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

10 files changed, 0 insertions, 841 deletions

diff --git a/web/webqtl/dataSharing/SharingBody.py b/web/webqtl/dataSharing/SharingBody.py
deleted file mode 100755
index 4445e0d1..00000000
--- a/web/webqtl/dataSharing/SharingBody.py
+++ /dev/null
@@ -1,290 +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
-
-sharing_body_string = """
-<TD vAlign=top width="100%" align="left" height=10 bgColor=#eeeeee>
-
-							<p style="font-size:18px;font-family:verdana;color:black"><B> Data Set Download</B></p>
-							<Form METHOD="get" ACTION="/webqtl/main.py" name="SEARCHFORM">
-
-								<TABLE width="800" border="0">
-					
-					<!--  SPECIES  SELECTION -->				
-									<TR>
-										<TD align=right height="35" style="font-size:14px;font-family:verdana;color:black" width="16%">
-											<B>Species:</B>
-										</TD>
-										<TD width="3%">
-										</TD>
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu0">
-												<Select NAME="species" size=1 id="species" onchange="fillOptions('species');">
-												</Select>
-											</DIV>
-										</TD>
-									</TR>
-				
-					<!--  GROUP  SELECTION -->	
-									<TR>
-										<TD align="right" height="35" style="font-size:14px;font-family:verdana;color:black">
-											<B>Group:</B>
-										</TD>
-										<TD>
-										</TD>
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu1">
-
-												<Select NAME="cross" size=1 id="cross" onchange="fillOptions('cross');">
-												</Select>
-											<input type="button" class="button" value=" Info " onCLick="javascript:crossinfo();">
-											</DIV>
-										</TD>
-									</TR>
-
-					<!--  TYPE  SELECTION -->		
-									<TR>
-										<TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-											<B>Type:</B>
-										</TD>
-										<TD>
-										</TD>
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu2">
-												<Select NAME="tissue" size=1 id="tissue" onchange="fillOptions('tissue');">
-
-												</Select>
-											</DIV>
-										</TD>
-									</TR>
-
-					<!--  DATABASE  SELECTION -->		
-									<TR>
-										<TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-											<B>Database:</B>
-										</TD>
-										<TD>
-										</TD>
-										<TD NOWRAP width="85%" align="left">
-											<DIV Id="menu3">
-												<Select NAME="database" size=1 id="database"> 
-												</Select>
-												<input type="button" class="button" value=" Info " onCLick="javascript:databaseinfo();">
-											</DIV>
-										</TD>
-									</TR>
-
-<!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-									<TR>
-										<td></td>
-										<td></td>
-										<TD ALIGN="left" HEIGHT="40">
-											&nbsp;&nbsp;&nbsp;<INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE="&nbsp;&nbsp;Download&nbsp;&nbsp;" onCLick="javascript:datasetinfo();">
-										</TD>
-									</TR>
-								</TABLE>
-
-								<SCRIPT SRC="/javascript/selectDatasetMenu.js"></SCRIPT>
-							</FORM>
-							
-							<p style="font-size:18px;font-family:verdana;color:black"><B> GeneNetwork Accession Number</B></p>
-							<form method="get" action="/webqtl/main.py" name="f2" target="_blank">
-								<INPUT TYPE="hidden" NAME="FormID" VALUE="sharinginfo">
-								<TABLE width="800" border="0">
-									<tr>
-										<td align=right height="35" style="font-size:14px;font-family:verdana;color:black" width="16%"><b>GN:</b></td>
-										<td width=3%></td>
-										<td><input type="text" name="GN_AccessionId" size="40" />&nbsp;&nbsp;E.g. 112</td>
-									</tr>
-									<tr>
-										<td></td>
-										<td></td>
-										<td HEIGHT="40">
-											&nbsp;&nbsp;&nbsp;<input type="Submit" class="button" STYLE="font-size:12px" VALUE="&nbsp;&nbsp;&nbsp;Submit&nbsp;&nbsp;&nbsp;">
-										</td>
-									</tr>
-								</table>
-							</form>
-							
-</td>
-"""
-
-sharinginfo_body_string = """<td>
-<a href="/webqtl/main.py?FormID=sharingListDataset">List of DataSets</a><br>
-<H1 class="title" id="parent-fieldname-title">%s
-<a href="/webqtl/main.py?FormID=sharinginfoedit&GN_AccessionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>
-<span style="color:red;">%s</span>
-</H1>
-<table border="0" width="100%%">
-<tr>
-<td valign="top" width="50%%">
-<TABLE cellSpacing=0 cellPadding=5 width=100%% border=0>
-                      <TR><td><b>GN Accession:</b> GN%s</TD></tr>
-                      <TR><TD><b>GEO Series:</b> %s</TD></TR>
-                      <TR><TD><b>Title:</b> %s</TD></TR> 
-                      <TR><TD><b>Organism:</b> <a href=http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=%s>%s</a></TD></tr>
-                      <tr><TD><b>Group:</b> %s</TD></TR>
-                      <TR><TD><b>Tissue:</b> %s</TD></tr>
-                      <tr><TD><b>Dataset Status:</b> %s</TD></tr>
-                      <TR><TD><b>Platforms:</b> %s</TD></TR>
-                      <TR><TD><b>Normalization:</b> %s</TD></TR>
-                      <TR><TD><!--Code below to Show hide Contact information -->
-                       <a href="#" onclick="colapse('answer1')">See Contact Information</a><br>
-                       <span id="answer1" style="display: none; return: false;">
-					   %s<br>
-                       %s<br>
-                       %s<br>
-                       %s<br>
-                       %s, %s %s %s<br>
-                       Tel. %s<br>
-                       %s<br>
-                       <a href="%s">%s</a>
-                       </span><!--Code above to Show hide Contact information --></TD></TR>
-</TABLE>
-</td>
-<td valign="top" width="50%%">
-<table border="0" width="100%%">
-<tr>
-	<td bgcolor="#dce4e1"><b>Download datasets and supplementary data files</b></td>
-</tr>
-<tr>
-	<td>%s</td>
-</tr>
-</table>
-</td>
-</tr>
-</table>
-<HR>
-<p>
-<table width="100%%" border="0" cellpadding="5" cellspacing="0">
-<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">About the cases used to generate this set of data:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">About downloading this data set:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">About the array platform:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">About data values and data processing:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Data source acknowledgment:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Experiment Type:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Overall Design:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Contributor:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Citation:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Submission Date:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Laboratory:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-<tr><td><span style="font-size:115%%;font-weight:bold;">Samples:</span></td></tr>
-	<tr><td> %s<br><br></td></tr>
-</table>
-</p>
-</td>
-"""
-
-sharinginfoedit_body_string = """<td>
-<H1 class="title">%s</H1>
-<script language="javascript">
-function CheckGNAccesionId(){
-	if (document.sharinginfoupdate.GN_AccesionId.value.length  ==  0){
-		alert("Please input GN Accesion Id");
-		document.sharinginfoupdate.GN_AccesionId.focus();
-		return false;
-	} else {
-		return true;
-	}
-}
-</script>
-<table border="0" CELLSPACING="0" CELLPADDING="8">
-<form name="sharinginfoupdate" method="post" action="/webqtl/main.py?FormID=sharinginfoupdate" onsubmit="return CheckGNAccesionId();">
-<input type="hidden" name="Id" value="%s">
-
-  <tr><TH COLSPAN=2><h2 class="title">Principal Investigator</h2></TH></tr>
