Re: [Neo] Limits of Neo4j

2010-04-19 Thread Todd Stavish
Hi Chris,

Neo4j should be suitable for your problem. I just built a similar
application (using an email corpus for relationships not facebook).

The size of the system was the following:

Nodes: 100,030,002
Edges:  3,041,030,000
Attributes: 140,120,000

We did standard friend-of-a-friend and other navigational queries.
Most of our queries came back under 50 milliseconds (often under 10
milliseconds).  In an EC2 instance we were able to ingest the entire
95GB graph in 100m39.661s. I don't think we did a really good job
optimizing Neo4j or the VMs, plus it was all virtualized in EC2
(dedicated hardware would have been faster). But with those speeds and
at that scale, we were happy without spending any time optimizing. :)

-Todd


On Mon, Apr 19, 2010 at 2:21 PM, snacktime snackt...@gmail.com wrote:
  Would Neo4j scale to handle the friend relationships handled by Facebook?
 Where I work we run a number of large social games mostly on Facebook, and
 for a number of reasons we end up caching a lot of the friend data (mostly
 because their api can be unreliable and slow).  I'd like to have a more
 intelligent caching system where our side is relationship aware, so when
 relationships change we can show that to users, as opposed to doing stuff
 like caching your friends list for 48 hours, regardless of whether it's
 changed.

 Is Ne04j even in the ballpark for something like this?

 Chris
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Re: [Neo] Connecting to Neo4j DB from ActionScript

2010-03-12 Thread Todd Stavish
Hi Amir,

I used GSON (google's json package) on the Neo side and Flex's json
AS3 classes to make the connection.

-Todd



On Fri, Mar 12, 2010 at 4:31 PM, Amir Hossein Jadidinejad
amir.jad...@yahoo.com wrote:
 Hi,
 Is it possible to connect a Neo4j instance using ActionScript and Adobe Flex?!
 Thanks.




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Re: [Neo] Graph Algo Problems

2010-03-03 Thread Todd Stavish
Hi Peter,

I have the centrality stuff working now, no further help required. :)   
My nodeset  had to be larger.

-Todd

On Mar 1, 2010, at 10:02 PM, Todd Stavish t...@stavi.sh wrote:

 Hi Everyone,

 I am running into some null pointer exceptions when I try to feed
 things into some of the graph algos. The test cases can be found in
 the link below. It is all maven based and the pre-built graph is
 included. Queries19 (Floyd-Warshall), 20 (Eigenvector Centrality with
 the Arnoldi iteration), and 21 (Eigenvector Centrality with the
 Power method) are the problematic ones.

 To run each query, change the query number in the
 configuration.properties in the resources directory. Then, mvn
 compile, mvn exec:exec.

 http://www.stavi.sh/backend.zip

 I constrained the sub-graph to be the smallest possible one. I also
 tried setting the max iterations and calling calculate before the
 getCentrality call. I followed the same pattern I used for the
 BFS-Centrality and Dijikstra for shortest path (which seem to be
 working). Not sure what I am doing wrong here.

 Any help would be appreciated.

 Thanks,
 Todd
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Re: [Neo] Graph Algo Problems

2010-03-03 Thread Todd Stavish

Those exceptions seem like it might not be setup properly. No matter,  
I changed the implementation.

I am seeing different centrality calculations for Arnoldi versus  
Power. I tweaked the iterations to see if it made a difference. Is it  
the precision setting causing the difference maybe? The target and  
nodeset are the same for each.

-Todd

On Mar 3, 2010, at 11:04 AM, Peter Neubauer  
peter.neuba...@jayway.com wrote:

 Ok, great,

 I am just now looking at it and noticed a NPE in Node topicNodes =
 referenceNode.getSingleRelationship(RelationshipTypes.TOPICS,
 Direction.OUTGOING).getEndNode();

 The referenceNode.getSingleRelationship(RelationshipTypes.TOPICS,
 Direction.OUTGOING) is returning NULL ...

 Cheers,

 /peter neubauer

 COO and Sales, Neo Technology

 GTalk:  neubauer.peter
 Skype   peter.neubauer
 Phone   +46 704 106975
 LinkedIn   http://www.linkedin.com/in/neubauer
 Twitter  http://twitter.com/peterneubauer

 http://www.neo4j.org - Your high performance graph  
 database.
 http://www.tinkerpop.com  - Processing for Internet-scale graphs.
 http://www.thoughtmade.com - Scandinavias coolest Bring-a-Thing party.



 On Wed, Mar 3, 2010 at 6:55 PM, Todd Stavish toddstav...@gmail.com  
 wrote:
 Hi Peter,

 I have the centrality stuff working now, no further help required. :)
 My nodeset  had to be larger.

 -Todd

 On Mar 1, 2010, at 10:02 PM, Todd Stavish t...@stavi.sh wrote:

 Hi Everyone,

 I am running into some null pointer exceptions when I try to feed
 things into some of the graph algos. The test cases can be found in
 the link below. It is all maven based and the pre-built graph is
 included. Queries19 (Floyd-Warshall), 20 (Eigenvector Centrality  
 with
 the Arnoldi iteration), and 21 (Eigenvector Centrality with the
 Power method) are the problematic ones.

 To run each query, change the query number in the
 configuration.properties in the resources directory. Then, mvn
 compile, mvn exec:exec.

 http://www.stavi.sh/backend.zip

 I constrained the sub-graph to be the smallest possible one. I also
 tried setting the max iterations and calling calculate before the
 getCentrality call. I followed the same pattern I used for the
 BFS-Centrality and Dijikstra for shortest path (which seem to be
 working). Not sure what I am doing wrong here.

 Any help would be appreciated.

 Thanks,
 Todd
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Re: [Neo] Graph Algo Problems

2010-03-02 Thread Todd Stavish
Hi Peter,

Thanks for the help. It is critical. I need to provide feedback to my
customer on the suitability of using the in-built Neo4J graph algos.
Or if someone has a working testcase of Floyd-Warshall or either
Eigenvector implementation, I could use that to compare with my code /
graph.

Thanks,
Todd


On Tue, Mar 2, 2010 at 3:10 AM, Peter Neubauer neubauer.pe...@gmail.com wrote:
 Thanks Todd for the pointers!

