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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/textUI/cmdHelp.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/textUI/cmdHelp.py')
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1 files changed, 105 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py
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+# 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))
+
+
+