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>

3 files changed, 0 insertions, 103 deletions

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/gn3/db/__init__.py
+++ /dev/null
diff --git a/gn3/db/calls.py b/gn3/db/calls.py
deleted file mode 100644
index 547bccf..0000000
--- a/gn3/db/calls.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""module contains calls method for db"""
-import json
-import urllib
-from flask import g
-from gn3.utility.logger import getLogger
-logger = getLogger(__name__)
-# should probably put this is env
-USE_GN_SERVER = False
-LOG_SQL = False
-
-GN_SERVER_URL = None
-
-
-def fetch1(query, path=None, func=None):
-    """fetch1 method"""
-    if USE_GN_SERVER and path:
-        result = gn_server(path)
-        if func is not None:
-            res2 = func(result)
-
-        else:
-            res2 = result
-
-        if LOG_SQL:
-            pass
-            # should probably and logger
-            # logger.debug("Replaced SQL call", query)
-
-        # logger.debug(path,res2)
-        return res2
-
-    return fetchone(query)
-
-
-def gn_server(path):
-    """Return JSON record by calling GN_SERVER
-
-    """
-    res = urllib.request.urlopen(GN_SERVER_URL+path)
-    rest = res.read()
-    res2 = json.loads(rest)
-    return res2
-
-
-def fetchone(query):
-    """method to fetchone item from  db"""
-    def helper(query):
-        res = g.db.execute(query)
-        return res.fetchone()
-
-    return logger.sql(query, helper)
diff --git a/gn3/db/webqtlDatabaseFunction.py b/gn3/db/webqtlDatabaseFunction.py
deleted file mode 100644
index 9e9982b..0000000
--- a/gn3/db/webqtlDatabaseFunction.py
+++ /dev/null
@@ -1,52 +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)
-"""
-
-from gn3.db.calls import fetch1
-
-from gn3.utility.logger import getLogger
-logger = getLogger(__name__)
-
-###########################################################################
-# output: cursor instance
-# function: connect to database and return cursor instance
-###########################################################################
-
-
-def retrieve_species(group):
-    """Get the species of a group (e.g. returns string "mouse" on "BXD"
-
-    """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
-        group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
-    # logger.debug("retrieve_species result:", result)
-    return result
-
-
-def retrieve_species_id(group):
-    """retrieve species id method"""
-
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
-        group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
-    logger.debug("retrieve_species_id result:", result)
-    return result