 Is this absolutely critical for you? Otherwise, we will put it into
 our backlog and do as time permits. Great you got testcases, so I'm
 sure we should be able to sort it out. The graph algos are written
 some time ago and would need some general review - we are not quite
 satisfied with the semantics and logic of things.

 Meanwhile, another possibility would be to look at the JUNG algos via
 Gremlin, see 
 http://wiki.github.com/tinkerpop/gremlin/working-with-jung-algorithms.
 They do not use traversers, but the algos themselfes should be very
 good and otherwise performance is prolly ok.

 Cheers,

 /peter neubauer

 COO and Sales, Neo Technology

 GTalk:      neubauer.peter
 Skype       peter.neubauer
 Phone       +46 704 106975
 LinkedIn   http://www.linkedin.com/in/neubauer
 Twitter      http://twitter.com/peterneubauer

 http://www.neo4j.org             - Your high performance graph database.
 http://www.tinkerpop.com      - Processing for Internet-scale graphs.
 http://www.thoughtmade.com - Scandinavias coolest Bring-a-Thing party.



 On Tue, Mar 2, 2010 at 6:02 AM, Todd Stavish t...@stavi.sh wrote:
 Hi Everyone,

 I am running into some null pointer exceptions when I try to feed
 things into some of the graph algos. The test cases can be found in
 the link below. It is all maven based and the pre-built graph is
 included. Queries19 (Floyd-Warshall), 20 (Eigenvector Centrality with
 the Arnoldi iteration), and 21 (Eigenvector Centrality with the
 Power method) are the problematic ones.

 To run each query, change the query number in the
 configuration.properties in the resources directory. Then, mvn
 compile, mvn exec:exec.

 http://www.stavi.sh/backend.zip

 I constrained the sub-graph to be the smallest possible one. I also
 tried setting the max iterations and calling calculate before the
 getCentrality call. I followed the same pattern I used for the
 BFS-Centrality and Dijikstra for shortest path (which seem to be
 working). Not sure what I am doing wrong here.

 Any help would be appreciated.

 Thanks,
 Todd
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[Neo] Graph Algo Problems

2010-03-01 Thread Todd Stavish
Hi Everyone,

I am running into some null pointer exceptions when I try to feed
things into some of the graph algos. The test cases can be found in
the link below. It is all maven based and the pre-built graph is
included. Queries19 (Floyd-Warshall), 20 (Eigenvector Centrality with
the Arnoldi iteration), and 21 (Eigenvector Centrality with the
Power method) are the problematic ones.

To run each query, change the query number in the
configuration.properties in the resources directory. Then, mvn
compile, mvn exec:exec.

http://www.stavi.sh/backend.zip

I constrained the sub-graph to be the smallest possible one. I also
tried setting the max iterations and calling calculate before the
getCentrality call. I followed the same pattern I used for the
BFS-Centrality and Dijikstra for shortest path (which seem to be
working). Not sure what I am doing wrong here.

Any help would be appreciated.

Thanks,
Todd
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Re: [Neo] Porting to RC1 for algos?

2010-02-06 Thread Todd Stavish
Hi Mattias,

Thanks, I've already upgraded to RC1 and 0.3-SNAPSHOT . It was pretty
straightforward and painless. So if anyone that is thinking of
upgrading and hasn't, it's not a big deal. Don't let the initial
compilation errors scare you. :)

Regards,
Todd



On Sat, Feb 6, 2010 at 5:14 PM, Mattias Persson
matt...@neotechnology.com wrote:
 which version are you using? If you're using maven then that component
 have changed name to (artifactId) neo4j-graph-algo and uses the latest
 kernel snapshot, so my thought would be to try that. (version
 0.3-SNAPSHOT)

 2010/2/6, Todd Stavish t...@stavi.sh:
 Hi Everyone,

 Is it better for us to port to RC1 if we are trying to use graph-algos
 or stay on the old stuff?

 Thanks
 Todd
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[Neo] Graph Algos

2010-02-03 Thread Todd Stavish
Hello,

When I migrated from:

dependency
groupIdorg.neo4j/groupId
artifactIdgraph-algo/artifactId
version0.2-SNAPSHOT/version
/dependency

to:

dependency
groupIdorg.neo4j/groupId
artifactIdneo4j-graph-algo/artifactId
version0.3-SNAPSHOT/version
/dependency

It gave me the following compilation errors:

NeoQuery.java:[719,35] cannot find symbol
symbol  : constructor
SingleSourceShortestPathBFS(nulltype,org.neo4j.api.core.Direction,com.cisco.collectiveintelligence.RelationshipTypes)
location: class org.neo4j.graphalgo.shortestpath.SingleSourceShortestPathBFS

NeoQuery.java:[736,44] getCentrality(org.neo4j.graphdb.Node) in
org.neo4j.graphalgo.centrality.ShortestPathBasedCentralityjava.lang.Double,java.lang.Integer
cannot be applied to (org.neo4j.api.core.Node)


Looking in SVN, the constructor seems to be there, but getCentrality is gone?

Thanks,
Todd




ListNode nodeList = findPeopleByATopic(person,topic);

// Set up shortest path algorithm.
// Observe that we don't need to specify a start node.
SingleSourceShortestPathInteger singleSourceShortestPath;
singleSourceShortestPath = new SingleSourceShortestPathBFS(
person,
Direction.BOTH,
RelationshipTypes.KNOWS);

System.out.println(after single sorce shortest path);

// Set up betweenness centrality algorithm.
Set nodeSet = new HashSet(nodeList);
BetweennessCentralityInteger betweennessCentrality;
betweennessCentrality = new BetweennessCentralityInteger(
singleSourceShortestPath,
nodeSet);

System.out.println(after betweeness centrality constructor);

// Get centrality value for a node.
Double value = betweennessCentrality.getCentrality(person);
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[Neo] Does anyone have Prefuse (not flare) with Neo4j sample code?

2010-01-01 Thread Todd Stavish
In particular, how to use their graph reader class or custom mapping?

Thanks,
Todd
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Re: [Neo] Neo Shell listing a relationship's property

2009-12-12 Thread Todd Stavish
Ah, I was trying to cd to the relationship ID without the -r. Works
perfectly. Thanks Mattias.





On Sat, Dec 12, 2009 at 5:54 AM, Mattias Persson
matt...@neotechnology.com wrote:
 This can be done. You're using b11 right? In that case you do a:

 ls -rv to list your relationships with their ids (the -v flag)

 then you take the relationship's id and do a:

 cd -r relationship-id

 you're now standing on that relationship and can do operations like
 ls, set, rm a.s.o. From there you can then do cd .. to get back or
 cd start or cd end to go to its start/end node
 2009/12/11, Todd Stavish toddstav...@gmail.com:
 Is there a way to list a property of a relationship in Neo Shell? If
 not, is there another way to do this without using Neoclipse? I am
 SSHing into an EC2 instance.

 Thanks,
 Todd
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Re: [Neo] SingleValueIndex org.neo4j.api.core.NotFoundException: More than one relationship

2009-12-11 Thread Todd Stavish
Hi Arin,

I just ran into this same problem. I am not sure about the scalability
of my solution, but I only had 20,000 users. It may scale, but I just
wanted you to know that I didn't test for it. My goal was to step
into the graph using a string based query, that is supplying a user's
name. An index seemed like overkill to me.

I created my users with all of the relationships that I needed for
modeling, however I created one extra relationship that attached to a
sub-reference node that attached to the reference node.  So when I
needed to needed a user, I could open the reference node, got to the
people sub-reference node, and traverse to all of my people nodes
adding them to a hashmapstring:name,long:nodeId. This hashmap can be
used to resolve users to their nodeId for other queries along the
graph.

Code is below.

-Todd

private static HashMapString,Long getMap(String type, NeoService neo)
{
long referenceNodeId = 0;
HashMapString,Long map = new HashMapString,Long();
Node referenceNode = neo.getNodeById(referenceNodeId);
if (type.equals(topic))
{
Node topicNodes =
referenceNode.getSingleRelationship(RelationshipTypes.TOPICS,
Direction.OUTGOING).getEndNode();
for (Relationship topic :
topicNodes.getRelationships(RelationshipTypes.TOPIC,
Direction.OUTGOING))
{
Node topicNode = topic.getEndNode();

map.put(topicNode.getProperty(topic).toString(), topicNode.getId());
}
}
else if (type.equals(person))
{
Node personNodes =
referenceNode.getSingleRelationship(RelationshipTypes.PEOPLE,
Direction.OUTGOING).getEndNode();
for (Relationship person :
personNodes.getRelationships(RelationshipTypes.PERSON,
Direction.OUTGOING))
{
Node personNode = person.getEndNode();

map.put(personNode.getProperty(name).toString(), personNode.getId());
}
}
return map;
}





On Thu, Dec 10, 2009 at 2:19 PM, Arin Sarkissian a...@rspot.net wrote:
 Hey guys,

 I'm pretty new to Neo4j, especially the indexing stuff.

 Here's my situation. I want to be able to get nodes via one of their
 properties; in this case let's say the Nodes represent a user  I want
 to be able to grab a User's node via their username.

 So, my initial attempt may be naive (no batching etc) but I've been
 reading thru a a large text file (CSV format: username, userid),
 creating a node for each of these lines  indexing the username
 component.

 Now this needs to be unique (given that usernames are unique) so I've
 been using the SingleValueIndex and have run into a problem: It looks
 like the SingleValueIndex actually does allow multiple values for a
 given lookup (ex: username = phatduckk) however when trying to fetch a
 Node from the index that has multiples (ie: username=phatduckk was
 indexed twice) I get a NotFoundException with More than one
 relationship  as the message.

 I have posted a skeleton piece of code that surfaces this problem over
 at: http://gist.github.com/253553
 This code does not make sure that the Node being indexed for a key is
 always the same - it actually does the opposite: it tries to index
 username=phatduckk w/ a different node each time.

 The bit of code at http://gist.github.com/253569 does the opposite: i
 tries to index the same node for the index username=phatduckk each
 time.

 I also have a few random questions sprinkled in the code as comments
 which illustrate my noobiness =)

 Honestly, I'm not claiming this is a bug - I may be completely
 misusing and misunderstanding the indexing functionality but with my
 limited experience it doesn't seem that SingleValueIndex is single
 at all (hopefully - i'm just wrong and made a dumb mistake).

 Thanks for the help guys,
 Arin
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[Neo] Neo Shell listing a relationship's property

2009-12-11 Thread Todd Stavish
Is there a way to list a property of a relationship in Neo Shell? If
not, is there another way to do this without using Neoclipse? I am
SSHing into an EC2 instance.

Thanks,
Todd
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Re: [Neo] LuceneIndexBatchInserter doubt

2009-12-07 Thread Todd Stavish
Hi Mattias, Núria.

I am also running into scalability problems with the Lucene batch
inserter at much smaller numbers, 30,000 indexed nodes. I tried
calling optimize more. Increasing ulimit didn't help.

INFO] Exception in thread main java.lang.RuntimeException:
java.io.FileNotFoundException:
/Users/todd/Code/neo4Jprototype/target/classes/data/graph/lucene/name/_0.cfx
(Too many open files)
[INFO]  at 
org.neo4j.util.index.LuceneIndexBatchInserterImpl.getNodes(LuceneIndexBatchInserterImpl.java:186)
[INFO]  at 
org.neo4j.util.index.LuceneIndexBatchInserterImpl.getSingleNode(LuceneIndexBatchInserterImpl.java:238)
[INFO]  at 
com.collectiveintelligence.QueryNeo.loadDataToGraph(QueryNeo.java:277)
[INFO]  at com.collectiveintelligence.QueryNeo.main(QueryNeo.java:57)
[INFO] Caused by: java.io.FileNotFoundException:
/Users/todd/Code/neo4Jprototype/target/classes/data/graph/lucene/name/_0.cfx
(Too many open files)

I tried breaking up to separate batchinserter instances, and it hangs
now. Can I create more than one batch inserter per process if they run
sequentially and non-threaded?