-   <tr><td align="right" width="100"><b>Contact Name:</b></td><td width="200"><input type='text' name='Contact_Name' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Emails:</b></td><td><input type='text' name='Emails' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Phone:</b></td><td><input type='text' name='Phone' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>URL:</b></td><td><input type='text' name='URL' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Organization Name:</b></td><td><input type='text' name='Organization_Name' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Department:</b></td><td><input type='text' name='Department' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Laboratory:</b></td><td><input type='text' name='Laboratory' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Address:</b></td><td><input type='text' name='Street' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>City:</b></td><td><input type='text' name='City' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>State:</b></td><td><input type='text' name='State' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>ZIP:</b></td><td><input type='text' name='ZIP' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Country:</b></td><td><input type='text' name='Country' size='90' value='%s'></td></tr>
-   
-  <tr><TH COLSPAN=2><h2 class="title">Summary</h2></TH></tr>
-  <tr><td align="right"><b>Summary: </b></td><td><TEXTAREA NAME="Summary" cols="77" rows="15">%s</textarea></td></tr>
-   
-  <tr><TH COLSPAN=2><h2 class="title">Biology</h2></TH></tr>
-  <tr><td align="right"><b>Experiment Design:</b></td><td><TEXTAREA NAME="Experiment_Type" cols="77" rows="15">%s</textarea></td></tr>
-  <tr><td align="right"><b>About the cases used to<br>generate this set of data:</b></td><td><TEXTAREA NAME="About_Cases" cols="77" rows="15">%s</textarea></td></tr>
-  <tr><td align="right"><b>About the tissue used to<br>generate this set of data:</b></td><td><TEXTAREA NAME="About_Tissue" cols="77" rows="15">%s</textarea></td></tr>
-  
-  <tr><TH COLSPAN=2><h2 class="title">Technique</h2></TH></tr>
-  <tr><td align="right"><b>About downloading this data set:</b></td><td><TEXTAREA NAME="About_Download" cols="77" rows="15">%s</textarea></td></tr>
-  <tr><td align="right"><b>About the array platform:</b></td><td><TEXTAREA NAME="About_Array_Platform" cols="77" rows="15">%s</textarea></td></tr>
-  
-  <tr><TH COLSPAN=2><h2 class="title">Bioinformatics</h2></TH></tr>
-  <tr><td align="right"><b>About data values and<br>data processing:</b></td><td><TEXTAREA NAME="About_Data_Values_Processing" cols="77" rows="15">%s</textarea></td></tr>
-  <tr><td align="right"><b>Overall Design:</b></td><td><TEXTAREA NAME="Overall_Design" cols="77" rows="15">%s</textarea></td></tr>
-  
-  <tr><TH COLSPAN=2><h2 class="title">Misc</h2></TH></tr>
-  <tr><td align="right"><b>Contributor:</b></td><td><TEXTAREA NAME="Contributor" cols="77" rows="15">%s</textarea></td></tr>
-  <tr><td align="right"><b>Citation:</b></td><td><TEXTAREA NAME="Citation" cols="77" rows="5">%s</textarea></td></tr>
-  <tr><td align="right"><b>Data source acknowledgment:</b></td><td><TEXTAREA NAME="Data_Source_Acknowledge" cols="77" rows="15">%s</textarea></td></tr>
-
-  <tr><TH COLSPAN=2><h2 class="title">Administrator ONLY</h2></TH></tr>
-  <tr><td align="right"><b>GN Accesion Id:</b></td><td><input type='text' name='GN_AccesionId' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>DB Title in GN:</b></td><td><input type='text' name='InfoPageTitle' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>GEO Series:</b></td><td><input type='text' name='GEO_Series' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Status:</b></td><td><input type='text' name='Status' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Title:</b></td><td><input type='text' name='Title' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Organism_Id (Taxonomy ID):</b></td><td><input type='text' name='Organism_Id' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Organism:</b></td><td><input type='text' name='Organism' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Submission Date:</b></td><td><input type='text' name='Submission_Date' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Platforms:</b></td><td><input type='text' name='Platforms' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Species:</b></td><td><input type='text' name='Species' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Tissue:</b></td><td><input type='text' name='Tissue' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Normalization:</b></td><td><input type='text' name='Normalization' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Inbred Set:</b></td><td><input type='text' name='InbredSet' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Info Page Name:</b></td><td><input type='text' name='InfoPageName' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Samples:</b></td><td><input type='text' name='Samples' size='90' value='%s'></td></tr>
