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

[Joseph Guhlin]

Thanks, I'll try to run some tests on this this week. Is there a limit to
the number of things you can do? Should I stagger at 10k or 100k or
somewhere or do you know, or will it handle it itself?

Best,
--Joseph

On Sun, Sep 23, 2012 at 4:46 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

> 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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> >>> >>> ===========================================================
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>>
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> >>> --
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> >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> >>> ===========================================================
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> >>>
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