This project forked from rdfostrich/bear
🏋 Fork of the BEAR benchmark with additional evaluations: https://github.com/webdata/BEAR
License: GNU Lesser General Public License v3.0
Querying SPARQL endpoint http://Starvers:7200/repositories/cbng_bearb_day with query lookup_queries_p_q32_v2.txt
Following row cannot be removed: ['http://dbpedia.org/resource/Islamic_State_of_Iraq_and_the_Levant', 'http://dbpedia.org/resource/Template:Infobox_war_faction']
Cause: Error in filter clause in string comparison in SPARQL query:
filter (str(?graph) <= "http://starvers_eval/v2/added" || str(?graph) <= "http://starvers_eval/v2/deleted")
The triple
http://open-data.europa.eu/en/data/dataset/0019c864-1b5d-48da-ad41-d4bb2c18ce7b http://purl.org/dc/terms/description "Frontex Annual Risk Analysis (ARA) 2014 presents a European summary of trends and developments along the external borders of the Member States of the EU. It focuses on describing current challenges that are likely to impact on operations coordinated along the external borders. It presents the latest update\r\nregarding the situation before the border, at the border and after the border." .
in /starvers_eval/rawdata/bearc/alldata.IC.nt/26.nt turns into following erroneous triple in /starvers_eval/rawdata/bearc/alldata.TB_star_hierarchical.ttl where the part in bold is missing
<< << http://open-data.europa.eu/en/data/dataset/0019c864-1b5d-48da-ad41-d4bb2c18ce7b http://purl.org/dc/terms/description "Frontex Annual Risk Analysis (ARA) 2014 presents a European summary of trends and developments along the external borders of the Member States of the EU. It focuses on describing current challenges that are likely to impact on operations coordinated along the\nregarding the situation before the border, at the border and after the border.">>https://github.com/GreenfishK/DataCitation/versioning/valid_from "2022-10-01T12:00:25.000+00:00"^^http://www.w3.org/2001/XMLSchema#dateTime >>https://github.com/GreenfishK/DataCitation/versioning/valid_until "2022-10-01T12:00:26.000+00:00"^^http://www.w3.org/2001/XMLSchema#dateTime .
Evaluate.sh runs through but the result sets are all empty.
Stack trace
2023-02-08 Wednesday 13:48:01 root:INFO:Build snapshot version 0363 from endpoint http://Starvers:3030/cb_sr_ng_bearb_hour/sparql
2023-02-08 Wednesday 13:48:20 root:INFO:Shutting down fuseki server and finishing evaluation of cb_sr_ng_bearb_hour.
Docker stack trace
evaluate_single_1 | Traceback (most recent call last):
evaluate_single_1 | File "/starvers_eval/scripts/6_evaluate/query.py", line 232, in <module>
evaluate_single_1 | build_snapshot(snapshot_g)
evaluate_single_1 | File "/starvers_eval/scripts/6_evaluate/query.py", line 221, in build_snapshot
evaluate_single_1 | del_set = engine.query().convert()
evaluate_single_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
evaluate_single_1 | return QueryResult(self._query())
evaluate_single_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
evaluate_single_1 | response = urlopener(request)
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 222, in urlopen
evaluate_single_1 | return opener.open(url, data, timeout)
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 525, in open
evaluate_single_1 | response = self._open(req, data)
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 542, in _open
evaluate_single_1 | result = self._call_chain(self.handle_open, protocol, protocol +
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 502, in _call_chain
evaluate_single_1 | result = func(*args)
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 1383, in http_open
evaluate_single_1 | return self.do_open(http.client.HTTPConnection, req)
evaluate_single_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 1358, in do_open
evaluate_single_1 | r = h.getresponse()
evaluate_single_1 | File "/usr/local/lib/python3.8/http/client.py", line 1348, in getresponse
evaluate_single_1 | response.begin()
evaluate_single_1 | File "/usr/local/lib/python3.8/http/client.py", line 316, in begin
evaluate_single_1 | version, status, reason = self._read_status()
evaluate_single_1 | File "/usr/local/lib/python3.8/http/client.py", line 285, in _read_status
evaluate_single_1 | raise RemoteDisconnected("Remote end closed connection without"
evaluate_single_1 | http.client.RemoteDisconnected: Remote end closed connection without response
Seems that it is not due to memory overflow
2023-03-19 Sunday 11:46:00 root:INFO:Querying SPARQL endpoint http://Starvers:3030/tb_sr_rs_bearb_hour/sparql with query lookup_queries_po_q11_v1298.txt
2023-03-19 Sunday 11:46:00 root:WARNING:The query execution lookup_queries_po_q11_v1298.txt reached the timeout of Nones. The execution_time will be set to -1. The results will not be serialized.
