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[Obo-discuss] DAG-Edit can't read GO OBO file?

From: <gary.merrill@gs...> - 2004-09-24 16:02

Attachments: Message as HTML

I have just installed DAG-Edit 1.417 (1.418 seems inaccessible at the 
moment and my previous attempts to install it met with no success).  This 
is on a Win 2000 Advanced Server system, and it is using the j2rre1.4.2_05 
runtime.  When I attempt to load the gene_ontology_obo file I get the 
error

     org.bdgp.io.DataAdapterException: Load error

Contents of the stderr file are appended at the end of this message. There 
appeared to be no installation problems and I believe I followed all of 
the directions correctly.  This is the first time I've attempted to 
install and use DAG-Edit, and I sort of expected it to work on the gene 
ontology obo file without problems.

Can anyone offer some insight on what might be wrong here?  Thanks.

Contents of stderr file:

Starting DAG-Edit 1.417: Fri Sep 24 12:03:31 EDT 2004
java.net.UnknownHostException: E
        at java.net.PlainSocketImpl.connect(Unknown Source)
        at java.net.Socket.connect(Unknown Source)
        at java.net.Socket.connect(Unknown Source)
        at sun.net.NetworkClient.doConnect(Unknown Source)
        at sun.net.NetworkClient.openServer(Unknown Source)
        at sun.net.ftp.FtpClient.openServer(Unknown Source)
        at sun.net.ftp.FtpClient.<init>(Unknown Source)
        at sun.net.www.protocol.ftp.FtpURLConnection.connect(Unknown 
Source)
        at 
sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(Unknown Source)
        at 
org.bdgp.io.ProgressableURLInputStream.<init>(ProgressableURLInputStream.java:10)
        at org.bdgp.io.IOUtil.getProgressableStream(IOUtil.java:19)
        at 
org.bdgp.apps.dagedit.dataadapter.GOBOParseEngine.doParse(GOBOParseEngine.java:270)
        at 
org.bdgp.apps.dagedit.dataadapter.GOBOParseEngine.parse(GOBOParseEngine.java:398)
        at 
org.bdgp.apps.dagedit.dataadapter.GOBOAdapter.getRoot(GOBOAdapter.java:353)
        at 
org.bdgp.apps.dagedit.dataadapter.GOBOAdapterGUI.readTerms(GOBOAdapterGUI.java:794)
        at 
org.bdgp.apps.dagedit.dataadapter.GOBOAdapterGUI.doOperation(GOBOAdapterGUI.java:783)
        at 
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:355)
        at 
org.bdgp.swing.widget.DataAdapterChooser.doCommit(DataAdapterChooser.java:408)
        at 
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:132)
        at java.lang.Thread.run(Unknown Source)


--------------------------------------
Gary H. Merrill
Director and Principal Scientist, New Applications
Data Exploration Sciences
GlaxoSmithKline Inc.
(919) 483-8456

Re: [Obo-discuss] DAG-Edit can't read GO OBO file?

From: John Day-Richter <john.richter@ay...> - 2004-09-25 02:54

On Friday 24 September 2004 09:02, gary.h.merrill@... wrote:
> I have just installed DAG-Edit 1.417 (1.418 seems inaccessible at the
> moment and my previous attempts to install it met with no success).  This
> is on a Win 2000 Advanced Server system, and it is using the j2rre1.4.2_05
> runtime.  When I attempt to load the gene_ontology_obo file I get the
> error
>
>      org.bdgp.io.DataAdapterException: Load error
>
> Can anyone offer some insight on what might be wrong here?  Thanks.

Sorry about this. First off, I recommend downloading the latest beta version. 
It's pretty stable, and it should solve this problem...

The problem you are having is a bug that only occurs under Windows, where Java 
reports to DAG-Edit that the E: before the file name is NOT a drive letter, 
but the name of an internet protocol. Since DAG-Edit can load files either 
from a local disk or a URL, it tries to figure out what to do with URLs that 
start with E, and promptly fails. A workaround in version 1.417 is to append 
the string "file:" to the front of your file name. This tells DAG-Edit that 
you are trying to load a file, and everything works out fine.

In any case, I suggest you download the latest beta version, available from 
the sourceforge site. It contains a work around for this problem.

	-John

P.S. I'm sorry you had difficulty with your very first use of DAG-Edit. Please 
let me know if you have any further problems. I'm always glad to help.

Open Biomedical Ontologies

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