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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/textUI/cmdGet.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/textUI/cmdGet.py')
-rwxr-xr-xweb/webqtl/textUI/cmdGet.py86
1 files changed, 86 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.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 cmdClass import cmdClass
+
+#########################################
+# Get trait value Class
+#########################################
+class cmdGet(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
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+ if self.accessError:
+ return
+ if not self.error:
+ self.readDB()
+ else:
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+
+ def readDB(self):
+ prefix, dbId = self.getDBId(self.database)
+
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ try:
+ if not traitdata:
+ raise ValueError
+ traitdata = heads + list(traitdata)
+ if self.format == 'col':
+ self.formatCols(traitdata)
+ else:
+ self.formatRows(traitdata)
+ except:
+ self.contents.append('Error: no record was found')
+ self.contents.append(self.accessCode)
+ return
+
+ def formatCols(self, traitdata):
+ for item in traitdata:
+ lines = []
+ for item2 in item:
+ lines.append(item2)
+ lines = string.join(map(str,lines), '\t')
+ self.contents.append(lines)
+
+ def formatRows(self, traitdata):
+ for i in range(len(traitdata[0])):
+ lines = []
+ for j in range(len(traitdata)):
+ lines.append(traitdata[j][i])
+ lines = string.join(map(str,lines), '\t')
+ self.contents.append(lines)
+
+