Re: [galaxy-dev] filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum
On Wed, Jan 23, 2013 at 4:03 PM, Ross <ross.lazarus(a)gmail.com> wrote:
> Hi, Dan
> Glad it worked and thanks for pointing out a more general mimetype - does
> any one else (other than me) want to vote to add
> <datatype extension="rda" type="galaxy.datatypes.binary:Binary
> mimetype="application/x-gzip" subclass="True" />
> to datatypes_conf.xml.sample permanently ?
>
I do. This would be great as I am automating the creation of galaxy
tools and I'd like to be able to enable this feature without requiring
(either manual or programmatic) editing of datatypes_conf.xml.
Note that serialized R objects also sometimes have the .RData
extension -- both are valid -- so it would be good to support that as
well.
But now that I think about it, serialized objects are not always gzip
files--depending on the value of the 'compression' flag used with the
save() function, it may be gzip, bzip, xz, or even ascii!
So maybe the mime type should be changed back to something different,
like application/x-rlang-transport as you suggested.
I tried this and it seemed to work; It did the filtering I wanted and
I was still able to download a history item with this type.
Dan
Thanks,
Dan
>
> On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum <dtenenba(a)fhcrc.org> wrote:
>>
>> On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus(a)gmail.com> wrote:
>> > Hi, Dan.
>> > Using format="rda" will restrict the list to history items of the 'rda'
>> > datatype - but ONLY if the rda datatype has been defined!
>> > The easiest way to do that is to define a new datatype in
>> > datatypes_conf.xml
>> > and since rData is binary, you should subclass binary.
>> > Something like (untested - especially the mimetype !)
>> > <datatype extension="rda" type="galaxy.datatypes.binary:Binary"
>> > mimetype="application/x-rlang-transport" subclass="True" />
>> > might work. A server restart is always required to load any new
>> > datatypes.
>> > Good luck!
>> >
>>
>> It works! I changed the mime type to application/x-gzip, since
>> serialized R objects are gzipped.
>>
>> Thanks,
>> Dan
>>
>>
>> >
>> >
>> > On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum <dtenenba(a)fhcrc.org>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> I have a tool wrapper with a <param> of type="data".
>> >>
>> >> Currently, this renders as a text box with a drop down list that has
>> >> 52 items in it (the number of things I have in my history, I guess).
>> >>
>> >> I'd like to filter this list so that only some items in the history
>> >> (in my case any item whose name ends with '.rda') are shown in this
>> >> dropdown.
>> >>
>> >> It seems like maybe the 'format' parameter to the 'param' tag is what
>> >> I want, but:
>> >> 1) I tried format="rda" and that didn't seem to change anything.
>> >> 2) "rda" is not in the datatypes.conf file which the documentation
>> >> suggests is required?
>> >>
>> >> (.rda is an extension used for serialized R objects.)
>> >>
>> >> The tool I'm working on only accepts rda files as input and the reason
>> >> I'm asking for this is that it is all too easy to accidentally feed it
>> >> a file of some other type. If the dropdown could be filtered so that
>> >> only items which will work with the tool are shown, that would be
>> >> great.
>> >>
>> >> Is there a way to do that?
>> >> Thanks,
>> >> Dan
>> >> ___________________________________________________________
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>> >
>> >
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--
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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--
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
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