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[Pymerase-cvs-commit] htdocs/docs index.shtml,1.14,1.15

From: <ki...@us...> - 2003-03-21 02:57:14

Update of /cvsroot/pymerase/htdocs/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv11277

Modified Files:
	index.shtml 
Log Message:
formatting


Index: index.shtml
===================================================================
RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** index.shtml	21 Mar 2003 02:56:41 -0000	1.14
--- index.shtml	21 Mar 2003 02:57:11 -0000	1.15
***************
*** 29,33 ****
            <a href="input">Input Modules</a>
            - Documentation about Input Modules<br>
! 	  <a href="output">Output Modules</a> ] - Documentation about Output Modules<br>
  	  </td>
          </tr>
--- 29,33 ----
            <a href="input">Input Modules</a>
            - Documentation about Input Modules<br>
! 	  <a href="output">Output Modules</a> ] - Documentation about Output Modules<br><br>
  	  </td>
          </tr>

[Pymerase-cvs-commit] htdocs/docs index.shtml,1.13,1.14

From: <ki...@us...> - 2003-03-21 02:56:44

Update of /cvsroot/pymerase/htdocs/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv10986

Modified Files:
	index.shtml 
Log Message:
formatting update


Index: index.shtml
===================================================================
RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** index.shtml	21 Mar 2003 02:51:22 -0000	1.13
--- index.shtml	21 Mar 2003 02:56:41 -0000	1.14
***************
*** 23,33 ****
          <tr>
            <td width="100%" bgcolor="#6C8AFF">
! 	  <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> | pdf ]<br>
! 	  Running Pymerase [ <a href="running">html</a> |
            <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=144835">
            pdf</a> ] - Information about running pymerase<br>
!           Input Modules [ <a href="input">html</a> ] 
            - Documentation about Input Modules<br>
! 	  Output Modules [ <a href="output">html</a> ] - Documentation about Output Modules<br>
  	  </td>
          </tr>
--- 23,33 ----
          <tr>
            <td width="100%" bgcolor="#6C8AFF">
! 	  <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> ]<br>
! 	  <a href="running">Running Pymerase</a> [
            <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=144835">
            pdf</a> ] - Information about running pymerase<br>
!           <a href="input">Input Modules</a>
            - Documentation about Input Modules<br>
! 	  <a href="output">Output Modules</a> ] - Documentation about Output Modules<br>
  	  </td>
          </tr>

[Pymerase-cvs-commit] Docs/running_pymerase Makefile,1.1,1.2

From: <ki...@us...> - 2003-03-21 02:53:29

Update of /cvsroot/pymerase/Docs/running_pymerase
In directory sc8-pr-cvs1:/tmp/cvs-serv9509

Modified Files:
	Makefile 
Log Message:
updated for html generation


Index: Makefile
===================================================================
RCS file: /cvsroot/pymerase/Docs/running_pymerase/Makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile	7 Mar 2003 02:54:07 -0000	1.1
--- Makefile	21 Mar 2003 02:53:21 -0000	1.2
***************
*** 2,4 ****
  	latex Run_Pymerase.tex
  	dvipdf Run_Pymerase.dvi
! 	gv Run_Pymerase.pdf
\ No newline at end of file
--- 2,7 ----
  	latex Run_Pymerase.tex
  	dvipdf Run_Pymerase.dvi
! 	gv Run_Pymerase.pdf
! 
! html:
! 	tth Run_Pymerase.tex
\ No newline at end of file

[Pymerase-cvs-commit] htdocs/docs index.shtml,1.12,1.13

From: <ki...@us...> - 2003-03-21 02:51:24

Update of /cvsroot/pymerase/htdocs/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv8468

Modified Files:
	index.shtml 
Log Message:
updated for latest release of Running Pymerase


Index: index.shtml
===================================================================
RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** index.shtml	21 Mar 2003 02:48:42 -0000	1.12
--- index.shtml	21 Mar 2003 02:51:22 -0000	1.13
***************
*** 25,29 ****
  	  <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> | pdf ]<br>
  	  Running Pymerase [ <a href="running">html</a> |
!           <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=141350">
            pdf</a> ] - Information about running pymerase<br>
            Input Modules [ <a href="input">html</a> ] 
--- 25,29 ----
  	  <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> | pdf ]<br>
  	  Running Pymerase [ <a href="running">html</a> |
!           <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=144835">
            pdf</a> ] - Information about running pymerase<br>
            Input Modules [ <a href="input">html</a> ]

[Pymerase-cvs-commit] htdocs/docs index.shtml,1.11,1.12

From: <ki...@us...> - 2003-03-21 02:48:45

Update of /cvsroot/pymerase/htdocs/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv7538

Modified Files:
	index.shtml 
Log Message:
updated with FAQ


Index: index.shtml
===================================================================
RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** index.shtml	5 Mar 2003 00:46:38 -0000	1.11
--- index.shtml	21 Mar 2003 02:48:42 -0000	1.12
***************
*** 22,34 ****
          </tr>
          <tr>
!           <td width="100%" bgcolor="#6C8AFF">&nbsp;Running 
!           Pymerase [ <a href="running">html</a> |
            <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=141350">
            pdf</a> ] - Information about running pymerase<br>
!           &nbsp;Input Modules [ <a href="input">html</a> ] 
            - Documentation about Input Modules<br>
! &nbsp;Output Modules [ <a href="output">html</a> ] - Documentation about 
!           Output Modules<br>
! &nbsp;</td>
          </tr>
  
