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From: <ki...@us...> - 2003-04-16 03:12:05
|
Update of /cvsroot/pymerase/pymerase
In directory sc8-pr-cvs1:/tmp/cvs-serv11869
Modified Files:
setup.py
Log Message:
added command line arg --prefix=
still need to seperate out bin/docs paths
added documentation
Index: setup.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/setup.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** setup.py 27 Feb 2003 01:56:21 -0000 1.4
--- setup.py 16 Apr 2003 03:11:59 -0000 1.5
***************
*** 58,68 ****
"pymerase.output.PythonAPI"]
! if sys.platform == 'linux2':
! prefix = '/usr'
! docs = os.path.join(prefix, 'share/doc/pymerase')
else:
! prefix = 'pymerase'
! docs = 'pymerase'
BIN_TUPLE=(os.path.join(prefix, 'bin'),
['bin/pymerase', 'bin/pymerasegui.py'])
--- 58,103 ----
"pymerase.output.PythonAPI"]
!
!
! ########################################
! # Process Commandline Args
!
! #list of items to remove from sys.argv when done
! rmList = []
!
! #set prefix to None for later error checking
! prefix = None
!
! #look for custom command line args
! for item in sys.argv:
!
! #If prefix command line arg exists, set new prefix and mark
! # item to be removed from sys.argv
! if item[:9] == '--prefix=':
! prefix = item[9:]
! rmList.append(item)
!
! #Remove processed items from sys.argv
! for item in rmList:
! sys.argv.remove(item)
!
! #If user overrides command line args, then don't need to
! # use logic to figure them out.
! if prefix is None:
! #Set default for linux 2.x systems
! if sys.platform == 'linux2':
! prefix = '/usr'
! docs = os.path.join(prefix, 'share/doc/pymerase')
! #set default for all others
! #FIXME: should add more defaults
! #NOTE: can override with command line
! else:
! prefix = 'pymerase'
! docs = 'pymerase'
else:
! docs = os.path.join(prefix, 'share/doc/pymerase')
+ #################################
+ # Setup Data Files
BIN_TUPLE=(os.path.join(prefix, 'bin'),
['bin/pymerase', 'bin/pymerasegui.py'])
***************
*** 84,87 ****
--- 119,124 ----
#FIXME: Grabs .cvsignore files, need to add filter
+
+ #Run setup! =o)
setup(name="Pymerase",
version="0.1",
|
|
From: <ki...@us...> - 2003-04-16 01:22:04
|
Update of /cvsroot/pymerase/pymerase/pymweb
In directory sc8-pr-cvs1:/tmp/cvs-serv27280
Added Files:
setup.py
Log Message:
setup.py script for installing pymweb
--- NEW FILE: setup.py ---
#!/usr/bin/env python
###########################################################################
# #
# C O P Y R I G H T N O T I C E #
# Copyright (c) 2003 by: #
# * California Institute of Technology #
# #
# All Rights Reserved. #
# #
# Permission is hereby granted, free of charge, to any person #
# obtaining a copy of this software and associated documentation files #
# (the "Software"), to deal in the Software without restriction, #
# including without limitation the rights to use, copy, modify, merge, #
# publish, distribute, sublicense, and/or sell copies of the Software, #
# and to permit persons to whom the Software is furnished to do so, #
# subject to the following conditions: #
# #
# The above copyright notice and this permission notice shall be #
# included in all copies or substantial portions of the Software. #
# #
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
# SOFTWARE. #
###########################################################################
#
# Authors: Brandon King
# Last Modified: $Date: 2003/04/16 01:22:01 $
#
import os
import sys
from distutils.core import setup
#from distutils.core import Command
#######################################
# Install Paths
#Default (Debian) CGI installation path
CGI_PATH = '/usr/lib/cgi-bin/'
#Default (Debian) Apache WWW path
WWW_PATH = '/var/www/'
#Default (Debian) Apache Conf path
CONF_PATH = '/etc/apache/conf/'
#######################################
# Files to be copied
CGI_SCRIPT = (os.path.join(CGI_PATH, 'pymweb.py'),
['cgi/pymweb.py'])
HTML_FORM = (os.path.join(WWW_PATH, 'pymweb.html'),
['www/pymweb.html'])
LOGO_IMG = (os.path.join(WWW_PATH, 'images', 'pymerase-title.jpg'),
['www/images/pymerase-title.jpg'])
CONF_FILE = (os.path.join(CONF_PATH, 'pymweb.conf'),
['conf/pymweb.conf'])
DTD_FILE = (os.path.join(WWW_PATH, 'table.dtd'),
['dtd/table.dtd'])
DATA_FILES=[CGI_SCRIPT,
HTML_FORM,
LOGO_IMG,
CONF_FILE,
DTD_FILE]
#List of argv items to be removed after being processed
# Need to be removed before passing to setup() below
rmList = []
#Command line options available for passing non debian paths
for item in sys.argv:
#cgi install path from commandline
if item[:10] == '--cgiPath=' and len(item) > 10:
CGI_PATH = item[10:]
rmList.append(item)
#www install path from commandline
if item[:10] == '--wwwPath=' and len(item) > 10:
WWW_PATH = item[10:]
rmList.append(item)
#conf install path from commandline
if item[:11] == '--confPath=' and len(item) > 11:
CONF_PATH = item[11:]
rmList.append(item)
#Remove processed argv items
if len(rmList) > 0:
for item in rmList:
sys.argv.remove(item)
#class install_paths(Command):
