Re: [galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-25 Thread Dannon Baker
Leandro,

Thanks for reporting this, I'm able to reproduce it and will let you know when 
I have a fix.

-Dannon


On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:

 Hi,
 
 There seems to be a weird bug with the Input dataset workflow
 control feature, hard to explain clearly but I'll try my best.
 
 If you define a custom datatype that is a simple subclass of an
 existing galaxy datatype, e.g.:
 
 datatype extension=myext type=galaxy.datatypes.data:Text
 subclass=True display_in_upload=true/
 
 And if this datatype will be the input to a workflow where you want to
 use the multiple input files feature you must put into your workflow
 editor an Input dataset box at the beginning and connect it.
 
 If you define a custom datatype that's it's own custom class, e.g.:
 
 datatype extension=myext type=galaxy.datatypes.data:MyExt
 display_in_upload=true/
 
 with a simple class in lib/galaxy/datatypes/data.py e.g.:
 
 class MyExt( Data ):
file_ext = myext
 
 And if this datatype will be the input data to a workflow if you have
 an Input dataset box at the beginning for some reason the drop-down
 menu (or multi-select) won't not have files of this type from your
 history it just ignores them. Now what is strange is if I edit the
 workflow and remove the beginning Input dataset box and start the
 workflow with just the first tool which has this custom datatype as an
 input parameter then when I try to run the workflow everything shows
 up properly :-/
 
 Hope I explained this ok, seems like something is broken with the
 Input dataset workflow control feature.
 
 best,
 Leandro
 ___
 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/

___
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/


Re: [galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-25 Thread Leandro Hermida
Hi Dannon,

Thanks I'm glad you could reproduce it! One thing I was thinking about
since you are working in that code area is whether you could make it that
the Input Dataset workflow control feature is not required. When you use
this feature it cannot filter out the dataset history for a particular
datatype, although when don't use it and start a workflow with a tool that
has an input data parameter it is able to filter out for the desired
datatype.  It used to be in old galaxy-dist versions that if you didn't
start with the Input Dataset control feature then you couldn't use the
multiple input files workflow parallelization feature but now it doesn't
seem to be the case which is very good.

thanks,
Leandro

On Wed, Jan 25, 2012 at 2:55 PM, Dannon Baker dannonba...@me.com wrote:

 Leandro,

 Thanks for reporting this, I'm able to reproduce it and will let you know
 when I have a fix.

 -Dannon


 On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:

  Hi,
 
  There seems to be a weird bug with the Input dataset workflow
  control feature, hard to explain clearly but I'll try my best.
 
  If you define a custom datatype that is a simple subclass of an
  existing galaxy datatype, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:Text
  subclass=True display_in_upload=true/
 
  And if this datatype will be the input to a workflow where you want to
  use the multiple input files feature you must put into your workflow
  editor an Input dataset box at the beginning and connect it.
 
  If you define a custom datatype that's it's own custom class, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:MyExt
  display_in_upload=true/
 
  with a simple class in lib/galaxy/datatypes/data.py e.g.:
 
  class MyExt( Data ):
 file_ext = myext
 
  And if this datatype will be the input data to a workflow if you have
  an Input dataset box at the beginning for some reason the drop-down
  menu (or multi-select) won't not have files of this type from your
  history it just ignores them. Now what is strange is if I edit the
  workflow and remove the beginning Input dataset box and start the
  workflow with just the first tool which has this custom datatype as an
  input parameter then when I try to run the workflow everything shows
  up properly :-/
 
  Hope I explained this ok, seems like something is broken with the
  Input dataset workflow control feature.
 
  best,
  Leandro
  ___
  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/


___
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/

Re: [galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-25 Thread Dannon Baker
Input Dataset datatype filtering actually used to work, this is a regression 
that happened in changeset 6329:ab90893a7cf5.  I should have a fix for it today 
and you'll be back in business.

-Dannon

On Jan 25, 2012, at 10:53 AM, Leandro Hermida wrote:

 Hi Dannon,
 
 Thanks I'm glad you could reproduce it! One thing I was thinking about since 
 you are working in that code area is whether you could make it that the Input 
 Dataset workflow control feature is not required. When you use this feature 
 it cannot filter out the dataset history for a particular datatype, although 
 when don't use it and start a workflow with a tool that has an input data 
 parameter it is able to filter out for the desired datatype.  It used to be 
 in old galaxy-dist versions that if you didn't start with the Input Dataset 
 control feature then you couldn't use the multiple input files workflow 
 parallelization feature but now it doesn't seem to be the case which is very 
 good.
 
 thanks,
 Leandro
 
 On Wed, Jan 25, 2012 at 2:55 PM, Dannon Baker dannonba...@me.com wrote:
 Leandro,
 
 Thanks for reporting this, I'm able to reproduce it and will let you know 
 when I have a fix.
 
