Hi Rajan, > *05:11:41,851 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - Indexed 0 items in 2059467sec (Infinityms/item):
'You have not indexed a single entity. So something in your indexing configuration is wrong. Most likely you are not correctly building the URIs of the entities from the incoming_links.txt file. Can you provide me an example line of the 'incoming_links.txt' file and the contents of the 'iditerator.properties' file. Those specify how Entity URIs are built. Short answers to the other questions On Fri, May 22, 2015 at 2:10 PM, Rajan Shah <raja...@gmail.com> wrote: > it ran for almost 3 days and generated index. Thats good. It means you do have now the Freebase dump in your Jena TDB triple store. You will not need to repeat this (until you want to use a newer dump. On the next call to the indexing tool it will immediately start with the indexing step. > > Couple questions come to mind: > > a. Is there any particular log/error file the process generates besides > printing out on stdout/stderr? The indexer writes a zip archive with the IDs of all the indexed entities. Its in the indexing/destination folder. > b. Is it a must-have to have stanbol full launcher running all the time > while indexing is going on? No Stanbol instance is needed by the indexing process. > c. Is it possible that, if the machine is not connected to internet for > couple minutes could cause some issues? No Internet connectivity is needed during indexing. Only if you want to use the namespace prefix mappings of prefix.cc you need to have internet connectivity when starting the indexing tool. best Rupert > > I would really appreciate, if you can shed some light on "what could be > wrong" or "potential approach to nail down this issue"? If you need, I am > happy to share any additional logs/properties. > > With best regards, > Rajan > > *1. Configuration changes* > > a. set ns-prefix-state=false* > [within /indexing/config/iditerator.properties]* > b. add empty space mapping to http://rdf.freebase.com/ns/* > [within namespaceprefix.mappings]* > c. enable bunch of properties within mappings.txt such as following > > fb:music.artist.genre > fb:music.artist.label > fb:music.artist.album > > *2. Contents of indexing/dist directory* > > -rw-r--r-- 108899 May 22 05:11 freebase.solrindex.zip > -rw-r--r-- 3457 May 22 05:11 > org.apache.stanbol.data.site.freebase-1.0.0.jar > > *3. Contents of /tmp/freebase/indexing/resources/imported directory* > > -rw-r--r-- 1 31026810858 May 20 07:32 freebase.nt.gz > > *4. Contents of /tmp/freebase/indexing/resources directory* > > -rw-r--r-- 1 1206745360 May 19 09:38 incoming_links.txt > > *5. The indexer log* > > *04:31:57,236 [Thread-3] INFO jenatdb.RdfResourceImporter - Add: > 570,850,000 triples (Batch: 2,604 / Avg: 3,621)* > *04:32:00,727 [Thread-3] INFO jenatdb.RdfResourceImporter - Filtered: > 2429800000 triples (80.97554853864854%)* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Finish > triples data phase* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - ** Data: > 570,859,352 triples loaded in 157,619.39 seconds [Rate: 3,621.76 per > second]* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Start > triples index phase* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Finish > triples index phase* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Finish > triples load* > *04:32:01,157 [Thread-3] INFO jenatdb.RdfResourceImporter - ** Completed: > 570,859,352 triples loaded in 157,619.39 seconds [Rate: 3,621.76 per > second]* > 04:32:56,880 [Thread-3] INFO source.ResourceLoader - ... moving > imported file freebase.nt.gz to imported/freebase.nt.gz > 04:32:56,883 [Thread-3] INFO source.ResourceLoader - - completed in > 157675 seconds > 04:32:56,883 [Thread-3] INFO source.ResourceLoader - > loading > '/private/tmp/freebase/indexing/resources/rdfdata/fixit.sh' ... > 04:32:56,944 [Thread-3] WARN jenatdb.RdfResourceImporter - ignore File {} > because of unknown extension > 04:32:56,958 [Thread-3] INFO source.ResourceLoader - - completed in 0 > seconds > 04:32:56,958 [Thread-3] INFO source.ResourceLoader - ... 