#
# # Brief (40-50 characters) description of the command
# description = "Allows paths to be given in command line."
#
# # List of option tuples: long name, short name (None if no short
# # name), and help string.
# user_options = [('cgiPath=', None,
# "Path to cgi-bin directory"),
# ('wwwPath=', None,
# "Path to the apache www directory"),
# ('confPath=', None,
# "Path to the apache conf directory")
# ]
#
#
# def initialize_options (self):
# self.cgiPath = None
# self.wwwPath = None
# self.confPath = None
#
# # initialize_options()
#
#
# def finalize_options (self):
# pass
#
# # finalize_options()
#
#
# def run (self):
# #print self.cgiPath
# if self.cgiPath is not None:
# CGI_PATH = self.cgiPath
#
# #print self.wwwPath
# if self.wwwPath is not None:
# WWW_PATH = self.wwwPath
#
# #print self.confPath
# if self.confPath is not None:
# CONF_PATH = self.confPath
#
# # run()
#
## class install_paths
setup(name="Pymweb",
version="0.1.0",
description="Pymweb is a web front end for running Pymerase.",
author="Brandon King",
author_email="ki...@ca...",
url="http://pymerase.sf.net/",
data_files=DATA_FILES,
#cmdclass= {'install_paths': install_paths},
)
|
|
From: <ki...@us...> - 2003-04-15 19:38:13
|
Update of /cvsroot/pymerase/pymerase In directory sc8-pr-cvs1:/tmp/cvs-serv8893 Modified Files: INSTALL Log Message: minor update Index: INSTALL =================================================================== RCS file: /cvsroot/pymerase/pymerase/INSTALL,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** INSTALL 5 Apr 2003 01:11:17 -0000 1.3 --- INSTALL 15 Apr 2003 19:38:08 -0000 1.4 *************** *** 5,9 **** do with it. ! ** Debian Packages Need (partial list) ------------------------------------- python2.2 --- 5,9 ---- do with it. ! ** Debian Packages Required (partial list) ------------------------------------- python2.2 |
|
From: <ki...@us...> - 2003-04-15 19:36:28
|
Update of /cvsroot/pymerase/Docs/install
In directory sc8-pr-cvs1:/tmp/cvs-serv7559
Modified Files:
install.tex
Log Message:
updated install docs with debian package requirements
Index: install.tex
===================================================================
RCS file: /cvsroot/pymerase/Docs/install/install.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** install.tex 3 Apr 2003 00:46:58 -0000 1.1
--- install.tex 15 Apr 2003 19:36:24 -0000 1.2
***************
*** 28,32 ****
\author{Diane Trout \\
Copyright \copyright California Institute of Technology}
! \date{Version 0.1.1\\\today}
\maketitle
\thispagestyle{empty}
--- 28,32 ----
\author{Diane Trout \\
Copyright \copyright California Institute of Technology}
! \date{Version 0.1.2\\\today}
\maketitle
\thispagestyle{empty}
***************
*** 44,47 ****
--- 44,55 ----
Pymerase depends on several components depending on what you'd like to
do with it.
