Hi, Ed
> A work around is to have a read only account to the database for
> loading the data and then users can enter their own credentials at the
> time of saving (if you wish to allow direct database access).
Yes, my goal is to have it saved directly to the Chado DB, and
immediately having the changes available on GBrowse, after a suitable
reload of course. So, no XML files to email to each other and wait until
the changes are added to the database and all the additional
complexities of that, etc.
That's a great idea, the read-only approach. I'll try to implement it
and see what happens. That would actually be useful in another level --
regular (outside of the project) users of the website could open Apollo
to have a better view of the genome, but would not be able to change the
database.
> However, IT departments usually are opposed to opening up non standard
> ports to the outside world (only an issue if the curators are outside
> your intranet), in which case you'll want to take a look at the work
> Scott Cain has done for CAS (Community Annnotation System):
> http://gmod.org/wiki/CAS
Yeah, I know, we're working on convincing our IT guys that this is OK.
The site for CAS is where I got the idea (and lots of help from the disk
image) of what I'm doing now. I guess I missed something though...
Doesn't his approach need the Postgresql port open for people using
web-start Apollo?
Thanks
J
P.S.: Re: the wrong coordinates in the analysis window. Well, very
weird, but... Now it is working here (Linux computer, haven't tested
again on the Mac) even with Java 1.6 and the correct coordinates show!
The .dtd error continues though.
Ed Lee wrote:
Hi J,
- 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).
The command line for Apollo was setup to automatically load data for
the user to curate, rather than requiring user feedback on loading
the data. So to read specific data from the database, all the
credentials need to be provided when connecting to the database.
A work around is to have a read only account to the database for
loading the data and then users can enter their own credentials at the
time of saving (if you wish to allow direct database access). However,
IT departments usually are opposed to opening up non standard ports to
the outside world (only an issue if the curators are outside your
intranet), in which case you'll want to take a look at the work
Scott Cain has done for CAS (Community Annnotation System):
http://gmod.org/wiki/CAS
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...
You can view the e-mail archives at the mailing list website, but
unfortunately I don't think it supports a search feature =(
Cheers,
Ed
--
-------------------------------
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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