Fwd: Fw: [DAS] LDAS web browser connection setup

[DOBBO@THEVILLAS.ECLIPSE.CO.UK]

Hi,
it appears to be the case that I had something wrong 
with my Bio::DB::Fasta module that had slipped through 
the net (didn't notice on initial scans of the apache 
logs, thought the log was spitting out a Bio::DB::GFF 
error). The LDAS setup is fine

bioperl 'make test' produced the following

t/DBFasta...........AnyDBM_File doesn't define an 
EXISTS method at Bio/DB/Fasta.pm line 789
indexing was interrupted, so 
unlinking ./t/data/dbfa/directory.index at 
Bio/DB/Fasta.pm line 948.
t/DBFasta...........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-11
        Failed 11/11 tests, 0.00% okay

Thanks
Rich

>Is there an error in the server error log?  The most 
>common problem is a 
>password error in the config file.  Early versions of 
>the Bioperl 
>Bio::DB::GFF module did not handle username password 
>right, but this was 
>fixed before the 1.0 release.

Lincoln

On Friday 19 July 2002 05:31 am, 
dobbo@thevillas.eclipse.co.uk wrote:
>> Hello,
>>
>> When I do an 'entry_points' query with my test 
database,
>> dicty, I get the
>> following output returned to my web browser:
>>
>>
>>  Could not open database
>>
>> The browser returns the relevant entry from the
>> dicty.conf file when viewing the dsn's.
>> I'm able to use ldasdump.pl to query my test 
database.
>> I'm also able to
>> log in as the user 'root' and do a query using mysql.
>>
>> Does anyone have any suggestions on how to debug my
>> installation?
>>
>> Here is the DATA SOURCE portion of my dicty.conf file
>> that is in the
>> das.conf subdirectory of the Apache conf directory.
>>
>> [DATA SOURCE]
>> description = Test annotations
>> adaptor     = dbi::mysqlopt
>> mapmaster   = http://192.168.1.110/cgi-bin/das/dicty
>> database    = dbi:mysql:database=dicty;host=localhost
>> fasta_files = /var/annotation/dna
>> user        = root
>> passwd      = xxxxxxx
>>
>> I noticed when searching the archives somebody 
reported
>> the same error way back in December. I pressume the 
fix
>> is now in the 1.06 release?
>>
>> Any help would be greatly appreciated,
>>
>> Rich
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS@biodas.org
>> http://biodas.org/mailman/listinfo/das

-- 
========================================================
================
Lincoln D. Stein                           Cold Spring 
Harbor Laboratory
lstein@cshl.org                   Cold Spring Harbor, NY
========================================================
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