def __init__(self): #watch("neo4j.bolt") self.graph = Graph(super().graph_url) tx = self.graph.begin() tx.run(SnomedConceptProcessor.create_index_concept_id) tx.run(SnomedConceptProcessor.create_index_term) tx.commit()
def get_graph_context(config): if config is None: return Graph(auth=('neo4j', 'pass'), host='localhost') login = config.get('NEO4J_LOGIN', 'neo4j') password = config.get('NEO4J_PASS', 'pass') host = config.get('NEO4J_HOST', 'localhost') return Graph(auth=(login, password), host=host)
def __init__(self, uri=None, **settings): self.output_file = settings.pop("file", None) verbose = settings.pop("verbose", False) connection_data = get_connection_data(uri, **settings) try: self.graph = Graph(uri, **settings) except ServiceUnavailable as error: raise ConsoleError("Could not connect to {} -- {}".format( connection_data["uri"], error)) try: makedirs(HISTORY_FILE_DIR) except OSError: pass self.history = FileHistory(path_join(HISTORY_FILE_DIR, HISTORY_FILE)) self.prompt_args = { "history": self.history, "lexer": PygmentsLexer(CypherLexer), "style": merge_styles([ style_from_pygments_cls(NativeStyle), style_from_pygments_dict({ Token.Prompt: "#ansi{}".format(self.prompt_colour.replace( "cyan", "teal")), Token.TxCounter: "#ansi{} bold".format( self.tx_colour.replace("cyan", "teal")), }) ]) } self.lexer = CypherLexer() self.result_writer = Table.write if verbose: from neobolt.diagnostics import watch self.watcher = watch("neo4j.%s" % connection_data["scheme"]) self.commands = { "//": self.set_multi_line, "/e": self.edit, "/?": self.help, "/h": self.help, "/help": self.help, "/x": self.exit, "/exit": self.exit, "/play": self.play, "/csv": self.set_csv_result_writer, "/table": self.set_tabular_result_writer, "/tsv": self.set_tsv_result_writer, "/config": self.config, "/kernel": self.kernel, } self.tx = None self.tx_counter = 0
def __init__(self, profile=None, *_, **settings): super(ClientConsole, self).__init__(__name__, verbosity=settings.get("verbosity", 0)) self.output_file = settings.pop("file", None) welcome = settings.get("welcome", True) if welcome: self.write(TITLE) self.write() self.write(dedent(QUICK_HELP)) self.write() self.profile = ConnectionProfile(profile, **settings) try: self.graph = Graph(self.profile) except OSError as error: self.critical("Could not connect to <%s> (%s)", self.profile.uri, " ".join(map(str, error.args))) raise else: self.debug("Connected to <%s>", self.graph.service.uri) try: makedirs(HISTORY_FILE_DIR) except OSError: pass self.history = FileHistory(path_join(HISTORY_FILE_DIR, HISTORY_FILE)) self.lexer = CypherLexer() self.result_writer = Table.write self.commands = { "//": self.set_multi_line, "/e": self.edit, "/?": self.help, "/h": self.help, "/help": self.help, "/x": self.exit, "/exit": self.exit, "/play": self.play, "/csv": self.set_csv_result_writer, "/table": self.set_tabular_result_writer, "/tsv": self.set_tsv_result_writer, "/config": self.config, "/kernel": self.kernel, } self.tx = None self.qid = 0
class SnomedConceptProcessor(BaseItemProcessor): statement = Template( "CREATE (c:Concept:FSA:$label {conceptId: \"$id\", term: \"$term\", descType: $descType});" ) create_index_concept_id = "CREATE INDEX ON :Concept(conceptId)" create_index_term = "CREATE INDEX ON :Concept(term)" def __init__(self): #watch("neo4j.bolt") self.graph = Graph(super().graph_url) tx = self.graph.begin() tx.run(SnomedConceptProcessor.create_index_concept_id) tx.run(SnomedConceptProcessor.create_index_term) tx.commit() def process(self, record, tx): label = self.extract_label(record['term']) if label is None or label[0].isdigit(): label = 'NO_LABEL' term = record["term"].replace('"', '\\"') local_statement = SnomedConceptProcessor.statement.substitute( id=record["id"], term=term, descType=record["descType"], label=label) tx.run(local_statement) def extract_label(self, text): search_match = re.search(r"\([^)]*\)$", text.rstrip()) if search_match is not None: match_text = re.sub(r"[^a-zA-Z0-9_\s]", "", search_match.group(0)).upper() return "_".join(match_text.split()) else: return None
def __init__(self): #watch("neo4j.bolt") self.graph = Graph(super().graph_url) tx = self.graph.begin() tx.run(SnomedConceptProcessor.create_index_concept_id) tx.run(SnomedConceptProcessor.create_index_term) tx.commit()
class SnomedConceptProcessor(BaseItemProcessor): statement = Template("CREATE (c:Concept:FSA:$label {conceptId: \"$id\", term: \"$term\", descType: $descType});") create_index_concept_id = "CREATE INDEX ON :Concept(conceptId)" create_index_term = "CREATE INDEX ON :Concept(term)" def __init__(self): #watch("neo4j.bolt") self.graph = Graph(super().graph_url) tx = self.graph.begin() tx.run(SnomedConceptProcessor.create_index_concept_id) tx.run(SnomedConceptProcessor.create_index_term) tx.commit() def process(self, record, tx): label = self.extract_label(record['term']) if label is None or label[0].isdigit(): label = 'NO_LABEL' term = record["term"].replace('"','\\"') local_statement = SnomedConceptProcessor.statement.substitute(id=record["id"], term=term, descType=record["descType"], label=label) tx.run(local_statement) def extract_label(self, text): search_match = re.search(r"\([^)]*\)$", text.rstrip()) if search_match is not None: match_text = re.sub(r"[^a-zA-Z0-9_\s]", "", search_match.group(0)).upper() return "_".join(match_text.split()) else: return None
def connectGraph(self): # graph = Graph(user = self.user, password = self.password) authenticate(self.service_ip, self.user, self.password) graph = Graph('http://%s/db/data/' % self.service_ip) # authenticate("localhost:7474", self.user, self.password) # graph = Graph("http://localhost:7474/db/data/") return graph
def __init__(self, content_type, uri, name=None): self._content_type = content_type key_value_pos = uri.find("/{key}/{value}") if key_value_pos >= 0: self._searcher = ResourceTemplate(uri) self.__remote__ = Resource(uri[:key_value_pos]) else: self.__remote__ = Resource(uri) self._searcher = ResourceTemplate(uri.string + "/{key}/{value}") uri = remote(self).uri self._create_or_fail = Resource( uri.resolve("?uniqueness=create_or_fail")) self._get_or_create = Resource( uri.resolve("?uniqueness=get_or_create")) self._query_template = ResourceTemplate(uri.string + "{?query,order}") self._name = name or uri.path.segments[-1] self.__searcher_stem_cache = {} self.graph = Graph(uri.resolve("/db/data/").string)
