genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 17)

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[Genex-cvs-commit] genex-www/status/2003/feb status_main.ssi,1.2,1.3

From: <ki...@us...> - 2003-03-07 02:46:41

Update of /cvsroot/genex/genex-www/status/2003/feb
In directory sc8-pr-cvs1:/tmp/cvs-serv6878

Modified Files:
	status_main.ssi 
Log Message:
had wrong year


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/feb/status_main.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_main.ssi	5 Mar 2003 01:57:59 -0000	1.2
--- status_main.ssi	7 Mar 2003 02:46:37 -0000	1.3
***************
*** 4,8 ****
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>February 28th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">
--- 4,8 ----
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>February 28th, 2003</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">
***************
*** 67,71 ****
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>February 7th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">
--- 67,71 ----
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>February 7th, 2003</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">

[Genex-cvs-commit] genex-server INSTALL,1.26,1.27

From: <de...@us...> - 2003-03-07 01:49:03

Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv18595

Modified Files:
	INSTALL 
Log Message:
Updated the apt sources lines, libxerces17 is currently named
libxercesc17 (should I change it to not have the c?) 
Also removed the comment about not having a libbio-mage-perl debian
package. (go dh-make-perl!)


Index: INSTALL
===================================================================
RCS file: /cvsroot/genex/genex-server/INSTALL,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** INSTALL	13 Feb 2003 20:35:31 -0000	1.26
--- INSTALL	7 Mar 2003 01:48:57 -0000	1.27
***************
*** 54,67 ****
      
      #Diane trout's libxerces site
!     deb http://woldlab.caltech.edu/software woldlab main
!     
      The following command (as root) will install everything you need to support
!     GeneX (except the Perl Bio::MAGE package, which hasn't been packaged for
!     Debian yet and the DBD::Pg pkg as the Debian woody pkg is too old (req.
      >=1.12):
  
      apt-get install postgresql postgresql-dev postgresql-client \
!     postgresql-doc libpgtcl libpgperl expat  perlSGML libxerces17 \
!     libxerces17-dev libxml-xerces-perl libxaw7-dev  apache-dev \
      libapache-mod-perl libdevel-symdump-perl odbc-postgresql  libpgjava \
      pgaccess unixodbc-bin xgobi vncserver  perlSGML libcgi-pm-perl \
--- 54,67 ----
      
      #Diane trout's libxerces site
!     deb http://woldlab.caltech.edu/software/ genex2/$(ARCH)/
!     deb http://woldlab.caltech.edu/software/ genex2/all/
! 
      The following command (as root) will install everything you need to support
!     GeneX and the DBD::Pg pkg as the Debian woody pkg is too old (req.
      >=1.12):
  
      apt-get install postgresql postgresql-dev postgresql-client \
!     postgresql-doc libpgtcl libpgperl expat  perlSGML libxercesc17 \
!     libxercesc17-dev libxml-xerces-perl libxaw7-dev  apache-dev \
      libapache-mod-perl libdevel-symdump-perl odbc-postgresql  libpgjava \
      pgaccess unixodbc-bin xgobi vncserver  perlSGML libcgi-pm-perl \
***************
*** 69,75 ****
      libdigest-md5-perl libdbd-pg-perl libdbi-perl  libhtml-mason-perl \
      libtie-ixhash-perl libclass-objecttemplate-perl \
!     libclass-objecttemplate-db-perl libxerces17 libxerces17-dev \
      libxml-xerces-perl r-base-core r-recommended  r-base r-base-dev \
!     r-base-html
      
      for genespring/odbc connectivity
--- 69,75 ----
      libdigest-md5-perl libdbd-pg-perl libdbi-perl  libhtml-mason-perl \
      libtie-ixhash-perl libclass-objecttemplate-perl \
!     libclass-objecttemplate-db-perl  \
      libxml-xerces-perl r-base-core r-recommended  r-base r-base-dev \
!     r-base-html libbio-mage-perl
      
      for genespring/odbc connectivity

[Genex-cvs-commit] genex-www/status/2003/feb status_main.ssi,1.1,1.2

From: <ki...@us...> - 2003-03-05 01:58:02

Update of /cvsroot/genex/genex-www/status/2003/feb
In directory sc8-pr-cvs1:/tmp/cvs-serv18564

Modified Files:
	status_main.ssi 
Log Message:
link update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/feb/status_main.ssi,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** status_main.ssi	28 Feb 2003 22:13:13 -0000	1.1
--- status_main.ssi	5 Mar 2003 01:57:59 -0000	1.2
***************
*** 10,14 ****
  	
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  <p>
--- 10,14 ----
  	
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  <p>
***************
*** 44,48 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>
--- 44,48 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>
***************
*** 50,60 ****
  </p>
  <p>
!    On another note, my laptop has suffered from a RAM Slot Failure. It has been sent back to sony for repairs. Unfortunately, it had our only copy of GeneX 2.x. So, we are going to install GeneX 2.x on our database server soon, as Joe Roden would like to use the database. Any comments or suggestions about installation from a CVS checkout? Is it in a stable state? Any big changes planed soon?
  </p>
  <p>
!    Joe is hoping to load Affy U133 data into the database. Are the MAGE-ML file available to doing such a thing?
  </p>
  <p>
!    My goal for the next couple of weeks is to continue preparing <a href="http://pymerase.sf.net/">Pymerase</a> for release in the hope that other will use it and maybe even contribute to it. I also would like to get a better understanding of where GeneX 2.x currently stands?  We would love to see GeneX 2.x regain the momentum it had before the holidays... Maybe it has, but we've just been out of touch?
  </p>
  
--- 50,60 ----
  </p>
  <p>
!    On another note, my laptop has suffered from a RAM Slot Failure. It has been sent back to sony for repairs. Unfortunately, it had our only copy of <a href="http://genex.sf.net/">GeneX 2.x</a>. So, we are going to install <a href="http://genex.sf.net/">GeneX 2.x</a> on our database server soon, as Joe Roden would like to use the database. Any comments or suggestions about installation from a CVS checkout? Is it in a stable state? Any big changes planed soon?
  </p>
  <p>
!    Joe is hoping to load Affy U133 data into the database. Are the <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML file available to doing such a thing?
  </p>
  <p>
!    My goal for the next couple of weeks is to continue preparing <a href="http://pymerase.sf.net/">Pymerase</a> for release in the hope that other will use it and maybe even contribute to it. I also would like to get a better understanding of where <a href="http://genex.sf.net/">GeneX 2.x</a> currently stands?  We would love to see <a href="http://genex.sf.net/">GeneX 2.x</a> regain the momentum it had before the holidays... Maybe it has, but we've just been out of touch?
  </p>
  
***************
*** 73,77 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>
--- 73,77 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>
***************
*** 88,96 ****
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  <p>
  - Jodi cleaned up the schema some. We added a table to the security system so we can keep track of primary investigators (PI). Traditional groups aren't enough<br>
! -- the Microarray Center (called the BRF here at UVa) wants to know who the PI is. Jodi also removed loads of legacy stuff in the schema that isn't being used.
  </p>
  <p>
--- 88,96 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  <p>
  - Jodi cleaned up the schema some. We added a table to the security system so we can keep track of primary investigators (PI). Traditional groups aren't enough<br>
! -- the Microarray Center (called the BRF here at <a href="http://www.virginia.edu/">UVa</a>) wants to know who the PI is. Jodi also removed loads of legacy stuff in the schema that isn't being used.
  </p>
  <p>
***************
*** 119,123 ****
  </p>
  <p>
! - Patrick at George Washington U. has installed Va GeneX and found a bug in loading XLS Affy MAS5 data. I fixed that, added a new item to our test plan (since we missed the bug) and generally did some much needed cleaning in the loading scripts.
  </p>
  <p>
--- 119,123 ----
  </p>
  <p>
! - Patrick at George Washington U. has installed Va GeneX and found a bug in loading XLS Affy <a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a> data. I fixed that, added a new item to our test plan (since we missed the bug) and generally did some much needed cleaning in the loading scripts.
  </p>
  <p>

[Genex-cvs-commit] genex-www/status/2003/jan status_main.ssi,1.4,1.5

From: <ki...@us...> - 2003-03-05 01:56:21

Update of /cvsroot/genex/genex-www/status/2003/jan
In directory sc8-pr-cvs1:/tmp/cvs-serv17903

Modified Files:
	status_main.ssi 
Log Message:
link update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/jan/status_main.ssi,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** status_main.ssi	4 Mar 2003 19:50:01 -0000	1.4
--- status_main.ssi	5 Mar 2003 01:56:14 -0000	1.5
***************
*** 11,15 ****
  
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  <p>
--- 11,15 ----
  
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  <p>
***************
*** 43,47 ****
          <hr>
  	<p>
! 	<b><u>UVa Update - Jodi Kanter</u></b>
  	</p>
  <p>
--- 43,47 ----
          <hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Jodi Kanter</u></b>
  	</p>
  <p>
***************
*** 55,59 ****
  For Next Week:<br>
  - clean up schema SQL script to reflect tables, indexes, etc.. actually in use.<br>
! - focus on Postgres and query performance<br>
  - work on adding foreign key constraints, necessary indexes, etc. to GeneX schema<br>
  </p>
--- 55,59 ----
  For Next Week:<br>
  - clean up schema SQL script to reflect tables, indexes, etc.. actually in use.<br>
! - focus on <a href="http://www.postgresql.org/">Postgres</a> and query performance<br>
  - work on adding foreign key constraints, necessary indexes, etc. to GeneX schema<br>
  </p>
***************
*** 61,65 ****
  	<hr>
  	<p>
! 	<b><u>UCI Update - Harry Mangalam</u></b>
  	</p>
  <p>
--- 61,65 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b>
  	</p>
  <p>
***************
*** 70,77 ****
  </p>
  <p>
! Recently, used indexing, and experimented with float -> int conversion to represent data in a custom table to increase speed of query > 1000X on GMU server on some queries.  Also learned many unpleasant but useful things about GeneSpring, DB drivers, PostgreSQL, Perl, & Python.
  </p>
  <p>
! GeneSpring connectivity is back (SiG changed the way it distributes it over the holidays) and once Jennifer tells me more about their Genome format, we can start putting together a complete connection package (finish HOWTO, provide example views and tables to query with it, etc).
  </p>
  
--- 70,77 ----
  </p>
  <p>
! Recently, used indexing, and experimented with float -> int conversion to represent data in a custom table to increase speed of query > 1000X on <a href="http://www.gmu.edu/">GMU</a> server on some queries.  Also learned many unpleasant but useful things about <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a>, DB drivers, <a href="http://www.postgresql.org/">PostgreSQL</a>, <a href="http://www.perl.com">Perl</a>, & Python.
  </p>
  <p>
! <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> connectivity is back (SiG changed the way it distributes it over the holidays) and once Jennifer tells me more about their Genome format, we can start putting together a complete connection package (finish HOWTO, provide example views and tables to query with it, etc).
  </p>
  
***************
*** 91,95 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  
--- 91,95 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  
***************
*** 123,131 ****
  
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>	
  Accomplishments:<br>
! -Can now generate basic Python/Tk GUI widget library using Pymerase<br>
  --Entry Widgets (Validated entry boxes for a give table)<br>
  --Save Widget (Tells a given entry widget to save the data)<br>
--- 123,131 ----
  
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>	
  Accomplishments:<br>
! -Can now generate basic Python/Tk GUI widget library using <a href="http://pymerase.sf.net/">Pymerase</a><br>
  --Entry Widgets (Validated entry boxes for a give table)<br>
  --Save Widget (Tells a given entry widget to save the data)<br>
***************
*** 146,150 ****
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  <p>
--- 146,150 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  <p>
***************
*** 175,179 ****
  
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  	<p>
--- 175,179 ----
  
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  	<p>

[Genex-cvs-commit] genex-www/status/2002/dec status_main.ssi,1.4,1.5

From: <ki...@us...> - 2003-03-05 01:48:29

Update of /cvsroot/genex/genex-www/status/2002/dec
In directory sc8-pr-cvs1:/tmp/cvs-serv15156

Modified Files:
	status_main.ssi 
Log Message:
link update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/dec/status_main.ssi,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** status_main.ssi	28 Feb 2003 20:55:23 -0000	1.4
--- status_main.ssi	5 Mar 2003 01:48:26 -0000	1.5
***************
*** 19,23 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Brandon King</u></b><br>
  	</p>
  <p>Summery:<br>
--- 19,23 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b><br>
  	</p>
  <p>Summery:<br>
***************
*** 30,39 ****
  -Add support for other datatypes to Python Tk Widget generation<br>
  -Automaticly hook up the Python Tk Widgets to generate Python Tk Widgets as a option<br>
! -Test GeneSpring connection<br>
  </p>
  
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Diane Trout</u></b>
  	</p>
  <p>
--- 30,39 ----
  -Add support for other datatypes to Python Tk Widget generation<br>
  -Automaticly hook up the Python Tk Widgets to generate Python Tk Widgets as a option<br>
! -Test <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> connection<br>
  </p>
  
