Re: [Neo4j] Python embedding: problems with shutdown and threads

2011-11-02 Thread Tim McNamara
Here are a few notes of my own from using Neo4j with Python embedded.
I know that this isn't the right place .

Ubuntu doesn't set $JAVA_HOME. I ended up hard coding the location of my JVM.

I seem to encounter unclean shutdowns all the time when running with
the iPython REPL. Is there a db.shutdown() command that I've been
neglecting to use?

Tim


On 3 November 2011 17:28, Michael Rene Armida m...@marmida.com wrote:
 I'm having some weird problems with threading on shutdown.  As I previously
 discovered, using neo4j in a multi-threaded Python app requires complete
 segregation of neo4j into a single thread.  That all works fine for
 creating a database, however, it appears that shutting one down is a bit of
 a mystery.  I wrote a test program to minimally illustrate the difficulty:

 http://pastebin.com/gg204kae

 Threading is always easy to get wrong, so I added a simple switch to remove
 neo4j from the picture.  When I disable neo, the program starts up and
 shuts down cleanly.  When I re-enable neo, some of the print statements
 never get run, and the app mysteriously exits.

 I am testing this by saving it into a script and running it on the command
 line.  Any time after the worker thread finishes creating the neo db, I hit
 ctrl-c, and the two scenarios play out as above.

 It seems that the embedded Python API is not exactly at the forefront of
 popular use, and so I understand if nobody knows what's up with this.  I
 just thought I should add something, for the record.  I hope my script
 doesn't have an obvious bug.

 Thanks,
 Michael
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Re: [Neo4j] Embedded neo4j in Python up to date again

2011-10-10 Thread Tim McNamara
This is great news. I love that it uses context managers for transactions.

On 7 October 2011 02:06, Jacob Hansson jacob.hans...@neotechnology.com wrote:
 On Thu, Oct 6, 2011 at 1:57 PM, Peter Neubauer 
 peter.neuba...@neotechnology.com wrote:

 Yes Javier,
 that would be great! Do you think you could open an issue and provide
 some details on how to go about it?

 Cheers,

 /peter neubauer

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 On Wed, Oct 5, 2011 at 5:15 PM, Javier de la Rosa ver...@gmail.com
 wrote:
  On Wed, Oct 5, 2011 at 07:48, Jacob Hansson
  jacob.hans...@neotechnology.com wrote:
  there is now a first stable release of the new neo4j-embedded
  python package available from PyPi.
 
  This news is really great! And I'm very glad to see that some methods
  are seemed to the neo4j-rest-client [1]. Is there any chance to find
  some day from neo4j import restgraphdatabase and to make both
  API's totally equal?
 
  Thank you very much for all the work involved.
  Regards!
 
 
 
  [1] https://github.com/versae/neo4j-rest-client
 
  --
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  http://versae.es
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 Javier,

 it would be really awesome to combine the two, or at least make sure the
 APIs are completely compatible.

 I'm hesitant to bundle them together, because the REST client is pure
 python, and can keep a very small footprint. The embedded package, on the
 other hand, bundles the full Neo4j distribution, and so it's a full 10MB
 large.

 In most settings, this won't matter much, but it still feels unnecessary to
 force people who just want the REST client to include the full DB
 distribution in their projects.


 Architecture-wise, perhaps we can have a common front for them, that can
 then be powered either by the embedded implementation, or by the REST
 client, and then use something like the db path to determine which one to
 use:

 from neo4j import GraphDatabase

 embeddeddb = GraphDatabase('/home/data')
 serverdb = GraphDatabase('http://localhost:7474')


 There is one major hurdle we need to get past first, we need to implement
 transaction support in the REST API that is feature-compatible with the
 embedded transaction API. When that is in place, the REST client will be
 able to behave exactly like the embedded client, and we can combine them.

 /Jake

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Re: [Neo4j] List all indexed key/values for an entity

2011-09-21 Thread Tim McNamara
+1

But the plural of index is indices.
On 22/09/2011 1:56 AM, Peter Neubauer peter.neuba...@neotechnology.com
wrote:
 Josh,
 very reasonable request. Could you please put that into an issue? I
 suspect this is in line with better auto indexing support, I am not
 sure how much of it there already is, so let's keep track of it in the
 issue.

 Thanks!

 /peter neubauer

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 On Mon, Sep 19, 2011 at 4:15 PM, jadell josh.ad...@gmail.com wrote:
 Is there any way via the REST API to list all the indexes and keys/values
 that a given entity is indexed on?  Something like:

 GET http://0.0.0.0:7474/db/data/node/123/indexes

 returns:

 [
 http://0.0.0.0:7474/db/data/index/node/favorites/color/blue;,
 http://0.0.0.0:7474/db/data/index/node/favorites/food/pizza;,
 http://0.0.0.0:7474/db/data/index/node/users/name/josh;,
 http://0.0.0.0:7474/db/data/index/node/authors/post/456;,
 ]

 Does anything exist that gives this functionality or similar?

 -- Josh Adell

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 Sent from the Neo4j Community Discussions mailing list archive at
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[Neo4j] Course materials code for Graph and Network Analysis freely available

2011-07-24 Thread Tim McNamara
New to graphs? FYI http://mlg.ucd.ie/summer


Tim McNamara
Professional \\  paperlessprojects.com
Personal \\  @timClicks  |  timmcnamara.co.nz
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Re: [Neo4j] Demand for native python bindings?

2011-06-02 Thread Tim McNamara
Thanks Aaron- I'll remove my pypi package of the same name. Can you upload
it into there?
On 2/06/2011 10:54 PM, Aaron Moffatt aja.moff...@gmail.com wrote:
 Python/JCC bindings are uploaded to github:

 https://github.com/OneSaidWho/neo4py

 Feedback, suggestions, and testing are much appreciated!

 Regards,
 Aaron

 On Wed, Jun 1, 2011 at 11:35 PM, Aaron Moffatt aja.moff...@gmail.com
wrote:

 I have new native python-neo4j bindings via JCC (mostly based on the
 current neo4j.py, but only supporting a JCC backend). They aren't
 thoroughly tested and don't yet support 'models' (that's the next step),
but
 most stuff is in place (including fulltext indexing for nodes and
 relationships). I'm curious if there's a demand for me to put up a page
 with download and basic usage docs. There isn't a super clean install
 process yet, but they're not difficult to setup, at least in my test
 environment (OSX 10.6, python 2.6)

 Thanks,
 Aaron

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[Neo4j] Open Data Manual - contributions welcome

2011-06-02 Thread Tim McNamara
Hi all,

Sorry if this is off topic. I am the editor of the Open Data Manual[0]. It's
an ever improving manual on how to go about open data. At the moment, it's
mostly focused on government data, but that is changing.

A great enhancement would be some information on graphs. In particular, an
outline of moving data housed in relational tables into a graph would be
excellent. The manual has a large readership and it could be a great way to
become a published author.*  If you would like to assist, please email me
off the list.

Tim McNamara
Professional \\  paperlessprojects.com
Personal \\  @timClicks http://twitter.com/timClicks  |  timmcnamara.co.nz

[0] http://opendatamanual.org

* We're investigating options for creating printed material, but that hasn't
happened yet.
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Re: [Neo4j] Password sent in plain text via email?

2011-06-01 Thread Tim McNamara
That's standard with mailman. There's a big warning when you add your
password that explains this: https://lists.neo4j.org/mailman/listinfo/user

Tim McNamara
Professional \\  paperlessprojects.com
Personal \\  @timClicks http://twitter.com/timClicks  |  timmcnamara.co.nz



On 1 June 2011 23:42, Todd Chaffee t...@mikamai.com wrote:

 I was kind of shocked to see my password sent via email in plain text at
 the
 bottom of the monthly mailing list notification from
 mailman-ow...@lists.neo4j.org.  Any way to suppress that part of the
 message?

