def setUp(self):
registerplugins()
store = plugin.get("SQLAlchemy", Store)(identifier=self.ident)
self.graph = Graph(store, identifier=self.ident)
self.graph.open(self.uri, create=True)
g = self.graph
sid = BNode()
g.add((sid, RDF.subject, URIRef("http://www.google.com/")))
def test_registerplugins(self):
# I doubt this is quite right for a fresh pip installation,
# this test is mainly here to fill a coverage gap.
registerplugins()
self.assert_(plugin.get("SQLAlchemy", Store) is not None)
p = plugin._plugins
self.assert_(("SQLAlchemy", Store) in p, p)
del p[("SQLAlchemy", Store)]
plugin._plugins = p
registerplugins()
self.assert_(("SQLAlchemy", Store) in p, p)
def test_registerplugins(self):
# I doubt this is quite right for a fresh pip installation,
# this test is mainly here to fill a coverage gap.
from rdflib_sqlalchemy import registerplugins
from rdflib import plugin
from rdflib.store import Store
registerplugins()
self.assert_(plugin.get('SQLAlchemy', Store) is not None)
p = plugin._plugins
self.assert_(('SQLAlchemy', Store) in p, p)
del p[('SQLAlchemy', Store)]
plugin._plugins = p
registerplugins()
self.assert_(('SQLAlchemy', Store) in p, p)
def generate_graph():
"""Main function that, will parse all the cache folder and will generate a graph with all its content
Run this using python graph.py <path_to_dir_with_lattes_pages>
Parameters
----------
Returns
-------
"""
sys.excepthook = exception_handler
registerplugins()
# This is our ontology
schema = Namespace("http://schema.org/version/latest/schema.nt#")
identifier = URIRef("knowlattes_uriref")
# Create the Graph ###
SQLALCHEMY_URL = "sqlite:///%(here)s/database.sqlite" % {
"here": os.getcwd()
}
print(f"Creating the file to output: {SQLALCHEMY_URL}")
store = plugin.get("SQLAlchemy", Store)(identifier=identifier)
graph = Graph(store, identifier=identifier)
graph.open(SQLALCHEMY_URL, create=True)
# Get the lattes list
base_path = sys.argv[1]
lattes_profile_list = all_the_files_in_directory(base_path)
non_lattes_page = find_non_lattes_pages(base_path, lattes_profile_list)
lattes_pages = [i for i in lattes_profile_list if i not in non_lattes_page]
for lattes_page in tqdm(lattes_pages):
lattes_id = re.sub(".html", "", lattes_page)
file = open(base_path + "/" + lattes_page, "r", encoding="ISO-8859-1")
lattes_file = file.read()
file.close()
try:
lattes_page = ParserLattes(lattes_id, lattes_file)
add_lattes_reasercher_to_graph(lattes_page, graph, schema)
except Exception as inst:
print(f"{inst}")
graph.close()
def setup(graph_id):
rdf_store_ident = URIRef(sys.argv[1])
# Note that this DBURI does not specify host or username: instead, connection is
# made via UNIX domain sockets, which are self-authenticating
# To use this, this code needs to be run as the user in question
# Note also that pip install is in general user-local
dburi = Literal('postgresql+psycopg2:///kendraio_facta')
registerplugins()
store = plugin.get("SQLAlchemy", Store)(identifier=rdf_store_ident)
graph = Graph(store, identifier=URIRef(graph_id))
graph.open(dburi, create=True)
return graph, rdf_store_ident
def load_grah(path=None):
registerplugins()
identifier = URIRef("knowlattes_uriref")
# Create the Graph
SQLALCHEMY_URL = "sqlite:///%(here)s/database.sqlite" % {
"here": os.getcwd() if path is None else path
}
print(f"Reading the file to output: {SQLALCHEMY_URL}")
store = plugin.get("SQLAlchemy", Store)(identifier=identifier)
graph = Graph(store, identifier=identifier)
graph.open(SQLALCHEMY_URL, create=False)
return graph
def open(self):
try:
from rdflib_sqlalchemy import registerplugins
except ImportError:
raise OpenFailError(
'The rdflib-sqlalchemy package is not installed.'
' You may need to install one of "sqlite_source", "mysql_source", or'
' "postgresql_source" extra for owmeta_core.'
' For example, change "owmeta_core" in your setup.py or'
' requirements.txt to "owmeta_core[sqlite_source]" and reinstall'
)
registerplugins()
store = plugin.get("SQLAlchemy", Store)(**self._initargs())
self.graph = ConjunctiveGraph(store)
cfg = self._openconfig()
self.graph.open(cfg, create=True)
import os
from rdflib import plugin, ConjunctiveGraph, Literal, URIRef
from rdflib.store import Store
from rdflib_sqlalchemy import registerplugins
def read_configuration_file(config_file_path):
if not os.path.isfile(config_file_path):
raise Exception("The config file does not exist!")
config_parser = configparser.ConfigParser()
config_parser.read(config_file_path)
return config_parser
registerplugins()
config_parser = read_configuration_file('config.ini')
server = config_parser.get('POSTGRES', 'server', fallback='localhost')
port = config_parser.get('POSTGRES', 'port', fallback='5432')
database = config_parser.get('POSTGRES', 'database', fallback='benchmark')
password = config_parser.get('POSTGRES',
'password',
fallback='mysecretpassword')
identifier = URIRef("benchmark")
db_uri = Literal('postgresql+psycopg2://postgres:{0}@{1}:{2}/{3}'.format(
password, server, port, database))
def do(action):
def setup_rdf_store(ident):
registerplugins()
store = plugin.get("SQLAlchemy", Store)(identifier=ident)
return store
self.graph.commit()
@classmethod
def _is_graph_add_exception_acceptable(cls, ex):
"""Checks if a graph-add exception can be safely ignored.
"""
# integrity errors due to violating unique constraints should be safe
# to ignore since the only unique constraints in rdflib-sqlalchemy are
# on index columns
return 'UNIQUE constraint failed' in text_type(ex)
_METADATA_CACHE = None
registerplugins()
def set_metadata_cache(cache):
"""Sets the metadata cache object to use.
"""
global _METADATA_CACHE
if _METADATA_CACHE and _METADATA_CACHE.is_open:
_METADATA_CACHE.close()
_METADATA_CACHE = cache
def get_metadata_cache():
# limitations under the License.
#
#===============================================================================
#
# A simple knowledge base...
#
#===============================================================================
from contextlib import ContextDecorator
#===============================================================================
import rdflib
import rdflib_sqlalchemy as sqlalchemy
sqlalchemy.registerplugins()
#from rdflib.plugins.sparql.results.jsonlayer import encode as JSON_results_encode
from rdflib.plugins.sparql.results.jsonresults import JSONResultSerializer
#===============================================================================
class KnowledgeBase(rdflib.Graph, ContextDecorator):
def __init__(self, kb_path, create=False):
SPARC = rdflib.URIRef('SPARC')
store = rdflib.plugin.get('SQLAlchemy',
rdflib.store.Store)(identifier=SPARC)
super().__init__(store, identifier=SPARC)
database = rdflib.Literal('sqlite:///{}'.format(kb_path))
self.open(database, create=create)