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Updating documentation update script to auto-generate documentation for ensemble metrics. #105

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f655c25
Updating documentation update script to auto-generate documentation f…
vmullig Feb 8, 2022
648bc8d
Update xsd_to_doc_fragments.py for python3.
vmullig Feb 25, 2022
165c8b9
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Apr 27, 2022
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61 changes: 31 additions & 30 deletions doc_tools/xsd_to_doc_fragments.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@

TYPE_ALIASES={ 'xs:string':'string', 'xs:integer':'integer', 'xs:decimal':'real', 'rosetta_bool':'bool' }
# SECTIONS are actually the top level groups (xs:group) entries in the XSD (though not the nonce ones).
SECTIONS = [ 'mover', 'filter', 'packer_palette', 'task_operation', 'residue_selector', 'simple_metric', 'res_lvl_task_op', 'res_filter', 'constraint_generator', 'features_reporter', 'pose_selector', 'scoring_grid', 'pose_property_reporter', 'denovo_perturber', 'compound_architect_pairing_group', 'jump_selector', 'loop_definer' ]
SECTIONS = [ 'mover', 'filter', 'packer_palette', 'task_operation', 'residue_selector', 'simple_metric', 'ensemble_metric', 'res_lvl_task_op', 'res_filter', 'constraint_generator', 'features_reporter', 'pose_selector', 'scoring_grid', 'pose_property_reporter', 'denovo_perturber', 'compound_architect_pairing_group', 'jump_selector', 'loop_definer' ]
# Nonce groups:
# ['loop_definer', 'layer_design_ss_layer', 'layer_design_ss_layer_or_taskop', 'denovo_architect', 'compound_architect_pairing_group', 'denovo_perturber', 'denovo_folder', 'rdf_function', 'pose_property_reporter', 'envclaim', 'scriptcm']

Expand All @@ -37,6 +37,7 @@
'task_operation':('TaskOperation Tag','Any of the [[RosettaScripts TaskOperation|TaskOperations-RosettaScripts]] tags'),
'residue_selector':('Residue Selector Tag','Any of the [[ResidueSelectors]]'),
'simple_metric':('Simple Metric Tag', 'Any of the [[SimpleMetrics]]'),
'ensemble_metric':('Ensemble Metric Tag', 'Any of the [[EnsembleMetrics]]'),
'jump_selector':('Jump Selector Tag','Any of the [[JumpSelectors]]'),
'res_lvl_task_op':('ResidueLevelTaskOperation Tag','Any of the [[Residue Level TaskOperations]]'),
'res_filter':('ResFilter Tag','Any of the [[ResFilters|OperateOnCertainResiduesOperation#ResFilters]]'),
Expand All @@ -63,9 +64,9 @@ def get_annotation(node, name1, name2=None):
if node.tag != '{http://www.w3.org/2001/XMLSchema}annotation': return ''
if len(node) < 1 or node[0].tag != '{http://www.w3.org/2001/XMLSchema}documentation':
if name2 is not None:
print "Error parsing annotation for entry", name1, "in", name2
print( "Error parsing annotation for entry", name1, "in", name2 )
else:
print "Error parsing annotation for entry", name1
print( "Error parsing annotation for entry", name1 )
return ''
return node[0].text

Expand All @@ -77,16 +78,16 @@ def parse_subelement( subelem, parentname ):
doc_lines = []

if 'name' not in subelem.attrib:
print 'Error: missing name when parsing subtag for ', parentname
print( 'Error: missing name when parsing subtag for ', parentname )
name = subelem.attrib['name']

if len(subelem) >=2:
print "Error: can't parse type for", name, "in", parentname
print( "Error: can't parse type for", name, "in", parentname )
return None

if len( subelem ) == 0:
if 'type' not in subelem.attrib:
print "Error: can't parse type entry for", name, "in", parentname
print( "Error: can't parse type entry for", name, "in", parentname )
return None
typename = subelem.attrib['type']
if typename in COMMON_TYPES:
Expand All @@ -98,14 +99,14 @@ def parse_subelement( subelem, parentname ):

# Parse complex type in ALL_ENTRIES
if typename not in ALL_ENTRIES:
print "Error: can't parse type of ", typename, " for", name, "in", parentname
print( "Error: can't parse type of ", typename, " for", name, "in", parentname )
return None
ctype = ALL_ENTRIES[typename]
elif len( subelem ) == 1:
ctype = subelem[0]

if ctype.tag != '{http://www.w3.org/2001/XMLSchema}complexType':
print "Error getting type for", name, "in", parentname
print( "Error getting type for", name, "in", parentname )
return None
sct = parse_complextype( name, parentname, ctype )
if sct is None:
Expand Down Expand Up @@ -164,7 +165,7 @@ def parse_multi( node, parentname ):
tag_lines.extend( subtag_lines )
doc_lines.extend( subdoc_lines )
else:
print "Error parsing subtag of", nodetype, "for", parentname, '::', subelem.tag
print( "Error parsing subtag of", nodetype, "for", parentname, '::', subelem.tag )
continue


Expand All @@ -181,7 +182,7 @@ def parse_group( node, parentname ):
#print "PARSING GROUP for ", parentname

if 'ref' not in node.attrib:
print "Error parsing group element for ", parentname
print( "Error parsing group element for ", parentname )
return None

ref = node.attrib['ref']
Expand All @@ -192,16 +193,16 @@ def parse_group( node, parentname ):
return '', '', [ tagline, ], ['',docline,]

if ref not in ALL_ENTRIES:
print "Error: can't parse group ", typename, " for in", parentname
print( "Error: can't parse group ", typename, " for in", parentname )
return None
ctype = ALL_ENTRIES[ref]
if ctype.tag != '{http://www.w3.org/2001/XMLSchema}group' or len(ctype) != 1:
print "Error: issue parsing group", ref, 'in', parentname
print( "Error: issue parsing group", ref, 'in', parentname )
return None
ctype = ctype[0]
if ctype.tag != '{http://www.w3.org/2001/XMLSchema}choice':
print 'Error: issue parsing group', ref, 'in', parentname
print '... putting group', ref, 'in-line for', parentname
print( 'Error: issue parsing group', ref, 'in', parentname )
print( '... putting group', ref, 'in-line for', parentname )
sc = parse_choice( ctype, parentname )
if sc is None:
return None
Expand All @@ -224,9 +225,9 @@ def parse_complextype( name, parentname, node ):
elif gc.tag == '{http://www.w3.org/2001/XMLSchema}attribute':
if 'name' not in gc.attrib:
if parentname is not None:
print "Error parsing attribute for entry", name, 'on', parentname
print( "Error parsing attribute for entry", name, 'on', parentname )
else:
print "Error parsing attribute for entry", name
print( "Error parsing attribute for entry", name )
continue
attrib = dict( gc.attrib )
docstring = ''
Expand Down Expand Up @@ -254,7 +255,7 @@ def parse_complextype( name, parentname, node ):
if sa is not None:
subtags.append( sa )
else:
print "Warning: skipping entry of type '"+ gc.tag+ "' in", name
print( "Warning: skipping entry of type '"+ gc.tag+ "' in", name )
pass

# Format the tags:
Expand Down Expand Up @@ -314,7 +315,7 @@ def process( name, node, outfilename ):
subtags = []

if node.tag != '{http://www.w3.org/2001/XMLSchema}complexType':
print "Error: expected complex type."
print( "Error: expected complex type." )
return

_, main_doc, tag_lines, doc_lines = parse_complextype( name, None, node )
Expand All @@ -341,13 +342,13 @@ def main( xsdfile, outdir ):
root = xsd.getroot()

if root.tag != '{http://www.w3.org/2001/XMLSchema}schema':
print "ERROR: Malformed XSD schema file."
print( "ERROR: Malformed XSD schema file." )
sys.exit()

entries = {}
for child in root:
if 'name' not in child.attrib:
print "Error in reading", child.tag
print( "Error in reading", child.tag )
continue

entries[ child.attrib['name'] ] = child
Expand All @@ -359,28 +360,28 @@ def main( xsdfile, outdir ):
to_process = {} # dictionary of lower-cased name:(xsd_type_name, display_name)
for section in SECTIONS:
if section not in entries:
print "ERROR: can't find section for", section, " in XSD."
print( "ERROR: can't find section for", section, " in XSD." )
continue
sec_entry = entries[ section ]
sec_choice = None
for se in sec_entry:
if se.tag != '{http://www.w3.org/2001/XMLSchema}choice':
continue
if sec_choice is not None:
print "ERROR: malformed entry for section", section
print( "ERROR: malformed entry for section", section )
continue
sec_choice = se
if sec_choice is None:
print "ERROR: malformed entry for section", section
print( "ERROR: malformed entry for section", section )
continue
for child in sec_choice:
if 'type' not in child.attrib or 'name' not in child.attrib:
print "ERROR: malformed entry in section", section
print( "ERROR: malformed entry in section", section )
continue
entry_type = child.attrib['type']
entry_name = child.attrib['name']
if entry_type not in entries:
print "ERROR: can't find definition for", entry_type
print( "ERROR: can't find definition for", entry_type )
continue
to_process.setdefault( entry_type.lower(), [] ).append( (entry_type, entry_name) )

Expand All @@ -390,7 +391,7 @@ def main( xsdfile, outdir ):
for key in to_process:
to_process[key].sort()
if len( to_process[key] ) > 1:
print "Case sensitivity conflict between: ", ' '.join( et for et, en in to_process[key] )
print( "Case sensitivity conflict between: ", ' '.join( et for et, en in to_process[key] ) )
for ii, (entry_type, entry_name) in enumerate( to_process[key] ):
if ii == 0:
outname = outdir + '/' + entry_type + '.md'
Expand All @@ -402,10 +403,10 @@ def main( xsdfile, outdir ):
if __name__ == "__main__":

if len(sys.argv) != 3:
print
print "ERROR: Usage: ./create_rosetta_scripts_docs.py <xsd file> <directory to write docs to>"
print
print __doc__
print( "\n" )
print( "ERROR: Usage: ./create_rosetta_scripts_docs.py <xsd file> <directory to write docs to>" )
print( "\n" )
print( __doc__ )
sys.exit()

main(sys.argv[1], sys.argv[2])
Expand Down