2 files imported > in 157675 seconds > 04:32:56,958 [Thread-3] INFO source.ResourceLoader - Loding 0 File ... > 04:32:56,958 [Thread-3] INFO source.ResourceLoader - ... 0 files imported > in 0 seconds > 04:32:56,971 [main] INFO impl.IndexerImpl - ... delete existing > IndexedEntityId file > /private/tmp/freebase/indexing/destination/indexed-entities-ids.zip > 04:32:56,982 [main] INFO impl.IndexerImpl - Initialisation completed > 04:32:56,982 [main] INFO impl.IndexerImpl - ... initialisation completed > 04:32:56,982 [main] INFO impl.IndexerImpl - start indexing ... > 04:32:56,982 [main] INFO impl.IndexerImpl - Indexing started ... > > > > 04:45:48,075 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'nsogi' valid , namespace ' > http://prefix.cc/nsogi:' invalid -> mapping ignored! > 04:45:48,076 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'category' valid , namespace ' > http://dbpedia.org/resource/Category:' invalid -> mapping ignored! > 04:45:48,077 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'chebi' valid , namespace ' > http://bio2rdf.org/chebi:' invalid -> mapping ignored! > 04:45:48,077 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'hgnc' valid , namespace ' > http://bio2rdf.org/hgnc:' invalid -> mapping ignored! > 04:45:48,077 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'dbptmpl' valid , namespace ' > http://dbpedia.org/resource/Template:' invalid -> mapping ignored! > 04:45:48,077 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'dbc' valid , namespace ' > http://dbpedia.org/resource/Category:' invalid -> mapping ignored! > 04:45:48,078 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'pubmed' valid , namespace ' > http://bio2rdf.org/pubmed_vocabulary:' invalid -> mapping ignored! > 04:45:48,078 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'dbt' valid , namespace ' > http://dbpedia.org/resource/Template:' invalid -> mapping ignored! > 04:45:48,078 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'dbrc' valid , namespace ' > http://dbpedia.org/resource/Category:' invalid -> mapping ignored! > 04:45:48,078 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'call' valid , namespace ' > http://webofcode.org/wfn/call:' invalid -> mapping ignored! > 04:45:48,078 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'dbcat' valid , namespace ' > http://dbpedia.org/resource/Category:' invalid -> mapping ignored! > 04:45:48,084 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'affymetrix' valid , namespace ' > http://bio2rdf.org/affymetrix_vocabulary:' invalid -> mapping ignored! > 04:45:48,084 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'bgcat' valid , namespace ' > http://bg.dbpedia.org/resource/Категория:' invalid -> mapping ignored! > 04:45:48,084 [pool-1-thread-1] WARN impl.NamespacePrefixProviderImpl - > Invalid Namespace Mapping: prefix 'condition' valid , namespace ' > http://www.kinjal.com/condition:' invalid -> mapping ignored! > 05:11:41,836 [Indexing: Entity Source Reader Deamon] INFO impl.IndexerImpl > - Indexing: Entity Source Reader Deamon completed (sequence=0) ... > 05:11:41,838 [Indexing: Entity Source Reader Deamon] INFO impl.IndexerImpl > - > current sequence : 0 > 05:11:41,838 [Indexing: Entity Source Reader Deamon] INFO impl.IndexerImpl > - > new sequence: 1 > 05:11:41,838 [Indexing: Entity Source Reader Deamon] INFO impl.IndexerImpl > - Send end-of-queue to Deamons with Sequence 1 > 05:11:41,839 [Indexing: Entity Processor Deamon] INFO impl.IndexerImpl - > Indexing: Entity Processor Deamon completed (sequence=1) ... > 05:11:41,839 [Indexing: Entity Processor Deamon] INFO