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, 84 deletions

diff --git a/gn3/base/webqtlCaseData.py b/gn3/base/webqtlCaseData.py
deleted file mode 100644
index 8395af8..0000000
--- a/gn3/base/webqtlCaseData.py
+++ /dev/null
@@ -1,84 +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
-
-
-# uncomment below
-
-# from utility.logger import getLogger
-# logger = getLogger(__name__)
-
-# import utility.tools
-
-# utility.tools.show_settings()
-# pylint: disable-all
-
-class webqtlCaseData:
-    """one case data in one trait"""
-
-    def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
-        self.name = name
-        self.name2 = name2                  # Other name (for traits like BXD65a)
-        self.value = value                  # Trait Value
-        self.variance = variance            # Trait Variance
-        self.num_cases = num_cases          # Number of individuals/cases
-        self.extra_attributes = None
-        self.this_id = None   # Set a sane default (can't be just "id" cause that's a reserved word)
-        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"
\ No newline at end of file