An exception is thrown but unfortunatelly we get not error message other than the warning. I improved the script so that we also print the actual error message. New execution is pending
GraphDB is stacking up the heap with every "activated" repository
A repository becomes activated as soon as it is queried
This is only an issue for "multi repository" policies. Currently, I am only using single repository policies where every version is stored within a named graph
Following two queries gets stuck when executing them against rdflib's Graph().
PREFIX dcat: <http://www.w3.org/ns/dcat#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
# version 00
Select *
{
?dataset rdf:type dcat:Dataset .
?dataset dc:title ?title .
?dataset dcat:distribution ?distribution .
?distribution dcat:accessURL ?URL .
?distribution dcat:mediaType "text/csv" .
?distribution dc:title ?filetitle .
?distribution dc:description ?description .
}
PREFIX dcat: <http://www.w3.org/ns/dcat#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
# version 00
Select *
{
?dataset rdf:type dcat:Dataset .
?dataset dc:title ?title .
?distr1 dcat:distribution ?dataset .
?distr1 dcat:accessURL ?URL1 .
?distr1 dcat:mediaType "text/csv" .
?distr1 dc:title ?titleFile1 .
?distr1 dc:description ?description1 .
?distr2 dcat:distribution ?dataset .
?distr2 dcat:accessURL ?URL2 .
?distr2 dcat:mediaType "text/tab-separated-values" .
?distr2 dc:title ?titleFile2 .
?distr2 dc:description ?description2 .
}
Stacktrace
evaluate_1 | cp: cannot stat '/starvers_eval/configs/jenatdb2_ic_sr_ng_bearc/*.ttl': No such file or directory
evaluate_1 | [2023-01-26 10:23:32] Server INFO Apache Jena Fuseki 4.0.0
evaluate_1 | [2023-01-26 10:23:32] Config INFO FUSEKI_HOME=/jena-fuseki
evaluate_1 | [2023-01-26 10:23:32] Config INFO FUSEKI_BASE=/run
evaluate_1 | [2023-01-26 10:23:32] Config INFO Shiro file: file:///run/shiro.ini
evaluate_1 | [2023-01-26 10:23:33] Server INFO System
evaluate_1 | [2023-01-26 10:23:33] Server INFO Memory: 90.0 GiB
evaluate_1 | [2023-01-26 10:23:33] Server INFO Java: 11.0.11
evaluate_1 | [2023-01-26 10:23:33] Server INFO OS: Linux 5.15.0-52-generic amd64
evaluate_1 | [2023-01-26 10:23:33] Server INFO PID: 158
evaluate_1 | [2023-01-26 10:23:33] Server INFO Started 2023/01/26 10:23:33 UTC on port 3030
evaluate_1 | Traceback (most recent call last):
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
evaluate_1 | response = urlopener(request)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 222, in urlopen
evaluate_1 | return opener.open(url, data, timeout)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 531, in open
evaluate_1 | response = meth(req, response)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 640, in http_response
evaluate_1 | response = self.parent.error(
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 569, in error
evaluate_1 | return self._call_chain(*args)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 502, in _call_chain
evaluate_1 | result = func(*args)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 649, in http_error_default
evaluate_1 | raise HTTPError(req.full_url, code, msg, hdrs, fp)
evaluate_1 | urllib.error.HTTPError: HTTP Error 404: Not Found
evaluate_1 |
evaluate_1 | During handling of the above exception, another exception occurred:
evaluate_1 |
evaluate_1 | Traceback (most recent call last):
evaluate_1 | File "/starvers_eval/scripts/6_evaluate/query.py", line 187, in <module>
evaluate_1 | result = engine.query()
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
evaluate_1 | return QueryResult(self._query())
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 932, in _query
evaluate_1 | raise EndPointNotFound(e.read())
evaluate_1 | SPARQLWrapper.SPARQLExceptions.EndPointNotFound: EndPointNotFound: It was not possible to connect to the given endpoint: check it is correct.
