Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

3 files changed, 0 insertions, 266 deletions

diff --git a/web/webqtl/misc/__init__.py b/web/webqtl/misc/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/misc/__init__.py
+++ /dev/null
diff --git a/web/webqtl/misc/editHtmlPage.py b/web/webqtl/misc/editHtmlPage.py
deleted file mode 100755
index 68595b83..00000000
--- a/web/webqtl/misc/editHtmlPage.py
+++ /dev/null
@@ -1,129 +0,0 @@
-# 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
deleted file mode 100755
index da679910..00000000
--- a/web/webqtl/misc/uploadFilePage.py
+++ /dev/null
@@ -1,137 +0,0 @@
-# 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