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b>
  	</p>
  <p>
***************
*** 46,50 ****
  </p>
  <p>
!  * Next week ** Try and generate python MAGE objects<br>
  ** More pymerase bug fixes.
  </p>
--- 46,50 ----
  </p>
  <p>
!  * Next week ** Try and generate python <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> objects<br>
  ** More pymerase bug fixes.
  </p>
***************
*** 60,64 ****
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  <p>- Implemented chgrp and chmod types of functionality in the web UI.</p>
--- 60,64 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  <p>- Implemented chgrp and chmod types of functionality in the web UI.</p>
***************
*** 72,76 ****
  	<hr>
  	<p>
! 	<b><u>UCI Update - Harry Mangalam</u></b>
  	</p>
  <p>
--- 72,76 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b>
  	</p>
  <p>
***************
*** 85,95 ****
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  <p>
  Progress:<br>
  * jamboree at Stanford - added support for persistence in XML::Reader<br>
! * added array tools to support MAS5 (fix-array, tab2AD, qtdim)<br>
! * loaded and verified MAS5 dataset<br>
  </p>
  <p>
--- 85,95 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  <p>
  Progress:<br>
  * jamboree at Stanford - added support for persistence in XML::Reader<br>
! * added array tools to support <a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a> (fix-array, tab2AD, qtdim)<br>
! * loaded and verified <a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a> dataset<br>
  </p>
  <p>
***************
*** 111,115 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  <p>
--- 111,115 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  <p>
***************
*** 141,151 ****
  	<hr>
  	<p>
! 	<b><u>UCI Update - Harry Mangalam</u></b>
  	</p>
  <p>
! Last week largely lost to travel prep and travel. Met and talked with a number of people at GMU, NRL.  Installed GeneX with some success and tried to load data, with less success.
  </p>
  <p>
! During last week, more time 'lost' to Thanksgiving, but GeneSpring connection up and running mostly.  Have documented the protocol level connection and am continuing to extend the connection to provide user-level useful data and provide mappings so that more of GeneSpring capabilities can be used.
  </p>
  <p>
--- 141,151 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b>
  	</p>
  <p>
! Last week largely lost to travel prep and travel. Met and talked with a number of people at <a href="http://www.gmu.edu/">GMU</a>, <a href="http://www.nrl.navy.mil/">NRL</a>.  Installed GeneX with some success and tried to load data, with less success.
  </p>
  <p>
! During last week, more time 'lost' to Thanksgiving, but <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> connection up and running mostly.  Have documented the protocol level connection and am continuing to extend the connection to provide user-level useful data and provide mappings so that more of <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> capabilities can be used.
  </p>
  <p>
***************
*** 153,166 ****
  </p>
  <p>
! Also for GeneSpring connectivity, am testing scalability of GeneX DB (sometimes by intent, sometimes by ignorance)...
  </p>
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>
  Summery:<br>
! -Created GenePix-GPR-1.0 FeatureExtractionSoftware<br>
! -Tested Uploading of GPR files (success)<br>
  -Documented the creation process of<br>
  ---FeatureExtractionSoftware<br>
--- 153,166 ----
  </p>
  <p>
! Also for <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> connectivity, am testing scalability of GeneX DB (sometimes by intent, sometimes by ignorance)...
  </p>
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>
  Summery:<br>
! -Created GenePix-<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>-1.0 FeatureExtractionSoftware<br>
! -Tested Uploading of <a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a> files (success)<br>
  -Documented the creation process of<br>
  ---FeatureExtractionSoftware<br>
***************
*** 168,177 ****
  ---ExperimentSet<br>
  ---Data Upload<br>
! -Finished Agilent 5.1.1 FeatureExtractionSoftware XML<br>
  -Created BioGenex Python package<br>
! ---GPR Parser (Diane's Creation)<br>
! ---Agilent Parser<br>
! ---GeneX 2.x Config Parser<br>
! ---bin/fixarray-gpr.py (for preparing arraydesigns from a GPR file)<br>
  ---bin/tab2ADgui.py (GUI for running tab2AD.pl)<br>
  ---setup.py for installing BioGeneX package<br>
--- 168,177 ----
  ---ExperimentSet<br>
  ---Data Upload<br>
! -Finished <a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a> 5.1.1 FeatureExtractionSoftware XML<br>
  -Created BioGenex Python package<br>
! ---<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a> Parser (Diane's Creation)<br>
! ---<a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a> Parser<br>
! ---<a href="http://genex.sf.net/">GeneX 2.x</a> Config Parser<br>
! ---bin/fixarray-gpr.py (for preparing arraydesigns from a <a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a> file)<br>
  ---bin/tab2ADgui.py (GUI for running tab2AD.pl)<br>
  ---setup.py for installing BioGeneX package<br>
***************
*** 179,194 ****
  <p>
  Next Week:<br>
! -Finish testing Agilent data upload<br>
! -Help Diane (if possible) with updatinge Pymerase for GeneX 2.x.<br>
! -Start on ideas for GeneX 2.x GUIs<br>
  </p>
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  	N/A Currently
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  	N/A Currently
--- 179,194 ----
  <p>
  Next Week:<br>
! -Finish testing <a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a> data upload<br>
! -Help Diane (if possible) with updatinge <a href="http://pymerase.sf.net/">Pymerase</a> for <a href="http://genex.sf.net/">GeneX 2.x</a>.<br>
! -Start on ideas for <a href="http://genex.sf.net/">GeneX 2.x</a> GUIs<br>
  </p>
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  	N/A Currently
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  	N/A Currently

[Genex-cvs-commit] genex-www/status/2002/nov status_main.ssi,1.8,1.9

From: <ki...@us...> - 2003-03-05 01:43:45

Update of /cvsroot/genex/genex-www/status/2002/nov
In directory sc8-pr-cvs1:/tmp/cvs-serv13518

Modified Files:
	status_main.ssi 
Log Message:
one more try!


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** status_main.ssi	5 Mar 2003 01:25:53 -0000	1.8
--- status_main.ssi	5 Mar 2003 01:43:41 -0000	1.9
***************
*** 18,22 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  <p>
--- 18,22 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  <p>
***************
*** 41,45 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>
--- 41,45 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>
***************
*** 59,63 ****
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  <p>
--- 59,63 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  <p>
***************
*** 93,97 ****
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  <p>
--- 93,97 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  <p>
***************
*** 111,115 ****
  <p>
  problems:
! * hit the wall with huge INSERT's into <a href="http://www.postgresql.org/">Postgres</a>  Got some info that I
    might need to a) drop indices before insert and re-create them
    afterwards, or b) do it outside of a transaction. Tom Lane, from the
--- 111,115 ----
  <p>
  problems:
! * hit the wall with huge INSERT's into <a href="http://www.postgresql.org/">Postgres</a>. Got some info that I
    might need to a) drop indices before insert and re-create them
    afterwards, or b) do it outside of a transaction. Tom Lane, from the
***************
*** 135,139 ****
  	<hr>
  	<p>
! 	<b><u>UCI Update - Harry Mangalam</u></b>
  	</p>
  Out of town
--- 135,139 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b>
  	</p>
  Out of town
***************
*** 150,154 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  
--- 150,154 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  
***************
*** 179,183 ****
  -----
  <p>
! <b>GeneX 2.x Task and Dependancy Outline</b>
  </p>
  
--- 179,183 ----
  -----
  <p>
! <b><a href="http://genex.sf.net/">GeneX 2.x</a> Task and Dependancy Outline</b>
  </p>
  
***************
*** 215,227 ****
  
  <p>
! <b>GeneX 2.x Project</b><br>
  -----------------<br>
  *ExperimentSet (Prototype Done)<br>
  *ArrayDesign (Prototype Done)<br>
  **Data-loader (Jason) [< 1 week, 75%]<br>
!  **Affy File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML (Jason) [< 1 week, 60%]<br>
!  **GenePix File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML (Brandon) [< 1 week, 90%]<br>
!  * <a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a> File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML (?) [ 0.8-1.2 * GenePix task time]<br>
!  **QuantArray File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML (done)<br>
    ***(Requires working data loader and >= 1 working File Format)<br>
    ***Data export [0-2 weeks, 80%]<br>
--- 215,227 ----
  
  <p>
! <b><a href="http://genex.sf.net/">GeneX 2.x</a> Project</b><br>
  -----------------<br>
  *ExperimentSet (Prototype Done)<br>
  *ArrayDesign (Prototype Done)<br>
  **Data-loader (Jason) [< 1 week, 75%]<br>
!  **Affy File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML (Jason) [< 1 week, 60%]<br>
!  **GenePix File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML (Brandon) [< 1 week, 90%]<br>
!  **<a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a> File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML (?) [ 0.8-1.2 * GenePix task time]<br>
!  **QuantArray File Format --> <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML (done)<br>
    ***(Requires working data loader and >= 1 working File Format)<br>
    ***Data export [0-2 weeks, 80%]<br>
***************
*** 263,267 ****
  <p>
  (Requires: Finished Security Model Implementation)<br>
! *Security model update to Pymerase<br>
  **Python API for GeneX (Beta/Final)<br>
  ***MLX connection through API (Beta/Final)<br>
--- 263,267 ----
  <p>
  (Requires: Finished Security Model Implementation)<br>
! *Security model update to <a href="http://pymerase.sf.net/">Pymerase</a><br>
  **Python API for GeneX (Beta/Final)<br>
  ***MLX connection through API (Beta/Final)<br>
***************
*** 270,274 ****
          <hr>
  	<p>	
! 	<b><u>UCI Update - Harry Mangalam</u></b><br>
  	</p>
  
--- 270,274 ----
          <hr>
  	<p>	
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b><br>
  	</p>
  
***************
*** 282,286 ****
  
  <p>
! Also, I've just about finished figuring out the <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> <-> GeneX 2 intereraction with both JDBC <-> ODBC <-> <a href="http://www.postgresql.org/">Postgres</a> l (on Windows clients) and JDBC <-> GeneX (on Linux clients).  The former I posted, the latter is being written up.
  </p>
  
--- 282,286 ----
  
  <p>
! Also, I've just about finished figuring out the <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> <-> GeneX 2 intereraction with both JDBC <-> ODBC <-> <a href="http://www.postgresql.org/">Postgres</a>ql (on Windows clients) and JDBC <-> GeneX (on Linux clients).  The former I posted, the latter is being written up.
  </p>
  
***************
*** 298,307 ****
          <hr>
  	<p>	
! 	<b><u>Caltech Update - Brandon King</u></b><br>
  	</p>
  
  <p>
  <b>Summery:</b><br>
! *Created GenePix <a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a> 1.0 FeatureExtractionSoftware xml file<br>
  *Found bugs in array-design.html and data-loader.html<br>
  *Worked on task/depandancy outline with Diane<br>
--- 298,307 ----
          <hr>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b><br>
  	</p>
  
  <p>
  <b>Summery:</b><br>
! *Created GenePix-<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>-1.0 FeatureExtractionSoftware xml file<br>
  *Found bugs in array-design.html and data-loader.html<br>
  *Worked on task/depandancy outline with Diane<br>
***************
*** 310,318 ****
   **Talked about <a href="http://www.caltech.edu/">Caltech</a> Deadlines<br>
     ***Two-week deadline (now one-week):<br>
!      ****Expression data imported and exported from GeneX 2.x<br>
     ***Christmas deadline:<br>
       ****Allow Biologists to easily get data into the database<br>
         *****Basic Analysis (Normalization, Quality Control, etc.)<br>
!    ** <a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> Connection<br>
     ***Annotation of experiments<br>
     ***I think there is more, but I am forgetting what it is... I'll get back to list on this.<br>
--- 310,318 ----
   **Talked about <a href="http://www.caltech.edu/">Caltech</a> Deadlines<br>
     ***Two-week deadline (now one-week):<br>
!      ****Expression data imported and exported from <a href="http://genex.sf.net/">GeneX 2.x</a><br>
     ***Christmas deadline:<br>
       ****Allow Biologists to easily get data into the database<br>
         *****Basic Analysis (Normalization, Quality Control, etc.)<br>
!    ***<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a> Connection<br>
     ***Annotation of experiments<br>
     ***I think there is more, but I am forgetting what it is... I'll get back to list on this.<br>
***************
*** 341,345 ****
  <b>Future:</b><br>
  *Discusion of GUI's<br>
! *GUI Widget Auto-generation with Pymerase<br>
  </p>
  
--- 341,345 ----
  <b>Future:</b><br>
  *Discusion of GUI's<br>
! *GUI Widget Auto-generation with <a href="http://pymerase.sf.net/">Pymerase</a><br>
  </p>
  
***************
*** 362,366 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  
--- 362,366 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  
***************
*** 390,394 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  	
--- 390,394 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  	
***************
*** 396,400 ****
  	<b>Summery:</b><br>
  	* Installed <a href="http://genex.sf.net/">GeneX 2.x</a> with help from Diane and Jason<br>
! 	* Started uploading QuantArray test data to GeneX 2.x<br>
  	* No form to upload ExperimentSets (looks like now fixed), used SQL as shorterm solution<br>
     	* Successfully generated and uploaded ArrayDesigns<br>
--- 396,400 ----
  	<b>Summery:</b><br>
  	* Installed <a href="http://genex.sf.net/">GeneX 2.x</a> with help from Diane and Jason<br>
! 	* Started uploading QuantArray test data to <a href="http://genex.sf.net/">GeneX 2.x</a><br>
  	* No form to upload ExperimentSets (looks like now fixed), used SQL as shorterm solution<br>
     	* Successfully generated and uploaded ArrayDesigns<br>
***************
*** 410,414 ****
  	* Create ArrayDesign from GenePix data<br>
  	* Upload GenePix expression data<br>
! 	* Help Diane update Pymerase<br>
  	</p>
  
