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-rw-r--r--.gitignore2
-rw-r--r--web/images/edit.pngbin0 -> 4322 bytes
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingBody.py290
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfo.py146
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoAddPage.py47
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoDeletePage.py55
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoEditPage.py51
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoPage.py64
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfoUpdatePage.py109
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingListDataSetPage.py99
-rwxr-xr-xwqflask/wqflask/dataSharing/SharingPage.py40
-rwxr-xr-xwqflask/wqflask/dataSharing/__init__.py0
-rwxr-xr-xwqflask/wqflask/docs.py1
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/my_pylmm/README.md21
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/__init__.py1
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gwas.py173
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/input.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/kinship.py22
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py142
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm2.py410
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/phenotype.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py75
-rwxr-xr-xwqflask/wqflask/news.py16
-rwxr-xr-xwqflask/wqflask/templates/docedit.html (renamed from wqflask/wqflask/templates/testhtmleditor.html)8
-rwxr-xr-xwqflask/wqflask/templates/docs.html5
-rwxr-xr-xwqflask/wqflask/templates/index_page.html1
-rwxr-xr-xwqflask/wqflask/templates/news.html21
-rwxr-xr-xwqflask/wqflask/views.py50
-rwxr-xr-xwqflask/wqflask/yaml_data/whats_new.yaml26
30 files changed, 864 insertions, 1017 deletions
diff --git a/.gitignore b/.gitignore
index 1111cbc7..1108f228 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,5 @@
web/new_genotypes/HSNIH.json
*.cross
*webqtlConfig.py
+wqflask/secure_server.py
+
diff --git a/web/images/edit.png b/web/images/edit.png
new file mode 100644
index 00000000..dda50521
--- /dev/null
+++ b/web/images/edit.png
Binary files differ
diff --git a/wqflask/wqflask/dataSharing/SharingBody.py b/wqflask/wqflask/dataSharing/SharingBody.py
deleted file mode 100755
index 880161f5..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfo.py b/wqflask/wqflask/dataSharing/SharingInfo.py
deleted file mode 100755
index 41a75222..00000000
--- a/wqflask/wqflask/dataSharing/SharingInfo.py
+++ /dev/null
@@ -1,146 +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 __future__ import print_function, division
-
-from pprint import pformat as pf
-from collections import namedtuple
-
-import requests
-
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-
-#import logging
-#logging.basicConfig(filename="/tmp/flask_gn_log", level=logging.INFO)
-#
-#_log = logging.getLogger("search")
-#_ch = logging.StreamHandler()
-#_log.addHandler(_ch)
-
-
-
-#########################################
-# Sharing Info
-#########################################
-class SharingInfo(object):
-
- def __init__(self, GN_AccessionId, InfoPageName):
- print("In SharingInfo")
- self.GN_AccessionId = GN_AccessionId
- self.InfoPageName = InfoPageName
-
- def getInfo(self):
- cursor = webqtlDatabaseFunction.getCursor()
- if (not cursor):
- return
-
- field_names = """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 """
-
- # We can use string interpolation here cause we own the string
- sql = """select %s from InfoFiles where """ % (field_names)
- 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 Exception('No correct parameter found')
- info = cursor.fetchone()
-
- info = todict(field_names, info)
-
- # fetch datasets file list
- filelist = []
- if info["GN_AccesionId"]:
- url = "http://atlas.uthsc.edu/scandatasets.php?GN_AccesionId=%s" % (
- info["GN_AccesionId"])
- try:
- response = requests.get(url)
- except Exception as why:
- log.exception("Problem conneting to:", url)
- if response:
- data = response.text
- filelist = data.split()
-
- 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 info, htmlfilelist
- #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])
-
-
-def todict(fields, values):
- """Converts sql results into a user friendly dictionary"""
- new_dict = {}
- fields = fields.split(",")
- for counter, field in enumerate(fields):
- field = field.strip()
- value = values[counter]
- if isinstance(value, str):
- value = unicode(value, "utf-8")
- new_dict[field] = value
- return new_dict
diff --git a/wqflask/wqflask/dataSharing/SharingInfoAddPage.py b/wqflask/wqflask/dataSharing/SharingInfoAddPage.py
deleted file mode 100755
index 452fb474..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoDeletePage.py b/wqflask/wqflask/dataSharing/SharingInfoDeletePage.py
deleted file mode 100755
index a9c785c6..00000000
--- a/wqflask/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
diff --git a/wqflask/wqflask/dataSharing/SharingInfoEditPage.py b/wqflask/wqflask/dataSharing/SharingInfoEditPage.py
deleted file mode 100755
index c5f4ed22..00000000
--- a/wqflask/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/wqflask/dataSharing/SharingInfoPage.py b/wqflask/wqflask/dataSharing/SharingInfoPage.py
deleted file mode 100755
index c32eec50..00000000
--- a/wqflask/wqflask/dataSharing/SharingInfoPage.py
+++ /dev/null
@@ -1,64 +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 __future__ import print_function, division
-
-from pprint import pformat as pf
-
-import urlparse
-
-import flask
-
-from base import webqtlConfig
-from dbFunction import webqtlDatabaseFunction
-import SharingBody
-import SharingInfo
-
-
-#########################################
-# Sharing Info Page
-#########################################
-class SharingInfoPage():
-
- def __init__(self, fd):
- self.redirect_url = None # Set if you want a redirect
- print("fd is:", pf(fd.__dict__))
- # Todo: Need a [0] in line below????d
- GN_AccessionId = fd.get('GN_AccessionId') # Used under search datasharing
- InfoPageName = fd.get('database') # Might need to add a [0]
- 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()
- self.redirect_url = urlparse.urljoin(webqtlConfig.ROOT_URL, "/data_sharing?GN_AccessionId=%s" % GN_AccessionId)
- #self.redirect_url = flask.url_for('data_sharing', GN_AccessionId=GN_AccessionId[0])
- print("set self.redirect_url")
- #print("before redirect")
- #return flask.redirect(url)
- #print("after redirect")
- else:
- CauseError
diff --git a/wqflask/wqflask/dataSharing/SharingInfoUpdatePage.py b/wqflask/wqflask/dataSharing/SharingInfoUpdatePage.py
deleted file mode 100755
index 181f2eed..00000000
--- a/wqflask/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)
diff --git a/wqflask/wqflask/dataSharing/SharingListDataSetPage.py b/wqflask/wqflask/dataSharing/SharingListDataSetPage.py
deleted file mode 100755
index 8685ac65..00000000
--- a/wqflask/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)
diff --git a/wqflask/wqflask/dataSharing/SharingPage.py b/wqflask/wqflask/dataSharing/SharingPage.py
deleted file mode 100755
index b244a6bd..00000000
--- a/wqflask/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();"'
diff --git a/wqflask/wqflask/dataSharing/__init__.py b/wqflask/wqflask/dataSharing/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/wqflask/wqflask/dataSharing/__init__.py
+++ /dev/null
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 65255987..07b0b81a 100755
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,5 +11,6 @@ class Docs(object):
WHERE Docs.entry LIKE '%s'
"""
result = g.db.execute(sql % (entry)).fetchone()
+ self.entry = entry
self.title = result[0]
self.content = result[1]
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 3fb9915b..7708356b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -701,7 +701,7 @@ class MarkerRegression(object):
no_val_samples = self.identify_empty_samples()
trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
- genotype_matrix = np.array(trimmed_genotype_data).T
+ genotype_matrix = np.array(genotype_data).T
#print("pheno_vector: ", pf(pheno_vector))
#print("genotype_matrix: ", pf(genotype_matrix))
diff --git a/wqflask/wqflask/my_pylmm/README.md b/wqflask/wqflask/my_pylmm/README.md
new file mode 100644
index 00000000..f6b0e72d
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/README.md
@@ -0,0 +1,21 @@
+# RELEASE NOTES
+
+## 0.50-gn2-pre1 release
+
+This is the first test release of multi-core pylmm into GN2. Both
+kinship calculation and GWAS have been made multi-threaded by
+introducing the Python multiprocessing module. Note that only
+run_other has been updated to use the new routines (so human is still
+handled the old way). I have taken care that we can still run both
+old-style and new-style LMM (through passing the 'new_code'
+boolean). This could be an option in the web server for users to
+select and test for any unexpected differences (of which there should
+be none, naturally ;).
