I just discovered a scant reference to this on the ToolSyntax page, and tracked it down to something that looks like it was introduced around 2011: a "LibraryDatasetToolParameter"
http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user: kanwei date: 2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.
Now I can't quite fathom the syntax around this but it appears to be broken - python error displayed:
TypeError: get_initial_value() got an unexpected keyword argument 'history'
Which is because in the galaxy code the
def get_initial_value( self, trans, context )
function is missing a "history=None" parameter like other types have?!
But is this input type essentially discontinued (no other refs to it on the web) or is it supposed to be operational?
I was hoping for a tool input that would list a particular libraries datasets, so that I could obtain their file paths for use in my tool.
<param name="test" type="library_data" label="test" help="test help"/> <options library="Reference Bins"> </param>
Regards,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
It was only ever used for one tool that I know of, but we should make it work since we try to never break backward compatibility. If you add the 'history=None' kwarg is that sufficient to fix the problem?
However, I think a better solution to this problem is to build it into dataset parameters. Anywhere a dataset can be provided it should be an option to provide a library dataset. Then one could imagine an option to restrict to only library datasets and a specific library.
-- jt
On Wed, Jan 14, 2015 at 7:08 PM, Dooley, Damion Damion.Dooley@bccdc.ca wrote:
I just discovered a scant reference to this on the ToolSyntax page, and tracked it down to something that looks like it was introduced around 2011: a "LibraryDatasetToolParameter"
http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user: kanwei date: 2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.
Now I can't quite fathom the syntax around this but it appears to be broken - python error displayed:
TypeError: get_initial_value() got an unexpected keyword argument 'history'
Which is because in the galaxy code the
def get_initial_value( self, trans, context )
function is missing a "history=None" parameter like other types have?!
But is this input type essentially discontinued (no other refs to it on the web) or is it supposed to be operational?
I was hoping for a tool input that would list a particular libraries datasets, so that I could obtain their file paths for use in my tool.
<param name="test" type="library_data" label="test" help="test help"/> <options library="Reference Bins"> </param>
Regards,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Hi,
Almost!
def get_initial_value( self, trans, context, history=None ):
in /lib/galaxy/tools/parameters/basic.py under class LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a popup with "Grid failed" appears, with an OK button that cleanly exits (see attached). So I guess that part is still broken unless there is more to the input parameter setup. I had tested with
<param name="test" type="library_data" label="test" help="test help"/>
I do like your better solution though, esp. if above control can't be primed with the desired library or folder.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: James Taylor [james@jamestaylor.org] Sent: Thursday, January 15, 2015 12:53 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool param type "library_data"
It was only ever used for one tool that I know of, but we should make it work since we try to never break backward compatibility. If you add the 'history=None' kwarg is that sufficient to fix the problem?
However, I think a better solution to this problem is to build it into dataset parameters. Anywhere a dataset can be provided it should be an option to provide a library dataset. Then one could imagine an option to restrict to only library datasets and a specific library.
Hi Damion,
I will look into this.
Thanks, Sam
On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion Damion.Dooley@bccdc.ca wrote:
Hi,
Almost!
def get_initial_value( self, trans, context, history=None ):in /lib/galaxy/tools/parameters/basic.py under class LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a popup with "Grid failed" appears, with an OK button that cleanly exits (see attached). So I guess that part is still broken unless there is more to the input parameter setup. I had tested with
<param name="test" type="library_data" label="test" help="test help"/>
I do like your better solution though, esp. if above control can't be primed with the desired library or folder.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: James Taylor [james@jamestaylor.org] Sent: Thursday, January 15, 2015 12:53 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool param type "library_data"
It was only ever used for one tool that I know of, but we should make it work since we try to never break backward compatibility. If you add the 'history=None' kwarg is that sufficient to fix the problem?
However, I think a better solution to this problem is to build it into dataset parameters. Anywhere a dataset can be provided it should be an option to provide a library dataset. Then one could imagine an option to restrict to only library datasets and a specific library.
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: https://lists.galaxyproject.org/
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Hi Damion,
This change here https://bitbucket.org/galaxy/galaxy-central/pull-request/639/fix-for-library... might fix it.
Thanks for reporting the issue, Sam
On Thu, Jan 15, 2015 at 3:42 PM, Aysam Guerler aysam.guerler@gmail.com wrote:
Hi Damion,
I will look into this.
Thanks, Sam
On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion Damion.Dooley@bccdc.ca wrote:
Hi,
Almost!
def get_initial_value( self, trans, context, history=None ):in /lib/galaxy/tools/parameters/basic.py under class LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a popup with "Grid failed" appears, with an OK button that cleanly exits (see attached). So I guess that part is still broken unless there is more to the input parameter setup. I had tested with
<param name="test" type="library_data" label="test" help="test help"/>
I do like your better solution though, esp. if above control can't be primed with the desired library or folder.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: James Taylor [james@jamestaylor.org] Sent: Thursday, January 15, 2015 12:53 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool param type "library_data"
It was only ever used for one tool that I know of, but we should make it work since we try to never break backward compatibility. If you add the 'history=None' kwarg is that sufficient to fix the problem?
However, I think a better solution to this problem is to build it into dataset parameters. Anywhere a dataset can be provided it should be an option to provide a library dataset. Then one could imagine an option to restrict to only library datasets and a specific library.
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Just to summarize what I found about getting tool parameter <param type="library_data" > going again (though a future expansion of dataset parameters to handle this would be great, esp. if one can specify a particular data library):
1) Aysam's patch (thanks!) 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs that have a prefix so that needs adjustment:
$(".add-librarydataset").click(function() { var link = $(this); $.ajax({ url: "/visualization/list_libraries",
Now one gets the popup form in one's tool where one or more library datasets can be selected. Selecting one or more gets them listed in one's tool form.
However, I'm not understanding how to get those items submitted with galaxy form <command> params. I tried for example: -B "$library_datasets[0].file_name" and also tried a loop to enumerate the dataset file names.
I keep on getting:
File "cheetah_DynamicallyCompiledCheetahTemplate_1421706558_2_37415.py", line 203, in respond TypeError: object of type 'LibraryDatasetValueWrapper' has no len()
If anyone knows the solution, that would be appreciated.
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
galaxy-dev@lists.galaxyproject.org
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Aysam Guerler -
Dooley, Damion -
James Taylor