--- 410,414 ----
  	* Create ArrayDesign from GenePix data<br>
  	* Upload GenePix expression data<br>
! 	* Help Diane update <a href="http://pymerase.sf.net/">Pymerase</a><br>
  	</p>
  
***************
*** 436,440 ****
  	<hr>
  	<p>
! 	<b><u>UCI Update - Harry Mangalam</u></b>
  	</p>
  	<p>
--- 436,440 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.uci.edu/">UCI</a> Update - Harry Mangalam</u></b>
  	</p>
  	<p>
***************
*** 472,479 ****
  	
  	<p>
! 	Mostly this has been in pursuit of a <a href="http://www.perl.com">Perl</a> OpenDX link so that a module
  	can be added to a visual DX net allowing arbitrary <a href="http://www.perl.com">Perl</a> code to be run
  	on the input.  There are various problems - DX prefers to operate on
! 	particular types of data fields, not the simple string input that <a href="http://www.perl.com">Perl</a> 	favors, but there are many possibilitiess, high among them using <a href="http://www.perl.com">Perl</a> s
  	DBI to suck data from RDBs and format it for DX to do automated analysis
  	and visualization on.
--- 472,480 ----
  	
  	<p>
! 	Mostly this has been in pursuit of a <a href="http://www.perl.com">Perl</a>-OpenDX link so that a module
  	can be added to a visual DX net allowing arbitrary <a href="http://www.perl.com">Perl</a> code to be run
  	on the input.  There are various problems - DX prefers to operate on
! 	particular types of data fields, not the simple string input that <a href="http://www.perl.com">Perl</a>
! 	favors, but there are many possibilitiess, high among them using <a href="http://www.perl.com">Perl</a>'s
  	DBI to suck data from RDBs and format it for DX to do automated analysis
  	and visualization on.
***************
*** 481,485 ****
  	
  	<p>
! 	Status: I've gotten some DX <a href="http://www.perl.com">Perl</a> modules built, but am still a ways away
  	from a solid generic module.
  	</p>
--- 482,486 ----
  	
  	<p>
! 	Status: I've gotten some DX-<a href="http://www.perl.com">Perl</a> modules built, but am still a ways away
  	from a solid generic module.
  	</p>
***************
*** 528,532 ****
  	makes the output available as:
  	- tab-delimited spreadsheet-like files
! 	- <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML
  	- N-dimensional file such as netCDF/HDF/XDF
  	- maybe a few others
--- 529,533 ----
  	makes the output available as:
  	- tab-delimited spreadsheet-like files
! 	- <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML
  	- N-dimensional file such as netCDF/HDF/XDF
  	- maybe a few others
***************
*** 537,541 ****
  	cross-platform, using either the Qt designer (or BlackAdder if it EVER
  	sees the light of day).  The Python bindings seem to be more stable and
! 	coherent than for <a href="http://www.perl.com">Perl</a>  
  	</p>
  
--- 538,542 ----
  	cross-platform, using either the Qt designer (or BlackAdder if it EVER
  	sees the light of day).  The Python bindings seem to be more stable and
! 	coherent than for <a href="http://www.perl.com">Perl</a>. 
  	</p>
  
***************
*** 543,547 ****
  	<hr>
  	<p>
! 	<b><u>UVa Update - Tom Laudeman</u></b>
  	</p>
  	<p>
--- 544,548 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.virginia.edu/">UVa</a> Update - Tom Laudeman</u></b>
  	</p>
  	<p>
***************
*** 572,576 ****
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  <p>
--- 573,577 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  <p>
***************
*** 587,592 ****
  <p>
  <b>Hyojoo:</b><br>
! Created a Java GUI for creating QT Dimensions that uses the <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> Java
! API and thus can export <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML. The <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a> ML QT Dimension is needed to
  configure the data loader.
  </p>
--- 588,593 ----
  <p>
  <b>Hyojoo:</b><br>
! Created a Java GUI for creating QT Dimensions that uses the <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-Java
! API and thus can export <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML. The <a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>-ML QT Dimension is needed to
  configure the data loader.
  </p>
***************
*** 599,603 ****
  Planning<br>
  ========<br>
! I've been getting ready to switch to <a href="http://www.postgresql.org/">Postgres</a> .3
  </p>
  
--- 600,604 ----
  Planning<br>
  ========<br>
! I've been getting ready to switch to <a href="http://www.postgresql.org/">Postgres</a>7.3
  </p>
  
***************
*** 605,609 ****
  Service<br>
  =======<br>
! Helped Brandon get Genex-2.0a1 running at <a href="http://www.caltech.edu/">Caltech</a> </p>
  
  <p>
--- 606,611 ----
  Service<br>
  =======<br>
! Helped Brandon get Genex-2.0a1 running at <a href="http://www.caltech.edu/">Caltech</a>
! </p>
  
  <p>
***************
*** 666,668 ****
    </table>
  
! <!-- End of Content -->
--- 668,670 ----
    </table>
  
! <!-- End of Content -->
\ No newline at end of file

[Genex-cvs-commit] genex-www/status/2002/nov status_main.ssi,1.7,1.8

From: <ki...@us...> - 2003-03-05 01:25:57

Update of /cvsroot/genex/genex-www/status/2002/nov
In directory sc8-pr-cvs1:/tmp/cvs-serv7319

Modified Files:
	status_main.ssi 
Log Message:
formatting


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** status_main.ssi	5 Mar 2003 01:23:07 -0000	1.7
--- status_main.ssi	5 Mar 2003 01:25:53 -0000	1.8
***************
*** 1,143 ****
! <html><head>
! <!-- ViewCVS       -- http://viewcvs.sourceforge.net/
!      by Greg Stein -- mailto:gs...@ly...
!   -->
! 
! <title>genex/genex-www/status/2002/nov/status_main.ssi - view - 1.5</title></head>
! <body bgcolor="#eeeeee">
! <table width="100&#37;" border=0 cellspacing=0 cellpadding=1 bgcolor="#9999ee">
! <tr valign=bottom><td>
! <a href="status_main.ssi#rev1.5"><img src="/viewcvs/back.gif" alt="[BACK_ICON]" border=0 width=16 height=16></a>
[...1313 lines suppressed...]
! <p>
! Goals for next week<br>
! ===================<br>
  Finish rules code - need to fix problem with GroupSec table having
  ro/rw_groupname fkeys to itself.
! </p>
  
! <p>
  Ensure that ArrayDesign importer can handle Affy U133 files.
! </p>
  
! <p>
  Add ability to data loader to import .CEL data and <a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a> data.
! </p>
    
!       </td>
!     </tr>
!   </table>
  
! <!-- End of Content -->

[Genex-cvs-commit] genex-www/status/2002/nov status_main.ssi,1.6,1.7

From: <ki...@us...> - 2003-03-05 01:23:13

Update of /cvsroot/genex/genex-www/status/2002/nov
In directory sc8-pr-cvs1:/tmp/cvs-serv6155

Modified Files:
	status_main.ssi 
Log Message:
link update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** status_main.ssi	5 Mar 2003 01:12:17 -0000	1.6
--- status_main.ssi	5 Mar 2003 01:23:07 -0000	1.7
***************
*** 1,452 ****
! <!--Main content -->
! <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>November 28th, 2002</big></th>
!     </tr>
!     <tr bgcolor="#D8E4F7">
!       <td>
!        <b>Happy Thanksgiving!</b>
!       </td>
!     </tr>
[...1318 lines suppressed...]
  
! &lt;p&gt;
  Ensure that ArrayDesign importer can handle Affy U133 files.
! &lt;/p&gt;
  
! &lt;p&gt;
! Add ability to data loader to import .CEL data and <a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a> data.
! &lt;/p&gt;
    
!       &lt;/td&gt;
!     &lt;/tr&gt;
!   &lt;/table&gt;
  
! &lt;!-- End of Content --&gt;
! </pre>
! <hr noshade><table width="100&#37;" border=0 cellpadding=0 cellspacing=0><tr>
! <td align=left><address><a href="http://sourceforge.net/">Back to SourceForge</a></address></td>
! <td align=right>Powered by<br><a href="http://viewcvs.sourceforge.net/">ViewCVS 0.8</a>
! </td></tr></table>
! </body></html>

[Genex-cvs-commit] genex-www/status/2002/nov status_main.ssi,1.5,1.6

From: <ki...@us...> - 2003-03-05 01:12:22

Update of /cvsroot/genex/genex-www/status/2002/nov
In directory sc8-pr-cvs1:/tmp/cvs-serv1206

Modified Files:
	status_main.ssi 
Log Message:
updated with links


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** status_main.ssi	6 Dec 2002 19:07:47 -0000	1.5
--- status_main.ssi	5 Mar 2003 01:12:17 -0000	1.6
***************
*** 18,22 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  <p>
--- 18,22 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  <p>
***************
*** 41,59 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  <p>
  Summery:<br>
  -Worked on non-genex related work<br>
! -Worked more on getting GenePix GPR files to load into genex
  </p>
  <p>
  Next Week:<br>
! -Finish GPR loading (Monday Deadline)
  </p>
  <p>
  Problems:<br>
  -Too many things to do, too little time.<br>
! -Need to get GPR files loaded into GeneX 2.x ASAP<br>
  -Still fighting with the dataloader =o( (Altough, progress has been made =o)	</p>
  	<hr>
--- 41,59 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  <p>
  Summery:<br>
  -Worked on non-genex related work<br>
! -Worked more on getting GenePix<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>files to load into genex
  </p>
  <p>
  Next Week:<br>
! -Finish<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>loading (Monday Deadline)
  </p>
  <p>
  Problems:<br>
  -Too many things to do, too little time.<br>
! -Need to get<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>files loaded into <a href="http://genex.sf.net/">GeneX 2.x</a> ASAP<br>
  -Still fighting with the dataloader =o( (Altough, progress has been made =o)	</p>
  	<hr>
***************
*** 93,97 ****
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  <p>
--- 93,97 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  <p>
***************
*** 105,115 ****
    and sessioning mechanism in Genex-2<br>
  * Added some performance tweaks for the Mason apps by pre-loading
!   often used Perl modules at server initialization time (like
    XML::Xerces which takes forever to load)<br>
! * helped Caltech team with issues<br>
  </p>
  <p>
  problems:
! * hit the wall with huge INSERT's into Postgres. Got some info that I
    might need to a) drop indices before insert and re-create them
    afterwards, or b) do it outside of a transaction. Tom Lane, from the
--- 105,115 ----
    and sessioning mechanism in Genex-2<br>
  * Added some performance tweaks for the Mason apps by pre-loading
!   often used<a href="http://www.perl.com">Perl</a>modules at server initialization time (like
    XML::Xerces which takes forever to load)<br>
! * helped <a href="http://www.caltech.edu/">Caltech</a> team with issues<br>
  </p>
  <p>
  problems:
! * hit the wall with huge INSERT's into <a href="http://www.postgresql.org/">Postgres</a>. Got some info that I
    might need to a) drop indices before insert and re-create them
    afterwards, or b) do it outside of a transaction. Tom Lane, from the
***************
*** 150,154 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  
--- 150,154 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  
***************
*** 179,183 ****
  -----
  <p>
! <b>GeneX 2.x Task and Dependancy Outline</b>
  </p>
  
--- 179,183 ----
  -----
  <p>
! <b><a href="http://genex.sf.net/">GeneX 2.x</a> Task and Dependancy Outline</b>
  </p>
  
***************
*** 215,227 ****
  
  <p>
! <b>GeneX 2.x Project</b><br>
  -----------------<br>
  *ExperimentSet (Prototype Done)<br>
  *ArrayDesign (Prototype Done)<br>
  **Data-loader (Jason) [< 1 week, 75%]<br>
!  **Affy File Format --> MAGE-ML (Jason) [< 1 week, 60%]<br>
!  **GenePix File Format --> MAGE-ML (Brandon) [< 1 week, 90%]<br>
!  **Agilent File Format --> MAGE-ML (?) [ 0.8-1.2 * GenePix task time]<br>
!  **QuantArray File Format --> MAGE-ML (done)<br>
    ***(Requires working data loader and >= 1 working File Format)<br>
    ***Data export [0-2 weeks, 80%]<br>
--- 215,227 ----
  