-   <tr><td align="right"><b>Authorized Users:</b></td><td><input type='text' name='AuthorizedUsers' size='90' value='%s'></td></tr>  
-   <tr><td align="right"><b>Progress:</b></td><td><input type='text' name='Progress' size='90' value='%s'></td></tr>
-
-  <tr><td> <colspan='2' align="center"><input type="Submit" class="button" style="font-size:12px" value="  Submit  "></td></tr>
-
-</form>
-</table>
-</td>"""
diff --git a/web/webqtl/dataSharing/SharingInfo.py b/web/webqtl/dataSharing/SharingInfo.py
deleted file mode 100755
index 10abcefa..00000000
--- a/web/webqtl/dataSharing/SharingInfo.py
+++ /dev/null
@@ -1,98 +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 httplib
-
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-
-
-#########################################
-#      Sharing Info
-#########################################
-class SharingInfo:
-
-		def __init__(self, GN_AccessionId, InfoPageName):
-				self.GN_AccessionId = GN_AccessionId
-				self.InfoPageName = InfoPageName
-
-		def getInfo(self):
-				cursor = webqtlDatabaseFunction.getCursor()
-				if (not cursor):
-						return
-				sql = "select Id, GEO_Series, Status, Title, Organism, Experiment_Type, Summary, Overall_Design, Contributor, Citation, Submission_Date, Contact_Name, Emails, Phone, URL, Organization_Name, Department, Laboratory, Street, City, State, ZIP, Country, Platforms, Samples, Species, Normalization, InbredSet, InfoPageName, DB_Name, Organism_Id, InfoPageTitle, GN_AccesionId, Tissue, AuthorizedUsers, About_Cases, About_Tissue, About_Download, About_Array_Platform, About_Data_Values_Processing, Data_Source_Acknowledge, Progreso from InfoFiles where "
-				if(self.GN_AccessionId):
-						sql += "GN_AccesionId = %s"
-						cursor.execute(sql, self.GN_AccessionId)
-				elif (self.InfoPageName):
-						sql += "InfoPageName = %s"
-						cursor.execute(sql, self.InfoPageName)
-				else:
-						raise 'No correct parameter found'
-				info = cursor.fetchone()
-				# fetch datasets file list
-				try:
-					conn = httplib.HTTPConnection("atlas.uthsc.edu")
-					conn.request("GET", "/scandatasets.php?GN_AccesionId=%s" % (info[32]))
-					response = conn.getresponse()
-					data = response.read()
-					filelist = data.split()
-					conn.close()
-				except Exception:
-					filelist = []
-				return info, filelist
-				
-		def getBody(self, infoupdate=""):
-				info, filelist = self.getInfo()
-				if filelist:
-					htmlfilelist = '<ul style="line-height:160%;">\n'
-					for i in range(len(filelist)):
-							if i%2==0:
-									filename = filelist[i]
-									filesize = filelist[i+1]
-									htmlfilelist += "<li>"
-									htmlfilelist += '<a href="ftp://atlas.uthsc.edu/users/shared/Genenetwork/GN%s/%s">%s</a>' % (self.GN_AccessionId, filename, filename)
-									htmlfilelist += '&nbsp;&nbsp;&nbsp;'
-									#r=re.compile(r'(?<=\d)(?=(\d\d\d)+(?!\d))')
-									#htmlfilelist += '[%s&nbsp;B]' % r.sub(r',',filesize)
-									if 12<len(filesize):
-										filesize=filesize[0:-12]
-										filesize += ' T'
-									elif 9<len(filesize):
-										filesize=filesize[0:-9]
-										filesize += ' G'
-									elif 6<len(filesize):
-										filesize=filesize[0:-6]
-										filesize += ' M'
-									elif 3<len(filesize):
-										filesize=filesize[0:-3]
-										filesize += ' K'
-									htmlfilelist += '[%sB]' % filesize
-									htmlfilelist += "</li>\n"
-					htmlfilelist += "</ul>"
-				else:
-					htmlfilelist = "Data sets are not available or are not public yet."
