make drop down

Re: make drop down

hi Rochak,

why dont you first verify against live ensembl (using MartEditor) and 
see how your settings for the said filter differ from Region->Chromosome 
filter in ensembl.

Cheers
Syed

Rochak Neupane wrote:
> Does the "make drop down" context menu item not work if the field of 
> which unique values are to be the options contain multiple words?
> In the past, I've used it to to automate options creation, but before 
> the option's values were always one word.
> 
> I was trying to make a drop down menu in marteditor. But when i click 
> "make drop down" from the context menu to automate the choices, no 
> options are generated. the filter has its type changed to list, 
> displayType to list and style to menu.
> 
> I checked that the field, tableConstraint, and key are correct. So the 
> only change is that the field, which i want turned into options, has 
> multiple words.
> I also manually created the options, but the filter is not displayed on 
> the web page. Hide display is off.
> 
> any  insights?
> 
> Thanks,
> Rochak

Using MartView on vega mart with additional tables

Hello,

I am struggling to get the web-interface MartView to display
interesting data for an extended vega mart.

The extended vega mart is build from the homo sapiens vega schema with
an additional table 'gene_test' that has two columns 'gene_id' and
'annotation'. During the mart building process (with MartBuilder), I
can see in the dataset view that the key of the new table is correctly
associated with the gene table. I have then created the mart and after
updating the meta tables using MartEditor I got an additional choice
'NEW_ATTRIBUTES' besides 'Features', "Sequences' and 'Structures' for
constructing queries in MartView and MartExplorer. In MartEditor I
then dragged and dropped the 'AttributeGroup: new_attributes' so that
it now appears under 'AttributePage: feature_page'. I ran the mart
configuration again (perl bin/configure.pl ...) and now I can select
'Annotation 1077' besides other entries (e.g. 'VEGA Gene ID') in the
'Feature' panel. When I use MartExplorer, everything works fine, so
that I can query the mart and get results accordingly. However, in
MartView I can select the same checkboxes as in MartExplorer, but I
get the following output: "Validation Error: Attributes from multiple
attribute pages are not allowed".

Does anyone know what steps need to be undertaken in order to get the
same query results in MartView as I get in MartExplorer? Is it not
possible to arbitrarily move AttributeGroups and AttributeCollections
around in MartEditor?

Thanks,
Joachim

--

-- 
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom

RE: Using MartView on vega mart with additional tables

Dear Joachim,

Could you please send me (not the mart-dev list as it filters out attachments) your configuration files?
You can generate those XML files using MartEditor: File => Save All. You will find two files (???.xml and
???.template.xml) being saved in the folder you just chose. Please send me both files.

Best regards,
Junjun

> -----Original Message-----
> From: owner-mart-dev <at> ebi.ac.uk 
> [mailto:owner-mart-dev <at> ebi.ac.uk] On Behalf Of Joachim Baran
> Sent: Wednesday, April 08, 2009 11:47 AM
> To: mart-dev <at> ebi.ac.uk
> Subject: [mart-dev] Using MartView on vega mart with additional tables
> 
> Hello,
> 
> I am struggling to get the web-interface MartView to display 
> interesting data for an extended vega mart.
> 
> The extended vega mart is build from the homo sapiens vega 
> schema with an additional table 'gene_test' that has two 
> columns 'gene_id' and 'annotation'. During the mart building 
> process (with MartBuilder), I can see in the dataset view 
> that the key of the new table is correctly associated with 
> the gene table. I have then created the mart and after 
> updating the meta tables using MartEditor I got an additional 
> choice 'NEW_ATTRIBUTES' besides 'Features', "Sequences' and 
> 'Structures' for constructing queries in MartView and 
> MartExplorer. In MartEditor I then dragged and dropped the 
> 'AttributeGroup: new_attributes' so that it now appears under 
> 'AttributePage: feature_page'. I ran the mart configuration 
> again (perl bin/configure.pl ...) and now I can select 
> 'Annotation 1077' besides other entries (e.g. 'VEGA Gene ID') 
> in the 'Feature' panel. When I use MartExplorer, everything 
> works fine, so that I can query the mart and get results 
> accordingly. However, in MartView I can select the same 
> checkboxes as in MartExplorer, but I get the following 
> output: "Validation Error: Attributes from multiple attribute 
> pages are not allowed".
> 
> Does anyone know what steps need to be undertaken in order to 
> get the same query results in MartView as I get in 
> MartExplorer? Is it not possible to arbitrarily move 
> AttributeGroups and AttributeCollections around in MartEditor?
> 
> Thanks,
> Joachim
> 
> --
> B.1079 Michael Smith Building
> Faculty of Life Sciences
> The University of Manchester
> Oxford Road
> Manchester
> M13 9PT
> United Kingdom
> 

Re: Using MartView on vega mart with additional tables

Hi Joachim,

Could you please send us:

a- the query using XML button on MartView page
b- Using MartEditor, do 'Save All'. Send us these XML files.