--- 22,34 ----
          </tr>
          <tr>
!           <td width="100%" bgcolor="#6C8AFF">
! 	  <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> | pdf ]<br>
! 	  Running Pymerase [ <a href="running">html</a> |
            <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=141350">
            pdf</a> ] - Information about running pymerase<br>
!           Input Modules [ <a href="input">html</a> ] 
            - Documentation about Input Modules<br>
! 	  Output Modules [ <a href="output">html</a> ] - Documentation about Output Modules<br>
! 	  </td>
          </tr>

[Pymerase-cvs-commit] Docs/faq faq.tex,1.1,1.2

From: <ki...@us...> - 2003-03-21 02:43:32

Update of /cvsroot/pymerase/Docs/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv5559

Modified Files:
	faq.tex 
Log Message:
update


Index: faq.tex
===================================================================
RCS file: /cvsroot/pymerase/Docs/faq/faq.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** faq.tex	21 Mar 2003 00:36:40 -0000	1.1
--- faq.tex	21 Mar 2003 02:43:30 -0000	1.2
***************
*** 28,32 ****
  \author{Brandon King \& Diane Trout\\
  Copyright \copyright  California Institute of Technology}
! \date{Version 0.1.1\\\today}
  \maketitle
  \thispagestyle{empty}
--- 28,32 ----
  \author{Brandon King \& Diane Trout\\
  Copyright \copyright  California Institute of Technology}
! \date{Version 0.1.2\\\today}
  \maketitle
  \thispagestyle{empty}
***************
*** 40,43 ****
--- 40,44 ----
  \setcounter{page}{1}
  
+ %GENERAL
  \section{\cb FAQ - General}
  \subsection{\cb Why the name ''Pymerase''?}
***************
*** 53,56 ****
--- 54,63 ----
  Institute of Technology (Caltech).
  
+ \subsection{\cb What is the Wold Lab?}\label{woldlab}
+ The Wold Lab, run by Barbara Wold, is a Bioinformatics / Biology Lab at the
+ California Institute of Technology. The Lab consists of both
+ biologists and computational members. For more information visit
+ http://woldlab.caltech.edu/.
+ 
  \subsection{\cb Who originally developed Pymerase?}
  Diane Trout and Brandon King originally developed Pymerase in the Wold
***************
*** 65,68 ****
--- 72,128 ----
  including Sigmoid and MAGE.
  
+ \subsection{\cb What License is Pymerase distributed under?}
+ Pymerase is distributed under the MIT license which can be found in
+ the source code of Pymerase or on the web at
+ http://www.opensource.org/licenses/
+ 
+ \subsection{\cb Does Pymerase support all versions of ArgoUML and/or
+   XMI?}
+ Please see section \ref{argouml} for more information.
+ 
+ %CONTRIBUTING TO PYMERASE
+ \section{\cb FAQ - Contributing to Pymerase}
+ \subsection{\cb Can I contribute to Pymerase?}
+ Yes, anyone with the will to help may contribute to the Pymerase
+ project. Be it with programming skills, documention, examples, money
+ or good old moral support, we could use all the help we can get. If
+ you would like contribute in any way please send an e-mail to
+ pymerase-devel at lists.sourceforge.net or contact on of the curent
+ developers.
+ 
+ \subsection{\cb What ways can I contribute?}
+ Pymerase as an open source project servives from the support of the
+ Open Source community. Any help is welcome. Becoming a programmer
+ is probably the most obvious way to help, but is not the only way one
+ can contribute.
+ 
+ Here is just a small list of things one can do to help:
+ \begin{itemize}
+ \item writting documentation
+ \item testing code
+ \item creating examples
+ \item updating the web site
+ \item contributing expertice
+ \item contributing ideas
+ \item funding development
+ \end{itemize}
+ 
+ Please send e-mail to the mailing list pymerase-devel at
+ lists.sourceforge.net if you would like to contribute in any way.
+ 
+ \subsection{\cb How can I help fund development and how will it help?}
+ If you would like to help fund the Pymerase project or other projects
+ in the Wold Lab please contact Barbara Wold or send an e-mail to
+ pymerase-devel at lists.sourceforge.net. You can find out more about
+ the Wold Lab in section \ref{woldlab}
+ 
+ Additional funding for Pymerase would help in many ways. First of all,
+ Diane and myself (Brandon) also work on other projects in the Wold
+ Lab, so not all of our time goes into the project. Funding would help
+ with the continuing development by providing more time for us to work
+ on the project or the highering of more programmers to work on the
+ project.
+ 
+ %INPUT MODULES
  \section{\cb FAQ - Input Modules}
  \subsection{\cb parseGenexSchemaXML}
***************
*** 71,78 ****
  No. It's called parseGenexSchemaXML to give credit to the GeneX
  project for coming up with the file format used for this particular
! input module and the schema of the GeneX 2.x project. The format can
  be used to make any number of schemas using it. Special thanks goes to
  Jason Stewart of OpenInformatics.org for the original design of this
  XML format.
  