+
+ \subsubsection{\cb Debian Packages Required (Partial List)}
+ \begin{itemize}
+ \item python2.2
+ \item python2.2-dev
+ \item python2.2-egenix-mxdatetime
+ \item python2.2-pygresql
+ \end{itemize}
\subsubsection{\cb GeneX Table Definition Format}
|
|
From: <ki...@us...> - 2003-04-09 21:37:49
|
Update of /cvsroot/pymerase/htdocs/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv13283
Modified Files:
index.shtml
Log Message:
argouml 4 pymerase
Index: index.shtml
===================================================================
RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** index.shtml 9 Apr 2003 18:10:53 -0000 1.18
--- index.shtml 9 Apr 2003 21:13:24 -0000 1.19
***************
*** 30,33 ****
--- 30,34 ----
<a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=144835">
pdf</a> ] - Information about running pymerase<br>
+ ArgoUML for Pymerase [ <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151931">pdf</a> ]<br>
<a href="input">Input Modules</a>
- Documentation about Input Modules<br>
|
|
From: <ki...@us...> - 2003-04-09 21:37:15
|
Update of /cvsroot/pymerase/htdocs/docs In directory sc8-pr-cvs1:/tmp/cvs-serv14277 Modified Files: index.shtml Log Message: updated descriptions Index: index.shtml =================================================================== RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** index.shtml 9 Apr 2003 21:13:24 -0000 1.19 --- index.shtml 9 Apr 2003 21:15:55 -0000 1.20 *************** *** 26,34 **** <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=147810">pdf</a> ]<br> <a href="linkdb">LinkDB Tutorial</a> [ <a href="linkdb/linkdb-tutorial.html">html</a> | ! <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151884">pdf</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> ! ArgoUML for Pymerase [ <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151931">pdf</a> ]<br> <a href="input">Input Modules</a> - Documentation about Input Modules<br> --- 26,34 ---- <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=147810">pdf</a> ]<br> <a href="linkdb">LinkDB Tutorial</a> [ <a href="linkdb/linkdb-tutorial.html">html</a> | ! <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151884">pdf</a> ] - Fairly complete Pymerase Tutorial<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> ! ArgoUML for Pymerase [ <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151931">pdf</a> ] - How to use ArgoUML with Pymerase (Incomplete)<br> <a href="input">Input Modules</a> - Documentation about Input Modules<br> |
|
From: <ki...@us...> - 2003-04-09 18:10:56
|
Update of /cvsroot/pymerase/htdocs/docs In directory sc8-pr-cvs1:/tmp/cvs-serv24629 Modified Files: index.shtml Log Message: updated with linkdb tutorial Index: index.shtml =================================================================== RCS file: /cvsroot/pymerase/htdocs/docs/index.shtml,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** index.shtml 21 Mar 2003 03:23:28 -0000 1.17 --- index.shtml 9 Apr 2003 18:10:53 -0000 1.18 *************** *** 25,28 **** --- 25,30 ---- <a href="faq">Pymerase FAQ</a> [ <a href="faq/faq.html">html</a> | <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=147810">pdf</a> ]<br> + <a href="linkdb">LinkDB Tutorial</a> [ <a href="linkdb/linkdb-tutorial.html">html</a> | + <a href="http://sourceforge.net/project/showfiles.php?group_id=63836&release_id=151884">pdf</a> ]<br> <a href="running">Running Pymerase</a> [ <a href="https://sourceforge.net/project/showfiles.php?group_id=63836&release_id=144835"> |
|
From: <ki...@us...> - 2003-04-09 18:10:39
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb
In directory sc8-pr-cvs1:/tmp/cvs-serv24429
Added Files:
index.shtml
Log Message:
Pymerase Docs - LinkDB Tutorial
--- 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 - LinkDB Tutorial</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>
<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="linkdb-tutorial.html"-->
</td>
</tr>
</table>
Last Modified: <!--#echo var="LAST_MODIFIED" -->
</td>
</tr>
</table>
</div>
</body>
</html>
|
|
From: <ki...@us...> - 2003-04-09 18:08:01
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb
In directory sc8-pr-cvs1:/tmp/cvs-serv23231
Added Files:
linkdb-tutorial.html
Log Message:
linkdb-tutorial, html format.
--- NEW FILE: linkdb-tutorial.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 - LinkDB Tutorial</title>
<h1 align="center"><font color="#0000FF">Pymerase Docs - LinkDB Tutorial</font> </h1>
<h3 align="center">Brandon King <br />
Copyright © California Institute of Technology </h3>
<h3 align="center">Version 0.1.6<br />Apr 9, 2003
</h3>
[...1296 lines suppressed...]
version of this is in the tutorial dictory in Pymerase CVS module
Docs
<p>
<a name="tthFtNtABE"></a><a href="#tthFrefABE"><sup>14</sup></a>If no
documentation exist on the table.dtd XML format, please e-mail the
mailing list mentioned in section <a href="#pymdevel">3.2</a>.
<p>
<a name="tthFtNtABF"></a><a href="#tthFrefABF"><sup>15</sup></a>http://pymerase.sf.net/docs/output/
<p>
<a name="tthFtNtABG"></a><a href="#tthFrefABG"><sup>16</sup></a>http://pymerase.sf.net/docs/
<p>
<a name="tthFtNtABH"></a><a href="#tthFrefABH"><sup>17</sup></a>Check the
pymerase docs or e-mail the mailing list mentioned in section
<a href="#pymdevel">3.2</a> for more help.
