Add all the source codes into the github.

3 files changed, 266 insertions, 0 deletions

diff --git a/web/webqtl/misc/__init__.py b/web/webqtl/misc/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/misc/__init__.py
diff --git a/web/webqtl/misc/editHtmlPage.py b/web/webqtl/misc/editHtmlPage.py
new file mode 100755
index 00000000..68595b83
--- /dev/null
+++ b/web/webqtl/misc/editHtmlPage.py
@@ -0,0 +1,129 @@
+# 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
+import os
+import urlparse
+
+from htmlgen import HTMLgen2 as HT
+
+from base.templatePage import templatePage
+from base import webqtlConfig
+from utility import webqtlUtil
+
+
+#########################################
+#      Edit HTML Page
+#########################################
+
+class editHtmlPage(templatePage):
+	htmlPath = webqtlConfig.ChangableHtmlPath
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		self.templateInclude = 1
+		self.dict['title'] = "Editing HTML"
+
+		if not self.updMysql():
+			return
+
+		if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
+			pass
+		else:
+			heading = "Editing HTML"
+			detail = ["You don't have the permission to modify this file"]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+
+		path = fd.formdata.getvalue('path')
+		preview = fd.formdata.getvalue('preview')
+		newHtmlCode = fd.formdata.getvalue('htmlSrc')
+		if newHtmlCode:
+			#newHtmlCode = string.replace(newHtmlCode, "&image", "&image")
+			newHtmlCode = string.replace(newHtmlCode,"&", "&")
+		if path and preview:
+			#preview
+			self.templateInclude = 0
+			#print newHtmlCode
+			self.debug = newHtmlCode
+		elif path:
+			#edit result
+			fileName = self.htmlPath + path
+			newfileName = fileName +'.old'
+			os.system("/bin/cp -f %s %s" % (fileName, newfileName))
+			fp = open(fileName, 'wb')
+			fp.write(newHtmlCode)
+			fp.close()
+			#print "chown qyh %s" % fileName
+			TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#eeeeee", height=200)
+			mainTitle = HT.Paragraph("Edit HTML", Class="title")
+			url = HT.Href(text = "page", url =path, Class = "normal")
+			intro = HT.Blockquote("This ",url, " has been succesfully modified. ")
+			TD_LR.append(mainTitle, intro)
+			self.dict['body'] = TD_LR
+		#elif os.environ.has_key('HTTP_REFERER'):
+		elif fd.refURL:
+			#retrieve file to be edited
+			#refURL = os.environ['HTTP_REFERER']
+			addressing_scheme, network_location, path, parameters, query, fragment_identifier = urlparse.urlparse(fd.refURL)
+			if path[-1] == "/":
+				path += 'index.html'
+				
+			fileName = self.htmlPath + path
+			try:
+				fp = open(fileName,'rb')
+			except:
+				fp = open(os.path.join(self.htmlPath, 'temp.html'),'rb')
+			htmlCode = fp.read()
+			#htmlCode = string.replace(htmlCode, "&nbsp","&nbsp")
+			htmlCode = string.replace(htmlCode, "&","&")
+			fp.close()
+			form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), name='editHtml',submit=HT.Input(type='hidden'))
+			inputBox = HT.Textarea(name='htmlSrc', cols="100", rows=30,text=htmlCode)
+			
+			hddn = {'FormID':'editHtml', 'path':path, 'preview':''}
+			for key in hddn.keys():
+				form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+			previewButton = HT.Input(type='button',name='previewhtml', value='Preview',Class="button", onClick= "editHTML(this.form, 'preview');")
+			submitButton = HT.Input(type='button',name='submitchange', value='Submit Change',Class="button", onClick= "editHTML(this.form, 'submit');")
+			resetButton = HT.Input(type='reset',Class="button")
+			form.append(HT.Center(inputBox, HT.P(), previewButton, submitButton, resetButton))
+			
+			TD_LR = HT.TD(valign="top",colspan=2,bgcolor="#eeeeee")
+			mainTitle = HT.Paragraph("Edit HTML", Class="title")
+			intro = HT.Blockquote("You may edit the HTML source code in the editbox below, or you can copy the content of the editbox to your favorite HTML editor. ")
+			imgUpload = HT.Href(url="javascript:openNewWin('/upload.html', 'menubar=0,toolbar=0,location=0,resizable=0,status=1,scrollbars=1,height=400, width=600');", text="here", Class="fs14")
+			intro2 = HT.Blockquote("Click ", imgUpload, " to upload Images. ")
+			TD_LR.append(mainTitle, intro, intro2, HT.Center(form))
+			self.dict['body'] = TD_LR
+		else:
+			heading = "Editing HTML"
+			detail = ["Error occured while trying to edit the html file."]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+
diff --git a/web/webqtl/misc/uploadFilePage.py b/web/webqtl/misc/uploadFilePage.py
new file mode 100755
index 00000000..da679910
--- /dev/null
+++ b/web/webqtl/misc/uploadFilePage.py
@@ -0,0 +1,137 @@
+# 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 os
+import string
+
+from htmlgen import HTMLgen2 as HT
+
+from base.templatePage import templatePage
+from base import webqtlConfig
+from utility import webqtlUtil
+
+#########################################
+#      Upload File Page 
+#########################################
+
+class uploadFilePage(templatePage):
+
+	uploadPath = webqtlConfig.UPLOADPATH
+
+	def __init__(self, fd, formdata, cookies):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+                if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
+                        pass
+                else:
+                        heading = "Upload File"
+                        detail = ["You don't have the permission to upload file to the server."]
