Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 105 deletions

diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py
deleted file mode 100755
index 754ff5b5..00000000
--- a/web/webqtl/textUI/cmdHelp.py
+++ /dev/null
@@ -1,105 +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 GeneNetwork Core Team 2010/10/20
-
-import string
-
-from base import webqtlConfig
-from base.admin import ADMIN_tissue_alias
-from cmdClass import cmdClass
-
-#########################################
-#      Help Class
-#########################################
-
-#XZ, 03/23/2009: There are several issues need attention.
-#1. Some probeset datasets are not added into DBList.
-#2. Do NOT show confidential datasets. 
-#3. Get rid of ADMIN_tissue_alias. We should use info from database instead.
-
-class cmdHelp(cmdClass):
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-
-		machineParse = self.data.getvalue('parse')
-		topic = self.data.getvalue('topic')
-		if topic:
-			topic = topic.lower()
-			if topic == 'tissue':
-				self.contents.append("%s%s|          %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations"))
-				self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)"))
-				self.contents.append("%s|%s" %('_'*50, '_'*40))
-			
-				keys = ADMIN_tissue_alias.keys()
-				keys.sort()
-				for key in keys:
-					self.contents.append("%s%s|   %s" % (key , ' '*(50-len(key)),  string.join(ADMIN_tissue_alias[key], "  ")))
-					self.contents.append("%s|%s" %('_'*50, '_'*40))
-			else:	
-				pass
-		else:
-			self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use",
-					     "#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)]
-			self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time
-						from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id  and 
-						ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id) 
-						UNION 
-						(SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time
-						from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by 
-						PublishFreeze.CreateTime ,DBList.Name, DBList.Id) 
-						UNION
-						(SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime 
-						from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by 
-						GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH)
-			dbs = self.cursor.fetchall()
-			if machineParse =="machine":
-				pass
-			else:
-				self.contents.append("\n")
-				self.contents.append("%s%s|          %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name"))
-				self.contents.append("%s|%s" %('_'*50, '_'*40))
-			for dbInfo in dbs:
-				self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH))
-				results = self.cursor.fetchall()
-				if not results:
-					pass
-				else:
-					if machineParse =="machine":
-						self.contents.append(results[0][0]+ ',' +dbInfo[2])
-					else:
-						self.contents.append("%s%s|          %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2]))
-						self.contents.append("%s|%s" %('_'*50, '_'*40))
-	
-
-