impl.IndexerImpl - > > current sequence : 1 > 05:11:41,839 [Indexing: Entity Processor Deamon] INFO impl.IndexerImpl - > > new sequence: 2 > 05:11:41,839 [Indexing: Entity Processor Deamon] INFO impl.IndexerImpl - > Send end-of-queue to Deamons with Sequence 2 > 05:11:41,839 [Indexing: Entity Perstisting Deamon] INFO impl.IndexerImpl - > Indexing: Entity Perstisting Deamon completed (sequence=2) ... > 05:11:41,839 [Indexing: Entity Perstisting Deamon] INFO impl.IndexerImpl - > > current sequence : 2 > 05:11:41,839 [Indexing: Entity Perstisting Deamon] INFO impl.IndexerImpl - > > new sequence: 3 > 05:11:41,839 [Indexing: Entity Perstisting Deamon] INFO impl.IndexerImpl - > Send end-of-queue to Deamons with Sequence 3 > *05:11:41,851 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - Indexed 0 items in 2059467sec (Infinityms/item): > processing: -1.000ms/item | queue: -1.000ms* > 05:11:41,851 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - - source : -1.000ms/item > 05:11:41,851 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - - processing: -1.000ms/item > 05:11:41,851 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - - store : -1.000ms/item > 05:11:41,906 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - Indexing: Finished Entity Logger Deamon completed > (sequence=3) ... > 05:11:41,906 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - > current sequence : 3 > 05:11:41,906 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - > new sequence: 4 > 05:11:41,906 [Indexing: Finished Entity Logger Deamon] INFO > impl.IndexerImpl - Send end-of-queue to Deamons with Sequence 4 > 05:11:41,910 [Indexer: Entity Error Logging Daemon] INFO impl.IndexerImpl > - Indexer: Entity Error Logging Daemon completed (sequence=4) ... > 05:11:41,910 [Indexer: Entity Error Logging Daemon] INFO impl.IndexerImpl > - > current sequence : 4 > 05:11:41,910 [main] INFO impl.IndexerImpl - ... indexing completed > 05:11:41,910 [main] INFO impl.IndexerImpl - start post-processing ... > 05:11:41,910 [main] INFO impl.IndexerImpl - PostProcessing started ... > 05:11:41,910 [main] INFO impl.IndexerImpl - ... post-processing finished > ... > 05:11:41,911 [main] INFO impl.IndexerImpl - start finalisation.... > > > > On Wed, May 20, 2015 at 8:19 AM, Rupert Westenthaler < > rupert.westentha...@gmail.com> wrote: > >> On Tue, May 19, 2015 at 7:04 PM, Rajan Shah <raja...@gmail.com> wrote: >> > Hi Rupert and Antonio, >> > >> > Thanks a lot for the reply. >> > >> > I start to follow Rupert's suggestion, however it failed again at >> > >> > 10:56:34,152 [Thread-3] ERROR jena.riot - [line: 8722294, col: 88] >> illegal >> > escape sequence value: $ (0x24) -- Is there anyway it can be resolved for >> > the entire file? >> > >> >> The indexing tool uses Apache Jena. An those are Jena parsing errors. >> So the Jena Mailing lists would be the better place to look for >> answers. >> This specific issue looks like an invalid URI that is not fixed by the >> fixit script. >> >> >> > I requested an access to latest BaseKB bucket, as it doesn't seem to be >> > open. >> > >> > s3cmd ls s3://basekb-now/2015-04-15-18-54/ >> > --add-header="x-amz-request-payer: requester" >> > ERROR: Access to bucket 'basekb-now' was denied >> > >> > >> > *Couple additional questions:* >> > >> > *1. indexing enhancements:* >> > What settings/properties one can tweak to gain most out of the indexing. >> > >> >> In general you do only want information as needed for your application >> case in the index. >> For EntityLinking only labels and type are required. >> Additional properties will only be used for dereferencing Entities. So >> this will depend on your application needs (your dereferencing >> configuration). >> >> In general I try to exclude as much information as possible form the >> index to keep the size of the Solr Index as small as possible. >> >> > a. for ex. domain specific such as Pharmaceutical, Law etc... within >> > freebase >> > b. potential optimizations to speed up the overall indexing >> >> Most of the time will be needed to load the Freebase dump into Jena >> TDB. Even with an SSD equipped Server this will take several days. >> Assigning more RAM will speed up this process as Jena TDB can cache >> more things in RAM. >> >> Usually it is a good Idea to cancel the indexing process after the >> importing of the RDF data has finished (and the indexing of the >> Entities has started). This is because after indexing all the RAM will >> be used by Jena TDB for caching stuff that is no longer needed in the >> read-only operations during indexing. So a fresh start can speed up >> the indexing part of the process. >> >> Also have a look at the Freebase Indexing Tool Readme >> >> > >> > *2. demo:* >> > I see that, in recent github commit(s) the eHealth and other demos have >> > been commented out. How can I get demo source code and other components >> for >> > these demos. I prefer to build it myself to see the power of stanbol. >> > >> >> The eHealth demo is still in the 0.12 branch [1]. This is fully >> compatible to the trunk version. >> >> > *3. custom vocabulary:* >> > Suppose, I have custom vocabulary in CSV format. Is there a preferred way >> > to upload it to Stanbol and have it recognize my entities? >> >> Google Refine[2] with the RDF extension [3]. You can also try to use >> the (newer) Open Refine [4] with the RDF Refine 0.9.0 Alpha version >> but AFAIK this combination is not so stable and might not work at all. >> >> * Google Refine allows you to import your CSV file. >> * Clean it up (if necessary) >> * The RDF extension allows you to map your CSV data to RDF >> * based on this mapping you can save your data as RDF >> * after that you can import the RDF data to Apache Stanbol >> >> hope this helps >> best >> Rupert >> >> > >> > Thanks in advance, >> > Rajan >> > >> >> >> >> [1] >> http://svn.apache.org/repos/asf/stanbol/branches/release-0.12/demos/ehealth/ >> [2] https://code.google.com/p/google-refine/ >> [3] http://refine.deri.ie/ >> [4] http://openrefine.org/ >> >> > On Tue, May 19, 2015 at 3:01 AM, Rupert Westenthaler < >> > rupert.westentha...@gmail.com> wrote: >> > >> >> Hi Rajan, >> >> >> >> I think this is because you named you file >> >> "freebase-rdf-latest-fixed.gz". Jena assumes RDF/XML if the RDF format >> >> is not provided by the file extension. Renaming the file to >> >> "freebase-rdf-latest-fixed.nt.gz" should fix this issue. >> >> >> >> The suggestion of Antonio to use BaseKB is also a valid option. >> >> >> >> best >> >> Rupert >> >> >> >> On Tue, May 19, 2015 at 8:32 AM, Antonio David Perez Morales >> >> <ape...@zaizi.com> wrote: >> >> > Hi Rajan >> >> > >> >> > Freebase dump contains some things that does not fit very well with >> the >> >> > indexer. >> >> > I advise you to use the dump provided by BaseKB (http://basekb.com) >> >> which >> >> > is a curated Freebase dump. >> >> > I did not have any problem indexing it using that dump. >> >> > >> >> > Regards >> >> > >> >> > On Mon, May 18, 2015 at 8:48 PM, Rajan Shah <raja...@gmail.com> >> wrote: >> >> > >> >> >> Hi, >> >> >> >> >> >> I am working on indexing Freebase data within EntityHub and observed >> >> >> following issue: >> >> >> >> >> >> 01:06:01,547 [Thread-3] ERROR jena.riot - [line: 1, col: 7 ] Element >> or >> >> >> attribute do not match QName production: QName::=(NCName':')?NCName. >> >> >> >> >> >> I would appreciate any help pertaining to this issue. >> >> >> >> >> >> Thanks, >> >> >> Rajan >> >> >> >> >> >> *Steps followed:* >> >> >> >> >> >> *1. Initialization: * >> >> >> java -jar >> >> org.apache.stanbol.entityhub.indexing.freebase-1.0.0-SNAPSHOT.jar >> >> >> init >> >> >> >> >> >> *2. Download the data:* >> >> >> Download data and copy it to >> >> https://developers.google.com/freebase/data >> >> >> >> >> >> *3. Performed execution of fbrankings-uri.sh* >> >> >> It generated incoming_links.txt under resources directory as follows >> >> >> >> >> >> 10888430 m.0kpv11 >> >> >> 3741261 m.019h >> >> >> 2667858 m.0775xx5 >> >> >> 2667804 m.0775xvm >> >> >> 1875352 m.01xryvm >> >> >> 1739262 m.05zppz >> >> >> 1369590 m.01xrzlb >> >> >> >> >> >> *4. Performed execution of fixit script* >> >> >> >> >> >> gunzip -c ${FB_DUMP} | fixit | gzip > ${FB_DUMP_fixed} >> >> >> >> >> >> *5. Rename the fixed file to freebase.rdf.gz and copy it * >> >> >> to indexing/resources/rdfdata >> >> >> >> >> >> *6. config/iditer.properties file has following setting* >> >> >> #id-namespace=http://freebase.com/ >> >> >> ns-prefix-state=false >> >> >> >> >> >> *7. Performed run of following command:* >> >> >> java -jar -Xmx32g >> >> >> org.apache.stanbol.entityhub.indexing.freebase-1.0.0-SNAPSHOT.jar >> index >> >> >> >> >> >> The error dump on stdout is as follows: >> >> >> >> >> >> 01:37:32,884 [Thread-0] INFO solryard.SolrYardIndexingDestination - >> >> ... >> >> >> copy Solr Configuration form >> >> /private/tmp/freebase/indexing/config/freebase >> >> >> to >> /private/tmp/freebase/indexing/destination/indexes/default/freebase >> >> >> 01:37:32,895 [Thread-3] INFO jenatdb.RdfResourceImporter - - >> bulk >> >> >> loading File freebase.rdf.gz using Format Lang:RDF/XML >> >> >> 01:37:32,896 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Start >> >> >> triples data phase >> >> >> 01:37:32,896 [Thread-3] INFO jenatdb.RdfResourceImporter - ** Load >> >> empty >> >> >> triples table >> >> >> *01:37:32,948 [Thread-3] ERROR jena.riot - [line: 1, col: 7 ] >> Element or >> >> >> attribute do not match QName production: QName::=(NCName':')?NCName.* >> >> >> 01:37:32,948 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Finish >> >> >> triples data phase >> >> >> 01:37:32,948 [Thread-3] INFO jenatdb.RdfResourceImporter - -- Finish >> >> >> triples load >> >> >> 01:37:32,960 [Thread-3] INFO source.ResourceLoader - Ignore Error >> for >> >> File >> >> >> /private/tmp/freebase/indexing/resources/rdfdata/freebase.rdf.gz and >> >> >> continue >> >> >> >> >> >> Additional Reference Point: >> >> >> >> >> >> *Original Freebase dump size:* 31025015397 May 14 18:10 >> >> >> freebase-rdf-latest.gz >> >> >> *Fixed Freebase dump size:* 31026818367 May 15 12:45 >> >> >> freebase-rdf-latest-fixed.gz >> >> >> *Incoming Links size: *1206745360 May 17 00:42 incoming_links.txt >> >> >> >> >> > >> >> > -- >> >> > >> >> > ------------------------------ >> >> > This message should be regarded as confidential. If you have received >> >> this >> >> > email in error please notify the sender and destroy it immediately. >> >> > Statements of intent shall only become binding when confirmed in hard >> >> copy >> >> > by an authorised signatory. >> >> > >> >> > Zaizi Ltd is registered in England and Wales with the registration >> number >> >> > 6440931. The Registered Office is Brook House, 229 Shepherds Bush >> Road, >> >> > London W6 7AN. >> >> >> >> >> >> >> >> -- >> >> | Rupert Westenthaler rupert.westentha...@gmail.com >> >> | Bodenlehenstraße 11 ++43-699-11108907 >> >> | A-5500 Bischofshofen >> >> | REDLINK.CO >> >> >> .......................................................................... >> >> | http://redlink.co/ >> >> >> >> >> >> -- >> | Rupert Westenthaler rupert.westentha...@gmail.com >> | Bodenlehenstraße 11 ++43-699-11108907 >> | A-5500 Bischofshofen >> | REDLINK.CO >> .......................................................................... >> | http://redlink.co/ >> -- | Rupert Westenthaler rupert.westentha...@gmail.com | Bodenlehenstraße 11 ++43-699-11108907 | A-5500 Bischofshofen | REDLINK.CO .......................................................................... | http://redlink.co/