  \end{document}
--- 131,182 ----
  No. It's called parseGenexSchemaXML to give credit to the GeneX
  project for coming up with the file format used for this particular
! input module and the schema of the GeneX~2.x project. The format can
  be used to make any number of schemas using it. Special thanks goes to
  Jason Stewart of OpenInformatics.org for the original design of this
  XML format.
+ 
+ \subsubsection{\cb Does parseXMI support all versions of
+   XMI?}\label{argouml}
+ No. Unfortunately, the XMI standard is still developing rapidly, so
+ different versions of XMI can become incompatible with previous
+ versions. Supporting XMI was difficult in the first place as it's a
+ complicated standard. The XMI parser that was used in parseXMI was
+ written in Java, so Jython has to be used when running parseXMI.
+ 
+ I will have to find out what the latest version of ArgoUML that can be
+ used before they switch over to a new XMI parser. I know
+ ArgoUML~v0.10.* should work with Pymerase.
+ 
+ If you want to know more information on which versions of ArgoUML
+ export the version of XMI that Pymerase can read, please e-mail the
+ mailing list pymerase-devel at lists.sourceforge.net.
+ 
+ \subsubsection{\cb Why does parseGenexSchemaXML only work with
+   Jython?}
+ Finding an XMI parser that is developed enough and has documentation
+ on how to use it is difficult at this point in time. The XMI parser
+ that Diane used in parseXMI is written in Java, so Jython has to be
+ used when using the parseXMI input module.
+ 
+ %OUTPUT MODULES
+ \section{\cb FAQ - Output Modules}
+ \subsection{\cb General}
+ \subsubsection{\cb What modules do hope to include in the future?}
+ In the future we hope to include many more output modules. One of the
+ output modules we hope to develop is the generation of a C++ API which
+ then could be swig wrapped to allow many different languages like,
+ Python, Perl, and Java to use the same generate API.
+ 
+ \subsection{\cb CreateDBAPI}
+ \subsubsection{\cb What does CreateDBAPI do?}
+ CreateDBAPI generates a Python Database API for a given
+ schema. Currently the generated DBAPI is only compatible with
+ PostgreSQL databases. With some work, it could be ported to other
+ Relational Database Management Systems such as MySQL or Oracle.
+ 
+ \subsection{\cb CreateSQL}
+ \subsubsection{\cb What does CreateSQL do?}
+ CreateSQL generates a file containing SQL statements for the creation
+ of a PostgreSQL database for a given schema.
  
  \end{document}

[Pymerase-cvs-commit] htdocs/docs/faq index.shtml,NONE,1.1

From: <ki...@us...> - 2003-03-21 02:43:10

Update of /cvsroot/pymerase/htdocs/docs/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv5412

Added Files:
	index.shtml 
Log Message:
FAQ


--- NEW FILE: index.shtml ---
<html>

<head>
<meta name="GENERATOR" content="Microsoft FrontPage 5.0">
<meta name="ProgId" content="FrontPage.Editor.Document">
<meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
<link rel="SHORTCUT ICON" href="/images/pyfav.gif">
<title>Pymerase - FAQ</title>
</head>

<body>

<div align="left">
  <table border="0" cellpadding="0" cellspacing="0" style="border-collapse: collapse" bordercolor="#111111" id="AutoNumber1" width="100%">

  <!--#include virtual="/menus/docs_menu.shtml" -->

      <td align="center" valign="top"><br>
&nbsp;<table border="0" cellpadding="0" cellspacing="0" style="border-collapse: collapse" bordercolor="#111111" width="90%" id="AutoNumber2">
        <tr>
          <td width="100%" bgcolor="#6C8AFF">
	  <!--#include virtual="faq.html"-->
	  </td>
        </tr>
      </table>
      Last Modified: <!--#echo var="LAST_MODIFIED" -->
      </td>
    </tr>
  </table>
</div>

</body>

</html>

[Pymerase-cvs-commit] htdocs/docs/faq faq.html,NONE,1.1

From: <ki...@us...> - 2003-03-21 02:42:50

Update of /cvsroot/pymerase/htdocs/docs/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv5224

Added Files:
	faq.html 
Log Message:
first version of the FAQ


--- NEW FILE: faq.html ---
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"
           "http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<meta name="GENERATOR" content="TtH 2.92">

 
<title>Pymerase Docs - FAQ</title>
 
<h1 align="center"><font color="#0000FF">Pymerase Docs - FAQ</font> </h1>

<h3 align="center">Brandon King &amp; Diane Trout<br />
Copyright &#169;  California Institute of Technology </h3>

