From 83c982d26c5ffa12b53edfae7154ccc24fca210f Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 22 Jul 2013 12:20:19 -0700 Subject: [PATCH] turtle writing improvements. * Update namespaces added to default writer. * Add a function to generate a default turtle prefix header. --- htsworkflow/util/rdfhelp.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py index 90b0e6a..cbe2a91 100644 --- a/htsworkflow/util/rdfhelp.py +++ b/htsworkflow/util/rdfhelp.py @@ -329,7 +329,7 @@ def add_default_schemas(model, schema_path=None): namespace = 'file://localhost/htsworkflow/schemas/'+s add_schema(model, schema, namespace) - if schema_path: + if schema_path: if type(schema_path) in types.StringTypes: schema_path = [schema_path] @@ -423,11 +423,19 @@ def get_serializer(name='turtle'): writer.set_namespace('wot', wotNS._prefix) # should these be here, kind of specific to an application - writer.set_namespace('libraryOntology', libraryOntology._prefix) + writer.set_namespace('htswlib', libraryOntology._prefix) writer.set_namespace('ucscSubmission', submissionOntology._prefix) writer.set_namespace('ucscDaf', dafTermOntology._prefix) + writer.set_namespace('geoSoft', geoSoftNS._prefix) + writer.set_namespace('encode3', encode3NS._prefix) return writer +def get_turtle_header(): + """Return a turtle header with our typical namespaces + """ + serializer = get_serializer() + empty = get_model() + return serializer.serialize_model_to_string(empty) def dump_model(model, destination=None): if destination is None: -- 2.30.2