-				return SharingBody.sharinginfo_body_string % (info[31], info[32], infoupdate, info[32], info[1], info[3], info[30], info[4], info[27], info[33], info[2], info[23], info[26], info[11], info[15], info[16], info[18], info[19], info[20], info[21], info[22], info[13], info[12], info[14], info[14], htmlfilelist, info[6], info[35], info[36], info[37], info[38], info[39], info[40], info[5], info[7], info[8], info[9], info[10], info[17], info[24])
diff --git a/web/webqtl/dataSharing/SharingInfoAddPage.py b/web/webqtl/dataSharing/SharingInfoAddPage.py
deleted file mode 100755
index 8174bf68..00000000
--- a/web/webqtl/dataSharing/SharingInfoAddPage.py
+++ /dev/null
@@ -1,47 +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
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-import SharingBody
-import SharingInfo
-
-
-#########################################
-#      Sharing Info Edit Page
-#########################################
-class SharingInfoAddPage(templatePage):
-
-		def __init__(self, fd=None):
-				templatePage.__init__(self, fd)
-				if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
-						pass
-				else:
-						heading = "Adding Info"
-						detail = ["You don't have the permission to add new dataset"]
-						self.error(heading=heading,detail=detail,error="Error")
-						return
-				self.dict['body'] = SharingBody.sharinginfoedit_body_string % ("Add new dataset", "-1", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "")
diff --git a/web/webqtl/dataSharing/SharingInfoDeletePage.py b/web/webqtl/dataSharing/SharingInfoDeletePage.py
deleted file mode 100755
index edc0be7d..00000000
--- a/web/webqtl/dataSharing/SharingInfoDeletePage.py
+++ /dev/null
@@ -1,55 +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
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-import SharingInfo
-
-
-#########################################
-#      Sharing Info Delete Page
-#########################################
-class SharingInfoDeletePage(templatePage):
-
-		def __init__(self, fd=None):
-				templatePage.__init__(self, fd)
-				if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
-						pass
-				else:
-						heading = "Deleting Info"
-						detail = ["You don't have the permission to delete this dataset"]
-						self.error(heading=heading,detail=detail,error="Error")
-						return
-				cursor = webqtlDatabaseFunction.getCursor()
-				if (not cursor):
-						return
-				GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
-				sql = "delete from InfoFiles where GN_AccesionId=%s"
-				cursor.execute(sql, GN_AccessionId)
-				re = cursor.fetchone()
-				self.dict['body'] = "Delete dataset info record (GN_AccesionId=%s) successfully." % GN_AccessionId
\ No newline at end of file
diff --git a/web/webqtl/dataSharing/SharingInfoEditPage.py b/web/webqtl/dataSharing/SharingInfoEditPage.py
deleted file mode 100755
index 266b8602..00000000
--- a/web/webqtl/dataSharing/SharingInfoEditPage.py
+++ /dev/null
@@ -1,51 +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
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-import SharingBody
-import SharingInfo
-
-
-#########################################
-#      Sharing Info Edit Page
-#########################################
-class SharingInfoEditPage(templatePage):
-
-		def __init__(self, fd=None):
-				templatePage.__init__(self, fd)
-				if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
-						pass
-				else:
-						heading = "Editing Info"
-						detail = ["You don't have the permission to edit this dataset"]
-						self.error(heading=heading,detail=detail,error="Error")
-						return
-				GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
-				InfoPageName = fd.formdata.getvalue('InfoPageName')
-				sharingInfoObject = SharingInfo.SharingInfo(GN_AccessionId, InfoPageName)
-				info, filelist = sharingInfoObject.getInfo()
-				self.dict['body'] = SharingBody.sharinginfoedit_body_string % (info[31], info[0], info[11], info[12], info[13], info[14], info[15], info[16], info[17], info[18], info[19], info[20], info[21], info[22], info[6], info[5], info[35], info[36], info[37], info[38], info[39], info[7], info[8], info[9], info[40], info[32], info[31], info[1], info[2], info[3], info[30], info[4], info[10], info[23], info[25], info[33], info[26], info[27], info[28], info[24], info[34], info[41])
diff --git a/web/webqtl/dataSharing/SharingInfoPage.py b/web/webqtl/dataSharing/SharingInfoPage.py
