忘れがちな記憶へ GraphDB

2012-02-02(Thu)

neo4j-server Mismatching store version found (Uknown while expecting v0.A.0)

/usr/lib/python2.6/site-packages/jpype/_pykeywords.py:18: DeprecationWarning: the sets module is deprecated
  import sets
DEBUG:root:trans_contents start
org.neo4j.graphdb.TransactionFailureException: Could not create data source [nioneodb], see nested exception for cause of error
	at org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:161)
	at org.neo4j.kernel.GraphDbInstance.start(GraphDbInstance.java:104)
	at org.neo4j.kernel.EmbeddedGraphDbImpl.(EmbeddedGraphDbImpl.java:187)
	at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:80)
Caused by: java.lang.IllegalStateException: Mismatching store version found (Uknown while expecting v0.A.0) and the store is not cleanly shutdown. Recover the database with the previous database version and then attempt to upgrade
	at org.neo4j.kernel.impl.nioneo.store.NeoStore.checkVersion(NeoStore.java:125)
	at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.(CommonAbstractStore.java:103)
	at org.neo4j.kernel.impl.nioneo.store.AbstractStore.(AbstractStore.java:119)
	at org.neo4j.kernel.impl.nioneo.store.NeoStore.(NeoStore.java:78)
	at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.(NeoStoreXaDataSource.java:165)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
	at org.neo4j.kernel.impl.transaction.XaDataSourceManager.create(XaDataSourceManager.java:77)
	at org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:155)
	... 3 more

確かにneo4j-community-1.4.M01で古いバージョンだ。
新しいバージョンで試してみる。
ココから最新版をダウンロード。
最新版はneo4j-community-1.6-unix.tar.gzだ。

これで再起動して実行してみる。
よし、OK！

スポンサーサイト

2012-02-01(Wed)

neo4j-server Unable to lock store Error

CentOSでpython neo4j-embedded-1.6を使ってDBに書きこもうとすると以下のエラー
が発生したのでメモる。

DEBUG:root:trans_contents start
org.neo4j.graphdb.TransactionFailureException: Could not create data source [nioneodb], see nested exception for cause of error
	at org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:161)
	at org.neo4j.kernel.GraphDbInstance.start(GraphDbInstance.java:104)
	at org.neo4j.kernel.EmbeddedGraphDbImpl.(EmbeddedGraphDbImpl.java:187)
	at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:80)
Caused by: java.lang.IllegalStateException: Unable to lock store [/vol/tools/neo4j-community-1.4.M01/data/graph.db/neostore], this is usually a result of some other Neo4j kernel running using the same store.
	at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.checkStorage(CommonAbstractStore.java:174)
	at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.(CommonAbstractStore.java:102)
	at org.neo4j.kernel.impl.nioneo.store.AbstractStore.(AbstractStore.java:119)
	at org.neo4j.kernel.impl.nioneo.store.NeoStore.(NeoStore.java:78)
	at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.(NeoStoreXaDataSource.java:165)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
	at org.neo4j.kernel.impl.transaction.XaDataSourceManager.create(XaDataSourceManager.java:77)
	at org.neo4j.kernel.impl.transaction.TxModule.registerDataSource(TxModule.java:155)

同じプロセスが動いている可能性がある。

$ ps -aux | grep neo4j
[neo4j@ip-10-156-117-25 uki2neo4j]$ ps aux | grep neo4j
root     12423  0.0  2.4 421668 41424 ?        Sl   12:15   0:06 java -Dwrapper.pidfile=/vol/tools/neo4j-community-1.4.M01/data/neo4j-server.pid -Dwrapper.service=true -Dwrapper.visible=false -Xrs -jar /vol/tools/neo4j-community-1.4.M01/bin/wrapper.jar -c /vol/tools/neo4j-community-1.4.M01/conf/neo4j-wrapper.conf
neo4j    13263  2.6  2.0 420156 34608 pts/1    Sl+  20:33   0:00 java -Dwrapper.pidfile=/vol/tools/neo4j-community-1.4.M01/data/neo4j-server.pid -Dwrapper.service=true -Dwrapper.visible=false -jar /vol/tools/neo4j-community-1.4.M01/bin/wrapper.jar -px /vol/tools/neo4j-community-1.4.M01/conf/neo4j-wrapper.conf
一度殺して再起動させてみたらこの問題はクリア。

参考：
Pythonスタートブック
みんなのPython

2012-01-29(Sun)

