[Biojava-dev] Problem with read RichFormat file from an applet

[Mark Schreiber]

Consulting a good book on the java security model may reveal a way
that you can modify the policy to allow this.

However, I think you should give serious consideration to why you
would want to use an applet in any context. The technology has major
limitations and has been long since superceeded by either severlet or
other technologies for server side stuff or webstart for client side
apps distributed from a server.

- Mark

On Jan 9, 2008 4:38 PM, Richard Holland <holland at ebi.ac.uk> wrote:
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> Hello.
>
> This is the root of your problem:
>
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
>  GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>
> The applet runtime environment is not allowing BioJava to create a
> custom class loader. It's not to do with disk access at all unfortunately.
>
> I don't know of a solution myself as I've not done much work with applets.
>
> Does anyone else on this list have any suggestions?
>
> cheers,
> Richard
>
>
>
> Minh Duc, Cao wrote:
> > Hi,
> >
> > I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> > alone application, it works perfectly. However, when the code is called from
> > an applet, the following exception is thrown
> >
> > Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
> >     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
> >     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> > SimpleFeatureHolder.java:54)
> >     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> > RichFeature.java:167)
> >     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> > :61)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:100)
> >     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> > SimpleRichSequenceBuilder.java:81)
> >     at
> > org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> > (SimpleRichSequenceBuilderFactory.java:68)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> > RichStreamReader.java:92)
> >     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> > ReadFormatFileFunction.java:134)
> >     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> > Caused by: java.security.AccessControlException: access denied (
> > java.lang.RuntimePermission createClassLoader)
> >     at java.security.AccessControlContext.checkPermission(Unknown Source)
> >     at java.security.AccessController.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkPermission(Unknown Source)
> >     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
> >     at java.lang.ClassLoader.<init>(Unknown Source)
> >     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> > GeneratedClassLoader.java:29)
> >     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :51)
> >     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> > :58)
> >     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> > FeatureFilter.java:1270)
> >     ... 11 more
> >
> > It is noted that the applet is signed and can read files from client
> > harddisk if other method is used.
> >
> > Do anyone have an idea how can I go about to fix this problem?
> >
> > Thank you very much
> >
> > Minh
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
> - --
> Richard Holland (BioMart)
> EMBL EBI, Wellcome Trust Genome Campus,
> Hinxton, Cambridgeshire CB10 1SD, UK
> Tel. +44 (0)1223 494416
>
> http://www.biomart.org/
> http://www.biojava.org/
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