filtering a <param> of type 'data' so only one type is available
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
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! On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum <dtenenba@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 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus@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@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 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
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 ? On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus@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@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 ___________________________________________________________ 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:
Struggling with this now...you have my vote! From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Ross Sent: donderdag 24 januari 2013 1:04 To: Dan Tenenbaum Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] filtering a <param> of type 'data' so only one type is available 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 ? On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>> wrote: On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus@gmail.com<mailto:ross.lazarus@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@fhcrc.org<mailto:dtenenba@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 ___________________________________________________________ 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:
You would have my vote too for this, is there a trello card for it? Stef ----- Original message ----- From: "Lukasse, Pieter" <pieter.lukasse@wur.nl> To: Ross <ross.lazarus@gmail.com> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] filtering a <param> of type 'data' so only one type is available Date: Wed, 22 Oct 2014 11:52:13 +0000 Struggling with this now...you have my vote! *From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *Ross *Sent:* donderdag 24 januari 2013 1:04 *To:* Dan Tenenbaum *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] filtering a <param> of type 'data' so only one type is available 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 ? On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus@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@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
___________________________________________________________
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:
_____________________________________________________________ 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/
participants (4)
-
Dan Tenenbaum -
Lukasse, Pieter -
Ross -
Stef van Lieshout