Re: [Neo4j] neo4j 1.1 Download? -- for Use with Current Python Bindings

2011-02-03 Thread Tobias Ivarsson
Server did not exist for Neo4j 1.1, it was first released with 1.2.

Cheers,
Tobias

On Thu, Feb 3, 2011 at 12:57 AM, James Thornton ja...@jamesthornton.comwrote:

 Thank you. Is the the neo4j 1.1 server download still available?

 On Mon, Jan 31, 2011 at 8:59 PM, James Thornton ja...@jamesthornton.com
 wrote:
  Since the current python bindings only work with neo4j 1.1 (as per
  this bug report https://trac.neo4j.org/ticket/302 and
  http://wiki.neo4j.org/content/Getting_Started_With_Python), where can
  you download neo4j 1.1 in the meantime until the python bindings are
  updated?
 
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Re: [Neo4j] Non-exact index queries with the REST API

2011-02-03 Thread Peter Neubauer
Maximilian,
for the time being, you can always write a fast Server Plugin to do
this for you, should not be much work, see
http://components.neo4j.org/neo4j-examples/snapshot/server-plugins.html
where you can expose the fulltext queries.

Would that help?

Cheers,

/peter neubauer

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On Thu, Feb 3, 2011 at 8:49 AM, Mattias Persson
matt...@neotechnology.com wrote:
 The index framework in neo4j (lucene integration) supports wildcards and all
 that, but it isn't exposed in the REST API as of yet, as Jim mentioned.

 2011/2/3 Jim Webber j...@neotechnology.com

 Hi Max,

 I don't think there is a way to search for non-exact queries in the REST
 API today. I'll add it to the feature backlog for future releases.

 Jim
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[Neo4j] Visualization options for graphs

2011-02-03 Thread Luanne Misquitta
Hi,

 

Would be good to include Arbor.js (http://arborjs.org/) to the
JavaScript options listed in the Neo4J wiki
(http://wiki.neo4j.org/content/Visualization_options_for_graphs)

Have just started playing with it and it renders very nice graphs indeed
(HTML5 + JavaScript).

 

Regards

Luanne M.
Tech Lead

twitter / @luannem http://twitter.com/luannem
linkedin / http://in.linkedin.com/in/luannemisquitta
http://in.linkedin.com/in/luannemisquitta  
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Re: [Neo4j] Visualization options for graphs

2011-02-03 Thread Peter Neubauer
Done.

Feel free to let us know if you happen to anything generic up!

Cheers,

/peter neubauer

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On Thu, Feb 3, 2011 at 11:04 AM, Luanne Misquitta lmisqui...@saba.com wrote:
 Hi,



 Would be good to include Arbor.js (http://arborjs.org/) to the
 JavaScript options listed in the Neo4J wiki
 (http://wiki.neo4j.org/content/Visualization_options_for_graphs)

 Have just started playing with it and it renders very nice graphs indeed
 (HTML5 + JavaScript).



 Regards

 Luanne M.
 Tech Lead

 twitter / @luannem http://twitter.com/luannem
 linkedin / http://in.linkedin.com/in/luannemisquitta
 http://in.linkedin.com/in/luannemisquitta
 skype / luanne.misquitta
 blog / http://thought-bytes.blogspot.com/
 http://thought-bytes.blogspot.com/
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Massimo Lusetti
On Wed, Feb 2, 2011 at 1:20 PM, Tobias Ivarsson
tobias.ivars...@neotechnology.com wrote:

 You are doing I/O bound work. More then two threads is most likely just
 going to add overhead and make things slower!

I'm certainly doing something wired cause the performance of my tests
aren't linear.

I've run the app and let it process two big data files and this are
the results: 298 rows in 3465742 ms and 2897177 rows in 3483767 ms
which are values not in line with the performance of the other test
which used just only 10 rows. With more rows the performance
dropped down to values between 1.160404947 ms per row and 1.202469507
ms per row. The overall DB size (I measure only the db directory) has
grown as well far behond the expected values: 4.9G ...

Do you or anyone else have any clue?

Thanks
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Mattias Persson
2011/2/3 Massimo Lusetti mluse...@gmail.com

 On Wed, Feb 2, 2011 at 1:20 PM, Tobias Ivarsson
 tobias.ivars...@neotechnology.com wrote:

  You are doing I/O bound work. More then two threads is most likely just
  going to add overhead and make things slower!

 I'm certainly doing something wired cause the performance of my tests
 aren't linear.

 I've run the app and let it process two big data files and this are
 the results: 298 rows in 3465742 ms and 2897177 rows in 3483767 ms
 which are values not in line with the performance of the other test
 which used just only 10 rows. With more rows the performance
 dropped down to values between 1.160404947 ms per row and 1.202469507
 ms per row. The overall DB size (I measure only the db directory) has
 grown as well far behond the expected values: 4.9G ...

 Do you or anyone else have any clue?


Lucene lookup performance degrades the bigger the index gets. That may be a
reason.


 Thanks
 --
 Massimo
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Massimo Lusetti
On Thu, Feb 3, 2011 at 11:30 AM, Mattias Persson
matt...@neotechnology.com wrote:

 Lucene lookup performance degrades the bigger the index gets. That may be a
 reason.

I don't think Lucene cannot handle an index with 6/7 million of
entries. Maybe are some logs around?

Cheers
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http://meridio.blogspot.com
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Re: [Neo4j] Visualization options for graphs

2011-02-03 Thread Tobias Ivarsson
It's a wiki, why didn't you just do it yourself?