<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 9 Apr 2003, 10:52.</small>
</html>
|
|
From: <ki...@us...> - 2003-04-09 18:04:09
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb/images In directory sc8-pr-cvs1:/tmp/cvs-serv21374 Added Files: nameLinkPairDb-widget.jpg Log Message: figure for tutorial --- NEW FILE: nameLinkPairDb-widget.jpg --- (This appears to be a binary file; contents omitted.) |
|
From: <ki...@us...> - 2003-04-09 18:03:09
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb/images In directory sc8-pr-cvs1:/tmp/cvs-serv20761 Added Files: groupdb-widget2.jpg Log Message: figure for tutorial --- NEW FILE: groupdb-widget2.jpg --- (This appears to be a binary file; contents omitted.) |
|
From: <ki...@us...> - 2003-04-09 18:02:15
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb/images In directory sc8-pr-cvs1:/tmp/cvs-serv20277 Added Files: dbConnect-widget.jpg Log Message: figure for tutorial --- NEW FILE: dbConnect-widget.jpg --- (This appears to be a binary file; contents omitted.) |
|
From: <ki...@us...> - 2003-04-09 18:01:47
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb/images In directory sc8-pr-cvs1:/tmp/cvs-serv19890 Added Files: linkdb-argouml.jpg Log Message: figure for tutorial --- NEW FILE: linkdb-argouml.jpg --- (This appears to be a binary file; contents omitted.) |
|
From: <ki...@us...> - 2003-04-09 18:01:09
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb/images In directory sc8-pr-cvs1:/tmp/cvs-serv19689/images Log Message: Directory /cvsroot/pymerase/htdocs/docs/linkdb/images added to the repository |
|
From: <ki...@us...> - 2003-04-09 18:00:58
|
Update of /cvsroot/pymerase/htdocs/docs/linkdb In directory sc8-pr-cvs1:/tmp/cvs-serv19562/linkdb Log Message: Directory /cvsroot/pymerase/htdocs/docs/linkdb added to the repository |
|
From: <ki...@us...> - 2003-04-09 17:32:50
|
Update of /cvsroot/pymerase/Docs/linkDB-tutorial
In directory sc8-pr-cvs1:/tmp/cvs-serv6816
Modified Files:
linkdb-tutorial.tex
Log Message:
minor update, change python2.1 requirement to python2.2
Index: linkdb-tutorial.tex
===================================================================
RCS file: /cvsroot/pymerase/Docs/linkDB-tutorial/linkdb-tutorial.tex,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** linkdb-tutorial.tex 14 Mar 2003 03:43:59 -0000 1.5
--- linkdb-tutorial.tex 9 Apr 2003 17:32:46 -0000 1.6
***************
*** 33,37 ****
\author{Brandon King \\
Copyright \copyright California Institute of Technology}
! \date{Version 0.1.5\\\today}
\maketitle
\thispagestyle{empty}
--- 33,37 ----
\author{Brandon King \\
Copyright \copyright California Institute of Technology}
! \date{Version 0.1.6\\\today}
\maketitle
\thispagestyle{empty}
***************
*** 64,68 ****
\subsection{\cb Software Requirements}
\begin{itemize}
! \item Python 2.1\footnote{http://www.python.org} or greater
\begin{itemize}
\item Pymerase\footnote{\pymlink}
--- 64,68 ----
\subsection{\cb Software Requirements}
\begin{itemize}
! \item Python 2.2\footnote{http://www.python.org} or greater
\begin{itemize}
\item Pymerase\footnote{\pymlink}
|
|
From: <ki...@us...> - 2003-04-09 15:50:53
|
Update of /cvsroot/pymerase/pymerase/pymweb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv25990
Modified Files:
pymweb.html
Log Message:
added .tar.gz XML schemas as an option for upload. =o)
Index: pymweb.html
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/www/pymweb.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** pymweb.html 9 Apr 2003 14:18:19 -0000 1.6
--- pymweb.html 9 Apr 2003 15:50:45 -0000 1.7
***************
*** 14,18 ****
<table>
<tr>
! <td><div align="right">Schema (.xmi):</div></td><td><input type="file" name="schema" size="25"></td>
</tr>
<tr>
--- 14,18 ----
<table>
<tr>
! <td><div align="right">Schema (.xmi or .tar.gz XML):</div></td><td><input type="file" name="schema" size="25"></td>
</tr>
<tr>
|
|
From: <ki...@us...> - 2003-04-09 15:45:16
|
Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv23518/cgi
Modified Files:
pymweb.py
Log Message:
added a check to see if the user is trying to upload a file that
already exists, if so, raise error.
Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** pymweb.py 9 Apr 2003 15:26:21 -0000 1.10
--- pymweb.py 9 Apr 2003 15:45:09 -0000 1.11
***************
*** 217,220 ****
--- 217,232 ----
+ def checkSchema(fileName):
+ if fileName[-7:] == '.tar.gz':
+ fileName = fileName[:-7]
+
+ if fileName == 'driver.sh' \
+ or fileName == 'driver.py' \
+ or fileName == 'index.html' \
+ or fileName == 'untar.sh':
+ return 0
+
+ return 1
+
def checkDest(dest):
block = ['\\', '/']
***************
*** 224,227 ****
--- 236,245 ----
return 0
+ if dest == 'driver.sh' \
+ or dest == 'driver.py' \
+ or dest == 'index.html' \
+ or dest == 'untar.sh':
+ return 0
+
return 1
***************
*** 252,255 ****
--- 270,278 ----
fileName = file.filename
fileName = checkFileName(fileName)
+
+ if checkSchema(fileName) != 1:
+ text = 'File name %s invalid! File already exists.<br>\n' % (fileName)
+ print text
+ raise ValueError, text
saved = saveFile(fileName, file.file.read())
|
|
From: <ki...@us...> - 2003-04-09 15:26:27
|
Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv15981/cgi
Modified Files:
pymweb.py
Log Message:
updated to prevent tar & zip to be run unless the files exist to compress.
Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** pymweb.py 9 Apr 2003 14:17:53 -0000 1.9
--- pymweb.py 9 Apr 2003 15:26:21 -0000 1.10
***************
*** 46,51 ****
cd %s
/home/king/jython-2.1/jython ./driver.py > /dev/null
! tar cvzf %s.tar.gz %s > /dev/null
! """ % (DIRPATH, dest, dest)
elif compress == 'Zip' and inputMod == "parseXMI":
text = """#!/bin/bash
--- 46,56 ----
cd %s
/home/king/jython-2.1/jython ./driver.py > /dev/null
! if [ -e %s ] ; then
! tar cvzf %s.tar.gz %s > /dev/null
! else
! cat %s.bs
! fi
! """ % (DIRPATH, dest, dest, dest, dest)
!
elif compress == 'Zip' and inputMod == "parseXMI":
text = """#!/bin/bash
***************
*** 53,70 ****
cd %s
/home/king/jython-2.1/jython ./driver.py > /dev/null
! zip %s.zip %s > /dev/null
! """ % (DIRPATH, dest, dest)
elif compress == 'Tar&Gzip' and inputMod == 'parseGenexSchemaXML':
text = """#!/bin/bash
cd %s
python ./driver.py > /dev/null
! tar cvzf %s.tar.gz %s > /dev/null
! """ % (DIRPATH, dest, dest)
elif compress == 'Zip' and inputMod == 'parseGenexSchemaXML':
text = """#!/bin/bash
cd %s
python ./driver.py > /dev/null
! zip %s.zip %s > /dev/null
! """ % (DIRPATH, dest, dest)
else:
--- 58,89 ----
cd %s
/home/king/jython-2.1/jython ./driver.py > /dev/null
! if [ -e %s ] ; then
! zip %s.zip %s > /dev/null
! else
! cat %s.bs
! fi
! """ % (DIRPATH, dest, dest, dest, dest)
!
elif compress == 'Tar&Gzip' and inputMod == 'parseGenexSchemaXML':
text = """#!/bin/bash
cd %s
python ./driver.py > /dev/null
! if [ -e %s ] ; then
! tar cvzf %s.tar.gz %s > /dev/null
! else
! cat %s.bs
! fi
! """ % (DIRPATH, dest, dest, dest, dest)
!
elif compress == 'Zip' and inputMod == 'parseGenexSchemaXML':
text = """#!/bin/bash
cd %s
python ./driver.py > /dev/null
! if [ -e %s ] ; then
! zip %s.zip %s > /dev/null
! else
! cat %s.bs
! fi
! """ % (DIRPATH, dest, dest, dest, dest)
else:
|
|
From: <ki...@us...> - 2003-04-09 14:18:22
|
Update of /cvsroot/pymerase/pymerase/pymweb/www In directory sc8-pr-cvs1:/tmp/cvs-serv20086/www Modified Files: pymweb.html Log Message: added support for parseGenexSchemaXML Index: pymweb.html =================================================================== RCS file: /cvsroot/pymerase/pymerase/pymweb/www/pymweb.html,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** pymweb.html 8 Apr 2003 18:30:24 -0000 1.5 --- pymweb.html 9 Apr 2003 14:18:19 -0000 1.6 *************** *** 17,21 **** </tr> <tr> ! <td><div align="right">Input Module:</div></td><td><input type="text" name="input" value="parseXMI" size="25"></td> </tr> <tr> --- 17,26 ---- </tr> <tr> ! <td><div align="right">Input Module:</div></td> ! <td><select name="input" size="1"> ! <option value="parseXMI" label="parseXMI">parseXMI</option> ! <option value="parseGenexSchemaXML" label="parseGenexSchemaXML">parseGenexSchemaXML</option> ! </select> ! </td> </tr> <tr> *************** *** 39,42 **** --- 44,48 ---- <option value="Tar&Gzip" label="Tar&Gzip" selected="1">Tar&Gzip</option> <option value="Zip" label="Zip">Zip</option> + </select> </td> <tr> |
|
From: <ki...@us...> - 2003-04-09 14:17:56
|
Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv19827/cgi
Modified Files:
pymweb.py
Log Message:
Added support for parseGenexSchemaXML input module =o)
Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** pymweb.py 9 Apr 2003 01:38:50 -0000 1.8
--- pymweb.py 9 Apr 2003 14:17:53 -0000 1.9
***************
*** 38,44 ****
import tempfile
import re
! def getDriverScript(dest, compress):
! if compress == 'Tar&Gzip':
text = """#!/bin/bash
export CLASSPATH=/home/king/downloads/novasoft/nsuml-0.4.19.jar:/usr/share/java/xerces.jar
--- 38,45 ----
import tempfile
import re
+ import glob
! def getDriverScript(dest, compress, inputMod):
! if compress == 'Tar&Gzip' and inputMod == "parseXMI":
text = """#!/bin/bash
export CLASSPATH=/home/king/downloads/novasoft/nsuml-0.4.19.jar:/usr/share/java/xerces.jar
***************
*** 47,51 ****
tar cvzf %s.tar.gz %s > /dev/null
""" % (DIRPATH, dest, dest)
! elif compress == 'Zip':
text = """#!/bin/bash
export CLASSPATH=/home/king/downloads/novasoft/nsuml-0.4.19.jar:/usr/share/java/xerces.jar
--- 48,52 ----
tar cvzf %s.tar.gz %s > /dev/null
""" % (DIRPATH, dest, dest)
! elif compress == 'Zip' and inputMod == "parseXMI":
text = """#!/bin/bash
export CLASSPATH=/home/king/downloads/novasoft/nsuml-0.4.19.jar:/usr/share/java/xerces.jar
***************
*** 54,57 ****
--- 55,71 ----
zip %s.zip %s > /dev/null
""" % (DIRPATH, dest, dest)
+ elif compress == 'Tar&Gzip' and inputMod == 'parseGenexSchemaXML':
+ text = """#!/bin/bash
+ cd %s
+ python ./driver.py > /dev/null
+ tar cvzf %s.tar.gz %s > /dev/null
+ """ % (DIRPATH, dest, dest)
+ elif compress == 'Zip' and inputMod == 'parseGenexSchemaXML':
+ text = """#!/bin/bash
+ cd %s
+ python ./driver.py > /dev/null
+ zip %s.zip %s > /dev/null
+ """ % (DIRPATH, dest, dest)
+
else:
raise ValueError, 'Compression type of %s is invalid.' % (compress)
***************
*** 87,90 ****
--- 101,112 ----
+ def getDecompress(fileName):
+ text = """#!/bin/bash
+ tar xzf %s
+ """ % (fileName)
+
+ return text
+
+
ROOTPATH = '/tmp/pymweb'
if not os.path.exists(ROOTPATH):
***************
*** 109,112 ****
--- 131,152 ----
+ def processSchemaXML(schemaPath):
+ obj = re.compile('SYSTEM \".*\"')
+
+ xmlSearch = os.path.join(schemaPath[:-7], '*.xml')
+ fileList = glob.glob(xmlSearch)
+
+ for file in fileList:
+ f = open(file, 'r')
+ xmlFile = f.read()
+ f.close()
+
+ xmlFile = obj.sub('SYSTEM \"http://localhost/table.dtd\"', xmlFile)
+
+ f = open(file, 'w')
+ f.write(xmlFile)
+ f.close()
+
+
def saveFile(fileName, file):
***************
*** 117,120 ****
--- 157,179 ----
f.close()
+ if fileName[-7:] == '.tar.gz':
+ curPath = os.getcwd()
+ os.chdir(DIRPATH)
+
+ untarPath = os.path.join(DIRPATH, 'untar.sh')
+
+ f = open(untarPath, 'w')
+ f.write(getDecompress(fileName))
+ f.close()
+
+ os.chmod(untarPath, 0755)
+
+ errCode = os.spawnl(os.P_WAIT, 'untar.sh', 'untar.sh')
+ #print 'Decompress Exit Code: %s<br><br>' % \
+ # (errCode)
+ if str(errCode) == '0':
+ processSchemaXML(filePath)
+
+ os.chdir(curPath)
return filePath
***************
*** 140,144 ****
def checkDest(dest):
! block = ['\\', '/', '..']
for item in block:
--- 199,203 ----
def checkDest(dest):
! block = ['\\', '/']
for item in block:
***************
*** 175,179 ****
fileName = checkFileName(fileName)
! saved = saveFile(fileName, file.file.read())
#print 'File %s saved.<br><br>' % (saved)
--- 234,238 ----
fileName = checkFileName(fileName)
! saved = saveFile(fileName, file.file.read())
#print 'File %s saved.<br><br>' % (saved)
***************
*** 201,209 ****
html += text
text = '<b>Destination:</b> %s<br>\n' % (dest)
print text
html += text
! if checkDest == 1:
pass
else:
--- 260,281 ----
html += text
+ if fileName[-7:] == '.tar.gz':
+ uploadedFile = fileName
+ fileName = fileName[:-7]
+
+ if os.path.isdir(os.path.join(DIRPATH, fileName)):
+ #tar xvzf fileName worked
+ pass
+ else:
+ text = "Error: %s does not exist, is %s a valid file?<br>" % \
+ (fileName, uploadedFile)
+ print text
+ raise ValueError, text
+
text = '<b>Destination:</b> %s<br>\n' % (dest)
print text
html += text
! if checkDest(dest) == 1:
pass
else:
***************
*** 227,231 ****
driverPath = saveFile('driver.py', driver)
! script = getDriverScript(dest, compression)
scriptPath = saveFile('driver.sh', script)
--- 299,303 ----
driverPath = saveFile('driver.py', driver)
! script = getDriverScript(dest, compression, input)
scriptPath = saveFile('driver.sh', script)
|
|
From: <ki...@us...> - 2003-04-09 14:17:19
|
Update of /cvsroot/pymerase/pymerase/pymweb In directory sc8-pr-cvs1:/tmp/cvs-serv19600 Modified Files: Makefile Log Message: added installation of table.dtd file Index: Makefile =================================================================== RCS file: /cvsroot/pymerase/pymerase/pymweb/Makefile,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Makefile 4 Apr 2003 23:18:21 -0000 1.1 --- Makefile 9 Apr 2003 14:17:14 -0000 1.2 *************** *** 5,8 **** --- 5,9 ---- install: cp cgi/pymweb.py /usr/lib/cgi-bin/ + cp dtd/table.dtd /var/www/ cp www/pymweb.html /var/www/ cp -r www/images/ /var/www/ |
|
From: <ki...@us...> - 2003-04-09 01:38:54
|
Update of /cvsroot/pymerase/pymerase/pymweb/cgi
In directory sc8-pr-cvs1:/tmp/cvs-serv9983/cgi
Modified Files:
pymweb.py
Log Message:
fixes a potential security problem. Checks to see if the destination is a valid file name or directory name. /, \\, and .. are invalid file name chars.
Index: pymweb.py
===================================================================
RCS file: /cvsroot/pymerase/pymerase/pymweb/cgi/pymweb.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** pymweb.py 8 Apr 2003 20:56:38 -0000 1.7
--- pymweb.py 9 Apr 2003 01:38:50 -0000 1.8
***************
*** 93,96 ****
--- 93,105 ----
f.write("Pymweb")
f.close()
+
+ f = open(os.path.abspath('table.dtd'), 'r')
+ dtd = f.read()
+ f.close()
+
+ f = open(os.path.join(ROOTPATH, 'table.dtd'), 'w')
+ f.write(dtd)
+ f.close()
+
tempfile.tempdir = ROOTPATH
DIRPATH = tempfile.mktemp()
***************
*** 128,131 ****
--- 137,150 ----
return file
+
+
+ def checkDest(dest):
+ block = ['\\', '/', '..']
+
+ for item in block:
+ if item in dest:
+ return 0
+
+ return 1
***************
*** 154,158 ****
fileName = file.filename
-
fileName = checkFileName(fileName)
--- 173,176 ----
***************
*** 166,174 ****
html += text
! text = '<b>Input:</b> %s<br>\n' % (form['input'].value)
print text
html += text
! text = '<b>Output:</b> %s<br>\n' % (form['output'].value)
print text
html += text
--- 184,197 ----
html += text
! input = form['input'].value
! output = form['output'].value
! dest = form['dest'].value
! compression = form['compression'].value
!
! text = '<b>Input:</b> %s<br>\n' % (input)
print text
html += text
! text = '<b>Output:</b> %s<br>\n' % (output)
print text
html += text
***************
*** 178,186 ****
html += text
! text = '<b>Destination:</b> %s<br>\n' % (form['dest'].value)
print text
html += text
! text = '<b>Compression:</b> %s<br>\n' % (form['compression'].value)
print text
html += text
--- 201,216 ----
html += text
! text = '<b>Destination:</b> %s<br>\n' % (dest)
print text
html += text
! if checkDest == 1:
! pass
! else:
! text = "<b>Error: Destination %s Invalid!</b><br>" % (dest)
! print text
! raise ValueError, text
!
