On 12 Jan 2007, at 17:08, Richard Holland wrote:
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What you're talking about is linking two datasets in the same query.
You
have to do this by establishing an exportable and importable in each
dataset - this means identifying the attributes in one dataset whose
values can be applied to the filters in the other dataset to produce a
meaningful join, and vice versa.
Then, you have a choice. You could leave your registry as it is (a
single MartDBLocation with includeDatasets containing an empty string
so
that all datasets are picked up automatically), which will
automatically
allow users to choose the second dataset by clicking on the second
dataset link on the left, therefore joining it to the results from the
first dataset. Or, you can use placeholder filters/attributes to point
filters from one dataset at filters in the other whilst appearing
visually to the user to all be in the same place.
I'm copying Arek on this in case he has any helpful things to add.
or ideally have a dimension "container" in the reagents dataset
and the dimension "reagent" in the container dataset. Then this would
be the easiest as they both would appear in one dataset and you
wouldn't have
to do anything special ei exportables, importables or pointer
attributes.
It is interesting that MBuilder did not pick up this option.
Is there anything in common between container and reagent dataset?
eg an identifer of some sort? If so tell me what it is and I'll
investigate
why the transformation like this has not happened and get back to you
a.
cheers,
Richard
PS. The pairwise drop-downs in compara mart don't refer to different
datasets in each dropdown - each unique combination of the three
dropdowns refers to just one dataset. This was something we set up
specifically for Compara, it's not intended for wider use.
Marina Olhovsky wrote:
Hi Richard,
Sorry, I didn't express myself well: I want multiple datasets
belonging
to the same database and schema to show in Martview in SEPARATE
dropdown
lists - similar to the Ensembl search page, where Pairwise Alignment
database is selected - you see 3 different dropdowns in the Dataset
section. The rationale is being able to link search information
between
different datasets. E.g. in my case MBuilder created 2 separate
datasets for 'reagents' and 'containers'. I want to search for
reagents
stored in container XYZ - i.e. I need all the filters from both
datasets
shown in the filters page. That was, in a sense, what I tried doing
from the beginning. I appreciate any suggestions you could give.
Thanks so much.
Best regards,
Marina.
---------------------------------------------------------
Marina Olhovsky
Software Engineer, Pawson Laboratory
Mount Sinai Hospital
600 University Avenue, Room 1060
Toronto, Ontario, M5G 1X5
[EMAIL PROTECTED]
---------------------------------------------------------
-----Original Message-----
From: Richard Holland [mailto:[EMAIL PROTECTED]
Sent: Fri 1/12/2007 3:55 AM
To: Marina Olhovsky
Cc: [EMAIL PROTECTED]
Subject: Re: URL registry config
The way to get more than one dataset appearing in MartView is to
enclose
multiple MartDBLocation/MartURLLocations inside a virtualSchema tag:
<MartRegistry>
<virtualSchema name="bloggs" default="1">
<MartDBLocation ..... />
<MartDBLocation ..... />
<MartURLLocation ..... />
<MartURLLocation ..... />
</virtualSchema>
</MartRegistry>
Exactly one of the locations inside the virtualSchema tag must also
have
default="1" inside it. This is the one that will be selected by
default
when the user starts a new query.
The datasets will appear in the interface in the same order as they
appear in the registry file.
You can have multiple virtualSchemas in the registry - if so, an
additional Schema drop-down appears in the MartView automatically to
allow users to switch between them. This way you can keep many
datasets
with the same name - this can be useful when presenting archived
copies
of datasets, for instance.
Lastly, your error message is caused because your MartURLLocation
points
to itself in effect. MartURLLocations need to point to an existing
MartView server that is already running at the time that you run the
configure script. In essence it is saying 'take all the datasets from
that server over there and make them appear like they're on this one'.
cheers,
Richard
Marina Olhovsky wrote:
Hi Arek/Richard,
I'm trying to custommize my Martview to look like the one on your
server, making several datasets available for search. I've changed
the
XML config file from MartDBLocation to MartURLLocation as follows:
<MartRegistry>
<MartURLLocation
name = "test_mart"
displayName = "test_mart"
host = "localhost"
port = "5555"
visible = "1"
default = "1"
includeDatasets = "my_dataset"
martUser = ""
/>
</MartRegistry>
I'm getting the following command-line errors:
% perl bin/configure.pl --clean -r conf/myRegistry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n
Checking several common Apache locations...done.
Select either one of the detected httpd paths on the list, OR enter
the
path you wish to use:
/usr/local/bin/httpd
/usr/sbin/httpd2
[1]:
Got usable Apache in /usr/local/bin/httpd, probing for version &
ModPerl
configuration
Have Apache DSO-support and ModPerl library file present,
configuring
ModPerl in httpd.conf.
Enter the server host OR default [p53]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Libdir /home/olhovsky/biomart-perl/lib is not in @INC, adding to
@INC
Optional setting for serverVirtualSchema in MartURLLocation
location:test_mart not defined - setting to default values
Optional setting for path in MartURLLocation location:test_mart not
defined - setting to default values
Use of uninitialized value in string eq at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Configuration/
MartURLLocation.pm
line 135.
ERROR something wrong with your registry:
No datasets available with given parameters for
Location:
test_mart
Trace begun at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line
1001
BioMart::Initializer::_populateRegistry('BioMart::
Initializer=HASH(0x93a05c4)')
called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x93a05c4)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line
393
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x93a05c4)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line
160
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x93a05c4)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action',
'clean',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/configureBioMart.pl line 339
eval {...} at /home/olhovsky/biomart-perl/bin/configureBioMart.pl
line 338
Your help is most appreciated.
Best regards,
Marina.
---------------------------------------------------------
Marina Olhovsky
Software Engineer, Pawson Laboratory
Mount Sinai Hospital
600 University Avenue, Room 1060
Toronto, Ontario, M5G 1X5
[EMAIL PROTECTED]
---------------------------------------------------------
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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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