graphdb | Project has moved to : neo4j/community | Graph Database library

 by   neo4j-attic Java Version: Current License: AGPL-3.0

kandi X-RAY | graphdb Summary

kandi X-RAY | graphdb Summary

graphdb is a Java library typically used in Database, Graph Database, Neo4j applications. graphdb has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has high support. You can download it from GitHub.

The contents of this repository has been migrated to the Community edition of Neo4j, now available here: For more information, visit:
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            kandi-support Support

              graphdb has a highly active ecosystem.
              It has 84 star(s) with 5 fork(s). There are 1 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 0 open issues and 1 have been closed. There are 3 open pull requests and 0 closed requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of graphdb is current.

            kandi-Quality Quality

              graphdb has 0 bugs and 0 code smells.

            kandi-Security Security

              graphdb has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              graphdb code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              graphdb is licensed under the AGPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              graphdb releases are not available. You will need to build from source code and install.
              Build file is available. You can build the component from source.
              graphdb saves you 80275 person hours of effort in developing the same functionality from scratch.
              It has 88750 lines of code, 7380 functions and 803 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed graphdb and discovered the below as its top functions. This is intended to give you an instant insight into graphdb implemented functionality, and help decide if they suit your requirements.
            • Starts the Neo4j
            • Assign memory to memory
            • Start the NodeManager
            • Parse the parameters from the map
            • Enlist an XAResource
            • Writes start record to the transaction log
            • Get the branch ID for a resource
            • Rebuilds the internal id generator
            • Finds the high - id for the next record in the file
            • Enlist a resource
            • Returns the JMX service URL
            • Read a dynamic record from the given byte buffer
            • Rollback the transaction
            • Deletes a relationship record
            • Decodes a long
            • Removes a property
            • Loads the dynamic store
            • Prepares the transaction
            • Reads a command from a channel buffer
            • Commits the transaction
            • Sets the number of blocks to fit in the file
            • Process a Watched event
            • Rebuilds the id generator
            • Initialize the TransactionManager
            • Write to log buffer
            • Handles a request
            Get all kandi verified functions for this library.

            graphdb Key Features

            No Key Features are available at this moment for graphdb.

            graphdb Examples and Code Snippets

            No Code Snippets are available at this moment for graphdb.

            Community Discussions

            QUESTION

            SPARQL Inference with SKOS
            Asked 2021-Jun-08 at 12:26

            We are trying to showcase inference with linked-data.

            The simple graph looks like the following in turtle-format:

            ...

            ANSWER

            Answered 2021-Jun-08 at 12:26

            To complete the question, I'm posting my comment above as an answer...

            To make it work, You need to define some meaning to your properties ex:isPartOf and ex:livesIn. Suggest to make ex:isPartOf transitive and then to define ex:livesIn as a property chain over ex:isPartOf, e.g.:

            Source https://stackoverflow.com/questions/67786448

            QUESTION

            Embedded Neo4j with Graph Data Science - BFS Procedure appears to be missing
            Asked 2021-Jun-04 at 20:45

            The documentation here https://neo4j.com/docs/graph-data-science/1.1/algorithms/bfs/#algorithms-bfs describes a callable "gds.alpha.bfs.stream".

            In order to call that, to the best of my knowledge, it needs to be registered with the embedded DB. Something along the lines of

            ...

            ANSWER

            Answered 2021-Jun-04 at 20:45

            The required procedure is conveniently called "TraverseProc" and allows use of both BFS and DFS.

            The file doesn't include the name of the callable, either. Discovered it through search of all my neo4j dependencies with

            Source https://stackoverflow.com/questions/67843656

            QUESTION

            Adding jdbc driver when creating Ontop Virtual repository problem
            Asked 2021-Jun-04 at 19:51

            I'm having problems adding a jdbc driver when creating an Ontop virtual SPARQL repository. I follow the instructions here. The interface already warns that there is no JDBC driver found in the classpath. There is also a link to the download site where you can get the drivers. That all works. But adding the driver to the lib path (in the case of a Linux installation \opt\graphdb-free\app\lib) and then restarting GraphDB does not work. GraphDB is still reporting that the driver is not found.

            I did try a lot of things. Adding the correct .jar to the CLASSPATH did not work. Using several other potential lib directories (the instructions are not precise on which directory to choose) also changed nothing. Then I took a look in the files you can create under Help - System Information - New Report. I found that all the .jar files in \opt\graphdb-free\app\lib were 'registered' (don't know if that is the correct term), but not the new one I placed there.

