"""Helper features for working with librdf
"""
+import collections
from datetime import datetime
+from glob import glob
from urlparse import urlparse, urlunparse
from urllib2 import urlopen
import logging
import os
+import sys
import types
+from pkg_resources import resource_listdir, resource_string
import lxml.html
import lxml.html.clean
logger = logging.getLogger(__name__)
-# standard ontology namespaces
-owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
-dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
-rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
-rdfsNS = RDF.NS("http://www.w3.org/2000/01/rdf-schema#")
-xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
-
-# internal ontologies
-submissionOntology = RDF.NS(
- "http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#")
-dafTermOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/UcscDaf#")
-libraryOntology = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
-inventoryOntology = RDF.NS(
- "http://jumpgate.caltech.edu/wiki/InventoryOntology#")
-submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
-geoSoftNS = RDF.NS('http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#')
+from htsworkflow.util.rdfns import *
+
+SCHEMAS_URL='http://jumpgate.caltech.edu/phony/schemas'
+INFERENCE_URL='http://jumpgate.caltech.edu/phony/inference'
ISOFORMAT_MS = "%Y-%m-%dT%H:%M:%S.%f"
ISOFORMAT_SHORT = "%Y-%m-%dT%H:%M:%S"
-
-def sparql_query(model, query_filename):
+def sparql_query(model, query_filename, output_format='text'):
"""Execute sparql query from file
"""
logger.info("Opening: %s" % (query_filename,))
query_body = open(query_filename, 'r').read()
query = RDF.SPARQLQuery(query_body)
results = query.execute(model)
- display_query_results(results)
+ if output_format == 'html':
+ html_query_results(results)
+ else:
+ display_query_results(results)
def display_query_results(results):
print "{0}: {1}".format(k, v)
print
+def html_query_results(result_stream):
+ from django.conf import settings
+ from django.template import Context, loader
+
+ # I did this because I couldn't figure out how to
+ # get simplify_rdf into the django template as a filter
+ class Simplified(object):
+ def __init__(self, value):
+ self.simple = simplify_rdf(value)
+ if value.is_resource():
+ self.url = value
+ else:
+ self.url = None
+
+ template = loader.get_template('rdf_report.html')
+ results = []
+ for row in result_stream:
+ new_row = collections.OrderedDict()
+ row_urls = []
+ for k,v in row.items():
+ new_row[k] = Simplified(v)
+ results.append(new_row)
+ context = Context({'results': results,})
+ print template.render(context)
def blankOrUri(value=None):
"""Return a blank node for None or a resource node for strings.
return node
-def toTypedNode(value):
+def toTypedNode(value, language="en"):
"""Convert a python variable to a RDF Node with its closest xsd type
"""
if type(value) == types.BooleanType:
if value_type is not None:
node = RDF.Node(literal=value, datatype=value_type)
else:
- node = RDF.Node(literal=unicode(value).encode('utf-8'))
+ node = RDF.Node(literal=unicode(value).encode('utf-8'), language=language)
return node
def fromTypedNode(node):
"""Convert a typed RDF Node to its closest python equivalent
"""
- if node is None:
- return None
+ if not isinstance(node, RDF.Node):
+ return node
+ if node.is_resource():
+ return node
value_type = get_node_type(node)
literal = node.literal_value['string']
return value_type.replace(str(xsdNS[''].uri), '')
-def simplifyUri(namespace, term):
+def simplify_rdf(value):
+ """Return a short name for a RDF object
+ e.g. The last part of a URI or an untyped string.
+ """
+ if isinstance(value, RDF.Node):
+ if value.is_resource():
+ name = simplify_uri(str(value.uri))
+ elif value.is_blank():
+ name = '<BLANK>'
+ else:
+ name = value.literal_value['string']
+ elif isinstance(value, RDF.Uri):
+ name = split_uri(str(value))
+ else:
+ name = value
+ return str(name)
+
+
+def simplify_uri(uri):
+ """Split off the end of a uri
+
+ >>> simplify_uri('http://asdf.org/foo/bar')
+ 'bar'
+ >>> simplify_uri('http://asdf.org/foo/bar#bleem')
+ 'bleem'
+ >>> simplify_uri('http://asdf.org/foo/bar/')
+ 'bar'
+ >>> simplify_uri('http://asdf.org/foo/bar?was=foo')
+ 'was=foo'
+ """
+ if isinstance(uri, RDF.Node):
+ if uri.is_resource():
+ uri = uri.uri
+ else:
+ raise ValueError("Can't simplify an RDF literal")
+ if isinstance(uri, RDF.Uri):
+ uri = str(uri)
+
+ parsed = urlparse(uri)
+ if len(parsed.query) > 0:
+ return parsed.query
+ elif len(parsed.fragment) > 0:
+ return parsed.fragment
+ elif len(parsed.path) > 0:
+ for element in reversed(parsed.path.split('/')):
+ if len(element) > 0:
+ return element
+ raise ValueError("Unable to simplify %s" % (uri,))
+
+def strip_namespace(namespace, term):
"""Remove the namespace portion of a term
returns None if they aren't in common
return term_s.replace(namespace._prefix, "")
-def get_model(model_name=None, directory=None):
+def get_model(model_name=None, directory=None, use_contexts=True):
if directory is None:
directory = os.getcwd()
+ contexts = 'yes' if use_contexts else 'no'
+
if model_name is None:
- storage = RDF.MemoryStorage()
+ storage = RDF.MemoryStorage(options_string="contexts='{}'".format(contexts))
logger.info("Using RDF Memory model")
else:
- options = "hash-type='bdb',dir='{0}'".format(directory)
+ options = "contexts='{0}',hash-type='bdb',dir='{1}'".format(contexts, directory)
storage = RDF.HashStorage(model_name,
options=options)
logger.info("Using {0} with options {1}".format(model_name, options))
def load_into_model(model, parser_name, path, ns=None):
+ if type(ns) in types.StringTypes:
+ ns = RDF.Uri(ns)
+
+ if isinstance(path, RDF.Node):
+ if path.is_resource():
+ path = str(path.uri)
+ else:
+ raise ValueError("url to load can't be a RDF literal")
+
url_parts = list(urlparse(path))
- if len(url_parts[0]) == 0:
+ if len(url_parts[0]) == 0 or url_parts[0] == 'file':
url_parts[0] = 'file'
url_parts[2] = os.path.abspath(url_parts[2])
+ if parser_name is None or parser_name == 'guess':
+ parser_name = guess_parser_by_extension(path)
url = urlunparse(url_parts)
- logger.info("Opening %s" % (url,))
- req = urlopen(url)
- logger.debug("request status: %s" % (req.code,))
- if parser_name is None:
- content_type = req.headers.get('Content-Type', None)
- parser_name = guess_parser(content_type, path)
- logger.debug("Guessed parser: %s" % (parser_name,))
- data = req.read()
- load_string_into_model(model, parser_name, data, ns)
+ logger.info("Opening {0} with parser {1}".format(url, parser_name))
+ rdf_parser = RDF.Parser(name=parser_name)
+
+ statements = []
+ retries = 3
+ succeeded = False
+ while retries > 0:
+ try:
+ retries -= 1
+ statements = rdf_parser.parse_as_stream(url, ns)
+ retries = 0
+ succeeded = True
+ except RDF.RedlandError, e:
+ errmsg = "RDF.RedlandError: {0} {1} tries remaining"
+ logger.error(errmsg.format(str(e), retries))
+
+ if not succeeded:
+ logger.warn("Unable to download %s", url)
+
+ for s in statements:
+ conditionally_add_statement(model, s, ns)
def load_string_into_model(model, parser_name, data, ns=None):
- if ns is None:
- ns = RDF.NS("http://localhost/")
- imports = owlNS['imports']
+ ns = fixup_namespace(ns)
+ logger.debug("load_string_into_model parser={0}, len={1}".format(
+ parser_name, len(data)))
rdf_parser = RDF.Parser(name=parser_name)
+
for s in rdf_parser.parse_string_as_stream(data, ns):
- if s.predicate == imports:
- obj = str(s.object)
- logger.info("Importing %s" % (obj,))
- load_into_model(model, None, obj, ns)
- if s.object.is_literal():
- value_type = get_node_type(s.object)
- if value_type == 'string':
- s.object = sanitize_literal(s.object)
- model.add_statement(s)
+ conditionally_add_statement(model, s, ns)
+
+
+def fixup_namespace(ns):
+ if ns is None:
+ ns = RDF.Uri("http://localhost/")
+ elif type(ns) in types.StringTypes:
+ ns = RDF.Uri(ns)
+ elif not(isinstance(ns, RDF.Uri)):
+ errmsg = "Namespace should be string or uri not {0}"
+ raise ValueError(errmsg.format(str(type(ns))))
+ return ns
+
+
+def conditionally_add_statement(model, s, ns):
+ imports = owlNS['imports']
+ if s.predicate == imports:
+ obj = str(s.object)
+ logger.info("Importing %s" % (obj,))
+ load_into_model(model, None, obj, ns)
+ if s.object.is_literal():
+ value_type = get_node_type(s.object)
+ if value_type == 'string':
+ s.object = sanitize_literal(s.object)
+ model.add_statement(s)
+
+
+def add_default_schemas(model, schema_path=None):
+ """Add default schemas to a model
+ Looks for turtle files in either htsworkflow/util/schemas
+ or in the list of directories provided in 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)
+
+ if schema_path:
+ if type(schema_path) in types.StringTypes:
+ schema_path = [schema_path]
+
+ 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
+ a RDFlib context so I can remove them later.