def setup(): author_nodes = [] pmid_nodes = [] written_by = [] count = 0 g = Graph(uri="bolt://localhost:7687", auth=("neo4j", "justjournals")) g.schema.create_uniqueness_constraint('PMID', 'name') g.schema.create_uniqueness_constraint('Person', 'title') g.schema.create_uniqueness_constraint('Factor', 'dID') g.schema.create_uniqueness_constraint('Qualifier', 'qID')
def main(args): logger = log.getdebuglogger("dbmanager") graph = Graph(host=NEO4J_HOST, user=NEO4J_USERNAME, password=NEO4J_PASSWORD) args_obj = parse_args(args) if args_obj.verbose: logger.setLevel(log.LEVELS[-1]) else: logger.setLevel(log.LEVELS[0]) args_obj.func(args_obj, graph, logger)
def graph_session(yield_graph=False, *args, **kwargs): '''Generate a Neo4j graph transaction object with safe commit/rollback built-in. Args: {*args, **kwargs}: Any arguments for py2neo.database.Graph Yields: py2neo.database.Transaction ''' graph = Graph(*args, **kwargs) transaction = graph.begin() try: if yield_graph: yield (graph, transaction) else: yield transaction transaction.commit() except: transaction.rollback() raise finally: del transaction del graph
def __init__(self, content_type, uri, name=None): self._content_type = content_type key_value_pos = uri.find("/{key}/{value}") if key_value_pos >= 0: self._searcher = ResourceTemplate(uri) self.__remote__ = Resource(uri[:key_value_pos]) else: self.__remote__ = Resource(uri) self._searcher = ResourceTemplate(uri.string + "/{key}/{value}") uri = remote(self).uri self._create_or_fail = Resource(uri.resolve("?uniqueness=create_or_fail")) self._get_or_create = Resource(uri.resolve("?uniqueness=get_or_create")) self._query_template = ResourceTemplate(uri.string + "{?query,order}") self._name = name or uri.path.segments[-1] self.__searcher_stem_cache = {} self.graph = Graph(uri.resolve("/db/data/").string)
import os import sys import pytest from py2neo.database import Graph from py2neo.data import Node, Relationship ROOT_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) sys.path.append(ROOT_PATH) from schemes.graph import GraphNode, GraphRelation from graph.graph import NLMGraph nlmg = NLMGraph(graph=Graph(port=7688)) nlmg.graph.delete_all() def test_graph_connected(): assert nlmg.graph.database.name != None @pytest.fixture def make_node(): props = {"age": 20, "sex": "female"} node = GraphNode("Person", "Alice", props) return node @pytest.fixture def make_node_no_props(): return GraphNode("Person", "Alice")
import os import sys import pytest ROOT_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) sys.path.append(ROOT_PATH) from py2neo.database import Graph from schemes.graph import GraphNode, GraphRelation from schemes.extractor import Entity, ExtractorInput from nlm import NLMLayer graph = Graph(port=7688) mem = NLMLayer(graph=graph) def test_nlm_instance_call_graphnode(): start = GraphNode("Person", "AliceThree") res = mem(start) query = res[0] assert isinstance(query, GraphNode) == True assert query.label == "Person" assert query.name == "AliceThree" assert query.props == {'age': 22, 'sex': 'male'} def test_nlm_instance_call_graphrelation(): start = GraphNode("Person", "AliceThree") end = GraphNode("Person", "AliceOne") relation = GraphRelation(start, end, "LOVES")
import os from py2neo.database import Graph h = os.environ.get('GRAPHENEDB_HOST', 'localhost') u = os.environ.get('NEO4J_USERNAME', 'neo4j') p = os.environ.get('NEO4J_PASSWORD', '111111') graph = Graph(host=h, user=u, password=p) def query_on_constraint(constraint): matcher = NodeMatcher(graph) return graph.nodes.match('Label', Constraint=constraint).first() def list_all(): return list(graph.nodes.match('Label'))
to_node = Node('manufacturer', manuf_name=to_node_name[0], manuf_comment=to_node_name[1]) if None in [from_node, to_node]: raise Exception('Unknown connection type', connection) rel = Relationship(from_node, connection, to_node) graph.merge(rel) def worker(mac_address): print(mac_address) manuf_data = mac_parser.get_all(mac_address) if manuf_data is None or manuf_data.manuf is None: return register_connection('ETHER/GEN/OUI/MANUFACTURED_BY', mac_address, (manuf_data.manuf, manuf_data.comment)) graph = Graph( password='******') # TODO: parameterize, don't hardcode password mac_parser = manuf.MacParser(update=True) if __name__ == '__main__': pool = multiprocessing.Pool(multiprocessing.cpu_count()) manuf.MacParser(update=True) macs = [ _['d.mac_address'] for _ in graph.run( 'MATCH (d:device) WHERE NOT (d)-[:`ETHER/GEN/OUI/MANUFACTURED_BY`]-() RETURN d.mac_address' ) ] pool.map(worker, macs)
def gdb(self): """The graph database service instance as a property, for convenience. Note: The property will use these configuration variables ``CONNECTION_RETRY`` ``RETRY_INTERVAL`` :return: the graph database service as a property """ retry = False if 'CONNECTION_RETRY' in self.app.config: retry = self.app.config['CONNECTION_RETRY'] retry_interval = 5 if 'RETRY_INTERVAL' in self.app.config: retry_interval = self.app.config['RETRY_INTERVAL'] retry_count = 0 try: log.info("flask.ext.Neo4j gdb trying to connect to DB") host_port = '' host_database = self.app.config['GRAPH_DATABASE'] neo_user = self.app.config['GRAPH_USER'] neo_pass = self.app.config['GRAPH_PASSWORD'] host_port_idx = host_database.find('://') if host_port_idx >= 0: # extract the host and port from the host_database host_port_idx = host_port_idx + 3 host_port = host_database[host_port_idx:] host_port = host_port[:host_port.find('/')] except Exception as e: log.error( "Error with database parameters, they may not have been specified in your config: {}" .format(e)) try: #authenticate( # host_port, # self.app.config['GRAPH_USER'], # self.app.config['GRAPH_PASSWORD'] #) #v4: #"bolt://myserver:7687", auth=("neo4j", "psswrd") self.graph_db = Graph(host_database, auth=(neo_user, neo_pass)) except Exception as se: log.error('SocketError: {0}'.format(se)) if retry: while retry_count < 3: log.debug( 'Waiting {0}secs before Connection Retry to GraphDatabaseService' .format(retry_interval)) time.sleep(retry_interval) #time.sleep(1) retry_count += 1 try: self.graph_db = Graph(host_database, auth=(neo_user, neo_pass)) except Exception as sse: log.error('SocketError: {0}'.format(sse.message)) if not hasattr(self, 'index'): self.index = {} # add all the indexes as app attributes if self._indexes is not None: for i, i_type in iter(list(self._indexes.items())): log.debug('getting or creating graph index:{0} {1}'.format( i, i_type)) self.index[i] = \ self.graph_db.legacy.get_or_create_index(i_type, i) return self.graph_db
