joelib-help

[Joelib-help] Problems with whitespaces in pathnames

[Gerd M. <Ger...@sm...>]

Hi,

If I call 
java -jar joelib.jar:myclasses.jar my.Main.Class

and try to load a molecule from a file I get an error that 
joelib can't load the file atomtypes.txt although the jar contains
it. If I unpack joelib.jar it works. 

I found out that the error occurs if the jar resists in a directory 
with whitespaces in the pathname. Also I saw that wsi.ra.tools.ResourceLoader
replaces '%20' in the pathname with ' ' which seems to be the
problem here. Why is this done ? Any hints for fixing this problem ?

Best Regards,
gerd

________________________________________________________________
Gerd Mueller                                    ge...@sm...     
SMB GmbH                                  http://www.smb-tec.com

Re: [Joelib-help] Problems with whitespaces in pathnames

[Joerg K. W. <we...@in...>]

Hi Gerd,

> and try to load a molecule from a file I get an error that 
> joelib can't load the file atomtypes.txt although the jar contains
> it. If I unpack joelib.jar it works. 
> I found out that the error occurs if the jar resists in a directory 
> with whitespaces in the pathname. Also I saw that wsi.ra.tools.ResourceLoader
> replaces '%20' in the pathname with ' ' which seems to be the
> problem here. Why is this done ? Any hints for fixing this problem ?

111. As you can see also the replacement takes only an effect for 
'files' which are not contained in a .zip or .jar file !

So the question is, why is this not recognized (line 161) ?

Switch
log4j.category.wsi.ra.tool.ResourceLoader=INFO
to
log4j.category.wsi.ra.tool.ResourceLoader=DEBUG
in build/log4.properties and src/log4j.properties

and try again. Then you could see a little bit more informations ! 
Otherwise you should add some System.out.println("abc"); to the 
ResourceLoader class to see why this check fails !

So three way plan:
1. increase verbosity in logging
2. add console informations and recompile sources
3. check again your example.

I added the replacement of white space characters (FOR FILES), because 
other users had the same path problem. So, we must find a way to combine 
the solutions for both problems at once.

222. Which way are you using for loading your file. ?
Stream, SimpleReader, ResourceLoader, ... ?

333. Have you anything changed in joelib.properties ?
There you can define another 'atomtype.txt'-path. Typically JOELib uses 
the resource-load mechanism to be independant from user-paths.

Regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                          E. Hemingway

Re: [Joelib-help] Problems with whitespaces in pathnames

[Gerd M. <Ger...@sm...>]

On Mon, 08 Dec 2003 15:51:34 +0100
"Joerg K. Wegner" <we...@in...> wrote:

> Hi Gerd,
> 
> > and try to load a molecule from a file I get an error that 
> > joelib can't load the file atomtypes.txt although the jar contains
> > it. If I unpack joelib.jar it works. 
> > I found out that the error occurs if the jar resists in a directory 
> > with whitespaces in the pathname. Also I saw that
> > wsi.ra.tools.ResourceLoader replaces '%20' in the pathname with ' ' which
> > seems to be the problem here. Why is this done ? Any hints for fixing this
> > problem ?
> 
> 111. As you can see also the replacement takes only an effect for 
> 'files' which are not contained in a .zip or .jar file !

Yes, and this seems to be the problem. I've used java.net.URLDecoder 
to decode the urlToZipArchive in getBytesFromArchive() and everything
works fine. So the solution seems to be move the '%20' replacement
code a few lines up, so that also archive paths are handled. Also
I would recomment to use java.net.URLDecoder instead of using 
regexp. This way you don't need to care about other %-sign that
may occur.

best regards,
gerd

________________________________________________________________
Gerd Mueller                                    ge...@sm...     
SMB GmbH                                  http://www.smb-tec.com

Re: [Joelib-help] Problems with whitespaces in pathnames

[Joerg K. W. <we...@in...>]

Hi Gerd,

could you please change these things and send me the complete 
ResourceLoader, so i must not check these things on my own.

Thanks and best regards, Joerg

> On Mon, 08 Dec 2003 15:51:34 +0100
> "Joerg K. Wegner" <we...@in...> wrote:
> 
> 
>>Hi Gerd,
>>
>>
>>>and try to load a molecule from a file I get an error that 
>>>joelib can't load the file atomtypes.txt although the jar contains
>>>it. If I unpack joelib.jar it works. 
>>>I found out that the error occurs if the jar resists in a directory 
>>>with whitespaces in the pathname. Also I saw that
>>>wsi.ra.tools.ResourceLoader replaces '%20' in the pathname with ' ' which
>>>seems to be the problem here. Why is this done ? Any hints for fixing this
>>>problem ?
>>
>>111. As you can see also the replacement takes only an effect for 
>>'files' which are not contained in a .zip or .jar file !
> 
> 
> Yes, and this seems to be the problem. I've used java.net.URLDecoder 
> to decode the urlToZipArchive in getBytesFromArchive() and everything
> works fine. So the solution seems to be move the '%20' replacement
> code a few lines up, so that also archive paths are handled. Also
> I would recomment to use java.net.URLDecoder instead of using 
> regexp. This way you don't need to care about other %-sign that
> may occur.
> 
> best regards,
> gerd
> 
> ________________________________________________________________
> Gerd Mueller                                    ge...@sm...     
> SMB GmbH                                  http://www.smb-tec.com
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                          E. Hemingway