diff options
Diffstat (limited to 'web/webqtl/base')
| -rwxr-xr-x | web/webqtl/base/GeneralObject.py | 71 | ||||
| -rwxr-xr-x | web/webqtl/base/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/base/admin.py | 88 | ||||
| -rwxr-xr-x | web/webqtl/base/cgiData.py | 70 | ||||
| -rwxr-xr-x | web/webqtl/base/cookieData.py | 52 | ||||
| -rwxr-xr-x | web/webqtl/base/footer.py | 6 | ||||
| -rwxr-xr-x | web/webqtl/base/header.py | 6 | ||||
| -rwxr-xr-x | web/webqtl/base/indexBody.py | 291 | ||||
| -rwxr-xr-x | web/webqtl/base/myCookie.py | 55 | ||||
| -rwxr-xr-x | web/webqtl/base/sessionData.py | 53 | ||||
| -rwxr-xr-x | web/webqtl/base/template.py | 123 | ||||
| -rwxr-xr-x | web/webqtl/base/templatePage.py | 222 | ||||
| -rwxr-xr-x | web/webqtl/base/webqtlCaseData.py | 54 | ||||
| -rwxr-xr-x | web/webqtl/base/webqtlConfig.py | 73 | ||||
| -rwxr-xr-x | web/webqtl/base/webqtlConfigLocal.py | 17 | ||||
| -rwxr-xr-x | web/webqtl/base/webqtlDataset.py | 160 | ||||
| -rwxr-xr-x | web/webqtl/base/webqtlFormData.py | 289 | ||||
| -rw-r--r-- | web/webqtl/base/webqtlTrait.py | 590 |
18 files changed, 0 insertions, 2220 deletions
diff --git a/web/webqtl/base/GeneralObject.py b/web/webqtl/base/GeneralObject.py deleted file mode 100755 index 311c9e22..00000000 --- a/web/webqtl/base/GeneralObject.py +++ /dev/null @@ -1,71 +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 - -class GeneralObject: - """ - Base class to define an Object. - a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] - a.sort(lambda x, y: cmp(x.eggs, y.eggs)) - """ - - def __init__(self, *args, **kw): - self.contents = list(args) - for name, value in kw.items(): - setattr(self, name, value) - - def __setitem__(self, key, value): - setattr(self, key, value) - - def __getitem__(self, key): - return getattr(self, key) - - def __getattr__(self, key): - if key in self.__dict__.keys(): - return self.__dict__[key] - else: - return eval("self.__dict__.%s" % key) - - def __len__(self): - return len(self.__dict__) - 1 - - def __str__(self): - s = '' - for key in self.__dict__.keys(): - if key != 'contents': - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __repr__(self): - s = '' - for key in self.__dict__.keys(): - s += '%s = %s\n' % (key,self.__dict__[key]) - return s - - def __cmp__(self,other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) - - - diff --git a/web/webqtl/base/__init__.py b/web/webqtl/base/__init__.py deleted file mode 100755 index e69de29b..00000000 --- a/web/webqtl/base/__init__.py +++ /dev/null diff --git a/web/webqtl/base/admin.py b/web/webqtl/base/admin.py deleted file mode 100755 index a04df2da..00000000 --- a/web/webqtl/base/admin.py +++ /dev/null @@ -1,88 +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 - - - - - -#XZ, 04/02/2009: we should put this into database. - - -###LIST of databases used into gene name query - - -ADMIN_search_dbs = { - 'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'], - 'KIDNEY': ['KI_2A_0405_Rz'], - 'ADRENAL GLAND': ['HXB_Adrenal_1208'], - 'HEART': ['HXB_Heart_1208'] - }, - 'mouse': {'CEREBELLUM': ['CB_M_0305_R'], - 'STRIATUM': ['SA_M2_0905_R', 'SA_M2_0405_RC', 'UTHSC_1107_RankInv', 'Striatum_Exon_0209'], - 'HIPPOCAMPUS': ['HC_M2_0606_R', 'UMUTAffyExon_0209_RMA'], - 'WHOLE BRAIN': ['BR_M2_1106_R', 'IBR_M_0106_R', 'BRF2_M_0805_R', 'UCLA_BHF2_BRAIN_0605'], - 'LIVER': ['LV_G_0106_B', 'UCLA_BHF2_LIVER_0605'], - 'EYE': ['Eye_M2_0908_R'], - 'HEMATOPOIETIC STEM CELLS': ['HC_U_0304_R'], - 'KIDNEY': ['MA_M2_0806_R'], - 'MAMMARY TUMORS': ['MA_M_0704_R', 'NCI_Agil_Mam_Tum_RMA_0409'], - 'PREFRONTAL CORTEX': ['VCUSal_1206_R'], - 'SPLEEN': ['IoP_SPL_RMA_0509'], - 'NUCLEUS ACCUMBENS': ['VCUSalo_1007_R'], - 'NEOCORTEX': ['HQFNeoc_0208_RankInv'], - 'ADIPOSE': ['UCLA_BHF2_ADIPOSE_0605'], - 'RETINA': ['Illum_Retina_BXD_RankInv0410'] - }, - 'human': { - 'LYMPHOBLAST B CELL': ['Human_1008', 'UT_CEPH_RankInv0909'], - 'WHOLE BRAIN': ['GSE5281_F_RMA0709', 'GSE15222_F_RI_0409'] - } - } - - -###LIST of tissue alias - -ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'], - 'STRIATUM': ['Str'], - 'HIPPOCAMPUS': ['Hip'], - 'WHOLE BRAIN': ['Brn'], - 'LIVER': ['Liv'], - 'EYE': ['Eye'], - 'PERITONEAL FAT': ['Fat'], - 'HEMATOPOIETIC STEM CELLS': ['Hsc'], - 'KIDNEY': ['Kid'], - 'ADRENAL GLAND': ['Adr'], - 'HEART': ['Hea'], - 'MAMMARY TUMORS': ['Mam'], - 'PREFRONTAL CORTEX': ['Pfc'], - 'SPLEEN': ['Spl'], - 'NUCLEUS ACCUMBENS': ['Nac'], - 'NEOCORTEX': ['Ctx'], - 'ADIPOSE': ['Wfat'], - 'RETINA': ['Ret'] - } - - diff --git a/web/webqtl/base/cgiData.py b/web/webqtl/base/cgiData.py deleted file mode 100755 index 57416060..00000000 --- a/web/webqtl/base/cgiData.py +++ /dev/null @@ -1,70 +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 - -######################################### -#convert Field storage object to Dict object -#in order to be able to saved into a session file -######################################### - -class cgiData(dict): - '''convert Field storage object to Dict object - Filed storage object cannot be properly dumped - ''' - - def __init__(self, field_storage=None): - - if not field_storage: - field_storage={} - - for key in field_storage.keys(): - temp = field_storage.getlist(key) - if len(temp) > 1: - temp = map(self.toValue, temp) - elif len(temp) == 1: - temp = self.toValue(temp[0]) - else: - temp = None - self[key]= temp - - def toValue(self, obj): - '''fieldstorge returns different type of objects, \ - need to convert to string or None''' - try: - return obj.value - except: - return "" - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default - - getfirst = getvalue - - - - diff --git a/web/webqtl/base/cookieData.py b/web/webqtl/base/cookieData.py deleted file mode 100755 index 4b7c9046..00000000 --- a/web/webqtl/base/cookieData.py +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -######################################### -#convert mod_python object to Dict object -#in order to be able to be pickled -######################################### - -class cookieData(dict): - 'convert mod python Cookie object to Dict object' - - def __init__(self, cookies=None): - - if not cookies: - cookies={} - - for key in cookies.keys(): - self[key.lower()]= cookies[key].value - - def getvalue(self, k, default= None): - try: - return self[k.lower()] - except: - return default - - getfirst = getvalue - - - diff --git a/web/webqtl/base/footer.py b/web/webqtl/base/footer.py deleted file mode 100755 index 6f92fdf8..00000000 --- a/web/webqtl/base/footer.py +++ /dev/null @@ -1,6 +0,0 @@ -import webqtlConfig - -footer_html = open(webqtlConfig.HTMLPATH + 'footer.html', 'r').read() -footer = footer_html.replace('%"','%%"') - -footer_string = footer.replace('<!-- %s -->', '%s') diff --git a/web/webqtl/base/header.py b/web/webqtl/base/header.py deleted file mode 100755 index b6136b51..00000000 --- a/web/webqtl/base/header.py +++ /dev/null @@ -1,6 +0,0 @@ -import webqtlConfig - -header_string = open(webqtlConfig.HTMLPATH + 'header.html', 'r').read() -header_string = header_string.replace("\\'", "'") -header_string = header_string.replace('%"','%%"') -header_string = header_string.replace('<!-- %s -->', '%s') \ No newline at end of file diff --git a/web/webqtl/base/indexBody.py b/web/webqtl/base/indexBody.py deleted file mode 100755 index e73409a5..00000000 --- a/web/webqtl/base/indexBody.py +++ /dev/null @@ -1,291 +0,0 @@ -index_body_string = """ -<TD vAlign=top width="40%" align="left" height=10 bgColor=#eeeeee> - <p style="font-size:18px;font-family:verdana;color:black"><B> Select and Search</B> - <Form METHOD="POST" ACTION="/webqtl/main.py" ENCTYPE="multipart/form-data" NAME="SEARCHFORM"> - - <TABLE width="100%"> - - <!-- 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 width="3%"> - </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 width="3%"> - </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>Data Set:</B> - </TD> - - <TD width="3%"> - </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> - - <!-- USER HELP --> - <TR> - <TD align=right height=20 width="10%"> - </TD> - <TD width="3%"> - </TD> - - <TD align="left" width="85%"> - <P class="fs12"> Databases marked with <B>**</B> suffix are not public yet. - <BR> Access requires <A HREF="/account.html" target="_blank" class="fs14"><small>user login</small></A>.</P> - </TD> - </TR> - - -<!-- GET ANY SEARCH --> - <TR> - <TD align=right height=35 NOWRAP="on" style="font-size:14px;font-family:verdana;color:black" width="10%"> - <B>Get Any:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - - <input id="tfor" name="ORkeyword" style="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500"> - </TD> - </TR> - - - -<!-- GET ANY HELP --> - <TR> - <TD align=right height=20 width="10%"> - </TD> - <TD width="3%"> - - </TD> - <TD width="85%" align="left"> - <P class="fs12"> Enter terms, genes, ID numbers in the <B>Get Any</B> field. - <BR> Use <B>*</B> or <B>?</B> wildcards (Cyp*a?, synap*). - <BR> Use <B>Combined</B> for terms such as <I>tyrosine kinase</I>.</P> - - </TD> - </TR> - - - -<!-- COMBINED SEARCH --> - - <TR> - <TD align=right height=35 NOWRAP="on" STYLE="font-size:14px;font-family:verdana;color:black" width="10%"> - <B>Combined:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <input id="tfand" NAME="ANDkeyword" STYLE="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500"> - <input name="matchwhole" type="hidden" value="ON"> - </TD> - </TR> - - - -<!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH --> - - <TR ALIGN="center"> - <TD width="3%"> - </TD> - <TD width="3%"> - </TD> - <TD ALIGN="left" HEIGHT="40" COLSPAN=3> - <INPUT id="btsearch" TYPE="Submit" CLASS="button" STYLE="font-size:12px" VALUE=" Search "> - <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Make Default " onClick = "setDefault(this.form);"> - <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Advanced Search " onClick="javascript:window.open('/index3.html', '_self');"> - - </TD> - </TR> - </TABLE> - <INPUT TYPE="hidden" NAME="FormID" VALUE="searchResult"> - <INPUT TYPE="hidden" NAME="RISet" VALUE="BXD"> - <SCRIPT SRC="/javascript/selectDatasetMenu.js"></SCRIPT> - </FORM> - </CENTER> - - - - - -<!-- QUICK HELP --> - -<P><LEFT> ______________________________________________________ - -<P STYLE="font-size:13px;font-family:verdana;color:black"><B> - -Quick HELP Examples and </B> -<A HREF="http://www.genenetwork.org/index4.html" target="_blank" class="fs14"><B> - User's Guide</B></A></P> - -</CENTER style="font-size:12px;font-family:verdana;color:black"> - You can also use advanced commands. Copy these simple examples -<BR> into the <B>Get Any</B> or <B>Combined</B> search fields: -<UL style="font-size:12px;font-family:verdana;color:black"> - -<LI><B><I>POSITION=(chr1 25 30)</I></B> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb. - -<LI><B><I>MEAN=(15 16) LRS=(23 46)</I></B> in the <B>Combined</B> field finds highly expressed genes (15 to 16 log2 units) AND with peak <A HREF="http://www.genenetwork.org/glossary.html#L" target="_blank" class="fs14"><small>LRS</small></A> linkage between 23 and 46. - - -<LI><B><I>RIF=mitochondrial</I></B> searches RNA databases for <A HREF="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank" class="fs14"><small>GeneRIF</small></A> links. - -<LI><B><I>WIKI=nicotine</I></B> searches <A HREF="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class="fs14"><small>GeneWiki</small></A> for genes that you or other users have annotated with the word <I>nicotine</I>. - -<LI><B><I>GO:0045202</I></B> searches for synapse-associated genes listed in the <A HREF="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class="fs14"><small>Gene Ontology</small></A>. - - -<LI><B><I>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds synapse-associated genes with <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank" class="fs14"><small>cis eQTL</small></A> on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999. - -<LI><B><I>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds diabetes-associated transcripts with peak <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank" class="fs14"><small>trans eQTLs</small></A> on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999. - - -</UL> -</DIR> - </TD> -<!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) --> - -<!-- START OF TOP RIGHT PANEL --> - -<TD vAlign=top width="40%" bgColor=#FFFFFF> - <p style="font-size:15px;font-family:verdana;color:black"><B>Websites Affiliated with GeneNetwork</B></p> - <p style="font-size:12px;font-family:verdana;color:black"> - <ul> - <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome Browser</a> at UTHSC</li> - <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at UTHSC</li> - <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon Cloud (EC2)</a></li> - <li>GeneNetwork Source Codes at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li> - <li>GeneNetwork Source Codes at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li> - </ul> - </p> - <P>____________________________ - - <p style="font-size:15px;font-family:verdana;color:black"><B>Getting Started</B> </p> - <OL style="font-size:12px;font-family:verdana;color:black"> - <LI>Select <B>Species</B> (or select All) - <LI>Select <B>Group</B> (a specific sample) - <LI>Select <B>Type</B> of data: - <UL> - <LI>Phenotype (traits) - <LI>Genotype (markers) - <LI>Expression (mRNAs) - </UL> - <LI>Select a <B>Database</B> - <LI>Enter search terms in the <B>Get Any</B> or <B>Combined</B> field: words, genes, ID numbers, probes, advanced search commands - <LI>Click on the <B>Search</B> button - <LI>Optional: Use the <B>Make Default</B> button to save your preferences - </OL> - - <P>____________________________ - -<p style="font-size:14px;font-family:verdana;color:black"><B>How to Use GeneNetwork</B> - - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute GeneNetwork <A HREF="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14"><small>Tour</small></A> that includes screen shots and typical steps in the analysis.