<h3 align="center">Version 0.1.2<br />Mar 20, 2003
</h3>




<p>

<h1>Contents </h1><a href="#tth_sEc1"
>1&nbsp; <font color="#0000FF">FAQ - General</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.1"
>1.1&nbsp; <font color="#0000FF">Why the name ''Pymerase''?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.2"
>1.2&nbsp; <font color="#0000FF">Where was Pymerase originally developed?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.3"
>1.3&nbsp; <font color="#0000FF">What is the Wold Lab?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.4"
>1.4&nbsp; <font color="#0000FF">Who originally developed Pymerase?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.5"
>1.5&nbsp; <font color="#0000FF">Why was the original purpose of Pymerase?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.6"
>1.6&nbsp; <font color="#0000FF">What License is Pymerase distributed under?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc1.7"
>1.7&nbsp; <font color="#0000FF">Does Pymerase support all versions of ArgoUML and/or XMI?</font></a><br />
<a href="#tth_sEc2"
>2&nbsp; <font color="#0000FF">FAQ - Contributing to Pymerase</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc2.1"
>2.1&nbsp; <font color="#0000FF">Can I contribute to Pymerase?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc2.2"
>2.2&nbsp; <font color="#0000FF">What ways can I contribute?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc2.3"
>2.3&nbsp; <font color="#0000FF">How can I help fund development and how will it help?</font></a><br />
<a href="#tth_sEc3"
>3&nbsp; <font color="#0000FF">FAQ - Input Modules</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc3.1"
>3.1&nbsp; <font color="#0000FF">parseGenexSchemaXML</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc3.1.1"
>3.1.1&nbsp; <font color="#0000FF">Can the parseGenexSchemaXML input module only parse the GeneX project schema?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc3.1.2"
>3.1.2&nbsp; <font color="#0000FF">Does parseXMI support all versions of XMI?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc3.1.3"
>3.1.3&nbsp; <font color="#0000FF">Why does parseGenexSchemaXML only work with Jython?</font></a><br />
<a href="#tth_sEc4"
>4&nbsp; <font color="#0000FF">FAQ - Output Modules</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.1"
>4.1&nbsp; <font color="#0000FF">General</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.1.1"
>4.1.1&nbsp; <font color="#0000FF">What modules do hope to include in the future?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.2"
>4.2&nbsp; <font color="#0000FF">CreateDBAPI</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.2.1"
>4.2.1&nbsp; <font color="#0000FF">What does CreateDBAPI do?</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.3"
>4.3&nbsp; <font color="#0000FF">CreateSQL</font></a><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#tth_sEc4.3.1"
>4.3.1&nbsp; <font color="#0000FF">What does CreateSQL do?</font></a><br />
 



<p>


<p>

 <h2><a name="tth_sEc1">
1</a>&nbsp;&nbsp;<font color="#0000FF">FAQ - General</font></h2>

     <h3><a name="tth_sEc1.1">
1.1</a>&nbsp;&nbsp;<font color="#0000FF">Why the name ''Pymerase''?</font></h3>
Pymerase is the combination of 'Python', the primary language Pymerase
is written in, and 'Polymerase'. Polymerase, in short, is a molecule
which copies/converts DNA into RNA. We figured that Pymerase had
similar functionality in that it took table.dtd XML (DNA) files and
converted them into other things, such as SQL statements (RNA) which
is then used to create a database (Protein).

<p>
     <h3><a name="tth_sEc1.2">
1.2</a>&nbsp;&nbsp;<font color="#0000FF">Where was Pymerase originally developed?</font></h3>
Pymerase was originally developed in the Wold Lab at the California
Institute of Technology (Caltech).

<p>
     <h3><a name="tth_sEc1.3">
1.3</a>&nbsp;&nbsp;<font color="#0000FF">What is the Wold Lab?</font></h3><a name="woldlab">
</a>
The Wold Lab, run by Barbara Wold, is a Bioinformatics / Biology Lab at the
California Institute of Technology. The Lab consists of both
biologists and computational members. For more information visit
http://woldlab.caltech.edu/.

<p>
     <h3><a name="tth_sEc1.4">
1.4</a>&nbsp;&nbsp;<font color="#0000FF">Who originally developed Pymerase?</font></h3>
Diane Trout and Brandon King originally developed Pymerase in the Wold
Lab at Caltech. Barbara Wold is the principal invesigator incharge of
the project at Caltech, along with collaborator Eric Mjolsness of
UC&nbsp;Irvine.

<p>
     <h3><a name="tth_sEc1.5">
1.5</a>&nbsp;&nbsp;<font color="#0000FF">Why was the original purpose of Pymerase?</font></h3>
The original purpose of pymerase was to generate a Python Database API
for the GeneX Microarray Gene Expression Database. As development
progressed Pymerase was made more generic to support other projects
including Sigmoid and MAGE.

<p>
     <h3><a name="tth_sEc1.6">
1.6</a>&nbsp;&nbsp;<font color="#0000FF">What License is Pymerase distributed under?</font></h3>
Pymerase is distributed under the MIT license which can be found in
the source code of Pymerase or on the web at
http://www.opensource.org/licenses/

<p>
     <h3><a name="tth_sEc1.7">
1.7</a>&nbsp;&nbsp;<font color="#0000FF">Does Pymerase support all versions of ArgoUML and/or
  XMI?</font></h3>
Please see section <a href="#argouml">3.1.2</a> for more information.

<p>

 <h2><a name="tth_sEc2">
2</a>&nbsp;&nbsp;<font color="#0000FF">FAQ - Contributing to Pymerase</font></h2>

     <h3><a name="tth_sEc2.1">
2.1</a>&nbsp;&nbsp;<font color="#0000FF">Can I contribute to Pymerase?</font></h3>
Yes, anyone with the will to help may contribute to the Pymerase
project. Be it with programming skills, documention, examples, money
or good old moral support, we could use all the help we can get. If
you would like contribute in any way please send an e-mail to
pymerase-devel at lists.sourceforge.net or contact on of the curent
developers.

<p>
     <h3><a name="tth_sEc2.2">
2.2</a>&nbsp;&nbsp;<font color="#0000FF">What ways can I contribute?</font></h3>
Pymerase as an open source project servives from the support of the
Open Source community. Any help is welcome. Becoming a programmer
is probably the most obvious way to help, but is not the only way one
can contribute.

<p>
Here is just a small list of things one can do to help:

<ul><p>
<li> writting documentation</li>
<p>
<li> testing code</li>
<p>
<li> creating examples</li>
<p>
<li> updating the web site</li>
<p>
<li> contributing expertice</li>
<p>
<li> contributing ideas</li>
<p>
<li> funding development</li>
</ul>

<p>
Please send e-mail to the mailing list pymerase-devel at
lists.sourceforge.net if you would like to contribute in any way.

