Added dataSharing to flask directory

10 files changed, 841 insertions, 0 deletions

diff --git a/wqflask/dataSharing/SharingBody.py b/wqflask/dataSharing/SharingBody.py
new file mode 100755
index 00000000..4445e0d1
--- /dev/null
+++ b/wqflask/dataSharing/SharingBody.py
@@ -0,0 +1,290 @@
+# 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
new file mode 100755
index 00000000..10abcefa
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfo.py
@@ -0,0 +1,98 @@
+# 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
new file mode 100755
index 00000000..8174bf68
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfoAddPage.py
@@ -0,0 +1,47 @@
+# 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
new file mode 100755
index 00000000..edc0be7d
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfoDeletePage.py
@@ -0,0 +1,55 @@
+# 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
new file mode 100755
index 00000000..266b8602
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfoEditPage.py
@@ -0,0 +1,51 @@
+# 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
new file mode 100755
index 00000000..230ba2f3
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfoPage.py
@@ -0,0 +1,52 @@
+# 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
new file mode 100755
index 00000000..a70238b9
--- /dev/null
+++ b/wqflask/dataSharing/SharingInfoUpdatePage.py
@@ -0,0 +1,109 @@
+# 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
new file mode 100755
index 00000000..ec90f5f3
--- /dev/null
+++ b/wqflask/dataSharing/SharingListDataSetPage.py
@@ -0,0 +1,99 @@
+#
+# 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
new file mode 100755
index 00000000..cf1d9ac3
--- /dev/null
+++ b/wqflask/dataSharing/SharingPage.py
@@ -0,0 +1,40 @@
+# 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
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/dataSharing/__init__.py