Hi,
First of all, thanks for the great software that Apollo is. It has
helped us tremendously a few years back, and I'm hoping it will be even
greater help now.
I am trying to get Apollo to work using webstart. It is started directly
from a GBrowse instance (data from a Chado DB). It is mostly working but
I encountered some problems.
- The first one is independent of whether I'm running locally or as
webstart. When I start Apollo from the command line with the following
command: apollo -i chadoDB -t gene -u genename
I get the error:
apollo.dataadapter.ApolloAdapterException: Unable to access database: A
connection error has occurred: org.postgresql.util.PSQLException: FATAL:
password authentication failed for user "username"
Followed by a null pointer error and the program exits.
If I then add -D userpasswd it then works normally.
The problem is that I was hoping the window "Apollo: load data" would
appear, so the user could THEN enter the password (and change the user
name), when it is not provided as a command-line argument (as it happens
when one just types "apollo" on the CLI, for example).
All the same behavior happens using the corresponding <argument> pairs
in the .jnlp file -- with -D, all fine; without, no dice.
Having the add -D is a big pain, specially considering the webstart
aspect. That would increase the complexity of my setup lot: the user
would have to enter a user and password on GBrowse (not a big deal), but
the password would be clear text unless I move the whole thing to SSL to
get encrypted communication, or the net security people here won't be
very happy with me. Doable, but a pain.
Compounded to that is the fact that "The user property is missing. It is
mandatory." So, if I hard-code one user in the chado-adapter.xml file
and the other users provide their passwords, the combination will be wrong.
So, am I missing something and doing something wrong, or is Apollo's
behavior intended to be like that? Is there a way to "catch the error"
here and, when a password is not provided, open the "load data" window
-- with the other parameters passed filled in (in my case, gene name),
of course?
Since this is getting quite long, I'll send my other questions in
different emails. By the way, is there a way to search this mailing
list? Using "site:http://mail.fruitfly.org/"; on Google did not work, as
expected...
Now, what I am running...
My setup for the local version:
INFO : OS name: Linux
INFO : OS arch: i386
INFO : Java version: 1.6.0_16
INFO : this is Apollo Genome Annotation and Curation Tool, version
1.11.2, last updated Oct 5 2009
The webstart was compiled from the latest (as of 2009-01-04) version
from SVN, downloaded as follows:
svn co https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk
Thanks a lot for any help
Cheers
J
--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897
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