diff --git a/pyontutils/ontload.py b/pyontutils/ontload.py index b987ab1e..49dcea14 100755 --- a/pyontutils/ontload.py +++ b/pyontutils/ontload.py @@ -579,13 +579,15 @@ def inner(local_filepath, remote=False): def loadall(git_local, repo_name, local=False, dobig=False): local_base = jpth(git_local, repo_name) lb_ttl = os.path.realpath(jpth(local_base, 'ttl')) - + #match = (rdflib.term.URIRef('http://purl.org/dc/elements/1.1/member'), # iao.owl #rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), #rdflib.term.URIRef('http://www.w3.org/2002/07/owl#AnnotationProperty')) done = [] - filenames = [f for g in ('*', '*/*', '*/*/*') for f in glob(lb_ttl + '/' + g + '.ttl')] + git_path = '/home/tmsincomb/Dropbox/git/' + hardcoded_files = [repo_name + '/' + 'extra.ttl'] + [git_path+'sparc-view.ttl', git_path+'fma_slim.ttl', git_path+'emapa.ttl', git_path+'uberon.ttl', git_path+'mondo.ttl'] + filenames = hardcoded_files + [f for g in ('*', '*/*', '*/*/*') for f in glob(lb_ttl + '/' + g + '.ttl')] graph = OntGraph() for f in filenames: print(f) @@ -598,12 +600,17 @@ def repeat(dobig=dobig): # we don't really know when to stop, so just adjust for s, o in graph.subject_objects(owl.imports): if os.path.basename(o) not in done and o not in done: #if (o, rdf.type, owl.Ontology) not in graph: + if not o.startswith('/home/tmsincomb'): + continue print(o) done.append(o) ext = os.path.splitext(o)[1] fmt = 'turtle' if ext == '.ttl' else 'xml' if noneMembers(o, *bigleaves) or dobig: - graph.parse(o, format=fmt) + try: + graph.parse(o, format=fmt) + except: + print('FAILED:', o) #if match in graph: #raise BaseException('Evil file found %s' % o) @@ -670,7 +677,7 @@ def inner(graph): records = {c:[l, s, p] for c, l, s, p in inner(graph) if l or s} with open(os.path.expanduser('~/files/ontology-classes-with-labels-synonyms-parents.json'), 'wt') as f: - json.dump(records, f, sort_keys=True, indent=2) + json.dump(records, f, sort_keys=True, indent=2) def make_post_clone(git_local, repo_name, remote_base):