I have a legacy dataset (ENRON data represented as GraphML) that I would like to query. In an comment in a related question, #StefanArmbruster suggests that I use Cypher to query the database. My query use case is simple: given a message id (a property of the Message node), retrieve the node that has that id, and also retrieve the sender and recipient nodes of that message.
It seems that to do this in Cypher, I first have to create an index of the nodes. Is there a way to do this automatically when the data is loaded from the graphML file? (I had used Gremlin to load the data and create the database.)
I also have an external Lucene index of the data (I need it for other purposes). Does it make sense to have two indexes? I could, for example, index the Neo4J node ids into my external index, and then query the graph based on those ids. My concern is about the persistence of these ids. (By analogy, Lucene document ids should not be treated as persistent.)
So, should I:
Index the Neo4j graph internally to query on message ids using Cypher? (If so, what is the best way to do that: regenerate the database with some suitable incantation to get the index built? Build the index on the already-existing db?)
Store Neo4j node ids in my external Lucene index and retrieve nodes via these stored ids?
UPDATE
I have been trying to get auto-indexing to work with Gremlin and an embedded server, but with no luck. In the documentation it says
The underlying database is auto-indexed, see Section 14.12, “Automatic Indexing” so the script can return the imported node by index lookup.
But when I examine the graph after loading a new database, no indexes seem to exist.
The Neo4j documentation on auto indexing says that a bunch of configuration is required. In addition to setting node_auto_indexing = true, you have to configure it
To actually auto index something, you have to set which properties
should get indexed. You do this by listing the property keys to index
on. In the configuration file, use the node_keys_indexable and
relationship_keys_indexable configuration keys. When using embedded
mode, use the GraphDatabaseSettings.node_keys_indexable and
GraphDatabaseSettings.relationship_keys_indexable configuration keys.
In all cases, the value should be a comma separated list of property
keys to index on.
So is Gremlin supposed to set the GraphDatabaseSettings parameters? I tried passing in a map into the Neo4jGraph constructor like this:
Map<String,String> config = [
'node_auto_indexing':'true',
'node_keys_indexable': 'emailID'
]
Neo4jGraph g = new Neo4jGraph(graphDB, config);
g.loadGraphML("../databases/data.graphml");
but that had no apparent effect on index creation.
UPDATE 2
Rather than configuring the database through Gremlin, I used the examples given in the Neo4j documentation so that my database creation was like this (in Groovy):
protected Neo4jGraph getGraph(String graphDBname, String databaseName) {
boolean populateDB = !new File(graphDBName).exists();
if(populateDB)
println "creating database";
else
println "opening database";
GraphDatabaseService graphDB = new GraphDatabaseFactory().
newEmbeddedDatabaseBuilder( graphDBName ).
setConfig( GraphDatabaseSettings.node_keys_indexable, "emailID" ).
setConfig( GraphDatabaseSettings.node_auto_indexing, "true" ).
setConfig( GraphDatabaseSettings.dump_configuration, "true").
newGraphDatabase();
Neo4jGraph g = new Neo4jGraph(graphDB);
if (populateDB) {
println "Populating graph"
g.loadGraphML(databaseName);
}
return g;
}
and my retrieval was done like this:
ReadableIndex<Node> autoNodeIndex = graph.rawGraph.index()
.getNodeAutoIndexer()
.getAutoIndex();
def node = autoNodeIndex.get( "emailID", "<2614099.1075839927264.JavaMail.evans#thyme>" ).getSingle();
And this seemed to work. Note, however, that the getIndices() call on the Neo4jGraph object still returned an empty list. So the upshot is that I can exercise the Neo4j API correctly, but the Gremlin wrapper seems to be unable to reflect the indexing state. The expression g.idx('node_auto_index') (documented in Gremlin Methods) returns null.
the auto indexes are created lazily. That is - when you have enabled the auto-indexing, the actual index is first created when you index your first property. Make sure you are inserting data before checking the existence of the index, otherwise it might not show up.
For some auto-indexing code (using programmatic configuration), see e.g. https://github.com/neo4j-contrib/rabbithole/blob/master/src/test/java/org/neo4j/community/console/IndexTest.java (this is working with Neo4j 1.8
/peter
Have you tried the automatic index feature? It's basically the use case you're looking for--unfortunately it needs to be enabled before you import the data. (Otherwise you have to remove/add the properties to reindex them.)
http://docs.neo4j.org/chunked/milestone/auto-indexing.html
Related
spring-data-neo4j query using dynamic key and dynamic value,
like following code:
public interface NodeReposity extends Neo4jRepository<Node,Long> {
#Query("MATCH(n:Node{{key}={value}})return n")
Iterable<Node> queryByProperty(#Param("key")String key,#Param("value") String value);
}
But it says the {key} must be something like variable in string, such as MATCH(n:Node{name={value}})return n.Can't be {key}. But My property's key is dynamic like the value, how to implement it and is it possible?
