Protege Wiki - Recent changes [en]

User:Jguerra42

2009-11-21T03:41:12Z

New user account

New page

User:Chuangifan

2009-11-20T02:36:16Z

New user account

New page

ClearingP4Preferences

2009-11-19T19:53:49Z

← Older revision		Revision as of 19:53, November 19, 2009
Line 9:		Line 9:
	[[File:JavaPreferences-JPUI.png]]		[[File:JavaPreferences-JPUI.png]]

-	This user interface will allow one to ~~delete all~~ the Protege java preferences and ~~start from~~ a clean slate.	+	This user interface will allow one to modify the Protege java preferences. In particular to delete the Protege Java preferences and return to a clean slate, select PROTEGE_PREFERENCES, click the Node menu and click delete.

File:JavaPreferences-JPUI.png

2009-11-19T19:52:42Z

uploaded a new version of "[[File:JavaPreferences-JPUI.png]]"

New page

ClearingP4Preferences

2009-11-19T18:39:39Z

← Older revision		Revision as of 18:39, November 19, 2009
(One intermediate revision not shown)
Line 5:		Line 5:
	java -jar jpui-0.4.0.jar		java -jar jpui-0.4.0.jar
	</pre>		</pre>
		+	Here is a screenshot.
		+
		+	[[File:JavaPreferences-JPUI.png]]
		+
		+	This user interface will allow one to delete all the Protege java preferences and start from a clean slate.

File:JavaPreferences-JPUI.png

2009-11-19T18:38:12Z

uploaded "[[File:JavaPreferences-JPUI.png]]" Example of the java preferences user interface

New page

ClearingP4Preferences

2009-11-19T18:37:35Z

← Older revision		Revision as of 18:37, November 19, 2009
Line 1:		Line 1:
	Protege 4 uses java preferences to store user preferences and activity. This can be very nice because when a new version of Protege 4 is installed, it will remember such things as recent ontologies visited, the location of owl viz, rendering preferences and other such stuff. But sometimes, when Protege is misbehaving, this becomes saved state about Protege that persists when everything else is cleared. For some operating systems, one can find the location of the java preferences and adjust them there. For example, on linux machines the java preferences can be found in ~/.java/.userPrefs and on OS X machines the preferences can be found in ~/Library/Preferences/com.apple.java.util.prefs.plist. On windows machines I believe that the java preferences are found in the registry but I could be wrong.		Protege 4 uses java preferences to store user preferences and activity. This can be very nice because when a new version of Protege 4 is installed, it will remember such things as recent ontologies visited, the location of owl viz, rendering preferences and other such stuff. But sometimes, when Protege is misbehaving, this becomes saved state about Protege that persists when everything else is cleared. For some operating systems, one can find the location of the java preferences and adjust them there. For example, on linux machines the java preferences can be found in ~/.java/.userPrefs and on OS X machines the preferences can be found in ~/Library/Preferences/com.apple.java.util.prefs.plist. On windows machines I believe that the java preferences are found in the registry but I could be wrong.

-	However, there is a much nicer portable way of interacting with the java preferences directly. There is a simple but very useful utility calls [http://sourceforge.net/projects/jpui/ Java Preferences User Interface]. It allows one to easily clear or update ~~preferencs~~ and it is pretty clear where the Protege preferences live.	+	However, there is a much nicer portable way of interacting with the java preferences directly. There is a simple but very useful utility calls [http://sourceforge.net/projects/jpui/ Java Preferences User Interface]. It allows one to easily clear or update preferences and it is pretty clear where the Protege preferences live. To use it type the following at the command line:
		+	<pre>
		+	java -jar jpui-0.4.0.jar
		+	</pre>

CompileProtege4InEclipse

2009-11-18T20:25:58Z

← Older revision		Revision as of 20:25, November 18, 2009
Line 8:		Line 8:
	[[Protege4DevDocs#Protege-OWL_editor_in_a_Generic_IDE\|generic ide instructions]].		[[Protege4DevDocs#Protege-OWL_editor_in_a_Generic_IDE\|generic ide instructions]].

