Adding the 'name' content of the selection parameter
Hello, Continuing the discussion from Dec. 19th, http://mail.bx.psu.edu/pipermail/galaxy-user/2008-December/000422.html The following hack adds an additional key/value which contains the 'name' of the selected option in a <select> input parameter. With this hack, the following tool configuration is possible (note the output/label option): ========================== <tool> .. <inputs> <input format="fasta" type="data" name="input"> <input type="select" name="database" label="Database"> <option value="/home/gordon/long/path/hg18.fa">Human (hg18)</option> <option value="/home/gordon/long/path/dm3.fa">Fly (dm3)</option> <option value="/home/gordon/long/path/mm9.fa">Mouse (mm9)</option> </input> </inputs> <outputs> <!-- old way --> <data format="txt" name="output" label="Blat $input1 on $database" /> <!-- new way --> <data format="txt" name="output" label="Blat $input1 on $database_name" /> </outputs> ========================== Currently, using "$database" in the output/label part will put the *value* of the selected option (e.g. "/home/gordon/long/path/hg18.fa") in the dataset's name. This doesn't really help the user understand what the dataset contains. With this hack, for each <select> input, a new variable is created (with the "_name" suffix) which will contain the *name* of the selected option (e.g. "Human (hg18)"). For example, if the user selected the second option, Then "$database" will contain "/home/gordon/long/path/dm3.fa", and "$database_name" will contain "Fly (dm3)". I'm well aware this is an ugly hack. A better way would be to have each parameter (in the incoming dictionary) be an object (e.g. ToolParameter) and not a string. Then we could write something like "$database.name" or "$database.value". The hack contains two patches. The first add support for 'value_to_display_text' with dynamic options, in "Parameters/Basic.py": ============================================================== --- galaxy_prod/lib/galaxy/tools/parameters/basic.py +++ galaxy_devel/lib/galaxy/tools/parameters/basic.py @@ -576,7 +576,7 @@ elif len( value ) == 1: value = value[0] return value - def value_to_display_text( self, value, app ): + def value_to_display_text( self, value, app, other_values={} ): if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" value = value.value @@ -584,10 +584,11 @@ suffix = "" if not isinstance( value, list ): value = [ value ] - # FIXME: Currently only translating values back to labels if they - # are not dynamic if self.is_dynamic: - rval = map( str, value ) + rval = [ ] + for name in self.options.get_options ( app , other_values ) : + if ( name[1] in value ): + rval.append ( name[0] ) else: options = list( self.static_options ) rval = [] ============================================================== The second patch iterates the tool's parameters, and for each <select> type parameter, adds the additional key/value for the selected option: ============================================================== --- galaxy_prod/lib/galaxy/tools/actions/__init__.py +++ galaxy_devel/lib/galaxy/tools/actions/__init__.py @@ -96,6 +96,18 @@ on_text = "" # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey + + ##28dec2008, gordon + ## For every 'Select' parameter, we get only the 'value' part of the selection from the HTTP request. + ## The following code gets the 'name' part for the selected option + selection_parameter_names = {} + for param_name, param_selected_value in incoming.iteritems(): + param_obj = tool.get_param ( param_name ) + if isinstance( param_obj, basic.SelectToolParameter): + param_selected_name = param_obj.value_to_display_text( param_selected_value, trans, incoming ) + selection_parameter_names [ param_name + "_name" ] = param_selected_name.replace("\n","") + incoming.update( selection_parameter_names ) + # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] ============================================================== I tried to make the changes as non intrusive as possible. I hope the added 'other_value' parameter doesn't affect other places that call 'value_to_display_text' - but I'm not quite sure about it (I'm still very new to python). I've tested this hack with several tools, and it seems to work (or at least not crash horribly). Comments are welcomed, Gordon.
Hello Assaf, Thanks very much for this request. This feature was completed in rev 1706. Since SelectToolParameters already have a "name" attribute, the tool in your example can now have a tag like this: <data format="txt" name="output" label="Blat $input1 on ${database.value_label}" /> Of course, any other attribute of a SelectToolParameter will now work as well, e.g., <data format="txt" name="output" label="Blat $input1 on ${database.name}" /> The following will display the value as before: <data format="txt" name="output" label="Blat $input1 on ${database}" /> Greg Von Kuster Galaxy Development Team Assaf Gordon wrote:
Hello,
Continuing the discussion from Dec. 19th, http://mail.bx.psu.edu/pipermail/galaxy-user/2008-December/000422.html
The following hack adds an additional key/value which contains the 'name' of the selected option in a <select> input parameter.
