Add all the source codes into the github.

1 files changed, 86 insertions, 0 deletions

diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.py
new file mode 100755
index 00000000..a11c97a3
--- /dev/null
+++ b/web/webqtl/textUI/cmdGet.py
@@ -0,0 +1,86 @@
+# 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)
+
+