-	# Download the protege plug-ins with linked source. Currently these can be found [http://~~www~~.~~tigraworld~~.~~com~~/~~p4plugins~~/Protege4SourcePlugins.zip here] (version information is [http://~~www~~.~~tigraworld~~.~~com~~/~~p4plugins~~/~~version~~.txt here]). Soon there will be a standard download page connected to each of our releases. It is also possible to follow all of these steps by using the plugins from any installation of Protege 4 but these plugins-ins will not include the source. The minimal set of plugins needed is	+	# Download the protege plug-ins with linked source. Currently these can be found [http://smi-protege.stanford.edu/protege4/Protege4SourcePlugins.zip here] (version information is [http://smi-protege.stanford.edu/protege4/Protege4SourcePluginsVersion.txt here]). Soon there will be a standard download page connected to each of our releases. It is also possible to follow all of these steps by using the plugins from any installation of Protege 4 but these plugins-ins will not include the source. The minimal set of plugins needed is
	## org.protege.common.jar		## org.protege.common.jar
	## org.protege.editor.core.application.jar		## org.protege.editor.core.application.jar

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2009-11-18T18:13:50Z

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User:Buycialis

2009-11-18T18:06:11Z

New user account

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WebProtege

2009-11-17T20:11:35Z

← Older revision		Revision as of 20:11, November 17, 2009
Line 3:		Line 3:

	<div style="background:#F7F7F7; border:1px solid #999999; padding:1em; width:75%;">		<div style="background:#F7F7F7; border:1px solid #999999; padding:1em; width:75%;">
-	'''[[ID::WebProtege]]''' is an open source, lightweight, web-based ontology editor. Our main goal in developing WebProtege is to support the process of collaborative ontology development in a web environment. Try out WebProtege on our demo server:	+	'''[[ID::WebProtege]]''' is an open source, lightweight, web-based ontology editor. Our main goal in developing WebProtege is to support the process of collaborative ontology development in a web environment. Try out WebProtege on our '''demo server''':

	http://bmir-protege-dev1.stanford.edu/webprotege/		http://bmir-protege-dev1.stanford.edu/webprotege/
		+
		+
		+	<div style="color:#CC0000;font-weight:bold;">Help us evaluate WebProtege by taking the 3-minute survey from [http://www.surveymonkey.com/s.aspx?sm=WuTpnqnBem7JD77fSFDJLQ_3d_3d here].</div>

User:Jinkydo

2009-11-17T11:09:45Z

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User:Jinkydo

2009-11-17T11:07:47Z

New user account

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Main Page

2009-11-17T01:41:10Z

added link to homepage for march 2010 protege-owl shortcourse

← Older revision		Revision as of 01:41, November 17, 2009
Line 10:		Line 10:
	== Upcoming Events ==		== Upcoming Events ==
	<ul>		<ul>
-	<li style="padding-bottom:5px; list-style:circle;">Protege-OWL Short Course, March 24-26, 2010, Stanford, California (register for the [http://mailman.stanford.edu/mailman/listinfo/protege-users protege-users mailing list] to receive notification when registration opens)</li>	+	<li style="padding-bottom:5px; list-style:circle;">[http://protege.stanford.edu/shortcourse/protege-owl/201003/index.html Protege-OWL Short Course], March 24-26, 2010, Stanford, California (register for the [http://mailman.stanford.edu/mailman/listinfo/protege-users protege-users mailing list] to receive notification when registration opens)</li>
	</ul><br />		</ul><br />

User:Koroswesley

2009-11-16T23:29:46Z

New user account

New page

Apple's missing Java 6

2009-11-16T15:09:35Z

Dealing with Java5 Compiler issues:

← Older revision		Revision as of 15:09, November 16, 2009
(6 intermediate revisions not shown)
Line 1:		Line 1:
		+	=The Problem and Our Current Options =

		+	It looks as though Apple has stopped development on the powerpc and the 32 bit intel macs. Apple has always had a very hard time keeping up with Java development but they are now working on being four years behind on these two platforms. Even for Apple this is excessive. Though there does not appear to be any information coming from Cupertino, my suspicion is that there will never be an apple or sun supported java 6 on the powerpc. This creates a problem for the Protege group who are now considering the possibility that java 6 will never arrive. Here is my analysis of the options that I see. All the choices are bad.

