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authorAlexander Kabui2021-03-16 11:38:13 +0300
committerGitHub2021-03-16 11:38:13 +0300
commit56ce88ad31dec3cece63e9370ca4e4c02139753b (patch)
tree766504dfaca75a14cc91fc3d88c41d1e775d415f /gn3/db
parent43d1bb7f6cd2b5890d5b3eb7c357caafda25a35c (diff)
downloadgenenetwork3-56ce88ad31dec3cece63e9370ca4e4c02139753b.tar.gz
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>
Diffstat (limited to 'gn3/db')
-rw-r--r--gn3/db/__init__.py0
-rw-r--r--gn3/db/calls.py51
-rw-r--r--gn3/db/webqtlDatabaseFunction.py52
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