Opengrok UI shows incorrect results

[chkp-baselz]

I'm using

• OpenGrok v1.7.33 rev 9bbba82
• CentOS Linux release 8.5.2111
• OpenJDK Runtime Environment 18.9 (build 11.0.13+8-LTS)

I'm getting incorrect results in Opengrok UI, let's say for example in a specific file I have 3 rehearsals of a specific string, it shows me four rehearsals, the forth one is incorrect (the original line does not contains the string, seems it think like it's a duplication of the first result) and it's in incorrect line order
for example

As you can see line 2237 does not contains the string

Under /opengrok/data folder I see that the file has "org_opengrok" extension, I tried to delete the file and touch the src file so it'll be reindex, but it keeps failing and re generating the file with "org_opengrok" extension

I use this command to index
java -Djavax.net.debug=all -Djavax.net.ssl.trustStore=/usr/share/apache-tomcat-9.0.40/conf/keystore/opengrok.jks -Djavax.net.ssl.trustStoreType=jks -Djavax.net.ssl.keyStorePassword= -Djava.util.logging.config.file=/opengrok/etc/logging.properties -jar /opengrok/dist/lib/opengrok.jar -c /usr/local/bin/ctags -s /opengrok/src -d /opengrok/data -H -P -S -G -W /opengrok/etc/configuration.xml -U https://opengrok.com:8443/source/

special output in indexing command for this project

10:58:01 WARNING: Could not notify the webapp that project jaguar_main:indexed=true,history=true was indexed
jakarta.ws.rs.ProcessingException: Cannot find trust store file "/usr/share/apache-tomcat-9.0.40/conf/keystore/opengrok.jks".
        at org.glassfish.jersey.client.ClientRuntime.invoke(ClientRuntime.java:309)
        at org.glassfish.jersey.client.JerseyInvocation.lambda$invoke$0(JerseyInvocation.java:662)
        at org.glassfish.jersey.client.JerseyInvocation.call(JerseyInvocation.java:697)
        at org.glassfish.jersey.client.JerseyInvocation.lambda$runInScope$3(JerseyInvocation.java:691)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
        at org.glassfish.jersey.internal.Errors.process(Errors.java:205)
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:390)
        at org.glassfish.jersey.client.JerseyInvocation.runInScope(JerseyInvocation.java:691)
        at org.glassfish.jersey.client.JerseyInvocation.invoke(JerseyInvocation.java:661)
        at org.glassfish.jersey.client.JerseyInvocation$Builder.method(JerseyInvocation.java:439)
        at org.glassfish.jersey.client.JerseyInvocation$Builder.put(JerseyInvocation.java:328)
        at org.opengrok.indexer.index.IndexDatabase.markProjectIndexed(IndexDatabase.java:403)
        at org.opengrok.indexer.index.IndexDatabase.update(IndexDatabase.java:681)
        at org.opengrok.indexer.index.IndexDatabase.lambda$updateAll$1(IndexDatabase.java:247)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalStateException: Cannot find trust store file "/usr/share/apache-tomcat-9.0.40/conf/keystore/opengrok.jks".
        at org.glassfish.jersey.SslConfigurator.createSSLContext(SslConfigurator.java:729)
        at org.glassfish.jersey.SslConfigurator.getDefaultContext(SslConfigurator.java:278)
        at org.glassfish.jersey.SslConfigurator.getDefaultContext(SslConfigurator.java:263)
        at org.glassfish.jersey.client.JerseyClient$1.getDefaultSslContext(JerseyClient.java:62)
        at org.glassfish.jersey.client.JerseyClient$2.get(JerseyClient.java:202)
        at org.glassfish.jersey.client.JerseyClient$2.get(JerseyClient.java:199)
        at org.glassfish.jersey.internal.util.collection.Values$LazyUnsafeValueImpl.get(Values.java:402)
        at org.glassfish.jersey.client.JerseyClient.getSslContext(JerseyClient.java:378)
        at org.glassfish.jersey.client.internal.HttpUrlConnector$1.get(HttpUrlConnector.java:134)
        at org.glassfish.jersey.client.internal.HttpUrlConnector$1.get(HttpUrlConnector.java:131)
        at org.glassfish.jersey.internal.util.collection.Values$LazyValueImpl.get(Values.java:317)
        at org.glassfish.jersey.client.internal.HttpUrlConnector.secureConnection(HttpUrlConnector.java:311)
        at org.glassfish.jersey.client.internal.HttpUrlConnector._apply(HttpUrlConnector.java:335)
        at org.glassfish.jersey.client.internal.HttpUrlConnector.apply(HttpUrlConnector.java:266)
        at org.glassfish.jersey.client.ClientRuntime.invoke(ClientRuntime.java:297)
        ... 19 more
Caused by: java.io.FileNotFoundException: /usr/share/apache-tomcat-9.0.40/conf/keystore/opengrok.jks (Permission denied)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:112)
        at org.glassfish.jersey.SslConfigurator.createSSLContext(SslConfigurator.java:713)
        ... 33 more

13:01:31 SEVERE: Problem updating index database in directory /opengrok/data/index/jaguar_main:
java.lang.IllegalStateException: cannot close: prepareCommit was already called with no corresponding call to commit
        at org.apache.lucene.index.IndexWriter.shutdown(IndexWriter.java:1225)
        at org.apache.lucene.index.IndexWriter.close(IndexWriter.java:1278)
        at org.opengrok.indexer.index.IndexDatabase.update(IndexDatabase.java:702)
        at org.opengrok.indexer.index.IndexDatabase.lambda$updateAll$1(IndexDatabase.java:247)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)

[vladak]

The files with org_opengrok extension are temporary xref files generated during reindex. At the end of reindex they are moved to their final destination, i.e. without the suffix. When such operation fails, there is either some problem with the I/O or some grave problem in the indexing (like shortage or memory). For the former one can try to repair by moving the files to their correct destinations, however as you note the search returns incorrect results (which has nothing to do with xref content) so I'd say the indexing of given project lead to inconsistent/corrupted index so my advice would be to reindex from scratch.

The IllegalStateException: cannot close: prepareCommit was already called with no corresponding call to commit might be a consequence of something else (see e.g. #718 (comment)).

As for the previous exception (ProcessingException: Cannot find trust store file) I suspect this is related to the fact that the webapp URI uses HTTPS for connection. Most likely related to certificate processing.