I know there are hundreds of questions out there (and I have been looking prior to asking this!!) because whatever I try, Neo4j will not run the APOC export function.
CALL apoc.export.graphml.all('/tmp/complete-graph.graphml', {useTypes:true, storeNodeIds:false})
Failed to invoke procedure apoc.export.graphml.all: Caused by: java.lang.RuntimeException: Export to files not enabled, please set apoc.export.file.enabled=true in your neo4j.conf
Here is the bottom of my neo4j.conf file:
dbms.security.procedures.unrestricted=apoc.*
dbms.directories.plugins=/var/lib/neo4j/plugins`
apoc.export.file.enabled=true
apoc.import.file.enabled=true
Here is the contents of /var/lib/neo4j/plugins:
-rwxr-xr-x 1 neo4j adm 15949360 Apr 16 2020 apoc-3.5.0.11-all.jar
I am running v 3.5 on Ubuntu 18.
So it turns out the plugins was duplicated and also I needed the whitelist:
dbms.security.procedures.unrestricted=apoc.*
dbms.security.procedures.whitelist=*
apoc.import.file.enabled=true
apoc.export.file.enabled=true
Along with this, I set dbms.directories.import=/ which then allowed me to export along with creating the graph.xml file and setting permissions on it before neo4j could write to it.
If in doubt - pray about it! God always answers.
This still didn't fix it.
Using Neo4j with DBMS 5.2
//EXPORT til CYPHER CALL apoc.export.cypher.all("all-plain.cypher", { format: "plain", useOptimizations: {type: "UNWIND_BATCH", unwindBatchSize: 20} }) YIELD file, batches, source, format, nodes, relationships, properties, time, rows, batchSize RETURN file
gives same error:
and the neo4j.conf-file for this DBMS has this added:
Related
Our Perfino server crashed recently, logging since then the ERROR shown below. (There are some clues hinting to an OutOfMemory resulting in a corrupt db.)
It is suggested: 'Possible solution: use the recovery tool'. But neither the official perfino documentation nor the logs offer more instructions on how to proceed.
So here the question: how to use the recovery tool?
Stacktrace:
ERROR [collector] server: could not load transaction data
org.h2.jdbc.JdbcSQLException: File corrupted while reading record: "[495834] stream data key:64898 pos:11 remaining:0". Possible solution: use the recovery tool; SQL statement:
SELECT value FROM transaction_names WHERE id=? [90030-176]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:178)
at org.h2.message.DbException.get(DbException.java:154)
at org.h2.index.PageDataIndex.getPage(PageDataIndex.java:242)
at org.h2.index.PageDataNode.getNextPage(PageDataNode.java:233)
at org.h2.index.PageDataLeaf.getNextPage(PageDataLeaf.java:400)
at org.h2.index.PageDataCursor.nextRow(PageDataCursor.java:95)
at org.h2.index.PageDataCursor.next(PageDataCursor.java:53)
at org.h2.index.IndexCursor.next(IndexCursor.java:278)
at org.h2.table.TableFilter.next(TableFilter.java:361)
at org.h2.command.dml.Select.queryFlat(Select.java:533)
at org.h2.command.dml.Select.queryWithoutCache(Select.java:646)
at org.h2.command.dml.Query.query(Query.java:323)
at org.h2.command.dml.Query.query(Query.java:291)
at org.h2.command.dml.Query.query(Query.java:37)
at org.h2.command.CommandContainer.query(CommandContainer.java:91)
at org.h2.command.Command.executeQuery(Command.java:197)
at org.h2.jdbc.JdbcPreparedStatement.executeQuery(JdbcPreparedStatement.java:109)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:353)
at com.perfino.a.f.b.a.a(ejt:70)
at com.perfino.a.f.o.a(ejt:880)
at com.perfino.a.f.o.a(ejt:928)
at com.perfino.a.f.o.a(ejt:60)
at com.perfino.a.f.aa.a(ejt:783)
at com.perfino.a.f.o.a(ejt:847)
at com.perfino.a.f.o.a(ejt:792)
at com.perfino.a.f.o.a(ejt:787)
at com.perfino.a.f.o.a(ejt:60)
at com.perfino.a.f.ac.a(ejt:1011)
at com.perfino.b.a.b(ejt:68)
at com.perfino.b.a.c(ejt:82)
at com.perfino.a.f.o.a(ejt:1006)
at com.perfino.a.i.b.d.a(ejt:168)
at com.perfino.a.i.b.d.b(ejt:155)
at com.perfino.a.i.b.d.b(ejt:52)
at com.perfino.a.i.b.d.a(ejt:45)
at com.perfino.a.i.a.b.a(ejt:94)
at com.perfino.a.c.a.b(ejt:105)
at com.perfino.a.c.a.a(ejt:37)
at com.perfino.a.c.c.run(ejt:57)
at java.lang.Thread.run(Thread.java:745)
Notice: I couldn't recover my database with the procedure described below. I'm still keeping this post as reference, as the probability of a successful recovery will depend on how broken the database is, and there is no evidence that this procedure is invalid.
Perfino uses by default the H2 Database Engine as its persistence storage. H2 has a recovery tool and a run script tool to import sql statements:
# 1. Create a dump of the current database using the tool [1]
# This tool creates a 'config.h2.sql' and a 'perfino.h2.sql' db dump
cd ${PERFINO_DATA_DIR}
java -cp ${PATH_TO_H2_LIB}/h2*.jar org.h2.tools.Recover
# 2. Rename the corrupt database file to e.g. *bkp
mv perfino.h2.db perfino.h2.db.bkp
# 3. Import the dump from step 1, ignoring errors
java -cp ${PATH_TO_H2_LIB}/h2*.jar \
org.h2.tools.RunScript \
-url jdbc:h2:${PERFINO_DATA_DIR}/db/perfino \
-script perfino.h2.sql -checkResults
[1]: Perfino includes a version of the h2.jar under ${PERFINO_INSTALL_DIR}/lib/common/h2.jar. You could of course download the official jar and try with it, but in my case, I could only restore the database with the jar supplied with perfino.
This failed for me with a
Exception in thread "main" org.h2.jdbc.JdbcSQLException: Feature not supported: "Restore page store recovery SQL script can only be restored to a PageStore file".
If this happens to you, try:
# 1. Delete database and mv files
cd ${PERFINO_DATA_DIR}
rm perfino.h2.db perfino.mv.db
# 2. Create a PageStore database manually
touch perfino.h2.db
# 3. try with MV_STORE=FALSE on the url [2]
java -cp ${PATH_TO_H2_LIB}/h2*.jar \
org.h2.tools.RunScript \
-url jdbc:h2:${PERFINO_DATA_DIR}/db/perfino;MV_STORE=FALSE \
-checkResults \
-continueOnError
[2]: force h2 to recreate a pagestore db instead of the new storage engine (See this thread in metabase)
I found this article trying to repair a Confluence internal h2 database and this worked for me. Here's a shell script as a gist on my GitHub with what I did - you'll have to adjust for your environment.
I'm in a big trouble, I can't start Elasticsearch and I need it for run my rails locally, please tell me what's going on. I installed Elasticsearch in the normal fashion then I did the following:
elasticsearch --config=/usr/local/opt/elasticsearch/config/elasticsearch.yml
But it shows the following error: [2015-11-01 20:36:50,574][INFO ][bootstrap] es.config is no longer supported. elasticsearch.yml must be placed in the config directory and cannot be renamed.
I tried several alternative ways of run it, like:
elasticsearch -f -D
But then I get the following error, and I can't find any useful for solve it, it seems to be related with file perms but not sure:
java.io.IOException: Resource not found: "org/joda/time/tz/data/ZoneInfoMap" ClassLoader: sun.misc.Launcher$AppClassLoader#33909752
at org.joda.time.tz.ZoneInfoProvider.openResource(ZoneInfoProvider.java:210)
at org.joda.time.tz.ZoneInfoProvider.<init>(ZoneInfoProvider.java:127)
at org.joda.time.tz.ZoneInfoProvider.<init>(ZoneInfoProvider.java:86)
at org.joda.time.DateTimeZone.getDefaultProvider(DateTimeZone.java:514)
at org.joda.time.DateTimeZone.getProvider(DateTimeZone.java:413)
at org.joda.time.DateTimeZone.forID(DateTimeZone.java:216)
at org.joda.time.DateTimeZone.getDefault(DateTimeZone.java:151)
at org.joda.time.chrono.ISOChronology.getInstance(ISOChronology.java:79)
at org.joda.time.DateTimeUtils.getChronology(DateTimeUtils.java:266)
at org.joda.time.format.DateTimeFormatter.selectChronology(DateTimeFormatter.java:968)
at org.joda.time.format.DateTimeFormatter.printTo(DateTimeFormatter.java:672)
at org.joda.time.format.DateTimeFormatter.printTo(DateTimeFormatter.java:560)
at org.joda.time.format.DateTimeFormatter.print(DateTimeFormatter.java:644)
at org.elasticsearch.Build.<clinit>(Build.java:51)
at org.elasticsearch.node.Node.<init>(Node.java:135)
at org.elasticsearch.node.NodeBuilder.build(NodeBuilder.java:145)
at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:170)
at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:270)
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:35)
[2015-11-01 20:40:57,602][INFO ][node ] [Centurius] version[2.0.0], pid[22063], build[de54438/2015-10-22T08:09:48Z]
[2015-11-01 20:40:57,605][INFO ][node ] [Centurius] initializing ...
Exception in thread "main" java.lang.IllegalStateException: failed to load bundle [] due to jar hell
Likely root cause: java.security.AccessControlException: access denied ("java.io.FilePermission" "/usr/local/Cellar/elasticsearch/2.0.0/libexec/antlr-runtime-3.5.jar" "read")
at java.security.AccessControlContext.checkPermission(AccessControlContext.java:472)
at java.security.AccessController.checkPermission(AccessController.java:884)
at java.lang.SecurityManager.checkPermission(SecurityManager.java:549)
at java.lang.SecurityManager.checkRead(SecurityManager.java:888)
at java.util.zip.ZipFile.<init>(ZipFile.java:210)
at java.util.zip.ZipFile.<init>(ZipFile.java:149)
at java.util.jar.JarFile.<init>(JarFile.java:166)
at java.util.jar.JarFile.<init>(JarFile.java:103)
at org.elasticsearch.bootstrap.JarHell.checkJarHell(JarHell.java:173)
at org.elasticsearch.plugins.PluginsService.loadBundles(PluginsService.java:340)
at org.elasticsearch.plugins.PluginsService.<init>(PluginsService.java:113)
at org.elasticsearch.node.Node.<init>(Node.java:144)
at org.elasticsearch.node.NodeBuilder.build(NodeBuilder.java:145)
at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:170)
at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:270)
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:35)
Refer to the log for complete error details.
Thanks for your help.
There are some changes with libexec with Elasticsearch/homebrew installation and that is why it is failing to start. There is a PR #45644 currently being worked on. Till the PR gets accepted, you can use the same formula to fix the installation of Elasticsearch.
First uninstall the earlier/older version. Then edit the formula of Elasticsearch:
$ brew edit elasticsearch
And use the formula from the PR.
Then do brew install elasticsearch, it should work fine.
To start Elasticsearch, just do:
$ elasticsearch
config option is no longer valid. For custom config, use path.config:
$ elasticsearch --path.conf=/usr/local/opt/elasticsearch/config
I am trying to use the export-graphml function in Neo4j 2.2. I have downloaded neo4j shell tools and extract it into the lib directory. I am able to export the entire database as a graphml file. However, if I try to export a subset using a query, I receive the following error:
Error occurred in server thread; nested exception is:
java.lang.NoSuchMethodError: org.neo4j.cypher.export.CypherResultSubGraph.from(Lorg/neo4j/cypher/javacompat/ExecutionResult;Lorg/neo4j/graphdb/GraphDatabaseService;Z)Lorg/neo4j/cypher/export/SubGraph;
The statement I used is:
export-graphml -o /path/to/file/out.graphml match (n:Person)-[r:RELATIONSHIP]-() WHERE n.id = 12345 return n, r
I have tried different variations with the different options (-r, -t) and none work
I've been using the Neo4j batch loader for a while now and tonight started running into issues building my graph from a fresh database export. Running it yields the following:
> java -servjava -server -Xmx4G -jar ~/Dev/github.com/jexp/batch-import/target/batch-import-jar-with-dependencies.jar ./graph.db nodes.csv rels.csv node_index entities exact entities_idx.csv
Usage: Importer data/dir nodes.csv relationships.csv [node_index node-index-name fulltext|exact nodes_index.csv rel_index rel-index-name fulltext|exact rels_index.csv ....]
Using: Importer ./graph.db nodes.csv rels.csv node_index entities exact entities_idx.csv
Using Existing Configuration File
........................
Importing 2412268 Nodes took 4 seconds
.....................
Total import time: 9 seconds
Exception in thread "main" org.neo4j.graphdb.NotFoundException: id=2412269
at org.neo4j.unsafe.batchinsert.BatchInserterImpl.getNodeRecord(BatchInserterImpl.java:917)
at org.neo4j.unsafe.batchinsert.BatchInserterImpl.createRelationship(BatchInserterImpl.java:471)
at org.neo4j.batchimport.Importer.importRelationships(Importer.java:136)
at org.neo4j.batchimport.Importer.doImport(Importer.java:214)
at org.neo4j.batchimport.Importer.main(Importer.java:78)
I was able to successfully run the batch loader for the nodes.csv and rels.csv that are included in its own repository, so I'm thinking that the issue is somewhere in my rels.csv file. However, it's a pretty big file and I would like to know what id=2412269 means, as it seems like the best starting point for diagnosing the failure.
Any ideas?
_howard
This means that in the rels.csv file, you are trying to create a relationship for a node referenced by id = 2412269 . But no such node has been created in your nodes.csv file.
After working through the issue with the author of the importer, it turns out that the issue was that I had single, unescaped quotes in my nodes.csv file. So the rels.csv record was pointing to a node that could not be created in nodes.csv. Unfortunately, the error reported on the console was not exactly the error causing the issue.
I am seeing this error for quite sometime now.
I am running ant build on CYGWIN which inturn runs on WindowsXP.
The resolution(bad one) I found was to delete my gcct/first directory and run ant build again (which runs from another directory). It runs successfully but if I modify some code under gcct/first, I do not want to delete it because of this error.
I did see this link. The resolution here does not apply to me since I do not have .cvspass defined anywhere in the build.xml.
C:\svn\CEL_v3681\buildCore.xml:1883: cvs exited with error code 1
Command line was [Executing 'cvs' with arguments:
'checkout'
'-A'
'-rfirst_v2_126'
'gcct/first'
The ' characters around the executable and arguments are
not part of the command.
environment:
ALLUSERSPROFILE=C:\Documents and Settings\All Users
ANT_HOME=C:/Apps/Apache/apache-ant-1.7.0
APPDATA=C:\Documents and Settings\shankarc\Application Data
CLASSPATH=./;C:/Program Files/Java/jre1.5.0_07/lib/ext/QTJava.zip
COMMONPROGRAMFILES=C:\Program Files\Common Files
COMPUTERNAME=NYKPWM2035798
COMSPEC=C:\WINNT\system32\cmd.exe
CUSTPROF=Roaming700Live
CVSROOT=:pserver:shankarc#amcvs2.lehman.com:/home/eqcvs/cmte
CVS_RSH=/bin/ssh
FP_NO_HOST_CHECK=NO
HOME=C:\Apps\CYGWIN\home\shankarc
HOMEDRIVE=F:
HOMEPATH=\
HOSTNAME=nykpwm2035798
IDEA_PROPERTIES=C:\Documents and Settings\shankarc\idea.properties
INFOPATH=/usr/local/info:/usr/share/info:/usr/info:
JAVA_HOME=C:/Program Files/Java/jdk1.6.0_21/
JDK_HOME=C:\Program Files\Java\jdk1.6.0_21\
LOGONSERVER=\\NYKPSM00069
MANPATH=/usr/local/man:/usr/share/man:/usr/man::/usr/ssl/man
NUMBER_OF_PROCESSORS=2
OS=Windows_NT
PATH=C:\Apps\CYGWIN\usr\local\bin;C:\Apps\CYGWIN\bin;C:\Apps\CYGWIN\bin;C:\Apps\CYGWIN\usr\X11R6\bin;C:\Apps\Apache\apache-ant-1.7.0\bin;C:\Program Files\Java\jdk1.6.0_21\bin\;C:\Apps\CYGWIN\bin;C:\Program Files\VisualSVN Server\bin;C:\Program Files\Sudowin\Clients\Console;C:\Program Files\Fortify Software\Fortify 360 v2.5.0\bin
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.PSC1
PRINTER=\\NYKPSM04020\NYKLPR1301-03-03C05
PROCESSOR_ARCHITECTURE=x86
PROCESSOR_IDENTIFIER=x86 Family 6 Model 15 Stepping 6, GenuineIntel
PROCESSOR_LEVEL=6
PROCESSOR_REVISION=0f06
PROFGROUP=FONP
PROGRAMFILES=C:\Program Files
PROMPT=$P$G
PWD=/cygdrive/c/svn/CEL_v3681/gcct/cel
QHOME=c:\q
QTJAVA=C:\Program Files\Java\jre1.5.0_07\lib\ext\QTJava.zip
SESSIONNAME=Console
SHLVL=1
SITECODE=NYK
SITEIDENT=NYK
SVN_ASP_DOT_NET_HACK=1
SYSTEMDRIVE=C:
SYSTEMROOT=C:\WINNT
TEMP=C:\TEMP
TERM=cygwin
TMP=C:\TEMP
UATDATA=C:\WINNT\system32\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77
USER=shankarc
USERDNSDOMAIN=INTRANET.BARCAPINT.COM
USERDOMAIN=INTRANET
USERNAME=shankarc
USERPROFILE=C:\Documents and Settings\shankarc
WINDIR=C:\WINNT
CVS_PASSFILE=C:\Apps\CYGWIN\home\shankarc\.cvspass]
Total time: 58 seconds
How I resolve this?
I had the same issue and found that even though I was not using .cvspass I did have a build property of cvs.pass set which needed to be reset to OVERRIDE to function depending on how you set up your cvs access (though it looked similar from your post). This needed to be changed in build.properties and .build.properties. Hope this helps!