Neo4j-serverのconfig設定

Neo4j-serverのconfig設定はココをみればだいたいわかる。

propertiesファイルは４つあるそうだ。

Quick info
①The server’s primary configuration file is found under conf/neo4j-server.properties
②The conf/log4j.properties file contains the default server logging configuration
③Low-level performance tuning parameters are found in conf/neo4j.properties
④Configuraion of the deamonizing wrapper are found in conf/neo4j-wrapper.properties

まずは、ほとんどデフォルトでも動く。
conf/neo4j-server.properties設定だけでも見ておこう。

$ vim /usr/local/neo4j/conf/neo4j-server.properties
# location of the database directory(DBの設定)
org.neo4j.server.database.location=data/graph.db
 
# http port (for all data, administrative, and UI access)（DBポートの設定）
org.neo4j.server.webserver.port=7474

#allow any client to connect（アクセス許可IP設定）
org.neo4j.server.webserver.address=0.0.0.0

# location of the servers round-robin database directory(ラウンドロビンで使うDBディレクトリの設定)
org.neo4j.server.webadmin.rrdb.location=data/graph.db/../rrd
------

パフォーマンスチューニングはconf/neo4j.propertiesで設定する。
メモリとかが主かな。

2012-01-28(Sat)

Ubuntuでneo4jサーバーを起動させる

neo4j サーバーを起動させてみる。
だいたいココをみればわかる。

今回はUbuntuで挑戦。

(1).neo4j-serverの最新版をダウンロード
http://neo4j.org/download
このディレクトリに解答する。
/usr/local/neo4j-community-1.4.M01
でリンクをはる。

$ ln -s /usr/local/neo4j-community-1.4.M01 neo4j

(2).bashrc設定

$ vim ~/.bashrc
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
export PATH=$PATH:$JAVA_HOME/bin
export CLASSPATH=.:$JAVA_HOME/jre/lib:$JAVA_HOME/lib:$JAVA_HOME/lib/tools.jar
export NEO4J_HOME=/usr/local/neo4j
export PATH=$PATH:$NEO4J_HOME/bin
$ source ~/.bashrc

(3).neo4j-server起動

$ cd /usr/local/neo4j/bin
$ sudo ./neo4j install
************* INSTALLING neo4j-server ***********************
Service neo4j-server installed

サービス登録されているか確認してみる。

$ chkconfig -l | grep neo
neo4j-server              0:off  1:off  2:on   3:off  4:off  5:off  6:off

やっと起動

$ sudo /etc/init.d/neo4j-server start
Starting neo4j-server ...
Jan 28, 2012 8:41:14 PM org.apache.commons.vfs.VfsLog info
INFO: Using "/tmp/vfs_cache" as temporary files store.
Jan 28, 2012 8:41:14 PM org.rzo.yajsw.os.posix.PosixService init
INFO: /etc/init.d/neo4j-server already exists
************* STARTING neo4j-server ***********************

Jan 28, 2012 8:41:14 PM org.rzo.yajsw.os.posix.PosixService getPid
INFO: wrapper pid file: /usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid
Jan 28, 2012 8:41:14 PM org.rzo.yajsw.os.posix.PosixService startProcess
INFO: calling "java" "-Dwrapper.pidfile=/usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid" "-Dwrapper.service=true" "-Dwrapper.visible=false" "-Xrs" "-jar" "/usr/local/neo4j-community-1.4.M01/bin/wrapper.jar" "-c" "/usr/local/neo4j-community-1.4.M01/conf/neo4j-wrapper.conf" 
Jan 28, 2012 8:41:14 PM org.rzo.yajsw.os.posix.PosixService getPid
INFO: wrapper pid file: /usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid
Jan 28, 2012 8:41:16 PM org.rzo.yajsw.os.posix.PosixService getPid
INFO: wrapper pid file: /usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid
Jan 28, 2012 8:41:18 PM org.rzo.yajsw.os.posix.PosixService getPid
INFO: wrapper pid file: /usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid
rudi 0

Jan 28, 2012 8:41:34 PM org.rzo.yajsw.os.posix.PosixService getPid
INFO: wrapper pid file: /usr/local/neo4j-community-1.4.M01/data/neo4j-server.pid
rudi 0
Service neo4j-server started

よし、起動した。

2012-01-23(Mon)

Gephiを使ってグラフ化画像を生成する(2)

今回はpostgreSQLとDephiライブラリーを連携させようと試みる。
今日は、そのDBを構築しておく。

必要なテーブルは以下の２テーブル。
①Node用テーブル
②edge_t用テーブル

まずデータベースを作成する。

createdb -W -E UTF-8 buddydb

ついでにデータもいくつか入れておこう。

BEGIN;
--
-- PostgreSQL database dump
--

SET statement_timeout = 0;
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SET check_function_bodies = false;
SET client_min_messages = warning;

--
-- Name: plpgsql; Type: EXTENSION; Schema: -; Owner:_
--

CREATE EXTENSION IF NOT EXISTS plpgsql WITH SCHEMA pg_catalog;


--
-- Name: EXTENSION plpgsql; Type: COMMENT; Schema: -; Owner:_
--

COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';


SET search_path = public, pg_catalog;

SET default_tablespace = '';

SET default_with_oids = false;

--
-- Name: egender_t; Type: TABLE; Schema: public; Owner: postgres; Tablespace:_
--

CREATE TABLE node_t (
    id integer NOT NULL,
    idnode integer,
    label text,
    url text
);

ALTER TABLE public.node_t OWNER TO postgres;
CREATE SEQUENCE node_t_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;

ALTER TABLE public.node_t_id_seq OWNER TO postgres;
ALTER SEQUENCE node_t_id_seq OWNED BY node_t.id;
SELECT pg_catalog.setval('node_t_id_seq', 1, true);
ALTER TABLE node_t ALTER COLUMN id SET DEFAULT nextval('node_t_id_seq'::regclass);

CREATE TABLE edge_t (
    id integer NOT NULL,
    source integer,
    target integer,
    name text,
    weight integer
);

ALTER TABLE public.edge_t OWNER TO postgres;
CREATE SEQUENCE edge_t_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;

ALTER TABLE public.edge_t_id_seq OWNER TO postgres;
ALTER SEQUENCE edge_t_id_seq OWNED BY edge_t.id;
SELECT pg_catalog.setval('edge_t_id_seq', 1, true);
ALTER TABLE edge_t ALTER COLUMN id SET DEFAULT nextval('edge_t_id_seq'::regclass);

INSERT INTO  node_t (id, idnode, label, url) VALUES (1, 0, '桑田佳祐', 'http://www.uki2view.jp/ukimedia/icon/joy.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (2, 1, '及川光博', 'http://www.uki2view.jp/ukimedia/icon/sad.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (3, 2, '小栗旬', 'http://www.uki2view.jp/ukimedia/icon/angry.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (4, 3, '浜崎あゆみ', 'http://www.uki2view.jp/ukimedia/icon/smile.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (5, 4, '仲間由紀江', 'http://www.uki2view.jp/ukimedia/icon/joy.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (6, 5, '金城武', 'http://www.uki2view.jp/ukimedia/icon/sad.png');
INSERT INTO  node_t (id, idnode, label, url) VALUES (7, 6, '佐々木望', 'http://www.uki2view.jp/ukimedia/icon/smile.png');

INSERT INTO  edge_t (id, source, target, name, weight) VALUES (1, 0, 1, 'knows', 1); 
INSERT INTO  edge_t (id, source, target, name, weight) VALUES (2, 0, 2, 'knows', 1); 
INSERT INTO  edge_t (id, source, target, name, weight) VALUES (3, 0, 3, 'knows', 1); 
INSERT INTO  edge_t (id, source, target, name, weight) VALUES (4, 0, 4, 'knows', 2); 
INSERT INTO  edge_t (id, source, target, name, weight) VALUES (5, 4, 5, 'knows', 1); 
INSERT INTO  edge_t (id, source, target, name, weight) VALUES (6, 4, 6, 'knows', 1); 

ALTER TABLE ONLY node_t
    ADD CONSTRAINT node_t_pkey PRIMARY KEY (id);

ALTER TABLE ONLY edge_t
    ADD CONSTRAINT edge_t_pkey PRIMARY KEY (id);


CREATE INDEX node_t_id_idx ON node_t USING btree (id);
CREATE INDEX node_t_idnode_idx ON node_t USING btree (idnode);

CREATE INDEX edge_t_id_idx ON edge_t USING btree (id);
CREATE INDEX edge_t_source_idx ON edge_t USING btree (source);
CREATE INDEX edge_t_target_idx ON edge_t USING btree (target);

COMMIT;

つづくー
(参考)
PostgreSQL徹底入門第3版
PostgreSQL全機能リファレンス (アドバンストリファレンスシリーズ)