Can't setup query-filters: exclude by query id

[bouillon]

I am new to CodeQL and have successfully run analyses on our Python codebase locally using the full set of Python queries like this:

codeql database analyze /tmp/codeql_db codeql/python-queries --format csv --output /tmp/codeql-report.csv --download

I would like to exclude certain queries and found the query-filters option:

query-filters:
  - exclude:
      id: py/missing-docstring
  - exclude:
      id: py/todo-comment

The documentation for this is found in this issue: #7937

However, I'm unsure about where or how to apply the configuration file. The codeql database analyze --help command doesn't accept a configuration file parameter.

I've tried adding this configuration to .github/workflows/codeql-analysis.yml, but it didn't work.

Could you show me what the content of the configuration file should look like and what its name should be?

[mbg]

Hi @bouillon 👋

The issue you linked to discusses how to filter out queries when running CodeQL in a GitHub Actions workflow. For usage with the CLI, you can put together a custom query suite. There is an example of what such a file would look like to filter out some queries from an existing suite.

[bouillon]

Thanks.
I created a file codeqlfilter.qls with very simple content

- qlpack: codeql/python-queries

I would expect this a call like

codeql database analyze /tmp/codeql_db/ codeqlfilter.qls --format csv --output /tmp/codeql-report.csv --download --threads=12

produce me the same result as without codeqlfilter.qls but a get much less results (only errors)

all recommendations, like missing doc-string are missing.

$ codeql resolve queries codeqlfilter.qls
Recording pack reference codeql/python-queries at .../python-queries/0.9.9.
Running the default query suite of codeql/python-queries. In order to run all queries in the query suite, use a clause like this:
- queries: '.'
  from: codeql/python-queries
  version: 0.9.9 # Optional
Recording pack reference codeql/suite-helpers at .../python-queries/0.9.9/.codeql/libraries/codeql/suite-helpers/0.7.9.
.../python-queries/0.9.9/Expressions/UseofInput.ql
.../python-queries/0.9.9/Security/CVE-2018-1281/BindToAllInterfaces.ql
.../python-queries/0.9.9/Security/CWE-020/IncompleteHostnameRegExp.ql
.../python-queries/0.9.9/Security/CWE-020/IncompleteUrlSubstringSanitization.ql
.../python-queries/0.9.9/Security/CWE-020/OverlyLargeRange.ql
.../python-queries/0.9.9/Security/CWE-022/PathInjection.ql
.../python-queries/0.9.9/Security/CWE-078/CommandInjection.ql
.../python-queries/0.9.9/Security/CWE-079/ReflectedXss.ql
.../python-queries/0.9.9/Security/CWE-089/SqlInjection.ql
.../python-queries/0.9.9/Security/CWE-090/LdapInjection.ql
.../python-queries/0.9.9/Security/CWE-094/CodeInjection.ql
.../python-queries/0.9.9/Security/CWE-116/BadTagFilter.ql
.../python-queries/0.9.9/Security/CWE-209/StackTraceExposure.ql
.../python-queries/0.9.9/Security/CWE-215/FlaskDebug.ql
.../python-queries/0.9.9/Security/CWE-285/PamAuthorization.ql
.../python-queries/0.9.9/Security/CWE-295/MissingHostKeyValidation.ql
.../python-queries/0.9.9/Security/CWE-312/CleartextLogging.ql
.../python-queries/0.9.9/Security/CWE-312/CleartextStorage.ql
.../python-queries/0.9.9/Security/CWE-326/WeakCryptoKey.ql
.../python-queries/0.9.9/Security/CWE-327/BrokenCryptoAlgorithm.ql
.../python-queries/0.9.9/Security/CWE-327/InsecureDefaultProtocol.ql
.../python-queries/0.9.9/Security/CWE-327/InsecureProtocol.ql
.../python-queries/0.9.9/Security/CWE-327/WeakSensitiveDataHashing.ql
.../python-queries/0.9.9/Security/CWE-352/CSRFProtectionDisabled.ql
.../python-queries/0.9.9/Security/CWE-377/InsecureTemporaryFile.ql
.../python-queries/0.9.9/Security/CWE-502/UnsafeDeserialization.ql
.../python-queries/0.9.9/Security/CWE-601/UrlRedirect.ql
.../python-queries/0.9.9/Security/CWE-611/Xxe.ql
.../python-queries/0.9.9/Security/CWE-643/XpathInjection.ql
.../python-queries/0.9.9/Security/CWE-730/PolynomialReDoS.ql
.../python-queries/0.9.9/Security/CWE-730/ReDoS.ql
.../python-queries/0.9.9/Security/CWE-730/RegexInjection.ql
.../python-queries/0.9.9/Security/CWE-776/XmlBomb.ql
.../python-queries/0.9.9/Security/CWE-918/FullServerSideRequestForgery.ql
.../python-queries/0.9.9/Diagnostics/ExtractedFiles.ql
.../python-queries/0.9.9/Diagnostics/ExtractionWarnings.ql
.../python-queries/0.9.9/Summary/LinesOfCode.ql
.../python-queries/0.9.9/Summary/LinesOfUserCode.ql

Also i wondering if the file has content

- qlpack: codeql/python-queries
- include:
    id:
      - py/missing-docstring
      - py/todo-comment

$ codeql resolve queries codeqlfilter.qls
Recording pack reference codeql/python-queries at .../codeql/codeql/qlpacks/codeql/python-queries/0.9.9.
Running the default query suite of codeql/python-queries. In order to run all queries in the query suite, use a clause like this:
- queries: '.'
  from: codeql/python-queries
  version: 0.9.9 # Optional
Recording pack reference codeql/suite-helpers at .../codeql/qlpacks/codeql/python-queries/0.9.9/.codeql/libraries/codeql/suite-helpers/0.7.9.
WARNING: No queries found in query suite. (..../active/api/codeqlfilter.qls:1,1-1)

It seem codeql not found all queries for python as by default?

[mbg]

@bouillon you could try to change

- qlpack: codeql/python-queries

to

- queries: .
  from: codeql/python-queries

to include all Python queries, not just the default ones.

[bouillon]

Thanks this include all queries but i get an exception and the output file is not generated.
Is there any way to ignore exceptions like this:

-queries/0.9.9/Security/CWE-020-ExternalAPIs/ExternalAPIsUsedWithUntrustedData.ql.
Error was: Unknown kind "Table". [UNSUPPORTED_KIND]

I found this but how to configure it #13839

How to configure and include only compatible queries?

[bouillon]

Ok my config

- queries: .
  from: codeql/python-queries
- include:
    kind: problem
- exclude:
    id:
      - py/missing-docstring
      - py/todo-comment

Any comments are wellcome

[mbg]

This seems like unintended behaviour on our end and I have passed this on to our Python team to have a look to see if there's a Python-specific issue which triggers this error here.

In the meantime, you could try to explicitly exclude table queries from the query suite:

- queries: .
  from: codeql/python-queries
- include:
    kind: problem
- exclude:
    id:
      - py/missing-docstring
      - py/todo-comment
- exclude:
    kind: table

Let me know if that works for you.

[bouillon]

Thank you for support