		+	We could stick with Java 5 as the final Protege development platform. I am having a great deal of trouble stomaching this option.
		+
		+	We have also considered dropping the problematic platforms. All of us in the protege group are uncomfortable with this option. In particular we know people who are using protege (including me!) on the laptops and desktops in question. This option has not entirely been ruled out but we are favoring rejecting it. Over time this may become more palatable.
		+
		+	I have looked into building java 6 on the problematic platforms using openjdk. This is cool but I think there are several problems that make me think that this is not workable. First we would then be supporting our own java distribution - a game that I really don't want to get involved in. Also my experiments indicate that openjdk will have several dependencies. So we would have to install several packages multiplying the problems that will arise. Alternatively there is this macports technology (very cool!!) that will automatically build java 6 openjdk. It doesn't work now on the powerpc but probably will soon. But this is time consuming (several hours to build java 6) and I suspect that there will be build issues. I have pretty much decided to reject this option.
		+
		+	The final two options - which is where I am beginning to go - both involve maintaining code bases for java 5 and the latest java. To support this we would do nightly builds and junit runs in both java 5 and java 6. We would only have to take further measures if, for some reason, the nightly java 5 builds and junits started to fail. It may very well be that there will not be too many cases where the code bases are different. There will be many issues that we have not yet figured out like whether a java 5 client can safely connect to a java 6 server.
		+
		+	So there are two different remaining proposals. First we could create a java 5 branch for the projects that need some additional work. We would create nightly scripts that would merge changes from the trunk into the java 5 branch. If the compile, junits or merge failed then the merge would not be committed. We would have to be somewhat careful with the script but we would probably get it right after a few tries. An advantage of this approach is that regular java 6 developers would not have to be aware of the java 5 issue.
		+
		+	Alternatively, we would not create a branch. Instead we would create multiple source trees. Regular developers would use src and src.java6. Developers maintaining the java 5 platforms would use src and src.java5. The advantage of this would be that there would be no branches and all the additional sources of error associated with this would be removed. It would also be very easy to switch between java 6 and java 5 builds. But I think that this is a bit awkward because classes could move between the src and src.java6. The packages would remain the same but there would be movement of classes from src to src.java6 when issues are discovered.
		+
		+	Actually I guess we could also do this in a single source tree and distinguish the java 6 vs java 5 specific code with a package name. This is easy to manage in the build files but might be more awkward in ides such as eclipse.
		+
		+	We haven't taken the plunge yet but I think that we are getting closer to doing this.
		+
		+	== Building Java 6 on the PowerPC ==
		+
		+	There is a [http://wikis.sun.com/display/OpenJDK/BSDPort new wiki] starting up about this. The mac ports didn't work on the g4 when I tried it because the bootstrap openjdk did not include a g4 version.

	If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that apple users will probably be unhappy about needing to install and run on X11.		If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that apple users will probably be unhappy about needing to install and run on X11.
Line 32:		Line 53:

	From this [http://lists.freebsd.org/pipermail/freebsd-questions/2008-April/172377.html] I found that pkg.m4 needs to be in autoconf's library path. I'm using fink and found that pkg.m4 was already in /sw/share/aclocal. I stuck a command line parameter (-B) into autogen.sh, but next time I'd just symlink /usr/local/share/aclocal.		From this [http://lists.freebsd.org/pipermail/freebsd-questions/2008-April/172377.html] I found that pkg.m4 needs to be in autoconf's library path. I'm using fink and found that pkg.m4 was already in /sw/share/aclocal. I stuck a command line parameter (-B) into autogen.sh, but next time I'd just symlink /usr/local/share/aclocal.
		+
		+	== Dealing with Java5 Compiler issues ==
		+
		+	Sometimes there are problems getting correct files to compile in java 5. Here is a page I made about how to troubleshoot these problems.
		+	[[DealingWithJava5CompilerIssues\|dealing with Java 5 compiler issues]]

ProtegeDevDocsGeneral

2009-11-15T19:09:35Z

Building Java 6 on the PowerPC:

← Older revision		Revision as of 19:09, November 15, 2009
Line 22:		Line 22:
	[[Category:Protege developer documentation]]		[[Category:Protege developer documentation]]

-	== ~~Building~~ Java 6 ~~on the PowerPC~~ ==	+	== Where is Java 6? ==

	I am working on solving the problem of [[Apple's missing Java 6]].		I am working on solving the problem of [[Apple's missing Java 6]].

Apple's missing Java 6

2009-11-15T19:08:57Z

Created page with ' If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that ap...'

New page

If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that apple users will probably be unhappy about needing to install and run on X11.

