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

[Minh Duc, Cao]

Hi,
I figured out the problem. Once the biojava jar file is signed, the applet
can read files without any problems.  Many thanks to you both.

Also thank Mark for your suggestions, I will certainly try WebStart out.

Cheers
Minh


On Jan 9, 2008 7:50 PM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> 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:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > 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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> >
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