With this hack, the following tool configuration is possible (note the output/label option): ========================== <tool> .. <inputs> <input format="fasta" type="data" name="input"> <input type="select" name="database" label="Database"> <option value="/home/gordon/long/path/hg18.fa">Human (hg18)</option> <option value="/home/gordon/long/path/dm3.fa">Fly (dm3)</option> <option value="/home/gordon/long/path/mm9.fa">Mouse (mm9)</option> </input> </inputs> <outputs> <!-- old way --> <data format="txt" name="output" label="Blat $input1 on $database" />
<!-- new way --> <data format="txt" name="output" label="Blat $input1 on $database_name" /> </outputs> ==========================
Currently, using "$database" in the output/label part will put the *value* of the selected option (e.g. "/home/gordon/long/path/hg18.fa") in the dataset's name. This doesn't really help the user understand what the dataset contains.
With this hack, for each <select> input, a new variable is created (with the "_name" suffix) which will contain the *name* of the selected option (e.g. "Human (hg18)").
For example, if the user selected the second option, Then "$database" will contain "/home/gordon/long/path/dm3.fa", and "$database_name" will contain "Fly (dm3)".
I'm well aware this is an ugly hack. A better way would be to have each parameter (in the incoming dictionary) be an object (e.g. ToolParameter) and not a string. Then we could write something like "$database.name" or "$database.value".
The hack contains two patches.
The first add support for 'value_to_display_text' with dynamic options, in "Parameters/Basic.py": ============================================================== --- galaxy_prod/lib/galaxy/tools/parameters/basic.py +++ galaxy_devel/lib/galaxy/tools/parameters/basic.py @@ -576,7 +576,7 @@ elif len( value ) == 1: value = value[0] return value - def value_to_display_text( self, value, app ): + def value_to_display_text( self, value, app, other_values={} ): if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" value = value.value @@ -584,10 +584,11 @@ suffix = "" if not isinstance( value, list ): value = [ value ] - # FIXME: Currently only translating values back to labels if they - # are not dynamic if self.is_dynamic: - rval = map( str, value ) + rval = [ ] + for name in self.options.get_options ( app , other_values ) : + if ( name[1] in value ): + rval.append ( name[0] ) else: options = list( self.static_options ) rval = [] ==============================================================
The second patch iterates the tool's parameters, and for each <select> type parameter, adds the additional key/value for the selected option: ============================================================== --- galaxy_prod/lib/galaxy/tools/actions/__init__.py +++ galaxy_devel/lib/galaxy/tools/actions/__init__.py @@ -96,6 +96,18 @@ on_text = "" # Add the dbkey to the incoming parameters incoming[ "dbkey" ] = input_dbkey + + ##28dec2008, gordon + ## For every 'Select' parameter, we get only the 'value' part of the selection from the HTTP request. + ## The following code gets the 'name' part for the selected option + selection_parameter_names = {} + for param_name, param_selected_value in incoming.iteritems(): + param_obj = tool.get_param ( param_name ) + if isinstance( param_obj, basic.SelectToolParameter): + param_selected_name = param_obj.value_to_display_text( param_selected_value, trans, incoming ) + selection_parameter_names [ param_name + "_name" ] = param_selected_name.replace("\n","") + incoming.update( selection_parameter_names ) + # Keep track of parent / child relationships, we'll create all the # datasets first, then create the associations parent_to_child_pairs = [] ==============================================================
I tried to make the changes as non intrusive as possible. I hope the added 'other_value' parameter doesn't affect other places that call 'value_to_display_text' - but I'm not quite sure about it (I'm still very new to python). I've tested this hack with several tools, and it seems to work (or at least not crash horribly).
Comments are welcomed, Gordon. _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
participants (2)
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Assaf Gordon -
Greg Von Kuster