This is actually a general question to everyone on the list:
What is the main hurdle preventing you from contributing to the wiki?

Cheers,
Tobias

On Thu, Feb 3, 2011 at 11:04 AM, Luanne Misquitta lmisqui...@saba.comwrote:

 Hi,



 Would be good to include Arbor.js (http://arborjs.org/) to the
 JavaScript options listed in the Neo4J wiki
 (http://wiki.neo4j.org/content/Visualization_options_for_graphs)

 Have just started playing with it and it renders very nice graphs indeed
 (HTML5 + JavaScript).



 Regards

 Luanne M.
 Tech Lead

 twitter / @luannem http://twitter.com/luannem
 linkedin / http://in.linkedin.com/in/luannemisquitta
 http://in.linkedin.com/in/luannemisquitta
 skype / luanne.misquitta
 blog / http://thought-bytes.blogspot.com/
 http://thought-bytes.blogspot.com/
 Saba. Power Up Your People.



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 User@lists.neo4j.org
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Re: [Neo4j] Difference between properties and nodes

2011-02-03 Thread Craig Taverner
I can comment also, that while it is possible to store properties as a
sub-graph as Tim suggests, that would be inefficient (in disk space and
performance). Neo4j stores properties in a special property store, not
actually within each node or relationship, but directly retrievable from the
node or relationship. The implications of this are that you do not load
properties when loading the nodes (faster traversal).

Read Chris Gioran's excellent blog on the subject at
http://digitalstain.blogspot.com/2010/10/neo4j-internals-file-storage.html

http://digitalstain.blogspot.com/2010/10/neo4j-internals-file-storage.htmlAnother
angle on this discussion is whether or not to model your domain using
properties or graph structure, and there are many domain models that could
be done both ways. That discussion is certainly beyond the scope of this
thread :-)

On Wed, Feb 2, 2011 at 7:29 PM, Rick Bullotta 
rick.bullo...@burningskysoftware.com wrote:

 Nodes are linked by relationships, and properties are attached to a node
 or relationship.  Relationships have a type associated with them also
 (worksFor, livesIn, etc.), whereas nodes are essentially typeless.
 Properties are general data/attributes attached to a node or relationship.


 -Original Message-
 From: user-boun...@lists.neo4j.org [mailto:user-boun...@lists.neo4j.org]
 On
 Behalf Of Tim McNamara
 Sent: Wednesday, February 02, 2011 1:25 PM
 To: Neo4j user discussions
 Subject: Re: [Neo4j] Difference between properties and nodes

 Sorry for the terseness of the initial email. I had intended to expand it.
 I
 was wondering whether properties are shorthand for creating edges on the
 graph. Are properties linked via relationships, or do nodes carry all of
 their data/properties with them?

 For example, in YAML a node could with properties looks like this:

 4
  type: person
  name: Neo

 Could also be represented as a tree:

 4  HAS_PROPERTY(name)  HAS_VALUE(Neo)

 Thanks for responding.

 On 2 February 2011 22:54, Mattias Persson matt...@neotechnology.com
 wrote:

  Hi Tim,
 
  In what aspect? performance, or semantics? Could you supply a little more
  context, please...
 
  2011/1/31 Tim McNamara paperl...@timmcnamara.co.nz
 
   Is there much difference between a creating property and creating a
 child
   node?
  
   Tim
  
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Re: [Neo4j] Visualization options for graphs

2011-02-03 Thread Luanne Misquitta
It asked me to log in- at the time I did not really notice the Create
account link at the top right, so I assumed wiki editing was reserved
for certain people only.
I shall contribute directly the next time :-)

-Luanne M.

-Original Message-
From: user-boun...@lists.neo4j.org [mailto:user-boun...@lists.neo4j.org]
On Behalf Of Tobias Ivarsson
Sent: Thursday, February 03, 2011 4:42 PM
To: Neo4j user discussions
Subject: Re: [Neo4j] Visualization options for graphs

It's a wiki, why didn't you just do it yourself?

This is actually a general question to everyone on the list:
What is the main hurdle preventing you from contributing to the wiki?

Cheers,
Tobias

On Thu, Feb 3, 2011 at 11:04 AM, Luanne Misquitta
lmisqui...@saba.comwrote:

 Hi,



 Would be good to include Arbor.js (http://arborjs.org/) to the
 JavaScript options listed in the Neo4J wiki
 (http://wiki.neo4j.org/content/Visualization_options_for_graphs)

 Have just started playing with it and it renders very nice graphs
indeed
 (HTML5 + JavaScript).



 Regards

 Luanne M.
 Tech Lead

 twitter / @luannem http://twitter.com/luannem
 linkedin / http://in.linkedin.com/in/luannemisquitta
 http://in.linkedin.com/in/luannemisquitta
 skype / luanne.misquitta
 blog / http://thought-bytes.blogspot.com/
 http://thought-bytes.blogspot.com/
 Saba. Power Up Your People.



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Re: [Neo4j] Visualization options for graphs

2011-02-03 Thread Anders Nawroth
Hi!

Just make sure to confirm your email address with the wiki, and it will 
happily accept you edits after that!

/anders

2011-02-03 13:10, Luanne Misquitta skrev:
 It asked me to log in- at the time I did not really notice the Create
 account link at the top right, so I assumed wiki editing was reserved
 for certain people only.
 I shall contribute directly the next time :-)

 -Luanne M.

 -Original Message-
 From: user-boun...@lists.neo4j.org [mailto:user-boun...@lists.neo4j.org]
 On Behalf Of Tobias Ivarsson
 Sent: Thursday, February 03, 2011 4:42 PM
 To: Neo4j user discussions
 Subject: Re: [Neo4j] Visualization options for graphs

 It's a wiki, why didn't you just do it yourself?

