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 12:08 PM
To: Marina Olhovsky
Cc: Arek Kasprzyk
Subject: Re: URL registry config
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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.
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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