Short answer: The query will be send "as it is" to the database and because cypher does only support placeholders for values, this will cause an error.
Slightly longer answer: When it comes to executing the method Spring Data Neo4j will look if it has already pre-processed the query and either process and cache it or just load it from the cache. This is done to improve the time it takes to execute the method from the application.
Pre-processing means SDN knows what parameters are in there and just adds the values in the right place when the method is called.
If SDN would provide more features for the query than cypher, the query would have to be processed every time the method gets called to create a new query that can be used with Neo4j.
I have the following code
PagedResultList res = myService.getPage(paginateParams, ...)
println res.size() // returns 2
println res.getTotalCount() // returns 1
getPage looks like:
def criteria = MyDomain.createCriteria()
criteria.list(max: paginateParams.max, offset: paginateParams.offset) { // max is 10, offset is 0, sortBy is updatedAt and sortOrder is desc
eq('org', org)
order(paginateParams.sortBy, paginateParams.sortOrder)
}
why do the two method return different values? The documentation doesn't explain the difference, but does mention that getTotalCount is for number of records
currently on grails 2.4.5
edits:
println on res prints out:
res: [
com.<hidden>.MyDomain: 41679f98-a7c5-4193-bba8-601725007c1a,
com.<hidden>.MyDomain: 41679f98-a7c5-4193-bba8-601725007c1a]
Yes, res has a SINGLE object twice - that's the bug I'm trying to fix. How do I know that? I have an primary key on MyDomain's ID, and when I inspect the database, it's also showing one record for this particular org (see my criteria)
edit 2: I found this comment (http://docs.grails.org/2.4.5/ref/Domain%20Classes/createCriteria.html)
listDistinct If subqueries or associations are used, one may end up
with the same row multiple times in the result set. In Hibernate one
would do a "CriteriaSpecification.DISTINCT_ROOT_ENTITY". In Grails one
can do it by just using this method.
Which, if I understand correctly, is their way of saying "list" method doesn't work in this scenario, use listDistinct instead but then they go on to warn:
The listDistinct() method does not work well with the pagination
options maxResult and firstResult. If you need distinct results with
pagination, we currently recommend that you use HQL. You can find out
more information from this blog post.
However, the blog post is a dead link.
Related: GORM createCriteria and list do not return the same results : what can I do?
Not related to actual problem after question edited but this quote seems useful
Generally PagedResultList .size() perform size() on resultList property (in-memory object represent database record), while .getTotalCount() do count query against database. If this two value didn't match your list may contain duplicate.
After viewing related issues (GORM createCriteria and list do not return the same results : what can I do?) I determined that there were several approaches:
Use grails projection groupBy('id') - doesn't work b/c i need the entire object
USe HSQL - Domain.executeQuery - actually this didn't work for my scenario very well because this returns a list, whereas criteria.list returns a PagedResultList from which I previously got totalCount. This solution had me learning HSQL and also made me break up my existing logic into two components - one that returned PagedResultList and one that didn't
Simply keep a set of IDs as I process my PagedResultList and make sure that I didn't have any duplicates.
I ended up going with option 3 because it was quick, didn't require me to learn a new language (HSQL) and I felt that I could easily write the code to do it and I'm not limited by the CPU to do such a unique ID check.
I'm using BatchInserter to initialise my Neo4j database - the data is coming from XML files on my local filesystem.
Suppose one set of files contains node information / properties, and another set has relationship information. I wanted to do two passes: create all the nodes, then set about creating the relationships.
However, the createRelationship method accepts a long id for the nodes, which I don't have in my relationship XML - all of my nodes have a GUID as a property called ID which I use to reference them.
Does BatchInsert mean it hasn't been indexed yet, so I won't be able to create relationships on nodes based on some other property?
I usually just keep the node-attribute to id mapping in a cache in memory in an efficient collection implementation like Trove or so.
Then for the relationships you can look up the node-id by attribute.
I found I was able to add nodes to the index as I go.