+
+The current version can handle missing phenotypes, but as they are
+removed there is no way for GN2 to know what SNPs the P-values belong
+to. A future version will pass a SNP index to allow for missing
+phenotypes.
+
+
+ \ No newline at end of file
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/__init__.py b/wqflask/wqflask/my_pylmm/pyLMM/__init__.py
index e69de29b..c40c3221 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/__init__.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/__init__.py
@@ -0,0 +1 @@
+PYLMM_VERSION="0.50-gn2-pre1"
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
new file mode 100644
index 00000000..b901c0e2
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
@@ -0,0 +1,173 @@
+# pylmm-based GWAS calculation
+#
+# Copyright (C) 2013 Nicholas A. Furlotte (nick.furlotte@gmail.com)
+# Copyright (C) 2015 Pjotr Prins (pjotr.prins@thebird.nl)
+#
+# 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.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#!/usr/bin/python
+
+import pdb
+import time
+import sys
+# from utility import temp_data
+import lmm2
+
+import os
+import numpy as np
+import input
+from optmatrix import matrix_initialize
+from lmm2 import LMM2
+
+import multiprocessing as mp # Multiprocessing is part of the Python stdlib
+import Queue
+
+def formatResult(id,beta,betaSD,ts,ps):
+ return "\t".join([str(x) for x in [id,beta,betaSD,ts,ps]]) + "\n"
+
+def compute_snp(j,n,snp_ids,lmm2,REML,q = None):
+ # print("COMPUTE SNP",j,snp_ids,"\n")
+ result = []
+ for snp_id in snp_ids:
+ snp,id = snp_id
+ x = snp.reshape((n,1)) # all the SNPs
+ # print "X=",x
+ # if refit:
+ # L.fit(X=snp,REML=REML)
+ ts,ps,beta,betaVar = lmm2.association(x,REML=REML,returnBeta=True)
+ # result.append(formatResult(id,beta,np.sqrt(betaVar).sum(),ts,ps))
+ result.append( (ts,ps) )
+ if not q:
+ q = compute_snp.q
+ q.put([j,result])
+ return j
+ # PS.append(ps)
+ # TS.append(ts)
+ # return len(result)
+ # compute.q.put(result)
+ # return None
+
+def f_init(q):
+ compute_snp.q = q
+
+def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
+ """
+ Execute a GWAS. The G matrix should be n inds (cols) x m snps (rows)
+ """
+ matrix_initialize()
+ cpu_num = mp.cpu_count()
+ numThreads = None # for now use all available threads
+ kfile2 = False
+ reml = restricted_max_likelihood
+
+ sys.stderr.write(str(G.shape)+"\n")
+ n = G.shape[1] # inds
+ inds = n
+ m = G.shape[0] # snps
+ snps = m
+ sys.stderr.write(str(m)+" SNPs\n")
+ # print "***** GWAS: G",G.shape,G
+ assert snps>inds, "snps should be larger than inds (snps=%d,inds=%d)" % (snps,inds)
+
+ # CREATE LMM object for association
+ # if not kfile2: L = LMM(Y,K,Kva,Kve,X0,verbose=verbose)
+ # else: L = LMM_withK2(Y,K,Kva,Kve,X0,verbose=verbose,K2=K2)
+
+ lmm2 = LMM2(Y,K) # ,Kva,Kve,X0,verbose=verbose)
+ if not refit:
+ if verbose: sys.stderr.write("Computing fit for null model\n")
+ lmm2.fit() # follow GN model in run_other
+ if verbose: sys.stderr.write("\t heritability=%0.3f, sigma=%0.3f\n" % (lmm2.optH,lmm2.optSigma))
+
+ # outFile = "test.out"
+ # out = open(outFile,'w')
+ out = sys.stderr
+
+ def outputResult(id,beta,betaSD,ts,ps):
+ out.write(formatResult(id,beta,betaSD,ts,ps))
+ def printOutHead(): out.write("\t".join(["SNP_ID","BETA","BETA_SD","F_STAT","P_VALUE"]) + "\n")
+
+ # printOutHead()
+ res = []
+
+ # Set up the pool
+ # mp.set_start_method('spawn')
+ q = mp.Queue()
+ p = mp.Pool(numThreads, f_init, [q])
+ collect = []
+
+ # Buffers for pvalues and t-stats
+ # PS = []
+ # TS = []
+ count = 0
+ job = 0
+ jobs_running = 0
+ for snp in G:
+ snp_id = (snp,'SNPID')
+ count += 1
+ if count % 1000 == 0:
+ job += 1
+ if verbose:
+ sys.stderr.write("Job %d At SNP %d\n" % (job,count))
+ if numThreads == 1:
+ print "Running on 1 THREAD"
+ compute_snp(job,n,collect,lmm2,reml,q)
+ collect = []
+ j,lst = q.get()
+ if verbose:
+ sys.stderr.write("Job "+str(j)+" finished\n")
+ res.append((j,lst))
+ else:
+ p.apply_async(compute_snp,(job,n,collect,lmm2,reml))
+ jobs_running += 1
+ collect = []
+ while jobs_running > cpu_num:
+ try:
+ j,lst = q.get_nowait()
+ if verbose:
+ sys.stderr.write("Job "+str(j)+" finished\n")
+ res.append((j,lst))
+ jobs_running -= 1
+ except Queue.Empty:
+ time.sleep(0.1)
+ pass
+ if jobs_running > cpu_num*2:
+ time.sleep(1.0)
+ else:
+ break
+
+ collect.append(snp_id)
+
+ if numThreads==1 or count<1000 or len(collect)>0:
+ job += 1
+ print "Collect final batch size %i job %i @%i: " % (len(collect), job, count)
+ compute_snp(job,n,collect,lmm2,reml,q)
+ collect = []
+ j,lst = q.get()
+ res.append((j,lst))
+ print "count=",count," running=",jobs_running," collect=",len(collect)
+ for job in range(jobs_running):
+ j,lst = q.get(True,15) # time out
+ if verbose:
+ sys.stderr.write("Job "+str(j)+" finished\n")
+ res.append((j,lst))
+
+ print "Before sort",[res1[0] for res1 in res]
+ res = sorted(res,key=lambda x: x[0])
+ # if verbose:
+ # print "res=",res[0][0:10]
+ print "After sort",[res1[0] for res1 in res]
+ print [len(res1[1]) for res1 in res]
+ ts = [item[0] for j,res1 in res for item in res1]
+ ps = [item[1] for j,res1 in res for item in res1]
+ return ts,ps
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/input.py b/wqflask/wqflask/my_pylmm/pyLMM/input.py
index f7b556a5..7063fedf 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/input.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/input.py
@@ -135,6 +135,8 @@ class plink:
def normalizeGenotype(self,G):
