Hi Mummi,
I haven't tested setting the attributes and filters using a URL a lot,
but what I did test all worked fine (except on the PRIDE BioMart, where
a problem with the filter configuration messed it up, but that's not a
URL problem).
Regards,
Roger.
Gudmundur A. Thorisson wrote:
Thanks Syed. From your explanation (and I'll RTFM as well!) it seems
the URLs do in fact do what I was expecting them to do. I must have
just done my test URL wrong! I'll try and do it properly this time and
get back to you if I am still stuck.
Mummi, Leicester
On 22 Feb 2008, at 13:46, Syed Haider wrote:
Hi Mummi,
We have a URL request (some call it direct URL, some call it URL API and
few other derivates), what it does is that it provides you with a
mechanism to write the query with attributes and filters preset. The
moment you fire it through web-browser against a BioMart server, it sets
all the attributes and filters in MartView and jumps directly to the
results page. From this point onwards, users can further modify the
selection. However, as you are well familiar with the session IDs system
of MartView, it does not show anything in address field of the browser,
just a session ID, which it creates from the set of attributes/filters
you supplied.
please see user-docs.pdf
page 68m section 6.7 MartView URL Requests
hope that explains it. Ensembl Genome browser is using the said
mechanism to jump directly to Ensembl MartView from Ensembl GENE VIEW,
CONTIG VIEW, EXON VIEW etc. please see the left panel on these views
where you will see options like:
Export Gene info in region
Export SNP info in region
Export Vega info in region
hope this explains these requests.
PS: if you are happy with the functioning and do not wish the MartView
to jump to results page, that I can help you to modify this.
cheers
syed
On Fri, 2008-02-22 at 10:27 +0000, Gudmundur A. Thorisson wrote:
Syed, we're looking to do a similar thing with our project over here
in Leicester, with respect to canned queries and also URLs from
various pages on our site. I'd like to ask you this: is there
currently a way to pass a previous Mart query straight to the CGI-
script and not only have it show the results, but also pre-fill out
the filters and attributes and other parts of the form, so the user
could then modify the parameters at will?
I ask because it's far from straight-forward to construct martview
URLs, and the one time I tried this and got it show me results as
desired, it did not set up the filters & attributes. Or is the direct-
URL method supposed to do this and I was just missing some key pieces
from the URL?
Best regards,
Mummi, Leicester
Begin forwarded message:
From: Syed Haider <[EMAIL PROTECTED]>
Date: 22 February 2008 09:40:50 GMT
To: Roger Hull <[EMAIL PROTECTED]>
Cc: [email protected]
Subject: Re: [mart-dev] Adding canned queries to MartView
Hi Roger,
On Thu, 2008-02-21 at 23:33 +0000, Roger Hull wrote:
Hi Syed,
Thanks for your comments.
Well, just getting the xml of the biomart query is a possibility - it
might be possible to get back to what the user had selected/typed
from
the xml. But really I want to store my own data which makes it
easy to
reinitialise my form (in header.tt) to what the user had
selected/typed. (Also in some cases the same biomart query might have
arisen from more than one canned query.)
I guess AJAX is still an option for this job (with a simple perl
script to handle the request). Originally I thought of adding some
extra GET or POST parameters to the martview page to pass it this
information, but then I would need to be able to run a CGI script as
the page loads, which would involve hacking into your martview code.
As far as I can see you don't provide anywhere official for me to put
a CGI script which gets run when martview loads.
So I wondered if you have any other suggestions?
Looks to me the best option if you declare your own <form>...</
form> and
have a PERL CGI script talking to it. would be easy to maintain and
eliminates the need to hack martview.
cheers
syed
If I write such a conversion function (xml -> URL parameters) I'll
certainly share it.
Regards,
Roger.
Syed Haider wrote:
Hi Roger,
On Thu, 2008-02-21 at 17:36 +0000, Roger Hull wrote:
Hi,
I am in the process of adding some preformed queries to
MartView. The
user will select from a list of queries, possibly enter some
parameters (depending upon the query), and I have code (either
perl or
javascript) which will send the query to MartView using a Mart URL
Request. This works fine for my first test query. This is
implemented
in javascript added to header.tt and footer.tt.
My main problem is how best to find out using javascript what query
was requested when I come back into the martview page (so I can
reselect the user's canned query and re-enter the parameters).
Can you
suggest how I could do this, minimising the changes to the biomart
code as far as possible?
One idea I had is to handle the generation of the query URL from
perl,
and store the canned query somewhere (in a session parameter
maybe).
Then when I come back to the martview page, use an ajax request to
find out the details of the canned query.
by storing a 'canned query' in session param, what exactly do you
intend
to store ? is it just like an XML query which our XML button
generates ? then of course write a simple AJAX javascript request
and
ask from XML query. Currently, if you see the code behind OnClick
() of
XML button, it asks for XML by setting the target to a new
window, you
can call it exactly the same way and just avoid the target window
bit.
AJAX code is already available in javascript 'martview.js' which
can be
reused.
This seems rather complicated, but could all be done without
changing
any biomart code, just adding javascript to header.tt, and some
extra
scripts on my server to handle the requests. But if you can suggest
something better (simpler :-) ) I would be grateful.
Also, do you have handy perl and/or javascript functions to convert
between a query in xml format (for MartService) and URL format? It
would be convenient to store the canned queries as xml templates
(ready to fill in parameters), then convert the completed xml
into a
URL query. I guess I can write such a function if necessary, but
don't
want to re-invent the wheel.
I am afraid, we never felt a need to do this conversion, please feel
free to write such a conversion function. This may help other
users in
the future.
good luck!
cheers
syed
Regards,
Roger
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
