I'm working on an RDF files importer but I have a problem, my data files have duplicate nodes. For this reason, I use a big ids to insert the nodes using batch inserter but the proccess is slow. I have seen this post when Michael recommends to use a index but the process remains slow.
Another option would be to merge duplicate nodes but I think there is no automatic option to do so in Neo4J. Am I wrong?
Could anyone help me? :)
Thanks!
There is no duplicate handling in the CSV batch importer yet (it's planned for the next version), as it is non-trivial and memory expensive.
Best to de-duplicate on your side.
Don't use externally supplied id's as node-id's that can get large from the beginning that just doesn't work. Use an efficient map (like trove) to keep the mapping between your key and the node-id.
I usually use a two-pass and an array for it then sort the array, array index becomes node-id and after sorting you can do another pass that nulls-out duplicate entries
Perfect :) The data would have the following structure:
chembl_activity:CHEMBL_ACT_102540 bao:BAO_0000208 bao:BAO_0002146 .
chembl_document:CHEMBL1129248 cco:hasActivity
chembl_activity:CHEMBL_ACT_102551 .
chembl_activity:CHEMBL_ACT_102540 cco:hasDocument
chembl_document:CHEMBL1129248 .
Each line corresponds with a relationship between two nodes and we could see that the node chembl_activity:CHEMBL_ACT_102540 is duplicated.
I wanted to save as id the hashcode of the node name but that hashcode is a very large number that slows the process. So I could check for ids to only create the relationship and not the nodes.
Thanks for all! :)
Related
I've always worked with relational DBs and recently decided to migrate a performance-critial service from SQL Server to Tarantool with a hope to take advantage of the fast in-memory search and processing. I've got a couple of questions while planning for the migration.
I've got a table with about one million records containing pricing information which means I'm dealing mostly with numbers and uuids. First, I need to run a select containing multiple conditions to get a subset of the data, like
SELECT * FROM rates WHERE SupplierId = #SupplierId AND ProductId = #ProductId AND (LocalDistributionZoneId = #LocalDistributionZoneId OR LocalDistributionZoneId IS NULL)
Q1: What is the strategy of running such a query in Lua? Do I create an index for each field in the predicate or I can go along with one secondary composite index?
Q2: Will it be more covenient to run such a query in SQL (box.sql.execute) rather than in pure Lua? Will it be considerably slower than running the same query in pure Lua?
Q3: If I use SQL, is it possible to review the execusion plan to make sure that the query I run really uses the indexes I've defined in the space?
Ok, after I've get the results from the first query I need to analyse the data and then based on the results of analysis, run one more query on the dataset returned by the first query.
Q4: Can Tarantool help me in dealing with the intermediate dataset? More specifically, may I somehow run more queries against the intermediate subset of tuples leveraging the indexes created in the space? Or, I would need to implement alternative strategies like re-add the intrim results to a temporary space with pre-defined indexes and then do another select, or implement further search myself?
Thank you!
Don't. Use SQL, it's faster: it doesn't create garbage collected objects for intermediate execution results.
Yes, please use our SQL features for that.
Use EXPLAIN statement.
I don't know what you exactly mean by "help". You could try to whatever strategy works best: create a more complex query, save the original query in a view to use in the resulting query, create a temporary table and work with it. To give more details let's look if the execution plan Tarantool chooses is good enough or you have to manually optimize it.
We are working on a system where users can define their own nodes and connections, and can query them with arbitrary queries. A user can create a "branch" much like in SCM systems and later can merge back changes into the main graph.
Is it possible to create an efficient data model for that in Neo4j? What would be the best approach? Of course we don't want to duplicate all the graph data for every branch as we have several million nodes in the DB.
I have read Ian Robinson's excellent article on Time-Based Versioned Graphs and Tom Zeppenfeldt's alternative approach with Network versioning using relationnodes but unfortunately they are solving a different problem.
I Would love to know what you guys think, any thoughts appreciated.
I'm not sure what your experience level is. Any insight into that would be helpful.
It would be my guess that this system would rely heavily on tags on the nodes. maybe come up with 5-20 node types that are very broad, including the names and a few key properties. Then you could allow the users to select from those base categories and create their own spin-offs by adding tags.
