def sparql():
"""
A POST or GET method to query the Open Annotations index with a SPARQL Query
This method has READ access to the Annotations index.
Required parameters:
query: The SPARQL query to execute
"""
sparql_xml_results = ""
try:
if request.method == 'POST':
q = request.form.get('query', None)
else:
q = request.args.get('query', None)
query = QueryFactory.create(String(q))
# Start dataset READ transaction
dataset = TDBFactory.createDataset(app.config['STORE_LOCATION'])
dataset.begin(ReadWrite.READ)
try:
qexec = QueryExecutionFactory.create(query, dataset)
results = qexec.execSelect()
try:
sparql_xml_results = ResultSetFormatter.asXMLString(results)
finally:
qexec.close()
finally:
dataset.end()
except AnnotationError, ex:
return jsonify({'value' : ex.value, 'trace' : traceback.format_stack()})
def test_store_creation(self):
from com.hp.hpl.jena.tdb import TDBFactory
from java.io import ByteArrayInputStream
from java.lang import String
db_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'OAC-testing.tdb')
dataset = TDBFactory.createDataset(db_path)
# Make sure the store was created
assert os.path.isdir(db_path)
# Make InputStream triples
rdf_text = '<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:about="info:fedora/changeme:651"><rdf:type rdf:resource="oa:Annotation"></rdf:type><oa:hasBody xmlns:oa="http://www.w3.org/ns/openannotation/core/" rdf:resource="info:fedora/changeme:650"></oa:hasBody><oa:modelVersion xmlns:oa="http://www.w3.org/ns/openannotation/core/" rdf:resource="http://www.openannotation.org/spec/core/20120509.html"></oa:modelVersion><oa:generated xmlns:oa="http://www.w3.org/ns/openannotation/core/">2012-06-07T03:50:55.993000Z</oa:generated></rdf:Description><rdf:Description rdf:about="info:fedora/changeme:650"><rdf:type rdf:resource="oa:Body"></rdf:type><dc:format xmlns:dc="http://purl.org/dc/elements/1.1/">text/xml</dc:format></rdf:Description></rdf:RDF>'
rdfxml = String(rdf_text)
input_stream = ByteArrayInputStream(rdfxml.getBytes())
model = dataset.getDefaultModel()
model.begin()
model.read(input_stream, None)
model.commit()
model.close()
# Were all of the triples added?
assert model.size() == 6
shutil.rmtree(db_path)
# Was the store removed?
assert not os.path.isdir(db_path)
def rebuild():
"""
A GET method that will rebuild the internal TDB index
with all of the Annotation objects in Fedora
"""
try:
query = "prefix fm: <info:fedora/fedora-system:def/model#> select ?s where {?s fm:hasModel <info:fedora/%s> }" \
% app.config.get('DEFUALT_ANNOTATION_CONTENT_MODEL')
all_pids = (p.lstrip('info:fedora/') for p in Fedora.get_sparql_query_resuts(query))
result, mimetype = Annotation.serialize(all_pids, format='nt', check_object=False)
dataset = TDBFactory.createDataset(app.config['STORE_LOCATION'])
# Remove all entries from the default model
dataset.begin(ReadWrite.WRITE)
try:
model = dataset.getDefaultModel()
model.begin()
model.removeAll()
model.commit()
model.close()
dataset.commit()
except Exception, exc:
raise
finally:
dataset.end()
TDB.sync(dataset)
# Load the triples
dataset.begin(ReadWrite.WRITE)
try:
model = dataset.getDefaultModel()
model.begin()
n3_input_stream = ByteArrayInputStream(String(result).getBytes())
model.read(n3_input_stream, None, "N-TRIPLE")
model.commit()
model.close()
dataset.commit()
except Exception, exc:
raise
def rebuild_one():
"""
A POST method that will rebuild the internal TDB index
with a specific PID from Fedora
"""
pid = request.form.get('pid', None)
if pid is None:
raise AnnotationError("Please pass a PID parameter to the rebuild POST request")
print "calling 'rebuild_one' with PID: %s" % pid
try:
# Get PID from Fedora and serialize it
result, mimetype = Annotation.serialize([pid], format='nt', check_object=True)
# Don't do anything if this there are no serialization results
# ie. was not an Annotation object
dataset = TDBFactory.createDataset(app.config['STORE_LOCATION'])