  <p>
! <b><a href="http://genex.sf.net/">GeneX 2.x</a> Project</b><br>
  -----------------<br>
  *ExperimentSet (Prototype Done)<br>
  *ArrayDesign (Prototype Done)<br>
  **Data-loader (Jason) [< 1 week, 75%]<br>
!  **Affy File Format --><a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML (Jason) [< 1 week, 60%]<br>
!  **GenePix File Format --><a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML (Brandon) [< 1 week, 90%]<br>
!  *<a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a>File Format --><a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML (?) [ 0.8-1.2 * GenePix task time]<br>
!  **QuantArray File Format --><a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML (done)<br>
    ***(Requires working data loader and >= 1 working File Format)<br>
    ***Data export [0-2 weeks, 80%]<br>
***************
*** 256,260 ****
  <p>
  (Requires: Possible now)<br>
! *Updates to Pymerase for GeneX support<br>
  **Python API for Genex (Prototype) (Diane & Brandon) [ 2d, 70% - 3d, 90%]<br>
  ***MLX connection through API (Prototype)<br>
--- 256,260 ----
  <p>
  (Requires: Possible now)<br>
! *Updates to <a href="http://pymerase.sf.net/">Pymerase</a> for GeneX support<br>
  **Python API for Genex (Prototype) (Diane & Brandon) [ 2d, 70% - 3d, 90%]<br>
  ***MLX connection through API (Prototype)<br>
***************
*** 263,267 ****
  <p>
  (Requires: Finished Security Model Implementation)<br>
! *Security model update to Pymerase<br>
  **Python API for GeneX (Beta/Final)<br>
  ***MLX connection through API (Beta/Final)<br>
--- 263,267 ----
  <p>
  (Requires: Finished Security Model Implementation)<br>
! *Security model update to <a href="http://pymerase.sf.net/">Pymerase</a><br>
  **Python API for GeneX (Beta/Final)<br>
  ***MLX connection through API (Beta/Final)<br>
***************
*** 278,294 ****
  
  <p>
! With a fresh Debian system, GeneX2 installs pretty much as described (now) in the INSTALL doc.  I collected the .deb requirements (and some more Perl peculiarities) for later installs.  Next week, I'll find out just how well I recorded them with a new series of installs at GMU and at the NRL (talk about installing under the gun..).
  </p>
  
  <p>
! Also, I've just about finished figuring out the GeneSpring <-> GeneX 2 intereraction with both JDBC <-> ODBC <-> Postgresql (on Windows clients) and JDBC <-> GeneX (on Linux clients).  The former I posted, the latter is being written up.
  </p>
  
  <p>
! What remains is the actual mapping of GeneSpring data columns to GeneX data columns, for which I may need a bit more time to learn the how each is laid out, or (if the financing is OK) Mark Wilkinson may finish it off.
  </p>
  
  <p>
! However, GeneSpring IS talking to GeneX; from sniffing the tcp packets go back and forth, I can see that the only reason data isn't showing up in GeneSpring is because there is a data mismatch (as well as a lack of data).
  </p>
  
--- 278,294 ----
  
  <p>
! With a fresh Debian system, GeneX2 installs pretty much as described (now) in the INSTALL doc.  I collected the .deb requirements (and some more<a href="http://www.perl.com">Perl</a>peculiarities) for later installs.  Next week, I'll find out just how well I recorded them with a new series of installs at<a href="http://www.gmu.edu/">GMU</a>and at the<a href="http://www.nrl.navy.mil/">NRL</a>(talk about installing under the gun..).
  </p>
  
  <p>
! Also, I've just about finished figuring out the<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a><-> GeneX 2 intereraction with both JDBC <-> ODBC <-> <a href="http://www.postgresql.org/">Postgres</a>ql (on Windows clients) and JDBC <-> GeneX (on Linux clients).  The former I posted, the latter is being written up.
  </p>
  
  <p>
! What remains is the actual mapping of<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a>data columns to GeneX data columns, for which I may need a bit more time to learn the how each is laid out, or (if the financing is OK) Mark Wilkinson may finish it off.
  </p>
  
  <p>
! However,<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a>IS talking to GeneX; from sniffing the tcp packets go back and forth, I can see that the only reason data isn't showing up in<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a>is because there is a data mismatch (as well as a lack of data).
  </p>
  
***************
*** 298,318 ****
          <hr>
  	<p>	
! 	<b><u>Caltech Update - Brandon King</u></b><br>
  	</p>
  
  <p>
  <b>Summery:</b><br>
! *Created GenePix-GPR-1.0 FeatureExtractionSoftware xml file<br>
  *Found bugs in array-design.html and data-loader.html<br>
  *Worked on task/depandancy outline with Diane<br>
  *Had strategy meeting with Barbara Wold, Jose Luis Riechmann, Eric Mjolsness, and Jennifer Weller<br>
  *Created tasklist, with estimated development times and dependancies (see Diane's status update)<br>
!  **Talked about Caltech Deadlines<br>
     ***Two-week deadline (now one-week):<br>
!      ****Expression data imported and exported from GeneX 2.x<br>
     ***Christmas deadline:<br>
       ****Allow Biologists to easily get data into the database<br>
         *****Basic Analysis (Normalization, Quality Control, etc.)<br>
!    ***GeneSpring Connection<br>
     ***Annotation of experiments<br>
     ***I think there is more, but I am forgetting what it is... I'll get back to list on this.<br>
--- 298,318 ----
          <hr>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b><br>
  	</p>
  
  <p>
  <b>Summery:</b><br>
! *Created GenePix<a href="http://www.axon.com/gn_GenePix_File_Formats.html#ResultsFormat">GPR</a>1.0 FeatureExtractionSoftware xml file<br>
  *Found bugs in array-design.html and data-loader.html<br>
  *Worked on task/depandancy outline with Diane<br>
  *Had strategy meeting with Barbara Wold, Jose Luis Riechmann, Eric Mjolsness, and Jennifer Weller<br>
  *Created tasklist, with estimated development times and dependancies (see Diane's status update)<br>
!  **Talked about <a href="http://www.caltech.edu/">Caltech</a> Deadlines<br>
     ***Two-week deadline (now one-week):<br>
!      ****Expression data imported and exported from <a href="http://genex.sf.net/">GeneX 2.x</a><br>
     ***Christmas deadline:<br>
       ****Allow Biologists to easily get data into the database<br>
         *****Basic Analysis (Normalization, Quality Control, etc.)<br>
!    **<a href="http://www.silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf">GeneSpring</a>Connection<br>
     ***Annotation of experiments<br>
     ***I think there is more, but I am forgetting what it is... I'll get back to list on this.<br>
***************
*** 328,334 ****
  <p>
  <b>Next Week:</b><br>
! *Update GeneX 2.x installation with Jason's fixes<br>
  *Test GenePix upload<br>
! *Create Agilent FeatureExtractionSoftware and/or supply data for testing<br>
  </p>
  
--- 328,334 ----
  <p>
  <b>Next Week:</b><br>
! *Update <a href="http://genex.sf.net/">GeneX 2.x</a> installation with Jason's fixes<br>
  *Test GenePix upload<br>
! *Create<a href="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547">Agilent</a>FeatureExtractionSoftware and/or supply data for testing<br>
  </p>
  
***************
*** 341,345 ****
  <b>Future:</b><br>
  *Discusion of GUI's<br>
! *GUI Widget Auto-generation with Pymerase<br>
  </p>
  
--- 341,345 ----
  <b>Future:</b><br>
  *Discusion of GUI's<br>
! *GUI Widget Auto-generation with <a href="http://pymerase.sf.net/">Pymerase</a><br>
  </p>
  
***************
*** 362,366 ****
        <td>
  	<p>	
! 	<b><u>Caltech Update - Diane Trout</u></b><br>
  	</p>
  
--- 362,366 ----
        <td>
  	<p>	
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Diane Trout</u></b><br>
  	</p>
  
***************
*** 390,405 ****
  	<hr>
  	<p>
! 	<b><u>Caltech Update - Brandon King</u></b>
  	</p>
  	
  	<p>
  	<b>Summery:</b><br>
! 	* Installed GeneX 2.x with help from Diane and Jason<br>
! 	* Started uploading QuantArray test data to GeneX 2.x<br>
  	* No form to upload ExperimentSets (looks like now fixed), used SQL as shorterm solution<br>
     	* Successfully generated and uploaded ArrayDesigns<br>
     	* Tested uploading of existing FeatureExtractionSoftware, detected entry and didn't upload. =o)<br>
     	* Tried to upload QuantArray expression data, ran into bugs, submited bug reports<br>
! 	* Worked on testing and updating pymerase to help prerpare for GeneX 2.x and MAGE support.<br>
  	</p>
  
--- 390,405 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.caltech.edu/">Caltech</a> Update - Brandon King</u></b>
  	</p>
  	
  	<p>
  	<b>Summery:</b><br>
! 	* Installed <a href="http://genex.sf.net/">GeneX 2.x</a> with help from Diane and Jason<br>
! 	* Started uploading QuantArray test data to <a href="http://genex.sf.net/">GeneX 2.x</a><br>
  	* No form to upload ExperimentSets (looks like now fixed), used SQL as shorterm solution<br>
     	* Successfully generated and uploaded ArrayDesigns<br>
     	* Tested uploading of existing FeatureExtractionSoftware, detected entry and didn't upload. =o)<br>
     	* Tried to upload QuantArray expression data, ran into bugs, submited bug reports<br>
! 	* Worked on testing and updating pymerase to help prerpare for <a href="http://genex.sf.net/">GeneX 2.x</a> and<a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>support.<br>
  	</p>
  
***************
*** 410,414 ****
  	* Create ArrayDesign from GenePix data<br>
  	* Upload GenePix expression data<br>
! 	* Help Diane update Pymerase<br>
  	</p>
  
--- 410,414 ----
  	* Create ArrayDesign from GenePix data<br>
  	* Upload GenePix expression data<br>
! 	* Help Diane update <a href="http://pymerase.sf.net/">Pymerase</a><br>
  	</p>
  
***************
*** 472,480 ****
  	
  	<p>
! 	Mostly this has been in pursuit of a Perl-OpenDX link so that a module
! 	can be added to a visual DX net allowing arbitrary Perl code to be run
  	on the input.  There are various problems - DX prefers to operate on
! 	particular types of data fields, not the simple string input that Perl
! 	favors, but there are many possibilitiess, high among them using Perl's
  	DBI to suck data from RDBs and format it for DX to do automated analysis
  	and visualization on.
--- 472,479 ----
  	
  	<p>
! 	Mostly this has been in pursuit of a<a href="http://www.perl.com">Perl</a>OpenDX link so that a module
! 	can be added to a visual DX net allowing arbitrary<a href="http://www.perl.com">Perl</a>code to be run
  	on the input.  There are various problems - DX prefers to operate on
! 	particular types of data fields, not the simple string input that<a href="http://www.perl.com">Perl</a>	favors, but there are many possibilitiess, high among them using<a href="http://www.perl.com">Perl</a>s
  	DBI to suck data from RDBs and format it for DX to do automated analysis
  	and visualization on.
***************
*** 482,486 ****
  	
  	<p>
! 	Status: I've gotten some DX-Perl modules built, but am still a ways away
  	from a solid generic module.
  	</p>
--- 481,485 ----
  	
  	<p>
! 	Status: I've gotten some DX<a href="http://www.perl.com">Perl</a>modules built, but am still a ways away
  	from a solid generic module.
  	</p>
***************
*** 489,493 ****
  	A close second priority is the integration of the R statistical language
  	in the same way - compile it as a shared lib and have it communicate to
! 	DX via sockets in the same way that I have Perl doing.  R is actually a
  	better fit as it has an idea about data objects and already has support
  	for many of the interconversions of data types that DX supports.
--- 488,492 ----
  	A close second priority is the integration of the R statistical language
  	in the same way - compile it as a shared lib and have it communicate to
! 	DX via sockets in the same way that I have<a href="http://www.perl.com">Perl</a>doing.  R is actually a
  	better fit as it has an idea about data objects and already has support
  	for many of the interconversions of data types that DX supports.
***************
*** 496,500 ****
  	<p>
  	A logical 3rd candidate would be Python, as it theoretically integrates
! 	more easily with C apps than Perl and there is already a Python project
  	for interacting with DX (tho it seems to be for controlling DX from
  	Python than rolling Python into DX.)
--- 495,499 ----
  	<p>
  	A logical 3rd candidate would be Python, as it theoretically integrates
! 	more easily with C apps than<a href="http://www.perl.com">Perl</a>and there is already a Python project
  	for interacting with DX (tho it seems to be for controlling DX from
  	Python than rolling Python into DX.)
***************
*** 529,533 ****
  	makes the output available as:
  	- tab-delimited spreadsheet-like files
! 	- MAGE-ML
  	- N-dimensional file such as netCDF/HDF/XDF
  	- maybe a few others
--- 528,532 ----
  	makes the output available as:
  	- tab-delimited spreadsheet-like files
! 	-<a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML
  	- N-dimensional file such as netCDF/HDF/XDF
  	- maybe a few others
***************
*** 538,542 ****
  	cross-platform, using either the Qt designer (or BlackAdder if it EVER
  	sees the light of day).  The Python bindings seem to be more stable and
! 	coherent than for Perl. 
  	</p>
  
--- 537,541 ----
  	cross-platform, using either the Qt designer (or BlackAdder if it EVER
  	sees the light of day).  The Python bindings seem to be more stable and
! 	coherent than for<a href="http://www.perl.com">Perl</a> 
  	</p>
  
***************
*** 573,577 ****
  	<hr>
  	<p>
! 	<b><u>Open Informatics Update - Jason Stewart</u></b>
  	</p>
  <p>
--- 572,576 ----
  	<hr>
  	<p>
! 	<b><u><a href="http://www.openinformatics.org/">Open Informatics</a> Update - Jason Stewart</u></b>
  	</p>
  <p>
***************
*** 588,593 ****
  <p>
  <b>Hyojoo:</b><br>
! Created a Java GUI for creating QT Dimensions that uses the MAGE-Java
! API and thus can export MAGE-ML. The MAGE-ML QT Dimension is needed to
  configure the data loader.
  </p>
--- 587,592 ----
  <p>
  <b>Hyojoo:</b><br>
! Created a Java GUI for creating QT Dimensions that uses the<a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>Java
! API and thus can export<a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML. The<a href="http://www.mged.org/Workgroups/MAGE/mage.html">MAGE</a>ML QT Dimension is needed to
  configure the data loader.
  </p>
***************
*** 600,604 ****
  Planning<br>
  ========<br>
! I've been getting ready to switch to Postgres7.3
  </p>
  