 This is actually a general question to everyone on the list:
 What is the main hurdle preventing you from contributing to the wiki?

 Cheers,
 Tobias

 On Thu, Feb 3, 2011 at 11:04 AM, Luanne Misquitta
 lmisqui...@saba.comwrote:

 Hi,



 Would be good to include Arbor.js (http://arborjs.org/) to the
 JavaScript options listed in the Neo4J wiki
 (http://wiki.neo4j.org/content/Visualization_options_for_graphs)

 Have just started playing with it and it renders very nice graphs
 indeed
 (HTML5 + JavaScript).



 Regards

 Luanne M.
 Tech Lead

 twitter / @luannemhttp://twitter.com/luannem
 linkedin / http://in.linkedin.com/in/luannemisquitta
 http://in.linkedin.com/in/luannemisquitta
 skype / luanne.misquitta
 blog / http://thought-bytes.blogspot.com/
 http://thought-bytes.blogspot.com/
 Saba. Power Up Your People.



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 User@lists.neo4j.org
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[Neo4j] neo4j with Sun Grid Engine

2011-02-03 Thread Joan Marc Riera Duocastella
Hello everybody,

this is my first post here, so any kind of advice, tip , trick , link or 
question will be nicely accepted.

I'm a linux system administrator on a reserch foundation, some of the 
social media coworkers are interested on neo4j software and its 
potential. So they asked me to install it for testing pourposes. I hope 
this is understood as compliment to the developers. :)

On the other hand, I know they are kind of heavy users, they work with 
heavy datasets, and I have a sun grid engine deployed on several servers.


I do not know much about neo4j, so if someone can point me on how to use 
it with sun grid engine, or similar grid HPC service, I will make them 
test it that way.


Many thanks.

Marc



-- 
Fundació Barcelona Media
*


  Joan Marc Riera Duocastella

*


Barcelona Media - Centre d'Innovació
Av. Diagonal, 177, planta 9 08018 - BARCELONA
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Peter Neubauer
Massimo,
I yesterday just tried to import the Germany OpenStreetMap dataset
into Neo4j using Lucene indexing. There are around 60M nodes that all
are indexed into Lucene, and then looked up when the Ways, consisting
of a number of nodes each, are calculated. Lucene is not fast, but it
works on these 60M entries. And in inserts, it does scale reasonably
even after a couple of million inserts, which wasn't the case when I
tried BerkeleyDB (Java), JDBM or other K/V stores.

Actually, if anyone knows a better index for exact lookups that is
configurable to have good insert and lookup performance, any hint
would be greatly appreciated. This is what right now limits insert
performance when you use the Neo4j Batchinserter. The BatchInserter
itself can insert around 200K-400K nodes or relationships per second,
but the indexing subsystems are just not up to that speed.

Help is greatly appreciated!

Cheers,

/peter neubauer

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.thoughtmade.com - Scandinavia's coolest Bring-a-Thing party.



On Thu, Feb 3, 2011 at 11:52 AM, Massimo Lusetti mluse...@gmail.com wrote:
 On Thu, Feb 3, 2011 at 11:30 AM, Mattias Persson
 matt...@neotechnology.com wrote:

 Lucene lookup performance degrades the bigger the index gets. That may be a
 reason.

 I don't think Lucene cannot handle an index with 6/7 million of
 entries. Maybe are some logs around?

 Cheers
 --
 Massimo
 http://meridio.blogspot.com
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Re: [Neo4j] Ignore Relationships while indexing

2011-02-03 Thread vaibhav adlakha
Hi Peter,

Thanks for your response. That helped me a lot.


I have to appreciate this community for being so prompt and helpful.

Thanks,
Vaibhav

On Tue, Feb 1, 2011 at 7:15 PM, Peter Neubauer 
peter.neuba...@neotechnology.com wrote:

 Vaibhav,
 youi can use the new combined Evaluator to control what will be
 included in the result set or not. See

 https://github.com/neo4j/examples/blob/master/src/test/java/org/neo4j/examples/orderedpath/OrderedPathTest.java#L71
 for an example. If you want to continue traversing, and include the
 current node in the result, use

 return Evaluation.INCLUDE_AND_CONTINUE and so on.

 Does that help?

 Cheers,

 /peter neubauer

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

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 http://www.thoughtmade.com - Scandinavia's coolest Bring-a-Thing party.



 On Tue, Feb 1, 2011 at 1:26 PM, vaibhav adlakha
 adlakha.vaib...@gmail.com wrote:
  Hi,
 
  I wish to traverse from node A to node B in the graph and find all
  relationships having certain properties. If the relationship does not
 have
  that property  say propertyName != desired value, then this relationship
  should be ignored and move to next relationships.
 
  In the end desired output is all nodes and relationships traversed
 between
  node A and node B. Using traverser and its Stop or return evaluator, we
 can
  ignore nodes while traversing them. Can any one please help me solve this
  problem.
 
 
  Thanks and Regards,
  Vaibhav Adlakha
 
  The thing that we call failure is not the falling down but the staying
  down
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Massimo Lusetti
On Thu, Feb 3, 2011 at 2:01 PM, Peter Neubauer
peter.neuba...@neotechnology.com wrote:

 Massimo,
 I yesterday just tried to import the Germany OpenStreetMap dataset
 into Neo4j using Lucene indexing. There are around 60M nodes that all
 are indexed into Lucene, and then looked up when the Ways, consisting
 of a number of nodes each, are calculated. Lucene is not fast, but it
 works on these 60M entries. And in inserts, it does scale reasonably
 even after a couple of million inserts, which wasn't the case when I
 tried BerkeleyDB (Java), JDBM or other K/V stores.

Happy to see good results so the question seems how to fine tune
Lucene or the usage which neo4j make of Lucene...

 Actually, if anyone knows a better index for exact lookups that is
 configurable to have good insert and lookup performance, any hint
 would be greatly appreciated. This is what right now limits insert
 performance when you use the Neo4j Batchinserter. The BatchInserter
 itself can insert around 200K-400K nodes or relationships per second,
 but the indexing subsystems are just not up to that speed.

I'm not using the BatchInserter cause I will need to do that work on a
daily basis and the normal operations are a lot slower.

 Help is greatly appreciated!

Indeed. Thanks in advance

Cheers
-- 
Massimo
http://meridio.blogspot.com
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Re: [Neo4j] Lucene index commit rate and NoSuchElementException

2011-02-03 Thread Mattias Persson
2011/2/3 Massimo Lusetti mluse...@gmail.com

 On Thu, Feb 3, 2011 at 2:01 PM, Peter Neubauer
 peter.neuba...@neotechnology.com wrote:

  Massimo,
  I yesterday just tried to import the Germany OpenStreetMap dataset
  into Neo4j using Lucene indexing. There are around 60M nodes that all
  are indexed into Lucene, and then looked up when the Ways, consisting
  of a number of nodes each, are calculated. Lucene is not fast, but it
  works on these 60M entries. And in inserts, it does scale reasonably
  even after a couple of million inserts, which wasn't the case when I
  tried BerkeleyDB (Java), JDBM or other K/V stores.

 Happy to see good results so the question seems how to fine tune
 Lucene or the usage which neo4j make of Lucene...


That was just one suggestion I had, maybe there's other things affecting the
performance, I mean if we stop guessing and actually measures bottle necks.


  Actually, if anyone knows a better index for exact lookups that is
  configurable to have good insert and lookup performance, any hint
  would be greatly appreciated. This is what right now limits insert
  performance when you use the Neo4j Batchinserter. The BatchInserter
  itself can insert around 200K-400K nodes or relationships per second,
  but the indexing subsystems are just not up to that speed.

 I'm not using the BatchInserter cause I will need to do that work on a
 daily basis and the normal operations are a lot slower.

  Help is greatly appreciated!

 Indeed. Thanks in advance

 Cheers
 --
 Massimo
 http://meridio.blogspot.com
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 User@lists.neo4j.org
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Re: [Neo4j] InvalidRecordException during traversal after unclean shutdown

2011-02-03 Thread Tobias Ivarsson
I've been able to manually put the store into a consistent state. I did this
by simply skipping the references to Relationship[2055394] that had somehow
gotten into the relationship chain of Node[1]. I haven't, however, been able
to reproduce or find the cause of this.

It would have been interesting to look at the logical log Neo4j created
while working on your store. Could you in the future configure Neo4j with:
keep_logical_logs=true
That way all the logical logs will be kept and I could use that to analyze
the problem, should this happen again, and you could use it to recreate your
store from scratch to a consistent state.

I'll continue my investigation a bit more, but I'm not sure I can get
anywhere further since the faulty record has been removed.

For my continued investigation I have a few questions:

Does your application ever remove any relationships during normal operation?
Or was the removal of the invalid relationship record the only that ever
occurred?
It looks like at least one other, Relationship[2055617], has been removed at
some point.

If this ever happens again, send the faulty store to me immediately, don't
try to fix it on your own. I'd love to see the actual corrupted data. As it
looks at the moment it is tempting to blame vmware (not going to do that
without evidence though), I don't know how well they propagate filesystem
flush() operations to the host file system, I'll have to investigate that.

Was the file system in the vmware vm an actual partition on disk, or was it
a virtual file system stored in an image file on the host?

The non-clean shutdown that caused this, was that a JVM crash, a vmware vm
crash, or a host machine crash?

Cheers,
Tobias

On Tue, Feb 1, 2011 at 7:12 PM, Lars Hvile lars.hv...@fovea.no wrote:

 -- directly after successful recovery
 org.neo4j.kernel.impl.nioneo.store.InvalidRecordException: Node[1] is
 neither firstNode[2055881] nor secondNode[2055876] for Relationship[2055394]


 -- after manual deletion of Relationship[2055394], in a desperate
 recovery-attempt =)


 Unfortunately I don't have a copy of the database at it's original corrupt
 state, I do however have a copy of it after I deleted the the relationship..
 788MiB zipped


It really is a shame that you removed that relationship. It would have been
super useful to look at what that record looked like.
Although I think that record was fine, more likely it was the reference to
it that was faulty.

-- 
Tobias Ivarsson tobias.ivars...@neotechnology.com
Hacker, Neo Technology
www.neotechnology.com
Cellphone: +46 706 534857
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[Neo4j] getting non-deterministic results with getAllNodes()

2011-02-03 Thread Raghava Mutharaju
Hi all,

I want to iterate over all the nodes in the graph and then do a tranversal
on each of them. To do this, I used the getAllNodes() method of
GraphDatabaseService class. But the number of nodes I get always varies on
each run. I checked the number of nodes I created during graph creation time
and they were as expected. The results of getAllNodes() return each node
many number of times.

Nodes created: 413,
Nodes obtained by getAllNodes(): 6506, 5426, 7021, 7434, ..

What might be going wrong here?

Another question I had is, it looks like a start/root node would be
created by default. Is this the case? If so, how can I avoid/recognize it in
the getAllNodes() results?


Thank you.

Regards,
Raghava.
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Re: [Neo4j] getting non-deterministic results with getAllNodes()

2011-02-03 Thread David Montag
Hi Raghava,

Could you please provide the code used to create the store? Could you also
please provide the code you use to iterate all nodes?

The reference node always has id 0, so you can filter by ID to ensure that
you don't process that node.

David

On Thu, Feb 3, 2011 at 10:41 AM, Raghava Mutharaju 
m.vijayaragh...@gmail.com wrote:

 Hi all,

 I want to iterate over all the nodes in the graph and then do a tranversal
 on each of them. To do this, I used the getAllNodes() method of
 GraphDatabaseService class. But the number of nodes I get always varies on
 each run. I checked the number of nodes I created during graph creation
 time
 and they were as expected. The results of getAllNodes() return each node
 many number of times.

 Nodes created: 413,
 Nodes obtained by getAllNodes(): 6506, 5426, 7021, 7434, ..

 What might be going wrong here?

 Another question I had is, it looks like a start/root node would be
 created by default. Is this the case? If so, how can I avoid/recognize it
 in
 the getAllNodes() results?


 Thank you.

 Regards,
 Raghava.
 ___
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 User@lists.neo4j.org
 https://lists.neo4j.org/mailman/listinfo/user




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Re: [Neo4j] getting non-deterministic results with getAllNodes()

2011-02-03 Thread Andreas Kollegger
Hi Raghava,

Also,  are you sure you're only creating the nodes once? Looking at your 
numbers, (7434-7021=413) happens to be true, though the other intervals don't 
match. Is this from a single run starting with a clean database (the db 
directory is empty)?

-Andreas

On Feb 3, 2011, at 7:51 PM, David Montag wrote:

 Hi Raghava,
 
 Could you please provide the code used to create the store? Could you also
 please provide the code you use to iterate all nodes?
 
 The reference node always has id 0, so you can filter by ID to ensure that
 you don't process that node.
 
 David
 
 On Thu, Feb 3, 2011 at 10:41 AM, Raghava Mutharaju 
 m.vijayaragh...@gmail.com wrote:
 
 Hi all,
 
 I want to iterate over all the nodes in the graph and then do a tranversal
 on each of them. To do this, I used the getAllNodes() method of
 GraphDatabaseService class. But the number of nodes I get always varies on
 each run. I checked the number of nodes I created during graph creation
 time
 and they were as expected. The results of getAllNodes() return each node
 many number of times.
 
 Nodes created: 413,
 Nodes obtained by getAllNodes(): 6506, 5426, 7021, 7434, ..
 
 What might be going wrong here?
 
 Another question I had is, it looks like a start/root node would be
 created by default. Is this the case? If so, how can I avoid/recognize it
 in
 the getAllNodes() results?
 
 
 Thank you.
 
 Regards,
 Raghava.
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 Cell: 650.556.4411
 david.mon...@neotechnology.com
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Re: [Neo4j] getting non-deterministic results with getAllNodes()

2011-02-03 Thread Raghava Mutharaju
Hi David  Andreas,

Aah, I deleted the contents of the db and ran it, this time I got the
expected result of 413 nodes. I was running the same program which creates 
traverses the graph multiple times, so the inconsistent results. Silly of
me :)

Thank you for pointing it out.

Regards,
Raghava.

On Thu, Feb 3, 2011 at 1:54 PM, Andreas Kollegger 
andreas.kolleg...@neotechnology.com wrote:

 Hi Raghava,

 Also,  are you sure you're only creating the nodes once? Looking at your
 numbers, (7434-7021=413) happens to be true, though the other intervals
 don't match. Is this from a single run starting with a clean database (the
 db directory is empty)?

 -Andreas

 On Feb 3, 2011, at 7:51 PM, David Montag wrote:

  Hi Raghava,
 
  Could you please provide the code used to create the store? Could you
 also
  please provide the code you use to iterate all nodes?
 
  The reference node always has id 0, so you can filter by ID to ensure
 that
  you don't process that node.
 
  David
 
  On Thu, Feb 3, 2011 at 10:41 AM, Raghava Mutharaju 
  m.vijayaragh...@gmail.com wrote:
 
  Hi all,
 
  I want to iterate over all the nodes in the graph and then do a
 tranversal
  on each of them. To do this, I used the getAllNodes() method of
  GraphDatabaseService class. But the number of nodes I get always varies
 on
  each run. I checked the number of nodes I created during graph creation
  time
  and they were as expected. The results of getAllNodes() return each node
  many number of times.
 
  Nodes created: 413,
  Nodes obtained by getAllNodes(): 6506, 5426, 7021, 7434, ..
 
  What might be going wrong here?
 
  Another question I had is, it looks like a start/root node would be
  created by default. Is this the case? If so, how can I avoid/recognize
 it
  in
  the getAllNodes() results?
 
 
  Thank you.
 
  Regards,
  Raghava.
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  Neo Technology, www.neotechnology.com
  Cell: 650.556.4411
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Re: [Neo4j] InvalidRecordException during traversal after unclean shutdown

2011-02-03 Thread Lars Hvile
We're actually using the logical logs already for backups now, I'll let you 
know if we get this kind of problem again..

How can we use these logs to go back to a known good state, are there any 
tools, and is it documented somewhere?

As for your questions..
- in this test we didn't delete nodes or relationships at all, except my little 
recovery attempt
- vmware.. we're using vmware for our production environment as well, but not 
vmware workstation.. we're also considering ec2 for this particular project, I 
can't imagine that disk are more reliable there?
- the file system is just regular files on the host
- the unclean shutdown was me terminating the jvm on purpose while doing inserts



Lars

- Reply message -
Fra: Tobias Ivarsson tobias.ivars...@neotechnology.com
Til: Neo4j user discussions user@lists.neo4j.org
Emne: [Neo4j] InvalidRecordException during traversal after unclean shutdown
Dato: tor., feb. 3, 2011 18:45



I've been able to manually put the store into a consistent state. I did this
by simply skipping the references to Relationship[2055394] that had somehow
gotten into the relationship chain of Node[1]. I haven't, however, been able
to reproduce or find the cause of this.

It would have been interesting to look at the logical log Neo4j created
while working on your store. Could you in the future configure Neo4j with:
keep_logical_logs=true
That way all the logical logs will be kept and I could use that to analyze
the problem, should this happen again, and you could use it to recreate your
store from scratch to a consistent state.

I'll continue my investigation a bit more, but I'm not sure I can get
anywhere further since the faulty record has been removed.

For my continued investigation I have a few questions:

Does your application ever remove any relationships during normal operation?
Or was the removal of the invalid relationship record the only that ever
occurred?
It looks like at least one other, Relationship[2055617], has been removed at
some point.

If this ever happens again, send the faulty store to me immediately, don't
try to fix it on your own. I'd love to see the actual corrupted data. As it
looks at the moment it is tempting to blame vmware (not going to do that
without evidence though), I don't know how well they propagate filesystem
flush() operations to the host file system, I'll have to investigate that.

Was the file system in the vmware vm an actual partition on disk, or was it
a virtual file system stored in an image file on the host?

The non-clean shutdown that caused this, was that a JVM crash, a vmware vm
crash, or a host machine crash?

Cheers,
Tobias

On Tue, Feb 1, 2011 at 7:12 PM, Lars Hvile lars.hv...@fovea.no wrote:

 -- directly after successful recovery
 org.neo4j.kernel.impl.nioneo.store.InvalidRecordException: Node[1] is
 neither firstNode[2055881] nor secondNode[2055876] for Relationship[2055394]


 -- after manual deletion of Relationship[2055394], in a desperate
 recovery-attempt =)


 Unfortunately I don't have a copy of the database at it's original corrupt
 state, I do however have a copy of it after I deleted the the relationship..
 788MiB zipped


It really is a shame that you removed that relationship. It would have been
super useful to look at what that record looked like.
Although I think that record was fine, more likely it was the reference to
it that was faulty.

--
Tobias Ivarsson tobias.ivars...@neotechnology.com
Hacker, Neo Technology
www.neotechnology.comhttp://www.neotechnology.com
Cellphone: +46 706 534857
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Re: [Neo4j] getting non-deterministic results with getAllNodes()

2011-02-03 Thread David Montag
Andreas' rain man style subtraction skills to the rescue :)  Glad it worked
out.

Happy hacking!

David

On Thu, Feb 3, 2011 at 12:16 PM, Raghava Mutharaju 
m.vijayaragh...@gmail.com wrote:

 Hi David  Andreas,

 Aah, I deleted the contents of the db and ran it, this time I got the
 expected result of 413 nodes. I was running the same program which creates
 
 traverses the graph multiple times, so the inconsistent results. Silly of
 me :)

 Thank you for pointing it out.

 Regards,
 Raghava.

 On Thu, Feb 3, 2011 at 1:54 PM, Andreas Kollegger 
 andreas.kolleg...@neotechnology.com wrote:

  Hi Raghava,
 
  Also,  are you sure you're only creating the nodes once? Looking at your
  numbers, (7434-7021=413) happens to be true, though the other intervals
  don't match. Is this from a single run starting with a clean database
 (the
  db directory is empty)?
 
  -Andreas
 
  On Feb 3, 2011, at 7:51 PM, David Montag wrote:
 
   Hi Raghava,
  
   Could you please provide the code used to create the store? Could you
  also
   please provide the code you use to iterate all nodes?
  
   The reference node always has id 0, so you can filter by ID to ensure
  that
   you don't process that node.
  
   David
  
   On Thu, Feb 3, 2011 at 10:41 AM, Raghava Mutharaju 
   m.vijayaragh...@gmail.com wrote:
  
   Hi all,
  
   I want to iterate over all the nodes in the graph and then do a
  tranversal
   on each of them. To do this, I used the getAllNodes() method of
   GraphDatabaseService class. But the number of nodes I get always
 varies
  on
   each run. I checked the number of nodes I created during graph
 creation
   time
   and they were as expected. The results of getAllNodes() return each
 node
   many number of times.
  
   Nodes created: 413,
   Nodes obtained by getAllNodes(): 6506, 5426, 7021, 7434, ..
  
   What might be going wrong here?
  
   Another question I had is, it looks like a start/root node would be
   created by default. Is this the case? If so, how can I avoid/recognize
  it
   in
   the getAllNodes() results?
  
  
   Thank you.
  