class Console(object): def echo(self, text, file=None, nl=True, err=False, color=None, **styles): return click.secho(text, file=file, nl=nl, err=err, color=color, **styles) def prompt(self, *args, **kwargs): return prompt(*args, **kwargs) multi_line = False watcher = None tx_colour = "yellow" err_colour = "reset" meta_colour = "cyan" prompt_colour = "cyan" def __init__(self, uri=None, **settings): self.output_file = settings.pop("file", None) verbose = settings.pop("verbose", False) connection_data = get_connection_data(uri, **settings) try: self.graph = Graph(uri, **settings) except ServiceUnavailable as error: raise ConsoleError("Could not connect to {} -- {}".format( connection_data["uri"], error)) try: makedirs(HISTORY_FILE_DIR) except OSError: pass self.history = FileHistory(path_join(HISTORY_FILE_DIR, HISTORY_FILE)) self.prompt_args = { "history": self.history, "lexer": PygmentsLexer(CypherLexer), "style": style_from_pygments( VimStyle, { Token.Prompt: "#ansi{}".format(self.prompt_colour.replace( "cyan", "teal")), Token.TxCounter: "#ansi{} bold".format( self.tx_colour.replace("cyan", "teal")), }) } self.lexer = CypherLexer() self.result_writer = Table.write if verbose: from neo4j.util import watch self.watcher = watch("neo4j.%s" % connection_data["scheme"]) self.commands = { "//": self.set_multi_line, "/e": self.edit, "/?": self.help, "/h": self.help, "/help": self.help, "/x": self.exit, "/exit": self.exit, "/play": self.play, "/csv": self.set_csv_result_writer, "/table": self.set_tabular_result_writer, "/tsv": self.set_tsv_result_writer, "/config": self.config, "/kernel": self.kernel, } self.tx = None self.tx_counter = 0 def loop(self): self.echo(TITLE, err=True) self.echo("Connected to {}".format(self.graph.database.uri).rstrip(), err=True) self.echo(u"", err=True) self.echo(dedent(QUICK_HELP), err=True) while True: try: source = self.read() except KeyboardInterrupt: continue except EOFError: return 0 try: self.run(source) except ServiceUnavailable: return 1 def run_all(self, sources): gap = False for s in sources: if gap: self.echo("") self.run(s) if not is_command(s): gap = True return 0 def run(self, source): source = source.strip() if not source: return try: if is_command(source): self.run_command(source) else: self.run_source(source) except CypherError as error: if error.classification == "ClientError": pass elif error.classification == "DatabaseError": pass elif error.classification == "TransientError": pass else: pass self.echo("{}: {}".format(error.title, error.message), err=True) except TransactionError: self.echo("Transaction error", err=True, fg=self.err_colour) except ServiceUnavailable: raise except Exception as error: self.echo("{}: {}".format(error.__class__.__name__, str(error)), err=True, fg=self.err_colour) def begin_transaction(self): if self.tx is None: self.tx = self.graph.begin() self.tx_counter = 1 self.echo(u"--- BEGIN at {} ---".format(datetime.now()), err=True, fg=self.tx_colour, bold=True) else: self.echo(u"Transaction already open", err=True, fg=self.err_colour) def commit_transaction(self): if self.tx: try: self.tx.commit() self.echo(u"--- COMMIT at {} ---".format(datetime.now()), err=True, fg=self.tx_colour, bold=True) finally: self.tx = None self.tx_counter = 0 else: self.echo(u"No current transaction", err=True, fg=self.err_colour) def rollback_transaction(self): if self.tx: try: self.tx.rollback() self.echo(u"--- ROLLBACK at {} ---".format(datetime.now()), err=True, fg=self.tx_colour, bold=True) finally: self.tx = None self.tx_counter = 0 else: self.echo(u"No current transaction", err=True, fg=self.err_colour) def read(self): if self.multi_line: self.multi_line = False return self.prompt(u"", multiline=True, **self.prompt_args) def get_prompt_tokens(_): tokens = [] if self.tx is None: tokens.append((Token.Prompt, "\n-> ")) else: tokens.append((Token.Prompt, "\n-(")) tokens.append((Token.TxCounter, "{}".format(self.tx_counter))) tokens.append((Token.Prompt, ")-> ")) return tokens return self.prompt(get_prompt_tokens=get_prompt_tokens, **self.prompt_args) def run_source(self, source): for i, statement in enumerate(self.lexer.get_statements(source)): if i > 0: self.echo(u"") if statement.upper() == "BEGIN": self.begin_transaction() elif statement.upper() == "COMMIT": self.commit_transaction() elif statement.upper() == "ROLLBACK": self.rollback_transaction() elif self.tx is None: self.run_cypher(self.graph.run, statement, {}) else: self.run_cypher(self.tx.run, statement, {}, line_no=self.tx_counter) self.tx_counter += 1 def run_cypher(self, runner, statement, parameters, line_no=0): t0 = timer() result = runner(statement, parameters) record_count = self.write_result(result) status = u"{} record{} from {} in {:.3f}s".format( record_count, "" if record_count == 1 else "s", address_str(result.summary().server.address), timer() - t0, ) if line_no: self.echo(u"(", err=True, fg=self.meta_colour, bold=True, nl=False) self.echo(u"{}".format(line_no), err=True, fg=self.tx_colour, bold=True, nl=False) self.echo(u")->({})".format(status), err=True, fg=self.meta_colour, bold=True) else: self.echo(u"({})".format(status), err=True, fg=self.meta_colour, bold=True) def write_result(self, result, page_size=50): table = Table(result) table_size = len(table) for skip in range(0, table_size, page_size): self.result_writer(table, file=self.output_file, header={ "fg": "cyan", "bold": True }, skip=skip, limit=page_size) self.echo("\r\n", nl=False) return table_size def run_command(self, source): source = source.lstrip() assert source terms = shlex.split(source) command_name = terms[0] try: command = self.commands[command_name] except KeyError: self.echo("Unknown command: " + command_name, err=True, fg=self.err_colour) else: args = [] kwargs = {} for term in terms[1:]: if "=" in term: key, _, value = term.partition("=") kwargs[key] = value else: args.append(term) command(*args, **kwargs) def set_multi_line(self, **kwargs): self.multi_line = True def edit(self, **kwargs): initial_message = b"" with NamedTemporaryFile(suffix=".cypher") as f: f.write(initial_message) f.flush() call([EDITOR, f.name]) f.seek(0) source = f.read().decode("utf-8") self.echo(source) self.run(source) def help(self, **kwargs): self.echo(DESCRIPTION, err=True) self.echo(u"", err=True) self.echo(FULL_HELP.replace("\b\n", ""), err=True) def exit(self, **kwargs): exit(0) def play(self, file_name): work = self.load_unit_of_work(file_name=file_name) with self.graph.begin() as tx: work(tx) def load_unit_of_work(self, file_name): """ Load a transaction function from a cypher source file. """ with open(expanduser(file_name)) as f: source = f.read() def unit_of_work(tx): for line_no, statement in enumerate( self.lexer.get_statements(source), start=1): if line_no > 0: self.echo(u"") self.run_cypher(tx.run, statement, {}, line_no=line_no) return unit_of_work def set_csv_result_writer(self, **kwargs): self.result_writer = Table.write_csv def set_tabular_result_writer(self, **kwargs): self.result_writer = Table.write def set_tsv_result_writer(self, **kwargs): self.result_writer = Table.write_tsv def config(self, **kwargs): result = self.graph.run("CALL dbms.listConfig") records = None last_category = None for record in result: name = record["name"] category, _, _ = name.partition(".") if category != last_category: if records is not None: Table(records, ["name", "value"]).write(auto_align=False, padding=0, separator=u" = ") self.echo(u"") records = [] records.append((name, record["value"])) last_category = category if records is not None: Table(records, ["name", "value"]).write(auto_align=False, padding=0, separator=u" = ") def kernel(self, **kwargs): result = self.graph.run( "CALL dbms.queryJmx", {"query": "org.neo4j:instance=kernel#0,name=Kernel"}) records = [] for record in result: attributes = record["attributes"] for key, value_dict in sorted(attributes.items()): value = value_dict["value"] if key.endswith("Date") or key.endswith("Time"): try: value = datetime.fromtimestamp(value / 1000).isoformat(" ") except: pass records.append((key, value)) Table(records, ["key", "value"]).write(auto_align=False, padding=0, separator=u" = ")
class ClientConsole(Console): multi_line = False def __init__(self, profile=None, *_, **settings): super(ClientConsole, self).__init__("py2neo", verbosity=settings.get("verbosity", 0)) self.output_file = settings.pop("file", None) welcome = settings.get("welcome", True) if welcome: self.write(TITLE) self.write() self.write(dedent(QUICK_HELP)) self.write() self.profile = ConnectionProfile(profile, **settings) routing = settings.get("routing", False) try: self.graph = Graph(self.profile, routing=routing) # TODO: use Connector instead except OSError as error: self.critical("Could not connect to <%s> (%s)", self.profile.uri, " ".join(map(str, error.args))) raise else: self.debug("Connected to <%s>", self.graph.service.uri) try: makedirs(HISTORY_FILE_DIR) except OSError: pass self.history = FileHistory(path_join(HISTORY_FILE_DIR, HISTORY_FILE)) self.lexer = CypherLexer() self.result_writer = Table.write self.commands = { "//": self.set_multi_line, "/e": self.edit, "/?": self.help, "/h": self.help, "/help": self.help, "/x": self.exit, "/exit": self.exit, "/play": self.play, "/csv": self.set_csv_result_writer, "/table": self.set_tabular_result_writer, "/tsv": self.set_tsv_result_writer, "/config": self.config, "/kernel": self.kernel, } self.tx = None self.qid = 0 def process_all(self, lines, times=1): gap = False for _ in range(times): for line in lines: if gap: self.write("") self.process(line) if not is_command(line): gap = True return 0 def process(self, line): line = line.strip() if not line: return try: if is_command(line): self.run_command(line) else: self.run_source(line) except (Neo4jError, Failure) as error: # TODO: once this class wraps a Connector instead of a # Graph and the errors raised by that class are only # Failures and not Neo4jErrors, this only needs to # catch Failure. if hasattr(error, "title") and hasattr(error, "message"): self.error("%s: %s", error.title, error.message) else: self.error("%s: %s", error.__class__.__name__, " ".join(map(str, error.args))) except OSError as error: self.critical("Service Unavailable (%s)", error.args[0]) except Exception as error: self.exception(*error.args) def begin_transaction(self): if self.tx is None: self.tx = self.graph.begin() self.qid = 1 else: self.warning("Transaction already open") def commit_transaction(self): if self.tx: try: self.tx.commit() self.info("Transaction committed") finally: self.tx = None self.qid = 0 else: self.warning("No current transaction") def rollback_transaction(self): if self.tx: try: self.tx.rollback() self.info("Transaction rolled back") finally: self.tx = None self.qid = 0 else: self.warning("No current transaction") def read(self): prompt_args = { "history": self.history, "lexer": PygmentsLexer(CypherLexer), "style": merge_styles([ style_from_pygments_cls(NativeStyle), style_from_pygments_dict({ Token.Prompt.User: "******", Token.Prompt.At: "#ansiteal", Token.Prompt.Host: "#ansiteal", Token.Prompt.QID: "#ansiyellow", Token.Prompt.Arrow: "#808080", }) ]) } self.write() if self.multi_line: self.multi_line = False return prompt(u"", multiline=True, **prompt_args) def get_prompt_tokens(): tokens = [ ("class:pygments.prompt.user", self.profile.user), ("class:pygments.prompt.at", "@"), ("class:pygments.prompt.host", self.profile.host), ] if self.tx is None: tokens.append(("class:pygments.prompt.arrow", " -> ")) else: tokens.append(("class:pygments.prompt.arrow", " ")) tokens.append(("class:pygments.prompt.qid", str(self.qid))) tokens.append(("class:pygments.prompt.arrow", "> ")) return tokens return prompt(get_prompt_tokens, **prompt_args) def run_source(self, source): for i, statement in