<p>
     <h3><a name="tth_sEc2.3">
2.3</a>&nbsp;&nbsp;<font color="#0000FF">How can I help fund development and how will it help?</font></h3>
If you would like to help fund the Pymerase project or other projects
in the Wold Lab please contact Barbara Wold or send an e-mail to
pymerase-devel at lists.sourceforge.net. You can find out more about
the Wold Lab in section <a href="#woldlab">1.3</a>

<p>
Additional funding for Pymerase would help in many ways. First of all,
Diane and myself (Brandon) also work on other projects in the Wold
Lab, so not all of our time goes into the project. Funding would help
with the continuing development by providing more time for us to work
on the project or the highering of more programmers to work on the
project.

<p>

 <h2><a name="tth_sEc3">
3</a>&nbsp;&nbsp;<font color="#0000FF">FAQ - Input Modules</font></h2>

     <h3><a name="tth_sEc3.1">
3.1</a>&nbsp;&nbsp;<font color="#0000FF">parseGenexSchemaXML</font></h3>

      <h4><a name="tth_sEc3.1.1">
3.1.1</a>&nbsp;&nbsp;<font color="#0000FF">Can the parseGenexSchemaXML input module only parse the
  GeneX project schema?</font></h4>
No. It's called parseGenexSchemaXML to give credit to the GeneX
project for coming up with the file format used for this particular
input module and the schema of the GeneX&nbsp;2.x project. The format can
be used to make any number of schemas using it. Special thanks goes to
Jason Stewart of OpenInformatics.org for the original design of this
XML format.

<p>
      <h4><a name="tth_sEc3.1.2">
3.1.2</a>&nbsp;&nbsp;<font color="#0000FF">Does parseXMI support all versions of
  XMI?</font></h4><a name="argouml">
</a>
No. Unfortunately, the XMI standard is still developing rapidly, so
different versions of XMI can become incompatible with previous
versions. Supporting XMI was difficult in the first place as it's a
complicated standard. The XMI parser that was used in parseXMI was
written in Java, so Jython has to be used when running parseXMI.

<p>
I will have to find out what the latest version of ArgoUML that can be
used before they switch over to a new XMI parser. I know
ArgoUML&nbsp;v0.10.* should work with Pymerase.

<p>
If you want to know more information on which versions of ArgoUML
export the version of XMI that Pymerase can read, please e-mail the
mailing list pymerase-devel at lists.sourceforge.net.

<p>
      <h4><a name="tth_sEc3.1.3">
3.1.3</a>&nbsp;&nbsp;<font color="#0000FF">Why does parseGenexSchemaXML only work with
  Jython?</font></h4>
Finding an XMI parser that is developed enough and has documentation
on how to use it is difficult at this point in time. The XMI parser
that Diane used in parseXMI is written in Java, so Jython has to be
used when using the parseXMI input module.

<p>

 <h2><a name="tth_sEc4">
4</a>&nbsp;&nbsp;<font color="#0000FF">FAQ - Output Modules</font></h2>

     <h3><a name="tth_sEc4.1">
4.1</a>&nbsp;&nbsp;<font color="#0000FF">General</font></h3>

      <h4><a name="tth_sEc4.1.1">
4.1.1</a>&nbsp;&nbsp;<font color="#0000FF">What modules do hope to include in the future?</font></h4>
In the future we hope to include many more output modules. One of the
output modules we hope to develop is the generation of a C++ API which
then could be swig wrapped to allow many different languages like,
Python, Perl, and Java to use the same generate API.

<p>
     <h3><a name="tth_sEc4.2">
4.2</a>&nbsp;&nbsp;<font color="#0000FF">CreateDBAPI</font></h3>

      <h4><a name="tth_sEc4.2.1">
4.2.1</a>&nbsp;&nbsp;<font color="#0000FF">What does CreateDBAPI do?</font></h4>
CreateDBAPI generates a Python Database API for a given
schema. Currently the generated DBAPI is only compatible with
PostgreSQL databases. With some work, it could be ported to other
Relational Database Management Systems such as MySQL or Oracle.

<p>
     <h3><a name="tth_sEc4.3">
4.3</a>&nbsp;&nbsp;<font color="#0000FF">CreateSQL</font></h3>

      <h4><a name="tth_sEc4.3.1">
4.3.1</a>&nbsp;&nbsp;<font color="#0000FF">What does CreateSQL do?</font></h4>
CreateSQL generates a file containing SQL statements for the creation
of a PostgreSQL database for a given schema.

<p>

<br /><br /><hr /><small>File translated from
T<sub><font size="-1">E</font></sub>X
by <a href="http://hutchinson.belmont.ma.us/tth/">
T<sub><font size="-1">T</font></sub>H</a>,
version 2.92.<br />On 20 Mar 2003, 18:36.</small>
</html>

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Added Files:
	Makefile 
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--- NEW FILE: Makefile ---
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	dvipdf faq.dvi pymerase-faq.pdf
	gv pymerase-faq.pdf

[Pymerase-cvs-commit] Docs/faq faq.tex,NONE,1.1

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First FAQ for Pymerase


--- NEW FILE: faq.tex ---
% Pymerase Docs - FAQ
% Copyright (c) California Institute of Technology
%
% Authors: Brandon King
% $Revision: 1.1 $
% Modified $Date: 2003/03/21 00:36:40 $

\documentclass{article}
\usepackage{graphicx}
\usepackage{color}
\usepackage[margin=3cm,noheadfoot]{geometry}