Please send us the attachments off the list as mart-dev wont accept 
attachments.

Thanks
Syed

Joachim Baran wrote:
> Hello,
> 
> I am struggling to get the web-interface MartView to display
> interesting data for an extended vega mart.
> 
> The extended vega mart is build from the homo sapiens vega schema with
> an additional table 'gene_test' that has two columns 'gene_id' and
> 'annotation'. During the mart building process (with MartBuilder), I
> can see in the dataset view that the key of the new table is correctly
> associated with the gene table. I have then created the mart and after
> updating the meta tables using MartEditor I got an additional choice
> 'NEW_ATTRIBUTES' besides 'Features', "Sequences' and 'Structures' for
> constructing queries in MartView and MartExplorer. In MartEditor I
> then dragged and dropped the 'AttributeGroup: new_attributes' so that
> it now appears under 'AttributePage: feature_page'. I ran the mart
> configuration again (perl bin/configure.pl ...) and now I can select
> 'Annotation 1077' besides other entries (e.g. 'VEGA Gene ID') in the
> 'Feature' panel. When I use MartExplorer, everything works fine, so
> that I can query the mart and get results accordingly. However, in
> MartView I can select the same checkboxes as in MartExplorer, but I
> get the following output: "Validation Error: Attributes from multiple
> attribute pages are not allowed".
> 
> Does anyone know what steps need to be undertaken in order to get the
> same query results in MartView as I get in MartExplorer? Is it not
> possible to arbitrarily move AttributeGroups and AttributeCollections
> around in MartEditor?
> 
> Thanks,
> Joachim
> 

RE: Using MartView on vega mart with additional tables

Dear Joachim,

Thanks for sending the XML files, I looked into it and started MartView with it, everything seems fine to me.
Could you please let me know which attributes you chose when error occurred? Or even better: after you
chose those attributes, you can just click the "XML" button on the top right corner of MartView web
interface, then you will get the query in XML format, please send it to me. I would try them here to reproduce
the problem.

From what you described in your first email, it seemed you had run configure.pl twice, one was before
drag-drop the new attribute, and the other was after that. This leads me thinking you might have conflict
GUI templates. If you were running configure.pl without --clean option, please make sure you do so, this
may help solve the problem.

Kind regards,
Junjun

> -----Original Message-----
> From: owner-mart-dev <at> ebi.ac.uk 
> [mailto:owner-mart-dev <at> ebi.ac.uk] On Behalf Of Junjun Zhang
> Sent: Wednesday, April 08, 2009 12:08 PM
> To: Joachim Baran; mart-dev <at> ebi.ac.uk
> Subject: RE: [mart-dev] Using MartView on vega mart with 
> additional tables
> 
> Dear Joachim,
> 
> Could you please send me (not the mart-dev list as it filters 
> out attachments) your configuration files? You can generate 
> those XML files using MartEditor: File => Save All. You will 
> find two files (???.xml and ???.template.xml) being saved in 
> the folder you just chose. Please send me both files.
> 
> Best regards,
> Junjun
>  
> 
> > -----Original Message-----
> > From: owner-mart-dev <at> ebi.ac.uk
> > [mailto:owner-mart-dev <at> ebi.ac.uk] On Behalf Of Joachim Baran
> > Sent: Wednesday, April 08, 2009 11:47 AM
> > To: mart-dev <at> ebi.ac.uk
> > Subject: [mart-dev] Using MartView on vega mart with 
> additional tables
> > 
> > Hello,
> > 
> > I am struggling to get the web-interface MartView to display 
> > interesting data for an extended vega mart.
> > 
> > The extended vega mart is build from the homo sapiens vega 
> schema with 
> > an additional table 'gene_test' that has two columns 'gene_id' and 
> > 'annotation'. During the mart building process (with 
> MartBuilder), I 
> > can see in the dataset view that the key of the new table 
> is correctly 
> > associated with the gene table. I have then created the 
> mart and after 
> > updating the meta tables using MartEditor I got an 
> additional choice 
> > 'NEW_ATTRIBUTES' besides 'Features', "Sequences' and 
> 'Structures' for 
> > constructing queries in MartView and MartExplorer. In MartEditor I 
> > then dragged and dropped the
> > 'AttributeGroup: new_attributes' so that it now appears under
> > 'AttributePage: feature_page'. I ran the mart configuration again 
> > (perl bin/configure.pl ...) and now I can select 'Annotation 1077' 
> > besides other entries (e.g. 'VEGA Gene ID') in the 'Feature' panel. 
> > When I use MartExplorer, everything works fine, so that I can query 
> > the mart and get results accordingly. However, in MartView I can 
> > select the same checkboxes as in MartExplorer, but I get 
> the following
> > output: "Validation Error: Attributes from multiple attribute pages 
> > are not allowed".
> > 
> > Does anyone know what steps need to be undertaken in order 
> to get the 
> > same query results in MartView as I get in MartExplorer? Is it not 
> > possible to arbitrarily move AttributeGroups and 
> AttributeCollections 
> > around in MartEditor?
> > 
> > Thanks,
> > Joachim
> > 
> > --
> > B.1079 Michael Smith Building
> > Faculty of Life Sciences
> > The University of Manchester
> > Oxford Road
> > Manchester
> > M13 9PT
> > United Kingdom
> > 
> 