deleted file mode 100755
index 230ba2f3..00000000
--- a/web/webqtl/dataSharing/SharingInfoPage.py
+++ /dev/null
@@ -1,52 +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
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-import SharingInfo
-
-
-#########################################
-#      Sharing Info Page
-#########################################
-class SharingInfoPage(templatePage):
-
-		def __init__(self, fd=None):
-				templatePage.__init__(self, fd)
-				GN_AccessionId = fd.formdata.getvalue('GN_AccessionId')
-				InfoPageName = fd.formdata.getvalue('InfoPageName')
-				cursor = webqtlDatabaseFunction.getCursor()
-				if InfoPageName and not GN_AccessionId:
-					sql = "select GN_AccesionId from InfoFiles where InfoPageName = %s"
-					cursor.execute(sql, InfoPageName)
-					GN_AccessionId = cursor.fetchone()
-					url = webqtlConfig.CGIDIR + "main.py?FormID=sharinginfo&GN_AccessionId=%s" % GN_AccessionId
-					self.redirection = url
-				else:
-					sharingInfoObject = SharingInfo.SharingInfo(GN_AccessionId, InfoPageName)
-					self.dict['body'] = sharingInfoObject.getBody(infoupdate="")
diff --git a/web/webqtl/dataSharing/SharingInfoUpdatePage.py b/web/webqtl/dataSharing/SharingInfoUpdatePage.py
deleted file mode 100755
index a70238b9..00000000
--- a/web/webqtl/dataSharing/SharingInfoUpdatePage.py
+++ /dev/null
@@ -1,109 +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 MySQLdb
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-import SharingInfo
-
-#########################################
-#      Sharing Info Update Page
-#########################################
-class SharingInfoUpdatePage(templatePage):
-
-		def __init__(self, fd=None):
-				templatePage.__init__(self, fd)
-				if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
-						pass
-				else:
-						heading = "Editing Info"
-						detail = ["You don't have the permission to modify this file"]
-						self.error(heading=heading,detail=detail,error="Error")
-						return
-				cursor = webqtlDatabaseFunction.getCursor()
-				if (not cursor):
-						return
-				Id=fd.formdata.getvalue('Id')
-				GN_AccesionId=fd.formdata.getvalue('GN_AccesionId')
-				GEO_Series=fd.formdata.getvalue('GEO_Series')
-				Status=fd.formdata.getvalue('Status')
-				Title=fd.formdata.getvalue('Title')
-				Organism_Id=fd.formdata.getvalue('Organism_Id')
-				Organism=fd.formdata.getvalue('Organism')
-				Experiment_Type =fd.formdata.getvalue('Experiment_Type') 
-				Summary=fd.formdata.getvalue('Summary')
-				Overall_Design=fd.formdata.getvalue('Overall_Design')
-				Contributor=fd.formdata.getvalue('Contributor')
-				Citation=fd.formdata.getvalue('Citation')
-				Submission_Date=fd.formdata.getvalue('Submission_Date')
-				Contact_Name=fd.formdata.getvalue('Contact_Name')
-				Emails=fd.formdata.getvalue('Emails')
-				Phone=fd.formdata.getvalue('Phone')
-				URL=fd.formdata.getvalue('URL')
-				Organization_Name=fd.formdata.getvalue('Organization_Name')
-				Department=fd.formdata.getvalue('Department')
-				Laboratory=fd.formdata.getvalue('Laboratory')
-				Street=fd.formdata.getvalue('Street')
-				City=fd.formdata.getvalue('City')
-				State=fd.formdata.getvalue('State')
-				ZIP=fd.formdata.getvalue('ZIP')
-				Country=fd.formdata.getvalue('Country')
-				Platforms=fd.formdata.getvalue('Platforms')
-				Samples=fd.formdata.getvalue('Samples')
-				Species=fd.formdata.getvalue('Species')
-				Tissue=fd.formdata.getvalue('Tissue')
-				Normalization=fd.formdata.getvalue('Normalization')
-				InbredSet=fd.formdata.getvalue('InbredSet')
-				InfoPageName=fd.formdata.getvalue('InfoPageName')
-				InfoPageTitle=fd.formdata.getvalue('InfoPageTitle')
-				About_Cases=fd.formdata.getvalue('About_Cases')
-				About_Tissue=fd.formdata.getvalue('About_Tissue')
-				About_Download=fd.formdata.getvalue('About_Download')
-				About_Array_Platform=fd.formdata.getvalue('About_Array_Platform')
-				About_Data_Values_Processing=fd.formdata.getvalue('About_Data_Values_Processing')
-				Data_Source_Acknowledge=fd.formdata.getvalue('Data_Source_Acknowledge')
-				AuthorizedUsers=fd.formdata.getvalue('AuthorizedUsers')
-				Progress=fd.formdata.getvalue('Progress')
-				if Id=='-1':
-						sharingInfoObject = SharingInfo.SharingInfo(GN_AccesionId, InfoPageName)
-						info, filelist = sharingInfoObject.getInfo()
-						if info:
-								heading = "Editing Info"
-								detail = ["The new dataset info record is duplicate."]
