Add all the source codes into the github.

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))
+	
+
+