data_columns

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data_columns

Jorrit Boekel
Dear list,

I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces.

Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does
if not dataset.metadata.columns: on line 1184 of the above mentioned file.

Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses.


I’m on changeset 14567:007f6a80629a in galaxy-dist.
 
cheers,

Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden




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Re: data_columns

Daniel Blankenberg
Hi Jorrit,

Are you subclassing your tsv datatypes from tabular?

If you can post your tool xml and datatype_conf.xml additions then we should be to provide more assistance.


Thanks for using Galaxy,

Dan


On Nov 7, 2014, at 12:27 PM, Jorrit Boekel <[hidden email]> wrote:

> Dear list,
>
> I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces.
>
> Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does
> if not dataset.metadata.columns: on line 1184 of the above mentioned file.
>
> Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses.
>
>
> I’m on changeset 14567:007f6a80629a in galaxy-dist.
>
> cheers,
> —
> Jorrit Boekel
> Proteomics systems developer
> BILS / Lehtiö lab
> Scilifelab Stockholm, Sweden
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>


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Re: data_columns

Jorrit Boekel
No, I am not subclassing from Tabular. But when I do, it suddenly works. Thanks loads Dan!

cheers,

Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



On 07 Nov 2014, at 19:07, Daniel Blankenberg <[hidden email]> wrote:

> Hi Jorrit,
>
> Are you subclassing your tsv datatypes from tabular?
>
> If you can post your tool xml and datatype_conf.xml additions then we should be to provide more assistance.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Nov 7, 2014, at 12:27 PM, Jorrit Boekel <[hidden email]> wrote:
>
>> Dear list,
>>
>> I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces.
>>
>> Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does
>> if not dataset.metadata.columns: on line 1184 of the above mentioned file.
>>
>> Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses.
>>
>>
>> I’m on changeset 14567:007f6a80629a in galaxy-dist.
>>
>> cheers,
>> —
>> Jorrit Boekel
>> Proteomics systems developer
>> BILS / Lehtiö lab
>> Scilifelab Stockholm, Sweden
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/