delete unwanted correlation stuff (#5)

* delete unwanted correlation stuff

* Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

* update guix scm file

* fix pylint error for correlations api

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

1 files changed, 0 insertions, 66 deletions

diff --git a/gn3/utility/webqtlUtil.py b/gn3/utility/webqtlUtil.py
deleted file mode 100644
index 1c76410..0000000
--- a/gn3/utility/webqtlUtil.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
-
-# from base import webqtlConfig
-
-# NL, 07/27/2010. moved from webqtlForm.py
-# Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
-
-"""
-ParInfo = {
-    'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
-    'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
-    'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-    'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
-    'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-    'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-    'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-    'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-    'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-    'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
-    'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-    'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
-    'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
-    'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-    'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-    'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
-    'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
-    'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-    'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
-    'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
-    'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
-    'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
-    'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
-}
-
-
-def has_access_to_confidentail_phenotype_trait(privilege, username, authorized_users):
-    """function to access to confidential phenotype Traits  further implementation needed"""
-    access_to_confidential_phenotype_trait = 0
-
-    results = (privilege, username, authorized_users)
-    return access_to_confidential_phenotype_trait