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

1 files changed, 0 insertions, 290 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>"""