Hi Daniel,
Thanks for the answer.
In my hands it does not work unfortunately but I’m a total python dummy.
Marc
From: Daniel Blankenberg [mailto:dan@bx.psu.edu]
Sent: Friday, February 22, 2013 4:10 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Filter tool: how to override automatic guessing of column types ?
Hi Marc,
You can force the metadata detection to search your entire file by adding a new set_meta method to your datatype class, e.g. (untested):
def set_meta( self, *args, **kwd ):
kwd['max_data_lines'] =
None
kwd['max_guess_type_data_lines']
= None
return super( CloneAdminTable, self ).set_meta( *args, **kwd )
and also define the default values for your datatype:
"""Add metadata elements"""
MetadataElement( name="column_types", default=['str','str','int','str','int'],
desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=['str','str','int','str','int']
)
MetadataElement( name="column_names",
default= ['Name', 'SeqInAlignment', 'Family', 'Animal/library', 'NR
Cluster'], desc="Column names",
readonly=True, visible=False,
optional=True, no_value=['Name', 'SeqInAlignment', 'Family', 'Animal/library', 'NR
Cluster'] )
alternatively, you can rewrite the set_meta method to handle setting the metadata in anyway that you like.
Thanks for using Galaxy,
Dan
On Feb 22, 2013, at 9:24 AM, Marc Logghe wrote:
Hi,
I have an issue with filtering using the Filter tool in the sense that the first line is considered invalid and I think it has to do with the automatic guessing
of column types.
The condition is like: c4 !='XXX'
The value of c4 for the first line is ‘NA’
When the paster.log is checked one can see that the last argument for filtering.py are the column types:
"str,str,int,int,int ". As you can see for whatever reason, the system thinks c4 is an int, it should be ‘str’. Indeed, most values for that field look like
numbers but they should be treated as string types.
In an attempt to override the guessing, a custom tabular type was defined in lib/galaxy/datatypes/tabular.py as such:
class CloneAdminTable( Tabular ):
"""
Tabular format Clone Administration
"""
column_names = ['Name', 'SeqInAlignment', 'Family', 'Animal/library', 'NR Cluster']
column_types = ['str','str','int','str','int']
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
But that seems not to help very much; the system still guesses the column types.
Any idea how to solve this ?
Thanks and regards,
Marc
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