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Diffstat (limited to 'web/webqtl/textUI/cmdHelp.py')
| -rwxr-xr-x | web/webqtl/textUI/cmdHelp.py | 105 |
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)) - - - |