 --

 MIKAMAI | Making Media Social
 http://mikamai.com
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Re: [Neo4j] GSoC 2011: OSM data mining and editing capabilities in uDig and Geotools

2011-05-02 Thread Tim McNamara
Congratulations Mirco. I look forward to hearing more about how your project
progresses over the course of the summer.

Tim McNamara  |  @timClicks http://twitter.com/timClicks  |
timmcnamara.co.nz


On 3 May 2011 10:24, Mirco Franzago mircofranz...@gmail.com wrote:

 Hi All,

 I am Mirco Franzago, a master course student in computer science. With my
 pleasure I want to announce that I’ve been selected for the Google Summer
 of
 Code 2011 for my proposal “OSM data mining and editing capabilities in uDig
 and Geotools”, a Neo4j and uDig project  in collaboration with Craig
 Taverner. The project is divided in 3 main steps. The first main target of
 this project is to enhance OSM data rendering in uDig. We will need a
 dynamic layers GUI support for the control of rendering and catalog actions
 functionalities. The second step will be on OSM editor improvement to allow
 a fine grained editing, using the existing uDig editing tools, but with
 different commands implementation. The last step concerns the OSM data
 synchronization into Neo4j database, for use them in the OSM editor.
 I’m very very happy to be part of this community and I’m sure it will be
 great to work with you. Ideas, tips and advices are welcome hopefully for a
 successful project.
 Best regards.

 -Mirco-
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Re: [Neo4j] REST results pagination

2011-04-20 Thread Tim McNamara
Data export, e.g. dumping everything as CSV, DOT or RDF?

On 20 April 2011 18:33, Michael Hunger michael.hun...@neotechnology.comwrote:

 Hi Javier,

 what would you need that for? I'm interested in the usecase.

 Cheers

 Michael

 Am 20.04.2011 um 06:17 schrieb Javier de la Rosa:

  On Tue, Apr 19, 2011 at 10:25, Jim Webber j...@neotechnology.com wrote:
  I've just checked and that's in our list of stuff we really should do
 because it annoys us that it's not there.
  No promises, but we do intend to work through at least some of that list
 for the 1.4 releases.
 
  If this finally is developed, it will possible to request for all
  nodes and all relationships in some URL?
 
 
  Jim
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Re: [Neo4j] Mac Pro Question ...

2011-04-14 Thread Tim McNamara
Rense-

You should explain what you have tried. Which commands have you used? What
error messages have you received?

Good luck

Tim McNamara  |  @timClicks http://twitter.com/timClicks  |
timmcnamara.co.nz


On 15 April 2011 16:19, Rense Lange rensela...@earthlink.net wrote:




 Is there anyone who is running neo4j on their Mac? How did you do it? I
 have a Mac pro, and I can't seem to get it going. Right now, the
 installation methods provided on the web don't work. I hope there is a way
 around this. Help!

 Rense Lange

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Re: [Neo4j] Neo4j rest server indexing

2011-02-20 Thread Tim McNamara
On Fri, Feb 18, 2011 at 12:42, francoisk6 francois_...@hotmail.com wrote:
  [...] is there an example to use fulltext search

On Saturday, 19 February 2011 at 6:08 AM, Maximilian Schulz wrote:
 Hi Francois,
 
 [...] I will write a brief post about it and add the source code as
 well. I could do it later… or maybe someone else already did it.
 
 Max

+1


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Re: [Neo4j] Difference between properties and nodes

2011-02-02 Thread Tim McNamara
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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[Neo4j] Implementing disambiguation algorithms in Neo4j

2011-02-01 Thread Tim McNamara
Say I have two nodes,


{ type: person, name: Neo }
{ type: person, name: Neo }



Over time, I learn their locations. They both live in the same city. This 
increases the chances that they're the same person. However, over time it turns 
out that their ages differ, therefore it's far less likely that they are the 
same Neo.