Thanks,
Todd





On Mon, Dec 7, 2009 at 7:28 AM, Núria Trench nuriatre...@gmail.com wrote:
 Hi again Mattias,

 I have tried to execute my application with the last version available in
 the maven repository and I still have the same problem. After creating and
 indexing all the nodes, the application calls the optimize method and,
 then, it creates all the edges by calling the method getNodes in order to
 select the tail and head node of the edge, but it doesn't work because many
 nodes are not found.

 I have tried to create only 30 nodes and 15 edges and it works properly, but
 if I try to create a big graph (180 million edges + 20 million nodes) it
 doesn't.

 I have also tried to call the optimize method every time the application
 has been created 1 million nodes but it doesn't work.

 Have you tried to create as many nodes as I have said with the newer
 index-util version?

 Thank you,

 Núria.

 2009/12/4 Núria Trench nuriatre...@gmail.com

 Hi Mattias,

 Thank you very much for fixing the problem so fast. I will try it as soon
 as the new changes will be available in the maven repository.

 Núria.


 2009/12/4 Mattias Persson matt...@neotechnology.com

 I fixed the problem and also added a cache per key for faster
 getNodes/getSingleNode lookup during the insert process. However the
 cache assumes that there's nothing in the index when the process
 starts (which almost always will be true) to speed things up even
 further.

 You can control the cache size and if it should be used by overriding
 the (this is also documented in the Javadoc):

 boolean useCache()
 int getMaxCacheSizePerKey()

 methods in your LuceneIndexBatchInserterImpl instance. The new changes
 should be available in the maven repository within an hour.

 2009/12/4 Mattias Persson matt...@neotechnology.com:
  I think I found the problem... it's indexing as it should, but it
  isn't reflected in getNodes/getSingleNode properly until you
  flush/optimize/shutdown the index. I'll try to fix it today!
 
  2009/12/3 Núria Trench nuriatre...@gmail.com:
  Thank you very much for your response.
  If you need more information, you only have to send an e-mail and I
 will try
  to explain it better.
 
  Núria.
 
  2009/12/3 Mattias Persson matt...@neotechnology.com
 
  This is something I'd like to reproduce and I'll do some testing on
  this tomorrow
 
  2009/12/3 Núria Trench nuriatre...@gmail.com:
   Hello,
  
   Last week, I decided to download your graph database core in order
 to use
   it. First, I created a new project to parse my CSV files and create
 a new
   graph database with Neo4j. This CSV files contain 150 milion edges
 and 20
   milion nodes.
  
   When I finished to write the code which will create the graph
 database, I
   executed it and, after six hours of execution, the program crashes
  because
   of a Lucene exception. The exception is related to the index merging
 and
  it
   has the following message:
   mergeFields produced an invalid result: docCount is 385282378 but
 fdx
  file
   size is 3082259028; now aborting this merge to prevent index
 corruption
  
   I have searched on the net and I found that it is a lucene bug. The
   libraries used for executing my project were:
   neo-1.0-b10
   index-util-0.7
   lucene-core-2.4.0
  
   So, I decided to use a newer Lucene version. I found that you have a
  newer
   index-util version so I updated the libraries:
   neo-1.0-b10
   index-util-0.9
   lucene-core-2.9.1
  
   When I had updated those libraries, I tried to execute my project
 again
  and
   I found that, in many occassions, it was not indexing properly. So,
 I
  tried
   to optimize the index after every time I indexed something. This was
 a
   solution because, after that, it was indexing properly but the time
   execution increased a lot.
  
   I am not using transactions, instead of this, I am using the Batch
  Inserter
   with 

[Neo] Maven Dependency For Neo Util for Lucene BatchInserter?

2009-12-04 Thread Todd Stavish
I am using the Lucene Batch Inserter with attributes that have a space
(combined first name and last name).

Exception in thread main java.lang.NoSuchMethodError:
org.neo4j.impl.util.FileUtils.fixSeparatorsInPath(Ljava/lang/String;)Ljava/lang/String;
at 
org.neo4j.util.index.LuceneIndexBatchInserterImpl.fixPath(LuceneIndexBatchInserterImpl.java:61)
at 
org.neo4j.util.index.LuceneIndexBatchInserterImpl.init(LuceneIndexBatchInserterImpl.java:51)
at com.cisco.collectiveintelligence.QueryNeo.addData(QueryNeo.java:135)
at com.cisco.collectiveintelligence.QueryNeo.main(QueryNeo.java:43)

I tried the obvious:

dependency
groupIdorg.neo4j/groupId
artifactIdutil/artifactId
version1.0-b9/version
/dependency

Anyone know where I can find this?

Thanks,
Todd
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Re: [Neo] Maven Dependency For Neo Util for Lucene BatchInserter?

2009-12-04 Thread Todd Stavish
Thanks Mattias. Just an FYI, there doesn't seem to be 1.0-b10 version
build for neo-utils yet.

 http://m2.neo4j.org/org/neo4j/neo-utils/

Regards,
Todd






On Fri, Dec 4, 2009 at 12:26 PM, Mattias Persson
matt...@neotechnology.com wrote:
 2009/12/4 Todd Stavish toddstav...@gmail.com:
 I am using the Lucene Batch Inserter with attributes that have a space
 (combined first name and last name).

 Exception in thread main java.lang.NoSuchMethodError:
 org.neo4j.impl.util.FileUtils.fixSeparatorsInPath(Ljava/lang/String;)Ljava/lang/String;
        at 
 org.neo4j.util.index.LuceneIndexBatchInserterImpl.fixPath(LuceneIndexBatchInserterImpl.java:61)
        at 
 org.neo4j.util.index.LuceneIndexBatchInserterImpl.init(LuceneIndexBatchInserterImpl.java:51)
        at 
 com.cisco.collectiveintelligence.QueryNeo.addData(QueryNeo.java:135)
        at com.cisco.collectiveintelligence.QueryNeo.main(QueryNeo.java:43)

 I tried the obvious:

 dependency
        groupIdorg.neo4j/groupId
        artifactIdutil/artifactId
 Try 'neo-utils' instead
        version1.0-b9/version
 /dependency

 Anyone know where I can find this?

 Thanks,
 Todd
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Re: [Neo] setProperty allowed objects

2009-11-22 Thread Todd Stavish
Plagiarizing the now defunct American anti-drug campaign, Just say
no...to object features.  The memory management and schema processing
of objects would decrease the speed (and arguably the elegance) of the
graph.



On Sun, Nov 22, 2009 at 1:26 PM, Emil Eifrem e...@neotechnology.com wrote:
 On Sun, Nov 22, 2009 at 18:34, Robert Lockhart bobby...@gmail.com wrote:
 it's super-lame that you only allow a basic set of objects to be the values
 of properties.  Any plans to open it up to arbitrary objects?

 No. We're not an object database. I think going down that path opens
 up a whole can of worms that I'd rather not get us into. For example,
 class/object versioning and activation depth.

 On the contrary, I've always agreed with the relational gurus that
 separating data and logic is a good thing. I.e., a programming
 language paradigm is not necessarily the most robust and effective
 data model. I disagree with the RDBMS guys, however, that tables is
 that data model. At least not for the majority of the applications in
 2009.

 Anyway, it seems to be easy enough to map any object down to the
 property data types Neo4j provides. If you think about it, you can
 recursively decompose most Java object's state to Strings + the JVM
 primitive types. What we need to add is more powerful wiring so you
 won't have to do as much of the get/setProperty that you need to do
 today.

 Cheers,

 --
 Emil Eifrém, CEO [e...@neotechnology.com]
 Neo Technology, www.neotechnology.com
 Cell: +46 733 462 271 | US: 206 403 8808
 http://blogs.neotechnology.com/emil
 http://twitter.com/emileifrem
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Re: [Neo] Garbage nodes

2009-11-11 Thread Todd Stavish
Based on my experience with Object Databases, I can't recommend a
persistent garbage collector implementation (PGC). Just like all parts
of your object model don't need to be expressed in your graph,
persistence doesn't need garbage collectors.

Based on what I've seen implemented by customers, GC's are meant for
dynamic memory allocation only.  One consequence, we found, is that
the PGC often delays the application. To avoid this, you end up
avoiding or delaying the PGC for a long time, which means there is no
automatic GC, so ultimately the application is making a manual process
of a supposedly automatic operation.

The delay also ends up bloating the database, ie the impact of not
deleting the nodes is that you end up using more storage space, when
you create new nodes you end up allocating more because the old ones
are still around.

Not sure about Neo4j, but this also ended up fragmenting the database
files. So for us,  we found that we were setting ourselves up for
bloat and fragmentation, and poor performance because you are going to
have access more data. It was also kind of fragile, because if you
make a mistake and not root something, you may end up having the PGC
accidentally delete something that you wanted. We had a tragically sad
experience were a customer was complaining about the PGC taking a long
time, the PGC was deleting more objects then they intended, good data
was lost (the performance was fine).

Please take this as a data point on the decision, it's possible that
PGCs could be implemented in a way that don't experience these
problems, and end-users could be guided to avoid pitfalls, or PGCs
might work for a certain class of applications and not others.

-Todd







On Fri, Nov 6, 2009 at 12:47 PM, Johan Svensson jo...@neotechnology.com wrote:
 I'll jump in on this one then.

 Node or relationship IDs will only be reused if they are deleted.
 There is no possibility that any IDs change without deleting.

 Regards,
 -Johan

 On Fri, Nov 6, 2009 at 3:11 PM, Andrea Puddu kiedi...@gmail.com wrote:
 Hi Peter,

 I'm sorry if I jump in the discussion. I have a question about
 garbage collection.
 Are node IDs reused only if some node is deleted? I mean, is there any
 possibility that some IDs change without deleting any nodes? And what
 about relationship IDs?

 Thank you in advance.
 Andrea

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Re: [Neo] Hadoop

2009-10-03 Thread Todd Stavish
I think you just have to import data into HDFS, a NeoInputFormat class -

http://hadoop.apache.org/common/docs/current/api/org/apache/hadoop/mapred/InputFormat.html

Relational implementation -

http://www.cloudera.com/blog/2009/03/06/database-access-with-hadoop/



On Sat, Oct 3, 2009 at 5:36 AM, Johan Svensson jo...@neotechnology.com wrote:
 Hi Oleg,

 On Wed, Sep 30, 2009 at 12:41 PM, Oleg Aravin oara...@griddynamics.com 
 wrote:
 Hello

 Can i use Hadooop to store neo4j storage ?

 I would say not possible at the moment. It might be possible to write
 some glue in-between but it will still not work as expected in some
 use-cases.

 What problem did you intend to solve by using Neo4j+Hadoop?

 Regards,
 -Johan
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[Neo] Traversing between two nodes

2009-09-15 Thread Todd Stavish
Does anybody have traversal code that shows if two nodes are
connected, and if so the nodes that connect them?

Thanks,
Todd
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Re: [Neo] Neo4J Scalability

2009-09-10 Thread Todd Stavish
Hi Johan,

Thanks! Quick summary, it was definitely a config issue. Changing to
the recommend config settings makes the exceptions go away. Weird
though, those config values are for VM memory management. But the
exceptions looked like file I/O issues. How does Neo4J get around the
OS max file size limitation, does it just overflow into a new file?

 I successfully ran the code resulting in roughly 190M nodes/properties
 and 390M relationships injected in 35min (the condition in one of your
 for loops probably has a typo, should have been personnumberOfPeople

Oh thanks, I thought that I was accessing a nodeID that didn't exist,
so I tried to go above the total number of nodes. I forgot to change
it back. Sorry.


 I first tried on my laptop but ran out of disk space (with a similar
 exception you got) since the full load requires 41GB of free space.
 Could you please try the injection again (using similar configuration
 and verifying you have enough disk space)?

I had enough disk space, 200GB+. I am still getting heap issues, I
don't have enough memory on my laptop, but I will run it on the cloud
later and they should go away.

 Also (maybe not important since this is just a test but) relationships
 can be treated as bi-directional/non directed using the enum constant
 Direction.BOTH, so the two relationships a-KNOWS-b  and b-KNOWS-a
 can be represented with one a-KNOWS-b.