# print "Before",G
# print G.shape
+ print "call input.normalizeGenotype"
+ raise "This should not be used"
x = True - np.isnan(G)
m = G[x].mean()
s = np.sqrt(G[x].var())
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index 28f2042d..0c43587e 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -21,6 +21,7 @@
import sys
import os
import numpy as np
+from scipy import linalg
import multiprocessing as mp # Multiprocessing is part of the Python stdlib
import Queue
import time
@@ -85,12 +86,13 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
m = G.shape[0] # snps
snps = m
sys.stderr.write(str(m)+" SNPs\n")
- assert m>n, "n should be larger than m (snps>inds)"
+ assert snps>inds, "snps should be larger than inds (%i snps, %i inds)" % (snps,inds)
q = mp.Queue()
p = mp.Pool(numThreads, f_init, [q])
cpu_num = mp.cpu_count()
print "CPU cores:",cpu_num
+ print snps,computeSize
iterations = snps/computeSize+1
# if testing:
# iterations = 8
@@ -153,5 +155,23 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
# np.savetxt(outFile+".kve",Kve)
return K
+def kvakve(K, verbose=True):
+ """
+ Obtain eigendecomposition for K and return Kva,Kve where Kva is cleaned
+ of small values < 1e-6 (notably smaller than zero)
+ """
+ if verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
+
+ Kva,Kve = linalg.eigh(K)
+ if verbose:
+ print("Kva is: ", Kva.shape, Kva)
+ print("Kve is: ", Kve.shape, Kve)
+
+ if sum(Kva < 1e-6):
+ if verbose: sys.stderr.write("Cleaning %d eigen values (Kva<0)\n" % (sum(Kva < 0)))
+ Kva[Kva < 1e-6] = 1e-6
+ return Kva,Kve
+
+
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 937d3340..53689071 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -43,15 +43,18 @@ Redis = Redis()
import sys
sys.path.append("/home/zas1024/gene/wqflask/")
-sys.path.append("/home/danny/GeneNetwork/wqflask/wqflask/my_pylmm/pyLMM/")
-print("sys.path2:", sys.path)
has_gn2=True
from utility.benchmark import Bench
from utility import temp_data
-from kinship import kinship, kinship_full
+
+sys.path.append("/home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/")
+
+from kinship import kinship, kinship_full, kvakve
import genotype
+import phenotype
+import gwas
try:
from wqflask.my_pylmm.pyLMM import chunks
@@ -254,7 +257,7 @@ def human_association(snp,
# refit=False,
# temp_data=None):
-def run_other(pheno_vector,
+def run_other_old(pheno_vector,
genotype_matrix,
restricted_max_likelihood=True,
refit=False,
@@ -270,7 +273,7 @@ def run_other(pheno_vector,
"""
- print("In run_other")
+ print("Running the original LMM engine in run_other (old)")
print("REML=",restricted_max_likelihood," REFIT=",refit)
with Bench("Calculate Kinship"):
kinship_matrix,genotype_matrix = calculate_kinship(genotype_matrix, tempdata)
@@ -278,25 +281,79 @@ def run_other(pheno_vector,
print("kinship_matrix: ", pf(kinship_matrix))
print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
- with Bench("Create LMM object"):
- lmm_ob = LMM(pheno_vector, kinship_matrix)
+ # with Bench("Create LMM object"):
+ # lmm_ob = LMM(pheno_vector, kinship_matrix)
- with Bench("LMM_ob fitting"):
- lmm_ob.fit()
+ # with Bench("LMM_ob fitting"):
+ # lmm_ob.fit()
- print("genotype_matrix: ", genotype_matrix.shape)
+ print("run_other_old genotype_matrix: ", genotype_matrix.shape)
print(genotype_matrix)
with Bench("Doing GWAS"):
t_stats, p_values = GWAS(pheno_vector,
- genotype_matrix,
- kinship_matrix,
- restricted_max_likelihood=True,
- refit=False,
- temp_data=tempdata)
+ genotype_matrix,
+ kinship_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ temp_data=tempdata)
Bench().report()
return p_values, t_stats
+def run_other_new(pheno_vector,
+ genotype_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ tempdata=None # <---- can not be None
+ ):
+
+ """Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics
+
+ restricted_max_likelihood -- whether to use restricted max likelihood; True or False
+ refit -- whether to refit the variance component for each marker
+ temp_data -- TempData object that stores the progress for each major step of the
+ calculations ("calculate_kinship" and "GWAS" take the majority of time)
+
+ """
+
+ print("Running the new LMM2 engine in run_other_new")
+ print("REML=",restricted_max_likelihood," REFIT=",refit)
+
+ # Adjust phenotypes
+ Y,G,keep = phenotype.remove_missing(pheno_vector,genotype_matrix,verbose=True)
+ print("Removed missing phenotypes",Y.shape)
+
+ # if options.maf_normalization:
+ # G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g )
+ # print "MAF replacements: \n",G
+ # if not options.skip_genotype_normalization:
+ # G = np.apply_along_axis( genotype.normalize, axis=1, arr=G)
+
+ with Bench("Calculate Kinship"):
+ K,G = calculate_kinship(G, tempdata)
+
+ print("kinship_matrix: ", pf(K))
+ print("kinship_matrix.shape: ", pf(K.shape))
+
+ # with Bench("Create LMM object"):
+ # lmm_ob = lmm2.LMM2(Y,K)
+ # with Bench("LMM_ob fitting"):
+ # lmm_ob.fit()
+
+ print("run_other_new genotype_matrix: ", G.shape)
+ print(G)
+
+ with Bench("Doing GWAS"):
+ t_stats, p_values = gwas.gwas(Y,
+ G.T,
+ K,
+ restricted_max_likelihood=True,
+ refit=False,verbose=True)
+ Bench().report()
+ return p_values, t_stats
+
+# def matrixMult(A,B):
+# return np.dot(A,B)
def matrixMult(A,B):
@@ -334,8 +391,10 @@ def calculate_kinship_new(genotype_matrix, temp_data=None):
Call the new kinship calculation where genotype_matrix contains
inds (columns) by snps (rows).
"""
+ print("call genotype.normalize")
G = np.apply_along_axis( genotype.normalize, axis=0, arr=genotype_matrix)
- return kinship(G.T),G
+ print("call calculate_kinship_new")
+ return kinship(G.T),G # G gets transposed, we'll turn this into an iterator (FIXME)
def calculate_kinship_old(genotype_matrix, temp_data=None):
"""
@@ -345,6 +404,7 @@ def calculate_kinship_old(genotype_matrix, temp_data=None):
normalizes the resulting vectors and returns the RRM matrix.
"""
+ print("call calculate_kinship_old")
n = genotype_matrix.shape[0]
m = genotype_matrix.shape[1]
print("genotype 2D matrix n (inds) is:", n)
@@ -375,7 +435,7 @@ def calculate_kinship_old(genotype_matrix, temp_data=None):
temp_data.store("percent_complete", percent_complete)
genotype_matrix = genotype_matrix[:,keep]
- print("genotype_matrix: ", pf(genotype_matrix))
+ print("After kinship (old) genotype_matrix: ", pf(genotype_matrix))
kinship_matrix = np.dot(genotype_matrix, genotype_matrix.T) * 1.0/float(m)
return kinship_matrix,genotype_matrix
@@ -533,11 +593,13 @@ class LMM:
print("this K is:", K.shape, pf(K))
if len(Kva) == 0 or len(Kve) == 0:
- if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
+ # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
begin = time.time()
- Kva,Kve = linalg.eigh(K)
+ # Kva,Kve = linalg.eigh(K)
+ Kva,Kve = kvakve(K)
end = time.time()
if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
+ print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve))
self.K = K
self.Kva = Kva
@@ -547,10 +609,11 @@ class LMM:
self.Y = Y
self.X0 = X0
self.N = self.K.shape[0]
-
- if sum(self.Kva < 1e-6):
- if self.verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(self.Kva < 0)))
- self.Kva[self.Kva < 1e-6] = 1e-6
+
+ # ----> Below moved to kinship.kvakve(K)
+ # if sum(self.Kva < 1e-6):
+ # if self.verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(self.Kva < 0)))
+ # self.Kva[self.Kva < 1e-6] = 1e-6
self.transform()
@@ -713,7 +776,10 @@ class LMM:
ts = beta / np.sqrt(var * sigma)
ps = 2.0*(1.0 - stats.t.cdf(np.abs(ts), self.N-q))
- if not len(ts) == 1 or not len(ps) == 1: raise Exception("Something bad happened :(")
+ if not len(ts) == 1 or not len(ps) == 1:
+ print("ts=",ts)
+ print("ps=",ps)
+ raise Exception("Something bad happened :(")
return ts.sum(),ps.sum()
def plotFit(self,color='b-',title=''):
@@ -739,7 +805,11 @@ class LMM:
pl.title(title)
-def gn2_redis(key,species):
+def gn2_redis(key,species,new_code=True):
+ """
+ Invoke pylmm using Redis as a container. new_code runs the new
+ version
+ """
json_params = Redis.get(key)
params = json.loads(json_params)
@@ -761,11 +831,18 @@ def gn2_redis(key,species):
geno = np.array(params['genotype_matrix'])
print('geno', geno.shape, geno)
- ps, ts = run_other(pheno_vector = np.array(params['pheno_vector']),
- genotype_matrix = geno,
- restricted_max_likelihood = params['restricted_max_likelihood'],
- refit = params['refit'],
- tempdata = tempdata)
+ if new_code:
+ ps, ts = run_other_new(pheno_vector = np.array(params['pheno_vector']),
+ genotype_matrix = geno,
+ restricted_max_likelihood = params['restricted_max_likelihood'],
+ refit = params['refit'],
+ tempdata = tempdata)
+ else:
+ ps, ts = run_other_old(pheno_vector = np.array(params['pheno_vector']),
+ genotype_matrix = geno,
+ restricted_max_likelihood = params['restricted_max_likelihood'],
+ refit = params['refit'],
+ tempdata = tempdata)
results_key = "pylmm:results:" + params['temp_uuid']
@@ -790,7 +867,7 @@ def gn2_main():
gn2_redis(key,species)
-def gn2_load_redis(key,species,kinship,pheno,geno):
+def gn2_load_redis(key,species,kinship,pheno,geno,new_code=True):
print("Loading Redis from parsed data")
if kinship == None:
k = None
@@ -811,7 +888,7 @@ def gn2_load_redis(key,species,kinship,pheno,geno):
Redis.set(key, json_params)
Redis.expire(key, 60*60)
- return gn2_redis(key,species)
+ return gn2_redis(key,species,new_code)
if __name__ == '__main__':
print("WARNING: Calling pylmm from lmm.py will become OBSOLETE, use runlmm.py instead!")
@@ -821,4 +898,3 @@ if __name__ == '__main__':
print("Run from runlmm.py instead")
-
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
new file mode 100644
index 00000000..d4b3ac82
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
@@ -0,0 +1,410 @@
+# pylmm is a python-based linear mixed-model solver with applications to GWAS
+
+# Copyright (C) 2013,2014 Nicholas A. Furlotte (nick.furlotte@gmail.com)
+#
+# 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.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+import sys
+import time
+import numpy as np
+from scipy.linalg import eigh, inv, det
+import scipy.stats as stats # t-tests
+from scipy import optimize
+from optmatrix import matrixMult
+import kinship
+
+def calculateKinship(W,center=False):
+ """
+ W is an n x m matrix encoding SNP minor alleles.
+
+ This function takes a matrix oF SNPs, imputes missing values with the maf,
+ normalizes the resulting vectors and returns the RRM matrix.
