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-rwxr-xr-xwqflask/dataSharing/SharingBody.py290
-rwxr-xr-xwqflask/dataSharing/SharingInfo.py98
-rwxr-xr-xwqflask/dataSharing/SharingInfoAddPage.py47
-rwxr-xr-xwqflask/dataSharing/SharingInfoDeletePage.py55
-rwxr-xr-xwqflask/dataSharing/SharingInfoEditPage.py51
-rwxr-xr-xwqflask/dataSharing/SharingInfoPage.py52
-rwxr-xr-xwqflask/dataSharing/SharingInfoUpdatePage.py109
-rwxr-xr-xwqflask/dataSharing/SharingListDataSetPage.py99
-rwxr-xr-xwqflask/dataSharing/SharingPage.py40
-rwxr-xr-xwqflask/dataSharing/__init__.py0
10 files changed, 0 insertions, 841 deletions
diff --git a/wqflask/dataSharing/SharingBody.py b/wqflask/dataSharing/SharingBody.py
deleted file mode 100755
index 4445e0d1..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfo.py b/wqflask/dataSharing/SharingInfo.py
deleted file mode 100755
index 10abcefa..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoAddPage.py b/wqflask/dataSharing/SharingInfoAddPage.py
deleted file mode 100755
index 8174bf68..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoDeletePage.py b/wqflask/dataSharing/SharingInfoDeletePage.py
deleted file mode 100755
index edc0be7d..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoEditPage.py b/wqflask/dataSharing/SharingInfoEditPage.py
deleted file mode 100755
index 266b8602..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoPage.py b/wqflask/dataSharing/SharingInfoPage.py
deleted file mode 100755
index 230ba2f3..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoUpdatePage.py b/wqflask/dataSharing/SharingInfoUpdatePage.py
deleted file mode 100755
index a70238b9..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingListDataSetPage.py b/wqflask/dataSharing/SharingListDataSetPage.py
deleted file mode 100755
index ec90f5f3..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingPage.py b/wqflask/dataSharing/SharingPage.py
deleted file mode 100755
index cf1d9ac3..00000000
--- a/wqflask/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/wqflask/dataSharing/__init__.py b/wqflask/dataSharing/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/wqflask/dataSharing/__init__.py
+++ /dev/null