Ran with database overwriting enabled, but the directory does not appear to be a CodeQL database or database cluster

[CaledoniaProject]

I'm creating a java database but maven fails:

codeql database create log4j-database -l=java -c="mvn clean install -file pom.xml -Dmaven.test.skip=true" --overwrite

When I run it again I got:

A fatal error occurred: Ran with database overwriting enabled, but the directory does not appear to be a CodeQL database or database cluster. Please check you do indeed wish to delete it, and do so manually.

When maven fails, codeql would fail to determine if it's a codeql database. That looks like a bug to me.

Here's the contents of log4j-database directory:

%> ls log4j-database/ -R
log4j-database/:
./  ../  log/  trap/

[smowton]

Can't reproduce this if I use -c false for a failing command. I'm using CodeQL CLI 2.8.2. What version are you using, and can you reproduce the problem using -c false? If not, what is the nature of the Maven failure that does reproduce this?

[hvitved]

I also tried to reproduce, and it works fine for me locally. Does the same thing happen if you first manually remove log4j-database, and then run the database create command twice?

[CaledoniaProject]

This happens every time in my environment:

1. Install jdk-17.0.2 on Mac
2. Download log4j source code: https://github.com/apache/logging-log4j2/archive/refs/tags/rel/2.11.0.zip
3. Run this command: codeql database create log4j-database -l=java -c="mvn clean install -file pom.xml -Dmaven.test.skip=true" --overwrite

And to reproduce the problem:

1. mkdir -p log4j-database/{log,trap}
2. codeql database create log4j-database -l=java -c="mvn clean install -file pom.xml -Dmaven.test.skip=true" --overwrite

[smowton]

That doesn't reproduce the problem for me:

$ codeql version
CodeQL command-line toolchain release 2.8.2.
...
$ unzip ~/Downloads/logging-log4j2-rel-2.11.0.zip
...
$ cd logging-log4j2-rel-2.11.0
$ codeql database create log4j-database -l=java -c="mvn clean install -file pom.xml -Dmaven.test.skip=true" --overwrite
... Maven fails, as you said: No toolchain found for type jdk ...
$ codeql database create log4j-database -l=java -c="mvn clean install -file pom.xml -Dmaven.test.skip=true" --overwrite
... The database is overwritten; Maven runs again and fails again in the same way.

I don't get the directory does not appear to be a CodeQL database error. I do get it if I mkdir -p log4j-database/{log,trap}, but that's expected as the database is missing the file codeql-database.yml.

[wac84s]

I am getting the same error reported above when using codeQL gitaction. Our runners dont clean up after themself always so passed the overwrite. Does the overwrite require a db to be there? Some runners wont be dirty.

Exit code was 2 and error was: A fatal error occurred: Ran with database overwriting enabled, but the directory does not appear to be a CodeQL database or database cluster. Please check you do indeed wish to delete it, and do so manually.