enumerate(self.lexer.get_statements(source)): if i > 0: self.write(u"") if statement.upper() == "BEGIN": self.begin_transaction() elif statement.upper() == "COMMIT": self.commit_transaction() elif statement.upper() == "ROLLBACK": self.rollback_transaction() elif self.tx is None: self.run_cypher(self.graph.run, statement, {}) else: self.run_cypher(self.tx.run, statement, {}, query_id=self.qid) self.qid += 1 def run_cypher(self, runner, statement, parameters, query_id=0): t0 = timer() result = runner(statement, parameters) record_count = self.write_result(result) summary = result.summary() if summary.connection: uri = summary.connection["uri"] else: uri = self.graph.service.uri msg = "Fetched %r %s from %r in %rs" args = [ record_count, "record" if record_count == 1 else "records", uri, timer() - t0, ] if query_id: msg += " for query (%r)" args.append(query_id) self.debug(msg, *args) def write_result(self, result, page_size=50): table = Table(result) table_size = len(table) if self.verbosity >= 0: for skip in range(0, table_size, page_size): self.result_writer(table, file=self.output_file, header="cyan", skip=skip, limit=page_size) self.write("\r\n", end='') return table_size def run_command(self, source): source = source.lstrip() assert source terms = shlex.split(source) command_name = terms[0] try: command = self.commands[command_name] except KeyError: self.info("Unknown command: " + command_name) else: args = [] kwargs = {} for term in terms[1:]: if "=" in term: key, _, value = term.partition("=") kwargs[key] = value else: args.append(term) command(*args, **kwargs) def set_multi_line(self, **kwargs): self.multi_line = True def edit(self, **kwargs): initial_message = b"" with NamedTemporaryFile(suffix=".cypher") as f: f.write(initial_message) f.flush() call([EDITOR, f.name]) f.seek(0) source = f.read().decode("utf-8") self.write(source) self.process(source) def help(self, **kwargs): self.info(DESCRIPTION) self.info(u"") self.info(FULL_HELP.replace("\b\n", "")) def play(self, file_name): work = self.load_unit_of_work(file_name=file_name) with self.graph.begin() as tx: work(tx) def load_unit_of_work(self, file_name): """ Load a transaction function from a cypher source file. """ with open(expanduser(file_name)) as f: source = f.read() def unit_of_work(tx): for line_no, statement in enumerate( self.lexer.get_statements(source), start=1): if line_no > 0: self.write(u"") self.run_cypher(tx.run, statement, {}, query_id=line_no) return unit_of_work def set_csv_result_writer(self, **kwargs): self.result_writer = Table.write_csv def set_tabular_result_writer(self, **kwargs): self.result_writer = Table.write def set_tsv_result_writer(self, **kwargs): self.result_writer = Table.write_tsv def config(self, **kwargs): result = self.graph.run("CALL dbms.listConfig") records = None last_category = None for record in result: name = record["name"] category, _, _ = name.partition(".") if category != last_category: if records is not None: Table(records, ["name", "value"]).write(auto_align=False, padding=0, separator=u" = ") self.write(u"") records = [] records.append((name, record["value"])) last_category = category if records is not None: Table(records, ["name", "value"]).write(auto_align=False, padding=0, separator=u" = ") def kernel(self, **kwargs): result = self.graph.run( "CALL dbms.queryJmx", {"query": "org.neo4j:instance=kernel#0,name=Kernel"}) records = [] for record in result: attributes = record["attributes"] for key, value_dict in sorted(attributes.items()): value = value_dict["value"] if key.endswith("Date") or key.endswith("Time"): try: value = datetime.fromtimestamp(value / 1000).isoformat(" ") except: pass records.append((key, value)) Table(records, ["key", "value"]).write(auto_align=False, padding=0, separator=u" = ")
def __init__(self): #watch("neo4j.bolt") self.graph = Graph(super().graph_url)
class ManualIndex(object): """ Searchable database index which can contain either nodes or relationships. """ def __init__(self, content_type, uri, name=None): self._content_type = content_type key_value_pos = uri.find("/{key}/{value}") if key_value_pos >= 0: self._searcher = ResourceTemplate(uri) self.__remote__ = Resource(uri[:key_value_pos]) else: self.__remote__ = Resource(uri) self._searcher = ResourceTemplate(uri.string + "/{key}/{value}") uri = remote(self).uri self._create_or_fail = Resource(uri.resolve("?uniqueness=create_or_fail")) self._get_or_create = Resource(uri.resolve("?uniqueness=get_or_create")) self._query_template = ResourceTemplate(uri.string + "{?query,order}") self._name = name or uri.path.segments[-1] self.__searcher_stem_cache = {} self.graph = Graph(uri.resolve("/db/data/").string) def __repr__(self): return "{0}({1}, {2})".format( self.__class__.__name__, self._content_type.__name__, repr(remote(self).uri.string) ) def _searcher_stem_for_key(self, key): if key not in self.__searcher_stem_cache: stem = self._searcher.uri_template.string.partition("{key}")[0] self.__searcher_stem_cache[key] = stem + percent_encode(key) + "/" return self.__searcher_stem_cache[key] def add(self, key, value, entity): """ Add an entity to this index under the `key`:`value` pair supplied. Note that while Neo4j indexes allow multiple entities to be added under a particular key:value, the same entity may only be represented once; this method is therefore idempotent. :param key: :param value: :param entity: """ remote(self).post({ "key": key, "value": value, "uri": remote(entity).uri.string, }) return entity def add_if_none(self, key, value, entity): """ Add an entity to this index under the `key`:`value` pair supplied if no entry already exists at that point. If added, this method returns the entity, otherwise :py:const:`None` is returned. """ rs = self._get_or_create.post({ "key": key, "value": value, "uri": remote(entity).uri.string, }) if rs.status_code == CREATED: return entity else: return None @property def content_type(self): """ Return the type of entity contained within this index. Will return either :py:class:`Node` or :py:class:`Relationship`. """ return self._content_type @property def name(self): """ Return the name of this index. """ return self._name def get(self, key, value): """ Fetch