It seems I made a mess with absolute and relative paths all together. So I created a minimal setup for testing: (I include the file-contents at the bottom)
$ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0 $ export PATH=$PATH:$JENA_HOME/bin $ tdb2.tdbloader --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl 13:50:54 INFO loader :: Loader = LoaderPhased 13:50:54 INFO loader :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl: 13 mm-loc-mini.ttl 0.06s (Avg: 232) 13:50:54 INFO loader :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50 mm-rdf.ttl 0.01s (Avg: 6,250) 13:50:55 INFO loader :: Finish - index SPO 13:50:55 INFO loader :: Start replay index SPO 13:50:55 INFO loader :: Index set: SPO => SPO->POS, SPO->OSP 13:50:55 INFO loader :: Index set: SPO => SPO->POS, SPO->OSP [63 items, 0.0 seconds] 13:50:55 INFO loader :: Finish - index POS 13:50:55 INFO loader :: Finish - index OSP $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/* jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory] org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417) at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159) at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348) at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251) at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141) at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64) at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104) at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72) at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50) at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) at jena.spatialindexer.exec(spatialindexer.java:110) at jena.cmd.CmdMain.mainMethod(CmdMain.java:93) at jena.cmd.CmdMain.mainRun(CmdMain.java:58) at jena.cmd.CmdMain.mainRun(CmdMain.java:45) at jena.spatialindexer.main(spatialindexer.java:53) I can get rid of the SLF4J warnings: $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417) at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159) at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348) at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251) at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150) at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141) at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64) at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104) at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72) at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50) at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) at jena.spatialindexer.exec(spatialindexer.java:110) at jena.cmd.CmdMain.mainMethod(CmdMain.java:93) at jena.cmd.CmdMain.mainRun(CmdMain.java:58) at jena.cmd.CmdMain.mainRun(CmdMain.java:45) at jena.spatialindexer.main(spatialindexer.java:53) There is no other java instance running at the time when I run those commands. All paths are fully qualified and double checked. The destination directory and the Lucene directory were cleared just before. The server does start and serve the data without errors or warnings in the log, but spatial queries do not work. Does anyone see a reason for the TransactionException? Thanks and best regards Markus Attachments: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix dcterms: <http://purl.org/dc/terms/> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> @prefix mm: <http://rdf.meteomatics.com/mm/> . <http://rdf.meteomatics.com/mm/> dcterms:publisher <http://api.meteomatics.com/Imprint.html> ; dcterms:title "Meteomatics RDF Vocabulary"@en . mm:location a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "location" ; dcterms:description "Location of a measurement"@en . mm:elevation a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "elevation" ; dcterms:description "Elevation of a location"@en . mm:validdate a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "validdate" ; dcterms:description "Temporal information describing when a Measurement is/was valid"@en . mm:value a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "value" ; dcterms:description "The (observed or predicted) value of a Measurement"@en . mm:parameter a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "parameter" ; dcterms:description "what was measured"@en . mm:station_name a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "station_name" ; dcterms:description "Name of a station"@en . mm:abbreviation a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "abbreviation" ; dcterms:description "Abbreviation of a station name"@en . mm:didok_id a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "didok_id" ; dcterms:description "didok id of a station"@en . mm:unit_symbol a rdf:Property ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "unit symbol" ; dcterms:description "unit symbol of a parameter"@en . mm:Measurement a rdf:Class ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "Measurement" ; dcterms:description "Measurement of a specific weather parameter at specific location at a specific date (both future or past)" . mm:Location a rdf:Class ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "Location" ; dcterms:description "A Point on the globe where we observe weather"@en . mm:Parameter a rdf:Class ; rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ; rdfs:label "Parameter" ; dcterms:description "A parameter describing an observable aspect of the weather"@en . /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> . @prefix geosparql: <http://www.opengis.net/ont/geosparql#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix dcterms: <http://purl.org/dc/terms/> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix mm: <http://rdf.meteomatics.com/mm/> . @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> . @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> . mm-locations:8500015 a mm:Location ; a geosparql:Geometry ; mm:didok_id 8500015 ; geo:lat 47.54259 ; geo:long 7.61574 ; mm:elevation 273 . mm-locations:8504238 a mm:Location ; a geosparql:Geometry ; geosparql:asWKT "POINT(6.86466645231 47.0840196485)"^^geosparql:wktLiteral ; mm:didok_id 8504238 ; geo:lat 47.08402 ; geo:long 6.86467 ; mm:elevation 1086 . /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl @prefix : <http://base/#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix tdb2: <http://jena.apache.org/2016/tdb#> . @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix fuseki: <http://jena.apache.org/fuseki#> . @prefix spatial: <http://jena.apache.org/spatial#> . @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> . @prefix geosparql: <http://www.opengis.net/ont/geosparql#> . # Spatial #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" . #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset . #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex . :service_tdb_all a fuseki:Service ; rdfs:label "TDB2 mm" ; fuseki:dataset :spatial_dataset ; fuseki:name "mm" ; fuseki:serviceQuery "query" , "sparql" ; fuseki:serviceReadGraphStore "get" ; fuseki:serviceReadWriteGraphStore "data" ; fuseki:serviceUpdate "update" ; fuseki:serviceUpload "upload" . :spatial_dataset a spatial:SpatialDataset ; spatial:dataset :tdb_dataset_readwrite ; spatial:index <#indexLucene> ; . <#indexLucene> a spatial:SpatialIndexLucene ; spatial:directory <file:Lucene> ; #spatial:directory "mem" ; spatial:definition <#definition> ; . <#definition> a spatial:EntityDefinition ; spatial:entityField "uri" ; spatial:geoField "geo" ; # custom geo predicates for 1) Latitude/Longitude Format spatial:hasSpatialPredicatePairs ( [ spatial:latitude geo:lat ; spatial:longitude geo:long ] ) ; # custom geo predicates for 2) Well Known Text (WKT) Literal spatial:hasWKTPredicates (geosparql:asWKT) ; #spatial:spatialContextFactory # "com.spatial4j.core.context.jts.JtsSpatialContextFactory" # "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory" . :tdb_dataset_readwrite a tdb2:DatasetTDB2 ; tdb2:location "/srv/linked_data_store/fuseki-server/run/databases/mm" . > Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>: > > I think you might have misunderstood the use of $JENA_HOME, or perhaps the > Java classpath. $JENA_HOME, which should generally be an absolute filepath, > allows the Jena scripts to find their libraries at runtime. Internally, the > scripts use $JENA_HOME to set up the classpaths with which to start running > Java code. But in this case, you're not using the scripts. You're calling a > Java class directly, which means you have to give it all the libraries > directly, using the classpath flag directly. For example, your second attempt: > > $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer > --desc=fuseki-server/run/configuration/mm.ttl > Error: Could not find or load main class > apache-jena-3.8.0.lib.commons-cli-1.4.jar > > may have failed because whatever directory you are in probably doesn't happen > to have a Jena distribution in it called "apache-jena-3.8.0". Perhaps try: > > java -cp $JENA_HOME/lib/* jena.spatialindexer > --desc=fuseki-server/run/configuration/mm.ttl > > Your first example looks like it might be misusing the -cp flag [1]. You > probably don't want the *.jar, just *, like > > java -cp lib/* jena.spatialindexer > --desc=../fuseki-server/run/configuration/mm.ttl > > especially if you happen to be using Windows. [2] That might not be the > entire story, but you can at least try those invocations and see if you get > anything different/better. > > ajs6f > > [1] > https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762 > > <https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762> > [2] > https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath > > <https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath> > > >> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneum...@meteomatics.com >> <mailto:mneum...@meteomatics.com>> wrote: >> >> Ok, that's exactly what I did here: >> $ java -cp lib/*.jar jena.spatialindexer >> --desc=../fuseki-server/run/configuration/mm.ttl >> Error: Could not find or load main class lib.commons-cli-1.4.jar >> >> Or from outside JENA_HOME: >> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer >> --desc=fuseki-server/run/configuration/mm.ttl >> Error: Could not find or load main class >> apache-jena-3.8.0.lib.commons-cli-1.4.jar >> >> Or did I missunderstand something? >> >>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <marco.neum...@gmail.com>: >>> >>> don't worry it's a common problem and frequent source of confusion not only >>> with jena but java projects. try to simply inlcude all the jars. >>> >>> I presume you run this on a linux box with OpenJDK 8. correct? >>> >>> now once you have set up jena just add the following >>> {replace_with_your_path}/apache-jena-3.8.0/lib/* >>> >>> >>> >>> >>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneum...@meteomatics.com >>> <mailto:mneum...@meteomatics.com> <mailto:mneum...@meteomatics.com >>> <mailto:mneum...@meteomatics.com>>> >>> wrote: >>> >>>> This is embarrassing but I don't get it. >>>> >>>> I've configured $JENA_HOME and adjusted the PATH. >>>> >>>> Now what classpath should I include when invoking the indexer? >>>> What I've tried so far: >>>> >>>> $ cd $JENA_HOME >>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer >>>> --desc=../fuseki-server/run/configuration/mm.ttl >>>> Error: Could not find or load main class jena.spatialindexer >>>> $ java -cp lib/*.jar jena.spatialindexer >>>> --desc=../fuseki-server/run/configuration/mm.ttl >>>> Error: Could not find or load main class lib.commons-cli-1.4.jar >>>> >>>> Thanks for your patience >>>> >>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <marco.neum...@gmail.com >>>>> <mailto:marco.neum...@gmail.com>>: >>>>> >>>>> yes correct, this looks good. now include the classpath during invocation >>>>> of the spatialindexer >>>>> >>>>> in addition it's always a good idea to properly configure jena along your >>>>> java runtime environment settings to avoid jdk / lib conflicts during >>>>> execution. >>>>> >>>>> https://jena.apache.org/documentation/tools/index.html >>>>> <https://jena.apache.org/documentation/tools/index.html> < >>>> https://jena.apache.org/documentation/tools/index.html >>>> <https://jena.apache.org/documentation/tools/index.html> >>>> <https://jena.apache.org/documentation/tools/index.html >>>> <https://jena.apache.org/documentation/tools/index.html>>> >>>>> >>>>> >>>>> >>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann < >>>> mneum...@meteomatics.com <mailto:mneum...@meteomatics.com> >>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com>> >>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com> >>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com>>>> >>>>> wrote: >>>>> >>>>>> 1.: what do you mean by indexer? >>>>>> Probably my biggest problem is, that I have no clue how to find out, >>>> where >>>>>> the jena.spatialindexer could be located except for asking here. >>>>>> >>>>>> Here is the content of the apache jena I downloaded: >>>>>> $ ls -lh ../apache-jena-3.8.0/lib >>>>>> total 17M >>>>>> -rw-r--r-- 1 process process 162K Oct 26 2017 collection-0.7.jar >>>>>> -rw-r--r-- 1 process process 53K Oct 26 2017 commons-cli-1.4.jar >>>>>> -rw-r--r-- 1 process process 328K Mar 5 2018 commons-codec-1.11.jar >>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar >>>>>> -rw-r--r-- 1 process process 41K Mar 5 2018 commons-csv-1.5.jar >>>>>> -rw-r--r-- 1 process process 210K Mar 5 2018 commons-io-2.6.jar >>>>>> -rw-r--r-- 1 process process 425K Oct 26 2017 commons-lang3-3.4.jar >>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar >>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01 >>>> httpclient-cache-4.5.5.jar >>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar >>>>>> -rw-r--r-- 1 process process 65K Oct 26 2017 >>>>>> jackson-annotations-2.9.0.jar >>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar >>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01 >>>> jackson-databind-2.9.5.jar >>>>>> -rw-r--r-- 1 process process 17K Oct 26 2017 jcl-over-slf4j-1.7.25.jar >>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 21K Jun 25 11:05 jena-dboe-index-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 74K Jun 25 11:05 >>>>>> jena-dboe-transaction-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 95K Jun 25 11:06 >>>>>> jena-dboe-trans-data-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 49K Jun 25 11:04 >>>> jena-rdfconnection-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01 >>>> jena-shaded-guava-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar >>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar >>>>>> -rw-r--r-- 1 process process 232K Mar 5 2018 libthrift-0.10.0.jar >>>>>> -rw-r--r-- 1 process process 479K Oct 26 2017 log4j-1.2.17.jar >>>>>> -rw-r--r-- 1 process process 41K Oct 26 2017 slf4j-api-1.7.25.jar >>>>>> -rw-r--r-- 1 process process 12K Oct 26 2017 slf4j-log4j12-1.7.25.jar >>>>>> >>>>>> 2.: Turns out, I don't need the jts. after commenting out the affected >>>>>> lines, the server still runs fine. (But still without spatial index) >>>>>> >>>>>> Best Markus >>>>>> >>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neum...@gmail.com >>>>>>> <mailto:marco.neum...@gmail.com> <mailto:marco.neum...@gmail.com >>>>>>> <mailto:marco.neum...@gmail.com>> >>>>> : >>>>>>> >>>>>>> Ok let's take a look at this. >>>>>>> >>>>>>> 1. please include in the indexer in the classpath. It's part of the >>>>>> current >>>>>>> jena distribution. >>>>>>> >>>>>>> 2. do you need jts? it's a package that allows you to index multi point >>>>>>> geometries. here a sample query would be helpful. If single point >>>>>>> geometries are indexed and used in conjunction with MBR range queries. >>>>>>> there is no need for jts. >>>>>>> >>>>>>> >>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann < >>>> mneum...@meteomatics.com <mailto:mneum...@meteomatics.com> >>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com>> >>>>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com> >>>>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com>> >>>>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com> >>>>>> <mailto:mneum...@meteomatics.com <mailto:mneum...@meteomatics.com>>>>> >>>>>>> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> (sorry for the long post) >>>>>>>> >>>>>>>> I've been struggling with the spatial index for a while now. >>>>>>>> I've read >>>>>> https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html>> < >>>> https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html>>> < >>>>>> https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html>> < >>>> https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html>>>> < >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html >>>>>>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>>>>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>>>>>> <https://jena.apache.org/documentation/query/spatial-query.html>> < >>>> https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html>>> < >>>>>> https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>>>> <https://jena.apache.org/documentation/query/spatial-query.html>> < >>>> https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html> >>>> <https://jena.apache.org/documentation/query/spatial-query.html >>>> <https://jena.apache.org/documentation/query/spatial-query.html>>>>> and >>>>>>>> skipped through about every spatial related thread here on the list. >>>>>>>> I managed to get an in-memory version up and running at some point >>>>>>>> following this >>>>>>>> >>>>>>>> >>>>>> >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>> < >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>>> >>>>>> < >>>>>> >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>> < >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>>> >>>>>>> >>>>>>>> < >>>>>>>> >>>>>> >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>> < >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>>> >>>>>> < >>>>>> >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>> < >>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 >>>> >>>> <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>> >>>>> >>>>>>> >>>>>>>>> >>>>>>>> and this >>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ >>>>>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> >>>>>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ >>>>>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>> >>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> < >>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> < >>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> >>>>>>>> >>>>>>>> But that was on a small dataset that I uploaded via the web-interface >>>> of >>>>>>>> Fuseki. >>>>>>>> >>>>>>>> Now the story is a bit different. I'm building the database using >>>>>>>> tdbloader2 and would like to create the spatial index upfront. >>>>>>>> >>>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file >>>>>>>> I could not figure out, how to get this line to work. I have the >>>>>> following >>>>>>>> possible scenarios: >>>>>>>> >>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the >>>>>> classpath: >>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer >>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl >>>>>>>> Error: Could not find or load main class jena.spatialindexer >>>>>>>> >>>>>>>> 2. I use the fuseki-server jar: >>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer >>>>>>>> --desc=./run/configuration/mm.ttl >>>>>>>> WARN Custom SpatialContextFactory lib is not ready in >>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory >>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a >>>>>>>> transaction >>>>>>>> >>>>>>>> I managed to eliminate the warning about jts by including that in the >>>>>>>> classpath, but the error remains the same (with full trace): >>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer >>>>>>>> --desc=./run/configuration/mm.ttl >>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a >>>>>>>> transaction >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141) >>>>>>>> at >>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) >>>>>>>> at >>>>>>>> >>>>>> >>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152) >>>>>>>> at jena.spatialindexer.exec(spatialindexer.java:110) >>>>>>>> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93) >>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:58) >>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:45) >>>>>>>> at jena.spatialindexer.main(spatialindexer.java:53) >>>>>>>> >>>>>>>> My configuration is the following: >>>>>>>> @prefix : <http://base/#> . >>>>>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . >>>>>>>> @prefix tdb2: <http://jena.apache.org/2016/tdb#> . >>>>>>>> @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> . >>>>>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . >>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> . >>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> . >>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> . >>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> . >>>>>>>> # Spatial >>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" . >>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset . >>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex . >>>>>>>> >>>>>>>> :service_tdb_all a fuseki:Service ; >>>>>>>> rdfs:label "TDB2 mm" ; >>>>>>>> fuseki:dataset :spatial_dataset ; >>>>>>>> fuseki:name "mm" ; >>>>>>>> fuseki:serviceQuery "query" , "sparql" ; >>>>>>>> fuseki:serviceReadGraphStore "get" ; >>>>>>>> fuseki:serviceReadWriteGraphStore >>>>>>>> "data" ; >>>>>>>> fuseki:serviceUpdate "update" ; >>>>>>>> fuseki:serviceUpload "upload" . >>>>>>>> >>>>>>>> :spatial_dataset a spatial:SpatialDataset ; >>>>>>>> spatial:dataset :tdb_dataset_readwrite ; >>>>>>>> spatial:index <#indexLucene> ; >>>>>>>> . >>>>>>>> >>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ; >>>>>>>> spatial:directory <file:Lucene> ; >>>>>>>> #spatial:directory "mem" ; >>>>>>>> spatial:definition <#definition> ; >>>>>>>> . >>>>>>>> >>>>>>>> <#definition> a spatial:EntityDefinition ; >>>>>>>> spatial:entityField "uri" ; >>>>>>>> spatial:geoField "geo" ; >>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format >>>>>>>> spatial:hasSpatialPredicatePairs ( >>>>>>>> [ spatial:latitude geo:lat ; spatial:longitude geo:long ] >>>>>>>> ) ; >>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal >>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ; >>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal >>>>>>>> spatial:spatialContextFactory >>>>>>>> # "com.spatial4j.core.context.jts.JtsSpatialContextFactory" >>>>>>>> >>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory" >>>>>>>> . >>>>>>>> >>>>>>>> :tdb_dataset_readwrite >>>>>>>> a tdb2:DatasetTDB2 ; >>>>>>>> tdb2:location >>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" . >>>>>>>> >>>>>>>> And I've changed the fuseki script to include the jts jar: >>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar >>>>>>>> >>>>>>>> I see no errors or warnings in the server log, when starting with that >>>>>>>> configuration, the Lucene folder is created and populated with >>>>>> something: >>>>>>>> $ ll run/configuration/Lucene/ >>>>>>>> total 4 >>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1 >>>>>>>> -rw-rw-r-- 1 process process 0 Sep 14 09:28 write.lock >>>>>>>> >>>>>>>> But any spatial query does not return any results. >>>>>>>> Any help on how to tackle this would be highly appreciated. >>>>>>>> >>>>>>>> Best >>>>>>>> Markus Neumann >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> >>>>>>> --- >>>>>>> Marco Neumann >>>>>>> KONA >>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> --- >>>>> Marco Neumann >>>>> KONA >>>> >>>> >>> >>> -- >>> >>> >>> --- >>> Marco Neumann >>> KONA