            Tried adding other .jars (for MS SQL, next to the MySQL that I needed). Same problem. Then I tried something weird that actually worked. I renamed a .jar that I thought I wouldn't need to .backup and then renamed the mysql driver .jar to that original .jar (hope this is not to confusing). Restarted Grapdb and it worked!

            What am I missing here? Is the list of .jars that are in the lib directory hardcoded somewhere? Very curious how to configure this the right way.

            ...

            ANSWER

            Answered 2021-Mar-11 at 11:36

            There is a config file, named graphdb-free.cfg, within graphdb-free/appfolder. Open it and alter the app.classpath property by adding the additional jar(s) for the JDBC driver to the list. Save and restart

            Source https://stackoverflow.com/questions/66318179

            QUESTION

            JSON-LD: Assign custom URIs to blank nodes within context
            Asked 2021-May-25 at 14:31

            I'm trying to convert a very large JSON file to JSON-LD. When I import the example code below into GraphDB, db:metadata becomes a property/predicate connecting each GeneSet:setX node with an automatically created blank node _:bX (gray in figure), from which the properties set_name and set_id then point to their corresponding values.

            ...

            ANSWER

            Answered 2021-May-25 at 14:31

            The sort of "templated" ID generation your after is (deliberately) not possible via the JSON-LD @context mechanism. The @context is for mapping tree data into graph data, not transforming it.

            Consequently, looking into injecting those ID values programmatically into the JSON-LD before you process it is one option.

            You might also want to ask on the JSON-LD WG's mailing list to get further options.

            Source https://stackoverflow.com/questions/67444075

            QUESTION

            Neo4j data loading performance: driver vs custom procedure
            Asked 2021-May-22 at 08:32

            I'm switching from Neo4j Java custom procedures to an approach based on the Neo4j Java driver. I want to end up with some sort of microservice running my graph algorithm, instead of calling the custom procedure through Cypher. I implemented the traversal using a bunch of standard HashMaps: Once the data is loaded from Neo4j to these HashMaps, the graph traversal is much faster than in my original custom procedure, so that's very promising.

            Now to my question: Within the custom procedure I was able to load the graph (40 mio edges, 10 mio nodes) to the Hashmaps like so:

            ...

            ANSWER

            Answered 2021-May-10 at 21:55

            Keep in mind that procedure code executes on the server itself, it is effectively embedded with Neo4j.

            Compare that to the need to transfer all nodes and their properties over the network. That's a lot of extra I/O that wasn't needed with procedures.

            Source https://stackoverflow.com/questions/67477156

            QUESTION

            The type GryoMessageSerializerV3d0 is deprecated
            Asked 2021-May-19 at 15:57

            I am using following code to connect to gremlin (JanusGraph) server and execute addV in transaction. My code works fine and it add Vertex properly, but code shows following warnings: "The type GryoMessageSerializerV3d0 is deprecated" & The method getInstance() from the type JanusGraphIoRegistry is deprecated

            So would like to know how can i get these warning resolved. Please find my code below:

            ...

            ANSWER

            Answered 2021-May-19 at 15:57

            The warning message is just letting you know that features you are using have been deprecated. If you look at the TinkerPop javadoc you can see how to resolve this problem - simply, prefer GraphBinaryMessageSerializerV1 to Gryo. You can often find helpful information for these sorts of things in the TinkerPop Upgrade Documentation. That said, you are using JanusGraph and depending on the version you are using I'm not sure that their IoRegistry implementation is supporting GraphBinary yet. While their latest code on their master branch shows support I don't see that code in a tagged version. It may be best to stay on Gryo a while longer until GraphBinary is fully supported as depending on the Gremlin you write you may hit some serialization problems. The warnings are just warnings - they should not impact your usage.

            As for the JanusGraphIoRegistry deprecation warning you can get rid of that pretty easily - simply prefer instance() rather than getInstance() (source code).

            Source https://stackoverflow.com/questions/67605955

            QUESTION

            Neo4j streams, fabric integration not working. Log reports "The `USE GRAPH` clause is not available in this implementation of Cypher"
            Asked 2021-May-12 at 07:51

            integrating my streams topics into fabric functionality is not working. Attempting to sink my first topic into a named graph produced the message below.
            I did follow the instructions provided by links to no avail.

            Am I missing someting?