a list of all entities from the index which are associated with the `key`:`value` pair supplied. :param key: :param value: """ return [ self.graph._hydrate(result) for result in self._searcher.expand(key=key, value=value).get().content ] def create(self, key, value, abstract): """ Create and index a new node or relationship using the abstract provided. :param key: :param value: :param abstract: """ batch = ManualIndexWriteBatch(self.graph) if self._content_type is Node: batch.create(abstract) batch.add_to_index(Node, self, key, value, 0) elif self._content_type is Relationship: batch.create(abstract) batch.add_to_index(Relationship, self, key, value, 0) else: raise TypeError(self._content_type) entity, index_entry = batch.run() return entity def _create_unique(self, key, value, abstract): """ Internal method to support `get_or_create` and `create_if_none`. """ if self._content_type is Node: body = { "key": key, "value": value, "properties": abstract } elif self._content_type is Relationship: body = { "key": key, "value": value, "start": abstract[0].uri.string, "type": abstract[1], "end": abstract[2].uri.string, "properties": abstract[3] if len(abstract) > 3 else None } else: raise TypeError(self._content_type) return self._get_or_create.post(body) def get_or_create(self, key, value, abstract): """ Fetch a single entity from the index which is associated with the `key`:`value` pair supplied, creating a new entity with the supplied details if none exists. """ return self.graph._hydrate(self._create_unique(key, value, abstract).content) def create_if_none(self, key, value, abstract): """ Create a new entity with the specified details within the current index, under the `key`:`value` pair supplied, if no such entity already exists. If creation occurs, the new entity will be returned, otherwise :py:const:`None` will be returned. """ rs = self._create_unique(key, value, abstract) if rs.status_code == CREATED: return self.graph._hydrate(rs.content) else: return None def remove(self, key=None, value=None, entity=None): """ Remove any entries from the index which match the parameters supplied. The allowed parameter combinations are: `key`, `value`, `entity` remove a specific entity indexed under a given key-value pair `key`, `value` remove all entities indexed under a given key-value pair `key`, `entity` remove a specific entity indexed against a given key but with any value `entity` remove all occurrences of a specific entity regardless of key and value """ if key and value and entity: t = ResourceTemplate(remote(self).uri.string + "/{key}/{value}/{entity}") t.expand(key=key, value=value, entity=remote(entity)._id).delete() elif key and value: uris = [ URI(remote(entity).metadata["indexed"]) for entity in self.get(key, value) ] batch = ManualIndexWriteBatch(self.graph) for uri in uris: batch.append_delete(uri) batch.run() elif key and entity: t = ResourceTemplate(remote(self).uri.string + "/{key}/{entity}") t.expand(key=key, entity=remote(entity)._id).delete() elif entity: t = ResourceTemplate(remote(self).uri.string + "/{entity}") t.expand(entity=remote(entity)._id).delete() else: raise TypeError("Illegal parameter combination for index removal") def query(self, query): """ Query the index according to the supplied query criteria, returning a list of matched entities. The query syntax used should be appropriate for the configuration of the index being queried. For indexes with default configuration, this should be Apache Lucene query syntax. """ resource = self._query_template.expand(query=query) for result in resource.get().content: yield self.graph._hydrate(result) def _query_with_score(self, query, order): resource = self._query_template.expand(query=query, order=order) for result in resource.get().content: yield self.graph._hydrate(result), result["score"] def query_by_index(self, query): return self._query_with_score(query, "index") def query_by_relevance(self, query): return self._query_with_score(query, "relevance") def query_by_score(self, query): return self._query_with_score(query, "score")
def connectGraph(self): authenticate(self.service_ip, self.user, self.password) graph = Graph('http://%s/db/data/' % self.service_ip) return graph
def graph(self): if self._graph is None: self._graph = Graph(**self.server) return self._graph
class Repository(object): """ Storage container for :class:`.GraphObject` instances. """ @classmethod def wrap(cls, graph): """ Wrap an existing :class:`.Graph` object as a :class:`.Repository`. """ obj = object.__new__(Repository) obj.graph = graph return obj def __init__(self, profile=None, name=None, **settings): self.graph = Graph(profile, name=name, **settings) def reload(self, obj): """ Reload data from the remote graph into the local object. """ self.graph.pull(obj) def save(self, *objects): """ Save data from the local object into the remote graph. """ def push_all(tx): for obj in objects: tx.push(obj) self.graph.play(push_all) def delete(self, obj): """ Delete the object in the remote graph. """ self.graph.delete(obj) def exists(self, obj): """ Check whether the object exists in the remote graph. """ return self.graph.exists(obj) def match(self, ogm_class, primary_value=None): """ Select one or more objects from the remote graph. :param ogm_class: the :class:`.GraphObject` subclass to match :param primary_value: value of the primary property (optional) :rtype: :class:`.GraphObjectMatch` """ return GraphObjectMatcher(ogm_class, self).match(primary_value) def get(self, ogm_class, primary_value=None): """ Match and return a single object from the remote graph. :param ogm_class: the :class:`.GraphObject` subclass to match :param primary_value: value of the primary property (optional) :rtype: :class:`.GraphObject` """ return self.match(ogm_class, primary_value).first() @deprecated("Repository.create is a compatibility alias, " "please use Repository.save instead") def create(self, obj): self.graph.create(obj) @deprecated("Repository.merge is a compatibility alias, " "please use Repository.save instead") def merge(self, obj): self.graph.merge(obj) @deprecated("Repository.pull is a compatibility alias, " "please use Repository.load instead") def pull(self, obj): self.graph.pull(obj) @deprecated("Repository.push is a compatibility alias, " "please use Repository.save instead") def push(self, obj): self.graph.push(obj)