--- 599,603 ----
  Planning<br>
  ========<br>
! I've been getting ready to switch to <a href="http://www.postgresql.org/">Postgres</a>7.3
  </p>
  
***************
*** 606,610 ****
  Service<br>
  =======<br>
! Helped Brandon get Genex-2.0a1 running at Caltech
  </p>
  
--- 605,609 ----
  Service<br>
  =======<br>
! Helped Brandon get Genex-2.0a1 running at <a href="http://www.caltech.edu/">Caltech</a>
  </p>
  
***************
*** 636,640 ****
  
  <p>
! Modifications to Perl API<br>
  --<br>
  * XMLUtils.pm - changed the internals of xml2sql() to use the new SQL
--- 635,639 ----
  
  <p>
! Modifications to<a href="http://www.perl.com">Perl</a>API<br>
  --<br>
  * XMLUtils.pm - changed the internals of xml2sql() to use the new SQL
***************
*** 661,665 ****
  
  <p>
! Add ability to data loader to import .CEL data and MAS5 data.
  </p>
    
--- 660,664 ----
  
  <p>
! Add ability to data loader to import .CEL data and<a href="http://www.affymetrix.com/products/software/specific/mas.affx">MAS5</a>data.
  </p>

[Genex-cvs-commit] genex-www/content devo.ssi,1.3,1.4

From: <ki...@us...> - 2003-03-05 00:13:28

Update of /cvsroot/genex/genex-www/content
In directory sc8-pr-cvs1:/tmp/cvs-serv2741/content

Modified Files:
	devo.ssi 
Log Message:
quick update


Index: devo.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/devo.ssi,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** devo.ssi	16 Feb 2002 15:39:11 -0000	1.3
--- devo.ssi	5 Mar 2003 00:13:22 -0000	1.4
***************
*** 75,78 ****
--- 75,85 ----
  	    </UL>
  	  </LI>
+ 	  
+ 	  <LI>Caltech - Wold Lab
+             <UL>
+               <LI>Brandon King</LI>
+ 	      <LI>Diane Trout</LI>
+             </UL>
+           </LI>
  	</UL>

[Genex-cvs-commit] genex-www/status/2003/jan status_main.ssi,1.3,1.4

From: <ki...@us...> - 2003-03-04 19:50:06

Update of /cvsroot/genex/genex-www/status/2003/jan
In directory sc8-pr-cvs1:/tmp/cvs-serv10006/2003/jan

Modified Files:
	status_main.ssi 
Log Message:
oops, missed a "


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/jan/status_main.ssi,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** status_main.ssi	4 Mar 2003 19:44:33 -0000	1.3
--- status_main.ssi	4 Mar 2003 19:50:01 -0000	1.4
***************
*** 155,159 ****
  </p>
  <p>
! - Revamped our History/Background page with links to all 3 GeneX projects and a description of Va GeneX and <a href="http://genex.ncgr.org/>GeneX-Lite</a>. We still don't have a description (2 to 3 paragraphs) from the GeneX 2 project
  *gentle hint*.
  </p>
--- 155,159 ----
  </p>
  <p>
! - Revamped our History/Background page with links to all 3 GeneX projects and a description of Va GeneX and <a href="http://genex.ncgr.org/">GeneX-Lite</a>. We still don't have a description (2 to 3 paragraphs) from the GeneX 2 project
  *gentle hint*.
  </p>
***************
*** 189,193 ****
  
  <p>
! - Added Todd's description of <a href="http://genex.ncgr.org/>GeneX-Lite</a> to our History/Background page, along with links to GeneX and <a href="http://genex.ncgr.org/>GeneX-Lite</a>.
  </p>
  
--- 189,193 ----
  
  <p>
! - Added Todd's description of <a href="http://genex.ncgr.org/">GeneX-Lite</a> to our History/Background page, along with links to GeneX and <a href="http://genex.ncgr.org/">GeneX-Lite</a>.
  </p>

[Genex-cvs-commit] genex-www/status/2003/jan status_main.ssi,1.2,1.3

From: <ki...@us...> - 2003-03-04 19:44:37

Update of /cvsroot/genex/genex-www/status/2003/jan
In directory sc8-pr-cvs1:/tmp/cvs-serv7465/2003/jan

Modified Files:
	status_main.ssi 
Log Message:
updated with Genex-Lite link


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/jan/status_main.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_main.ssi	28 Feb 2003 21:49:56 -0000	1.2
--- status_main.ssi	4 Mar 2003 19:44:33 -0000	1.3
***************
*** 155,159 ****
  </p>
  <p>
! - Revamped our History/Background page with links to all 3 GeneX projects and a description of Va GeneX and GeneX-Lite. We still don't have a description (2 to 3 paragraphs) from the GeneX 2 project
  *gentle hint*.
  </p>
--- 155,159 ----
  </p>
  <p>
! - Revamped our History/Background page with links to all 3 GeneX projects and a description of Va GeneX and <a href="http://genex.ncgr.org/>GeneX-Lite</a>. We still don't have a description (2 to 3 paragraphs) from the GeneX 2 project
  *gentle hint*.
  </p>
***************
*** 189,193 ****
  
  <p>
! - Added Todd's description of GeneX-Lite to our History/Background page, along with links to GeneX and GeneX-Lite.
  </p>
  
--- 189,193 ----
  
  <p>
! - Added Todd's description of <a href="http://genex.ncgr.org/>GeneX-Lite</a> to our History/Background page, along with links to GeneX and <a href="http://genex.ncgr.org/>GeneX-Lite</a>.
  </p>

[Genex-cvs-commit] genex-www/status index.shtml,1.5,1.6 status_main.ssi,1.2,1.3 status_menu.ssi,1.3,1.4

From: <ki...@us...> - 2003-02-28 22:15:01

Update of /cvsroot/genex/genex-www/status
In directory sc8-pr-cvs1:/tmp/cvs-serv13655

Modified Files:
	index.shtml status_main.ssi status_menu.ssi 
Log Message:
feb update


Index: index.shtml
===================================================================
RCS file: /cvsroot/genex/genex-www/status/index.shtml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** index.shtml	28 Feb 2003 21:47:01 -0000	1.5
--- index.shtml	28 Feb 2003 22:14:55 -0000	1.6
***************
*** 1 ****
! <!--#include virtual="/status/2003/jan/index.shtml"-->
\ No newline at end of file
--- 1 ----
! <!--#include virtual="/status/2003/feb/index.shtml"-->
\ No newline at end of file

Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/status_main.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_main.ssi	9 Nov 2002 05:46:06 -0000	1.2
--- status_main.ssi	28 Feb 2003 22:14:55 -0000	1.3
***************
*** 3,7 ****
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>November 7th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">
--- 3,7 ----
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>March 7th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">

Index: status_menu.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/status_menu.ssi,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** status_menu.ssi	28 Feb 2003 21:47:01 -0000	1.3
--- status_menu.ssi	28 Feb 2003 22:14:55 -0000	1.4
***************
*** 26,30 ****
  	  - <b>April</b><br>
  	  - <b>March</b><br>
! 	  - <b>February</b><br>
  	  - <b><a href="http://genex.sourceforge.net/status/2003/jan/">January</a></b><br>
        </td>
--- 26,30 ----
  	  - <b>April</b><br>
  	  - <b>March</b><br>
! 	  - <b><a href="http://genex.sourceforge.net/status/2003/feb/">February</a></b><br>
  	  - <b><a href="http://genex.sourceforge.net/status/2003/jan/">January</a></b><br>
        </td>

[Genex-cvs-commit] genex-www/status/2003/feb index.shtml,NONE,1.1 status_main.ssi,NONE,1.1

From: <ki...@us...> - 2003-02-28 22:13:17

Update of /cvsroot/genex/genex-www/status/2003/feb
In directory sc8-pr-cvs1:/tmp/cvs-serv12860

Added Files:
	index.shtml status_main.ssi 
Log Message:
feb update


--- NEW FILE: index.shtml ---
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<HTML>
  <HEAD> <TITLE>GeneX @ SourceForge</TITLE></HEAD>

  <BODY bgcolor="white">
    <center>
      <table border="1" cellpadding="0" cellspacing="0" width="800">
	  <tr>
	    <td bgcolor="#FFFFBB" colspan="2">
	      <img src="http://genex.sourceforge.net/graphics/genex_banner.png" alt="genex banner">
	    </td>
	  </tr> 
	  <tr> <!-- start Nav Bar table -->
	    <td width="25%" valign="top"> 

	      <!--#include virtual="/status/status_menu.ssi"-->

	    </td>
	    <td align="LEFT" VALIGN="top">

	      <!--#include virtual="status_main.ssi"-->

	    </td>
	  </tr>
	  <tr bgcolor="#8FB9AA">
	    <th colspan="2">
	      <!-- The Page Footer goes here -->
	      <!--#include virtual="/content/footer.ssi"-->
	    </th>
	  </tr>
      </table>
    </center>
  </BODY>
</HTML>


--- NEW FILE: status_main.ssi ---
<!--Main content -->


  <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
    <tr valign="top" bgcolor="#D8E4F7">
      <th><big>February 28th, 2002</big></th>
    </tr>
    <tr bgcolor="#D8E4F7">
      <td>
	
	<p>
	<b><u>UVa Update - Tom Laudeman</u></b>
	</p>
<p>
Things have been quiet lately. I hope everyone is making good progress.
</p>
<p>
We're putting a new version live today: 1.5.20
</p>

<p>
We just created a raft of changes/features requested mostly by the microarray center here (the BRF). They wanted all studies, experimental conditions, orders, samples, and hybridizations (arraymeasurement records) to be owned by the Primary Investigator, with a created_by field. That was exciting. In doing that I found some bugs.
</p>
<p>
We also added loading and viewing the Affy quality control data. I added quite a bit more detail to some of the curator's order views.
</p>
<p>
Teela got the back end for the Analysis Trees 98% complete. As far as we can tell there are a couple of tiny tweaks at the Web/UI side, and Analysis Trees will be fully functional.
</p>
<p>
BTW, we changed the logo from "Va GeneX" to "GeneX Va" due to an alternate (funny, unfortunate) way to understand the letter combination
</p>
<p>
v a g e n e x
</p>
<p>
Sadly, we neglected to do the "does this spell something funny" test before finalizing the name. Sheez.
</p>
<p>
Cheers! 
</p>

<p>	
	<hr>
	<p>
	<b><u>Caltech Update - Brandon King</u></b>
	</p>
<p>
   I've been busy trying to document and get <a href="http://pymerase.sf.net/">Pymerase</a> to the level where other developers would consider using it. One of these days we hope to make the changes which will make the generatedm Python API compatible with Genex 2.x. We have also just setup the Bug / Feature Request tracker for the <a href="http://pymerase.sf.net/">Pymerase</a> project. I personally like it and think it might be worth using in the GeneX world.
</p>
<p>
   On another note, my laptop has suffered from a RAM Slot Failure. It has been sent back to sony for repairs. Unfortunately, it had our only copy of GeneX 2.x. So, we are going to install GeneX 2.x on our database server soon, as Joe Roden would like to use the database. Any comments or suggestions about installation from a CVS checkout? Is it in a stable state? Any big changes planed soon?
</p>
<p>
   Joe is hoping to load Affy U133 data into the database. Are the MAGE-ML file available to doing such a thing?
</p>
<p>
   My goal for the next couple of weeks is to continue preparing <a href="http://pymerase.sf.net/">Pymerase</a> for release in the hope that other will use it and maybe even contribute to it. I also would like to get a better understanding of where GeneX 2.x currently stands?  We would love to see GeneX 2.x regain the momentum it had before the holidays... Maybe it has, but we've just been out of touch?
</p>


      </td>
    </tr>
  </table>


  <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
    <tr valign="top" bgcolor="#D8E4F7">
      <th><big>February 7th, 2002</big></th>
    </tr>
    <tr bgcolor="#D8E4F7">
      <td>
	<hr>
	<p>
	<b><u>Caltech Update - Brandon King</u></b>
	</p>
<p>
Accomplishments:<br>
-Generate Graphviz diagrams which look like UML using <a href="http://pymerase.sf.net/">Pymerase</a><br>
-Wrote setup script for installing <a href="http://pymerase.sf.net/">Pymerase</a><br>
</p>
<p>
Next Week:<br>
-<a href="http://pymerase.sf.net/">Pymerase</a> generation of GUIs<br>
-More setup script improvement<br>
</p>
	
	<hr>
	<p>
	<b><u>UVa Update - Tom Laudeman</u></b>
	</p>
<p>
- Jodi cleaned up the schema some. We added a table to the security system so we can keep track of primary investigators (PI). Traditional groups aren't enough<br>
-- the Microarray Center (called the BRF here at UVa) wants to know who the PI is. Jodi also removed loads of legacy stuff in the schema that isn't being used.
</p>
<p>
- Teela is back on our project for several weeks and is putting the final touches on the back end of the Analysis Trees.
</p>
<p>
After a couple of weeks working on other projects, I added some user requested features:
</p>
<p>
- Curator order view has a link to order owner's contact info
</p>
<p>
- Curator order view has a link to the QA data which is now being loaded from the RPT and EXP files.
</p>
<p>
- Curator order view has a link to the study. In yet another triumph for the security system, since the experimental conditions are not owned by the curator and therefore not writable, they render as text, not form fields. The triumph comes from not modifying the any existing code to achieve this.
</p>
<p>
- A couple of weeks ago I added a 'view one order' feature for the curators.
</p>
<p>
- I created the 'add PI to a specific user' and 'change user's PI' features.
</p>
<p>
- Fixed admin_cli.pl that we use to create new accounts to take PI as an argument.
</p>
<p>
- Patrick at George Washington U. has installed Va GeneX and found a bug in loading XLS Affy MAS5 data. I fixed that, added a new item to our test plan (since we missed the bug) and generally did some much needed cleaning in the loading scripts.
</p>
<p>
Next:<br>
- allow users to chown orders and studies to the PI. Current thinking is that chown'ed records keep their group and group permissions.
</p>
<p>
- allow curators chown orders to the PI so that when the data is loaded, the PI will own it. Loaded data is owned by whoever owns the order.
</p>
<p>
- Analysis Tree work continues
</p>
<p>
- Additional reports for the curators in the microarray center 
</p>	


      </td>
    </tr>
  </table>

<!-- End of Content -->

[Genex-cvs-commit] genex-www/status/2003/jan status_main.ssi,1.1,1.2

From: <ki...@us...> - 2003-02-28 21:50:00

Update of /cvsroot/genex/genex-www/status/2003/jan
In directory sc8-pr-cvs1:/tmp/cvs-serv3341a

Modified Files:
	status_main.ssi 
Log Message:
formatting update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2003/jan/status_main.ssi,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** status_main.ssi	28 Feb 2003 21:44:48 -0000	1.1
--- status_main.ssi	28 Feb 2003 21:49:56 -0000	1.2
***************
*** 9,13 ****
        <td>
  
!         <hr>
  	<p>	
  	<b><u>Caltech Update - Diane Trout</u></b><br>
--- 9,13 ----
        <td>
  
! 
  	<p>	
  	<b><u>Caltech Update - Diane Trout</u></b><br>
***************
*** 121,125 ****
      <tr bgcolor="#D8E4F7">
        <td>
! 	<hr>
  	<p>
  	<b><u>Caltech Update - Brandon King</u></b>
--- 121,125 ----
      <tr bgcolor="#D8E4F7">
        <td>
! 
  	<p>
  	<b><u>Caltech Update - Brandon King</u></b>
***************
*** 173,177 ****
      <tr bgcolor="#D8E4F7">
        <td>
! 	<hr>
  	<p>
  	<b><u>UVa Update - Tom Laudeman</u></b>
--- 173,177 ----
      <tr bgcolor="#D8E4F7">
        <td>
! 
  	<p>
  	<b><u>UVa Update - Tom Laudeman</u></b>

[Genex-cvs-commit] genex-www/status index.shtml,1.4,1.5 status_menu.ssi,1.2,1.3

From: <ki...@us...> - 2003-02-28 21:47:09

Update of /cvsroot/genex/genex-www/status
In directory sc8-pr-cvs1:/tmp/cvs-serv2274

Modified Files:
	index.shtml status_menu.ssi 
Log Message:
jan update


Index: index.shtml
===================================================================
RCS file: /cvsroot/genex/genex-www/status/index.shtml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** index.shtml	6 Dec 2002 19:20:32 -0000	1.4
--- index.shtml	28 Feb 2003 21:47:01 -0000	1.5
***************
*** 1 ****
! <!--#include virtual="/status/2002/dec/index.shtml"-->
\ No newline at end of file
--- 1 ----
! <!--#include virtual="/status/2003/jan/index.shtml"-->
\ No newline at end of file

Index: status_menu.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/status_menu.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_menu.ssi	6 Dec 2002 19:22:38 -0000	1.2
--- status_menu.ssi	28 Feb 2003 21:47:01 -0000	1.3
***************
*** 27,31 ****
  	  - <b>March</b><br>
  	  - <b>February</b><br>
! 	  - <b>January</b><br>
        </td>
  
--- 27,31 ----
  	  - <b>March</b><br>
  	  - <b>February</b><br>
! 	  - <b><a href="http://genex.sourceforge.net/status/2003/jan/">January</a></b><br>
        </td>

[Genex-cvs-commit] genex-www/status/2003/jan index.shtml,NONE,1.1 status_main.ssi,NONE,1.1

From: <ki...@us...> - 2003-02-28 21:44:51

Update of /cvsroot/genex/genex-www/status/2003/jan
In directory sc8-pr-cvs1:/tmp/cvs-serv1425

Added Files:
	index.shtml status_main.ssi 
Log Message:
status update


--- NEW FILE: index.shtml ---
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<HTML>
  <HEAD> <TITLE>GeneX @ SourceForge</TITLE></HEAD>

  <BODY bgcolor="white">
    <center>
      <table border="1" cellpadding="0" cellspacing="0" width="800">
	  <tr>
	    <td bgcolor="#FFFFBB" colspan="2">
	      <img src="http://genex.sourceforge.net/graphics/genex_banner.png" alt="genex banner">
	    </td>
	  </tr> 
	  <tr> <!-- start Nav Bar table -->
	    <td width="25%" valign="top"> 

	      <!--#include virtual="/status/status_menu.ssi"-->

	    </td>
	    <td align="LEFT" VALIGN="top">

	      <!--#include virtual="status_main.ssi"-->

	    </td>
	  </tr>
	  <tr bgcolor="#8FB9AA">
	    <th colspan="2">
	      <!-- The Page Footer goes here -->
	      <!--#include virtual="/content/footer.ssi"-->
	    </th>
	  </tr>
      </table>
    </center>
  </BODY>
</HTML>


--- NEW FILE: status_main.ssi ---
<!--Main content -->


  <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
    <tr valign="top" bgcolor="#D8E4F7">
      <th><big>January 24th, 2002</big></th>
    </tr>
    <tr bgcolor="#D8E4F7">
      <td>

        <hr>
	<p>	
	<b><u>Caltech Update - Diane Trout</u></b><br>
	</p>
<p>
Accomplishments:<br>
-Unhacked some workstations :(<br>
-Discovered Poseidon 1.5.1 is no longer using the novosoft UML reader
 instead they're using one from the netbeans project. (it supports a
 newer version of the XMI/UML file format).<br>
-Fixed bug in pymerase that prevented the bool type from being saved
 to the database correctly<br>
</p>
<p>
Next Week:<br>
-Fix several bugs that brandon found.<br>
-Choose and start implementing a solution to UML parsing.<br>
</p>
<p>
Problems:<br>
-Dealing with the switch of UML parsers<br>
--Ended up being distracted by trying to understand netbeans.<br>
--I'm getting tempted to extend pymerase to support generating C++
  classes. Using the current UML reader I could hopefully generate C++
  classes representing the UML specification. <br>
</p>
<p>
  Add a little XML parsing and some swig wrapping and I'm hopefully
  free of this annoying java dependency with my own scripting language
  friendly UML parser.
</p>

        <hr>
	<p>
	<b><u>UVa Update - Jodi Kanter</u></b>
	</p>
<p>
Accomplishments this week:<br>
-spent a lot of time on schema design for two other projects.<br>
- updating Va-GeneX schema drawings for web site.<br>
- ongoing Va-GeneX user assistance with training, accounts, data load, etc..<br>
- first historical data load to Va-GeneX complete.<br>
</p>
<p>
For Next Week:<br>
- clean up schema SQL script to reflect tables, indexes, etc.. actually in use.<br>
- focus on Postgres and query performance<br>
- work on adding foreign key constraints, necessary indexes, etc. to GeneX schema<br>
</p>

	<hr>
	<p>
	<b><u>UCI Update - Harry Mangalam</u></b>
	</p>
<p>
Updates:
</p>
<p>
Over Holidays did not do much of anything :) & :(
</p>
<p>
Recently, used indexing, and experimented with float -> int conversion to represent data in a custom table to increase speed of query > 1000X on GMU server on some queries.  Also learned many unpleasant but useful things about GeneSpring, DB drivers, PostgreSQL, Perl, & Python.
</p>
<p>
GeneSpring connectivity is back (SiG changed the way it distributes it over the holidays) and once Jennifer tells me more about their Genome format, we can start putting together a complete connection package (finish HOWTO, provide example views and tables to query with it, etc).
</p>

<p>Working on:<br>
- Learning about Python, Qt, & SWIG (thanks, Diane), so as to be able to design independent apps to connect the DB to other apps.<br>
- continuing to optimize the DB so as to make it responsive enough for real work (in realish time).<br>
- writing some PG routines to do the table conversion in-place rather than exporting tables, converting with Pl/Py, then importing them (latter is site dependent; former will be site-independent).<br>
</p>
-- 
<p>
Note:  Michael Pear, an old-time GeneX contributor who went to work for ISIS's GeneTrove div contacted me to tell me that they have decided not to release the SW as a separate product, but will instead be Open-Sourcing it (the value to them is the content, not the SW).  It's a relatively generic gene expression DB browser and query composer, written in Java, for MySQL, but relatively agnostic.  I'll be meeting with them at the O'Reilly BioCon in San Diego Feb 3-6 to get the details, but it sounds like it might be worth looking into as another front-end for GeneX.
</p>
<p>
I'll post a follow-up abstract from their group in another note.	
</p>

	<hr>
	<p>
	<b><u>Caltech Update - Brandon King</u></b>
	</p>

<p>	
Accomplishments:<br>
-Unhacked two computers<br>
-Discoverd the cause thanks to Diane and a few others (Affymetrix software installs MSDE with a huge security hole!)<br>
-Documented how to secure a computer with Affymetrix software installed.<br>
</p>
<p>
Next Week:<br>
-Back to auto-generating python/tk gui library using pymerase<br>
</p>
<p>
Problems:<br>
-Windows and Security, or lack there of!<br>
</p>
	

      </td>
    </tr>
  </table>


  <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
    <tr valign="top" bgcolor="#D8E4F7">
      <th><big>January 17th, 2002</big></th>
    </tr>
    <tr bgcolor="#D8E4F7">
      <td>
	<hr>
	<p>
	<b><u>Caltech Update - Brandon King</u></b>
	</p>
<p>	
Accomplishments:<br>
-Can now generate basic Python/Tk GUI widget library using Pymerase<br>
--Entry Widgets (Validated entry boxes for a give table)<br>
--Save Widget (Tells a given entry widget to save the data)<br>
--NavBar Widget (For a given Entry widget navigates through entries)<br>
--Generic database connection widget<br>
--DbEntry Widgets (Inherited from Entry; Uses Save/NavBar and DBAPI to connect to a database)<br>
</p>
<p>
Next Week:<br>
-DbEntry Widget Fk/Obj linking<br>
-Entry/DbEntry Widget combos (For combining 2 table Entry widgets into one entry widget)<br>
</p>
<p>
Problems:<br>
-Got thrown off by the holidays when it comes to status updates. (Hopefully back to normal now) =o)<br>
</p>

	<hr>
	<p>
	<b><u>UVa Update - Tom Laudeman</u></b>
	</p>
<p>
- Updated the production server with version 1.5.19. This is a few bug fixes and a few new features. All the edit/delete UI has a consistent look and feel. The data export was upgraded with improved (optional) headers.
</p>
<p>
- We've deployed a simple script to vacuum the db.
</p>
<p>
- Revamped our History/Background page with links to all 3 GeneX projects and a description of Va GeneX and GeneX-Lite. We still don't have a description (2 to 3 paragraphs) from the GeneX 2 project
*gentle hint*.
</p>
<p>
- This week we are mostly working on a couple of other web enabled database projects both of which include annotated protein encyclopedias.  GeneX work will consist of collecting requests from users and from the microarray center for new features (and bugs)
</p>

      </td>
    </tr>
  </table>


  <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
    <tr valign="top" bgcolor="#D8E4F7">
      <th><big>January 10th, 2002</big></th>
    </tr>
    <tr bgcolor="#D8E4F7">
      <td>
	<hr>
	<p>
	<b><u>UVa Update - Tom Laudeman</u></b>
	</p>
	<p>
	Better on Monday than not at all :-)
	<p>
<p>
- Preparing for a new release 1.5.19 with some bug fixes, and improved UI, and a new view of orders for the curators. This version also includes more features in Analysis Trees, including doing all the user parameters. Testing of the new version is complete, so we'll roll it out tomorrow (Tuesday the 14th).
</p>

<p>
- Created a new project Va Genex at SourceForge. We a no longer using the Rel-1_0_1-branch of GeneX.
</p>

<p>
- Added Todd's description of GeneX-Lite to our History/Background page, along with links to GeneX and GeneX-Lite.
</p>

<p>
- We may have a small bug-fix release at the beginning of February. Teela and I will spend February finishing the Analysis Tree code.
</p>	

