diff options
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingBody.py | 290 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfo.py | 146 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfoAddPage.py | 47 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfoDeletePage.py | 55 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfoEditPage.py | 51 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfoPage.py | 64 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingInfoUpdatePage.py | 109 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingListDataSetPage.py | 99 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/SharingPage.py | 40 | ||||
| -rwxr-xr-x | wqflask/wqflask/dataSharing/__init__.py | 0 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page.html | 1 |
11 files changed, 0 insertions, 902 deletions
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"> - <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Download " 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" /> E.g. 112</td> - </tr> - <tr> - <td></td> - <td></td> - <td HEIGHT="40"> - <input type="Submit" class="button" STYLE="font-size:12px" VALUE=" Submit "> - </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 += ' ' - #r=re.compile(r'(?<=\d)(?=(\d\d\d)+(?!\d))') - #htmlfilelist += '[%s 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(" ") - 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/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> |