Re: [galaxy-dev] Input parameter validation dependent on another parameter?
On Mon, Oct 21, 2013 at 1:55 PM, Bjoern Gruening wrote: > On 21.10.2013, Peter Cock wrote: >> On Mon, Oct 21, 2013 at 12:22 PM, Bjoern Gruening wrote: >> > >> > In the meantime you can use a code file to check your variables. Please >> > have a look at our wip DeSeq2 warpper: >> > >> > https://github.com/bgruening/galaxytools/tree/master/deseq2 >> > >> > or the excellent blog post from Ross: >> > >> > http://cloudimaging.blogspot.com.au/2013/05/input-validation-in-galaxy.html >> > >> > Hope that helps, >> > Bjoern >> >> Yes, a helper Python script linked via the tag containing >> a validate_input function may work here - thanks Bjoern :) >> >> However, according to the wiki the tag is deprecated :( > > Yes :( But I don't think it will go away really soon. To much tools > using it and no alternative is available. Thank you for those example links Bjoern. Ross mentioned on the blog post that we should see a "Log messages" popup from printing with the validate_input() function - I didn't, should that still work? I also found if I returned a non-empty dictionary in error_map (even with no error messages) then this was treated as a failure. Even with some working code to refer to this wasn't very straightforward, but I managed to get this to work: https://github.com/peterjc/pico_galaxy/commit/fee450c0bcee6935cc3e65da3e3281e96800f1b7 (I would love to write some unit tests for error conditions, something we talked about at GCC2013, but sadly that is still not possible yet.) Regards, Peter P.S. I wonder if the validate_input function is still used when running a tool via the API... ___ 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/
Re: [galaxy-dev] Input parameter validation dependent on another parameter?
Am Montag, den 21.10.2013, 12:33 +0100 schrieb Peter Cock: > On Mon, Oct 21, 2013 at 12:22 PM, Bjoern Gruening > wrote: > > Hi Peter, > > > >> Hello all, > >> > >> I'm currently trying to define a pair of integer parameters for > >> min/max values: > >> > >> >> label="Minimum" help="Optional, but if used you must also supply a > >> maximum value." /> > >> >> label="Maximum" help="Optional, but if used you must also supply a > >> minimum value." /> > >> > >> As far as I can tell from the documentation, there is no way to write > >> a validator which links the two parameters, for example in order to > >> insist that min_size <= max_size? > > > > I think you are right, there is no such easy mechanism. I would vote for > > a more powerful validator set. > > > > In the meantime you can use a code file to check your variables. Please > > have a look at our wip DeSeq2 warpper: > > > > https://github.com/bgruening/galaxytools/tree/master/deseq2 > > > > or the excellent blog post from Ross: > > > > http://cloudimaging.blogspot.com.au/2013/05/input-validation-in-galaxy.html > > > > Hope that helps, > > Bjoern > > Yes, a helper Python script linked via the tag containing > a validate_input function may work here - thanks Bjoern :) > > However, according to the wiki the tag is deprecated :( Yes :( But I don't think it will go away really soon. To much tools using it and no alternative is available. Cheers, Bjoern > Peter ___ 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/
Re: [galaxy-dev] Input parameter validation dependent on another parameter?
On Mon, Oct 21, 2013 at 12:22 PM, Bjoern Gruening wrote: > Hi Peter, > >> Hello all, >> >> I'm currently trying to define a pair of integer parameters for >> min/max values: >> >> > label="Minimum" help="Optional, but if used you must also supply a >> maximum value." /> >> > label="Maximum" help="Optional, but if used you must also supply a >> minimum value." /> >> >> As far as I can tell from the documentation, there is no way to write >> a validator which links the two parameters, for example in order to >> insist that min_size <= max_size? > > I think you are right, there is no such easy mechanism. I would vote for > a more powerful validator set. > > In the meantime you can use a code file to check your variables. Please > have a look at our wip DeSeq2 warpper: > > https://github.com/bgruening/galaxytools/tree/master/deseq2 > > or the excellent blog post from Ross: > > http://cloudimaging.blogspot.com.au/2013/05/input-validation-in-galaxy.html > > Hope that helps, > Bjoern Yes, a helper Python script linked via the tag containing a validate_input function may work here - thanks Bjoern :) However, according to the wiki the tag is deprecated :( Peter ___ 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/
Re: [galaxy-dev] Input parameter validation dependent on another parameter?
Hi Peter,
> Hello all,
>
> I'm currently trying to define a pair of integer parameters for
> min/max values:
>
> label="Minimum" help="Optional, but if used you must also supply a
> maximum value." />
> label="Maximum" help="Optional, but if used you must also supply a
> minimum value." />
>
> As far as I can tell from the documentation, there is no way to write
> a validator which links the two parameters, for example in order to
> insist that min_size <= max_size?
I think you are right, there is no such easy mechanism. I would vote for
a more powerful validator set.
In the meantime you can use a code file to check your variables. Please
have a look at our wip DeSeq2 warpper:
https://github.com/bgruening/galaxytools/tree/master/deseq2
or the excellent blog post from Ross:
http://cloudimaging.blogspot.com.au/2013/05/input-validation-in-galaxy.html
Hope that helps,
Bjoern
> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
>
> Alternatively, is it possible in the Cheetah section to raise an
> exception? That way at least the error should happen almost
> immediately (without having to wait for the cluster queue etc),
> e.g.
>
> raise ValueError("Requires minimum size is less than maximum!")
>
> Or, perhaps this particular use-case is common enough to warrant
> a new param type="integer-range" which shows two text boxes?
>
> Thanks,
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
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___
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[galaxy-dev] Input parameter validation dependent on another parameter?
Hello all,
I'm currently trying to define a pair of integer parameters for
min/max values:
As far as I can tell from the documentation, there is no way to write
a validator which links the two parameters, for example in order to
insist that min_size <= max_size?
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Alternatively, is it possible in the Cheetah section to raise an
exception? That way at least the error should happen almost
immediately (without having to wait for the cluster queue etc),
e.g.
raise ValueError("Requires minimum size is less than maximum!")
Or, perhaps this particular use-case is common enough to warrant
a new param type="integer-range" which shows two text boxes?
Thanks,
Peter
___
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:
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