On 21 Dec 2006, at 14:43, Marina Olhovsky wrote:
>> [NEW CONFIGURATION] .... WITH MEMORY [default]
>> default ... Reagent Tracker .......... 001/001 ... reagents_tbl
>> .............................. (RDBMS) localhost:5432
>> ................ OK
>> Setting possible links between datasets
>> ....(scanning) 100%
>> ....(linking) 100%
>> ....(sorting) 100%
>> ....(clustering) 1/1 - 0 remain
>> ....(resolving) 100%
>> Building templates for visible datasets
>> Uh-oh, got some non-fatal warnings:
>>
>> Use of uninitialized value in print at
>> /home/olhovsky/biomart-perl/bin/configureBioMart.pl line 353.
>>
and the last thing, I am assuming that this is the last line of the
output you see or does it actually
go to the next step - 'Compiling templates for visible datasets'?
Yes, Arek, this is the last line of the output I see (just copied and
pasted the output from the terminal). I will send you the xml (which
address should I send it to off the mailing list?) Thanks so much for
your help.
Marina.
Hi Marina,
I have now uploaded your xml as sent to me on my laptop (macos x, psql
(PostgreSQL) 8.0.1, latest 'release-0_5' biomart-perl)
ran a test and seems to be perfectly fine, configured and started the
server correctly, can
see both datasets and all of the filters and attributes. Had no
warnings. See below:
registry:
bigmac: ~/websites/biomart-perl[arek] cat conf/marina.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "marina"
displayName = "Marina"
databaseType = "postgres"
host = "localhost"
port = "5432"
database = "marina"
schema = "public"
user = "arek"
password = ""
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
and the starup:
bigmac: ~/websites/biomart-perl[arek] perl bin/configure.pl -r
conf/marina.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
rm /Users/arek/websites/biomart-perl/conf/templates/default/*.ttc
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]:
Cached Registry Unavailable...
Running Complete Clean...
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... Marina ................... 001/002 ... wells_tbl
................................. (RDBMS) localhost:5432
................ OK
default ... Marina ................... 002/002 ... reagents_tbl
.............................. (RDBMS) localhost:5432 ................
OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 2/2 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
.... 100%
bigmac: ~/websites/biomart-perl[arek] apache $PWD
Processing Cached Registry:
/Users/arek/websites/biomart-perl/conf/cachedRegistries/
marina.xml.cached
All I can advise at this stage is to throw away all the code, re-check
the latest 'release-0_5' branch and
try to configure again.
a.
a.
>
> Hi Marina,
> yes this looks a bit weird. Your xml is pulled out ok but then it
dies
> on templates.
> There is nothing that immidiately strikes me as being a possible
> problem
> Is there a chance that you could send us (off the list) your xml so
we
> could investigate
> a bit here?
>
> (you need to use MEditor, connect to your mart and 'save all' to
the
> file) and please
> send us this file (probably tar.gz)
>
>
-----------------------------------------------------------------------
-
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
-----------------------------------------------------------------------
-
-------
------------------------------------------------------------------------
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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