   Regards,
   Raghava.
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   --
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   Neo Technology, www.neotechnology.com
   Cell: 650.556.4411
   david.mon...@neotechnology.com
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[Neo4j] Stability of neo4j graph database

2011-02-03 Thread John Howard
Hello,

We have been evaluating the neo4j for one of our critical applications.
When the server goes down abruptly without the clean shutdown of the graph
db, it looks like the recovery always fails.
It consistently throws the exception given below and then the graph db
becomes unusable.
I dont think graph had any uncommitted transactions before the abrupt
shutdown, because we loaded the graph couple of days ago and since then we
have been using only to read the data(though not in read only mode).
It's possible that we have not configured something right.
Your help is highly appreciated. I have attached our log stack trace and
message.log contents

Nodes: 20
Relationships:45
Properties:4,000,000
Rel types: 60

Our log stack trace:
18:48:25,455 INFO  [log]
Non clean shutdown detected on log [C:\JBoss\jboss-5.1.0.GA
\server\all\data\ssGraphNew\nioneo_logical.log
.1]. Recovery started ...
18:48:26,015 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
jboss-5.1.0.GA\server\all\data\ssGraphNew/lucene/lucene.log.
1]. Recovery started ...
18:48:26,047 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
jboss-5.1.0.GA\server\all\data\ssGraphNew/lucene-fulltext/lu
cene.log.1]. Recovery started ...
18:48:26,405 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
jboss-5.1.0.GA\server\all\data\ssGraphNew\index/lucene.log.1
]. Recovery started ...
18:48:30,087 ERROR [STDERR] org.neo4j.graphdb.TransactionFailureException:
Could not create data source lucene-index[lucene-index]
18:48:30,089 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:182)
18:48:30,089 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneIndexProvider.load(LuceneIndexProvider.java:110)
18:48:30,090 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneIndexProvider.init(LuceneIndexProvider.java:94)
18:48:30,090 ERROR [STDERR] at
org.neo4j.kernel.KernelExtension$KernelData.initAll(KernelExtension.java:153)
18:48:30,091 ERROR [STDERR] at
org.neo4j.kernel.EmbeddedGraphDbImpl$2.init(EmbeddedGraphDbImpl.java:160)
18:48:30,091 ERROR [STDERR] at
org.neo4j.kernel.GraphDbInstance.start(GraphDbInstance.java:155)
18:48:30,092 ERROR [STDERR] at
org.neo4j.kernel.EmbeddedGraphDbImpl.init(EmbeddedGraphDbImpl.java:168)
18:48:30,092 ERROR [STDERR] at
org.neo4j.kernel.EmbeddedGraphDatabase.init(EmbeddedGraphDatabase.java:81)
18:48:30,139 ERROR [STDERR] Caused by:
java.lang.reflect.InvocationTargetException
18:48:30,139 ERROR [STDERR] at
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
18:48:30,140 ERROR [STDERR] at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
18:48:30,140 ERROR [STDERR] at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.jav
a:27)
18:48:30,141 ERROR [STDERR] at
java.lang.reflect.Constructor.newInstance(Constructor.java:513)
18:48:30,142 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.XaDataSourceManager.create(XaDataSourceManager.java:74)
18:48:30,142 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:176)
18:48:30,142 ERROR [STDERR] ... 79 more
18:48:30,143 ERROR [STDERR] Caused by: java.lang.NullPointerException
18:48:30,144 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneDataSource.findDocument(LuceneDataSource.java:602)
18:48:30,144 ERROR [STDERR] at
org.neo4j.index.impl.lucene.CommitContext.getDocument(CommitContext.java:71)
18:48:30,145 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneCommand$AddRelationshipCommand.perform(LuceneCommand.java:212
)
18:48:30,146 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneTransaction.doCommit(LuceneTransaction.java:231)
18:48:30,146 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:319)
18:48:30,147 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.injectTwoPhaseCommit(XaResource
Manager.java:380)
18:48:30,148 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.applyTwoPhaseCommitEntry(XaLogicalLo
g.java:577)
18:48:30,149 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.applyEntry(XaLogicalLog.java:469)
18:48:30,149 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.doInternalRecovery(XaLogicalLog.java
:804)
18:48:30,150 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.open(XaLogicalLog.java:274)
18:48:30,151 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.open(XaLogicalLog.java:197)
18:48:30,151 ERROR [STDERR] at
org.neo4j.kernel.impl.transaction.xaframework.XaContainer.openLogicalLog(XaContainer.java:98)
18:48:30,152 ERROR [STDERR] at
org.neo4j.index.impl.lucene.LuceneDataSource.init(LuceneDataSource.java:207)
18:48:30,152 ERROR [STDERR] 

Re: [Neo4j] Stability of neo4j graph database

2011-02-03 Thread Michael Hunger
Hello John,

what version of Neo4j are you currently running?

As it tries to replay an AddRelationshipCommand and there was a recent fix 
around this issue, you might try to recover your db using
Neo4j version 1.3 (Abisko Lampa) M01. 
(http://blog.neo4j.org/2011/01/neo4j-13-abisko-lampa-m01-ha-growing-up.html)

Quote: Indexing bug fixes - A bug during reovery was removed that occurred 
when only relationship index commands were executed before the crash (Thanks to 
Andreas Bauer for reporting that).

