java.lang.IllegalArgumentException when building entity-linking

[CharlieUnderwood]

Hello, I encountered this java.lang.IllegalArgumentException error when building entity-linking. I successfully generate following files through "create_graph_full_pagelinks.sh".

But when I tried

./gradlew runPreprocess --args="-i Users/charlieunderwood/Documents/repository/program_YD/repository/pgx_samples_master/entity_linking/data/graph_data/graph.json -g test111 -p -n 100" ###,

the error shows as the following pic:

I have tried to modify GraphPreprocessingMain.scala as follows:

The error stiil occurs. Appreciate for your answer.

[rhpatra]

@AlbertoParravicini can you look into this error?

[CharlieUnderwood]

./gradlew runPreprocess --args="-i Users/charlieunderwood/Documents/repository/program_YD/repository/pgx_samples_master/entity_linking/data/graph_data/graph.json -g test111 -p -n 100"

Configuration on demand is an incubating feature.

Task :runPreprocessor
18:05:26.180 INFO : Starting graph preprocessing...
18:05:26.263 INFO : Setting up graph preprocessor...
18:05:26.265 INFO : Input graph: Users/charlieunderwood/Documents/repository/program_YD/repository/pgx_samples_master/entity_linking/data/graph_data/graph.json
18:05:26.273 INFO : Creating Pgx session...
Exception in thread "main" java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: the datasource white list should not be empty when local file system usage is allowed
at java.util.concurrent.CompletableFuture.reportGet(CompletableFuture.java:357)
at java.util.concurrent.CompletableFuture.get(CompletableFuture.java:1908)
at oracle.pgx.api.PgxFuture.get(PgxFuture.java:99)
at oracle.pgx.api.ServerInstance.createSession(ServerInstance.java:578)
at oracle.pgx.api.Pgx.createSession(Pgx.java:270)
at oracle.pgx.api.Pgx.createSession(Pgx.java:284)
at utils.PgxManager.(PgxManager.scala:21)
at graph_preprocessor.GraphPreprocessor.(GraphPreprocessor.scala:36)
at graph_preprocessor.GraphPreprocessorMain$.main(GraphPreprocessorMain.scala:62)
at graph_preprocessor.GraphPreprocessorMain.main(GraphPreprocessorMain.scala)
Caused by: java.lang.IllegalArgumentException: the datasource white list should not be empty when local file system usage is allowed
at oracle.pgx.config.AbstractEngineConfig.validateAllowLocalFileSystemSettings(AbstractEngineConfig.java:34)
at oracle.pgx.config.AbstractEngineConfig.validate(AbstractEngineConfig.java:26)
at oracle.pgx.config.AbstractConfig.initialize(AbstractConfig.java:107)
at oracle.pgx.config.PgxConfig.(PgxConfig.java:511)
at oracle.pgx.config.PgxConfig.parse(PgxConfig.java:475)
at oracle.pgx.config.AbstractPgxConfig.initPgxConfig(AbstractPgxConfig.java:87)
at oracle.pgx.config.AbstractPgxConfig.getInstance(AbstractPgxConfig.java:72)
at oracle.pgx.engine.admin.Ctrl.doLoadConfig(Ctrl.java:316)
at oracle.pgx.engine.admin.Ctrl.doLoadConfig(Ctrl.java:84)
at oracle.pgx.api.admin.AbstractEmbeddedControl.loadConfig(AbstractEmbeddedControl.java:55)
at oracle.pgx.engine.admin.Ctrl.access$600(Ctrl.java:84)
at oracle.pgx.engine.admin.Ctrl$1.call(Ctrl.java:185)
at oracle.pgx.engine.admin.Ctrl$1.call(Ctrl.java:171)
at oracle.pgx.api.admin.AbstractControl.runOnCallerThread(AbstractControl.java:38)
at oracle.pgx.engine.admin.Ctrl.start(Ctrl.java:171)
at oracle.pgx.api.admin.AbstractControl.start(AbstractControl.java:97)
at java.util.concurrent.CompletableFuture.uniComposeStage(CompletableFuture.java:995)
at java.util.concurrent.CompletableFuture.thenCompose(CompletableFuture.java:2137)
at oracle.pgx.api.PgxFuture.thenCompose(PgxFuture.java:152)
at oracle.pgx.api.admin.AbstractControl.start(AbstractControl.java:84)
at oracle.pgx.api.admin.AbstractControl.lambda$start$1(AbstractControl.java:64)
at java.util.concurrent.CompletableFuture.uniComposeStage(CompletableFuture.java:995)
at java.util.concurrent.CompletableFuture.thenCompose(CompletableFuture.java:2137)
at oracle.pgx.api.PgxFuture.thenCompose(PgxFuture.java:152)
at oracle.pgx.api.admin.AbstractControl.start(AbstractControl.java:60)
at java.util.concurrent.CompletableFuture.uniComposeStage(CompletableFuture.java:995)
at java.util.concurrent.CompletableFuture.thenCompose(CompletableFuture.java:2137)
at oracle.pgx.api.PgxFuture.thenCompose(PgxFuture.java:152)
at oracle.pgx.api.ServerInstance.onControl(ServerInstance.java:224)
at oracle.pgx.api.ServerInstance.startEngineAsync(ServerInstance.java:283)
at oracle.pgx.api.ServerInstance.lambda$getCore$0(ServerInstance.java:185)
at java.util.concurrent.CompletableFuture.uniComposeStage(CompletableFuture.java:995)
at java.util.concurrent.CompletableFuture.thenCompose(CompletableFuture.java:2137)
at oracle.pgx.api.PgxFuture.thenCompose(PgxFuture.java:152)
at oracle.pgx.api.ServerInstance.getCore(ServerInstance.java:178)
at oracle.pgx.api.ServerInstance.createSessionAsync(ServerInstance.java:211)
at oracle.pgx.api.ServerInstance.createSessionAsync(ServerInstance.java:162)
... 7 more