-								self.error(heading=heading, detail=detail, error="Error")
-								return
-						sql = """INSERT INTO InfoFiles SET GN_AccesionId=%s, GEO_Series=%s, Status=%s, Title=%s, Organism_Id=%s, Organism=%s, Experiment_Type=%s, Summary=%s, Overall_Design=%s, Contributor=%s, Citation=%s, Submission_Date=%s, Contact_Name=%s, Emails=%s, Phone=%s, URL=%s, Organization_Name=%s, Department=%s, Laboratory=%s, Street=%s, City=%s, State=%s, ZIP=%s, Country=%s, Platforms=%s, Samples=%s, Species=%s, Tissue=%s, Normalization=%s, InbredSet=%s, InfoPageName=%s, InfoPageTitle=%s, About_Cases=%s, About_Tissue=%s, About_Download=%s, About_Array_Platform=%s, About_Data_Values_Processing=%s, Data_Source_Acknowledge=%s, AuthorizedUsers=%s, Progreso=%s"""
-						cursor.execute(sql, tuple([GN_AccesionId, GEO_Series, Status, Title, Organism_Id, Organism, Experiment_Type, Summary, Overall_Design, Contributor, Citation, Submission_Date, Contact_Name, Emails, Phone, URL, Organization_Name, Department, Laboratory, Street, City, State, ZIP, Country, Platforms, Samples, Species, Tissue, Normalization, InbredSet, InfoPageName, InfoPageTitle, About_Cases, About_Tissue, About_Download, About_Array_Platform, About_Data_Values_Processing, Data_Source_Acknowledge, AuthorizedUsers, Progress]))
-						infoupdate="This record has been succesfully added."
-				else:
-						sql = """UPDATE InfoFiles SET GN_AccesionId=%s, GEO_Series=%s, Status=%s, Title=%s, Organism_Id=%s, Organism=%s, Experiment_Type=%s, Summary=%s, Overall_Design=%s, Contributor=%s, Citation=%s, Submission_Date=%s, Contact_Name=%s, Emails=%s, Phone=%s, URL=%s, Organization_Name=%s, Department=%s, Laboratory=%s, Street=%s, City=%s, State=%s, ZIP=%s, Country=%s, Platforms=%s, Samples=%s, Species=%s, Tissue=%s, Normalization=%s, InbredSet=%s, InfoPageName=%s, InfoPageTitle=%s, About_Cases=%s, About_Tissue=%s, About_Download=%s, About_Array_Platform=%s, About_Data_Values_Processing=%s, Data_Source_Acknowledge=%s, AuthorizedUsers=%s, Progreso=%s WHERE Id=%s"""
-						cursor.execute(sql, tuple([GN_AccesionId, GEO_Series, Status, Title, Organism_Id, Organism, Experiment_Type, Summary, Overall_Design, Contributor, Citation, Submission_Date, Contact_Name, Emails, Phone, URL, Organization_Name, Department, Laboratory, Street, City, State, ZIP, Country, Platforms, Samples, Species, Tissue, Normalization, InbredSet, InfoPageName, InfoPageTitle, About_Cases, About_Tissue, About_Download, About_Array_Platform, About_Data_Values_Processing, Data_Source_Acknowledge, AuthorizedUsers, Progress, Id]))
-						infoupdate="This record has been succesfully updated."