You can get it from here: http://neo4j.org/download

HTH

Michael

Am 04.02.2011 um 01:48 schrieb John Howard:

 Hello,
 
 We have been evaluating the neo4j for one of our critical applications.
 When the server goes down abruptly without the clean shutdown of the graph
 db, it looks like the recovery always fails.
 It consistently throws the exception given below and then the graph db
 becomes unusable.
 I dont think graph had any uncommitted transactions before the abrupt
 shutdown, because we loaded the graph couple of days ago and since then we
 have been using only to read the data(though not in read only mode).
 It's possible that we have not configured something right.
 Your help is highly appreciated. I have attached our log stack trace and
 message.log contents
 
 Nodes: 20
 Relationships:45
 Properties:4,000,000
 Rel types: 60
 
 Our log stack trace:
 18:48:25,455 INFO  [log]
 Non clean shutdown detected on log [C:\JBoss\jboss-5.1.0.GA
 \server\all\data\ssGraphNew\nioneo_logical.log
 .1]. Recovery started ...
 18:48:26,015 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
 jboss-5.1.0.GA\server\all\data\ssGraphNew/lucene/lucene.log.
 1]. Recovery started ...
 18:48:26,047 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
 jboss-5.1.0.GA\server\all\data\ssGraphNew/lucene-fulltext/lu
 cene.log.1]. Recovery started ...
 18:48:26,405 INFO  [log] Non clean shutdown detected on log [C:\JBoss\
 jboss-5.1.0.GA\server\all\data\ssGraphNew\index/lucene.log.1
 ]. Recovery started ...
 18:48:30,087 ERROR [STDERR] org.neo4j.graphdb.TransactionFailureException:
 Could not create data source lucene-index[lucene-index]
 18:48:30,089 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:182)
 18:48:30,089 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.LuceneIndexProvider.load(LuceneIndexProvider.java:110)
 18:48:30,090 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.LuceneIndexProvider.init(LuceneIndexProvider.java:94)
 18:48:30,090 ERROR [STDERR] at
 org.neo4j.kernel.KernelExtension$KernelData.initAll(KernelExtension.java:153)
 18:48:30,091 ERROR [STDERR] at
 org.neo4j.kernel.EmbeddedGraphDbImpl$2.init(EmbeddedGraphDbImpl.java:160)
 18:48:30,091 ERROR [STDERR] at
 org.neo4j.kernel.GraphDbInstance.start(GraphDbInstance.java:155)
 18:48:30,092 ERROR [STDERR] at
 org.neo4j.kernel.EmbeddedGraphDbImpl.init(EmbeddedGraphDbImpl.java:168)
 18:48:30,092 ERROR [STDERR] at
 org.neo4j.kernel.EmbeddedGraphDatabase.init(EmbeddedGraphDatabase.java:81)
 18:48:30,139 ERROR [STDERR] Caused by:
 java.lang.reflect.InvocationTargetException
 18:48:30,139 ERROR [STDERR] at
 sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 18:48:30,140 ERROR [STDERR] at
 sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
 18:48:30,140 ERROR [STDERR] at
 sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.jav
 a:27)
 18:48:30,141 ERROR [STDERR] at
 java.lang.reflect.Constructor.newInstance(Constructor.java:513)
 18:48:30,142 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.XaDataSourceManager.create(XaDataSourceManager.java:74)
 18:48:30,142 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:176)
 18:48:30,142 ERROR [STDERR] ... 79 more
 18:48:30,143 ERROR [STDERR] Caused by: java.lang.NullPointerException
 18:48:30,144 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.LuceneDataSource.findDocument(LuceneDataSource.java:602)
 18:48:30,144 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.CommitContext.getDocument(CommitContext.java:71)
 18:48:30,145 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.LuceneCommand$AddRelationshipCommand.perform(LuceneCommand.java:212
 )
 18:48:30,146 ERROR [STDERR] at
 org.neo4j.index.impl.lucene.LuceneTransaction.doCommit(LuceneTransaction.java:231)
 18:48:30,146 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:319)
 18:48:30,147 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.injectTwoPhaseCommit(XaResource
 Manager.java:380)
 18:48:30,148 ERROR [STDERR] at
 org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.applyTwoPhaseCommitEntry(XaLogicalLo
 g.java:577)
 18:48:30,149 ERROR [STDERR] at
 

Re: [Neo4j] Stability of neo4j graph database

2011-02-03 Thread John Howard
Am using the V1.2 (stable)
Will try your suggestion.

Thanks for the prompt response!



Date: Fri, 4 Feb 2011 01:59:21 +0100
From: Michael Hunger michael.hun...@neotechnology.com
Subject: Re: [Neo4j] Stability of neo4j graph database
To: Neo4j user discussions user@lists.neo4j.org
Message-ID: ac59f47e-9830-4d08-b334-ed908e53f...@neotechnology.com
Content-Type: text/plain; charset=us-ascii

Hello John,

what version of Neo4j are you currently running?

As it tries to replay an AddRelationshipCommand and there was a recent fix
around this issue, you might try to recover your db using
Neo4j version 1.3 (Abisko Lampa) M01. (
http://blog.neo4j.org/2011/01/neo4j-13-abisko-lampa-m01-ha-growing-up.html)

Quote: Indexing bug fixes - A bug during reovery was removed that occurred
when only relationship index commands were executed before the crash (Thanks
to Andreas Bauer for reporting that).

You can get it from here: http://neo4j.org/download

HTH

Michael
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[Neo4j] Finding All Available Paths

2011-02-03 Thread Saikat Kanjilal

Hi Folks,I'm slowly but surely climbing the learning path in the neo4j world.  
I'm using Dijkstra's algorithm for the shortest path calculation between two 
nodes which now seems to be working fine after some code rearranging, however 
I'd also like to get the list of available paths between two nodes regardless 
of the path length.  I tried to use the findAllPaths function for the 
dijkstraFinder but I noticed that if there is only one available path between 
two nodes it returns this same path multiple times and then crashes (this only 
happens when there is only 1 path between 2 nodes).  I was wondering whether I 
should be using some other finder like the finders that dont use weighted paths 
to get this information.  If not some help would be much appreciated here, is 
findAllPaths supposed to return the same path multiple times.

Thanks in advance 
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