# Remove all triples from TDB involving this PID using SPARQL
# This was my first attempt, but the SPARQL query does not
# seem to be working. Using the Jena API (below) also works.
"""
query = "DELETE { ?s ?p ?o } WHERE { <info:fedora/%s> ?p ?o }" % pid
update = UpdateFactory.create(String(query))
dataset.begin(ReadWrite.WRITE)
try:
graph_store = GraphStoreFactory.create(dataset.getDefaultModel())
update_processor = UpdateExecutionFactory.create(update, graph_store)
results = update_processor.execute()
except Exception, exc:
raise
finally:
dataset.end()
TDB.sync(dataset)
"""
# Remove all triples from TDB involving this PID using Jena API
# Start dataset WRITE transaction
dataset.begin(ReadWrite.WRITE)
try:
resource = ResourceFactory.createResource("info:fedora/%s" % pid)
model = dataset.getDefaultModel()
model.removeAll(resource, None, None)
model.commit()
model.close()
dataset.commit()
except Exception, exc:
raise
finally:
dataset.end()
TDB.sync(dataset)
# Add new triples to TDB
dataset.begin(ReadWrite.WRITE)
try:
model = dataset.getDefaultModel()
model.begin()
n3_input_stream = ByteArrayInputStream(String(result).getBytes())
model.read(n3_input_stream, None, "N-TRIPLE")
model.commit()
model.close()
dataset.commit()
except Exception, exc:
raise
def create():
"""
A POST method that creates an Annotation (A-1) object
based on a number of parameters.
Required Parameters:
source_uri: The URI for the whole target object
dc_title: Dublin Core title associated with the annotation,
i.e. "dublin core title goes here"
body_inline Plain text string to store as the body
OR
body_content: Contents of the body (XML, text, json, etc.)
AND
body_mimetype: Mimetype of the body_content
OR
body_uri: URI pointing to the body of the annotation
Optional Parameters:
annotator: A string representing a user ID (0 or more)
ie. 'Charly'
generator: A string representing what generated the annotation
ie. 'Web Client'
oax_style_uri: A URI for a XSLT stylesheet used to render the whole target object. (0 or 1)
oa_selector: A string with the selector value(0 or 1)
oa_selector_type_uri: Required if an oa_selector is passed in
ie. oa:Fragment
fragment_type: URI describing the oa_selector type Optional and only used if
an oa_selector is passed in.
ie. 'http://www.w3.org/TR/xpath/'
body_content_model: A string representing the body's content model
ie. 'tei-annotation'
Will create 1 or 2 Fedora objects. One will represent the actual annotation (A-1)
and one will be the body of text that annotates the Fedora object (B-1).
>>> import urllib
>>> import urllib2
>>> post_url = "http://localhost:5000/create"
>>> params = {
"source_uri" : "test:1#xpointer('/foo')",
"body_content" : "<TEI><body>text body</body></TEI>",
"body_mimetype" : "text/xml",
"dc_title" : "Open Annotation Collaboration Annotation object (A-1)"
}
>>> encoded_data = urllib.urlencode( params )
>>> request = urllib2.Request( post_url, encoded_data )
>>> response = urllib2.urlopen( request )
>>> print response.read()
{
"errors": [],
"body_pid": "changeme:180",
"annotation_pid": "changeme:181"
}
"""
try:
annote = Annotation(source_uri = request.form.get('source_uri'),
dc_title = request.form.get('dc_title'),
annotated = datetime.utcnow(),
body_inline = request.form.get('body_inline', None),
body_content = request.form.get('body_content', None),
body_mimetype = request.form.get('body_mimetype', None),
body_uri = request.form.get('body_uri', None),
body_content_model = request.form.get('body_content_model', None),
annotator = request.form.get('annotator', None),
generator = request.form.get('generator', None),
oax_style_uri = request.form.get('oax_style_uri', None),
oa_selector = request.form.get('oa_selector', None),
oa_selector_type_uri = request.form.get('oa_selector_type_uri', None),
fragment_type = request.form.get('fragment_type', None))
annote.create()
annote.submit()
if annote.validate():
# Start dataset transaction
dataset = TDBFactory.createDataset(app.config['STORE_LOCATION'])
dataset.begin(ReadWrite.WRITE)
try:
model = dataset.getDefaultModel()
model.begin()
if annote.annotation_rdf is not None:
anno_input_stream = ByteArrayInputStream(String(tostring(annote.annotation_rdf)).getBytes())
model.read(anno_input_stream, None)
anno_input_stream.close()
if annote.specific_target_rdf_element is not None:
spectaget_input_stream = ByteArrayInputStream(String(tostring(annote.specific_target_rdf_element)).getBytes())
model.read(spectaget_input_stream, None)
spectaget_input_stream.close()
if annote.selector_rdf_element is not None:
selector_input_stream = ByteArrayInputStream(String(tostring(annote.selector_rdf_element)).getBytes())
model.read(selector_input_stream, None)
selector_input_stream.close()
if annote.rels_ext_rdf_element is not None:
relsext_input_stream = ByteArrayInputStream(String(tostring(annote.rels_ext_rdf_element)).getBytes())
model.read(relsext_input_stream, None)
relsext_input_stream.close()
if annote.body_inline_rdf_element is not None:
body_inline_input_stream = ByteArrayInputStream(String(tostring(annote.body_inline_rdf_element)).getBytes())
model.read(body_inline_input_stream, None)
body_inline_input_stream.close()
model.commit()
model.close()
dataset.commit()
except Exception, exc:
raise
finally:
dataset.end()
TDB.sync(dataset)