This is just for traversals, no? You can't define it as bi-directional
on creation, can you?  I noticed that Neo doesn't explicitly define
cardinality (many-to-many, one-to-many, etc). Everything is supported
though. And the API is concise, which is prefereable.

Thanks again.

Regards,
Todd

 Regards,
 -Johan

 On Wed, Sep 9, 2009 at 3:11 AM, Todd Stavishtoddstav...@gmail.com wrote:
 He Johan,

 What OS do you run this on? The FileChannel.write fail with an
 exception saying buffer is too large is new to me.

 OSX. Snow Leopard.

 java -version
 java version 1.6.0_15
 Java(TM) SE Runtime Environment (build 1.6.0_15-b03-219)
 Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02-90, mixed mode)

 I can try it on centos too. I was  going to try to run in it in EC2,
 but lost momentum and ideas to try.

 Try decrease the amount of memory you give the store files (if you
 have modified default configuration) and make sure you at least have
 disk space to write out 1/10th of the dedicated memory for each store
 file.

 Plenty of disk space. Do you mean pre-allocate the database file? How
 do you do that?

 I will run some tests on this code first thing in the morning to see
 if I can reproduce it.

 Thanks. I will send you the input files. And other code.

 Regards,
 Todd


 -Johan

 On Tue, Sep 8, 2009 at 5:45 PM, Todd Stavishtoddstav...@gmail.com wrote:
 Hello All,

 I hope that I haven't been too demanding of this list. I am pushing a
 tight deadline. I can't seem to get Neo4J to scale above 1.5 million
 nodes. The code is simple, just create a node, give it one property.
 Then go back and randomly create relationships. I moved to the
 BatchInserter too. Is there a way to use more than one DB? Is it a
 file size limitation? Can I commit incrementally somehow? I looked at
 the BatchInterter source, and there doesn't seem to be anything that I
 can do.

 Exceptions and demo code below.

 Thanks,
 Todd




 Created 1516633 nodes in 33 seconds

 Exception in thread main
 org.neo4j.impl.nioneo.store.StoreFailureException: Unable to write
 record[1419120] @[188742960]
        at 
 org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.writeOut(AbstractPersistenceWindow.java:111)
        at 
 org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.force(AbstractPersistenceWindow.java:123)
        at 
 org.neo4j.impl.nioneo.store.PersistenceWindowPool.flushAll(PersistenceWindowPool.java:229)
        at 
 org.neo4j.impl.nioneo.store.PersistenceWindowPool.close(PersistenceWindowPool.java:203)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:503)
        at 
 org.neo4j.impl.nioneo.store.PropertyStore.closeStorage(PropertyStore.java:106)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
        at 
 org.neo4j.impl.nioneo.store.NeoStore.closeStorage(NeoStore.java:81)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
        at 
 org.neo4j.impl.batchinsert.BatchInserterImpl.shutdown(BatchInserterImpl.java:311)
        at 
 com.palantir.pathfind.GraphIngestBatch.main(GraphIngestBatch.java:78)
 Caused by: java.io.IOException: Result too large
        at sun.nio.ch.FileDispatcher.pwrite0(Native Method)
        at sun.nio.ch.FileDispatcher.pwrite(FileDispatcher.java:45)
        at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:100)
        at sun.nio.ch.IOUtil.write(IOUtil.java:75)
        at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:651)
        at 
 

Re: [Neo] Looking at DB contents

2009-09-09 Thread Todd Stavish
Hi Mattias,

Yes, that is correct. I think fundamentally I do not understand how your
locking works. I assumed that both the shell and traverser would have read
only locks. However, I left the shell open and the traverser was blocked. I
did not do anything in the shell other than read-only commands.

-Todd


On Wed, Sep 9, 2009 at 5:47 AM, Mattias Persson
matt...@neotechnology.comwrote:

 I don't follow entirely... you mean that the shell held locks on nodes
 which made another traverser (executed via script or something) wait?
 At the moment every command in the shell is wrapped in its own
 transaction.

 2009/9/7 Todd Stavish toddstav...@gmail.com:
  Hi Martin, Anders,
 
  The standalone version of neoclipse works like a charm, thanks. I was
  surprised that the shell locked out a non-updating traverse
  application that I wrote. Where do I explicitly declare locking? My
  natural assumption was in beginTx( kindOfLock ).
 
  Thanks,
  Todd
 
 
  On Mon, Sep 7, 2009 at 1:17 AM, Martin Filipczyk i...@mupitu.de wrote:
  Hi Todd,
 
  have you already tried the neoclipse standalone version?
 
  -Martin
 
  Todd Stavish schrieb:
  Thanks I'll give the shell a try.
 
 
  Was it crashing on opening the database or what happened?
 
 
  It shows the reference node and then just hangs. I am using Galileo
  though and maybe the wrong version of GEF. So no big deal.
 
  -Todd
 
 
 
 
  /anders
 
  --
  Anders Nawroth [and...@neotechnology.com]
  GTalk, Skype: anders.nawroth
  Phone: +46 737 894 163
  http://twitter.com/nawroth
  http://blog.nawroth.com/
 
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[Neo] Neo4J Scalability

2009-09-08 Thread Todd Stavish
Hello All,

I hope that I haven't been too demanding of this list. I am pushing a
tight deadline. I can't seem to get Neo4J to scale above 1.5 million
nodes. The code is simple, just create a node, give it one property.
Then go back and randomly create relationships. I moved to the
BatchInserter too. Is there a way to use more than one DB? Is it a
file size limitation? Can I commit incrementally somehow? I looked at
the BatchInterter source, and there doesn't seem to be anything that I
can do.

Exceptions and demo code below.

