From 56ce88ad31dec3cece63e9370ca4e4c02139753b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Tue, 16 Mar 2021 11:38:13 +0300 Subject: 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 * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz --- gn3/db/__init__.py | 0 gn3/db/calls.py | 51 --------------------------------------- gn3/db/webqtlDatabaseFunction.py | 52 ---------------------------------------- 3 files changed, 103 deletions(-) delete mode 100644 gn3/db/__init__.py delete mode 100644 gn3/db/calls.py delete mode 100644 gn3/db/webqtlDatabaseFunction.py (limited to 'gn3/db') diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py deleted file mode 100644 index e69de29..0000000 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 -- cgit v1.2.3