes):
-                    holder = holder.decode("utf-8", errors="ignore")
-                setattr(trait, field, holder)
-
-            if dataset.type == 'Publish':
-                if trait.group_code:
-                    trait.display_name = trait.group_code + "_" + str(trait.name)
-
-                trait.confidential = 0
-                if trait.pre_publication_description and not trait.pubmed_id:
-                    trait.confidential = 1
-
-                description = trait.post_publication_description
-
-                # If the dataset is confidential and the user has access to confidential
-                # phenotype traits, then display the pre-publication description instead
-                # of the post-publication description
-                trait.description_display = "N/A"
-                trait.abbreviation = "N/A"
-                if not trait.pubmed_id:
-                    if trait.pre_publication_abbreviation:
-                        trait.abbreviation = trait.pre_publication_abbreviation
-                    if trait.pre_publication_description:
-                        trait.description_display = trait.pre_publication_description
-                else:
-                    if trait.post_publication_abbreviation:
-                        trait.abbreviation = trait.post_publication_abbreviation
-                    if description:
-                        trait.description_display = description.strip()
-
-                if not trait.year.isdigit():
-                    trait.pubmed_text = "N/A"
-                else:
-                    trait.pubmed_text = trait.year
-
-                if trait.pubmed_id:
-                    trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
-
-            if dataset.type == 'ProbeSet' and dataset.group:
-                description_string = trait.description
-                target_string = trait.probe_target_description
-
-                if str(description_string or "") != "" and description_string != 'None':
-                    description_display = description_string
-                else:
-                    description_display = trait.symbol
-
-                if (str(description_display or "") != ""
-                    and description_display != 'N/A'
-                        and str(target_string or "") != "" and target_string != 'None'):
-                    description_display = description_display + '; ' + target_string.strip()
-
-                # Save it for the jinja2 template
-                trait.description_display = description_display
-
-                trait.location_repr = 'N/A'
-                if trait.chr and trait.mb:
-                    trait.location_repr = 'Chr%s: %.6f' % (
-                        trait.chr, float(trait.mb))
-
-            elif dataset.type == "Geno":
-                trait.location_repr = 'N/A'
-                if trait.chr and trait.mb:
-                    trait.location_repr = 'Chr%s: %.6f' % (
-                        trait.chr, float(trait.mb))
-
-            if get_qtl_info:
-                # LRS and its location
-                trait.LRS_score_repr = "N/A"
-                trait.LRS_location_repr = "N/A"
-                trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
-                if dataset.type == 'ProbeSet' and not trait.cellid:
-                    trait.mean = ""
-                    cursor.execute(
-                        "SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, "
-                        "ProbeSetXRef.pValue, ProbeSetXRef.mean, "
-                        "ProbeSetXRef.additive FROM ProbeSetXRef, "
-                        "ProbeSet WHERE "
-                        "ProbeSetXRef.ProbeSetId = ProbeSet.Id "
-                        "AND ProbeSet.Name = %s AND "
-                        "ProbeSetXRef.ProbeSetFreezeId = %s",
-                        (trait.name, dataset.id,)
-                    )
-                    trait_qtl = cursor.fetchone()
-                    if any(trait_qtl):
-                        trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl
-                        if trait.locus:
-                            cursor.execute(
-                                "SELECT Geno.Chr, Geno.Mb FROM "
-                                "Geno, Species WHERE "
-                                "Species.Name = %s AND "
-                                "Geno.Name = %s AND "
-                                "Geno.SpeciesId = Species.Id",
-                                (dataset.group.species, trait.locus,)
-                            )
-                            if result := cursor.fetchone() :
-                                trait.locus_chr = result[0]
-                                trait.locus_mb = result[1]
-                            else:
-                                trait.locus_chr = trait.locus_mb = ""
-                        else:
-                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-
-                if dataset.type == 'Publish':
-                    cursor.execute(
-                        "SELECT PublishXRef.Locus, PublishXRef.LRS, "
-                        "PublishXRef.additive FROM "
-                        "PublishXRef, PublishFreeze WHERE "
-                        "PublishXRef.Id = %s AND "
-                        "PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
-                        "AND PublishFreeze.Id = %s", (trait.name, dataset.id,)
-                    )
-                    if trait_qtl := cursor.fetchone():
-                        trait.locus, trait.lrs, trait.additive = trait_qtl
-                        if trait.locus:
-                            cursor.execute(
-                                "SELECT Geno.Chr, Geno.Mb FROM Geno, "
-                                "Species WHERE Species.Name = %s "
-                                "AND Geno.Name = %s AND "
-                                "Geno.SpeciesId = Species.Id",
-                                (dataset.group.species, trait.locus,)
-                            )
-                            if result := cursor.fetchone():
-                                trait.locus_chr = result[0]
-                                trait.locus_mb = result[1]
-                            else:
-                                trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-                        else:
-                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-                    else:
-                        trait.locus = trait.lrs = trait.additive = ""
-                if (dataset.type == 'Publish' or dataset.type == "ProbeSet"):
-                    if str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
-                        trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
-                            trait.locus_chr, float(trait.locus_mb))
-                    if str(trait.lrs or "") != "":
-                        trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
-        else:
-            raise KeyError(
-                f"{repr(trait.name)} information is not found in the database "
-                f"for dataset '{dataset.name}' with id '{dataset.id}'.")