</P> - </BLOCKQUOTE> - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">For information about resources and methods, select the <img src="http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border= 0 valign="middle"> buttons.</P> - - - -<p style="font-size:12px;font-family:verdana;color:black">Try the <A HREF="http://alexandria.uthsc.edu/" target="_blank" class="fs14"><small>Workstation</small></A> site to explore data and features that are being implemented.</P> - - -<p style="font-size:12px;font-family:verdana;color:black">Review the <A HREF="/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></A> and <A HREF="/statusandContact.html" target="_blank" class="fs14"><small>Contacts</small></A> pages for information on the status of data sets and advice on their use and citation.</P> - - - </BLOCKQUOTE> - - - - <p style="font-size:14px;font-family:verdana;color:black"><B>Mirror and Development Sites</B></P> - - <UL> - <LI><A HREF="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</A> (main site) - <LI><A HREF="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</A> - <LI><A HREF="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</A> - <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><A HREF="https://genenetwork.hubrecht.eu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</A> (Development) - <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><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><A HREF="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</A> - </UL> - - - <p style="font-size:14px;font-family:verdana;color:black"><B>History and Archive</B> - - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <A HREF="http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time Machine</small></A> links to earlier versions that correspond to specific publication dates.</P> - - </BLOCKQUOTE> - - -</P> - </TD> -""" diff --git a/web/webqtl/base/myCookie.py b/web/webqtl/base/myCookie.py deleted file mode 100755 index db5320df..00000000 --- a/web/webqtl/base/myCookie.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 - -######################################### -## python cookie and mod python cookie are -## not compatible -######################################### - -class myCookie(dict): - 'define my own cookie' - - def __init__(self, name="", value="", expire = None, path="/"): - self['name']= name - self['value']= value - self['expire']= expire - self['path']= path - - def __getattr__(self, key): - if key in self.keys(): - return self[key] - else: - return None - - def __nonzero__ (self): - if self['name']: - return 1 - else: - return 0 - - - - diff --git a/web/webqtl/base/sessionData.py b/web/webqtl/base/sessionData.py deleted file mode 100755 index 01555f87..00000000 --- a/web/webqtl/base/sessionData.py +++ /dev/null @@ -1,53 +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 - -######################################### -#convert mod_python object to Dict object -#in order to be able to be pickled -######################################### - -class sessionData(dict): - 'convert mod python Session object to Dict object' - - def __init__(self, mod_python_session=None): - - if not mod_python_session: - mod_python_session = {} - - for key in mod_python_session.keys(): - self[key]= mod_python_session[key] - - - def getvalue(self, k, default= None): - try: - return self[k] - except: - return default - - getfirst = getvalue - - - diff --git a/web/webqtl/base/template.py b/web/webqtl/base/template.py deleted file mode 100755 index 85bd86df..00000000 --- a/web/webqtl/base/template.py +++ /dev/null @@ -1,123 +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 - -template = """ -<?XML VERSION="1.0" ENCODING="UTF-8"> -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML> -<HEAD> -<TITLE>%s</TITLE> - -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> -<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine"> -<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." > -<META NAME="author" CONTENT ="GeneNetwork developers" > -<META NAME="geo.placename" CONTENT ="Memphis, TN" > -<META NAME="geo.region" CONTENT="US-TN"> -%s -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> -<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> -<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" /> -<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' /> -<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' /> - -<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script> -<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> -<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> -<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT> -<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT> -<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> -<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script> -%s - -<script type="text/javascript"> - var _gaq = _gaq || []; - _gaq.push(['_setAccount', 'UA-3782271-1']); - _gaq.push(['_trackPageview']); - (function() { - var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; - ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; - var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); - })(); -</script> -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s> -%s -<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0> - <TBODY> - <!-- Start of header --> - <TR> - %s - </TR> - <!-- End of header --> - - <!-- Start of body --> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%%" cellSpacing=0 cellPadding=5> - <TR> - %s - </TR> - </TABLE> - </TD> - </TR> - <!-- End of body --> - - <!-- Start of footer --> - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <TABLE width="90%%">%s</table> - </td> - </TR> - <!-- End of footer --> -</TABLE> - -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="/javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="/javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="/javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - // Don't try to position menu locating menu initialization block in - // some table cell or other HTML element. Always put it before </body> - // each menu gets two parameters (see demo files) - // 1. items structure - // 2. geometry structure - new menu (MENU_ITEMS, MENU_POS); - // make sure files containing definitions for these variables are linked to the document - // if you got some javascript error like "MENU_POS is not defined", then you've made syntax - // error in menu_tpl.js file or that file isn't linked properly. - - // also take a look at stylesheets loaded in header in order to set styles - //--> -</script> -</BODY> -</HTML> -""" diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py deleted file mode 100755 index 4dece24a..00000000 --- a/web/webqtl/base/templatePage.py +++ /dev/null @@ -1,222 +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 - -#templatePage.py -# -#--Genenetwork generates a lot of pages; this file is the generic version of them, defining routines they all use. -# -#Classes: -#templatePage -# -#Functions (of templatePage): -#__init__(...) -- class constructor, allows a more specific template to be used in addition to templatePage -#__str__(self) -- returns the object's elements as a tuple -#__del__(self) -- closes the current connection to MySQL, if there is one -#write -- explained below -#writefile -- explained below -#openMysql(self) -- opens a MySQL connection and stores the resulting cursor in the object's cursor variable -#updMysql(self) -- same as openMysql -#error -- explained below -#session -- explained below - - -import socket -import time -import shutil -import MySQLdb -import os - -from htmlgen import HTMLgen2 as HT - -import template -import webqtlConfig -import header -import footer -from utility import webqtlUtil - - - -class templatePage: - - contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer'] - - # you can pass in another template here if you want - def __init__(self, fd=None, template=template.template): - - # initiate dictionary - self.starttime = time.time() - self.dict = {} - self.template = template - - for item in self.contents: - self.dict[item] = "" - - self.dict['basehref'] = "" #webqtlConfig.BASEHREF - self.cursor = None - - self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed - self.content_type = 'text/html' - self.content_disposition = '' - self.redirection = '' - self.debug = '' - self.attachment = '' - - #XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!! - self.session_data_changed = {} - - self.userName = 'Guest' - self.privilege = 'guest' - if fd.input_session_data.has_key('user'): - self.userName = fd.input_session_data['user'] - if fd.input_session_data.has_key('privilege'): - self.privilege = fd.input_session_data['privilege'] - - def __str__(self): - - #XZ: default setting - thisUserName = self.userName - thisPrivilege = self.privilege - #XZ: user may just go through login or logoff page - if self.session_data_changed.has_key('user'): - thisUserName = self.session_data_changed['user'] - if self.session_data_changed.has_key('privilege'): - thisPrivilege = self.session_data_changed['privilege'] - - if thisUserName == 'Guest': - userInfo = 'Welcome! <a href=/account.html><U>Login</U></a>' - else: - userInfo = 'Hi, %s! <a href=/webqtl/main.py?FormID=userLogoff><U>Logout</U></a>' % thisUserName - - reload(header) - self.dict['header'] = header.header_string % userInfo - - serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn()) - reload(footer) - self.dict['footer'] = footer.footer_string % serverInfo - - slist = [] - for item in self.contents: - slist.append(self.dict[item]) - return self.template % tuple(slist) - - - def __del__(self): - if self.cursor: - self.cursor.close() - - def write(self): - 'return string representation of this object' - - if self.cursor: - self.cursor.close() - - return str(self) - - def writeFile(self, filename): - 'save string representation of this object into a file' - if self.cursor: - self.cursor.close() - - try: - 'it could take a long time to generate the file, save to .tmp first' - fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb') - fp.write(str(self)) - fp.close() - path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp') - path_html = os.path.join(webqtlConfig.TMPDIR, filename) - shutil.move(path_tmp,path_html) - except: - pass - - def openMysql(self): - try: - self.con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \ - user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) - self.cursor = self.con.cursor() - return 1 - except: - heading = "Connect MySQL Server" - detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \ - The server may be down at this time"] - self.error(heading=heading,detail=detail,error="Error 2003") - return 0 - - def updMysql(self): - try: - self.con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \ - user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD) - self.cursor = self.con.cursor() - return 1 - except: - heading = "Connect MySQL Server" - detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \ - The server may be down at this time "] - self.error(heading=heading,detail=detail,error="Error 2003") - return 0 - - def error(self,heading="",intro=[],detail=[],title="Error",error="Error"): - 'generating a WebQTL style error page' - Heading = HT.Paragraph(heading) - Heading.__setattr__("class","title") - - Intro = HT.Blockquote() - if intro: - for item in intro: - Intro.append(item) - else: - Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\ - your request.', HT.P(),'The nature of the error generated is as\ - follows:') - - Detail = HT.Blockquote() - Detail.append(HT.Span("%s : " % error,Class="fwb cr")) - if detail: - Detail2 = HT.Blockquote() - for item in detail: - Detail2.append(item) - Detail.append(HT.Italic(Detail2)) - - #Detail.__setattr__("class","subtitle") - TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top") - TD_LR.append(Heading,Intro,Detail) - self.dict['body'] = str(TD_LR) - self.dict['title'] = title - - def session(self,mytitle="",myHeading=""): - 'generate a auto-refreshing temporary html file(waiting page)' - self.filename = webqtlUtil.generate_session() - self.dict['title'] = mytitle - self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF - - TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee') - Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr") - # NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py; - TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR) - self.dict['body'] = TD_LR - self.writeFile(self.filename + '.html') - return self.filename - - diff --git a/web/webqtl/base/webqtlCaseData.py b/web/webqtl/base/webqtlCaseData.py deleted file mode 100755 index 4df32ca4..00000000 --- a/web/webqtl/base/webqtlCaseData.py +++ /dev/null @@ -1,54 +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 - -class webqtlCaseData: - """ - one case data in one trait - """ - - val = None #Trait Value - var = None #Trait Variance - N = None #Number of individuals - - def __init__(self, val=val, var=var, N=N): - self.val = val - self.var = var - self.N = N - - def __str__(self): - str = "" - if self.val != None: - str += "value=%2.3f" % self.val - if self.var != None: - str += " variance=%2.3f" % self.var - if self.N != None: - str += " ndata=%d" % self.N - return str - - __repr__ = __str__ - - - diff --git a/web/webqtl/base/webqtlConfig.py b/web/webqtl/base/webqtlConfig.py deleted file mode 100755 index 87e2f3d0..00000000 --- a/web/webqtl/base/webqtlConfig.py +++ /dev/null @@ -1,73 +0,0 @@ -from webqtlConfigLocal import * -#########################################' -# Environment Variables - public -######################################### - -#Debug Level -#1 for debug, mod python will reload import each time -DEBUG = 1 - -#USER privilege -USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} - -#minimum number of informative strains -KMININFORMATIVE = 5 - -#maximum number of traits for interval mapping -MULTIPLEMAPPINGLIMIT = 11 - -#maximum number of traits for correlation -MAXCORR = 100 - -#Daily download limit from one IP -DAILYMAXIMUM = 1000 - -#maximum LRS value -MAXLRS = 460.0 - -#temporary data life span -MAXLIFE = 86400 - -#MINIMUM Database public value -PUBLICTHRESH = 0 - -#NBCI address -NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" -UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" -GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" -OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" -UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s" -HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" -PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" -UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" -UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s" -ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' -UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s" -GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" -ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" - -SECUREDIR = GNROOT + 'secure/' -COMMON_LIB = GNROOT + 'support/admin' -HTMLPATH = GNROOT + 'web/' -IMGDIR = HTMLPATH +'image/' -IMAGESPATH = HTMLPATH + 'images/' -UPLOADPATH = IMAGESPATH + 'upload/' -TMPDIR = HTMLPATH +'tmp/' -GENODIR = HTMLPATH + 'genotypes/' -GENO_ARCHIVE_DIR = GENODIR + 'archive/' -TEXTDIR = HTMLPATH + 'ProbeSetFreeze_DataMatrix/' -CMDLINEDIR = HTMLPATH + 'webqtl/cmdLine/' -ChangableHtmlPath = GNROOT + 'web/' - -SITENAME = 'GN' -PORTADDR = "http://132.192.47.32" -BASEHREF = '<base href="http://132.192.47.32/">' -INFOPAGEHREF = '/dbdoc/%s.html' -GLOSSARYFILE = "/glossary.html" -CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' -SCRIPTFILE = 'main.py' -REFRESHSTR = '<meta http-equiv="refresh" content="5;url=%s' + SCRIPTFILE +'?sid=%s">' -REFRESHDIR = '%s' + SCRIPTFILE +'?sid=%s' diff --git a/web/webqtl/base/webqtlConfigLocal.py b/web/webqtl/base/webqtlConfigLocal.py deleted file mode 100755 index 1f986aa7..00000000 --- a/web/webqtl/base/webqtlConfigLocal.py +++ /dev/null @@ -1,17 +0,0 @@ -#########################################' -# Environment Variables - private -######################################### - -MYSQL_SERVER = 'localhost' -DB_NAME = 'db_webqtl_zas1024' -DB_USER = 'webqtlupd' -DB_PASSWD = 'webqtl' - -MYSQL_UPDSERVER = 'localhost' -DB_UPDNAME = 'db_webqtl_zas1024' -DB_UPDUSER = 'webqtlupd' -DB_UPDPASSWD = 'webqtl' - -GNROOT = '/home/zas1024/gn/' -PythonPath = '/usr/bin/python' -PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/' diff --git a/web/webqtl/base/webqtlDataset.py b/web/webqtl/base/webqtlDataset.py deleted file mode 100755 index da1b8601..00000000 --- a/web/webqtl/base/webqtlDataset.py +++ /dev/null @@ -1,160 +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 htmlgen import HTMLgen2 as HT - -import webqtlConfig - - - -class webqtlDataset: - """ - Database class defines a database in webqtl, can be either Microarray, - Published phenotype, genotype, or user input database(temp) - """ - - def __init__(self, dbName, cursor=None): - - assert dbName - self.id = 0 - self.name = '' - self.type = '' - self.riset = '' - self.cursor = cursor - - #temporary storage - if dbName.find('Temp') >= 0: - self.searchfield = ['name','description'] - self.disfield = ['name','description'] - self.type = 'Temp' - self.id = 1 - self.fullname = 'Temporary Storage' - self.shortname = 'Temp' - elif dbName.find('Publish') >= 0: - self.searchfield = ['name','post_publication_description','abstract','title','authors'] - self.disfield = ['name','pubmed_id', - 'pre_publication_description', 'post_publication_description', 'original_description', - 'pre_publication_abbreviation', 'post_publication_abbreviation', - 'lab_code', 'submitter', 'owner', 'authorized_users', - 'authors','title','abstract', 'journal','volume','pages','month', - 'year','sequence', 'units', 'comments'] - self.type = 'Publish' - elif dbName.find('Geno') >= 0: - self.searchfield = ['name','chr'] - self.disfield = ['name','chr','mb', 'source2', 'sequence'] - self.type = 'Geno' - else: #ProbeSet - self.searchfield = ['name','description','probe_target_description', - 'symbol','alias','genbankid','unigeneid','omim', - 'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score'] - self.disfield = ['name','symbol','description','probe_target_description', - 'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim', - 'refseq_transcriptid','blatseq','targetseq','chipid', 'comments', - 'strand_probe','strand_gene','probe_set_target_region', - 'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start', - 'probe_set_blat_mb_end', 'probe_set_strand', - 'probe_set_note_by_rw', 'flag'] - self.type = 'ProbeSet' - self.name = dbName - if self.cursor and self.id == 0: - self.retrieveName() - - def __str__(self): - return self.name - - __repr__ = __str__ - - - def getRISet(self): - assert self.cursor - if self.type == 'Publish': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, PublishFreeze - WHERE - PublishFreeze.InbredSetId = InbredSet.Id AND - PublishFreeze.Name = "%s" - ''' % self.name - elif self.type == 'Geno': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, GenoFreeze - WHERE - GenoFreeze.InbredSetId = InbredSet.Id AND - GenoFreeze.Name = "%s" - ''' % self.name - elif self.type == 'ProbeSet': - query = ''' - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, ProbeSetFreeze, ProbeFreeze - WHERE - ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % self.name - else: - return "" - self.cursor.execute(query) - RISet, RIID = self.cursor.fetchone() - if RISet == 'BXD300': - RISet = "BXD" - self.riset = RISet - self.risetid = RIID - return RISet - - - def retrieveName(self): - assert self.id == 0 and self.cursor - query = ''' - SELECT - Id, Name, FullName, ShortName - FROM - %sFreeze - WHERE - public > %d AND - (Name = "%s" OR FullName = "%s" OR ShortName = "%s") - '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name) - try: - self.cursor.execute(query) - self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone() - except: - raise KeyError, `self.name`+' doesn\'t exist.' - - - def genHTML(self, Class='c0dd'): - return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), - url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank") - - - - - diff --git a/web/webqtl/base/webqtlFormData.py b/web/webqtl/base/webqtlFormData.py deleted file mode 100755 index 84e41cae..00000000 --- a/web/webqtl/base/webqtlFormData.py +++ /dev/null @@ -1,289 +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 mod_python import Cookie -import string -import os - -import reaper - -import webqtlConfig -import cookieData -import sessionData -from cgiData import cgiData -from webqtlCaseData import webqtlCaseData -from utility import webqtlUtil - - - -class webqtlFormData: - 'Represents data from a WebQTL form