Change add_default_schema to use pkg_resources feature to find schemas.

I was trying to get py.test to work and it really wants to install
things, and my previous method to find the schema files wasn't working
very well with the egg distribution.

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index e5c8718d8906897b86069be8e88baf19bcc2709c..c116fc9236c1f06641365a8bc6d3680ab727abea 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -9,6 +9,7 @@ import logging
 import os
 import sys
 import types
+from pkg_resources import resource_listdir, resource_string
 
 import lxml.html
 import lxml.html.clean
@@ -322,17 +323,24 @@ def add_default_schemas(model, schema_path=None):
     or in the list of directories provided in schema_path
     """
 
-    if schema_path is None:
-        path, _ = os.path.split(__file__)
-        schema_path = [os.path.join(path, 'schemas')]
-    elif type(schema_path) in types.StringTypes:
-        schema_path = [schema_path]
+    schemas = resource_listdir(__name__, 'schemas')
+    for s in schemas:
+        schema = resource_string(__name__,  'schemas/' + s)
+        namespace = 'file://localhost/htsworkflow/schemas/'+s
+        add_schema(model, schema, namespace)
 
-    for p in schema_path:
-        for f in glob(os.path.join(p, '*.turtle')):
-            add_schema(model, f)
+    if schema_path:    
+        if type(schema_path) in types.StringTypes:
+            schema_path = [schema_path]
 
-def add_schema(model, filename):
+        for path in schema_path:
+            for pathname in glob(os.path.join(path, '*.turtle')):
+                url = 'file://' + os.path.splitext(pathname)[0]
+                stream = open(pathname, 'r')
+                add_schema(model, stream, url)
+                stream.close()
+
+def add_schema(model, schema, url):
     """Add a schema to a model.
 
     Main difference from 'load_into_model' is it tags it with
@@ -340,8 +348,7 @@ def add_schema(model, filename):
     """
     parser = RDF.Parser(name='turtle')
     context = RDF.Node(RDF.Uri(SCHEMAS_URL))
-    url = 'file://' + filename
-    for s in parser.parse_as_stream(url):
+    for s in parser.parse_string_as_stream(schema, url):
         try:
             model.append(s, context)
         except RDF.RedlandError as e: