details: http://www.bx.psu.edu/hg/galaxy/rev/f84112d155c0 changeset: 3504:f84112d155c0 user: Dan Blankenberg dan@bx.psu.edu date: Wed Mar 10 11:28:50 2010 -0500 description: Allow renaming of uploaded files in toolbox tests by including a <edit_attributes type="name" value="new dataset name" /> child tag. A rename directive is automatically assigned (no xml changes required) to uploaded composite datasets, so that they can be identified uniquely.
diffstat:
lib/galaxy/tools/__init__.py | 23 +++++++++++++++++++++++ lib/galaxy/tools/test.py | 11 +++++++---- test/functional/test_toolbox.py | 16 ++++++++++++++-- 3 files changed, 44 insertions(+), 6 deletions(-)
diffs (91 lines):
diff -r c73f093219aa -r f84112d155c0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Mar 10 11:24:49 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Wed Mar 10 11:28:50 2010 -0500 @@ -510,6 +510,7 @@ store in `self.tests`. """ self.tests = [] + composite_data_names_counter = 0 #composite datasets need a unique name: each test occurs in a fresh history, but we'll keep it unique per set of tests for i, test_elem in enumerate( tests_elem.findall( 'test' ) ): name = test_elem.get( 'name', 'Test-%d' % (i+1) ) maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) @@ -524,6 +525,28 @@ else: value = None attrib['children'] = list( param_elem.getchildren() ) + if attrib['children']: + #at this time, we can assume having children only occurs on DataToolParameter test items + #but this could change and would cause the below parsing to change based upon differences in children items + attrib['metadata'] = [] + attrib['composite_data'] = [] + attrib['edit_attributes'] = [] + composite_data_name = None #composite datasets need to be renamed uniquely + for child in attrib['children']: + if child.tag == 'composite_data': + attrib['composite_data'].append( child ) + if composite_data_name is None: + #generate a unique name; each test uses a fresh history + composite_data_name = '_COMPOSITE_RENAMED %i_' % ( composite_data_names_counter ) + composite_data_names_counter += 1 + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'edit_attributes': + attrib['edit_attributes'].append( child ) + if composite_data_name: + attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) #composite datasets need implicit renaming; inserted at front of list so explicit declarations take precedence test.add_param( attrib.pop( 'name' ), value, attrib ) for output_elem in test_elem.findall( "output" ): attrib = dict( output_elem.attrib ) diff -r c73f093219aa -r f84112d155c0 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Wed Mar 10 11:24:49 2010 -0500 +++ b/lib/galaxy/tools/test.py Wed Mar 10 11:28:50 2010 -0500 @@ -30,12 +30,15 @@ if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) == 0: + name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] + if name_change: + name_change = name_change[-1].get( 'value' ) #only the last name change really matters + if value is None and not name_change: assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name else: - self.required_files.append( ( value, extra ) ) - if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) > 0: - value = extra.get( 'ftype' ) + self.required_files.append( ( value, extra ) ) #these files will be uploaded + if name_change: + value = name_change #change value for select to renamed uploaded file for e.g. composite dataset except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) diff -r c73f093219aa -r f84112d155c0 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Wed Mar 10 11:24:49 2010 -0500 +++ b/test/functional/test_toolbox.py Wed Mar 10 11:28:50 2010 -0500 @@ -33,10 +33,22 @@ # Upload any needed files for fname, extra in testdef.required_files: children = extra.get( 'children', [] ) - metadata = [ child for child in children if child.tag == 'metadata' ] - composite_data = [ child for child in children if child.tag == 'composite_data' ] + metadata = extra.get( 'metadata', [] ) + composite_data = extra.get( 'composite_data', [] ) self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ), metadata = metadata, composite_data = composite_data ) print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra + #Post upload attribute editing + edit_attributes = extra.get( 'edit_attributes', [] ) + #currently only renaming is supported + for edit_att in edit_attributes: + if edit_att.get( 'type', None ) == 'name': + new_name = edit_att.get( 'value', None ) + assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag' + hda_id = self.get_history_as_data_list()[-1].get( 'id' ) + self.edit_hda_attribute_info( hda_id, new_name = new_name ) + print "Renamed uploaded file to:", new_name + else: + raise Exception( 'edit_attributes type (%s) is unimplemented' % edit_att.get( 'type', None ) ) # We need to handle the case where we've uploaded a valid compressed file since the upload # tool will have uncompressed it on the fly. all_inputs = {}