Is there anything inside of Neo4j that attempts to determine how close two 
nodes are? E.g. to what extent their subtrees and properties match? 
Additionally, can anyone suggest literature for algorithms for disambiguating 
the two entities?


If I wanted to implement something that searches for similarities, that returns 
a probability of a match, can I do this within the database or should I 
implement it within the application?


--
Tim McNamara
@timClicks
http://timmcnamara.co.nz



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[Neo4j] Difference between properties and nodes

2011-01-30 Thread Tim McNamara
Is there much difference between a creating property and creating a child node? 

Tim

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Re: [Neo4j] HTML5 graph viz library

2011-01-15 Thread Tim McNamara

 On 15 January 2011 15:58, Peter Neubauer
 peter.neuba...@neotechnology.com wrote:
  Mhh,
  interesting! I wonder if there is any support for using e.g. GeoTools
  to render arbitrary layouts apart from spatial. Would be worth to
  investigate. The nice thing is that these algos support, as you
  mention, zomming into a static structure, and espose more and more
  detail on every layer.


On 16 January 2011 05:44, Rick Bullotta 
rick.bullo...@burningskysoftware.com wrote:

 Out of curiosity, has anyone looked at re-doing the rendering engine of
 this
 in SVG?


Rick,

SVG is effectively still outsourcing the render to the client. Well, it's
really a bit of a middle ground. The Cartesian positions of each of the
nodes needs to be calculated by the server. However, I think that even only
needing to parse and render the pre-calculated plots would still cripple
most browsers at several million nodes.

Tim McNamara
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  http://timmcnamara.co.nz
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Re: [Neo4j] HTML5 graph viz library

2011-01-15 Thread Tim McNamara
On 16 January 2011 05:34, Peter Neubauer
peter.neuba...@neotechnology.comwrote:

 In this case, the graph layout could be computed server side by
 something like graphviz or so, and then sliced into zoom level
 information. Then  interactivity can be added via open layers .

 However, of course the question is how long it takes to calculate the
 layout for say 100.000 nodes. After that, the basic layout info is
 more or less static. Still, very interesting to think of this kind of
 mixed approach for big visualizations, switching to dynamic solutions
 under a certain threshold, like 500 nodes or so.

 WDYT?

 /peter


Is there any need for database software to provide visualisations? There are
graph visualisation packages that have Neo4j backends that provide this
functionality amazingly well. If you have four minutes today, I strongly
recommend watching a video on Gephi [1]. You'll be amazed by the
beauty, speed and utility that can be achieved when built for purpose tools
are used.

Tim McNamara
  @timClicks
  http://timmcnamara.co.nz

[1] http://vimeo.com/14899695
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Re: [Neo4j] HTML5 graph viz library

2011-01-15 Thread Tim McNamara
On 16 January 2011 10:08, Peter Neubauer neubauer.pe...@gmail.com wrote:

 For this discussion, we are looking for a good way to do limited but
 sufficiently powerful web based vizualisation that can be used for
 mostly introspection and validation of small portion the graph (e.g.
 in the web admin), and still operate on production on production size
 datasets.


arbor.js[1] is flavour of the month. It looks very good at handling small
sections. To visualise a particular node in the web UI, you could have a
max-depth recursive lookup occurring as nodes are inspected.

Are you able to expand on what you mean by still operate on production on
production size datasets? Does this mean that you want one tool that
handles both scenarios? That is, being able manipulate and inspect
individual nodes while being able to render the entire graph? I think a
geoserver is probably the best option.

Tim McNamara
  @timClicks
  http://timmcnamara.co.nz

[1] http://arborjs.org/
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Re: [Neo4j] Scala == Better Java?

2011-01-14 Thread Tim McNamara
Scala seems to be very trendy in some of the Java shops here in NZ.

