-props argument in JNLP

I have configured a JNLP by altering the following section (codebase is localhost/Jalview/webstart):

        <application-desc main-class="jalview.bin.Jalview">
                <argument>-props</argument>
                <argument>http://localhost/Jalview/webstart/local.properties</argument>
        </application-desc>

The properties are not read. Jalview prompts for google tracking and then loads the example file from jalview.org despite the properties indicating not to load an example file and to take it from localhost. Obviously I can't open the Java console until the application has started so can't see what is going on.

Any clues? Are null values allowed in the property fields?

local.properties contains the following (as does my .jalview_properties file)

#---JalviewX Properties File---
#Tue Mar 15 08:03:46 GMT 2011
WRAP_ALIGNMENT=false
AUTO_CALC_CONSENSUS=true
FONT_SIZE=10
SHOW_DBREFS_TOOLTIP=true
PFAM_JVSUFFIX=true
SHOW_CONSENSUS_LOGO=false
PAD_GAPS=false
BUILD_DATE=15 November 2010
FONT_NAME=SansSerif
MSF_JVSUFFIX=true
SHOW_JAVA_CONSOLE=true
SHOW_UNCONSERVED=false
LATEST_VERSION=2.6.1
DEFAULT_COLOUR=None
PILEUP_JVSUFFIX=true
SHOW_GROUP_CONSERVATION=false
ID_ITALICS=true
CLUSTAL_JVSUFFIX=true
ANTI_ALIAS=false
VERSION=2.6.1
RECENT_FILE=
SHOW_JWS1_SERVICES=false
FASTA_JVSUFFIX=true
SHOW_JVSUFFIX=true
SEQUENCE_LINKS=SRS|http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all\:$SEQUENCE_ID$]))+-view+SwissEntry
DEFAULT_FILE_FORMAT=Jalview
FONT_STYLE=plain
DAS_LOCAL_SOURCE=
SHOW_CONSENSUS_HISTOGRAM=true
SHOW_GROUP_CONSENSUS=false
VERSION_CHECK=true
SHOW_WSDISCOVERY_ERRORS=true
BLC_JVSUFFIX=true
SHOW_JWS2_SERVICES=true
DAS_REGISTRY_URL=http\://www.dasregistry.org/das1/sources/
SHOW_STARTUP_FILE=false
STARTUP_FILE=http\://localhost/Jalview/examples/exampleFile_2_3.jar
RECENT_URL=http\://localhost/Jalview/examples/exampleFile_2_3.jar
SHOW_FULLSCREEN=false
SHOW_QUALITY=true
SHOW_CONSERVATION=true
WSMENU_BYTYPE=true
GAP_SYMBOL=-
JWS2HOSTURLS=http\://localhost\:8080/jaba
SHOW_ANNOTATIONS=true
USAGESTATS=false
SHOW_IDENTITY=true
SHOW_NPFEATS_TOOLTIP=true
USE_PROXY=false
SORT_ALIGNMENT=No sort
WSMENU_BYHOST=true
DAS_ACTIVE_SOURCE=
PIR_MODELLER=false
LAST_DIRECTORY=
SHOW_ENFIN_SERVICES=true
PIR_JVSUFFIX=true
RIGHT_ALIGN_IDS=false
SHOW_OVERVIEW=false

David Martin PhD
College of Life Sciences
University of Dundee
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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Hi David.

I have configured a JNLP by altering the following section (codebase is localhost/Jalview/webstart):

        <application-desc main-class="jalview.bin.Jalview">
                <argument>-props</argument>
                <argument>http://localhost/Jalview/webstart/local.properties</argument>
        </application-desc>

The properties are not read. Jalview prompts for google tracking and then loads the example file from jalview.org despite the properties indicating not to load an example file and to take it from localhost.

What is happening here is that Jalview is failing to retrieve the
properties file, and defaulting to default configuration, because all
-props argument actually does in version 2.6.x is override the path
jalview uses to retrieve its properties file. Even worse, that version
assumes the argument is a filename - not a URL, so it simply fails to
read any properties file at all, and when you close Jalview, or modify
its config, it'll also fail to write the file out to the path you've
given it. I fixed the web retrieval part a month ago after Balasz
commented on this in another post (see
http://issues.jalview.org/browse/JAL-761).

Obviously I can't open the Java console until the application has started so can't see what is going on.

You can. If you enable the system java console as described in
www.jalview.org/faq.html (rather than just opening Jalview's console,
which starts up later on), then you would see everything that goes on.
Alternately, run javaws from the command line.

Any clues? Are null values allowed in the property fields?

This is totally dependent on the field. Empty values are correctly
treated as false if they are boolean, but will otherwise be parsed
according to the datatype. In your case, what you want to do is only
specify the properties that you actually want to control in the
web-based properties file, and leave the rest as default. Ideally,
Jalview should then gracefully merge these specific properties into the
user's own config.

I have a feeling the properties file is not actually the correct
approach for achieving the functionality you want, anyhow. You want to
launch jalview with specific server URLs preconfigured, and the best way
to do that would be to create some new arguments to allow JABA server
URLs to be specified on the command line directly (in the same way that
DAS sequence and annotation servers can be).

Jim.

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On 15/03/2011 10:35, David Martin wrote: