[BioMart Users] Martservice on 0.8 (rc6)

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[BioMart Users] Martservice on 0.8 (rc6)

Ellen Schofield
Hi All,

I am investigating using BioMart for our website and am trying to
understand BioMart 0.8.  To do so, I am using the martservice REST api
to interrogate the central biomart service and look at how things that
work are set up.

According to the docs (page 69, section 11.3.3.3), the following should
return me a list of datasets for a given mart name:-
http://central.biomart.org/martservice/datasets?mart=gene_ensembl

But all I am seeing is a page not found error.  Have I mis-understood
something or is something going wrong?  The same error (for a different
mart, of course) can be reproduced on the cancer portal and my own test
portal.  The martserive works for the portal & marts methods for me.

I look forward to hearing from somebody.

Yours,
Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215

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Re: [BioMart Users] Martservice on 0.8 (rc6)

Arek Kasprzyk
Dear Ellen,
The 0.8 REST api is not yet ready to be officially released. I have reviewed it recently and it requires a little bit of cleaning because the current implementation is not very intuitive. Basically, when you ask for a mart you actually supply its configuration as a parameter. It is our intenation that in the near future it will be changed such that you will be able to supply mart and it will use its default configuration while other configurations will become an optional parameter.

If you simply want to play with it, please supply config name as a mart argument.

e.g in the call:

http://central.biomart.org/martservice/marts

you willl get:

mart mart="gene_ensembl" config="gene_ensembl_config_3"

please use:

http://central.biomart.org/martservice/datasets?mart=gene_ensembl_config_3

instead of:

http://central.biomart.org/martservice/datasets?mart=gene_ensembl

I know this is unituitive and therefore i am reluctant to release it until we clean it up but if you want to play with it you are more than welcome

please look at the example on page 75 (11.3.5). this should make it more clear

a




On Wed, Dec 14, 2011 at 12:01 PM, Ellen Schofield <[hidden email]> wrote:
Hi All,

I am investigating using BioMart for our website and am trying to understand BioMart 0.8.  To do so, I am using the martservice REST api to interrogate the central biomart service and look at how things that work are set up.

According to the docs (page 69, section 11.3.3.3), the following should return me a list of datasets for a given mart name:-
http://central.biomart.org/martservice/datasets?mart=gene_ensembl

But all I am seeing is a page not found error.  Have I mis-understood something or is something going wrong?  The same error (for a different mart, of course) can be reproduced on the cancer portal and my own test portal.  The martserive works for the portal & marts methods for me.

I look forward to hearing from somebody.

Yours,
Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


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Re: [BioMart Users] Martservice on 0.8 (rc6)

Ellen Schofield
Thanks for the Arek, makes perfect sense and works a treat.  And thanks for the pointer to a different part of the docs.

Onwards and upwards :-)

Ellen.

On 14/12/11 17:27, Arek Kasprzyk wrote:
Dear Ellen,
The 0.8 REST api is not yet ready to be officially released. I have reviewed it recently and it requires a little bit of cleaning because the current implementation is not very intuitive. Basically, when you ask for a mart you actually supply its configuration as a parameter. It is our intenation that in the near future it will be changed such that you will be able to supply mart and it will use its default configuration while other configurations will become an optional parameter.

If you simply want to play with it, please supply config name as a mart argument.

e.g in the call:

http://central.biomart.org/martservice/marts

you willl get:

mart mart="gene_ensembl" config="gene_ensembl_config_3"

please use:

http://central.biomart.org/martservice/datasets?mart=gene_ensembl_config_3

instead of:

http://central.biomart.org/martservice/datasets?mart=gene_ensembl

I know this is unituitive and therefore i am reluctant to release it until we clean it up but if you want to play with it you are more than welcome

please look at the example on page 75 (11.3.5). this should make it more clear

a




On Wed, Dec 14, 2011 at 12:01 PM, Ellen Schofield <[hidden email]> wrote:
Hi All,

I am investigating using BioMart for our website and am trying to understand BioMart 0.8.  To do so, I am using the martservice REST api to interrogate the central biomart service and look at how things that work are set up.

According to the docs (page 69, section 11.3.3.3), the following should return me a list of datasets for a given mart name:-
http://central.biomart.org/martservice/datasets?mart=gene_ensembl

But all I am seeing is a page not found error.  Have I mis-understood something or is something going wrong?  The same error (for a different mart, of course) can be reproduced on the cancer portal and my own test portal.  The martserive works for the portal & marts methods for me.

I look forward to hearing from somebody.

Yours,
Ellen.

--
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


-- 
[hidden email]
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
Tel: 01223 763215

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users