page, needed to generate the next page' - attrs = ('formID','RISet','genotype','strainlist','allstrainlist', - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, req = None, mod_python_session=None, FieldStorage_formdata=None): - - for item in self.attrs: - setattr(self,item, None) - - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - if req and req.headers_in.has_key('referer'): - self.refURL = req.headers_in['referer'] - else: - self.refURL = None - - - self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. - - #XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. - self.input_session_data = sessionData.sessionData( mod_python_session ) - - #XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. - self.formdata = cgiData( FieldStorage_formdata ) - - #get Form ID - self.formID = self.formdata.getfirst('FormID') - - #get rest of the attributes - if self.formID: - for item in self.attrs: - value = self.formdata.getfirst(item) - if value != None: - setattr(self,item,string.strip(value)) - - self.ppolar = "" - self.mpolar = "" - if self.RISet: - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] - except: - f1 = f12 = self.mpolar = self.ppolar = None - - try: - self.nperm = int(self.nperm) - self.nboot = int(self.nboot) - except: - self.nperm = 2000 #XZ: Rob asked to change the default value to 2000 - self.nboot = 2000 #XZ: Rob asked to change the default value to 2000 - - if self.allstrainlist: - self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) - #self.readGenotype() - #self.readData() - - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - 'read genotype from .geno file' - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - assert self.RISet - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - self.genotype_1 = reaper.Dataset() - self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] - except: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 =self.genotype_1 - if self.genotype_1.type == "riset" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - self.strainlist = list(self.genotype.prgy) - self.f1list = self.parlist = [] - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - def readData(self, strainlst=[], incf1=[]): - 'read user input data or from trait data and analysis form' - - if not self.genotype: - self.readGenotype() - if not strainlst: - if incf1: - strainlst = self.f1list + self.strainlist - else: - strainlst = self.strainlist - - - traitfiledata = self.formdata.getfirst('traitfile') - traitpastedata = self.formdata.getfirst('traitpaste') - variancefiledata = self.formdata.getfirst('variancefile') - variancepastedata = self.formdata.getfirst('variancepaste') - Nfiledata = self.formdata.getfirst('Nfile') - - - if traitfiledata: - tt = string.split(traitfiledata) - vals = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = string.split(traitpastedata) - vals = map(webqtlUtil.StringAsFloat, tt) - else: - vals = map(self.FormDataAsFloat, strainlst) - - if len(vals) < len(strainlst): - vals += [None]*(len(strainlst) - len(vals)) - elif len(vals) > len(strainlst): - vals = vals[:len(strainlst)] - else: - pass - - - if variancefiledata: - tt = string.split(variancefiledata) - vars = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = string.split(variancepastedata) - vars = map(webqtlUtil.StringAsFloat, tt) - else: - vars = map(self.FormVarianceAsFloat, strainlst) - - if len(vars) < len(strainlst): - vars += [None]*(len(strainlst) - len(vars)) - elif len(vars) > len(strainlst): - vars = vars[:len(strainlst)] - else: - pass - - if Nfiledata: - tt = string.split(Nfiledata) - nstrains = map(webqtlUtil.IntAsFloat, tt) - if len(nstrains) < len(strainlst): - nstrains += [None]*(len(strainlst) - len(nstrains)) - else: - nstrains = map(self.FormNAsFloat, strainlst) - - ##vals, vars, nstrains is obsolete - self.allTraitData = {} - for i, _strain in enumerate(strainlst): - if vals[i] != None: - self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) - - - - def informativeStrains(self, strainlst=[], incVars = 0): - '''if readData was called, use this to output the informative strains - (strain with values)''' - if not strainlst: - strainlst = self.strainlist - strains = [] - vals = [] - vars = [] - for _strain in strainlst: - if self.allTraitData.has_key(_strain): - _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var - if _val != None: - if incVars: - if _var != None: - strains.append(_strain) - vals.append(_val) - vars.append(_var) - else: - strains.append(_strain) - vals.append(_val) - vars.append(None) - return strains, vals, vars, len(strains) - - - - def FormDataAsFloat(self, key): - try: - return float(self.formdata.getfirst(key)) - except: - return None - - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None - - def Sample(self): - 'Create some dummy data for testing' - self.RISet = 'BXD' - self.incparentsf1 = 'on' - #self.display = 9.2 - #self.significance = 16.1 - self.readGenotype() - self.identification = 'BXD : Coat color example by Lu Lu, et al' - #self.readGenotype() - #self.genotype.ReadMM('AXBXAforQTL') - #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) - #self.strainlist.sort() - self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), - 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), - 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), - 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), - 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), - 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), - 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), - 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), - 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), - 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), - 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), - 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), - 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} - diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py deleted file mode 100644 index 2469504f..00000000 --- a/web/webqtl/base/webqtlTrait.py +++ /dev/null @@ -1,590 +0,0 @@ -import string - -from htmlgen import HTMLgen2 as HT - -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from webqtlDataset import webqtlDataset -from dbFunction import webqtlDatabaseFunction -from utility import webqtlUtil - - -from __future__ import print_function, division - -from pprint import pformat as pf - -class webqtlTrait: - """ - Trait class defines a trait in webqtl, can be either Microarray, - Published phenotype, genotype, or user input trait - """ - - def __init__(self, cursor = None, **kw): - self.cursor = cursor - self.db = None # database object - self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = '' - self.identification = 'un-named trait' - self.riset = '' - self.haveinfo = 0 - self.sequence = '' # Blat sequence, available for ProbeSet - self.data = {} - for name, value in kw.items(): - if self.