Thanks,
Todd




Created 1516633 nodes in 33 seconds

Exception in thread main
org.neo4j.impl.nioneo.store.StoreFailureException: Unable to write
record[1419120] @[188742960]
at 
org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.writeOut(AbstractPersistenceWindow.java:111)
at 
org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.force(AbstractPersistenceWindow.java:123)
at 
org.neo4j.impl.nioneo.store.PersistenceWindowPool.flushAll(PersistenceWindowPool.java:229)
at 
org.neo4j.impl.nioneo.store.PersistenceWindowPool.close(PersistenceWindowPool.java:203)
at 
org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:503)
at 
org.neo4j.impl.nioneo.store.PropertyStore.closeStorage(PropertyStore.java:106)
at 
org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
at org.neo4j.impl.nioneo.store.NeoStore.closeStorage(NeoStore.java:81)
at 
org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
at 
org.neo4j.impl.batchinsert.BatchInserterImpl.shutdown(BatchInserterImpl.java:311)
at com.palantir.pathfind.GraphIngestBatch.main(GraphIngestBatch.java:78)
Caused by: java.io.IOException: Result too large
at sun.nio.ch.FileDispatcher.pwrite0(Native Method)
at sun.nio.ch.FileDispatcher.pwrite(FileDispatcher.java:45)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:100)
at sun.nio.ch.IOUtil.write(IOUtil.java:75)
at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:651)
at 
org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.writeOut(AbstractPersistenceWindow.java:105)


public class GraphIngestBatch
{

public static void main(String[] args)
{
try
{

// Create graph database service
BatchInserter neo = new BatchInserterImpl(graphDB/,
BatchInserterImpl.loadProperties(neo.props));

// Read raw text for name data
FileReader namesFile = new
FileReader(/Users/todd/Code/pathfind/target/classes/rawData/lastNames.txt);
BufferedReader namesBuffer = new 
BufferedReader(namesFile);
String name;

// Start timer and counter
Stopwatch timer = new Stopwatch();
timer.start();
long numberOfPeople = 1;

// Initialize root node
long person, neighbor;
MapString,Object properties = new 
HashMapString,Object();
properties.put(name, Philberto Anderossono);
neighbor = neo.createNode(properties);
neo.createRelationship(neighbor, 0,
DynamicRelationshipType.withName(ROOT), null);

// Create people and neighbor relationships
while ((name = namesBuffer.readLine()) != null)
{
properties.put(name, name);
person = neo.createNode(properties);

neo.createRelationship(person, neighbor,
DynamicRelationshipType.withName(KNOWS), null);
neo.createRelationship(neighbor, person,
DynamicRelationshipType.withName(KNOWS), null);

neighbor = person;
numberOfPeople++;
}
namesBuffer.close();
namesFile.close();

System.out.println(Number of people is:  + 
numberOfPeople);

// Randomly generate relationships (minimum four per 
person + both
neighbors, mean ten relationships / person)
Long friend;
int numberOfFriends = 1;
for (person=1; personnumberOfPeople; person++)
{
for (int i=0; inumberOfFriends; i++)
 

Re: [Neo] Neo4J Scalability

2009-09-08 Thread Todd Stavish
He Johan,

 What OS do you run this on? The FileChannel.write fail with an
 exception saying buffer is too large is new to me.

OSX. Snow Leopard.

java -version
java version 1.6.0_15
Java(TM) SE Runtime Environment (build 1.6.0_15-b03-219)
Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02-90, mixed mode)

I can try it on centos too. I was  going to try to run in it in EC2,
but lost momentum and ideas to try.

 Try decrease the amount of memory you give the store files (if you
 have modified default configuration) and make sure you at least have
 disk space to write out 1/10th of the dedicated memory for each store
 file.

Plenty of disk space. Do you mean pre-allocate the database file? How
do you do that?

 I will run some tests on this code first thing in the morning to see
 if I can reproduce it.

Thanks. I will send you the input files. And other code.

Regards,
Todd


 -Johan

 On Tue, Sep 8, 2009 at 5:45 PM, Todd Stavishtoddstav...@gmail.com wrote:
 Hello All,

 I hope that I haven't been too demanding of this list. I am pushing a
 tight deadline. I can't seem to get Neo4J to scale above 1.5 million
 nodes. The code is simple, just create a node, give it one property.
 Then go back and randomly create relationships. I moved to the
 BatchInserter too. Is there a way to use more than one DB? Is it a
 file size limitation? Can I commit incrementally somehow? I looked at
 the BatchInterter source, and there doesn't seem to be anything that I
 can do.

 Exceptions and demo code below.

 Thanks,
 Todd




 Created 1516633 nodes in 33 seconds

 Exception in thread main
 org.neo4j.impl.nioneo.store.StoreFailureException: Unable to write
 record[1419120] @[188742960]
        at 
 org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.writeOut(AbstractPersistenceWindow.java:111)
        at 
 org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.force(AbstractPersistenceWindow.java:123)
        at 
 org.neo4j.impl.nioneo.store.PersistenceWindowPool.flushAll(PersistenceWindowPool.java:229)
        at 
 org.neo4j.impl.nioneo.store.PersistenceWindowPool.close(PersistenceWindowPool.java:203)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:503)
        at 
 org.neo4j.impl.nioneo.store.PropertyStore.closeStorage(PropertyStore.java:106)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
        at org.neo4j.impl.nioneo.store.NeoStore.closeStorage(NeoStore.java:81)
        at 
 org.neo4j.impl.nioneo.store.CommonAbstractStore.close(CommonAbstractStore.java:500)
        at 
 org.neo4j.impl.batchinsert.BatchInserterImpl.shutdown(BatchInserterImpl.java:311)
        at 
 com.palantir.pathfind.GraphIngestBatch.main(GraphIngestBatch.java:78)
 Caused by: java.io.IOException: Result too large
        at sun.nio.ch.FileDispatcher.pwrite0(Native Method)
        at sun.nio.ch.FileDispatcher.pwrite(FileDispatcher.java:45)
        at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:100)
        at sun.nio.ch.IOUtil.write(IOUtil.java:75)
        at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:651)
        at 
 org.neo4j.impl.nioneo.store.AbstractPersistenceWindow.writeOut(AbstractPersistenceWindow.java:105)


 public class GraphIngestBatch
 {

        public static void main(String[] args)
        {
                try
                {

                        // Create graph database service
                        BatchInserter neo = new BatchInserterImpl(graphDB/,
 BatchInserterImpl.loadProperties(neo.props));

                        // Read raw text for name data
                        FileReader namesFile = new
 FileReader(/Users/todd/Code/pathfind/target/classes/rawData/lastNames.txt);
                        BufferedReader namesBuffer = new 
 BufferedReader(namesFile);
                        String name;

