[Neo4j] Enable port 7474 for embedded applications?

[Joseph Guhlin]

I have a comparative genomics database project I'm planning to release, and 
would like to enable port 7474 so that RNeo4j library (and others) can 
connect directly to it, without having to also download the correct neo4j 
version. I can't find it in the API but may have not seen it. I realize 
it's not the most common use-case as well.

Any ideas?

Thanks,
--Joseph

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[Neo4j] Re: Data Insertion into Neo4j

[Joseph Guhlin]

I've had lots of luck using the BatchInserters.  More info at their API 
Doc's.

http://neo4j.com/docs/2.3.5/javadocs/

On Monday, June 20, 2016 at 3:10:49 AM UTC-5, yayat...@innoplexus.com wrote:
>
> Hi,
> I am trying to read records from MongoDB and insert into Neo4j. Now i have 
> 2.6 million records in mongoDb and I am inserting the records since 
> Friday[I am from India] into my Neo4j Community Edition. so far I have 
> processed 45k records resulting in 2.9 million nodes.
>
> can anyone suggest a faster way for insertion? 
>
> PS: Neo4j does not support Multiprocessing in Py2neo
>
>
>
>
>

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Re: [Neo4j] import owl file with ontology to Neo4j (Cypher query)

[Joseph Guhlin]

I don't think there is a cypher query way of doing it (but haven't seen all 
of what Cypher can do recently) but I have an database application that can 
import many types of OBO files, which are similar to OWL, for genomic 
comparisons. Is the database you want imported also available in OBO 
format?  I'd be happy to help.

--Joseph

On Tuesday, March 1, 2016 at 5:02:05 PM UTC-6, Michael Hunger wrote:
>
> It is possible with some string function application
>
> Can you share a small example file?
>
> Von meinem iPhone gesendet
>
> Am 01.03.2016 um 22:14 schrieb Aneta M :
>
> Hi,
>
> it is possible to import ontology file (.owl) into Neo4j using only Cypher 
> query?
>
> best regards,
> Aneta
>
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Re: [Neo4j] Problems with structure after multiple BatchInserter runs and supernodes

[Joseph Guhlin]

I was able to create the database using only one instance of the 
BatchInserter, and am still having the error:

START x=node:main(id = Medtr2125s0010)
  MATCH (x)-[:EXPRESSED]-(y)
WITH x,y
  MATCH (y)-[:EXPRESSED]-(g)
RETURN x.id,y.id,g.id

Where x is never a g in the second part of the statement. Is there any way 
to regenerate the Relationship Store or Relationship Group Store?

I'll see if I can make this a test case and report it as a bug, unless 
anyone has any other ideas.

--Joseph

On Tuesday, October 21, 2014 1:35:05 PM UTC-5, Joseph Guhlin wrote:

 I did have that as an issue before, and it has been fixed (on the Neo4j 
 side), and the index query in the query above gives the proper result. 

 It is the relationship that seems to exist only when coming from node (x) 
 in the above example, not when coming from (y) (despite not listing it as a 
 directional relationship). Plus the missing several thousand relationships. 
 I'm not using a relationship index as I haven't had need to. 

 Sorry my first message wasn't more clear.

 Best,
 --Joseph


 On Tuesday, October 21, 2014 1:28:29 PM UTC-5, Michael Hunger wrote:

 Joseph, could it be that you write to the index only in one of the runs?
 I thought there was an issue once where, when you didn't write to an 
 index in one run it removed the index-definition? 

 Could you check that?

 Michael

 On Tue, Oct 21, 2014 at 10:25 AM, Joseph Guhlin joseph...@gmail.com 
 wrote:

 JDK: 1.8
 Neo4j: 2.1.5 -  Embedded and then stand-alone to test the data

 I'm using a program to insert a large amount of data to Neo4j. Because 
 of memory limitations and sped limitations I usually have to do this in a 
 few batches using BatchInserter (separate commands, long after the database 
 has shut down -- not multiple threads). I'm getting things like this:

 START x=node:main(id = Medtr2125s0010)
   MATCH (x)-[:EXPRESSED]-(y)
 WITH x,y
   MATCH (y)-[:EXPRESSED]-(g)
 RETURN x.id,y.id,g.id

 Results here (copy and paste from the Web Console wasn't pretty so this 
 is by hand):
 x.id: Medtr2125s0010
 y.id: Nodule
 g.id: PAC:26323170
 Returned 1 row in 110 ms

 Which doesn't make sense to me, not only should there be over 20,000 
 entries, even if it is finding just this one it should find the same 
 x.id where g.id is.
 I've had no trouble doing multiple BatchInserter calls before, but have 
 had lots of trouble with the 2.1.x line, I believe it is related to the 
 RelationshipGroupStore, which was causing a massive slowdown (see my 
 StackOverflow question here: 
 http://stackoverflow.com/questions/26451609/relationshipgroupstore-mapped-memory-setting-for-batchinserter
  
 ).

