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Diffstat (limited to 'web/webqtl/textUI/cmdHelp.py')
| -rwxr-xr-x | web/webqtl/textUI/cmdHelp.py | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py new file mode 100755 index 00000000..754ff5b5 --- /dev/null +++ b/web/webqtl/textUI/cmdHelp.py @@ -0,0 +1,105 @@ +# 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)) + + + |