Task :runPreprocessor FAILED

FAILURE: Build failed with an exception.

• What went wrong:
  Execution failed for task ':runPreprocessor'.

Process 'command '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/bin/java'' finished with non-zero exit value 1

• Try:
  Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

• Get more help at https://help.gradle.org

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
Use '--warning-mode all' to show the individual deprecation warnings.
See https://docs.gradle.org/4.10.1/userguide/command_line_interface.html#sec:command_line_warnings

[AlbertoParravicini]

It seems that the error is coming from the following line
val session: PgxSession = Pgx.createSession("session_1") located in https://github.com/oracle/pgx-samples/blob/master/entity-linking/src/main/scala/utils/PgxManager.scala

It's not related to the input arguments, but to something wrong in the Pgx startup.
@CharlieUnderwood can you provide additional information about your config, Pgx version, os, etc...
Also, are you able to start a Pgx session inside a minimal example (either in java or scala)?

[AlbertoParravicini]

The error message Caused by: java.lang.IllegalArgumentException: the datasource white list should not be empty when local file system usage is allowed makes me think that the error is related to the allow_local_filesystem": true, setting in https://github.com/oracle/pgx-samples/blob/master/entity-linking/conf/pgx.conf

@rpatra do you know if there was some recent change in the behaviour of this setting?

@CharlieUnderwood you could try setting that flag to false, or specifying the data directory in the datasource_dir_whitelist setting (see https://docs.oracle.com/cd/E56133_01/latest/reference/config/pgx.html)

[rhpatra]

@CharlieUnderwood below is an example

{
"datasource_dir_whitelist" : ["PUT_THE_ABSOLUTE_PATH_TO_DATA_DIRECTORY_HERE"],
"allow_local_filesystem": true,
"tmp_dir": "tmp_data"
}

[CharlieUnderwood]

@AlbertoParravicini I am using mac os 10.14.1 with java version "11.0.6".
After chaning the `allow_local_filesystem" from true to false, the code is running OK.
Thank you for your kind help.
@AlbertoParravicini @rpatra