def connectGraph(self): # graph = Graph(user = self.user, password = self.password) authenticate("localhost:7474", self.user, self.password) graph = Graph("http://localhost:7474/db/data/") return graph
def __init__(self, profile=None, name=None, **settings): self.graph = Graph(profile, name=name, **settings)
from flask import Flask from py2neo.database import Graph from settings import PLATFORM_DB, BLOWFISH_SECRET from Crypto.Cipher import Blowfish db = Graph(**PLATFORM_DB) blowfish = Blowfish.new(BLOWFISH_SECRET) def create_app(): app = Flask('Platform') # Load common settings app.config.from_object('settings') # Register blueprints from .views import register_blueprints register_blueprints(app) @app.route('/healthcheck', methods=['GET']) def healthcheck(): return 'HEALTHY' return app
If is, the props will never update.') parser.add_argument('-ai', dest='add_inexistence', type=bool, default=False, help='Whether to add an inexistent Node or Relation.') parser.add_argument('-up', dest='update_props', type=bool, default=False, help='Whether to update props of a Node or Relation.') args = parser.parse_args() graph = Graph(scheme=neo_sche, host=neo_host, port=neo_port, user=neo_user, password=neo_pass) mem = NLMLayer(graph=graph, fuzzy_node=args.fuzzy_node, add_inexistence=args.add_inexistence, update_props=args.update_props) class NLMService(nlm_pb2_grpc.NLMServicer): @raise_grpc_error(Exception, StatusCode.INTERNAL) @deco_log_error(logger) @convert_request_to(GraphNode) def NodeRecall(self, request, context): result = mem(request) gn = result[0] if result else request
class Repository(object): """ Storage container for :class:`.Model` instances. The constructor for this class has an identical signature to that for the :class:`.Graph` class. For example:: >>> from py2neo.ogm import Repository >>> from py2neo.ogm.models.movies import Movie >>> repo = Repository("bolt://neo4j@localhost:7687", password="******") >>> repo.match(Movie, "The Matrix").first() <Movie title='The Matrix'> *New in version 2020.0. In earlier versions, a :class:`.Graph` was required to co-ordinate all reads and writes to the remote database. This class completely replaces that, removing the need to import from any other packages when using OGM.* """ @classmethod def wrap(cls, graph): """ Wrap an existing :class:`.Graph` object as a :class:`.Repository`. """ obj = object.__new__(Repository) obj.graph = graph return obj def __init__(self, profile=None, name=None, **settings): self.graph = Graph(profile, name=name, **settings) def __repr__(self): return "<Repository profile=%r>" % (self.graph.service.profile, ) def reload(self, obj): """ Reload data from the remote graph into the local object. """ self.graph.pull(obj) def save(self, *objects): """ Save data from the local object into the remote graph. """ def push_all(tx): for obj in objects: tx.push(obj) self.graph.update(push_all) def delete(self, obj): """ Delete the object in the remote graph. """ self.graph.delete(obj) def exists(self, obj): """ Check whether the object exists in the remote graph. """ return self.graph.exists(obj) def match(self, model, primary_value=None): """ Select one or more objects from the remote graph. :param model: the :class:`.Model` subclass to match :param primary_value: value of the primary property (optional) :rtype: :class:`.ModelMatch` """ return ModelMatcher(model, self).match(primary_value) def get(self, model, primary_value=None): """ Match and return a single object from the remote graph. :param model: the :class:`.Model` subclass to match :param primary_value: value of the primary property (optional) :rtype: :class:`.Model` """ return self.match(model, primary_value).first() @deprecated("Repository.create is a compatibility alias, " "please use Repository.save instead") def create(self, obj): self.graph.create(obj) @deprecated("Repository.merge is a compatibility alias, " "please use Repository.save instead") def merge(self, obj): self.graph.merge(obj) @deprecated("Repository.pull is a compatibility alias, " "please use Repository.load instead") def pull(self, obj): self.graph.pull(obj) @deprecated("Repository.push is a compatibility alias, " "please use Repository.save instead") def push(self, obj): self.graph.push(obj)
class ManualIndex(object): """ Searchable database index which can contain either nodes or relationships. """ def __init__(self, content_type, uri, name=None): self._content_type = content_type key_value_pos = uri.find("/{key}/{value}") if key_value_pos >= 0: self._searcher = ResourceTemplate(uri) self.__remote__ = Resource(uri[:key_value_pos]) else: self.__remote__ = Resource(uri) self._searcher = ResourceTemplate(uri.string + "/{key}/{value}") uri = remote(self).uri self._create_or_fail = Resource( uri.resolve("?uniqueness=create_or_fail")) self._get_or_create = Resource( uri.resolve("?uniqueness=get_or_create")) self._query_template = ResourceTemplate(uri.string + "{?query,order}") self._name = name or uri.path.segments[-1] self.__searcher_stem_cache = {} self.graph = Graph(uri.resolve("/db/data/").string) def __repr__(self): return "{0}({1}, {2})".format(self.__class__.__name__, self._content_type.__name__, repr(remote(self).uri.string)) def _searcher_stem_for_key(self, key): if key not in self.__searcher_stem_cache: stem = self._searcher.uri_template.string.partition("{key}")[0] self.__searcher_stem_cache[key] = stem + percent_encode(key) + "/" return self.