fix: remove .py extension for addRif to prevent pylint checks

1 files changed, 0 insertions, 129 deletions

diff --git a/scripts/addRif.py b/scripts/addRif.py
deleted file mode 100755
index 4d33af3..0000000
--- a/scripts/addRif.py
+++ /dev/null
@@ -1,129 +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 Lei Yan 2011/02/08
-
-# created by Lei Yan 02/08/2011
-
-import os
-import sys
-import MySQLdb
-
-path1 = os.path.abspath(os.path.dirname(__file__))
-path2 = path1 + "/.."
-path3 = path1 + "/../../tmp"
-sys.path.insert(0, path2)
-
-
-def fetchrif():
-    try:
-        con = MySQLdb.Connect(db="gn3", host="localhost", user="gn2", passwd="password")
-        cursor = con.cursor()
-        print("You have successfully connected to mysql.\n")
-    except:
-        print("You entered incorrect password.\n")
-        sys.exit(0)
-
-    taxIds = {"10090": 1, "9606": 4, "10116": 2, "3702": 3}
-    taxIdKeys = taxIds.keys()
-
-    os.chdir(path3)
-    print("path3: %s" % (path3))
-    genedict = {}
-
-    os.system("rm -vf gene_info")
-    os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz")
-    os.system("gunzip gene_info.gz")
-
-    file = open("gene_info", "r")
-    i = 0
-    for line1 in file:
-        line1 = line1.strip()
-        if line1.startswith("#"):
-            continue
-        line2 = line1.strip().split("\t")
-        if line2[0] in taxIdKeys:
-            genedict[line2[1]] = line2[2]
-        i += 1
-        if i % 1000000 == 0:
-            print("finished: %d" % (i))
-    print("finished all: %d" % (i))
-    file.close()
-
-    os.system("rm -vf generifs_basic")
-    os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz")
-    os.system("gunzip generifs_basic.gz")
-
-    file = open("generifs_basic", "r")
-    i = 0
-    for line1 in file:
-        line1 = line1.strip()
-        if line1.startswith("#"):
-            continue
-        line2 = line1.strip().split("\t")
-        if line2[0] in taxIdKeys and len(line2) >= 5:
-            line2[0] = taxIds[line2[0]]
-            try:
-                symbol = genedict[line2[1]]
-            except:
-                symbol = ""
-            sql = """
-				SELECT COUNT(*)
-				FROM GeneRIF_BASIC
-				WHERE GeneRIF_BASIC.`SpeciesId`=%s
-				AND GeneRIF_BASIC.`GeneId`=%s
-				AND GeneRIF_BASIC.`PubMed_ID`=%s
-				AND GeneRIF_BASIC.`createtime`=%s
-				AND GeneRIF_BASIC.`comment`=%s
-				"""
-            cursor.execute(sql, (line2[0], line2[1], line2[2], line2[3], line2[4]))
-            c = cursor.fetchone()[0]
-            if c == 0:
-                print("to insert...")
-                sql = """
-					INSERT INTO GeneRIF_BASIC
-					SET GeneRIF_BASIC.`SpeciesId`=%s,
-						GeneRIF_BASIC.`GeneId`=%s,
-						GeneRIF_BASIC.`symbol`=%s,
-						GeneRIF_BASIC.`PubMed_ID`=%s,
-						GeneRIF_BASIC.`createtime`=%s,
-						GeneRIF_BASIC.`comment`=%s
-					"""
-                cursor.execute(
-                    sql, (line2[0], line2[1], symbol, line2[2], line2[3], line2[4])
-                )
-        i += 1
-        if i % 100000 == 0:
-            print("finished: %d" % (i))
-    print("finished all: %d" % (i))
-    file.close()
-    cursor.close()
-
-
-# /usr/bin/python addRif.py
-
-if __name__ == "__main__":
-    print("command line arguments:\n\t%s" % sys.argv)
-    fetchrif()
-    print("exit successfully")