Say you had your basic categories of (:Thing{Name:"",Place:""}) and (:Object{Category:"",Count:4})
Your users would have a drop-down or something with "Thing" and "Object". They'd select "Thing" for instance, and type a new label (Say "Cool"), values for "Name" and "Place", and add any custom properties (IsAwesome:True).
So now you've got a new node (:Thing:Cool{Name:"Rock",Place:"Here",IsAwesome:True}) Which allows you to query by broad categories or a users created categories. Hopefully this would keep each broad category to a proportional fraction of your overall node count.
Not sure if this is exactly what you're asking for. Good luck!
Hmm. While this isn't insane, think about the type of system you're replacing first. SQL. In SQL databases you wouldn't use branches because it's data storage. If you're trying to get data from multiple sources into one DB, I'd suggest exporting them all to CSV files and using a MERGE statement in cypher to bring them all into your DB at once.
This could manifest similar to branching by having each person run a script on their own copy of the DB when you merge that takes all the nodes and edges in their copy and puts them all into a CSV. IE
MATCH (n)-[:e]-(n2)
RETURN n,e,n2
Then comparing these CSV's as you pull them into your final DB to see what's already there from the other copies.
IMPORT CSV WITH HEADERS FROM "file:\\YourFile.CSV" AS file
MERGE (N:Node{Property1:file.Property1, Property2:file.Property2})
MERGE (N2:Node{Property1:file.Property1, Property2:file.Property2})
MERGE (N)-[E:Edge]-(N2)
This will work, as long as you're using node types that you already know about and each person isn't creating new data structures that you don't know about until the merge.
I am using a "BatchInserter" to build a graph (in a single thread). I want to make sure nodes (and possibly relationships) are unique. My current solution is to check whether the node exists in the following manner:
String name = (String) nodeProperties.get(IndexKeys.CATEGORY_KEY);
if(index.get(IndexKeys.CATEGORY_KEY, name).size() > 0)
return index.get(IndexKeys.CATEGORY_KEY, name).getSingle();
Long nodeID = inserter.createNode( nodeProperties,categoryLabel );
index.add(nodeID, nodeProperties);
index.flush();
It seems to be working fine but as you can see it is IO expensive (flushing on every new addition - which i believe is a lucene "commit" command). This is slowing down my code considerably.
I am aware of put if absent and uniqueFactory. As documented:
By using put-if-absent functionality, entity uniqueness can be guaranteed using an index.
Here the index acts as the lock and will only lock the smallest part
needed to guaranteed uniqueness across threads and transactions. To
get the more high-level get-or-create functionality make use of
UniqueFactory
However, these are for transaction based interactions with the graph. What I would like to do is to ensure uniqueness of nodes and possibly relationships in a batch insertion semantics, that is faster than my current setup.
Any pointers would be much appreciated.
Thank you
You should investigate the MERGE keyword in cypher. I believe this will permit you to exploit your autoindexes without requiring you to use them yourself. More broadly, you might want to see if you can formulate your bulk load in a way that is conducive to piping large volumes of cypher queries through the neo4j-shell.
Finally, as general pointers and background, you should check out this information on bulk loading
When I encountered this problem, I just decided to go tyrant and force index values in my own. Can't you do the same? I mean, ensure uniqueness before you do the insertions?
START names = node(*),
target=node:node_auto_index(target_name="TARGET_1")
MATCH names
WHERE NOT names-[:contains]->()
AND HAS (names.age)
AND (names.qualification =~ ".*(?i)B.TECH.*$"
OR names.qualification =~ ".*(?i)B.E.*$")
CREATE UNIQUE (names)-[r:contains{type:"declared"}]->(target)
RETURN names.name,names,names.qualification
Iam consisting of nearly 1,80,000 names nodes, i had iterated the above process to create unique relationships above 100 times by changing the target. its taking too much amount of time.How can i resolve it..
i build the query with java and iterated.iam using neo4j 2.0.0.5 and java 1.7 .
I edited your cypher query because I think I understand it, but I can barely read the rest of your question. If you edit it with white spaces and punctuation it might be easier to understand what you are trying to do. Until then, here are some thoughts about your query being slow.
You bind all the nodes in the graph, that's typically pretty slow.
