Hello Peter,

Thanks very much for this - I'm sure many will find it very helpful.  I've 
applied your patch to changeset revision 8096:0c56502c7fd7, which will be 
included in the next Galaxy release currently scheduled for  next Friday (not 
today's currently scheduled release).

Thanks again,

Greg Von Kuster


On Oct 22, 2012, at 7:03 AM, Peter Cock wrote:

> FAO the Galaxy dev team,
> 
> I've tested a patch (at end of email) which issues a warning if loading
> a loc file with inconsistent numbers of tabs. In the case of blastdb_p.loc
> this would result in showing the warning three times, since currently
> Galaxy appears to reload a *.loc file for each tool using it.
> 
> (If the error happens to be on the first list, then the warning is triggered
> for all the following lines in the file - because they won't have the same
> number of fields as the first line.)
> 
> Could someone apply this to the trunk as is, or tell me if you would
> prefer it as a pull request on bitbucket?
> 
> Furthermore, would a more invasive change to treat this as an error
> condition be acceptable?
> 
> Thanks,
> 
> Peter
> 
> 
> On Sun, Oct 21, 2012 at 5:53 AM, Fields, Christopher J
> <cjfie...@illinois.edu> wrote:
>> Yes, have to agree there, an error would be more informative.
>> 
>> chris
>> 
>> On Oct 20, 2012, at 2:38 PM, Shane Sturrock <sh...@biomatters.com> wrote:
>> 
>>> That would certainly have saved me a fair bit of time since the only 
>>> indication I got was an empty set of quotes in the error log.  I always 
>>> feel like tabs aren't the best separators for these sorts of files anyway 
>>> since they are usually invisible but since that isn't likely to change, 
>>> making it more obvious what the problem is would be the best approach.
>>> 
>>> Shane
>>> 
>>> On 21/10/2012, at 1:44 AM, Peter Cock wrote:
>>>> 
>>>> Another idea would be for Galaxy to issue a clear error if a loc file has 
>>>> an inconsistent  number of fields/tabs per line.
>>>> 
>>>> Peter
>>>> 
> 
> Suggested patch:
> 
> $ hg diff lib/galaxy/tools/parameters/dynamic_options.py
> diff -r c05a680cbc80 lib/galaxy/tools/parameters/dynamic_options.py
> --- a/lib/galaxy/tools/parameters/dynamic_options.py  Fri Oct 19
> 15:56:51 2012 +0100
> +++ b/lib/galaxy/tools/parameters/dynamic_options.py  Mon Oct 22
> 11:59:04 2012 +0100
> @@ -471,6 +471,7 @@
> 
>     def parse_file_fields( self, reader ):
>         rval = []
> +        field_count = None
>         for line in reader:
>             if line.startswith( '#' ) or ( self.line_startswith and
> not line.startswith( self.line_startswith ) ):
>                 continue
> @@ -478,6 +479,17 @@
>             if line:
>                 fields = line.split( self.separator )
>                 if self.largest_index < len( fields ):
> +                    if not field_count:
> +                        field_count = len(fields)
> +                    elif field_count != len(fields):
> +                        try:
> +                            name = reader.name
> +                        except AttributeError:
> +                            name = "a configuration file"
> +                        #Perhaps this should be an error, but even a
> warning is useful
> +                        log.warn("Inconsistent number of fields (%i
> vs %i) in %s using "
> +                                 "separator %r, check line: %r" \
> +                                 % (field_count, len(fields), name,
> self.separator, line))
>                     rval.append( fields )
>         return rval
> 
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