Re: Using MartView on vega mart with additional tables

Hello Junjun,

2009/4/8 Junjun Zhang <Junjun.Zhang <at> oicr.on.ca>:
> If you were running configure.pl without --clean option, please make sure you do so, this may help solve
the problem.
This solved the problem!

Thank you very much..

Best Wishes,
Joachim

--

-- 
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom

Attribute NOT FOUND

Hi to all,

I am trying to invoke the following R code,

ensembl = useMart("ensembl");
ensembl = useDataset("drerio_gene_ensembl", mart=ensembl);
ids <- getBM(attributes = c("ensembl_gene_id","agilent_g2519F"), filters 
= "with_agilent_g2519f", values =TRUE,mart=ensembl);

but the result is always the same:

1 Query ERROR: caught BioMart::Exception::Usage: Attribute 
agilent_g2519F NOT FOUND
Error en getBM(attributes = c("ensembl_gene_id", "agilent_g2519F"), 
filters = c("with_agilent_g2519f"),  :
  Number of columns in the query result doesn't equal number of 
attributes in query.  This is probably an internal error, please report.

However, if I retrieve the list of available attributes I can see 
"agilent_g2519F" in the list.

Can you help me? There is a mistake in my code or there is something 
wrong in biomart?

Thanks in advance,
Rubén.

Re: Attribute NOT FOUND

Hi Ruben,
I suspect that there is inconsistency between the spelling of the  
internal name of the filter and the attribute. I will look into it and  
try to fix it for release 54 (approx end of April). Many apologies for  
any inconvenience caused.
Regards,
Rhoda

On 14 Apr 2009, at 12:27, Ruben wrote:

> Hi to all,
>
> I am trying to invoke the following R code,
>
> ensembl = useMart("ensembl");
> ensembl = useDataset("drerio_gene_ensembl", mart=ensembl);
> ids <- getBM(attributes = c("ensembl_gene_id","agilent_g2519F"),  
> filters = "with_agilent_g2519f", values =TRUE,mart=ensembl);
>
> but the result is always the same:
>
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute  
> agilent_g2519F NOT FOUND
> Error en getBM(attributes = c("ensembl_gene_id", "agilent_g2519F"),  
> filters = c("with_agilent_g2519f"),  :
> Number of columns in the query result doesn't equal number of  
> attributes in query.  This is probably an internal error, please  
> report.
>
> However, if I retrieve the list of available attributes I can see  
> "agilent_g2519F" in the list.
>
> Can you help me? There is a mistake in my code or there is something  
> wrong in biomart?
>
> Thanks in advance,
> Rubén.

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

Re: Attribute NOT FOUND

Hi Rhoda,

ok, thanks for your answer.

Rubén.

Rhoda Kinsella wrote:
> Hi Ruben,
> I suspect that there is inconsistency between the spelling of the 
> internal name of the filter and the attribute. I will look into it and 
> try to fix it for release 54 (approx end of April). Many apologies for 
> any inconvenience caused.
> Regards,
> Rhoda
>
>
> On 14 Apr 2009, at 12:27, Ruben wrote:
>
>> Hi to all,
>>
>> I am trying to invoke the following R code,
>>
>> ensembl = useMart("ensembl");
>> ensembl = useDataset("drerio_gene_ensembl", mart=ensembl);
>> ids <- getBM(attributes = c("ensembl_gene_id","agilent_g2519F"), 
>> filters = "with_agilent_g2519f", values =TRUE,mart=ensembl);
>>
>> but the result is always the same:
>>
>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute 
>> agilent_g2519F NOT FOUND
>> Error en getBM(attributes = c("ensembl_gene_id", "agilent_g2519F"), 
>> filters = c("with_agilent_g2519f"),  :
>> Number of columns in the query result doesn't equal number of 
>> attributes in query.  This is probably an internal error, please report.
>>
>> However, if I retrieve the list of available attributes I can see 
>> "agilent_g2519F" in the list.
>>
>> Can you help me? There is a mistake in my code or there is something 
>> wrong in biomart?
>>
>> Thanks in advance,
>> Rubén.
>
> Rhoda Kinsella Ph.D.
> Ensembl Bioinformatician,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>