\setlength{\parindent}{0in}
\setlength{\parskip}{2mm}

%colors
\newcommand{\cb}{\color{blue}}

%new commands
\newcommand{\pymlink}{http://pymerase.sf.net}

%document
\begin{document}

%title page
\begin{titlepage}
\title{\cb Pymerase Docs - FAQ}
\author{Brandon King \& Diane Trout\\
Copyright \copyright  California Institute of Technology}
\date{Version 0.1.1\\\today}
\maketitle
\thispagestyle{empty}
\end{titlepage}

\tableofcontents
\thispagestyle{empty}
\newpage

%Document Body
\setcounter{page}{1}

\section{\cb FAQ - General}
\subsection{\cb Why the name ''Pymerase''?}
Pymerase is the combination of 'Python', the primary language Pymerase
is written in, and 'Polymerase'. Polymerase, in short, is a molecule
which copies/converts DNA into RNA. We figured that Pymerase had
similar functionality in that it took table.dtd XML (DNA) files and
converted them into other things, such as SQL statements (RNA) which
is then used to create a database (Protein).

\subsection{\cb Where was Pymerase originally developed?}
Pymerase was originally developed in the Wold Lab at the California
Institute of Technology (Caltech).

\subsection{\cb Who originally developed Pymerase?}
Diane Trout and Brandon King originally developed Pymerase in the Wold
Lab at Caltech. Barbara Wold is the principal invesigator incharge of
the project at Caltech, along with collaborator Eric Mjolsness of
UC~Irvine.

\subsection{\cb Why was the original purpose of Pymerase?}
The original purpose of pymerase was to generate a Python Database API
for the GeneX Microarray Gene Expression Database. As development
progressed Pymerase was made more generic to support other projects
including Sigmoid and MAGE.

\section{\cb FAQ - Input Modules}
\subsection{\cb parseGenexSchemaXML}
\subsubsection{\cb Can the parseGenexSchemaXML input module only parse the
  GeneX project schema?}
No. It's called parseGenexSchemaXML to give credit to the GeneX
project for coming up with the file format used for this particular
input module and the schema of the GeneX 2.x project. The format can
be used to make any number of schemas using it. Special thanks goes to
Jason Stewart of OpenInformatics.org for the original design of this
XML format.

\end{document}

[Pymerase-cvs-commit] Docs/faq - New directory

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[Pymerase-cvs-commit] Docs README,1.3,1.4

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	README 
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Index: README
===================================================================
RCS file: /cvsroot/pymerase/Docs/README,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** README	7 Mar 2003 23:26:08 -0000	1.3
--- README	20 Mar 2003 22:44:09 -0000	1.4
***************
*** 3,6 ****
--- 3,8 ----
  Web site: http://pymerase.sf.net/docs/
  
+ template	 - Template for creating new pymerase documentation
+ 
  running_pymerase - Documentation about how to run pymerase
  
***************
*** 8,11 ****
  		   example.
  
  tutorial         - Tutorial on how to use pymerase
! 		   OLD: Will be ArgoUML Tutorial in the near future.
--- 10,16 ----
  		   example.
  
+ argouml		 - Information on how to use ArgoUML with Pymerase,
+ 		   includes tutorial.
+ 
  tutorial         - Tutorial on how to use pymerase
! 		   OLD: Converted to Docs/argouml/argouml.tex revision 1.2

[Pymerase-cvs-commit] Docs/argouml argouml.tex,1.1,1.2

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Log Message:
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Index: argouml.tex
===================================================================
RCS file: /cvsroot/pymerase/Docs/argouml/argouml.tex,v
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*** argouml.tex	20 Mar 2003 21:23:45 -0000	1.1
--- argouml.tex	20 Mar 2003 21:51:04 -0000	1.2
***************
*** 33,37 ****
  \author{Brandon King \\
  Copyright \copyright  California Institute of Technology}
! \date{Version 0.1.1\\\today}
  \maketitle
  \thispagestyle{empty}
--- 33,37 ----
  \author{Brandon King \\
  Copyright \copyright  California Institute of Technology}
! \date{Version 0.1.2\\\today}
  \maketitle
  \thispagestyle{empty}
***************
*** 125,129 ****
  be using in this example.
  
! --FIGURE--
  
  \subsection{\cb Step 2 - Create new class}
--- 125,134 ----
  be using in this example.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig1-NewArgoUMLFile.eps}
! \caption{\cb Getting Familiar with ArgoUML}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 2 - Create new class}
***************
*** 131,135 ****
  be using in this example.
  
! --FIGURE--
  
  \subsection{\cb Step 3 - Change name of namespace}
--- 136,145 ----
  be using in this example.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig2-NewClass.eps}
! \caption{\cb Create new class}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 3 - Change name of namespace}
***************
*** 141,145 ****
  Checkout).
  
! --FIGURE--
  
  \subsection{\cb Step 4 - Change class name}
--- 151,160 ----
  Checkout).
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig3-ChangeNamespace.eps}
! \caption{\cb Change name of namespace}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 4 - Change class name}
***************
*** 147,151 ****
  'Dvd'.
  
! --FIGURE--
  
  \subsection{\cb Step 5 - Create attributes for Dvd class}
--- 162,171 ----
  'Dvd'.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig4-ChangeClassName.eps}
! \caption{\cb Change class name}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 5 - Create attributes for Dvd class}
***************
*** 156,160 ****
  Dvd class should look similar to the one shown in the figure below.
  