This will probably get more detailed when I do it the next time. I am trying the build from icedtea which I got with the following mercurial command.
<pre>
hg clone http://icedtea.classpath.org/hg/icedtea6
</pre>
I needed to get/install
* mercurial
* md5sum
* gawk
* eclipse-ecj.jar ([http://archive.eclipse.org/eclipse/downloads/drops/R-3.3.1.1-200710231652/index.php eclipse.org])
* xalan.jar ([http://xml.apache.org/xalan-j/downloads.html xml.apache.org])
* giflib-devel ([http://sourceforge.net/projects/giflib/ sourceforge.net])
Thus far my configure line looks like this:
<pre>
./configure --enable-zero=yes \
--with-project=bsd --with-gcj-home=/usr/local/lib/gcj-4.2.2 \
--with-ecj-jar=${jars}/eclipse-ecj.jar \
--with-xalan2-jar=${jars}/xalan.jar \
--with-xalan2-serializer-jar=${jars}/serializer.jar \
--with-xerces2-jar=${jars}/xercesImpl.jar \
--with-rhino=${jars}/js.jar
</pre>
My current error is
<pre>
./configure: line : syntax error near unexpected token `XPROTO,'
./configure: line 11028: `PKG_CHECK_MODULES(XPROTO, xproto,XPROTO_FOUND=yes,XPROTO_FOUND=no)'
</pre>

From this [http://lists.freebsd.org/pipermail/freebsd-questions/2008-April/172377.html] I found that pkg.m4 needs to be in autoconf's library path. I'm using fink and found that pkg.m4 was already in /sw/share/aclocal. I stuck a command line parameter (-B) into autogen.sh, but next time I'd just symlink /usr/local/share/aclocal.

ProtegeDevDocsGeneral

2009-11-15T19:08:39Z

Building Java 6 on the PowerPC:

← Older revision		Revision as of 19:08, November 15, 2009
Line 24:		Line 24:
	== Building Java 6 on the PowerPC ==		== Building Java 6 on the PowerPC ==

-	I am working on solving the problem of Apple's missing Java 6. If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that apple users will probably be unhappy about needing to install and run on X11.	+	I am working on solving the problem of [[Apple's missing Java 6]].
-		+
-	~~This will probably get more detailed when I do it the next time. I am trying the build from icedtea which I got with the following mercurial command.~~	+
-	~~<pre>~~	+
-	~~hg clone http://icedtea.classpath.org/hg/icedtea6~~	+
-	~~</pre>~~	+
-	~~I needed to get/install~~	+
-	* mercurial	+
-	* md5sum	+
-	* gawk	+
-	* eclipse-ecj.jar ([http://archive.eclipse.org/eclipse/downloads/drops/R-3.3.1.1-200710231652/index.php eclipse.org])	+
-	* xalan.jar ([http://xml.apache.org/xalan-j/downloads.html xml.apache.org])	+
-	* giflib-devel ([http://sourceforge.net/projects/giflib/ sourceforge.net])	+
-	~~Thus far my configure line looks like this:~~	+
-	~~<pre>~~	+
-	~~./configure --enable-zero=yes \~~	+
-	~~--with-project=bsd --with-gcj-home=/usr/local/lib/gcj-4.2.2 \~~	+
-	~~--with-ecj-jar=${jars}/eclipse-ecj.jar \~~	+
-	~~--with-xalan2-jar=${jars}/xalan.jar \~~	+
-	~~--with-xalan2-serializer-jar=${jars}/serializer.jar \~~	+
-	~~--with-xerces2-jar=${jars}/xercesImpl.jar \~~	+
-	~~--with-rhino=${jars}/js.jar~~	+
-	~~</pre>~~	+
-	~~My current error is~~	+
-	~~<pre>~~	+
-	~~./configure: line : syntax error near unexpected token `XPROTO,'~~	+
-	~~./configure: line 11028: `PKG_CHECK_MODULES(XPROTO, xproto,XPROTO_FOUND=yes,XPROTO_FOUND=no)'~~	+
-	~~</pre>~~	+
-		+
-	From this [http://lists.freebsd.org/pipermail/freebsd-questions/2008-April/172377.html] I found that pkg.m4 needs to be in autoconf's library path. I'm using fink and found that pkg.m4 was already in /sw/share/aclocal. I stuck a command line parameter (-B) into autogen.sh, but next time I'd just symlink /usr/local/share/aclocal.	+

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2009-11-14T10:38:09Z

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2009-11-14T10:34:45Z

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