__dict__.has_key(name): - setattr(self, name, value) - elif name == 'fullname': - name2 = value.split("::") - if len(name2) == 2: - self.db, self.name = name2 - elif len(name2) == 3: - self.db, self.name, self.cellid = name2 - else: - raise KeyError, `value` + ' parameter format error.' - else: - raise KeyError, `name`+' not a valid parameter for this class.' - - if self.db and type(self.db) == type("1"): - assert self.cursor - self.db = webqtlDataset(self.db, self.cursor) - - #if self.db == None, not from a database - if self.db: - if self.db.type == "Temp": - self.cursor.execute(''' - SELECT - InbredSet.Name - FROM - InbredSet, Temp - WHERE - Temp.InbredSetId = InbredSet.Id AND - Temp.Name = "%s" - ''' % self.name) - self.riset = self.cursor.fetchone()[0] - else: - self.riset = self.db.getRISet() - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - - #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. - # The variable self.sequence should be changed to self.BlatSeq - # It also should be changed in other places where it are used. - - if self.db: - if self.db.type == 'ProbeSet': - query = ''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and - ProbeSet.Name = "%s" and - ProbeSetFreeze.Name = "%s" - ''' % (self.name, self.db.name) - self.cursor.execute(query) - self.sequence = self.cursor.fetchone()[0] - - - def getName(self): - str = "" - if self.db and self.name: - str = "%s::%s" % (self.db, self.name) - if self.cellid: - str += "::" + self.cellid - else: - str = self.description - return str - - # - # when user enter a trait or GN generate a trait, user want show the name - # not the name that generated by GN randomly, the two follow function are - # used to give the real name and the database. displayName() will show the - # database also, getGivenName() just show the name. - # For other trait, displayName() as same as getName(), getGivenName() as - # same as self.name - # - # Hongqiang 11/29/07 - # - def getGivenName(self): - str = self.name - if self.db and self.name: - if self.db.type=='Temp': - self.cursor.execute('SELECT description FROM Temp WHERE Name=%s',self.name) - desc = self.cursor.fetchone()[0] - if desc.__contains__('PCA'): - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - str = desc - return str - - def displayName(self): - str = "" - if self.db and self.name: - if self.db.type=='Temp': - desc = self.description - if desc.__contains__('PCA'): - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - str = "%s::%s" % (self.db, desc) - else: - str = "%s::%s" % (self.db, self.name) - if self.cellid: - str += "::" + self.cellid - else: - str = self.description - - return str - - - #def __str__(self): - # #return "%s %s" % (self.getName(), self.riset) - # return self.getName() - __str__ = getName - __repr__ = __str__ - - def exportData(self, strainlist, type="val"): - """ - export data according to strainlist - mostly used in calculating correlation - """ - result = [] - for strain in strainlist: - if self.data.has_key(strain): - if type=='val': - result.append(self.data[strain].val) - elif type=='var': - result.append(self.data[strain].var) - elif type=='N': - result.append(self.data[strain].N) - else: - raise KeyError, `type`+' type is incorrect.' - else: - result.append(None) - return result - - def exportInformative(self, incVar=0): - """ - export informative strain - mostly used in qtl regression - """ - strains = [] - vals = [] - vars = [] - for strain, value in self.data.items(): - if value.val != None: - if not incVar or value.var != None: - strains.append(strain) - vals.append(value.val) - vars.append(value.var) - return strains, vals, vars - - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - def getSequence(self): - assert self.cursor - if self.db.type == 'ProbeSet': - query = ''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - ''' , (self.name, self.db.name) - self.cursor.execute(query) - results = self.fetchone() - - return results[0] - - - - def retrieveData(self, strainlist=[]): - assert self.db and self.cursor - - debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w") - debug_file.write("strianlist is:" + strainlist + "\n") - - if self.db.type == 'Temp': - query = ''' - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - ''' % self.name - #XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE - elif self.db.type == 'Publish': - query = ''' - SELECT - Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id - FROM - (PublishData, Strain, PublishXRef, PublishFreeze) - left join PublishSE on - (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) - left join NStrain on - (NStrain.DataId = PublishData.Id AND - NStrain.StrainId = PublishData.StrainId) - WHERE - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.name, self.db.id) - - #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE - elif self.cellid: - #Probe Data - query = ''' - SELECT - Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id - FROM - (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, - Strain, Probe, ProbeSet) - left join ProbeSE on - (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId) - WHERE - Probe.Name = '%s' AND ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id AND - ProbeXRef.ProbeId = Probe.Id AND - ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeXRef.DataId = ProbeData.Id AND - ProbeData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.cellid, self.name, self.db.name) - #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE - elif self.db.type == 'ProbeSet': - #ProbeSet Data - query = ''' - SELECT - Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id - FROM - (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) - left join ProbeSetSE on - (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) - WHERE - ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSetXRef.DataId = ProbeSetData.Id AND - ProbeSetData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (self.name, self.db.name) - #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE - else: - #Geno Data - #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search. - query = ''' - SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id - FROM - (GenoData, GenoFreeze, Strain, Geno, GenoXRef) - left join GenoSE on - (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) - WHERE - Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '%s' AND - GenoXRef.DataId = GenoData.Id AND - GenoData.StrainId = Strain.Id - Order BY - Strain.Name - ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name) - - - self.cursor.execute(query) - results = self.cursor.fetchall() - self.data.clear() - if results: - self.mysqlid = results[0][-1] - if strainlist: - for item in results: - if item[0] in strainlist: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) - #end for - else: - for item in results: - val = item[1] - if val != None: - var = item[2] - ndata = None - if self.db.type in ('Publish', 'Temp'): - ndata = item[3] - self.data[item[0]] = webqtlCaseData(val, var, ndata) - #end for - #end if - else: - pass - - debug_file.write("self.data is:", pf(self.data) + "\n") - - def keys(self): - return self.