! --FIGURE--
  
  \subsection{\cb Step 6 - Add Studio class and attributes}
--- 176,185 ----
  Dvd class should look similar to the one shown in the figure below.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig5-AddAttributesToClass.eps}
! \caption{\cb Create attributes for Dvd class}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 6 - Add Studio class and attributes}
***************
*** 162,166 ****
  should look similar to the figure below.
  
! --FIGURE--
  
  \subsection{\cb Step 7 - Create Association}
--- 187,196 ----
  should look similar to the figure below.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig6-AddStudioClass.eps}
! \caption{\cb Add Studio class and attributes}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 7 - Create Association}
***************
*** 171,175 ****
  below.
  
! --FIGURE--
  
  \subsection{\cb Step 8 - Studio Association End}
--- 201,210 ----
  below.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig7-CreateAssociation.eps}
! \caption{\cb Create Association}
! \end{figure}
! 
! \newpage
  
  \subsection{\cb Step 8 - Studio Association End}
***************
*** 185,191 ****
  '0..1'. Once you're done, it should look similar to the figure below.
  
! --FIGURE--
  
! \subsection{\cb Step 9 - DvdAssociation End}
  Now we need to add similar information to the other end of the
  association. To do this, click on the association and then click on
--- 220,231 ----
  '0..1'. Once you're done, it should look similar to the figure below.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig8-StudioAssociationEnd.eps}
! \caption{\cb Studio Association End}
! \end{figure}
  
! \newpage
! 
! \subsection{\cb Step 9 - Dvd Association End}
  Now we need to add similar information to the other end of the
  association. To do this, click on the association and then click on
***************
*** 194,198 ****
  below.
  
! --FIGURE--
  
  \subsection{\cb Step 10 - Save ArgoUML File}
--- 234,241 ----
  below.
  
! \begin{figure}[h]
! \includegraphics[width=\textwidth]{images/Fig9-DvdAssociationEnd.eps}
! \caption{\cb Dvd Association End}
! \end{figure}
  
  \subsection{\cb Step 10 - Save ArgoUML File}

[Pymerase-cvs-commit] Docs/tutorial/images Fig1-New_ArgoUML_File.jpg,1.2,NONE Fig2-New_Class.jpg,1.2,NONE Fig3-Change_Namespace.jpg,1.2,NONE Fig4-Change_Class_Name.jpg,1.2,NONE Fig5-Add_attributes_to_class.jpg,1.2,NONE Fig6-Add_studio_class.jpg,1.2,NONE Fig7-Create_association.jpg,1.2,NONE Fig8-StudioAssociationEnd.jpg,1.2,NONE Fig9-DvdAssociationEnd.jpg,1.2,NONE

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[Pymerase-cvs-commit] Docs/argouml/images - New directory

From: <ki...@us...> - 2003-03-20 21:51:30

Update of /cvsroot/pymerase/Docs/argouml/images
In directory sc8-pr-cvs1:/tmp/cvs-serv11927/images

Log Message:
Directory /cvsroot/pymerase/Docs/argouml/images added to the repository

[Pymerase-cvs-commit] Docs/argouml argouml.tex,NONE,1.1

From: <ki...@us...> - 2003-03-20 21:23:48

Update of /cvsroot/pymerase/Docs/argouml
In directory sc8-pr-cvs1:/tmp/cvs-serv27529

Added Files:
	argouml.tex 
Log Message:
first step in converting Docs/tutorial/ into ArgoUML for Pymerase documentation


--- NEW FILE: argouml.tex ---
% Pymerase Docs - ArgoUML for Pymerase
% Copyright (c) California Institute of Technology
%
% Authors: Brandon King
% $Revision: 1.1 $
% Modified $Date: 2003/03/20 21:23:45 $

\documentclass{article}
\usepackage{graphicx}
\usepackage{color}
\usepackage[margin=3cm,noheadfoot]{geometry}
%\usepackage{makeidx}

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\begin{titlepage}
\title{\cb Pymerase Docs - ArgoUML for Pymerase}
\author{Brandon King \\
Copyright \copyright  California Institute of Technology}
\date{Version 0.1.1\\\today}
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\section{\cb Introduction}
\subsection{\cb ArgoUML, XMI and Pymerase}
Unified Modeling Language (UML) allows you to draw an Object Model.
Given this object model in the form of XML Metadata Interchange (XMI),
Pymerase can produce many different types of output using it's
pluggable input/output module design. The ParseXMI input module reads
in the Object Model and populates the Pymerase API with information
that output modules need to use. Here is a list of just some of the
output modules that currently exist and a brief discription.

\begin{tabular}{ll}
\bf Output Modules & \bf Description\\
CreateSQL & SQL Statements for creating database\\
CreateDBAPI & Python Database API for a given database\\
CreatePyTkWidgets & Python Tkinter GUI Widgets\\
CreatePyTkDbWidgets & Python Tk Database GUI Widgets
\end{tabular}

In this document I will go through a tutorial explaining how to use
ArgoUML to create an Object Model that has the information that
Pymerase needs for it's output modules to work. The first example will
be a very simple Dvd Collection Database. The second example will
demonstrait how to use the inheritance features of Pymerase. 

Note that Pymerase, in it's current state, does not take advantage of
all the features provided by UML.  At the same time, UML does not
provide all the information you may want to provide to Pymerase.  In
this document, I will go over the features of ArgoUML which are
currently used in Pymerase.  If you find that UML does not provide all
the information, you can use the CreateTableXML output module to
create XML files that describes your model. This will provide you with
a way of adding more information to your model.