+ """
+ parser = RDF.Parser(name='turtle')
+ context = RDF.Node(RDF.Uri(SCHEMAS_URL))
+ for s in parser.parse_string_as_stream(schema, url):
+ try:
+ model.append(s, context)
+ except RDF.RedlandError as e:
+ logger.error("%s with %s", str(e), str(s))
+
+
+def remove_schemas(model):
+ """Remove statements labeled with our schema context"""
+ context = RDF.Node(RDF.Uri(SCHEMAS_URL))
+ model.context_remove_statements(context)
def sanitize_literal(node):
if not isinstance(node, RDF.Node):
raise ValueError("sanitize_literal only works on RDF.Nodes")
- element = lxml.html.fromstring(node.literal_value['string'])
- cleaner = lxml.html.clean.Cleaner(page_structure=False)
- element = cleaner.clean_html(element)
- text = lxml.html.tostring(element)
- p_len = 3
- slash_p_len = 4
+ s = node.literal_value['string']
+ if len(s) > 0:
+ element = lxml.html.fromstring(s)
+ cleaner = lxml.html.clean.Cleaner(page_structure=False)
+ element = cleaner.clean_html(element)
+ text = lxml.html.tostring(element)
+ p_len = 3
+ slash_p_len = 4
- args = {'literal': text[p_len:-slash_p_len]}
+ args = {'literal': text[p_len:-slash_p_len]}
+ else:
+ args = {'literal': ''}
datatype = node.literal_value['datatype']
if datatype is not None:
args['datatype'] = datatype
def guess_parser(content_type, pathname):
- if content_type in ('application/rdf+xml'):
+ if content_type in ('application/rdf+xml',):
return 'rdfxml'
- elif content_type in ('application/x-turtle'):
+ elif content_type in ('application/x-turtle',):
return 'turtle'
- elif content_type in ('text/html'):
+ elif content_type in ('text/html',):
return 'rdfa'
- elif content_type is None:
- _, ext = os.path.splitext(pathname)
- if ext in ('xml', 'rdf'):
- return 'rdfxml'
- elif ext in ('html'):
- return 'rdfa'
- elif ext in ('turtle'):
- return 'turtle'
- return 'guess'
+ elif content_type is None or content_type in ('text/plain',):
+ return guess_parser_by_extension(pathname)
+def guess_parser_by_extension(pathname):
+ _, ext = os.path.splitext(pathname)
+ if ext in ('.xml', '.rdf'):
+ return 'rdfxml'
+ elif ext in ('.html',):
+ return 'rdfa'
+ elif ext in ('.turtle',):
+ return 'turtle'
+ return 'guess'
def get_serializer(name='turtle'):
"""Return a serializer with our standard prefixes loaded
"""
writer = RDF.Serializer(name=name)
# really standard stuff
- writer.set_namespace('owl', owlNS._prefix)
writer.set_namespace('rdf', rdfNS._prefix)
writer.set_namespace('rdfs', rdfsNS._prefix)
+ writer.set_namespace('owl', owlNS._prefix)
+ writer.set_namespace('dc', dcNS._prefix)
+ writer.set_namespace('xml', xmlNS._prefix)
writer.set_namespace('xsd', xsdNS._prefix)
+ writer.set_namespace('vs', vsNS._prefix)
+ 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):
+def dump_model(model, destination=None):
+ if destination is None:
+ destination = sys.stdout
serializer = get_serializer()
- print serializer.serialize_model_to_string(model)
+ destination.write(serializer.serialize_model_to_string(model))
+ destination.write(os.linesep)
projects / htsworkflow.git / blobdiff