            The Neo4j log Error:

            ErrorData(originalTopic=twoPoly, timestamp=1620757269838, partition=0, offset=1481, exception=org.neo4j.graphdb.QueryExecutionException: The USE GRAPH clause is not available in this implementation of Cypher due to lack of support for USE graph selector. (line 1, column 29 (offset: 28)) "UNWIND $events AS event use integerpolys MERGE (i:IndexedBy {N:event.NN,RowCounter:event.flatFileRowCounterr,MaxN:event.nMaxx,Dimension:"2"} ) MERGE (t:TwoSeqFactor {twoSeq:event.tSeqDB} ) MERGE (v:VertexNode {Vertex:event.vertexDBVertex,Scalar:event.vertexScalarDB,Degree:event.vertexDegreeDB} ) MERGE (e:Evaluate {Value:event.targetEvaluate}) MERGE (i)-[ee:TwoFactor]->(t) MERGE (i) -[:IndexedByEvaluate]->(e) MERGE (i)-[:VertexIndexedBy]->(v)" ^, key=null, value={"NN":"7","nMaxx":"8","vertexDBVertex":"1 -8 1 0 0","bTermDB":"1","flatFileRowCounterr":"6","targetEvaluate":"128","vertexDB":"1 -8 1 0 0","vertexScalarDB":"-8","tSeqDB":"32","vertexDegreeDB":"1"}, executingClass=class streams.kafka.KafkaAutoCommitEventConsumer)

            Neo4j version 4.1.0

            Relevant neo4j.conf:

            ...

            ANSWER

            Answered 2021-May-12 at 07:51

            The USE clause is currently not supported in this setting (only when connected using a neo4j driver).

            Remove the use integerpolys from the query and instead configure the streams plugin with the target database directly, according to https://neo4j.com/labs/kafka/4.0/consumer/#_multi_database_support

            Source https://stackoverflow.com/questions/67493235

            QUESTION

            Blank nodes generating when adding object properties to the ontology
            Asked 2021-Apr-14 at 18:58

            I have an ontology in Protege.

            When I add an object property like X worksFor Y, and then load the rdf to graphdb, it generates 3 triples with subject = blank node, property = owl:someValuesFrom, owl:onProperty, owl:rdfType, and then it adds a triple that states X rdf:subClassOf Y.

            Is this correct?

            What is the logic behind this?

            Here is an example of what I'm doing:

            This is the ontology in Protege. I made a small version that addresses this specific issue. I save it as rdf and then load it in GraphDb

            And here is what I get in GraphDb after loading the rdf from the ontology.

            I hope this helps to better understand the question.

            ...

            ANSWER

            Answered 2021-Apr-10 at 09:37

            The query output that you obtain is perfectly meaningful.

            By stating that personaCliente (subject) is a SubClass Of (predicate) worksFor some empresaCliente (object), you're saying that if p is a client person then it must work for some client company. Note that the object is not a simple super-class, but a complex class expressed by a property restriction.

            In other words, you're stating that every client person p works for some blank node _, such that _ is a client company. If you know description logics, read this as persona ⊑ ∃worksFor.empresaCliente.

            Now, by querying ?s ?p ?o, you're searching for all the possible triples of your ontology.

            Let's focus on the following subset of results:

            Source https://stackoverflow.com/questions/66962410

            QUESTION

            how to know the directory where there are the GraphDB executables
            Asked 2021-Apr-13 at 10:18

            I have installed GraphDB on Ubunto 20.4. How can I get the directory where there are the GraphDB executables.

            ...

            ANSWER

            Answered 2021-Apr-13 at 10:18

            GraphDB directory is located in /opt/graphdb-free The data directory (repositories, logs, configurations) is in /home/user/.graphdb

            Source https://stackoverflow.com/questions/67056968

            QUESTION

            Serializer for type org.janusgraph.graphdb.relations.RelationIdentifier not found
            Asked 2021-Apr-08 at 23:03

            Following error shows up in JanusGraph v0.5.3 server logs while retrieving edges from java client

            ...

            ANSWER

            Answered 2021-Apr-08 at 23:03

            I believe that some of the fixes that allow the IORegistry to hook the GraphBinary serializer have not yet been released although I do see the work on the main JanusGraph branch. [1] I was having the same problem you reported but was able to get things working using the GraphSONMessageSerialializerV3d0 serializer.

            [1] https://github.com/JanusGraph/janusgraph/commit/1cb4b6e849e3f9c2802722fe7f84c760cd471429

            This setup code works for me:

            Source https://stackoverflow.com/questions/66881082

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install graphdb

            You can download it from GitHub.
            You can use graphdb like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the graphdb component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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