! text = '<b>Compression:</b> %s<br>\n' % (compression)
print text
html += text
***************
*** 190,201 ****
html += text
! driver = getDriverProgram(form['input'].value,
! form['output'].value,
fileName,
! form['dest'].value)
driverPath = saveFile('driver.py', driver)
! script = getDriverScript(form['dest'].value, form['compression'].value)
scriptPath = saveFile('driver.sh', script)
--- 220,231 ----
html += text
! driver = getDriverProgram(input,
! output,
fileName,
! dest)
driverPath = saveFile('driver.py', driver)
! script = getDriverScript(dest, compression)
scriptPath = saveFile('driver.sh', script)
***************
*** 226,242 ****
html += text
! if form['compression'].value == 'Tar&Gzip':
text = 'Download: <a href="/pymweb/%s/%s.tar.gz">%s.tar.gz</a>' % \
! (sessionDir, form['dest'].value, form['dest'].value)
print text
html += text
! elif form['compression'].value == 'Zip':
text = 'Download: <a href="/pymweb/%s/%s.zip">%s.zip</a>' % \
! (sessionDir, form['dest'].value, form['dest'].value)
print text
html += text
else:
! raise ValueError, '%s invalid compression type!' % (form['compression'].value)
htmlFile = open(os.path.join(DIRPATH, 'index.html'), 'w')
htmlFile.write(html)
--- 256,272 ----
html += text
! if compression == 'Tar&Gzip':
text = 'Download: <a href="/pymweb/%s/%s.tar.gz">%s.tar.gz</a>' % \
! (sessionDir, dest, dest)
print text
html += text
! elif compression == 'Zip':
text = 'Download: <a href="/pymweb/%s/%s.zip">%s.zip</a>' % \
! (sessionDir, dest, dest)
print text
html += text
else:
! raise ValueError, '%s invalid compression type!' % (compression)
htmlFile = open(os.path.join(DIRPATH, 'index.html'), 'w')
htmlFile.write(html)
|
|
From: <ki...@us...> - 2003-04-09 01:36:19
|
Update of /cvsroot/pymerase/pymerase/pymweb/dtd
In directory sc8-pr-cvs1:/tmp/cvs-serv9417
Added Files:
table.dtd
Log Message:
Jason Stewarts table.dtd file
--- NEW FILE: table.dtd ---
<!-- ====================================== -->
<!-- RDBMS Table Definition DTD (table.dtd) -->
<!-- ====================================== -->
<!-- Copyright 2001-2002 Jason E. Stewart
All rights reserved -->
<!-- Table Type Entities -->
<!ENTITY data_table "DATA" >
<!ENTITY validation_table
"VALIDATION" >
<!ENTITY subset_table "SUBSET" >
<!ENTITY linking_table "LINKING" >
<!ENTITY system_table "SYSTEM" >
<!ENTITY view "VIEW" >
<!-- Foreign Key Type Entities -->
<!ENTITY fkey_linking "LINKING_TABLE" >
<!ENTITY fkey_lookup "LOOKUP_TABLE" >
<!ENTITY fkey_oto "ONE_TO_ONE" >
<!ENTITY fkey_mto "MANY_TO_ONE" >
<!ELEMENT table (column|
unique|
index|
linking_keys|
foreign_key|
primary_key)* >
<!ATTLIST table
type CDATA #REQUIRED
name CDATA #REQUIRED
comment CDATA #IMPLIED
where CDATA #IMPLIED
inherits_from
CDATA "none"
can_self_reference
(true|false) "false"
is_abstract
(true|false) "false" >
<!ELEMENT column EMPTY >
<!ATTLIST column
name ID #REQUIRED
full_name CDATA #REQUIRED
type CDATA #REQUIRED
comment CDATA #IMPLIED
not_null (true|false) "false"
source_table
CDATA #IMPLIED >
<!ELEMENT unique EMPTY >
<!ATTLIST unique
column_ids IDREFS #REQUIRED >
<!ELEMENT primary_key EMPTY >
<!ATTLIST primary_key
column_id IDREF #REQUIRED
serial (true|false) "true" >
<!--
the write_sql attribute enables us to indicate where table
references exist, but we don't want them to be defined by an
actual FOREIGN KEY constraint in the DB. This will enable the
API to have a getter method for this value, but it just wont'
have a constraint in the DB.
the can_self_reference attribute is for those cases when a table
has a foreign key to itself, and that foreign key is permitted
to point to the same object. For example, this happens when
groups are used for setting permissions, and the groups themselves
have a group that defines the permissions for who can add or delete
members from the group.
-->
<!ELEMENT foreign_key EMPTY >
<!ATTLIST foreign_key
column_id IDREF #REQUIRED
foreign_table
CDATA #REQUIRED
foreign_table_pkey
CDATA #REQUIRED
fkey_type CDATA #REQUIRED
can_cascade
(true|false) "false"
write_sql (true|false) "true"
can_self_reference
(true|false) "false" >
<!ELEMENT linking_keys EMPTY >
<!ATTLIST linking_keys
link1 IDREF #REQUIRED
link2 IDREF #REQUIRED >
<!ELEMENT index EMPTY >
<!ATTLIST index
name CDATA #REQUIRED
column_id IDREF #REQUIRED >
<!--
Local Variables:
dtd-xml-flag: t
End:
-->
|
|
From: <ki...@us...> - 2003-04-09 01:35:49
|
Update of /cvsroot/pymerase/pymerase/pymweb/dtd In directory sc8-pr-cvs1:/tmp/cvs-serv9370/dtd Log Message: Directory /cvsroot/pymerase/pymerase/pymweb/dtd added to the repository |