-        return trait
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
deleted file mode 100644
index dd6fad04..00000000
--- a/wqflask/base/webqtlCaseData.py
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-
-
-import utility.tools
-
-utility.tools.show_settings()
-
-
-class webqtlCaseData:
-    """one case data in one trait"""
-
-    def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
-        self.name = name
-        # Other name (for traits like BXD65a)
-        self.name2 = name2
-        self.value = value                  # Trait Value
-        self.variance = variance            # Trait Variance
-        self.num_cases = num_cases          # Number of individuals/cases
-        self.extra_attributes = None
-        # Set a sane default (can't be just "id" cause that's a reserved word)
-        self.this_id = None
-        self.outlier = None   # Not set to True/False until later
-
-    def __repr__(self):
-        case_data_string = "<webqtlCaseData> "
-        if self.value is not None:
-            case_data_string += "value=%2.3f" % self.value
-        if self.variance is not None:
-            case_data_string += " variance=%2.3f" % self.variance
-        if self.num_cases:
-            case_data_string += " ndata=%s" % self.num_cases
-        if self.name:
-            case_data_string += " name=%s" % self.name
-        if self.name2:
-            case_data_string += " name2=%s" % self.name2
-        return case_data_string
-
-    @property
-    def class_outlier(self):
-        """Template helper"""
-        if self.outlier:
-            return "outlier"
-        return ""
-
-    @property
-    def display_value(self):
-        if self.value is not None:
-            return "%2.3f" % self.value
-        return "x"
-
-    @property
-    def display_variance(self):
-        if self.variance is not None:
-            return "%2.3f" % self.variance
-        return "x"
-
-    @property
-    def display_num_cases(self):
-        if self.num_cases is not None:
-            return "%s" % self.num_cases
-        return "x"
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
deleted file mode 100644
index a7dbed3d..00000000
--- a/wqflask/base/webqtlConfig.py
+++ /dev/null
@@ -1,107 +0,0 @@
-# '
-#      Environment Variables - public
-#
-# Note: much of this needs to handled by the settings/environment
-# scripts. But rather than migrating everything in one go, we'll
-# take it a step at a time. First the hard coded paths get replaced
-# with those in utility/tools.py
-#
-#########################################
-import os
-from 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
-DEBUG = 1
-
-# USER privilege
-USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root': 4}
-
-# Set privileges
-SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
-DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'}
-
-# minimum number of informative strains
-KMININFORMATIVE = 5
-
-# Daily download limit from one IP
-DAILYMAXIMUM = 1000
-
-# maximum LRS value
-MAXLRS = 460.0
-
-# MINIMUM Database public value
-PUBLICTHRESH = 0
-
-# Groups to treat as unique when drawing correlation dropdowns (not sure if this logic even makes sense or is necessary)
-BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD']
-
-# EXTERNAL LINK ADDRESSES
-PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-GENOMEBROWSER_URL = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
-NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s"
-GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
-OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"
-HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s"
-GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s"
-GTEX_URL = "https://www.gtexportal.org/home/gene/%s"
-GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s"
-GENEMANIA_URL = "https://genemania.org/search/%s/%s"
-UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
-BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s"
-STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s"
-PANTHER_URL = "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=%s"
-GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s"
-ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s"
-EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
-WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
-ENSEMBLETRANSCRIPT_URL = "http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
-DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
-PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
-OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
-UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
-RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
-PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn7&section=geneEQTL"
-RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
-RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
-
-# Temporary storage (note that this TMPDIR can be set as an
-# environment variable - use utility.tools.TEMPDIR when you
-# want to reach this base dir
-assert_writable_dir(TEMPDIR)
-
-TMPDIR = mk_dir(TEMPDIR + '/gn2/')
-assert_writable_dir(TMPDIR)
-
-CACHEDIR = mk_dir(TMPDIR + '/cache/')
-# We can no longer write into the git tree:
-GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/')
-GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/')
-
-# Make sure we have permissions to access these
-assert_writable_dir(CACHEDIR)
-assert_writable_dir(GENERATED_IMAGE_DIR)
-assert_writable_dir(GENERATED_TEXT_DIR)
-
-# Flat file directories
-GENODIR = flat_files('genotype') + '/'
-assert_dir(GENODIR)
-# assert_dir(GENODIR+'bimbam') # for gemma
-
-# JSON genotypes are OBSOLETE
-JSON_GENODIR = flat_files('genotype/json') + '/'
-if not valid_path(JSON_GENODIR):
-    # fall back on old location (move the dir, FIXME)
-    JSON_GENODIR = flat_files('json')
-
-
-TEXTDIR = os.path.join(os.environ.get(
-    "GNSHARE", "/gnshare/gn/"), "web/ProbeSetFreeze_DataMatrix")
-# Are we using the following...?
-PORTADDR = "http://50.16.251.170"
-INFOPAGEHREF = '/dbdoc/%s.html'
-CGIDIR = '/webqtl/'  # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'