      </td>
    </tr>
  </table>

<!-- End of Content -->

[Genex-cvs-commit] genex-www/status/2002/dec status_main.ssi,1.3,1.4

From: <ki...@us...> - 2003-02-28 20:55:28

Update of /cvsroot/genex/genex-www/status/2002/dec
In directory sc8-pr-cvs1:/tmp/cvs-serv12380

Modified Files:
	status_main.ssi 
Log Message:
update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/dec/status_main.ssi,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** status_main.ssi	26 Feb 2003 21:46:20 -0000	1.3
--- status_main.ssi	28 Feb 2003 20:55:23 -0000	1.4
***************
*** 1,3 ****
--- 1,15 ----
  <!--Main content -->
+ 
+   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
+     <tr valign="top" bgcolor="#D8E4F7">
+       <th><big>December 20th, 2002</big></th>
+     </tr>
+     <tr bgcolor="#D8E4F7">
+       <td>
+ 	HOLIDAY BREAK =o)
+       </td>
+     </tr>
+   </table>
+ 
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">

[Genex-cvs-commit] genex-www/status/2002/dec status_main.ssi,1.2,1.3

From: <ki...@us...> - 2003-02-26 21:46:24

Update of /cvsroot/genex/genex-www/status/2002/dec
In directory sc8-pr-cvs1:/tmp/cvs-serv5140

Modified Files:
	status_main.ssi 
Log Message:
wrong date


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/dec/status_main.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_main.ssi	26 Feb 2003 21:45:07 -0000	1.2
--- status_main.ssi	26 Feb 2003 21:46:20 -0000	1.3
***************
*** 2,6 ****
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>December 5th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">
--- 2,6 ----
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
      <tr valign="top" bgcolor="#D8E4F7">
!       <th><big>December 13th, 2002</big></th>
      </tr>
      <tr bgcolor="#D8E4F7">

[Genex-cvs-commit] genex-www/status/2002/dec status_main.ssi,1.1,1.2

From: <ki...@us...> - 2003-02-26 21:45:12

Update of /cvsroot/genex/genex-www/status/2002/dec
In directory sc8-pr-cvs1:/tmp/cvs-serv4110

Modified Files:
	status_main.ssi 
Log Message:
update


Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/dec/status_main.ssi,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** status_main.ssi	6 Dec 2002 19:19:48 -0000	1.1
--- status_main.ssi	26 Feb 2003 21:45:07 -0000	1.2
***************
*** 1,3 ****
--- 1,94 ----
  <!--Main content -->
+   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
+     <tr valign="top" bgcolor="#D8E4F7">
+       <th><big>December 5th, 2002</big></th>
+     </tr>
+     <tr bgcolor="#D8E4F7">
+       <td>
+ 	<p>	
+ 	<b><u>Caltech Update - Brandon King</u></b><br>
+ 	</p>
+ <p>Summery:<br>
+ -Worked on updating pymerase output modules<br>
+ -Wrote an output module for generating Python Tk Widgets. (Partially Implemented)<br>
+ --Currently handles varchar and text fields.<br>
+ </p>
+ <p>
+ Next Week:<br>
+ -Add support for other datatypes to Python Tk Widget generation<br>
+ -Automaticly hook up the Python Tk Widgets to generate Python Tk Widgets as a option<br>
+ -Test GeneSpring connection<br>
+ </p>
+ 
+ 	<hr>
+ 	<p>
+ 	<b><u>Caltech Update - Diane Trout</u></b>
+ 	</p>
+ <p>
+ * Current progress
+ </p>
+ <p>
+  ** sent to rosetta to investigate resolver. ** in getting the XMI
+  reader working for pymerase I broke the GeneX
+    Table.dtd reader. I'm currently fixing it.
+ </p>
+ <p>
+  * Next week ** Try and generate python MAGE objects<br>
+ ** More pymerase bug fixes.
+ </p>
+ <p>
+ * Thoughts
+ </p>
+ <p>
+ Since we're auto creating an API and database to for the user, would
+ it be possible to choose between storing array expression data as
+ relational records or as NetCDF (or similar open matrix file format)?
+ </p>
+ 
+ 	<hr>
+ 	<p>
+ 	<b><u>UVa Update - Tom Laudeman</u></b>
+ 	</p>
+ <p>- Implemented chgrp and chmod types of functionality in the web UI.</p>
+ 
+ <p>- Fixed a host of small bugs</p>
+ 
+ <p>- Tested, and installed a new version in production (1.5.15)</p>
+ 
+ <p>- Started integrating UI of the Analysis trees with the back end. The UI now reads user parameter values, and new nodes created from the UI get default values.</p>
+ 
+ 	<hr>
+ 	<p>
+ 	<b><u>UCI Update - Harry Mangalam</u></b>
+ 	</p>
+ <p>
+ * worked on getting the configure/installer to install the analysis apps again
+    (cybert, xcluster, rcluster)<br>
+ * the changes are just about ready to check in (the infamous Mangalam
+   Real Soon Now).  The installation works for CyberT, xcluster, but not yet
+   for rcluster (perl lib location problem).<br>
+ * in doing so, spent some time fixing the app cores and interfaces for cybert<br>
+ * another GeneX install from scratch; more mods to the installation docs.<br>
+ </p>
+ 	<hr>
+ 	<p>
+ 	<b><u>Open Informatics Update - Jason Stewart</u></b>
+ 	</p>
+ <p>
+ Progress:<br>
+ * jamboree at Stanford - added support for persistence in XML::Reader<br>
+ * added array tools to support MAS5 (fix-array, tab2AD, qtdim)<br>
+ * loaded and verified MAS5 dataset<br>
+ </p>
+ <p>
+ Goals for next week<br>
+ * be happy<br>
+ * build Genex persistence subclass for XML::Reader<br>
+ * load U133 array design <br>
+ * load .CEL data<br>
+ </p>
+       </td>
+     </tr>
+   </table>
  
    <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">

[Genex-cvs-commit] genex-server ChangeLog,1.121,1.122

From: <man...@us...> - 2003-02-13 21:01:06

Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv19448

Modified Files:
	ChangeLog 
Log Message:
updated ChangeLog

Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.121
retrieving revision 1.122
diff -C2 -d -r1.121 -r1.122
*** ChangeLog	13 Feb 2003 20:35:31 -0000	1.121
--- ChangeLog	13 Feb 2003 20:47:15 -0000	1.122
***************
*** 1,2 ****
--- 1,13 ----
+ 2003-02-13 Harry Mangalam <hj...@ta...>
+     * added or modified following documentation files:
+         GeneSpring.notes, 
+         GeneSpring_GeneX.database, 
+         GeneX_DB_tuning.txt,
+         HOWTO_Load_QuantArray_Data.txt
+     * added following Analysis-Only installation files:
+         AI_Configure,  AI_Install
+         to allow installation of the previous analysis apps
+     * modified my email addresses in number of files        
+ 
  2003-01-12  Jason E. Stewart  <ja...@op...>

[Genex-cvs-commit] genex-server/mergem mergem.html.in,1.2,1.3 mergem.in,1.1,1.2

From: <man...@us...> - 2003-02-13 20:32:57

Update of /cvsroot/genex/genex-server/mergem
In directory sc8-pr-cvs1:/tmp/cvs-serv11458/mergem

Modified Files:
	mergem.html.in mergem.in 
Log Message:
adding several documentation files

Index: mergem.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/mergem/mergem.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** mergem.html.in	6 Jan 2001 04:36:05 -0000	1.2
--- mergem.html.in	13 Feb 2003 20:32:54 -0000	1.3
***************
*** 69,73 ****
  <HR>
  
! <A HREF="mailto:man...@ho...">Mail me</A> if you have complaints or suggestions, or better still, patches to 
  contribute.
  <HR>
--- 69,73 ----
  <HR>
  
! <A HREF="mailto:hj...@ta...">Mail me</A> if you have complaints or suggestions, or better still, patches to 
  contribute.
  <HR>

Index: mergem.in
===================================================================
RCS file: /cvsroot/genex/genex-server/mergem/mergem.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** mergem.in	30 Dec 2000 03:23:52 -0000	1.1
--- mergem.in	13 Feb 2003 20:32:54 -0000	1.2
***************
*** 1,5 ****
  %%START_PERL%%
  # #!/usr/local/bin/perl
! # by Harry Mangalam; man...@ho...
  # this is free software; I place it in the public domain.  There are NO restrictions
  # on its use, except I'd appreciate a note if you find it useful or find/fix a bug, or
--- 1,5 ----
  %%START_PERL%%
  # #!/usr/local/bin/perl
! # by Harry Mangalam; hj...@ta...
  # this is free software; I place it in the public domain.  There are NO restrictions
  # on its use, except I'd appreciate a note if you find it useful or find/fix a bug, or

[Genex-cvs-commit] genex-server/CyberT-dist CTHelp.html.in,1.5,1.6

From: <man...@us...> - 2003-02-13 20:32:56

Update of /cvsroot/genex/genex-server/CyberT-dist
In directory sc8-pr-cvs1:/tmp/cvs-serv11458/CyberT-dist

Modified Files:
	CTHelp.html.in 
Log Message:
adding several documentation files

Index: CTHelp.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/CTHelp.html.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** CTHelp.html.in	14 Nov 2002 04:19:27 -0000	1.5
--- CTHelp.html.in	13 Feb 2003 20:32:53 -0000	1.6
***************
*** 10,14 ****
        Copyright (C) 2000 National Center for Genome Resources
        All rights reserved.
! 		Written by Harry J Mangalam (hj...@nc... || man...@ho...)
  -->
  
--- 10,14 ----
        Copyright (C) 2000 National Center for Genome Resources
        All rights reserved.
! 		Written by Harry J Mangalam (hj...@ta...)
  -->
  
***************
*** 26,30 ****
  <p>This form now handles Mac (&lt;CR>) and PC (&lt;CR>&lt;LF>) end-of-lines,
  as well as unix end-of-lines(&lt;LF>). If you find a bug or have comments,
! please send them either <a href="mailto:man...@ho...?subject=CyberT">Harry
  Mangalam</a> (problems with interface, presentation, results) or <a href="mailto:td...@uc...?CyberT">Tony
  Long</a> (algorithms, statistical features).
--- 26,30 ----
  <p>This form now handles Mac (&lt;CR>) and PC (&lt;CR>&lt;LF>) end-of-lines,
  as well as unix end-of-lines(&lt;LF>). If you find a bug or have comments,
! please send them either <a href="mailto:hj...@ta...?subject=CyberT">Harry
  Mangalam</a> (problems with interface, presentation, results) or <a href="mailto:td...@uc...?CyberT">Tony
  Long</a> (algorithms, statistical features).
***************
*** 78,82 ****
     <li>You may have found a genuine bug.  If you suspect this to be the case, 
     	we'd REALLY like to know.  
!       <a href="mailto:man...@ho...?subject=CyberT">So please tell me</a>.
  </ul>
  <a NAME="LabelCols"></a>
--- 78,82 ----
     <li>You may have found a genuine bug.  If you suspect this to be the case, 
     	we'd REALLY like to know.  
!       <a href="mailto:hj...@ta...?subject=CyberT">So please tell me</a>.
  </ul>
  <a NAME="LabelCols"></a>

[Genex-cvs-commit] genex-server/gxquery fetch_array.pl.in,1.12,1.13 fetch_es.pl.in,1.7,1.8 fetch_spot.pl.in,1.13,1.14 query_intro.pl.in,1.9,1.10

From: <man...@us...> - 2003-02-13 20:32:56

Update of /cvsroot/genex/genex-server/gxquery
In directory sc8-pr-cvs1:/tmp/cvs-serv11458/gxquery

Modified Files:
	fetch_array.pl.in fetch_es.pl.in fetch_spot.pl.in 
	query_intro.pl.in 
Log Message:
adding several documentation files

Index: fetch_array.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/gxquery/fetch_array.pl.in,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** fetch_array.pl.in	5 Feb 2001 16:25:03 -0000	1.12
--- fetch_array.pl.in	13 Feb 2003 20:32:53 -0000	1.13
***************
*** 3,7 ****
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@nc... || man...@ho...)
  #
  
--- 3,7 ----
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@ta...)
  #
  

Index: fetch_es.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/gxquery/fetch_es.pl.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** fetch_es.pl.in	21 Nov 2001 01:08:44 -0000	1.7
--- fetch_es.pl.in	13 Feb 2003 20:32:53 -0000	1.8
***************
*** 3,7 ****
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@nc... || man...@ho...)
  #
  
--- 3,7 ----
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@ta...)
  #
  

Index: fetch_spot.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/gxquery/fetch_spot.pl.in,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** fetch_spot.pl.in	2 Apr 2001 09:28:32 -0000	1.13
--- fetch_spot.pl.in	13 Feb 2003 20:32:53 -0000	1.14
***************
*** 3,7 ****
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@nc... || man...@ho...)
  #
  
--- 3,7 ----
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@ta...)
  #
  

Index: query_intro.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/gxquery/query_intro.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** query_intro.pl.in	5 Mar 2002 22:11:09 -0000	1.9
--- query_intro.pl.in	13 Feb 2003 20:32:53 -0000	1.10
***************
*** 3,7 ****
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@nc... || man...@ho...)
  #
  # Changelog
--- 3,7 ----
  # Copyright 2000, National Center for Genome Resources
  # All Rights Reserved  
! # Coding: Jason Stewart (je...@nc...) & Harry Mangalam (hj...@ta...)
  #
  # Changelog

[Genex-cvs-commit] genex-server/site/webtools/analysis add_analysis.pl,NONE,1.1.2.1

From: <td...@us...> - 2003-02-12 18:57:34

Update of /cvsroot/genex/genex-server/site/webtools/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv4832

Added Files:
      Tag: Rel-1_0_1-branch
	add_analysis.pl 
Log Message:
Moved from ..