\subsection{\cb Naming Conventions}
When it comes to programming, naming conventions vary from programmer
to programmer and from situation to situation. In the Java world, it's
common to haveThisConvention while databases most commonly
have\_this\_convention. This led to the development of Name Manglers in
Pymerase. This allows different naming conventions to be converted to
others. Here's a list of a least some of the NameManglers available.

\begin{tabular}{ll}
\bf Name Mangler & \bf Description\\
nullMangler & Does not convert users naming convention\\
CapsWord & CapitalizesFirstLetterOfEachWord, NoSpaces\\
underscore\_word & all\_lower\_case, underscore\_for\_seperation\\
English Word & Capitalizes first word and uses spaces for seperation\\
 & \\
\bf Avoid & \\
alllowercasenospaces & This is just a horrible naming convention in
general, but it also prevents\\ & the name manglers from converting to
other name mangling schemes.
\end{tabular}

In some cases you may find you need to generate code to use with code
or a database that uses allowercasenospaces convention. If this is the
case, it is possible to get Pymerase to do what you want. It's just a
little harder. You can accomplish this by using the nullMangler or
creating your own mangler.

\section{\cb Tutorial: Dvd Example}
\subsection{\cb Introduction}
Before we jump in to the tutorial, let me describe the model we wish
to create. The goal is quickly create a Database, Python DBAPI, and
GUI for keeping track of Dvds in a collection. To keep it simple all
we will just have two classes in our Dvd Database. The first will be a
Dvd class which will contain the title of the movie, the year the
movie was released, and a link to a single Studio class. The Studio
class will contain the name of the studio which produced the movie. We
will allow a Studio have 0 to N Dvds, but will only allow a Dvd to
have 0 to 1 Studios. 

Note that this may not be the best design for a Dvd Collection
Database, but it does get across the point of how to use Pymerase and
it will function. We would love to have more example databases or
expansions on existing ones. If you would like to contribute, please
visit http://pymerase.sf.net/ and send a message to the mailing list.

\subsection{\cb Step 1 - Getting familiar with ArgoUML}
The first step is to open ArgoUML and learn the basic features we will
be using in this example.

--FIGURE--

\subsection{\cb Step 2 - Create new class}
The first step is to open ArgoUML and learn the basic features we will
be using in this example.

--FIGURE--

\subsection{\cb Step 3 - Change name of namespace}
Click on the 'Namespace' entry box that contains the text
'untitledModel'. Then change the name from 'untitledModel' to the name
of the DBAPI directory you want to use. In this case you would change
the name to 'DvdAPI'. If you don't do this, you may have trouble using
the generated DBAPI in the current version of Pymerase (CVS
Checkout).

--FIGURE--

\subsection{\cb Step 4 - Change class name}
Click on the class you created in step one and give the class the name
'Dvd'.

--FIGURE--

\subsection{\cb Step 5 - Create attributes for Dvd class}
Click on the Dvd class and then press the 'Add Attribute' button shown
in the figure below. For the first attribute, the name should be
'title', and the type should be 'String'. For the second attribute,
the name should be 'yearReleased', and the type should be 'int'. Your
Dvd class should look similar to the one shown in the figure below.

--FIGURE--

\subsection{\cb Step 6 - Add Studio class and attributes}
Create a Studio class with a name attribute of type 'String'. It
should look similar to the figure below.

--FIGURE--

\subsection{\cb Step 7 - Create Association}
Click on the association button shown in the figure below. Then click
and hold down the left mouse button on the Dvd class and drag the
mouse over the Studio class. Then release the mouse button over the
Studio class. If everything went well, it should look like the figure
below.

--FIGURE--

\subsection{\cb Step 8 - Studio Association End}
Although we have an association, we are not done yet. It is currently
set so that a Dvd object can have 1 to 1 Studios and a Studio can have
1 to 1 Dvds. To change this, click on the association. The properties
should look similar to the previous figure. Once you've click on the
association, you should see two 'Association Ends'. One called
'Dvd[1..1]' and the other 'Studio[1..1]'. Click on 'Studio[1..1]'. In
the name entry box, type 'Studio'. This will become the name of the
function you will call from a dvd object to get the studio object (
i.e. dvdObj.getStudio() ). Next change the multiplicity from '1..1' to
'0..1'. Once you're done, it should look similar to the figure below.

--FIGURE--

\subsection{\cb Step 9 - DvdAssociation End}
Now we need to add similar information to the other end of the
association. To do this, click on the association and then click on
'Dvd[1..1]'. Type 'Dvd' into the name entry box and change the
multiplicity from '1..1' to '0..*'. Compare your diagram to the figure
below.

--FIGURE--

\subsection{\cb Step 10 - Save ArgoUML File}
Save you ArgoUML file as 'dvd\_example.zargo'.

\end{document}

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--- NEW FILE: template.tex ---
% Pymerase Docs - Template
% Copyright (c) California Institute of Technology
%
% Authors: Brandon King
% $Revision: 1.1 $
% Modified $Date: 2003/03/20 20:54:59 $

\documentclass{article}
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\title{\cb Pymerase Docs - Title}
\author{Author \\
Copyright \copyright  California Institute of Technology}
\date{Version 0.1.1\\\today}
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\end{titlepage}

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%Document Body
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\section{\cb Section One}
\subsection{\cb Subsection One}

\end{document}

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