evaluate_1 |
evaluate_1 | Response:
evaluate_1 | b'Error 404: Not Found\n'
construct_datasets_1 | # A fatal error has been detected by the Java Runtime Environment:
construct_datasets_1 | #
construct_datasets_1 | # SIGBUS (0x7) at pc=0x00007f74ff550c76, pid=48, tid=96
construct_datasets_1 | #
construct_datasets_1 | # JRE version: OpenJDK Runtime Environment 18.9 (11.0.11+9) (build 11.0.11+9)
construct_datasets_1 | # Java VM: OpenJDK 64-Bit Server VM 18.9 (11.0.11+9, mixed mode, tiered, g1 gc, linux-amd64)
construct_datasets_1 | # Problematic frame:
construct_datasets_1 | # v ~StubRoutines::jlong_disjoint_arraycopy
construct_datasets_1 | #
construct_datasets_1 | # Core dump will be written. Default location: Core dumps may be processed with "/lib/systemd/systemd-coredump %P %u %g %s %t 9223372036854775808 %h" (or dumping to //core.48)
construct_datasets_1 | #
construct_datasets_1 | # An error report file with more information is saved as:
construct_datasets_1 | # //hs_err_pid48.log
construct_datasets_1 | Compiled method (c2) 694701 5184 4 org.apache.jena.dboe.trans.bplustree.BPTreeRecords::promote (116 bytes)
construct_datasets_1 | total in heap [0x00007f7507373310,0x00007f7507376a88] = 14200
construct_datasets_1 | relocation [0x00007f7507373488,0x00007f75073735f0] = 360
construct_datasets_1 | main code [0x00007f7507373600,0x00007f7507374e80] = 6272
construct_datasets_1 | stub code [0x00007f7507374e80,0x00007f7507374ee0] = 96
construct_datasets_1 | oops [0x00007f7507374ee0,0x00007f7507374f00] = 32
construct_datasets_1 | metadata [0x00007f7507374f00,0x00007f7507375070] = 368
construct_datasets_1 | scopes data [0x00007f7507375070,0x00007f7507376070] = 4096
construct_datasets_1 | scopes pcs [0x00007f7507376070,0x00007f75073767f0] = 1920
construct_datasets_1 | dependencies [0x00007f75073767f0,0x00007f7507376810] = 32
construct_datasets_1 | handler table [0x00007f7507376810,0x00007f7507376918] = 264
construct_datasets_1 | nul chk table [0x00007f7507376918,0x00007f7507376a88] = 368
construct_datasets_1 | Could not load hsdis-amd64.so; library not loadable; PrintAssembly is disabled
construct_datasets_1 | #
construct_datasets_1 | # If you would like to submit a bug report, please visit:
construct_datasets_1 | # https://bugreport.java.com/bugreport/crash.jsp
construct_datasets_1 | #
Querying SPARQL endpoint http://Starvers:7200/repositories/cbng_bearb_day with query join17_q5_v36.txt
SELECT * {
graph ?graph
{
?s http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/ontology/SoccerPlayer .
?s http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://xmlns.com/foaf/0.1/Person .