Creating index:
BatchInserter inserter = BatchInserters.inserter( "data/folder" );
BatchInserterIndexProvider indexProvider = new LuceneBatchInserterIndexProvider( inserter );
BatchInserterIndex index = indexProvider.nodeIndex("myindex", MapUtil.stringMap( "type", "exact" ) );
Then each time I insert a node, add it to the index as well:
Label label = DynamicLabel.label("person");
Map<String, Object> properties = new HashMap<>();
properties.put("ID", <some-value-here>);
long newNode = inserter.createNode(properties, labek);
index.add(newNode, properties);
index.flush();
Which I can query as I like:
IndexHits<Long> hits = index.get("ID", <some-value-here>);
if(hits.size() > 0) {
long existing = hits.getSingle();
}
I have no idea whether this is any good. I guess calling flush on the index often is a bad idea, but it seems to work for me.
When running Neo4j embedded, the default configuration doesn't have the automatic node index set as fulltext (meaning that all Lucene queries are case sensitive). How can I configure the automatic index to be fulltext?
For starters, you must perform this on a new database. The automatic index is lazily created, which means that it isn't created until the first access. You have until the first access to perform this configuration. If you attempt to change the property after it's already been created, it won't work. So the first step is to load the database with automatic indexing enabled (node or relationship).
val db = new GraphDatabaseFactory().newEmbedddedDatabaseBuilder("path/to/db").
setConfig(GraphDatabaseSettings.node_keys_indexable, "label,username").
setConfig(GraphDatabaseSettings.node_auto_indexing, "true").newGraphDatabase()
Now, before you do anything, you have to set the configuration properties. You can find out about the possible properties and values here. To do this, we just need two more lines.
val autoIndex = db.index.forNodes("node_auto_index")
db.index.setConfiguration(autoIndex, "type", "fulltext")
And that's all there is to it. You can now create vertices and relationships and the automatic index will be created and populated. You can get use the following code to query it using any Lucene query.
autoIndex.getAutoIndex.query("label:*caseinsensitive*")
I am using Gremlin and Neo4j to manipulate the ENRON dataset from infochimps. This dataset has two types of vertexes, Message and Email Addresss and two types of edges, SENT and RECEVIED_BY. I would like to create a custom index on this dataset that creates a Lucene document for each vertex of type: 'Message' and incorporates information from associated vertexes (e.g., v.in(), v.out()) as additional fields in the Lucene document.
I am thinking of code along the lines of
g = new Neo4jGraph('enron');
PerFieldAnalyzerWrapper analyzer =
new PerFieldAnalyzerWrapper(new StandardAnalyzer());
analyzer.addAnalyzer("sender", new KeywordAnalyzer());
analyzer.addAnalyzer("recipient", new KeywordAnalyzer());
IndexWriter idx = new IndexWriter (dir,analyzer,IndexWriter.MaxFieldLength.UNLIMITED);
g.V.filter{it.type == 'Message'}.each { v ->
Document doc = new Document();
doc.add(new Field("subject", v.subject));
doc.add(new Field("body", v.body));
doc.add(new Field("sender", v.in().address);
v.out().each { recipient ->
doc.add(new Field("recipient", recipient.address));
}
idx.addDocument(doc);
}
idx.close();
My questions are:
Is there a better way to enumerate vertexes for indexing?
Can I use auto-indexing for this, and if so, how to I specify what should be indexed?
Can I specify my own Analyzer, or am I stuck with the default? What is the default?
If I must create my own index, should I be using gremlin for this, or am I better off with a Java program?
I will be talking about direct Neo4j access here since I'm not well travelled in Gremlin.
So you'd like to build a Lucene index "outside of" the graph itself? Otherwise you can use the built in graphDb.index().forNodes( "myIndex", configForMyIndex ) to get (created on demand) a Lucene index associated with neo4j. You can then add multiple fields to each document by calling index.add( node, key, value ), where each node will be represented by one document in that Lucene index.
1) In Gremiln... I don't know
2) See http://docs.neo4j.org/chunked/milestone/auto-indexing.html
3) See http://docs.neo4j.org/chunked/milestone/indexing-create-advanced.html
4) Do you need to create it outside of the db entirely? If so, why?
I just finished an import with a Java process and it's really easy, in my opinion better inclusive through Gremlin.
Anyway, if the process is failing is because of you CAN'T create a new object of StandardAnalyzer. All the constructors of that class require parameters, so you should create a wrapper class or create it with the right version of Lucene like paramater in the constructor.
Neo4J, until today, accepts only until the lucene version 36.