-				sharingInfoObject = SharingInfo.SharingInfo(GN_AccesionId, InfoPageName)
-				self.dict['body'] = sharingInfoObject.getBody(infoupdate=infoupdate)
\ No newline at end of file
diff --git a/web/webqtl/dataSharing/SharingListDataSetPage.py b/web/webqtl/dataSharing/SharingListDataSetPage.py
deleted file mode 100755
index ec90f5f3..00000000
--- a/web/webqtl/dataSharing/SharingListDataSetPage.py
+++ /dev/null
@@ -1,99 +0,0 @@
-#
-# 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
-
-from htmlgen import HTMLgen2 as HT
-from base import webqtlConfig
-
-from base.templatePage import templatePage
-
-
-#########################################
-#      Sharing List DataSet Page
-#########################################
-class SharingListDataSetPage(templatePage):
-
-    def __init__(self, fd=None):
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-
-        if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['admin']:
-            pass
-        else:
-            heading = "Editing Info"
-            detail = ["You don't have the permission to list the datasets"]
-            self.error(heading=heading,detail=detail,error="Error")
-            return
-
-
-        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
-
-        query = """select GN_AccesionId, InfoPageTitle, Progreso from InfoFiles order by GN_AccesionId"""
-        self.cursor.execute(query)
-        result = self.cursor.fetchall()
-
-        heading = HT.Paragraph('Dataset Table', Class="title")
-		
-        newrecord = HT.Href(text="New Record", url="/webqtl/main.py?FormID=sharinginfoadd")
-
-        info = "Click the accession id to view the dataset info. Click the dataset name to edit the dataset info."
-        
-        datasetTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0, Class="collap", width="100%")
-
-        tableHeaderRow = HT.TR()
-        tableHeaderRow.append(HT.TD("Accession Id", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
-        tableHeaderRow.append(HT.TD("Dataset name", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
-        tableHeaderRow.append(HT.TD("Progress", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
-        tableHeaderRow.append(HT.TD("Operation", Class='fs14 fwb ffl b1 cw cbrb', align="center"))
-        datasetTable.append(tableHeaderRow)
-
-        for one_row in result:
-            Accession_Id, InfoPage_title, Progress = one_row
-            datasetRow = HT.TR()
-            datasetRow.append(HT.TD(HT.Href(text="GN%s" % Accession_Id, url="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s" % Accession_Id, Class='fs12 fwn'), Class="fs12 fwn b1 c222"))
-            datasetRow.append(HT.TD(HT.Href(text="%s" % InfoPage_title, url="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s" % Accession_Id, Class='fs12 fwn'), Class="fs12 fwn b1 c222"))
-            datasetRow.append(HT.TD("%s" % Progress, Class='fs12 fwn ffl b1 c222'))
-            operation_edit = HT.Href(text="Edit", url="/webqtl/main.py?FormID=sharinginfoedit&GN_AccessionId=%s" % Accession_Id)
-            operation_delete = HT.Href(text="Delete", onClick="deleteRecord(%s); return false;" % Accession_Id)
-            operation = HT.TD(Class="fs12 fwn b1 c222", align="center")
-            operation.append(operation_edit)
-            operation.append("&nbsp;&nbsp;&nbsp;&nbsp;")
-            operation.append(operation_delete)
-            datasetRow.append(operation)
-            datasetTable.append(datasetRow)
-
-        TD_LR.append(heading, HT.P(), newrecord, HT.P(), info, HT.P(), datasetTable)
-		
-        js1 = """	<script language="javascript" type="text/javascript">
-					function deleteRecord(id){
-						question = confirm("Are you sure you want to delete the dataset info record (Accession Id="+id+")?")
-						if (question != "0"){
-							window.open("/webqtl/main.py?FormID=sharinginfodelete&GN_AccessionId="+id, "_self");
-						}
-					}
-					</script>"""
-        self.dict['js1'] = js1
-        self.dict['body'] =  str(TD_LR)
\ No newline at end of file
diff --git a/web/webqtl/dataSharing/SharingPage.py b/web/webqtl/dataSharing/SharingPage.py
deleted file mode 100755
index cf1d9ac3..00000000
--- a/web/webqtl/dataSharing/SharingPage.py
+++ /dev/null
@@ -1,40 +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
-
-from base.templatePage import templatePage
-import SharingBody
-
-#########################################
-#      SharingPage
-#########################################
-
-class SharingPage(templatePage):
-
-		def __init__(self, fd):
-				templatePage.__init__(self, fd)
-				self.dict['title'] = 'GeneNetwork Data Sharing Zone'
-				self.dict['body'] = SharingBody.sharing_body_string
-				self.dict['js2'] = 'onload="javascript:initialDatasetSelection();"'
\ No newline at end of file
diff --git a/web/webqtl/dataSharing/__init__.py b/web/webqtl/dataSharing/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/dataSharing/__init__.py
+++ /dev/null