Return count of relationships instead of all

See also questions close to this topic

• Connection failure when using airflow to run python script connecting to neo4j database

  I'm trying to use airflow to orchestrate a workflow where a neo4j docker is run and then a python script to query data from the neo4j database (the code runs on AWS EC2 instance). I am able to run the neo4j docker successfully. But when I ran the task of querying the database, I got connection error as:

  neo4j.exceptions.ServiceUnavailable: Connection to 127.0.0.1:7687 closed without handshake response

  If I manually ran the python script on EC2, it can connect to the neo4j database without any issue. The code I am using is as below:

  class Neo4jConnection:
  
      def __init__(self, uri, user, pwd):
          self.__uri = uri
          self.__user = user
          self.__pwd = pwd
          self.__driver = None
          try:
              self.__driver = GraphDatabase.driver(self.__uri, auth=(self.__user, self.__pwd))
              logger.info('SUCCESS: Connected to the Neo4j Database.')
          except Exception as e:
              logger.info('ERROR: Could not connect to the Neo4j Database. See console for details.')
              raise SystemExit(e)
  
      def close(self):
          if self.__driver is not None:
              self.__driver.close()
  
      def query(self, query, parameters=None, db=None):
          assert self.__driver is not None, "Driver not initialized!"
          session = None
          response = None
          try:
              session = self.__driver.session(database=db) if db is not None else self.__driver.session()
              response = list(session.run(query, parameters))
          except Exception as e:
              logger.info("Query failed:", e)
          finally:
              if session is not None:
                  session.close()
          return response 
  
  class LoadWikiPathway2Neo4j:
      def __init__(self):
          # replace localhost with 127.0.0.1
          self.connection = Neo4jConnection(uri="bolt://localhost:7687",
                                            user="neo4j",
                                            pwd="test")
      def loadData(self):
          WIKIPATHWAY_MOUNTED_DATA_VOLUME = "/home/ec2-user/wikipathway_neo4j/data/Human/"  # the volume is mounted to neo4j docker
          WIKIPATHWAY_DATA_DOCKER_VOLUME = "file:///var/lib/neo4j/data/Human"  # file path in neo4j docker
  
          # connect db
          graph = self.connection
          # only run once
          graph.query('''MATCH (n) DETACH DELETE n''')
          graph.query('''CALL n10s.graphconfig.init()''')
          graph.query('''CREATE CONSTRAINT n10s_unique_uri IF NOT EXISTS ON (r:Resource) ASSERT r.uri IS UNIQUE''')
          graph.query('''call n10s.nsprefixes.removeAll()''')
          cypher = '''WITH '@prefix biopax:  <http://www.biopax.org/release/biopax-level3.owl#> . \
          @prefix cito:    <http://purl.org/spar/cito/> . \
          @prefix dc:      <http://purl.org/dc/elements/1.1/> . \
          @prefix dcat:     <http://www.w3.org/ns/dcat#> . \
          @prefix dcterms: <http://purl.org/dc/terms/> . \
          @prefix foaf:    <http://xmlns.com/foaf/0.1/> . \
          @prefix freq:    <http://purl.org/cld/freq/> . \
          @prefix gpml:    <http://vocabularies.wikipathways.org/gpml#> . \
          @prefix hmdb:     <https://identifiers.org/hmdb/> . \
          @prefix ncbigene: <https://identifiers.org/ncbigene/> .\
          @prefix owl:     <http://www.w3.org/2002/07/owl#> . \
          @prefix pav:     <http://purl.org/pav/> . \
          @prefix prov:    <http://www.w3.org/ns/prov#> . \
          @prefix pubmed:   <http://www.ncbi.nlm.nih.gov/pubmed/> .\
          @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . \
          @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> . \
          @prefix skos:    <http://www.w3.org/2004/02/skos/core#> . \
          @prefix void:    <http://rdfs.org/ns/void#> . \
          @prefix wp:      <http://vocabularies.wikipathways.org/wp#> . \
          @prefix wprdf:   <http://rdf.wikipathways.org/> . \
          @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> . ' as txt \
          CALL n10s.nsprefixes.addFromText(txt) yield prefix, namespace RETURN prefix, namespace'''
          graph.query(cypher)
  
          fileLst = os.listdir(WIKIPATHWAY_MOUNTED_DATA_VOLUME)
          # load data
          for filename in fileLst:
              filePath = f'{WIKIPATHWAY_DATA_DOCKER_VOLUME}/{filename}'
              print(filePath)
              cypher = f'''CALL n10s.rdf.import.fetch("{filePath}","Turtle")'''
              logger.info(cypher)
              graph.query(cypher)
              logger.info(f"{filename} is loaded")
          graph.close()
  
  def load_wikipathway_files():
      data = LoadWikiPathway2Neo4j()
      data.loadData()
  
  with DAG(
          default_args=default,
          dag_id=os.path.basename(__file__).replace(".py", ""),
          schedule_interval=None,
          catchup=False,
          start_date=days_ago(1),
          tags=['s3', 'download_wikipathway'],
  ) as dag:
       loadWikipathwayFile = PythonOperator(
          task_id="load_wikipathway",
          python_callable=load_wikipathway_files
      )
  
• How to extract dynamic property names from a json file in Neo4J using Cypher Query

  The tags property names are dynamic. e.g. linux and cypher are dynamic in the json. I am trying to extract the dynamic tags and their values and associate them as properties to the Person node. Here is what I have so far:

  CALL apoc.load.json("file:///example.json")
  YIELD value
  MERGE (p:Person {name: value.name})
  ON CREATE SET 
  p.job = value.job,
  p.department = value.department
  
  RETURN p as Person;
  
  

  example.json:

  {
      "name": "Harry",
      "job": "Developer",
      "tags": {
          "linux": "awesome",
          "cypher": "Working on it"
      },
  
      "department": "IT"
  
  }
  
• how to ensure atomicity in neo4j cypher writes:

  I have never used the transaction lock features in neo4j cypher before so I not sure how to do this. I have a series of writes that I need all to complete or none complete:

  CREATE (e:Elections) SET e +=$electionObj,
                               e.election_id=apoc.create.uuid(),e.createdAt=date()
  
                              WITH e, $nominate_authorizers AS na
                              UNWIND na AS n_auth 
                              MATCH (nm:Member {member_id: n_auth.member_id})
                              CREATE (nm)-[nr:NOMINATE_AUTHORIZER]->(e)
  
                              WITH e, nm, $certify_authorizers AS ca
                              UNWIND ca AS c_auth 
                              MATCH (cm:Member {member_id: c_auth.member_id})
                              CREATE (cm)-[cr:CERTIFY_AUTHORIZER]->(e)
  
                              WITH e, nm,cm, $tally_authorizers AS ta
                              UNWIND ta AS t_auth 
                              MATCH (tm:Member {member_id: t_auth.member_id})
                              CREATE (tm)-[tr:TALLY_AUTHORIZER]->(e)
  
                              WITH e, nm,cm, tm, $audit_authorizers AS aa
                              UNWIND aa AS a_auth 
                              MATCH (am:Member {member_id: a_auth.member_id})
                              CREATE (am)-[ar:AUDIT_AUTHORIZER]->(e)
  
                              WITH e, nm,cm, tm, am, $races AS races
                              UNWIND races AS race 
                              CREATE (r:Race) 
                              SET r.name= race, 
                              r.race_id=apoc.create.uuid()
                              CREATE (r)-[rr:OF_ELECTION]->(e) 
                              
                              RETURN {election: e}
  

  The problem is ...if there's an error that causes one of these MATCH's to return 0 row the query moves right along and creates the nodes it found. What is the most efficient of achieving atomicity here. I have looked at the apoc library but not sure about it....any suggestion would be appreciated.