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Kiran Mukhyala | 7 Jan 2010 19:56

Re: update a mart

Thanks Joachim, that was a very useful blogpost! I successfully built my
local ensembl mart by following your instructions. As you predicted I
did see some error messages like:

Compiler warnings:
  line 170: Attribute 'graph' outside of element.
  line 183: Attribute 'autoCompletion' outside of element.
"Problem finding a placeholder dataset for chromosome_name push actions.
Have you set the correct databases in the schema database connection
box?"

which I ignored for now.  

One problem I have right now is that in MartView, I don't see the
Microarray section in the Feature Attributes page under the External
attributes group. I do see the microarray attributes in MartEditor when
I import from my local mart. 

During the 'Upload All' step, I uploaded the following xml files:
gene_ensembl_template.template.xml
probe_set_template.template.xml
probe_template.template.xml
hsapiens_gene_ensembl.xml
(as I was not interested in the other species)

But when I import (either from martdb or localmart) I only see
'gene_ensembl' as the template, I don't see the probe or probe_set
templates. I am not sure if this is related to the missing Microarray
attributes problem.
(Continue reading)

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Joachim Baran | 7 Jan 2010 20:21
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Re: update a mart

Hello Kiran,

2010/1/7 Kiran Mukhyala <mukhyala.kiran <at> gene.com>:
> One problem I have right now is that in MartView, I don't see the
> Microarray section in the Feature Attributes page under the External
> attributes group. I do see the microarray attributes in MartEditor when
> I import from my local mart.
We have the same problem, but we ignored it for now since we do not
focus on that data in particular.

It would be great if this issue could be resolved, because so far I
always assumed that uploading the meta-data into the custom-build mart
should be sufficient.

BW,
Joachim

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Joachim Baran | 13 Jan 2010 20:40
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Enabling Count/Results buttons

Hello,

I am having trouble finding the code that enables/disables the 'Count'
and 'Result' buttons in MartView. I assume it is somewhere hidden in
either Web.pm or perhaps in the .tt template files, but I am not sure
what to look for. Basically, I would like to enable my own form
elements that I have added to the interface, as soon as the user has
chosen a dataset.

Thanks,
Joachim

--

-- 
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
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Syed Haider | 13 Jan 2010 21:04
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Re: Enabling Count/Results buttons

Hello Joachim,

have a loot at:

biomart-perl/conf/templates/default/menupanel.tt

Best,
Syed

Joachim Baran wrote:
> Hello,
> 
> I am having trouble finding the code that enables/disables the 'Count'
> and 'Result' buttons in MartView. I assume it is somewhere hidden in
> either Web.pm or perhaps in the .tt template files, but I am not sure
> what to look for. Basically, I would like to enable my own form
> elements that I have added to the interface, as soon as the user has
> chosen a dataset.
> 
> Thanks,
> Joachim
>
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Joachim Baran | 13 Jan 2010 22:20
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Re: Enabling Count/Results buttons

2010/1/13 Syed Haider <syed.haider <at> oicr.on.ca>:
> biomart-perl/conf/templates/default/menupanel.tt
I had a look at that file, which is also the place where I inserted my
own form elements. Whilst I can see that the buttons check 'onclick'
whether there is a dataset available, I cannot see where the buttons
are activated though. By the latter I mean un-greyed-out, i.e. made
click-able.

As a side note, I have to admit that the function of handle_request in
Web.pm is not quite clear to me. It seems to get called when I click
my 'submit' button, but only when the user has freshly selected a
dataset. Once the user has run any other query and pressed 'Results',
it appears to me that the code which I have put right before the line
'my $returnaAfterSave = 0;' in handle_request of Web.pm is not called
anymore. I find that strange, since I only surround my code with a 'if
($CGI->Vars()->{'myButton'})'. Is handle_request not called anymore
after a query is made?

Sorry for asking these programming questions -- especially as the code
will be obsolete soon -- but I am sure that there is a simple and
straightforward solution to my questions that I am just not being able
to see.

Thanks,
Joachim

--

-- 
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
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Syed Haider | 13 Jan 2010 23:12
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Re: Enabling Count/Results buttons

Joachim,

please have a look at the htdocs/martview/martview_template.css

some of the buttons related functions are there.

Best,
Syed

Joachim Baran wrote:
> 2010/1/13 Syed Haider <syed.haider <at> oicr.on.ca>:
>> biomart-perl/conf/templates/default/menupanel.tt
> I had a look at that file, which is also the place where I inserted my
> own form elements. Whilst I can see that the buttons check 'onclick'
> whether there is a dataset available, I cannot see where the buttons
> are activated though. By the latter I mean un-greyed-out, i.e. made
> click-able.
> 
> As a side note, I have to admit that the function of handle_request in
> Web.pm is not quite clear to me. It seems to get called when I click
> my 'submit' button, but only when the user has freshly selected a
> dataset. Once the user has run any other query and pressed 'Results',
> it appears to me that the code which I have put right before the line
> 'my $returnaAfterSave = 0;' in handle_request of Web.pm is not called
> anymore. I find that strange, since I only surround my code with a 'if
> ($CGI->Vars()->{'myButton'})'. Is handle_request not called anymore
> after a query is made?
> 
> Sorry for asking these programming questions -- especially as the code
> will be obsolete soon -- but I am sure that there is a simple and
(Continue reading)

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David Withers | 14 Jan 2010 02:02
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Biomart Registry down

Hi,

The Biomart registry at
http://www.biomart.org/biomart/martservice?type=registry is currently
returning:

non-BioMart die():
not well-formed (invalid token) at line 1, column 11797, byte 11797 at
/usr/lib/perl5/XML/Parser.pm line 187

David.
--

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David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
+44 (0)161 275 0683
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Syed Haider | 14 Jan 2010 02:15
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Re: Biomart Registry down

Hi David,

apologies for the inconvenience, this is being resolved at the moment, 
wont take long.

Best,
Syed

David Withers wrote:
> Hi,
> 
> The Biomart registry at
> http://www.biomart.org/biomart/martservice?type=registry is currently
> returning:
> 
> non-BioMart die():
> not well-formed (invalid token) at line 1, column 11797, byte 11797 at
> /usr/lib/perl5/XML/Parser.pm line 187
> 
> David.
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Junjun Zhang | 14 Jan 2010 04:47
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RE: Biomart Registry down

The problem has been fixed, sorry for the inconvenience.
Junjun

________________________________________
From: owner-mart-dev <at> ebi.ac.uk [owner-mart-dev <at> ebi.ac.uk] On Behalf Of Syed Haider [syed.haider <at> oicr.on.ca]
Sent: Wednesday, January 13, 2010 8:15 PM
To: David Withers
Cc: mart-dev <at> ebi.ac.uk
Subject: Re: [mart-dev] Biomart Registry down

Hi David,

apologies for the inconvenience, this is being resolved at the moment,
wont take long.

Best,
Syed

David Withers wrote:
> Hi,
>
> The Biomart registry at
> http://www.biomart.org/biomart/martservice?type=registry is currently
> returning:
>
> non-BioMart die():
> not well-formed (invalid token) at line 1, column 11797, byte 11797 at
> /usr/lib/perl5/XML/Parser.pm line 187
>
> David.
(Continue reading)

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Arek Kasprzyk | 14 Jan 2010 17:07
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CyanoBase mart interface


FYI,

A new BioMart interface is now available for CyanoBase housed at the Kazusa
Genome institute. The database contains the data on cyanobacteria species
information, complete genome sequences, genome-scale experiment data, gene
information, gene annotations and mutant information.

http://mart.kazusa.or.jp/

a.
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Gmane