 -Dannon
 
 
 On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:
 
  Hi,
 
  There seems to be a weird bug with the Input dataset workflow
  control feature, hard to explain clearly but I'll try my best.
 
  If you define a custom datatype that is a simple subclass of an
  existing galaxy datatype, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:Text
  subclass=True display_in_upload=true/
 
  And if this datatype will be the input to a workflow where you want to
  use the multiple input files feature you must put into your workflow
  editor an Input dataset box at the beginning and connect it.
 
  If you define a custom datatype that's it's own custom class, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:MyExt
  display_in_upload=true/
 
  with a simple class in lib/galaxy/datatypes/data.py e.g.:
 
  class MyExt( Data ):
 file_ext = myext
 
  And if this datatype will be the input data to a workflow if you have
  an Input dataset box at the beginning for some reason the drop-down
  menu (or multi-select) won't not have files of this type from your
  history it just ignores them. Now what is strange is if I edit the
  workflow and remove the beginning Input dataset box and start the
  workflow with just the first tool which has this custom datatype as an
  input parameter then when I try to run the workflow everything shows
  up properly :-/
 
  Hope I explained this ok, seems like something is broken with the
  Input dataset workflow control feature.
 
  best,
  Leandro
  ___
  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/
 
 

___
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/


Re: [galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-25 Thread Dannon Baker
Ok, should be fixed in 6620:c60760713d26.  Let me know if you still have any 
issues.

-Dannon

On Jan 25, 2012, at 10:53 AM, Leandro Hermida wrote:

 Hi Dannon,
 
 Thanks I'm glad you could reproduce it! One thing I was thinking about since 
 you are working in that code area is whether you could make it that the Input 
 Dataset workflow control feature is not required. When you use this feature 
 it cannot filter out the dataset history for a particular datatype, although 
 when don't use it and start a workflow with a tool that has an input data 
 parameter it is able to filter out for the desired datatype.  It used to be 
 in old galaxy-dist versions that if you didn't start with the Input Dataset 
 control feature then you couldn't use the multiple input files workflow 
 parallelization feature but now it doesn't seem to be the case which is very 
 good.
 
 thanks,
 Leandro
 
 On Wed, Jan 25, 2012 at 2:55 PM, Dannon Baker dannonba...@me.com wrote:
 Leandro,
 
 Thanks for reporting this, I'm able to reproduce it and will let you know 
 when I have a fix.
 
 -Dannon
 
 
 On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote:
 
  Hi,
 
  There seems to be a weird bug with the Input dataset workflow
  control feature, hard to explain clearly but I'll try my best.
 
  If you define a custom datatype that is a simple subclass of an
  existing galaxy datatype, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:Text
  subclass=True display_in_upload=true/
 
  And if this datatype will be the input to a workflow where you want to
  use the multiple input files feature you must put into your workflow
  editor an Input dataset box at the beginning and connect it.
 
  If you define a custom datatype that's it's own custom class, e.g.:
 
  datatype extension=myext type=galaxy.datatypes.data:MyExt
  display_in_upload=true/
 
  with a simple class in lib/galaxy/datatypes/data.py e.g.:
 
  class MyExt( Data ):
 file_ext = myext
 
  And if this datatype will be the input data to a workflow if you have
  an Input dataset box at the beginning for some reason the drop-down
  menu (or multi-select) won't not have files of this type from your
  history it just ignores them. Now what is strange is if I edit the
  workflow and remove the beginning Input dataset box and start the
  workflow with just the first tool which has this custom datatype as an
  input parameter then when I try to run the workflow everything shows
  up properly :-/
 
  Hope I explained this ok, seems like something is broken with the
  Input dataset workflow control feature.
 
  best,
  Leandro
  ___
  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/
 
 

___
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/


[galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-20 Thread Leandro Hermida
Hi,

There seems to be a weird bug with the Input dataset workflow
control feature, hard to explain clearly but I'll try my best.

If you define a custom datatype that is a simple subclass of an
existing galaxy datatype, e.g.:

datatype extension=myext type=galaxy.datatypes.data:Text
subclass=True display_in_upload=true/

And if this datatype will be the input to a workflow where you want to
use the multiple input files feature you must put into your workflow
editor an Input dataset box at the beginning and connect it.

If you define a custom datatype that's it's own custom class, e.g.:

datatype extension=myext type=galaxy.datatypes.data:MyExt
display_in_upload=true/

with a simple class in lib/galaxy/datatypes/data.py e.g.:

class MyExt( Data ):
file_ext = myext

And if this datatype will be the input data to a workflow if you have
an Input dataset box at the beginning for some reason the drop-down
menu (or multi-select) won't not have files of this type from your
history it just ignores them. Now what is strange is if I edit the
workflow and remove the beginning Input dataset box and start the
workflow with just the first tool which has this custom datatype as an
input parameter then when I try to run the workflow everything shows
up properly :-/

Hope I explained this ok, seems like something is broken with the
Input dataset workflow control feature.

best,
Leandro
___
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/