Not sure if this list is active, but will give it one more try... I think this error may be a bug.
I am trying to load a large .ttl file. This file had been successfully loaded in Stardog7.0 on Ubuntu20.04. Now I am trying to load it into Stardog7.6.4, but it keeps failing with an AccessDeniedException.
Here is the command I am using to load, and its immediate output
$ sudo /opt/stardog/bin/stardog-admin db create -n umls --verbose SNOMEDCT.ttl
[sudo] password for bonnie:
Bulk loading data to new database umls.
Errors were encountered during loading:
/home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl: /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl
Loaded 0 triples to umls from 1 file(s) in 00:00:00.282 @ 0.0K triples/sec.
Successfully created database 'umls'.
Here is the output from stardog.log
NFO 2021-06-25 15:18:26,167 [stardog-user-3] com.complexible.stardog.StardogKernel:write(77): Bulk loading data to new database umls.
WARN 2021-06-25 15:18:26,167 [stardog-user-3] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(622): Error during loading /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl: /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl
java.nio.file.AccessDeniedException: /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:90) ~[?:?]
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) ~[?:?]
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) ~[?:?]
at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:219) ~[?:?]
at java.nio.file.Files.newByteChannel(Files.java:371) ~[?:?]
at java.nio.file.Files.newByteChannel(Files.java:422) ~[?:?]
at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:420) ~[?:?]
at java.nio.file.Files.newInputStream(Files.java:156) ~[?:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFFileStream.openInputStream(RDFStreamBuilder.java:425) ~[stardog-utils-rdf-7.6.4.jar:?]
at com.complexible.common.rdf.rio.RDFStreamBuilder$RDFAbstractStream.parse(RDFStreamBuilder.java:243) ~[stardog-utils-rdf-7.6.4.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor$ConcurrentLoadManagerImpl.add(RDFStreamProcessor.java:525) ~[stardog-utils-rdf-7.6.4.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor.add(RDFStreamProcessor.java:226) ~[stardog-utils-rdf-7.6.4.jar:?]
at com.complexible.stardog.action.CreateDatabaseKernelAction.bulkLoad(CreateDatabaseKernelAction.java:518) ~[stardog-7.6.4.jar:?]
at com.complexible.stardog.action.CreateDatabaseKernelAction.loadDatabase(CreateDatabaseKernelAction.java:371) ~[stardog-7.6.4.jar:?]
at com.complexible.stardog.action.CreateDatabaseKernelAction.execute(CreateDatabaseKernelAction.java:264) ~[stardog-7.6.4.jar:?]
at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1287) ~[stardog-7.6.4.jar:?]
at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1380) ~[stardog-7.6.4.jar:?]
at com.complexible.stardog.protocols.http.server.AdminDatabaseService.createNewDatabase(AdminDatabaseService.java:810) ~[stardog-protocols-http-server-7.6.4.jar:?]
at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.6.4.jar:?]
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.7.1.jar:1.7.1]
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.7.1.jar:1.7.1]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
INFO 2021-06-25 15:18:26,205 [stardog-user-3] com.complexible.stardog.plan.cache.SimplePlanCache:clear(137): Clearing 0 cached plans
INFO 2021-06-25 15:18:26,206 [stardog-user-3] com.complexible.stardog.StardogKernel:write(77): Errors were encountered during loading:
INFO 2021-06-25 15:18:26,206 [stardog-user-3] com.complexible.stardog.StardogKernel:write(77): /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl: /home/bonnie/Dropbox/ResearchProjects/UMLSFilesFromRedhat/output/SNOMEDCT.ttl
INFO 2021-06-25 15:18:26,208 [stardog-user-3] com.complexible.stardog.StardogKernel:write(77): Loaded 0 triples to umls from 1 file(s) in 00:00:00.282 @ 0.0K triples/sec.
INFO 2021-06-25 15:18:26,208 [stardog-user-3] com.complexible.stardog.StardogKernel:write(77): Successfully created database 'umls'.
INFO 2021-06-25 15:18:26,233 [stardog-user-3] com.complexible.stardog.docs.db.BitesConnectableFactory:createDocumentStore(133): Creating document store for umls at file:////var/opt/stardog/umls/docs
bonnie@system76-pc:/var/opt/stardog$
The file is readable as can be seen from this listing
$ ls -l
total 3463908
-rw-r--r-- 1 bonnie bonnie 3480419 Jul 29 2019 ATC.ttl
-rw-r--r-- 1 bonnie bonnie 739469352 Jul 29 2019 MESH.ttl
-rw-r--r-- 1 bonnie bonnie 781016225 Jul 29 2019 NCBITAXON.ttl
-rw-r--r-- 1 bonnie bonnie 270407576 Jul 29 2019 NCI.ttl
-rw-r--r-- 1 bonnie bonnie 32899 Jul 29 2019 NDDF.ttl
-rw-r--r-- 1 bonnie bonnie 77927446 Jul 29 2019 NDFRT.ttl
-rw-r--r-- 1 bonnie bonnie 19444642 Jul 29 2019 PDQ.ttl
-rw-r--r-- 1 bonnie bonnie 198606447 Jul 29 2019 RXNORM.ttl
-rw-r--r-- 1 bonnie bonnie 1456579263 Jul 29 2019 SNOMEDCT.ttl
-rw-r--r-- 1 bonnie bonnie 32566 Jul 29 2019 umls_semantictypes.ttl
All of the other ttl files in this directory load without incident. As you can see, SNOMEDCT.ttl is the largest file, so that may be an issue. But it did load into Stardog7.0.
In researching this AccessDeniedException, I have read of scenarios in which threads are keeping the file open too long, so that when another thread tries to read, it cannot get access. Perhaps that is what is happening here? If so, what is the workaround?