[Bioperl-l] New Perl ORM for graph db Neo4j

[Mark A. Jensen]

All, 
I have added support for batch processing to REST::Neo4p, please have a look at https://metacpan.org/module/REST::Neo4p::Batch.

To use it, you write in the context of the object framework, but surround your code with a "batch" block; e.g.:

#!perl
# loader...
use REST::Neo4p;
use REST::Neo4p::Batch;
 
open $f, shift() or die $!;
batch {
  while (<$f>) {
   chomp;
   ($name, $value) = split /\t/;
   REST::Neo4p::Node->new({name => $name, value => $value});
  } 'discard_objs';
exit(0);

The code takes care of packaging the contained individual API calls and sending them off to the server in neo4j's batch format. 

Please send me bugs on RT (https://rt.cpan.org/Public/Bug/Report.html?Queue=REST-Neo4p)

cheers MAJ

>-----Original Message-----
>From: Mark A. Jensen [mailto:maj at fortinbras.us]
>Sent: Monday, September 17, 2012 03:02 PM
>To: 'Joseph Guhlin', 'Hilmar Lapp'
>Cc: 'Fields, Christopher J', <bioperl-l at lists.open-bio.org>, 'Mark A. Jensen'
>Subject: Re: [Bioperl-l] New Perl ORM for graph db Neo4j
>
>W00t! Glad to see there is scope for this; now I can say I did one useful thing for BP in two years!
>
>There is batch support (as well as traversals) in the REST api; looks like the next two features I should add.
>
>cheers all MAJ
>
>Batch is an interesting problem,
>>-----Original Message-----
>>From: Joseph Guhlin [mailto:guhli007 at umn.edu]
>>Sent: Monday, September 17, 2012 02:21 PM
>>To: 'Hilmar Lapp'
>>Cc: 'Fields, Christopher J', <bioperl-l at lists.open-bio.org>, 'Mark A. Jensen'
>>Subject: Re: [Bioperl-l] New Perl ORM for graph db Neo4j
>>
>>Another project using Neo4j is Bio4j. The database is generated using java
>>but can be queried through the REST interface with CYPHER.
>>
>>I haven't had a chance to build it yet or look at it, but may do so in the
>>near future.
>>
>>I am using Neo4j for my own project and the only thing generic enough I
>>could contribute with (that also overlaps with another module) is The Gene
>>Ontology. I import it (~60k node, ~600k relationships, but I ignore a few
>>that others may consider key) and could clean up and contribute that code.
>>I do use a bulk import script written in java that uses the native
>>libraries to process everything so would have to make it work for this
>>module directly (or keep the java import, as it is open source).
>>
>>--Joseph
>>
>>On Mon, Sep 17, 2012 at 12:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>
>>> Yes, indeed. And lo and behold, the Open Tree of Life (
>>> http://opentreeoflife.org) folks are at present building their tree store
>>> on top of Neo4J. They're mostly Python, though. (Which I'm sure our
>>> Biopython colleagues will love to hear.)
>>>
>>>         -hilmar
>>>
>>> On Sep 17, 2012, at 11:28 AM, Fields, Christopher J wrote:
>>>
>>> > Following up on this, any specific modules where this would be a boon?
>>>  I could see this being very useful for Bio::Tree (and Jason's recent work
>>> on creating a persistent backend for storing tree info). Bio::Ontology also…
>>> >
>>> > chris
>>> >
>>> > On Sep 17, 2012, at 12:08 PM, "Fields, Christopher J" <
>>> cjfields at illinois.edu> wrote:
>>> >
>>> >> Agree, very nice!
>>> >>
>>> >> chris
>>> >>
>>> >> On Sep 17, 2012, at 10:00 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>> >>
>>> >>> Very nice, Mark! -hilmar
>>> >>>
>>> >>> On Sep 17, 2012, at 8:13 AM, Mark A. Jensen wrote:
>>> >>>
>>> >>>> Hello all,
>>> >>>> If anyone is experimenting with Neo4j (www.neo4j.org) and needs a
>>> full-featured Perl OO interface, please give REST::Neo4p (
>>> https://metacpan.org/module/REST::Neo4p) a try. Send me the bugs via RT!
>>> >>>> cheers,
>>> >>>> MAJ
>>> >>>>
>>> >>>>
>>> >>>> _______________________________________________
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>>> >>>
>>> >>> --
>>> >>> ===========================================================
>>> >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> >>> ===========================================================
>>> >>>
>>> >>>
>>> >>>
>>> >>>
>>> >>>
>>> >>> _______________________________________________
>>> >>> Bioperl-l mailing list
>>> >>> Bioperl-l at lists.open-bio.org
>>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> >>
>>> >>
>>> >> _______________________________________________
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>>> >
>>>
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
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>>
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