On 14 January 2011 20:59, Peter Neubauer
peter.neuba...@neotechnology.comwrote:

 Interesting and short read, thought I would share it ...

 http://www.dzone.com/links/r/scala_effective_java_.html

 Cheers,

 /peter neubauer

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[Neo4j] Trouble with neo4j.py - Ubuntu 10.10

2011-01-12 Thread Tim McNamara
Has anyone else experienced difficulty running neo4j.py on Ubuntu 10.10?

I'm having difficulty building the package. I've installed Jython, but
am receiving the following traceback:


$ ~/jython/jython -V
Jython 2.5.2rc2
$ ~/jython/jython setup.py install

setup.py:54: UserWarning: Setuptools is not available.
You will need to make sure that you either have JCC installed prior to
installing Neo4j.py, or that you have JPype installed alongside with
Neo4j.py. With setuptools these could have been automatically installed.

  warnings.warn(Setuptools is not available.
Traceback (most recent call last):
  File setup.py, line 146, in module
main()
  File setup.py, line 134, in main
args[attr] = pom[attr]
  File /home/tim/Sources/neo4j-python/pom.py, line 57, in __getitem__
return self.pattern.sub(lambda match:self[match.groupdict()['var']],
  File /home/tim/Sources/neo4j-python/pom.py, line 57, in lambda
return self.pattern.sub(lambda match:self[match.groupdict()['var']],
  File /home/tim/Sources/neo4j-python/pom.py, line 54, in __getitem__
element = self.parent[path]
  File /home/tim/Sources/neo4j-python/pom.py, line 91, in __getitem__
return replacement.get(path, lambda s,x:x)(self, self.__pom[path])
  File /home/tim/Sources/neo4j-python/pom.py, line 56, in __getitem__
raise KeyError(path)
KeyError: 'project.artifactId'

Tim McNamara
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Re: [Neo4j] Trouble with neo4j.py - Ubuntu 10.10

2011-01-12 Thread Tim McNamara
My CPython can find setuptools fine.. I wonder if it's just something I've
done incorrectly when I installed Jython.

On 12 January 2011 23:25, Peter Neubauer
peter.neuba...@neotechnology.comwrote:

 Tim,
 from the message, it sounds like you should setup
 http://pypi.python.org/pypi/setuptools which will simplify things?

 Cheers,

 /peter neubauer

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 On Wed, Jan 12, 2011 at 11:22 AM, Tim McNamara
 paperl...@timmcnamara.co.nz wrote:
  Has anyone else experienced difficulty running neo4j.py on Ubuntu 10.10?
 
  I'm having difficulty building the package. I've installed Jython, but
  am receiving the following traceback:
 
 
  $ ~/jython/jython -V
  Jython 2.5.2rc2
  $ ~/jython/jython setup.py install
 
  setup.py:54: UserWarning: Setuptools is not available.
  You will need to make sure that you either have JCC installed prior to
  installing Neo4j.py, or that you have JPype installed alongside with
  Neo4j.py. With setuptools these could have been automatically installed.
 
   warnings.warn(Setuptools is not available.
  Traceback (most recent call last):
   File setup.py, line 146, in module
 main()
   File setup.py, line 134, in main
 args[attr] = pom[attr]
   File /home/tim/Sources/neo4j-python/pom.py, line 57, in __getitem__
 return self.pattern.sub(lambda match:self[match.groupdict()['var']],
   File /home/tim/Sources/neo4j-python/pom.py, line 57, in lambda
 return self.pattern.sub(lambda match:self[match.groupdict()['var']],
   File /home/tim/Sources/neo4j-python/pom.py, line 54, in __getitem__
 element = self.parent[path]
   File /home/tim/Sources/neo4j-python/pom.py, line 91, in __getitem__
 return replacement.get(path, lambda s,x:x)(self, self.__pom[path])
   File /home/tim/Sources/neo4j-python/pom.py, line 56, in __getitem__
 raise KeyError(path)
  KeyError: 'project.artifactId'
 
  Tim McNamara
   @timClicks
   http://timmcnamara.co.nz/
   http://people.sugarlabs.org/~tim/
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