+ """
+ n = W.shape[0]
+ m = W.shape[1]
+ keep = []
+ for i in range(m):
+ mn = W[True - np.isnan(W[:,i]),i].mean()
+ W[np.isnan(W[:,i]),i] = mn
+ vr = W[:,i].var()
+ if vr == 0: continue
+
+ keep.append(i)
+ W[:,i] = (W[:,i] - mn) / np.sqrt(vr)
+
+ W = W[:,keep]
+ K = matrixMult(W,W.T) * 1.0/float(m)
+ if center:
+ P = np.diag(np.repeat(1,n)) - 1/float(n) * np.ones((n,n))
+ S = np.trace(matrixMult(matrixMult(P,K),P))
+ K_n = (n - 1)*K / S
+ return K_n
+ return K
+
+def GWAS(Y, X, K, Kva=[], Kve=[], X0=None, REML=True, refit=False):
+ """
+
+ Performs a basic GWAS scan using the LMM. This function
+ uses the LMM module to assess association at each SNP and
+ does some simple cleanup, such as removing missing individuals
+ per SNP and re-computing the eigen-decomp
+
+ Y - n x 1 phenotype vector
+ X - n x m SNP matrix (genotype matrix)
+ K - n x n kinship matrix
+ Kva,Kve = linalg.eigh(K) - or the eigen vectors and values for K
+ X0 - n x q covariate matrix
+ REML - use restricted maximum likelihood
+ refit - refit the variance component for each SNP
+
+ """
+ n = X.shape[0]
+ m = X.shape[1]
+ prins("Initialize GWAS")
+ print("genotype matrix n is:", n)
+ print("genotype matrix m is:", m)
+
+ if X0 == None:
+ X0 = np.ones((n,1))
+
+ # Remove missing values in Y and adjust associated parameters
+ v = np.isnan(Y)
+ if v.sum():
+ keep = True - v
+ keep = keep.reshape((-1,))
+ Y = Y[keep]
+ X = X[keep,:]
+ X0 = X0[keep,:]
+ K = K[keep,:][:,keep]
+ Kva = []
+ Kve = []
+
+ if len(Y) == 0:
+ return np.ones(m)*np.nan,np.ones(m)*np.nan
+
+ L = LMM(Y,K,Kva,Kve,X0)
+ if not refit: L.fit()
+
+ PS = []
+ TS = []
+
+ n = X.shape[0]
+ m = X.shape[1]
+
+ for i in range(m):
+ x = X[:,i].reshape((n,1))
+ v = np.isnan(x).reshape((-1,))
+ if v.sum():
+ keep = True - v
+ xs = x[keep,:]
+ if xs.var() == 0:
+ PS.append(np.nan)
+ TS.append(np.nan)
+ continue
+
+ Ys = Y[keep]
+ X0s = X0[keep,:]
+ Ks = K[keep,:][:,keep]
+ Ls = LMM(Ys,Ks,X0=X0s)
+ if refit:
+ Ls.fit(X=xs)
+ else:
+ Ls.fit()
+ ts,ps = Ls.association(xs,REML=REML)
+ else:
+ if x.var() == 0:
+ PS.append(np.nan)
+ TS.append(np.nan)
+ continue
+
+ if refit:
+ L.fit(X=x)
+ ts,ps = L.association(x,REML=REML)
+
+ PS.append(ps)
+ TS.append(ts)
+
+ return TS,PS
+
+class LMM2:
+
+ """
+ This is a simple version of EMMA/fastLMM.
+ The main purpose of this module is to take a phenotype vector (Y), a set of covariates (X) and a kinship matrix (K)
+ and to optimize this model by finding the maximum-likelihood estimates for the model parameters.
+ There are three model parameters: heritability (h), covariate coefficients (beta) and the total
+ phenotypic variance (sigma).
+ Heritability as defined here is the proportion of the total variance (sigma) that is attributed to
+ the kinship matrix.
+
+ For simplicity, we assume that everything being input is a numpy array.
+ If this is not the case, the module may throw an error as conversion from list to numpy array
+ is not done consistently.
+
+ """
+ def __init__(self,Y,K,Kva=[],Kve=[],X0=None,verbose=False):
+
+ """
+ The constructor takes a phenotype vector or array Y of size n.
+ It takes a kinship matrix K of size n x n. Kva and Kve can be computed as Kva,Kve = linalg.eigh(K) and cached.
+ If they are not provided, the constructor will calculate them.
+ X0 is an optional covariate matrix of size n x q, where there are q covariates.
+ When this parameter is not provided, the constructor will set X0 to an n x 1 matrix of all ones to represent a mean effect.
+ """
+
+ if X0 == None:
+ X0 = np.ones(len(Y)).reshape(len(Y),1)
+ self.verbose = verbose
+
+ x = True - np.isnan(Y)
+ x = x.reshape(-1,)
+ if not x.sum() == len(Y):
+ if self.verbose: sys.stderr.write("Removing %d missing values from Y\n" % ((True - x).sum()))
+ Y = Y[x]
+ K = K[x,:][:,x]
+ X0 = X0[x,:]
+ Kva = []
+ Kve = []
+ self.nonmissing = x
+
+ print("this K is:", K.shape, K)
+
+ if len(Kva) == 0 or len(Kve) == 0:
+ # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
+ begin = time.time()
+ # Kva,Kve = linalg.eigh(K)
+ Kva,Kve = kinship.kvakve(K)
+ end = time.time()
+ if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
+ print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve))
+
+ self.K = K
+ self.Kva = Kva
+ self.Kve = Kve
+ self.N = self.K.shape[0]
+ self.Y = Y.reshape((self.N,1))
+ self.X0 = X0
+
+ if sum(self.Kva < 1e-6):
+ if self.verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(self.Kva < 0)))
+ self.Kva[self.Kva < 1e-6] = 1e-6
+
+ self.transform()
+
+ def transform(self):
+
+ """
+ Computes a transformation on the phenotype vector and the covariate matrix.
+ The transformation is obtained by left multiplying each parameter by the transpose of the
+ eigenvector matrix of K (the kinship).
+ """
+
+ self.Yt = matrixMult(self.Kve.T, self.Y)
+ self.X0t = matrixMult(self.Kve.T, self.X0)
+ self.X0t_stack = np.hstack([self.X0t, np.ones((self.N,1))])
+ self.q = self.X0t.shape[1]
+
+ def getMLSoln(self,h,X):
+
+ """
+ Obtains the maximum-likelihood estimates for the covariate coefficients (beta),
+ the total variance of the trait (sigma) and also passes intermediates that can
+ be utilized in other functions. The input parameter h is a value between 0 and 1 and represents
+ the heritability or the proportion of the total variance attributed to genetics. The X is the
+ covariate matrix.
+ """
+
+ S = 1.0/(h*self.Kva + (1.0 - h))
+ Xt = X.T*S
+ XX = matrixMult(Xt,X)
+ XX_i = inv(XX)
+ beta = matrixMult(matrixMult(XX_i,Xt),self.Yt)
+ Yt = self.Yt - matrixMult(X,beta)
+ Q = np.dot(Yt.T*S,Yt)
+ sigma = Q * 1.0 / (float(self.N) - float(X.shape[1]))
+ return beta,sigma,Q,XX_i,XX
+
+ def LL_brent(self,h,X=None,REML=False):
+ #brent will not be bounded by the specified bracket.
+ # I return a large number if we encounter h < 0 to avoid errors in LL computation during the search.
+ if h < 0: return 1e6
+ return -self.LL(h,X,stack=False,REML=REML)[0]
+
+ def LL(self,h,X=None,stack=True,REML=False):
+
+ """
+ Computes the log-likelihood for a given heritability (h). If X==None, then the
+ default X0t will be used. If X is set and stack=True, then X0t will be matrix concatenated with
+ the input X. If stack is false, then X is used in place of X0t in the LL calculation.