__dict__.keys() - - def has_key(self, key): - return self.__dict__.has_key(key) - - def items(self): - return self.__dict__.items() - - def retrieveInfo(self, QTL = None): - assert self.db and self.cursor - if self.db.type == 'Publish': - #self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\ - # 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\ - # 'Units', 'comments'] - query = ''' - SELECT - PublishXRef.Id, Publication.PubMed_ID, - Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, - Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, - Publication.Authors, Publication.Title, Publication.Abstract, - Publication.Journal, Publication.Volume, Publication.Pages, - Publication.Month, Publication.Year, PublishXRef.Sequence, - Phenotype.Units, PublishXRef.comments - FROM - PublishXRef, Publication, Phenotype, PublishFreeze - WHERE - PublishXRef.Id = %s AND - Phenotype.Id = PublishXRef.PhenotypeId AND - Publication.Id = PublishXRef.PublicationId AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id =%s - ''' % (self.name, self.db.id) - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. - elif self.db.type == 'ProbeSet': - disfieldString = string.join(self.db.disfield,',ProbeSet.') - disfieldString = 'ProbeSet.' + disfieldString - query = """ - SELECT %s - FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' - """ % (disfieldString, self.db.name, self.name) - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name - # to avoid the problem of same marker name from different species. - elif self.db.type == 'Geno': - disfieldString = string.join(self.db.disfield,',Geno.') - disfieldString = 'Geno.' + disfieldString - query = """ - SELECT %s - FROM Geno, GenoFreeze, GenoXRef - WHERE - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Name = '%s' AND - Geno.Name = '%s' - """ % (disfieldString, self.db.name, self.name) - else: #Temp type - query = 'SELECT %s FROM %s WHERE Name = "%s"' % \ - (string.join(self.db.disfield,','), self.db.type, self.name) - - - self.cursor.execute(query) - traitInfo = self.cursor.fetchone() - if traitInfo: - self.haveinfo = 1 - - #XZ: assign SQL query result to trait attributes. - for i, field in enumerate(self.db.disfield): - setattr(self, field, traitInfo[i]) - - if self.db.type == 'Publish': - self.confidential = 0 - if self.pre_publication_description and not self.pubmed_id: - self.confidential = 1 - - self.homologeneid = None - if self.db.type == 'ProbeSet' and self.riset and self.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - try: - junk = float(self.geneid) - geneidIsNumber = 1 - except: - geneidIsNumber = 0 - - if geneidIsNumber: - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId =%s AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (self.geneid, self.riset) - self.cursor.execute(query) - result = self.cursor.fetchone() - else: - result = None - - if result: - self.homologeneid = result[0] - - if QTL: - if self.db.type == 'ProbeSet' and not self.cellid: - query = ''' - SELECT - ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean - FROM - ProbeSetXRef, ProbeSet - WHERE - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSet.Name = "%s" AND - ProbeSetXRef.ProbeSetFreezeId =%s - ''' % (self.name, self.db.id) - self.cursor.execute(query) - traitQTL = self.cursor.fetchone() - if traitQTL: - self.locus, self.lrs, self.pvalue, self.mean = traitQTL - else: - self.locus = self.lrs = self.pvalue = self.mean = "" - if self.db.type == 'Publish': - query = ''' - SELECT - PublishXRef.Locus, PublishXRef.LRS - FROM - PublishXRef, PublishFreeze - WHERE - PublishXRef.Id = %s AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id =%s - ''' % (self.name, self.db.id) - self.cursor.execute(query) - traitQTL = self.cursor.fetchone() - if traitQTL: - self.locus, self.lrs = traitQTL - else: - self.locus = self.lrs = "" - else: - raise KeyError, `self.name`+' information is not found in the database.' - - def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""): - if not self.haveinfo: - self.retrieveInfo() - - if self.db.type == 'Publish': - PubMedLink = "" - if self.pubmed_id: - PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id, - target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id) - else: - PubMedLink = HT.Span("Unpublished : ", Class="fs15") - - if formName: - setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % - (formName, self.db.name, self.name), Class = "fs14") - else: - setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % - (self.db.name,self.name), Class = "fs14") - - if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users): - setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description)) - else: - setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description)) - - #XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1. - #if self.sequence > 1: - # setDescription2.append(' btach %d' % self.sequence) - if self.authors: - a1 = string.split(self.authors,',')[0] - while a1[0] == '"' or a1[0] == "'" : - a1 = a1[1:] - setDescription2.append(' by ') - setDescription2.append(HT.Italic('%s, and colleagues' % a1)) - setDescription = HT.Span(PubMedLink, setDescription2) - - elif self.db.type == 'Temp': - setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\ - ('%s','%s','')" % (self.db.name,self.name), Class = "fs14") - setDescription = HT.Span(setDescription) - - elif self.db.type == 'Geno': # Genome DB only available for single search - if formName: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \ - (formName, self.db.name, self.name), Class = "fs14") - else: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \ - (self.db.name,self.name), Class = "fs14") - - setDescription = HT.Span(setDescription) - - else: - if self.cellid: - if formName: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\ - "javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\ - "javascript:showDatabase2('%s','%s','%s')" % (self.db.name,self.name,self.cellid), \ - Class = "fs14") - else: - if formName: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase3('%s','%s','%s','')" % (formName, self.db.name,self.name), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase2('%s','%s','')" % (self.db.name,self.name), \ - Class = "fs14") - if self.symbol and self.chr and self.mb: - setDescription.append(' [') - setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb")) - setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb)) - if self.description: - setDescription.append(': %s' % self.description) - if self.probe_target_description: - setDescription.append('; %s' % self.probe_target_description) - setDescription = HT.Span(setDescription) - - if self.db.type != 'Temp' and dispFromDatabase: - setDescription.append( ' --- FROM : ') - setDescription.append(self.db.genHTML(Class='cori')) - return setDescription - - |