WikiData Import 2020-09-11

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Goal

replicate original blazegraph environment see https://github.com/wikimedia/wikidata-query-rdf/blob/master/docs/getting-started.md

Git clone

git clone  --recurse-submodules https://gerrit.wikimedia.org/r/wikidata/query/rdf wikidata-query-rdf
Cloning into 'wikidata-query-rdf'...
remote: Counting objects: 195, done
remote: Finding sources: 100% (161/161)
remote: Getting sizes: 100% (146/146)
remote: Compressing objects: 100% (131311/131311)
remote: Total 17957 (delta 17), reused 17930 (delta 9)
Receiving objects: 100% (17957/17957), 2.98 MiB | 3.37 MiB/s, done.
Resolving deltas: 100% (8953/8953), done.

mvn package

# Mac OS X 
export JAVA_HOME=$(/usr/libexec/java_home -v 1.8.0_191)
java -version
java version "1.8.0_191"
Java(TM) SE Runtime Environment (build 1.8.0_191-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)
cd wikidata-query-rdf
mvn -version
Apache Maven 3.6.0 (97c98ec64a1fdfee7767ce5ffb20918da4f719f3; 2018-10-24T20:41:47+02:00)
Maven home: /opt/local/share/java/maven3
Java version: 1.8.0_191, vendor: Oracle Corporation, runtime: /Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Contents/Home/jre
Default locale: de_DE, platform encoding: UTF-8
OS name: "mac os x", version: "10.13.6", arch: "x86_64", family: "mac"
mvn package

issue

see https://phabricator.wikimedia.org/T263855 

2020-09-11 13:45:39 INFO  RocksDBStateBackend:899 - Attempting to load RocksDB native library and store it under '/var/folders/2t/2g54bjr10830rv00508_y13w0000gn/T/flink-io-6ec39247-613e-410a-a83f-712f841ce3a8'
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /private/var/folders/2t/2g54bjr10830rv00508_y13w0000gn/T/flink-io-6ec39247-613e-410a-a83f-712f841ce3a8/rocksdb-lib-396871de50f5fa7595c1071b59c34498/librocksdbjni-osx.jnilib (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /private/var/folders/2t/2g54bjr10830rv00508_y13w0000gn/T/flink-io-6ec39247-613e-410a-a83f-712f841ce3a8/rocksdb-lib-396871de50f5fa7595c1071b59c34498/librocksdbjni-osx.jnilib (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Try workaround

mvn package -D skipTests

service unzip

Note the usage of. tar x instead of unzip 

cd dist/target/
tar xvfz service-0.3.50-SNAPSHOT-dist.tar.gz
cd service-0.3.50-SNAPSHOT
ls
RWStore.properties                     loadRestAPI.sh
blazegraph-service-0.3.50-SNAPSHOT.war munge.sh
createNamespace.sh                     mw-oauth-proxy-0.3.50-SNAPSHOT.war
default.properties                     mwservices.json
docs                                   prefixes-sdc.conf
forAllCategoryWikis.sh                 prefixes.conf
jetty-runner-9.4.12.v20180830.jar      runBlazegraph.sh
ldf-config.json                        runStreamingUpdater.sh
lib                                    runUpdate.sh
loadCategoryDaily.sh                   summarizeEvents.sh
loadCategoryDump.sh                    wcqs-data-reload.sh
loadData.sh

download

The download of some 275 GB took 16h in total

first try

wget https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz
--2020-09-25 17:29:02--  https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz
Resolving dumps.wikimedia.org (dumps.wikimedia.org)... 2620::861:1:208:80:154:7, 208.80.154.7
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620::861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 275358642076 (256G) [application/octet-stream]
Saving to: ‘latest-all.ttl.gz’

latest-all.ttl.gz    16%[==>                 ]  43.12G  4.88MB/s    in 2h 39m  

2020-09-25 20:23:55 (4.60 MB/s) - Read error at byte 46303657641/275358642076 (Resource temporarily unavailable, try again.). Retrying.

--2020-09-25 20:23:56--  (try: 2)  https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620::861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 275358642076 (256G), 229054984435 (213G) remaining [application/octet-stream]
Saving to: ‘latest-all.ttl.gz’

latest-all.ttl.gz   100%[+++================>] 256.45G  5.01MB/s    in 13h 14m 

2020-09-26 09:38:36 (4.58 MB/s) - ‘latest-all.ttl.gz’ saved [275358642076/275358642076]

second try

wget https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz
--2020-09-27 07:51:51--  https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz
Resolving dumps.wikimedia.org (dumps.wikimedia.org)... 2620::861:1:208:80:154:7, 208.80.154.7
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620::861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 275358642076 (256G) [application/octet-stream]
Saving to: ‘latest-all.ttl.gz’

latest-all.ttl.gz   100%[===================>] 256.45G  4.65MB/s    in 16h 4m  

2020-09-27 23:56:45 (4.54 MB/s) - ‘latest-all.ttl.gz’ saved [275358642076/275358642076]

munge

nohup ./munge.sh -f data/latest-all.ttl.gz -d data/split -l en,de &

Issue

Problem

tail -f nohup.out 
#logback.classic pattern: %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n
07:44:31.400 [org.wikidata.query.rdf.tool.rdf.AsyncRDFHandler$RDFActionsReplayer] INFO  org.wikidata.query.rdf.tool.Munge - Switching to data/split/wikidump-000000001.ttl.gz
07:44:37.263 [main] ERROR org.wikidata.query.rdf.tool.Munge - Fatal error munging RDF
org.openrdf.rio.RDFParseException: Expected '.', found 's' [line 595492]
	at org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:440)
	at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:685)
	at org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1405)
	at org.openrdf.rio.turtle.TurtleParser.verifyCharacterOrFail(TurtleParser.java:1227)
	at org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:261)
	at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:214)
	at org.wikidata.query.rdf.tool.Munge.run(Munge.java:105)
	at org.wikidata.query.rdf.tool.Munge.main(Munge.java:59)

Diagnosis

Therapy

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