 I plan on trying only 1 BatchInserter incarnation tonight and running it 
 to see if it finishes properly and will report back. But this seems like a 
 bug.

 Any advice on speeding up when RelationshipGroupStore slows down during 
 the insert would also be greatly appreciated.

 Thanks,
 --Joseph

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[Neo4j] Problems with structure after multiple BatchInserter runs and supernodes

[Joseph Guhlin]

JDK: 1.8
Neo4j: 2.1.5 -  Embedded and then stand-alone to test the data

I'm using a program to insert a large amount of data to Neo4j. Because of 
memory limitations and sped limitations I usually have to do this in a few 
batches using BatchInserter (separate commands, long after the database has 
shut down -- not multiple threads). I'm getting things like this:

START x=node:main(id = Medtr2125s0010)
  MATCH (x)-[:EXPRESSED]-(y)
WITH x,y
  MATCH (y)-[:EXPRESSED]-(g)
RETURN x.id,y.id,g.id

Results here (copy and paste from the Web Console wasn't pretty so this is 
by hand):
x.id: Medtr2125s0010
y.id: Nodule
g.id: PAC:26323170
Returned 1 row in 110 ms

Which doesn't make sense to me, not only should there be over 20,000 
entries, even if it is finding just this one it should find the same x.id 
where g.id is.
I've had no trouble doing multiple BatchInserter calls before, but have had 
lots of trouble with the 2.1.x line, I believe it is related to the 
RelationshipGroupStore, which was causing a massive slowdown (see my 
StackOverflow question here: 
http://stackoverflow.com/questions/26451609/relationshipgroupstore-mapped-memory-setting-for-batchinserter
 
).

I plan on trying only 1 BatchInserter incarnation tonight and running it to 
see if it finishes properly and will report back. But this seems like a bug.

Any advice on speeding up when RelationshipGroupStore slows down during the 
insert would also be greatly appreciated.

Thanks,
--Joseph

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Re: [Neo4j] Problems with structure after multiple BatchInserter runs and supernodes

[Joseph Guhlin]

I did have that as an issue before, and it has been fixed (on the Neo4j 
side), and the index query in the query above gives the proper result. 

It is the relationship that seems to exist only when coming from node (x) 
in the above example, not when coming from (y) (despite not listing it as a 
directional relationship). Plus the missing several thousand relationships. 
I'm not using a relationship index as I haven't had need to. 

Sorry my first message wasn't more clear.

Best,
--Joseph


On Tuesday, October 21, 2014 1:28:29 PM UTC-5, Michael Hunger wrote:

 Joseph, could it be that you write to the index only in one of the runs?
 I thought there was an issue once where, when you didn't write to an index 
 in one run it removed the index-definition? 

 Could you check that?

 Michael

 On Tue, Oct 21, 2014 at 10:25 AM, Joseph Guhlin joseph...@gmail.com 
 javascript: wrote:

 JDK: 1.8
 Neo4j: 2.1.5 -  Embedded and then stand-alone to test the data

 I'm using a program to insert a large amount of data to Neo4j. Because of 
 memory limitations and sped limitations I usually have to do this in a few 
 batches using BatchInserter (separate commands, long after the database has 
 shut down -- not multiple threads). I'm getting things like this:

 START x=node:main(id = Medtr2125s0010)
   MATCH (x)-[:EXPRESSED]-(y)
 WITH x,y
   MATCH (y)-[:EXPRESSED]-(g)
 RETURN x.id,y.id,g.id

 Results here (copy and paste from the Web Console wasn't pretty so this 
 is by hand):
 x.id: Medtr2125s0010
 y.id: Nodule
 g.id: PAC:26323170
 Returned 1 row in 110 ms

 Which doesn't make sense to me, not only should there be over 20,000 
 entries, even if it is finding just this one it should find the same x.id 
 where g.id is.
 I've had no trouble doing multiple BatchInserter calls before, but have 
 had lots of trouble with the 2.1.x line, I believe it is related to the 
 RelationshipGroupStore, which was causing a massive slowdown (see my 
 StackOverflow question here: 
 http://stackoverflow.com/questions/26451609/relationshipgroupstore-mapped-memory-setting-for-batchinserter
  
 ).

 I plan on trying only 1 BatchInserter incarnation tonight and running it 
 to see if it finishes properly and will report back. But this seems like a 
 bug.

 Any advice on speeding up when RelationshipGroupStore slows down during 
 the insert would also be greatly appreciated.

 Thanks,
 --Joseph

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 Neo4j group.
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