}
filter (str(?graph) <= "http://starvers_eval/v36/added" || str(?graph) <= "http://starvers_eval/v36/deleted")
} order by ?graph
Docker-compose output
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Apache Jena Fuseki 4.0.0
eval_construct_datasets_1 | [2023-03-23 08:44:31] Config INFO FUSEKI_HOME=/jena-fuseki
eval_construct_datasets_1 | [2023-03-23 08:44:31] Config INFO FUSEKI_BASE=/run
eval_construct_datasets_1 | [2023-03-23 08:44:31] Config INFO Shiro file: file:///run/shiro.ini
eval_construct_datasets_1 | [2023-03-23 08:44:31] Config INFO Configuration file: /run/config.ttl
eval_construct_datasets_1 | [2023-03-23 08:44:31] Config INFO Load configuration: file:///run/configuration/tb_rs_sr_bearc.ttl
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Configuration file: /run/config.ttl
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Path = /tb_rs_sr_bearc
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO System
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Memory: 90.0 GiB
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Java: 11.0.11
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO OS: Linux 5.15.0-52-generic amd64
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO PID: 207
eval_construct_datasets_1 | [2023-03-23 08:44:31] Server INFO Started 2023/03/23 08:44:31 UTC on port 3030
eval_construct_datasets_1 | [2023-03-23 08:44:32] Fuseki INFO [1] POST http://Starvers:3030/tb_rs_sr_bearc/update
Query from logfile:
PREFIX vers: <https://github.com/GreenfishK/DataCitation/versioning/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
delete {
<< <<?s ?p ?o>> vers:valid_from ?valid_from >> vers:valid_until "9999-12-31T00:00:00.000+02:00"^^xsd:dateTime
}
insert {
<< <<?s ?p ?o>> vers:valid_from ?valid_from >> vers:valid_until ?newVersion. # outdate
}
where {
values (?s ?p ?o) {
( <http://open-data.europa.eu/en/data/dataset/a140d18d-1b9c-46b7-bff9-064dfa89d816/resource/3a763560-dd38-43e1-b259-5e42bddbc910> <http://purl.org/dc/terms/license> <http://ec.europa.eu/geninfo/legal_notices_en.htm> )
}
# versioning
<< <<?s ?p ?o>> vers:valid_from ?valid_from >> vers:valid_until "9999-12-31T00:00:00.000+02:00"^^xsd:dateTime.
BIND(xsd:dateTime("2022-10-01T12:00:01.000+00:00") AS ?newVersion).
}
This is a follow-up issue of issue #1. While ingesting into GraphDB went through without an error, JenaTDB2 is still hanging at 1.500.000 triples.
Querying SPARQL endpoint http://Starvers:3030/tb_sr_rs_bearc/sparql with query query9_q0_v0.txt
Query
PREFIX vers: <https://github.com/GreenfishK/DataCitation/versioning/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT ?description2 ?title ?distr1 ?URL2 ?description1 ?distr2 ?titleFile2 ?dataset ?titleFile1 ?URL1 {
<< <<?distr1 <http://www.w3.org/ns/dcat#mediaType> "text/csv">> vers:valid_from ?valid_from_1 >> vers:valid_until ?valid_until_1. filter(?valid_from_1 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_1)
<< <<?distr1 <http://www.w3.org/ns/dcat#distribution> ?dataset>> vers:valid_from ?valid_from_2 >> vers:valid_until ?valid_until_2. filter(?valid_from_2 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_2)
<< <<?distr2 <http://www.w3.org/ns/dcat#distribution> ?dataset>> vers:valid_from ?valid_from_3 >> vers:valid_until ?valid_until_3. filter(?valid_from_3 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_3)
<< <<?distr2 <http://www.w3.org/ns/dcat#mediaType> "text/tab-separated-values">> vers:valid_from ?valid_from_4 >> vers:valid_until ?valid_until_4. filter(?valid_from_4 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_4)
<< <<?dataset <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/dcat#Dataset>>> vers:valid_from ?valid_from_5 >> vers:valid_until ?valid_until_5. filter(?valid_from_5 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_5)
<< <<?distr1 <http://purl.org/dc/elements/1.1/description> ?description1>> vers:valid_from ?valid_from_6 >> vers:valid_until ?valid_until_6. filter(?valid_from_6 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_6)
<< <<?distr1 <http://purl.org/dc/elements/1.1/title> ?titleFile1>> vers:valid_from ?valid_from_7 >> vers:valid_until ?valid_until_7. filter(?valid_from_7 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_7)
<< <<?distr1 <http://www.w3.org/ns/dcat#accessURL> ?URL1>> vers:valid_from ?valid_from_8 >> vers:valid_until ?valid_until_8. filter(?valid_from_8 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_8)
<< <<?distr2 <http://purl.org/dc/elements/1.1/description> ?description2>> vers:valid_from ?valid_from_9 >> vers:valid_until ?valid_until_9. filter(?valid_from_9 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_9)
<< <<?distr2 <http://purl.org/dc/elements/1.1/title> ?titleFile2>> vers:valid_from ?valid_from_10 >> vers:valid_until ?valid_until_10. filter(?valid_from_10 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_10)
<< <<?distr2 <http://www.w3.org/ns/dcat#accessURL> ?URL2>> vers:valid_from ?valid_from_11 >> vers:valid_until ?valid_until_11. filter(?valid_from_11 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_11)
<< <<?dataset <http://purl.org/dc/elements/1.1/title> ?title>> vers:valid_from ?valid_from_12 >> vers:valid_until ?valid_until_12.
filter(?valid_from_12 <= ?tsBGP_0 && ?tsBGP_0 < ?valid_until_12) bind("2022-10-01T12:00:00.000+00:00"^^xsd:dateTime as ?tsBGP_0)}
Logs:
2023-01-31 Tuesday 18:55:33 root:INFO:Build snapshot version 24 from endpoint http://Starvers:3030/cb_sr_ng_bearc/sparql
2023-01-31 Tuesday 18:56:23 root:INFO:Shutting down fuseki server
After sucessfully executing jenatdb2, cb_sr_ng, bearc and jenatdb2, cb_sr_ng, bearb_hour the evaluation process gets stuck with jenatdb2, cb_sr_ng, bearb_day
RUN apt-get install curl=7.74.0-1.3+deb11u3 -y
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
curl : Depends: libcurl4 (= 7.74.0-1.3+deb11u3) but 7.74.0-1.3+deb11u5 is to be installed
During the execution of construct_tb_star_ds I get this error in the second iteration:
rm: cannot remove '/starvers_eval/databases/construct_datasets/graphdb/repositories/tb_rs_sr_bearb_day/storage/history': Directory not empty
rm: cannot remove '/starvers_eval/databases/construct_datasets/graphdb/repositories/tb_rs_sr_bearb_day/storage/literals-index': Directory not empty
17:16:59.185 [main] INFO c.ontotext.graphdb.importrdf.Preload - Input folders recursively: false
17:16:59.187 [main] INFO c.ontotext.graphdb.importrdf.Preload - Iterator cache set to: 'auto'
17:16:59.187 [main] INFO c.ontotext.graphdb.importrdf.Preload - Chunk size set to: 'auto'
17:16:59.188 [main] INFO c.ontotext.graphdb.importrdf.Preload - Parsing tasks: 2
17:16:59.188 [main] INFO c.ontotext.graphdb.importrdf.Preload - Temporary data folder: /.
17:16:59.190 [main] INFO c.ontotext.graphdb.importrdf.Preload - Restore point interval: 3,600s
17:16:59.190 [main] INFO c.ontotext.graphdb.importrdf.Preload - CONFIG FILE: /starvers_eval/configs/construct_datasets/graphdb_tb_rs_sr_bearb_day/graphdb-config.ttl
17:16:59.205 [main] INFO c.ontotext.graphdb.importrdf.Preload - Attaching to location: /starvers_eval/databases/construct_datasets/graphdb
org.eclipse.rdf4j.repository.RepositoryException: Failed to lock directory: /starvers_eval/databases/construct_datasets/graphdb/repositories. Is another GraphDB instance running?
at com.ontotext.graphdb.GraphDBRepositoryManager.init(GraphDBRepositoryManager.java:219)
at com.ontotext.graphdb.importrdf.BaseLoadTool.mainInternal(BaseLoadTool.java:161)
at com.ontotext.graphdb.importrdf.Preload.call(Preload.java:250)
at com.ontotext.graphdb.importrdf.Preload.call(Preload.java:53)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.ontotext.graphdb.importrdf.ImportRDF.main(ImportRDF.java:25)
/opt/graphdb/dist/bin/graphdb: line 75: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Exception in thread "main" org.apache.catalina.LifecycleException: Protocol handler initialization failed
at org.apache.catalina.connector.Connector.initInternal(Connector.java:1051)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)
at org.apache.catalina.core.StandardService.initInternal(StandardService.java:556)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)
at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:1045)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)
at org.apache.catalina.startup.Tomcat.init(Tomcat.java:475)
at com.ontotext.graphdb.server.GraphDB.start(GraphDB.java:171)
at com.ontotext.graphdb.server.GraphDBServer.main(GraphDBServer.java:10)
Caused by: java.net.BindException: Address already in use
at java.base/sun.nio.ch.Net.bind0(Native Method)
at java.base/sun.nio.ch.Net.bind(Net.java:459)
at java.base/sun.nio.ch.Net.bind(Net.java:448)
at java.base/sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:227)
at org.apache.tomcat.util.net.NioEndpoint.initServerSocket(NioEndpoint.java:275)
at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:230)
at org.apache.tomcat.util.net.AbstractEndpoint.bindWithCleanup(AbstractEndpoint.java:1227)
at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:1240)
at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:606)
at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:77)
at org.apache.catalina.connector.Connector.initInternal(Connector.java:1048)
... 8 more
/opt/graphdb/dist/bin/graphdb: line 75: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Traceback (most recent call last):
File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
response = urlopener(request)
File "/usr/local/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/lib/python3.8/urllib/request.py", line 531, in open
response = meth(req, response)
File "/usr/local/lib/python3.8/urllib/request.py", line 640, in http_response
response = self.parent.error(
File "/usr/local/lib/python3.8/urllib/request.py", line 569, in error
return self._call_chain(*args)
File "/usr/local/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/usr/local/lib/python3.8/urllib/request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404:
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/starvers_eval/scripts/3_construct_datasets/construct_datasets.py", line 411, in <module>
construct_tb_star_ds(source_ic0=f"{data_dir}/{snapshot_dir}/" + "1".zfill(ic_basename_lengths[dataset]) + ".nt",
File "/starvers_eval/scripts/3_construct_datasets/construct_datasets.py", line 145, in construct_tb_star_ds
rdf_star_engine.insert(triples=added_triples_raw, timestamp=vers_ts, chunk_size=chunk_size)
File "/starvers_eval/python_venv/lib/python3.8/site-packages/starvers/starvers.py", line 470, in insert
self.sparql_post.query()
File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
return QueryResult(self._query())
File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 932, in _query
raise EndPointNotFound(e.read())
SPARQLWrapper.SPARQLExceptions.EndPointNotFound: EndPointNotFound: It was not possible to connect to the given endpoint: check it is correct.
Malformed query: query10_q7_v0.txt
Stacktrace
Creating network "starvers_eval_default" with the default driver
Creating starvers_eval_evaluate_1 ... done
Attaching to starvers_eval_evaluate_1
evaluate_1 | /opt/graphdb/dist/bin/graphdb: line 75: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
evaluate_1 | Traceback (most recent call last):
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
evaluate_1 | response = urlopener(request)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 222, in urlopen
evaluate_1 | return opener.open(url, data, timeout)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 531, in open
evaluate_1 | response = meth(req, response)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 640, in http_response
evaluate_1 | response = self.parent.error(
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 569, in error
evaluate_1 | return self._call_chain(*args)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 502, in _call_chain
evaluate_1 | result = func(*args)
evaluate_1 | File "/usr/local/lib/python3.8/urllib/request.py", line 649, in http_error_default
evaluate_1 | raise HTTPError(req.full_url, code, msg, hdrs, fp)
evaluate_1 | urllib.error.HTTPError: HTTP Error 400:
evaluate_1 |
evaluate_1 | During handling of the above exception, another exception occurred:
evaluate_1 |
evaluate_1 | Traceback (most recent call last):
evaluate_1 | File "/starvers_eval/scripts/6_evaluate/query.py", line 187, in <module>
evaluate_1 | result = engine.query()
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
evaluate_1 | return QueryResult(self._query())
evaluate_1 | File "/starvers_eval/python_venv/lib/python3.8/site-packages/SPARQLWrapper/Wrapper.py", line 930, in _query
evaluate_1 | raise QueryBadFormed(e.read())
evaluate_1 | SPARQLWrapper.SPARQLExceptions.QueryBadFormed: QueryBadFormed: A bad request has been sent to the endpoint: probably the SPARQL query is badly formed.
evaluate_1 |
evaluate_1 | Response:
evaluate_1 | b'MALFORMED QUERY: Encountered " "order" "ORDER "" at line 17, column 1.\nWas expecting one of:\n "(" ...\n "{" ...\n "}" ...\n "[" ...\n "." ...\n <NIL> ...\n <ANON> ...\n "optional" ...\n "graph" ...\n "minus" ...\n "filter" ...\n "true" ...\n "false" ...\n "bind" ...\n "service" ...\n "values" ...\n <Q_IRI_REF> ...\n <PNAME_NS> ...\n <PNAME_LN> ...\n <BLANK_NODE_LABEL> ...\n <VAR1> ...\n <VAR2> ...\n <INTEGER> ...\n <INTEGER_POSITIVE> ...\n <INTEGER_NEGATIVE> ...\n <DECIMAL> ...\n <DECIMAL_POSITIVE> ...\n <DECIMAL_NEGATIVE> ...\n <DOUBLE> ...\n <DOUBLE_POSITIVE> ...\n <DOUBLE_NEGATIVE> ...\n <STRING_LITERAL1> ...\n <STRING_LITERAL2> ...\n <STRING_LITERAL_LONG1> ...\n <STRING_LITERAL_LONG2> ...\n "<<" ...\n '
This is the output from docker logs
OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
838651
Try using the -Djava.io.tmpdir= option to select an alternate temp location.
This happend after finishing the evaluation for tb_rs_sr, bearc and JenaTDB. On the start of the evaluation of tb_rs_sr, bearb_hour and JenaTDB I got this error:
Stacktrace
[2023-02-03 22:21:03] Server INFO Apache Jena Fuseki 4.0.0
[2023-02-03 22:21:03] Config INFO FUSEKI_HOME=/jena-fuseki
[2023-02-03 22:21:03] Config INFO FUSEKI_BASE=/run
[2023-02-03 22:21:03] Config INFO Shiro file: file:///run/shiro.ini
[2023-02-03 22:21:03] Config INFO Configuration file: /run/config.ttl
[2023-02-03 22:21:03] Config INFO Load configuration: file:///run/configuration/config.ttl
[2023-02-03 22:21:04] Server INFO Configuration file: /run/config.ttl
[2023-02-03 22:21:04] Server INFO Path = /tb_sr_rs_bearb_hour
[2023-02-03 22:21:04] Server INFO System
[2023-02-03 22:21:04] Server INFO Memory: 90.0 GiB
[2023-02-03 22:21:04] Server INFO Java: 11.0.11
[2023-02-03 22:21:04] Server INFO OS: Linux 5.15.0-52-generic amd64
[2023-02-03 22:21:04] Server INFO PID: 610
[2023-02-03 22:21:04] Server ERROR SPARQLServer: Failed to start server: Failed to bind to 0.0.0.0/0.0.0.0:3030
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