You bind all the nodes in the graph twice. First you bind universally in your start clause: names=node(*), and then you bind universally in your match clause: MATCH names, and only then you limit your pattern. I don't quite know what the Cypher engine makes of this (possibly it gets a migraine and goes off to make a pot of coffee). It's unnecessary, you can at least drop the names=node(*) from your start clause. Or drop the match clause, I suppose that could work too, since you don't really do anything there, and you will still need a start clause for as long as you use legacy indexing.
You are using Neo4j 2.x, but you use legacy indexing instead of labels, at least in this query. Without knowing your data and model it's hard to know what the difference would be for performance, but it would certainly make it much easier to write (and read) your queries. So, that's a different kind of slow. It's likely that if you had labels and label indices, the query performance would improve.
So, first try removing one of the universal bindings of nodes, then use the 2.x schema tools to structure your data. You should be able to write queries like
MATCH target:Target
WHERE target.target_name="TARGET_1"
WITH target
MATCH names:Name
WHERE NOT names-[:contains]->()
AND HAS (names.age)
AND (names.qualification =~ ".*(?i)B.TECH.*$"
OR names.qualification =~ ".*(?i)B.E.*$")
CREATE UNIQUE (names)-[r:contains{type:"declared"}]->(target)
RETURN names.name,names,names.qualification
I have no idea if such a query would be fast on your data, however. If you put the "Name" label on all your nodes, then MATCH names:Name will still bind all nodes in the database, so it'll probably still be slow.
P.S. The relationships you create have a TYPE called contains, and you give them a property called type with value declared. Maybe you have a good reason, but that's potentially very confusing.
Edit:
Reading through your question and my answer again I no longer think that I understand even your cypher query. (Why are you returning both the bound nodes and properties of those nodes?) Please consider posting sample data on console.neo4j.org and explain in more detail what your model looks like and what you are trying to do. Let me know if my answer meets your question at all or I'll consider removing it.
I have nodes with multiple "sourceIds" in one array-valued property called "sourceIds", just because there could be multiple resources a node could be derived from (I'm assembling multiple databases into one Neo4j model).
I want to be able to look up nodes by any of their source IDs. With legacy indexing this was no problem, I would just add a node to the index associated with each element of the sourceIds property array.
Now I wanted to switch to indexing with labels and I'm wondering how that kind of index works here. I can do
CREATE INDEX ON :<label>(sourceIds)
but what does that actually do? I hoped it would just create index entries for each array element, but that doesn't seem to be the case. With
MATCH n:<label> WHERE "testid" in n.sourceIds RETURN n
the query takes between 300ms and 500ms which is too long for an index lookup (other schema indexes work three to five times faster). With
MATCH n:<label> WHERE n.sourceIds="testid" RETURN n
I don't get a result. That's clear because it's an array property but I just gave it a try since it would make sense if array properties would be broken down to their elements for indexing purposes.
So, is there a way to handle array properties with schema indexing or are there plans or will I just have to stick to legacy indexing here? My problem with the legacy Lucene index was that I hit the max number of boolean clauses (1024). Another question thus would be: Can I raise this number? Lucene allows that, but can I do this with the Lucene index used by Neo4j?
Thanks and best regards!
Edit: A bit more elaboration on why I hit the boolean clauses max limit: I need to export specific parts of the database into custom file formats for text processing pipelines. These pipelines use components I cannot (be it for the sake of accessibility or time) change to query Neo4j directly, so I'd rather stay with the defined required file format(s). I do the export via the pattern "give me all IDs in the DB; now, for batches of IDs, query the desired information (e.g. specific paths) from Neo4j and store the results to file". Why I use batches at all? Well, if I don't, things are slowed down significantly via the connection overhead. Thus, large batches are a kind of optimization here.
Schema indexes can only do exact matches right now. Your "testid" in n.sourceIds does not use the index (as shown by your query times). I think there are plans to make this behave better, but I'm waiting for them just as eagerly as you are.
I've actually hit a lower max in the lucene query: 512. If there is a way to increase it I'd love to hear of it. The way I got around it is just doing more than one query if I have one of the rare cases that actually goes over 512 ids. What query are you doing where you need more?