+ REML is computed by adding additional terms to the standard LL and can be computed by setting REML=True.
+ """
+
+ if X == None: X = self.X0t
+ elif stack:
+ self.X0t_stack[:,(self.q)] = matrixMult(self.Kve.T,X)[:,0]
+ X = self.X0t_stack
+
+ n = float(self.N)
+ q = float(X.shape[1])
+ beta,sigma,Q,XX_i,XX = self.getMLSoln(h,X)
+ LL = n*np.log(2*np.pi) + np.log(h*self.Kva + (1.0-h)).sum() + n + n*np.log(1.0/n * Q)
+ LL = -0.5 * LL
+
+ if REML:
+ LL_REML_part = q*np.log(2.0*np.pi*sigma) + np.log(det(matrixMult(X.T,X))) - np.log(det(XX))
+ LL = LL + 0.5*LL_REML_part
+
+
+ LL = LL.sum()
+ return LL,beta,sigma,XX_i
+
+ def getMax(self,H, X=None,REML=False):
+
+ """
+ Helper functions for .fit(...).
+ This function takes a set of LLs computed over a grid and finds possible regions
+ containing a maximum. Within these regions, a Brent search is performed to find the
+ optimum.
+
+ """
+ n = len(self.LLs)
+ HOpt = []
+ for i in range(1,n-2):
+ if self.LLs[i-1] < self.LLs[i] and self.LLs[i] > self.LLs[i+1]:
+ HOpt.append(optimize.brent(self.LL_brent,args=(X,REML),brack=(H[i-1],H[i+1])))
+ if np.isnan(HOpt[-1]): HOpt[-1] = H[i-1]
+ #if np.isnan(HOpt[-1]): HOpt[-1] = self.LLs[i-1]
+ #if np.isnan(HOpt[-1][0]): HOpt[-1][0] = [self.LLs[i-1]]
+
+ if len(HOpt) > 1:
+ if self.verbose: sys.stderr.write("NOTE: Found multiple optima. Returning first...\n")
+ return HOpt[0]
+ elif len(HOpt) == 1: return HOpt[0]
+ elif self.LLs[0] > self.LLs[n-1]: return H[0]
+ else: return H[n-1]
+
+
+ def fit(self,X=None,ngrids=100,REML=True):
+
+ """
+ Finds the maximum-likelihood solution for the heritability (h) given the current parameters.
+ X can be passed and will transformed and concatenated to X0t. Otherwise, X0t is used as
+ the covariate matrix.
+
+ This function calculates the LLs over a grid and then uses .getMax(...) to find the optimum.
+ Given this optimum, the function computes the LL and associated ML solutions.
+ """
+
+ if X == None: X = self.X0t
+ else:
+ #X = np.hstack([self.X0t,matrixMult(self.Kve.T, X)])
+ self.X0t_stack[:,(self.q)] = matrixMult(self.Kve.T,X)[:,0]
+ X = self.X0t_stack
+
+ H = np.array(range(ngrids)) / float(ngrids)
+ L = np.array([self.LL(h,X,stack=False,REML=REML)[0] for h in H])
+ self.LLs = L
+
+ hmax = self.getMax(H,X,REML)
+ L,beta,sigma,betaSTDERR = self.LL(hmax,X,stack=False,REML=REML)
+
+ self.H = H
+ self.optH = hmax.sum()
+ self.optLL = L
+ self.optBeta = beta
+ self.optSigma = sigma.sum()
+
+ return hmax,beta,sigma,L
+
+ def association(self,X,h=None,stack=True,REML=True,returnBeta=False):
+ """
+ Calculates association statitics for the SNPs encoded in the vector X of size n.
+ If h == None, the optimal h stored in optH is used.
+
+ """
+ if False:
+ print "X=",X
+ print "h=",h
+ print "q=",self.q
+ print "self.Kve=",self.Kve
+ print "X0t_stack=",self.X0t_stack.shape,self.X0t_stack
+
+ if stack:
+ # X = np.hstack([self.X0t,matrixMult(self.Kve.T, X)])
+ m = matrixMult(self.Kve.T,X)
+ # print "m=",m
+ m = m[:,0]
+ self.X0t_stack[:,(self.q)] = m
+ X = self.X0t_stack
+
+ if h == None: h = self.optH
+
+ L,beta,sigma,betaVAR = self.LL(h,X,stack=False,REML=REML)
+ q = len(beta)
+ ts,ps = self.tstat(beta[q-1],betaVAR[q-1,q-1],sigma,q)
+
+ if returnBeta: return ts,ps,beta[q-1].sum(),betaVAR[q-1,q-1].sum()*sigma
+ return ts,ps
+
+ def tstat(self,beta,var,sigma,q,log=False):
+
+ """
+ Calculates a t-statistic and associated p-value given the estimate of beta and its standard error.
+ This is actually an F-test, but when only one hypothesis is being performed, it reduces to a t-test.
+ """
+
+ ts = beta / np.sqrt(var * sigma)
+ #ps = 2.0*(1.0 - stats.t.cdf(np.abs(ts), self.N-q))
+ # sf == survival function - this is more accurate -- could also use logsf if the precision is not good enough
+ if log:
+ ps = 2.0 + (stats.t.logsf(np.abs(ts), self.N-q))
+ else:
+ ps = 2.0*(stats.t.sf(np.abs(ts), self.N-q))
+ if not len(ts) == 1 or not len(ps) == 1:
+ raise Exception("Something bad happened :(")
+ return ts.sum(),ps.sum()
+
+ def plotFit(self,color='b-',title=''):
+
+ """
+ Simple function to visualize the likelihood space. It takes the LLs
+ calcualted over a grid and normalizes them by subtracting off the mean and exponentiating.
+ The resulting "probabilities" are normalized to one and plotted against heritability.
+ This can be seen as an approximation to the posterior distribuiton of heritability.
+
+ For diagnostic purposes this lets you see if there is one distinct maximum or multiple
+ and what the variance of the parameter looks like.
+ """
+ import matplotlib.pyplot as pl
+
+ mx = self.LLs.max()
+ p = np.exp(self.LLs - mx)
+ p = p/p.sum()
+
+ pl.plot(self.H,p,color)
+ pl.xlabel("Heritability")
+ pl.ylabel("Probability of data")
+ pl.title(title)
+
+ def meanAndVar(self):
+
+ mx = self.LLs.max()
+ p = np.exp(self.LLs - mx)
+ p = p/p.sum()
+
+ mn = (self.H * p).sum()
+ vx = ((self.H - mn)**2 * p).sum()
+
+ return mn,vx
+
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/phenotype.py b/wqflask/wqflask/my_pylmm/pyLMM/phenotype.py
index bb620052..682ba371 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/phenotype.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/phenotype.py
@@ -36,5 +36,5 @@ def remove_missing(y,g,verbose=False):
sys.stderr.write("runlmm.py: Cleaning the phenotype vector and genotype matrix by removing %d individuals...\n" % (v.sum()))
y1 = y[keep]
g1 = g[keep,:]
- return y1,g1
+ return y1,g1,keep
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 6bb79856..324c4f2c 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -21,7 +21,7 @@ from optparse import OptionParser
import sys
import tsvreader
import numpy as np
-from lmm import gn2_load_redis, calculate_kinship
+from lmm import gn2_load_redis, calculate_kinship_old
from kinship import kinship, kinship_full
import genotype
import phenotype
@@ -54,9 +54,12 @@ parser.add_option("--geno",dest="geno",
parser.add_option("--maf-normalization",
action="store_true", dest="maf_normalization", default=False,
help="Apply MAF genotype normalization")
-parser.add_option("--skip-genotype-normalization",
- action="store_true", dest="skip_genotype_normalization", default=False,
- help="Skip genotype normalization")
+parser.add_option("--genotype-normalization",
+ action="store_true", dest="genotype_normalization", default=False,
+ help="Force genotype normalization")
+parser.add_option("--remove-missing-phenotypes",
+ action="store_true", dest="remove_missing_phenotypes", default=False,
+ help="Remove missing phenotypes")
parser.add_option("-q", "--quiet",
action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
@@ -99,28 +102,58 @@ if options.geno:
g = tsvreader.geno(options.geno)
print g.shape
-if cmd == 'redis':
+if cmd == 'redis_new':
+ # The main difference between redis_new and redis is that missing
+ # phenotypes are handled by the first
+ Y = y
+ G = g
+ print "Original G",G.shape, "\n", G
+
+ gt = G.T
+ G = None
+ ps, ts = gn2_load_redis('testrun','other',k,Y,gt,new_code=True)
+ print np.array(ps)
+ print len(ps),sum(ps)
+ # Test results
+ p1 = round(ps[0],4)
+ p2 = round(ps[-1],4)
+ sys.stderr.write(options.geno+"\n")
+ if options.geno == 'data/small.geno':
+ assert p1==0.0708, "p1=%f" % p1
+ assert p2==0.1417, "p2=%f" % p2
+ if options.geno == 'data/small_na.geno':
+ assert p1==0.0897, "p1=%f" % p1
+ assert p2==0.0405, "p2=%f" % p2
+ if options.geno == 'data/test8000.geno':
+ # assert p1==0.8984, "p1=%f" % p1
+ # assert p2==0.9621, "p2=%f" % p2
+ assert round(sum(ps)) == 4070
+ assert len(ps) == 8000
+elif cmd == 'redis':
# Emulating the redis setup of GN2
G = g
print "Original G",G.shape, "\n", G
- if y != None:
+ if y != None and options.remove_missing_phenotypes:
gnt = np.array(g).T
- Y,g = phenotype.remove_missing(y,g.T,options.verbose)
+ Y,g,keep = phenotype.remove_missing(y,g.T,options.verbose)
G = g.T
print "Removed missing phenotypes",G.shape, "\n", G
+ else:
+ Y = y
if options.maf_normalization:
G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g )
print "MAF replacements: \n",G
- if not options.skip_genotype_normalization:
+ if options.genotype_normalization:
G = np.apply_along_axis( genotype.normalize, axis=1, arr=G)
g = None
gnt = None
gt = G.T
G = None
- ps, ts = gn2_load_redis('testrun','other',k,Y,gt)
+ ps, ts = gn2_load_redis('testrun','other',k,Y,gt, new_code=False)
print np.array(ps)
- # Test results
+ print len(ps),sum(ps)
+ # Test results 4070.02346579
p1 = round(ps[0],4)
p2 = round(ps[-1],4)
sys.stderr.write(options.geno+"\n")
@@ -128,15 +161,15 @@ if cmd == 'redis':
assert p1==0.0708, "p1=%f" % p1
assert p2==0.1417, "p2=%f" % p2
if options.geno == 'data/small_na.geno':
- assert p1==0.0958, "p1=%f" % p1
- assert p2==0.0435, "p2=%f" % p2
+ assert p1==0.0897, "p1=%f" % p1
+ assert p2==0.0405, "p2=%f" % p2
if options.geno == 'data/test8000.geno':
- assert p1==0.8984, "p1=%f" % p1
- assert p2==0.9623, "p2=%f" % p2
+ assert round(sum(ps)) == 4070
+ assert len(ps) == 8000
elif cmd == 'kinship':
G = g
print "Original G",G.shape, "\n", G
- if y != None:
+ if y != None and options.remove_missing_phenotypes:
gnt = np.array(g).T
Y,g = phenotype.remove_missing(y,g.T,options.verbose)
G = g.T
@@ -144,32 +177,32 @@ elif cmd == 'kinship':
if options.maf_normalization:
G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g )
print "MAF replacements: \n",G
- if not options.skip_genotype_normalization:
+ if options.genotype_normalization:
G = np.apply_along_axis( genotype.normalize, axis=1, arr=G)
g = None
gnt = None
if options.test_kinship:
- K = kinship_full(G)
+ K = kinship_full(np.copy(G))
print "Genotype",G.shape, "\n", G
print "first Kinship method",K.shape,"\n",K
k1 = round(K[0][0],4)
- K2 = calculate_kinship(np.copy(G.T),temp_data=None)
+ K2,G = calculate_kinship_old(np.copy(G).T,temp_data=None)
print "Genotype",G.shape, "\n", G
print "GN2 Kinship method",K2.shape,"\n",K2
k2 = round(K2[0][0],4)
print "Genotype",G.shape, "\n", G
- K3 = kinship(np.copy(G),options)
+ K3 = kinship(G.T)
print "third Kinship method",K3.shape,"\n",K3
sys.stderr.write(options.geno+"\n")
k3 = round(K3[0][0],4)
if options.geno == 'data/small.geno':
- assert k1==0.7939, "k1=%f" % k1
+ assert k1==0.8, "k1=%f" % k1
assert k2==0.7939, "k2=%f" % k2
assert k3==0.7939, "k3=%f" % k3
if options.geno == 'data/small_na.geno':
- assert k1==0.7172, "k1=%f" % k1
+ assert k1==0.8333, "k1=%f" % k1
assert k2==0.7172, "k2=%f" % k2
assert k3==0.7172, "k3=%f" % k3
if options.geno == 'data/test8000.geno':
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
new file mode 100755
index 00000000..62dc1bbb
--- /dev/null
+++ b/wqflask/wqflask/news.py
@@ -0,0 +1,16 @@
+from __future__ import absolute_import, print_function, division
+import sys
+reload(sys)
+sys.setdefaultencoding('utf8')
+from flask import g
+
+class News(object):
+
+ def __init__(self):
+ sql = """
+ SELECT News.id, News.date, News.details
+ FROM News
+ order by News.date desc
+ """
+ self.title = "GeneNetwork News"
+ self.newslist = g.db.execute(sql).fetchall()
diff --git a/wqflask/wqflask/templates/testhtmleditor.html b/wqflask/wqflask/templates/docedit.html
index 1d258d0e..1a9e8ca8 100755
--- a/wqflask/wqflask/templates/testhtmleditor.html
+++ b/wqflask/wqflask/templates/docedit.html
@@ -1,18 +1,18 @@
{% extends "base.html" %}
-{% block title %}Test html editor{% endblock %}
+{% block title %}Edit: {{title}}{% endblock %}
{% block content %}
<div class="container">
- <h2>Test HTML Editor</h2>
+ <h3>Edit: {{title}}</h3>
<form>
<textarea name="ckcontent" id="ckcontent">
- Test HTML
+ {{content|safe}}
</textarea>
<script type="text/javascript" src="/static/packages/ckeditor/ckeditor.js"></script>
<script type="text/javascript">
CKEDITOR.replace('ckcontent', {
- height: '500px',
+ height: '650px',
});
</script>
</form>
diff --git a/wqflask/wqflask/templates/docs.html b/wqflask/wqflask/templates/docs.html
index cbaf1e70..08f95721 100755
--- a/wqflask/wqflask/templates/docs.html
+++ b/wqflask/wqflask/templates/docs.html
@@ -5,6 +5,11 @@
{% block content %}
<div class="container">
<h3>{{title}}</h3>
+ <div style="text-align: right;">
+ <a href="docedit?entry={{entry}}">
+ <img style="width: 25px;" src="/static/images/edit.png">
+ </a>
+ </div>
{{content|safe}}
</div>
{% endblock %}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index ba017bfb..5e0a92e3 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -211,7 +211,6 @@
<li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
<li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
<li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
<li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
</ul>
</section>
diff --git a/wqflask/wqflask/templates/news.html b/wqflask/wqflask/templates/news.html
new file mode 100755
index 00000000..4f0032b8
--- /dev/null
+++ b/wqflask/wqflask/templates/news.html
@@ -0,0 +1,21 @@
+{% extends "base.html" %}
+
+{% block title %}{{title}}{% endblock %}
+
+{% block content %}
+<div class="container">
+ <h3>{{title}}</h3>
+ <table class="table table-hover table-striped" style="width: 600px;">
+ <tbody>
+ {% for newsitem in newslist %}
+ <tr>
+ <td style="width: 90px; text-wrap:none;" nowrap>
+ <span style="font-weight: bold;">{{newsitem.date}}</span>
+ </td>
+ <td>{{newsitem.details|safe}}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7fec0456..39004f07 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -33,6 +33,7 @@ from flask import (render_template, request, make_response, Response,
from wqflask import search_results
from wqflask import docs
+from wqflask import news
from base.data_set import DataSet # Used by YAML in marker_regression
from base.data_set import create_datasets_list
from wqflask.show_trait import show_trait
@@ -45,8 +46,6 @@ from wqflask.correlation_matrix import show_corr_matrix
from wqflask.correlation import corr_scatter_plot
from utility import temp_data
-from wqflask.dataSharing import SharingInfo, SharingInfoPage
-
from base import webqtlFormData
from utility.benchmark import Bench
@@ -100,20 +99,20 @@ def tmp_page(img_path):
img_base64 = bytesarray )
-@app.route("/data_sharing")
-def data_sharing_page():
- print("In data_sharing")
- fd = webqtlFormData.webqtlFormData(request.args)
- print("1Have fd")
- sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
- info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
- print("type(htmlfilelist):", type(htmlfilelist))
- htmlfilelist = htmlfilelist.encode("utf-8")
- #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
- print("1 Made it to rendering")
- return render_template("data_sharing.html",
- info=info,
- htmlfilelist=htmlfilelist)
+#@app.route("/data_sharing")
+#def data_sharing_page():
+# print("In data_sharing")
+# fd = webqtlFormData.webqtlFormData(request.args)
+# print("1Have fd")
+# sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
+# info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
+# print("type(htmlfilelist):", type(htmlfilelist))
+# htmlfilelist = htmlfilelist.encode("utf-8")
+# #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
+# print("1 Made it to rendering")
+# return render_template("data_sharing.html",
+# info=info,
+# htmlfilelist=htmlfilelist)
@app.route("/search", methods=('GET',))
@@ -152,9 +151,10 @@ def search_page():
else:
return render_template("search_result_page.html", **result)
-@app.route("/testhtmleditor")
-def testhtmleditor_page():
- return render_template("testhtmleditor.html")
+@app.route("/docedit")
+def docedit():
+ doc = docs.Docs(request.args['entry'])
+ return render_template("docedit.html", **doc.__dict__)
@app.route("/help")
def help():
@@ -162,15 +162,9 @@ def help():
return render_template("docs.html", **doc.__dict__)
@app.route("/news")
-def news():
- #variables = whats_new.whats_new()
- with open("/home/sam/gene/wqflask/wqflask/yaml_data/whats_new.yaml") as fh:
- contents = fh.read()
- yamilized = yaml.safe_load(contents)
- news_items = yamilized['news']
- for news_item in news_items:
- print("\nnews_item is: %s\n" % (news_item))
- return render_template("whats_new.html", news_items=news_items)
+def news_route():
+ newsobject = news.News()
+ return render_template("news.html", **newsobject.__dict__)
@app.route("/references")
def references():
diff --git a/wqflask/wqflask/yaml_data/whats_new.yaml b/wqflask/wqflask/yaml_data/whats_new.yaml
deleted file mode 100755
index 8f41a8f2..00000000
--- a/wqflask/wqflask/yaml_data/whats_new.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-news:
--
- date: 2012-1-20
- title: Mouse SNPs from dbSNP have been added to GeneNetwork
- details:
- 10 million mouse SNPs from dbSNP (build 128) have been added to Variant Browser.
- They could be searched by name (e.g. rs31192936) (Implemented by Xiaodong Zhou and Ning Liu).
-
--
- date: 2012-1-20
- title: Literature correlation has been update to 2011 version
- details:
- Dr. Ramin Homayouni and Dr. Lijing Xu kindly provide the 2011 version of mouse gene-gene
- literature correlation matrix to GeneNetwork. (Implemented by Xiaodong Zhou).
-
--
- date: 2012-1-16
- title: Expression data set for EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA ** has been entered in GeneNetwork
- details:
- Laboratory of Integrative and Systems Physiology
- (<a href="http://auwerx-lab.epfl.ch/">LISP</a>).
- This data set is not yet freely available for global analysis.
- This data set has not yet been used or described in any publication.
- Please contact Johan Auwerx or Evan Williams at evan.williams@epfl.ch
- regarding use of these data. (Implemented by J Auwerx, E Williams, LA Rose,
- RW Williams and A Centeno). \ No newline at end of file