__searcher_stem_cache[key] def add(self, key, value, entity): """ Add an entity to this index under the `key`:`value` pair supplied. Note that while Neo4j indexes allow multiple entities to be added under a particular key:value, the same entity may only be represented once; this method is therefore idempotent. :param key: :param value: :param entity: """ remote(self).post({ "key": key, "value": value, "uri": remote(entity).uri.string, }) return entity def add_if_none(self, key, value, entity): """ Add an entity to this index under the `key`:`value` pair supplied if no entry already exists at that point. If added, this method returns the entity, otherwise :py:const:`None` is returned. """ rs = self._get_or_create.post({ "key": key, "value": value, "uri": remote(entity).uri.string, }) if rs.status_code == CREATED: return entity else: return None @property def content_type(self): """ Return the type of entity contained within this index. Will return either :py:class:`Node` or :py:class:`Relationship`. """ return self._content_type @property def name(self): """ Return the name of this index. """ return self._name def get(self, key, value): """ Fetch a list of all entities from the index which are associated with the `key`:`value` pair supplied. :param key: :param value: """ return [ self.graph._hydrate(result) for result in self._searcher.expand( key=key, value=value).get().content ] def create(self, key, value, abstract): """ Create and index a new node or relationship using the abstract provided. :param key: :param value: :param abstract: """ batch = ManualIndexWriteBatch(self.graph) if self._content_type is Node: batch.create(abstract) batch.add_to_index(Node, self, key, value, 0) elif self._content_type is Relationship: batch.create(abstract) batch.add_to_index(Relationship, self, key, value, 0) else: raise TypeError(self._content_type) entity, index_entry = batch.run() return entity def _create_unique(self, key, value, abstract): """ Internal method to support `get_or_create` and `create_if_none`. """ if self._content_type is Node: body = {"key": key, "value": value, "properties": abstract} elif self._content_type is Relationship: body = { "key": key, "value": value, "start": abstract[0].uri.string, "type": abstract[1], "end": abstract[2].uri.string, "properties": abstract[3] if len(abstract) > 3 else None } else: raise TypeError(self._content_type) return self._get_or_create.post(body) def get_or_create(self, key, value, abstract): """ Fetch a single entity from the index which is associated with the `key`:`value` pair supplied, creating a new entity with the supplied details if none exists. """ return self.graph._hydrate( self._create_unique(key, value, abstract).content) def create_if_none(self, key, value, abstract): """ Create a new entity with the specified details within the current index, under the `key`:`value` pair supplied, if no such entity already exists. If creation occurs, the new entity will be returned, otherwise :py:const:`None` will be returned. """ rs = self._create_unique(key, value, abstract) if rs.status_code == CREATED: return self.graph._hydrate(rs.content) else: return None def remove(self, key=None, value=None, entity=None): """ Remove any entries from the index which match the parameters supplied. The allowed parameter combinations are: `key`, `value`, `entity` remove a specific entity indexed under a given key-value pair `key`, `value` remove all entities indexed under a given key-value pair `key`, `entity` remove a specific entity indexed against a given key but with any value `entity` remove all occurrences of a specific entity regardless of key and value """ if key and value and entity: t = ResourceTemplate( remote(self).uri.string + "/{key}/{value}/{entity}") t.expand(key=key, value=value, entity=remote(entity)._id).delete() elif key and value: uris = [ URI(remote(entity).metadata["indexed"]) for entity in self.get(key, value) ] batch = ManualIndexWriteBatch(self.graph) for uri in uris: batch.append_delete(uri) batch.run() elif key and entity: t = ResourceTemplate(remote(self).uri.string + "/{key}/{entity}") t.expand(key=key, entity=remote(entity)._id).delete() elif entity: t = ResourceTemplate(remote(self).uri.string + "/{entity}") t.expand(entity=remote(entity)._id).delete() else: raise TypeError("Illegal parameter combination for index removal") def query(self, query): """ Query the index according to the supplied query criteria, returning a list of matched entities. The query syntax used should be appropriate for the configuration of the index being queried. For indexes with default configuration, this should be Apache Lucene query syntax. """ resource = self._query_template.expand(query=query) for result in resource.get().content: yield self.graph._hydrate(result) def _query_with_score(self, query, order): resource = self._query_template.expand(query=query, order=order) for result in resource.get().content: yield self.graph._hydrate(result), result["score"] def query_by_index(self, query): return self._query_with_score(query, "index") def query_by_relevance(self, query): return self._query_with_score(query, "relevance") def query_by_score(self, query): return self._query_with_score(query, "score")
continue existing_rels.append(job_value) existing_rels = existing_rels[-100000:] register_connection(get_connection(*job_value)) elif job_type == 'update_rel': pass else: raise Exception('Unknown job_type', job_type) db_queue.task_done() except: pass logger = logging.getLogger() print('Connecting to graph') graph = Graph(password='******') # TODO: parameterize, don't hardcode password def main(): sniffer_count = min([cpu_count(), len(argv[1:])]) sniffer_queue = JoinableQueue() db_queue = JoinableQueue() for filename in argv[1:]: if os.path.isfile(filename): print('Will be loading from file', filename) else: print('Will sniff from interface', filename) sniffer_queue.put(filename) if argv[1:] == []: sniffer_queue.put('*') if sniffer_count == 0:
from dataclasses import dataclass from pnlp import piop from py2neo.database import Graph from batch_scheme import (Disease, Department, Producer, Symptom, Examination, Food, Drug) graph = Graph(scheme="bolt", host="localhost", port=7687, user="******", password="******") def create_node(item: dict): """ One item of the given data to a node. """ dise = Disease() dise.name = item.get("name", "") dise.description = item.get("desc", "") dise.prevent = item.get("prevent", "") dise.cause = item.get("cause", "") dise.susceptible = item.get("easy_get", "") dise.cause_prob = item.get("get_prob", "") dise.cured_prob = item.get("ured_prob", "") dise.method = item.get("cure_way", "") dise.cure_duration = item.get("cure_lasttime", "") return dise @dataclass class RelationUpdate: