Thanks for the tip! It ‘worked’ or at least got me a bit further. Now I have
some errors/warnings about the DB and a final error about not being able to
represent a timestamp. I don’t think the problem is with the data … but I can’t
be sure. I can save the data currently in the DB and start again if there is an
issue after the DB upgrade.
=== Error Log ===
10:45:20.009 [INFO] [o.a.m.l.k.KiWiLoaderHandler] - Initializing KiWiLoader for
jdbc:mysql://marmottadb.example.com:3306/marmotta?useUnicode=true&characterEncoding=UTF-8&rewriteBatchedStatements=true;
user: user, password: pass
10:45:20.064 [INFO] [o.a.m.k.c.GuavaCacheManager] - initialising Guava
in-memory caching backend ...
10:45:20.547 [INFO] [o.a.m.k.g.SnowflakeIDGenerator] - SNOWFLAKE: initialised
with datacenter ID 63
10:45:20.547 [INFO] [o.a.m.k.p.KiWiPersistence] - database key generation
strategy: Twitter Snowflake
10:45:20.671 [INFO] [o.a.m.k.p.KiWiPersistence] - upgrading existing KiWi
database from version 3 to version 4
10:45:20.687 [ERROR] [o.a.m.k.p.u.ScriptRunner] - Error executing: ALTER TABLE
nodes ADD COLUMN tzoffset int default 0 AFTER tvalue
10:45:20.688 [ERROR] [o.a.m.k.p.u.ScriptRunner] -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Duplicate column
name 'tzoffset'
10:45:20.689 [ERROR] [o.a.m.k.p.u.ScriptRunner] - Error executing: UPDATE
METADATA SET mvalue = '3' WHERE mkey = 'version'
10:45:20.689 [ERROR] [o.a.m.k.p.u.ScriptRunner] -
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table
'marmotta.METADATA' doesn't exist
10:45:20.694 [INFO] [o.a.m.l.k.KiWiLoaderHandler] - - using MySQL bulk loader
...
10:45:20.699 [INFO] [o.a.m.k.l.g.KiWiHandler] - KiWi Loader: namespaces enabled
10:45:20.699 [INFO] [o.a.m.k.l.g.KiWiHandler] - KiWiLoader: initialising RDF
handler
10:45:20.700 [INFO] [o.a.m.l.c.MarmottaLoader] - loading file uniprot.rdf ...
10:45:20.721 [INFO] [o.a.m.l.c.MarmottaLoader] - using auto-detected format
(RDF/XML)
10:45:20.731 [INFO] [o.a.m.l.c.MarmottaLoader] - no compression detected, using
plain input stream
10:45:21.382 [ERROR] [o.a.m.k.l.g.KiWiHandler] - database error, could not load
URI resource
java.sql.SQLException: Value '537389890485153792uri2http:// marmotta.example
.com:8080/marmotta/context/uniprot000000-00-00 00:00:000000000-00-00 00:00:00'
can not be represented as java.sql.Timestamp
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:996)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:935)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:924)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:870)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.ResultSetRow.getTimestampFast(ResultSetRow.java:928)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.BufferRow.getTimestampFast(BufferRow.java:555)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at
com.mysql.jdbc.ResultSetImpl.getTimestampInternal(ResultSetImpl.java:5943)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.ResultSetImpl.getTimestamp(ResultSetImpl.java:5629)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at
org.apache.marmotta.kiwi.persistence.KiWiConnection.constructNodeFromDatabase(KiWiConnection.java:1799)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.persistence.KiWiConnection.loadUriResource(KiWiConnection.java:595)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.createURI(KiWiHandler.java:439)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiBatchHandler.createURI(KiWiBatchHandler.java:175)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.convertNode(KiWiHandler.java:314)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.startRDF(KiWiHandler.java:207)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiBatchHandler.startRDF(KiWiBatchHandler.java:125)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.kiwi.KiWiLoaderHandler.startRDF(KiWiLoaderHandler.java:140)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.wrapper.LoaderHandlerWrapper.startRDF(LoaderHandlerWrapper.java:70)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.openrdf.rio.rdfxml.RDFXMLParser.startDocument(RDFXMLParser.java:491)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at org.openrdf.rio.rdfxml.SAXFilter.startDocument(SAXFilter.java:193)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startDocument(AbstractSAXParser.java:292)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startDocument(XMLDTDValidator.java:636)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.startEntity(XMLDocumentScannerImpl.java:546)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.startDocumentParsing(XMLVersionDetector.java:175)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:826)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
[na:1.8.0_11]
at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:356)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:233)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.load(MarmottaLoader.java:151)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.loadFile(MarmottaLoader.java:254)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.load(MarmottaLoader.java:125)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.main(MarmottaLoader.java:747)
[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
10:45:21.384 [WARN] [o.a.m.l.c.MarmottaLoader] - Exception Details:
java.lang.IllegalStateException: database error, could not load URI resource
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.createURI(KiWiHandler.java:456)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiBatchHandler.createURI(KiWiBatchHandler.java:175)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.convertNode(KiWiHandler.java:314)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.startRDF(KiWiHandler.java:207)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiBatchHandler.startRDF(KiWiBatchHandler.java:125)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.kiwi.KiWiLoaderHandler.startRDF(KiWiLoaderHandler.java:140)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.wrapper.LoaderHandlerWrapper.startRDF(LoaderHandlerWrapper.java:70)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.openrdf.rio.rdfxml.RDFXMLParser.startDocument(RDFXMLParser.java:491)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at org.openrdf.rio.rdfxml.SAXFilter.startDocument(SAXFilter.java:193)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startDocument(AbstractSAXParser.java:292)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startDocument(XMLDTDValidator.java:636)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.startEntity(XMLDocumentScannerImpl.java:546)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.startDocumentParsing(XMLVersionDetector.java:175)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:826)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
~[na:1.8.0_11]
at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
~[na:1.8.0_11]
at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:356)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at org.openrdf.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:233)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.load(MarmottaLoader.java:151)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.loadFile(MarmottaLoader.java:254)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.load(MarmottaLoader.java:125)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.loader.core.MarmottaLoader.main(MarmottaLoader.java:747)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
Caused by: java.sql.SQLException: Value '537389890485153792uri2http://
marmotta.example. com:8080/marmotta/context/uniprot000000-00-00
00:00:000000000-00-00 00:00:00' can not be represented as java.sql.Timestamp
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:996)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:935)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:924)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:870)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.ResultSetRow.getTimestampFast(ResultSetRow.java:928)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.BufferRow.getTimestampFast(BufferRow.java:555)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at
com.mysql.jdbc.ResultSetImpl.getTimestampInternal(ResultSetImpl.java:5943)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at com.mysql.jdbc.ResultSetImpl.getTimestamp(ResultSetImpl.java:5629)
~[mysql-connector-java-5.1.34.jar:5.1.34]
at
org.apache.marmotta.kiwi.persistence.KiWiConnection.constructNodeFromDatabase(KiWiConnection.java:1799)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.persistence.KiWiConnection.loadUriResource(KiWiConnection.java:595)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
at
org.apache.marmotta.kiwi.loader.generic.KiWiHandler.createURI(KiWiHandler.java:439)
~[marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar:3.3.0-SNAPSHOT]
... 23 common frames omitted
usage: MarmottaLoader -a <archive> | -d <dir> | -f <file> [-B <backend>]
[-b <base>] [-c <context>] -C <connect> [-D <property=value>]
[-h] [-I] [-j | -z] [-s <statistics>] [-t <type>] [-U <user>] [-W
<password>]
-a,--archive <archive> input archives(s) to load (zip, tar.gz)
-B,--backend <backend> backend to use (kiwi)
-b,--base <base> base URI to use for resolving relative
URIs
-c,--context <context> URI of a context to add the statement to
-C,--connect <connect> JDBC database URL used by KiWi to connect
to the database
-d,--dir <dir> input directories(s) to load
-D <property=value> set configuration property to value
-f,--file <file> input file(s) to load
-h,--help print this help
-I,--drop-indexes drop KiWi database indexes before
importing
-j,--bzip2 input is bzip2 compressed
-s,--statistics <statistics> collect statistics and write a graph into
the file given
-t,--type <type> input format to use for parsing (MIME
type) in case auto-guessing does not work
-U,--user <user> database user used by KiWi to connect to
the database
-W,--password <password> database password used by KiWi to connect
to the database
-z,--gzip input is gzip compressed
Thanks again,
-J
Joshua Dunham
Scientific Computing | Vertex
E: joshua_dun...@vrtx.com
P: 617-229-5157
W: http://www.vrtx.com
L: http://linkedin.com/in/joshuadunham
S: joshua.dunham
> On Nov 27, 2014, at 7:15 AM, Jakob Frank <ja...@apache.org> wrote:
>
> In Java, you cannot combine the -cp and the -jar option. So to have
> the mysql connector available, you need to use the following command:
>
> java -cp mysql-connector-java.jar:marmotta-loader-kiwi.jar
> org.apache.marmotta.loader.core.MarmottaLoader -f
> /data/file-to-import.rdf -c
> "https://urldefense.proofpoint.com/v2/url?u=http-3A__example.com-3A8080_marmotta_context_thiscontext&d=AAIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=EjhiT90xylIcLIkX_L1-DfhHQmiIg5hWdNx9dZyVLiA&m=Xh_0HNz776GIS6qOq9QLyNU5AXj4cTR8QI8D11fU3u4&s=2e5xV_2M7rHkYoAqvFfZVKiBDPMK-81ssph21NYEhk8&e=
> " -C
> "jdbc:mysql://mysqldb.example.com:3306/marmotta?useUnicode=true&characterEncoding=UTF-8&rewriteBatchedStatements=true"
> -U username -W password
>
> (the path separator is OS specific, on windows use ';' instead of ':')
>
> Best,
> Jakob
>
>
> On 24 November 2014 at 23:41, Joshua Dunham <joshua_dun...@vrtx.com> wrote:
>> Hi Marmotta Users,
>>
>> I’ve edited the marmotta-loader-kiwi pom to include mysql and then mvn
>> install and it builds just fine but it can’t get past an error on not being
>> able to load the mysql-connector-java.jar file. I’ve tried adding the folder
>> containing the jar to $CLASSPATH and/or adding the jar itself to the
>> $CLASSPATH and calling it by,
>>
>> java -cp $CLASSPATH -jar marmotta-loader-kiwi-3.3.0-SNAPSHOT.jar -f
>> /data/file-to-import.rdf -c
>> "https://urldefense.proofpoint.com/v2/url?u=http-3A__example.com-3A8080_marmotta_context_thiscontext&d=AAIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=EjhiT90xylIcLIkX_L1-DfhHQmiIg5hWdNx9dZyVLiA&m=Xh_0HNz776GIS6qOq9QLyNU5AXj4cTR8QI8D11fU3u4&s=2e5xV_2M7rHkYoAqvFfZVKiBDPMK-81ssph21NYEhk8&e=
>> " -C
>> "jdbc:mysql://mysqldb.example.com:3306/marmotta?useUnicode=true&characterEncoding=UTF-8&rewriteBatchedStatements=true"
>> -U username -W password
>>
>> but it still complains on not being able to find it. I’ve also used the jar
>> at maven repos and the oracle binary one without luck.
>>
>> Does anyone have tips they could share?
>>
>> -J
>>
>> Joshua Dunham
>> Exploratory App Development | Vertex
>>
>> This email message and any attachments are confidential and intended for use
>> by the addressee(s) only. If you are not the intended recipient, please
>> notify me immediately by replying to this message, and destroy all copies of
>> this message and any attachments. Thank you.
This email message and any attachments are confidential and intended for use by
the addressee(s) only. If you are not the intended recipient, please notify me
immediately by replying to this message, and destroy all copies of this message
and any attachments. Thank you.