+                        self.error(heading=heading,detail=detail)
+                        return
+		
+		self.cursor.close()
+
+		file1 = self.save_uploaded_file (formdata, 'imgName1')
+		file2 = self.save_uploaded_file (formdata, 'imgName2')
+		file3 = self.save_uploaded_file (formdata, 'imgName3')
+		file4 = self.save_uploaded_file (formdata, 'imgName4')
+		file5 = self.save_uploaded_file (formdata, 'imgName5')
+		
+		i = 0
+		uploaded = []
+
+		for filename in (file1, file2, file3, file4, file5):
+			if filename: 
+				i += 1
+				uploaded.append(filename)
+				
+		if i == 0:
+			heading = "Upload File"
+			detail = ["No file was selected, no file uploaded."]
+			self.error(heading=heading,detail=detail)
+			return
+		else:
+			TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
+
+			imgTbl = HT.TableLite(border=0, width = "90%",cellspacing=2, cellpadding=2, align="Center")
+			imgTbl.append(HT.TR(HT.TD("Thumbnail", width="%30", align='center',Class="colorBlue"), 
+					HT.TD("URL", width="%60",Class="colorBlue", align='center')))
+			for item in uploaded:
+				img = HT.Image("/images/upload/" + item, border = 0, width=80)
+
+				#url = "%s/images/upload/" % webqtlConfig.PORTADDR + item
+				#url = HT.Href(text=url, url = url, Class='normalsize', target="_blank")
+				url2 = "/images/upload/" + item
+				url2 = HT.Href(text=url2, url = url2, Class='normalsize', target="_blank")
+				imgTbl.append(HT.TR(HT.TD(img, width="%30", align='center',Class="colorWhite"), 
+					#HT.TD(url, HT.BR(), 'OR', HT.BR(), url2,  width="%60",Class="colorWhite", align='center')))
+					HT.TD(url2,  width="%60",Class="colorWhite", align='center')))
+
+			intro = HT.Paragraph('A total of %d files are uploaded' % i)
+			TD_LR.append( HT.Center(intro) )
+
+			TD_LR.append( imgTbl )
+		
+			self.dict['body'] = str(TD_LR)	
+		
+	def save_uploaded_file(self, form, form_field, upload_dir=""):
+		if not upload_dir:
+			upload_dir = self.uploadPath
+		if not form.has_key(form_field):
+			return None
+		fileitem = form[form_field]
+		
+		if not fileitem.filename or not fileitem.file:
+			return None
+		
+		seqs = [""] + range(200)
+		try:
+			newfileName =  string.split(fileitem.filename, ".")
+			for seq in seqs:
+				newfileName2 = newfileName[:]
+				if seq != "":
+					newfileName2[-2] = "%s-%s" % (newfileName2[-2], seq)
+				fileExist = glob.glob(os.path.join(upload_dir, string.join(newfileName2, ".")))
+				if not fileExist:
+					break
+		except:
+			pass
+		
+		newfileName = string.join(newfileName2, ".")
+		#print [newfileName, os.path.join(upload_dir, newfileName)]
+		#return
+		
+		fout = file (os.path.join(upload_dir, newfileName), 'wb')
+		while 1:
+			chunk = fileitem.file.read(100000)
+			if not chunk: break
+			fout.write (chunk)
+		fout.close()
+		return newfileName