Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN. So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<( ***************** For others who may need... tool form's param: <param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/> <command> tag contents.... #if $library_datasets -B " #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for " #end if Successfully submits either the full file path of selected dataset, or its id. ***************** However trying to rerun this history tool item gets us an error (not related to the above <command> contents): Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' .... Module galaxy.tools.parameters.basic:146 in value_to_basic view >> return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app <galaxy.app.UniverseApplication object at 0x59a0710> ldda 331 self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090> value [331] >> return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id' which is in /lib/galaxy/tools/parameters/basic.py: class LibraryDatasetToolParameter( ToolParameter ): """ Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """ ... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value] "Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?: Input Parameter Value Note for rerun BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>] Tabular Report Column Labels Short name HTML Report template templates.html_report ******************************** The other bug: 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",
Hey Damion, Thanks a lot for the description. We are currently switching the tool form to a newer version but I will look into this fix soon and should be able transfer it. Thanks, Sam On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN.
So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<(
***************** For others who may need...
tool form's param:
<param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/>
<command> tag contents....
#if $library_datasets -B " #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for " #end if
Successfully submits either the full file path of selected dataset, or its id.
***************** However trying to rerun this history tool item gets us an error (not related to the above <command> contents):
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' .... Module galaxy.tools.parameters.basic:146 in value_to_basic view >> return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app <galaxy.app.UniverseApplication object at 0x59a0710> ldda 331 self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090> value [331] >> return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id'
which is in /lib/galaxy/tools/parameters/basic.py:
class LibraryDatasetToolParameter( ToolParameter ): """ Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """
... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value]
"Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?:
Input Parameter Value Note for rerun BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>] Tabular Report Column Labels Short name HTML Report template templates.html_report
******************************** The other bug:
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", ___________________________________________________________ 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/
Hi Damion, An initial implementation of the library dataset tool parameter (which allows the selection of multiple library datasets) is currently in the pipeline https://github.com/galaxyproject/galaxy/pull/132. After some review the feature should be available in the default branch, however you may try it now if you are interested. Thanks, Sam On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN.
So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<(
***************** For others who may need...
tool form's param:
<param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/>
<command> tag contents....
#if $library_datasets -B " #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for " #end if
Successfully submits either the full file path of selected dataset, or its id.
***************** However trying to rerun this history tool item gets us an error (not related to the above <command> contents):
Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' .... Module galaxy.tools.parameters.basic:146 in value_to_basic view >> return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app <galaxy.app.UniverseApplication object at 0x59a0710> ldda 331 self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090> value [331] >> return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id'
which is in /lib/galaxy/tools/parameters/basic.py:
class LibraryDatasetToolParameter( ToolParameter ): """ Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """
... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value]
"Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?:
Input Parameter Value Note for rerun BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>] Tabular Report Column Labels Short name HTML Report template templates.html_report
******************************** The other bug:
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", ___________________________________________________________ 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/
Ok, thanks Sam. I will take a close look at this in the next week. 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: Aysam Guerler [aysam.guerler@gmail.com] ... Hi Damion, An initial implementation of the library dataset tool parameter (which allows the selection of multiple library datasets) is currently in the pipeline https://github.com/galaxyproject/galaxy/pull/132. After some review the feature should be available in the default branch, however you may try it now if you are interested. Thanks, Sam
participants (2)
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Aysam Guerler -
Dooley, Damion