planemo lint XSD check unaware of legacy parameter attribute default_value #593
Description
While <param value="..." ...> is prefered, Galaxy still supports <param default_value="..." ...> for a ColumnListParameter, as can be seen here:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters/basic.py#L1005
# Legacy style default value specification...
self.default_value = input_source.get( "default_value", None )
if self.default_value is None:
# Newer style... more in line with other parameters.
self.default_value = input_source.get( "value", None )
if self.default_value is not None:
self.default_value = ColumnListParameter._strip_c( self.default_value )The XSD should be aware of this legacy attribute, which currently causes lint failures, e.g. https://travis-ci.org/peterjc/galaxy_blast/jobs/167595623
+Linting tool /home/travis/build/peterjc/galaxy_blast/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml
Applying linter tests... CHECK
.. CHECK: 2 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 7 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.2].
.. CHECK: Tool defines a name [BLAST top hit descriptions].
.. CHECK: Tool defines an id [blastxml_to_top_descr].
Applying linter command... CHECK
.. INFO: Command uses deprecated 'interpreter' attribute.
.. INFO: Tool contains a command with interpreter of type [python].
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Applying linter tool_xsd... FAIL
.. ERROR: Invalid tmp6TctTh found. Errors [/tmp/tmp6TctTh:24:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'option', attribute 'select': The attribute 'select' is not allowed.
/tmp/tmp6TctTh:32:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'param', attribute 'default_value': The attribute 'default_value' is not allowed.
/tmp/tmp6TctTh:33:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'param', attribute 'default_value': The attribute 'default_value' is not allowed.
/tmp/tmp6TctTh:34:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'param', attribute 'default_value': The attribute 'default_value' is not allowed.]
Applying linter shed_metadata... CHECK
.. INFO: Found all shed metadata fields required for automated repository creation and/or updates.
Failed linting
See galaxyproject/galaxy@9128311 (originally only default_value was supported) and the option to use the more common value added in galaxyproject/galaxy@40f19d2