--- NEW FILE: add_analysis.pl ---
#!/usr/bin/perl -w

=head1 NAME
 
  add_analysis -  add an analysis to the list of possible analyses

=head1 SYNOPSIS

 ./add_analysis

=head1 DESCRIPTION
  The add_analysis is intended to configure an new analysis for use 
 with in the gene analsys system.  It does the following:
   - adds appropriate records to the database based on the config file
   #- puts supplied scripts in appropriate locations
   #- verifies syntax and runnability of scripts
   #- verifies the existence of documentation

=cut

    use strict;
    use DBI;

    use Getopt::Long 2.13;
    use AppConfig qw(:expand :argcount);
    require "sessionlib.pl";


    my $config = AppConfig->new();
    $config->define('name', {ARGCOUNT => ARGCOUNT_ONE},
        'cmdstr', {ARGCOUNT => ARGCOUNT_ONE},
        'up', { ARGCOUNT => ARGCOUNT_LIST },
        'filetype',{ ARGCOUNT => ARGCOUNT_LIST },
        'extension',{ ARGCOUNT => ARGCOUNT_LIST },
        'sp', { ARGCOUNT => ARGCOUNT_LIST },
        'analysisfile', { ARGCOUNT => ARGCOUNT_LIST,});
    $config->define('configfile', {ARGCOUNT => ARGCOUNT_ONE},
                    'action', {ARGCOUNT => ARGCOUNT_ONE},
                    'debug', {ARGCOUNT => ARGCOUNT_ONE});
    my $success = $config->getopt(\@ARGV);
    usage() if (! $success);


    my $cfgfile = $config->get('configfile');
    my $debug = $config->get('debug');
    usage() if (!defined $cfgfile);
    usage() if (!defined $config->get('action'));
    $success = $config->file($cfgfile);
    die "Invalid config file format" if (! $success);

    modifyDB($config);

# end main

sub modifyDB
{
    my ($config) = @_;

    my $action = $config->get('action');

    # open handle to database
    my $dbh = new_connection();
    my $stm;
    my $name = $config->get('name');

    $stm = $dbh->prepare("select an_pk from analysis where an_name = '$name'");
    $stm->execute();

    #get result
    my $an_fk= $stm->fetchrow_array();
    $stm->finish();

    if (($action eq 'insert') && (!defined $an_fk))
    {
        # insert appropriate values in appropriate tables

        # we need to add the analysis
        act_analysis($dbh, $config->get('name'), $config->get('cmdstr'),
             $action);  

        # we need to add filetypes (optional)
        my $keysref = act_filetype($dbh, $config->get('filetype'), $action);    

        # we need to add the links to filetypes
        act_file_links($dbh, $config->get('analysisfile'), 
            $config->get('name'), $action, $keysref);    

        # we need to add the sysparams
        act_sysparams($dbh, $config->get('sp'), $config->get('name'), $action); 

        # we need to add the userparams
        act_userparams($dbh, $config->get('up'), $config->get('name'), $action);    

        # insert appropriate values in extension table
        act_extension($dbh, $config->get('extension'), $action, $keysref);
    }
    elsif (($action eq "remove") && (defined $an_fk))
    {
        # note: removing must be done in a somewhat opposite
        # order to adding

        # delete appropriate values in extension table
        act_extension($dbh, $config->get('extension'), $action, []);

        # we need to delete the links to filetypes
        act_file_links($dbh, $config->get('analysisfile'),
            $config->get('name'), $action, []);    

        # we need to delete the sysparams
        act_sysparams($dbh, $config->get('sp'), $config->get('name'), $action);

        # we need to delete the userparams
        act_userparams($dbh, $config->get('up'), $config->get('name'), $action);

        # we need to delete the analysis
        act_analysis($dbh, $config->get('name'), $config->get('cmdstr'),
             $action);  

        # we need to delete filetypes (optional)
        act_filetype($dbh, $config->get('filetype'), $action);    
    } 
    elsif (!(($action eq "insert") || ($action eq "remove")))
    {
        print "Unrecognized action: $action\n";
        usage();
    }   
    #$dbh->commit();
    $dbh->disconnect(); 

} # addToDB

sub parse_into_records
{
  my @input = @_;
  my @return = ();
  my %rec = ();

  while (my $element = shift(@input))
  { 
    my ($key, $value) = split(/=/, $element);
    #remove spaces from key
    $key =~ tr/ //d;
    if (exists $rec{$key})
    {
      my %dup = %rec;
      push(@return, \%dup);
      %rec = ();
    }
    $rec{$key} = $value;
  }
  push(@return, \%rec);
  return(@return);
  
} #parse_into_record

sub act_filetype
{

  my ($dbh, $filetype, $action) = @_;
  
  my $stm = "";
  my $record;
  my $table = "filetypes";
  my @keys = ();

  my @records = parse_into_records(@$filetype);

  foreach $record (@records)
  {
    my %rec = %$record;
    my $name = $rec{name};
    my $comment = $rec{comment};
    my $arg_name = $rec{arg_name};


    if ($action eq "remove")
    {
      $stm = "delete from $table where ft_name = '$name'";
    }
    else
    {
        checkValidFields($table, [ "name", "arg_name" ], 
            ["name", "comment", "arg_name"], $record);
      $stm = "insert into $table (ft_name, ft_comments, arg_name) " . 
        "values ('$name', '$comment', '$arg_name');";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }
  $dbh->commit();
  
  foreach $record (@records)
  {
    my %rec = %$record;
    my $name = $rec{name};
    my $comment = $rec{comment};
    my $arg_name = $rec{arg_name};

    if ($action eq "insert")
    {
        $stm = "select ft_pk from $table where ft_name = '$name' " .
            " and ft_comments = '$comment' and arg_name = '$arg_name'";
        my $sth = $dbh->prepare( $stm ); 
        $sth->execute(); 
        my $lastkey;
        while (my @row = $sth->fetchrow_array())
        {
            ($lastkey) = @row;
        }
        push(@keys, $lastkey);
    }
  }
  return(\@keys);
} # act_filetype    

sub act_analysis
{
  my ($dbh, $name, $cmdstr, $action) = @_; 
  my $stm = "";

  if ($action eq "remove")
  {
    $stm = "delete from analysis where an_name = '$name'";
  }
  else
  {
    $stm = "insert into analysis (an_name, cmdstr) values ('$name', '$cmdstr');";
  }

  print "$stm\n" if $debug;
  my $sth = $dbh->prepare( $stm ); 
  $sth->execute();
  $dbh->commit();
} # act_analysis   

sub act_extension
{
  my ($dbh, $ext, $action, $keysref) = @_;    

  my $stm = "";
  my $record;
  my $table="extension";
  my @keys = @$keysref;

  my @records = parse_into_records(@$ext);

  foreach $record (@records)
  {
    my %rec = %$record;

    
    my $filetype = $rec{filetype};
    my $ext = $rec{ext};

    # select the filetypes pk for the filetype
    $stm = $dbh->prepare("select ft_pk from filetypes where ft_name= '$filetype'");
    $stm->execute();

    my $ft_fk = $stm->fetchrow_array();

    if ((!defined $ft_fk) && ($action eq "insert"))
    { 
      warn "Unable to get filetypes key value for $filetype";
    }
    
    if (($action eq "remove") && (defined $ft_fk))
    {
            $stm = "delete from $table where ft_fk = '$ft_fk'";
            print "$stm\n" if $debug;
            my $sth = $dbh->prepare( $stm ); 
            $sth->execute();
    }
    if (($action eq "insert") && (defined $ft_fk))
    {
            checkValidFields($table, [ "filetype","ext" ],
                 ["filetype", "ext"], $record);
            while (! numIn($ft_fk, @keys))
            {
                $ft_fk = $stm->fetchrow_array;
                break() if (!defined $ft_fk);
            }

            $stm = $dbh->prepare("select ext_pk from extension where " .
                " ft_fk = $ft_fk and extension = '$ext'");
            $stm->execute();
            my $exists = $stm->fetchrow_array();
            if (!defined $exists)
            {
                $stm = "insert into $table (ft_fk, extension) " . 
                    "values ($ft_fk, '$ext');";
                print "$stm\n" if $debug;
                my $sth = $dbh->prepare( $stm ); 
                $sth->execute();
            }
    }
  }
} # act_extension


sub act_file_links
{
  my ($dbh, $filelist, $name, $action, $keysref) = @_;    

  my $stm = "";
  my $record;
  my $table="analysis_filetypes_link";
  my @keys = @$keysref;

  my @records = parse_into_records(@$filelist);

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select an_pk from analysis where an_name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }
  
  foreach $record (@records)
  {
    my %rec = %$record;

    
    my $filetype = $rec{filetype};
    my $input = $rec{input};

    # select the filetypes pk for the filetype
    $stm = $dbh->prepare("select ft_pk from filetypes where ft_name= '$filetype' ");

    $stm->execute();

    my $ft_pk = $stm->fetchrow_array; 
    

    if ((!defined $ft_pk) && ($action eq "insert"))
    { 
      warn "Unable to get filetypes key value for $filetype";
    }

    if (($action eq "remove") && (defined $ft_pk))
    {
            $stm = "delete from $table where an_fk = '$an_fk'";
            print "$stm\n" if $debug;
            my $sth = $dbh->prepare( $stm ); 
            $sth->execute();
    }

    if (($action eq "insert") && (defined $ft_pk))
    {
       checkValidFields($table, [ "filetype","input"],
             ["filetype", "input"], $record);
       while (! numIn($ft_pk, @keys))
       {
           $ft_pk = $stm->fetchrow_array; 
           break() if (! defined $ft_pk);
       }
       $stm = "insert into $table (an_fk, ft_fk, input) " . 
          "values ('$an_fk', '$ft_pk', '$input');";
       print "$stm\n" if $debug;
       my $sth = $dbh->prepare( $stm ); 
       $sth->execute();
    }
  }
} # act_file_links

sub act_sysparams
{
  my ($dbh, $sp, $name, $action) = @_; 
  
  my $stm = "";
  my $record;
  my $table="sys_parameter_names"; 
  my @records = parse_into_records(@$sp);

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select an_pk from analysis where an_name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }

  foreach $record (@records)
  {
    my %rec = %$record;

    checkValidFields($table, [ "name" ], ["name", "default"], $record);

    my $name = $rec{name};
    my $default ="NULL";

    $default = "'$rec{default}'" if exists($rec{default});
    if ($action eq "remove")
    {
      $stm = "delete from $table where an_fk = '$an_fk'";
    }
    else
    {
      $stm = "insert into $table (an_fk, sp_name, sp_default) values ('$an_fk', '$name', $default);";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }

  $dbh->commit();
} # act_sysparams   

sub act_userparams
{
  my ($dbh, $up, $name, $action) = @_; 
  
  my $stm = "";
  my $record;
  my $table="user_parameter_names";

  my @records = parse_into_records(@$up);

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select an_pk from analysis where an_name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }

  foreach $record (@records)
  {
    my %rec = %$record;
    my $name = $rec{name};
    my $display_name = $rec{display_name};
    my $type = $rec{type};
    my $default ="NULL";

    $default = "'$rec{default}'" if exists($rec{default});

    checkValidFields($table, [ "name", "display_name", "type" ],
         ["name", "display_name", "type", "default"], $record);
    if ($action eq "remove")
    {
      $stm = "delete from $table where an_fk = '$an_fk'";
    }
    else
    {
      $stm = "insert into $table (an_fk, up_name, up_display_name, up_type, up_default) values ('$an_fk', '$name', '$display_name', '$type', $default);";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }
} # act_userparams 

sub checkValidFields
{
    my ($table, $reqref, $fieldsref, $record) = @_;

    my @req = @$reqref;
    my @fields = @$fieldsref;
    my %rec = %$record;

    foreach my $req (@req)
    {
        warn "Incorrect configuration. $table requires $req field.\n" 
            if (!exists $rec{$req});
    }

    foreach my $key (keys(%rec))
    {
        my $found = 0;
        foreach my $field (@fields)
        {
            $found = 1 if ($field eq $key);
        }
        if (! $found)
        {
            warn "Invalid sys param field: $key.\n";
            warn "Valid field names are: @fields\n";
        }
    }
} # checkValidFields

sub numIn
{
    my ($scalar) = shift;
    my @array = @_;

    my $in = 0;
    foreach my $item (@array)
    {
        if ($item == $scalar)
        {
            $in=1;
        }
    }
    return($in);
}

sub usage
{
      print "Usage: \n";
      print "./add_analysis.pl --configfile <filename> --action <insert|remove>\n";
      exit;
} # usage

=head1 NOTES

This script is not intended to be a great database configuration tool.
It is designed to load demo*.cfg for testing.  Note that if you remove
a cfg, it may remove extension types needed by other analysis.  I could
fix this, but have deemed that it isn't worth the time right now.

=head1 AUTHOR

Teela James

Flat | Threaded

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