                // Start timer and counter
                Stopwatch timer = new Stopwatch();
                timer.start();
                        long numberOfPeople = 1;

                        // Initialize root node
                        long person, neighbor;
                        MapString,Object properties = new 
 HashMapString,Object();
                        properties.put(name, Philberto Anderossono);
                        neighbor = neo.createNode(properties);
                        neo.createRelationship(neighbor, 0,
 DynamicRelationshipType.withName(ROOT), null);

                        // Create people and neighbor relationships
                        while ((name = namesBuffer.readLine()) != null)
                        {
                                properties.put(name, name);
                                person = neo.createNode(properties);

                                neo.createRelationship(person, neighbor,
 DynamicRelationshipType.withName(KNOWS), null);
                                neo.createRelationship(neighbor, person,
 DynamicRelationshipType.withName(KNOWS), null);

   

Re: [Neo] Looking at DB contents

2009-09-07 Thread Todd Stavish
Hi Martin, Anders,

The standalone version of neoclipse works like a charm, thanks. I was
surprised that the shell locked out a non-updating traverse
application that I wrote. Where do I explicitly declare locking? My
natural assumption was in beginTx( kindOfLock ).

Thanks,
Todd


On Mon, Sep 7, 2009 at 1:17 AM, Martin Filipczyk i...@mupitu.de wrote:
 Hi Todd,

 have you already tried the neoclipse standalone version?

 -Martin

 Todd Stavish schrieb:
 Thanks I'll give the shell a try.


 Was it crashing on opening the database or what happened?


 It shows the reference node and then just hangs. I am using Galileo
 though and maybe the wrong version of GEF. So no big deal.

 -Todd




 /anders

 --
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 GTalk, Skype: anders.nawroth
 Phone: +46 737 894 163
 http://twitter.com/nawroth
 http://blog.nawroth.com/

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[Neo] Looking at DB contents

2009-09-05 Thread Todd Stavish
Are there command line tools that can output the database \ nodes to
text? Or any quick way to inspect the contents of Neo? I didn't have
luck getting Neoclipse to work.

Thanks,
Todd
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[Neo] JTA Classes

2009-09-04 Thread Todd Stavish
Hello,

Sun's website is down. Not sure, maybe Oracle isn't paying the bill.
Anyway, can someone please email me the JTA classes. I used Maven to
download Neo / APOC, but no JTA in the repositories.

Thanks,
-Todd
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Re: [Neo] JTA Classes

2009-09-04 Thread Todd Stavish
Thanks Andreas.  Worked like a charm. Does anyone have any sample code
that does larger graphs? Like 100M or 1B nodes?

Thanks,
Todd



On Fri, Sep 4, 2009 at 9:47 AM, Andreas
Kolleggerakolleg...@tembopublic.org wrote:
 Add this to your pom:

 dependency
     groupIdorg.apache.geronimo.specs/groupId
     artifactIdgeronimo-jta_1.1_spec/artifactId
     version1.1.1/version
 /dependency



 On Sep 4, 2009, at 9:41 AM, Todd Stavish wrote:

 Hello,

 Sun's website is down. Not sure, maybe Oracle isn't paying the bill.
 Anyway, can someone please email me the JTA classes. I used Maven to
 download Neo / APOC, but no JTA in the repositories.

 Thanks,
 -Todd
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 User@lists.neo4j.org
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Re: [Neo] JTA Classes

2009-09-04 Thread Todd Stavish
I am writing a prototype to link the relationships between people
based on cell call records.  I was hoping someone had a large graph
sample that dynamically generated 100M nodes \ people. Even if it was
something entirely different like a massive social graph ala linkin \
facebook, I could just add in the phone number property and my own
traversal code.

-Todd


On Fri, Sep 4, 2009 at 10:42 AM, Dan Heaverdan.hea...@peepwl.com wrote:
 Todd, what are you trying to achieve?
 lots of us have large graphs and code that works with them. can you be more
 specific?

 Dan

 On Fri, Sep 4, 2009 at 3:40 PM, Todd Stavish toddstav...@gmail.com wrote:

 Thanks Andreas.  Worked like a charm. Does anyone have any sample code
 that does larger graphs? Like 100M or 1B nodes?

 Thanks,
 Todd



 On Fri, Sep 4, 2009 at 9:47 AM, Andreas
 Kolleggerakolleg...@tembopublic.org wrote:
  Add this to your pom:
 
  dependency
      groupIdorg.apache.geronimo.specs/groupId
      artifactIdgeronimo-jta_1.1_spec/artifactId
      version1.1.1/version
  /dependency
 
 
 
  On Sep 4, 2009, at 9:41 AM, Todd Stavish wrote:
 
  Hello,
 
  Sun's website is down. Not sure, maybe Oracle isn't paying the bill.
  Anyway, can someone please email me the JTA classes. I used Maven to
  download Neo / APOC, but no JTA in the repositories.
 
  Thanks,
  -Todd
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[Neo] getReferenceNode

2009-09-04 Thread Todd Stavish
How do you set a reference node? Or create a root node? Is the
examples.NeoclipseExample package published somewhere?


Thanks,
Todd
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Re: [Neo] getReferenceNode

2009-09-04 Thread Todd Stavish
Cool. Thanks guys, I have it know. Have you given thought to just
having a global persistent hash map to find root objects? That way,
you could have several root objects that were easily retrievable, and
then you could start your navigation / traversal from there.

Thanks again,
Todd



On Fri, Sep 4, 2009 at 6:25 PM, Anders Nawroth and...@neotechnology.com wrote:
 Hi!

 Just one small addition to this: don't assume that the reference node
 will always have an id of 0. To check if a node is the reference node,
 use the equals() method to compare the nodes!

 /anders

 Dan Heaver:
 Todd, the reference node is node 0

 It's there even if you have an empty graph.

 You don't set it it's just there from the start...

 Dan

 On 4 Sep 2009, at 23:00, Todd Stavish toddstav...@gmail.com wrote:


 How do you set a reference node? Or create a root node? Is the
 examples.NeoclipseExample package published somewhere?


 Thanks,
 Todd
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