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Migrating from the CodeQL runner to CodeQL CLI

In this article

You can use the CodeQL CLI to complete the same tasks as with the CodeQL runner.

Code scanning is available for organization-owned repositories in GitHub Enterprise Server. This feature requires a license for GitHub Advanced Security. For more information, see "About GitHub Advanced Security."

On April 1, 2022, the CodeQL runner was fully deprecated. You should use the CodeQL CLI version 2.6.2 and greater instead. This document describes how to migrate common workflows from the CodeQL runner to the CodeQL CLI.

Installation

Download the CodeQL bundle from the github/codeql-action repository. This bundle contains the CodeQL CLI and the standard CodeQL queries and libraries.

For more information on setting up the CodeQL CLI, see "Installing CodeQL CLI in your CI system."

Overview of workflow changes

A typical workflow that uses the CodeQL runner to analyze a codebase has the following steps.

  • codeql-runner-<platform> init to start creating CodeQL databases and read the configuration.
  • For compiled languages: set environment variables produced by the init step.
  • For compiled languages: run autobuild or manual build steps.
  • codeql-runner-<platform> analyze to finish creating CodeQL databases, run queries to analyze each CodeQL database, summarize the results in a SARIF file, and upload the results to GitHub.

A typical workflow that uses the CodeQL CLI to analyze a codebase has the following steps.

  • codeql database create to create CodeQL databases.
    • For compiled languages: Optionally provide a build command.
  • codeql database analyze to run queries to analyze each CodeQL database and summarize the results in a SARIF file. This command must be run once for each language or database.
  • codeql github upload-results to upload the resulting SARIF files to GitHub, to be displayed as code scanning alerts. This command must be run once for each language or SARIF file.

The CodeQL runner is multithreaded by default. The CodeQL CLI only uses a single thread by default, but allows you to specify the amount of threads you want it to use. If you want to replicate the behavior of the CodeQL runner to use all threads available on the machine when using the CodeQL CLI, you can pass --threads 0 to codeql database analyze.

For more information, see "Configuring CodeQL CLI in your CI system."

Examples of common uses for the CodeQL CLI

About the examples

These examples assume that the source code has been checked out to the current working directory. If you use a different directory, change the --source-root argument and the build steps accordingly.

These examples also assume that the CodeQL CLI is placed on the current PATH.

In these examples, a GitHub token with suitable scopes is stored in the $TOKEN environment variable and passed to the example commands via stdin, or is stored in the $GITHUB_TOKEN environment variable.

The ref name and commit SHA being checked out and analyzed in these examples are known during the workflow. For a branch, use refs/heads/BRANCH-NAME as the ref. For the head commit of a pull request, use refs/pull/NUMBER/head. For a GitHub-generated merge commit of a pull request, use refs/pull/NUMBER/merge. The examples below all use refs/heads/main. If you use a different branch name, you must modify the sample code.

Single non-compiled language (JavaScript)

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages javascript \
    --github-url https://github.com --github-auth-stdin

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo
    --github-url https://github.com --github-auth-stdin
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

codeql database create /codeql-dbs/example-repo --language=javascript \
    --source-root=.

# The default query suite is called `<language>-code-scanning.qls`.
codeql database analyze /codeql-dbs/example-repo \
    javascript-code-scanning.qls --sarif-category=javascript \
    --format=sarif-latest --output=/temp/example-repo-js.sarif

echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-js.sarif --github-auth-stdin

Single non-compiled language (JavaScript) using a different query suite (security-and-quality)

A similar approach can be taken for compiled languages, or multiple languages.

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages javascript \
    --github-url https://github.com --github-auth-stdin

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo \
    --queries security-and-quality \
    --github-url https://github.com --github-auth-stdin \
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

codeql database create /codeql-dbs/example-repo --language=javascript \
    --source-root=.

# Use `<language>-<suite name>.qls`
codeql database analyze /codeql-dbs/example-repo  \
    javascript-security-and-quality.qls --sarif-category=javascript
    --format=sarif-latest --output=/temp/example-repo-js.sarif

echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-js.sarif --github-auth-stdin

Single non-compiled language (JavaScript) using a custom configuration file

A similar approach can be taken for compiled languages, or multiple languages.

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages javascript \
    --config-file .github/codeql/codeql-config.yml \
    --github-url https://github.com --github-auth-stdin

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo \
    --github-url https://github.com --github-auth-stdin \
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

# Use `--codescanning-config` with the path to the YAML configuration file.
codeql database create /codeql-dbs/example-repo --language=javascript \
    --codescanning-config=.github/codeql/codeql-config.yml \
    --source-root=.

codeql database analyze /codeql-dbs/example-repo  \
    --sarif-category=javascript
    --format=sarif-latest --output=/temp/example-repo-js.sarif

echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-js.sarif --github-auth-stdin

Single compiled language using autobuild (Java)

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages java \
    --github-url https://github.com --github-auth-stdin

# Source the script generated by the init step to set up the environment to monitor the build.
. codeql-runner/codeql-env.sh

# Run the autobuilder for the given language.
codeql-runner-linux autobuild --language java

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo
    --github-url https://github.com --github-auth-stdin
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

# Run `codeql database create` without `--command`.
# This will run the autobuilder for the given language.
codeql database create /codeql-dbs/example-repo --language=java \
    --source-root=.

codeql database analyze /codeql-dbs/example-repo  \
    javascript-code-scanning.qls --sarif-category=java
    --format=sarif-latest --output=/temp/example-repo-java.sarif

echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-java.sarif --github-auth-stdin

Single compiled language using a custom build command (Java)

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages java \
    --github-url https://github.com --github-auth-stdin

# Source the script generated by the init step to set up the environment to monitor the build.
. codeql-runner/codeql-env.sh

# Run a custom build command.
mvn compile -DskipTests

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo
    --github-url https://github.com --github-auth-stdin
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

# Provide an explicit build command using `--command`.
codeql database create /codeql-dbs/example-repo --language=java \
    --command="mvn compile -DskipTests" --source-root=.

codeql database analyze /codeql-dbs/example-repo  \
    java-code-scanning.qls --sarif-category=java
    --format=sarif-latest --output=/temp/example-repo-java.sarif

echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-java.sarif --github-auth-stdin

Single compiled language using indirect build tracing (C# on Windows within Azure DevOps)

Indirect build tracing for a compiled language enables CodeQL to detect all build steps between the init and analyze steps, when the code cannot be built using the autobuilder or an explicit build command line. This is useful when using preconfigured build steps from your CI system, such as the VSBuild and MSBuild tasks in Azure DevOps.

Runner:

- task: CmdLine@1
  displayName: CodeQL Initialization
  inputs:
  script: "%CodeQLRunner%\\codeql-runner-win.exe init --repository my-org/example-repo --languages csharp --github-url https://github.com --github-auth $(Token)"
# Set the generated environment variables so they are available for subsequent commands, in the format required by Azure Pipelines.
- task: PowerShell@1
  displayName: Set CodeQL Environment Variables
  inputs:
      targetType: inline
      script: >
          $json = Get-Content $(System.DefaultWorkingDirectory)/codeql-runner/codeql-env.json | ConvertFrom-Json
          $json.PSObject.Properties | ForEach-Object {
              $template = "##vso[task.setvariable variable="
              $template += $_.Name
              $template += "]"
              $template += $_.Value
              echo "$template"
          }

# Execute a clean build using the VSBuild task.
- task: VSBuild@1
  inputs:
      solution: '**/*.sln'
      msbuildArgs: '/p:OutDir=$(Build.ArtifactStagingDirectory) /p:UseSharedCompilation=false'
      platform: Any CPU
      configuration: Release
      clean: True
  displayName: Visual Studio Build

# Analyze the database created as part of the build, by running the selected queries against it, and upload results to GitHub.
- task: CmdLine@2
  displayName: CodeQL Analyze
  inputs:
      script: '%CodeQLRunner%\codeql-runner-win.exe analyze --repository my-org/example-repo --commit $(Build.SourceVersion) --ref $(Build.SourceBranch) --github-url https://github.com --github-auth $(Token)'

CLI:

# Run any pre-build tasks, for example, restore NuGet dependencies...

# Initialize the CodeQL database using `codeql database init --begin tracing`.
- task: CmdLine@1
  displayName: Initialize CodeQL database
  inputs:
      # Assumes the source code is checked out to the current working directory.
      # Creates a database at `/codeql-dbs/example-repo`.
      # Running on Windows, so specifies a trace process level.
      script: "codeql database init --language csharp --trace-process-name Agent.Worker.exe --source-root . --begin-tracing /codeql-dbs/example-repo"

# For CodeQL to trace future build steps without knowing the explicit build commands,
# it requires certain environment variables to be set during the build.
# Read these generated environment variables and values, and set them so they are available for subsequent commands
# in the build pipeline. This is done in PowerShell in this example.
- task: PowerShell@1
  displayName: Set CodeQL environment variables
  inputs:
      targetType: inline
      script: >
         $json = Get-Content /codeql-dbs/example-repo/temp/tracingEnvironment/start-tracing.json | ConvertFrom-Json
         $json.PSObject.Properties | ForEach-Object {
             $template = "##vso[task.setvariable variable="
             $template += $_.Name
             $template += "]"
             $template += $_.Value
             echo "$template"
         }

# Execute the pre-defined build step. Note the `msbuildArgs` variable.
- task: VSBuild@1
    inputs:
      solution: '**/*.sln'
      # Disable MSBuild shared compilation for C# builds.
      msbuildArgs: /p:OutDir=$(Build.ArtifactStagingDirectory) /p:UseSharedCompilation=false
      platform: Any CPU
      configuration: Release
      # Execute a clean build, in order to remove any existing build artifacts prior to the build.
      clean: True
   displayName: Visual Studio Build

# Read and set the generated environment variables to end build tracing. This is done in PowerShell in this example.
- task: PowerShell@1
   displayName: Clear CodeQL environment variables
   inputs:
      targetType: inline
      script: >
         $json = Get-Content $(System.DefaultWorkingDirectory)/db/temp/tracingEnvironment/end-tracing.json | ConvertFrom-Json
         $json.PSObject.Properties | ForEach-Object {
             $template = "##vso[task.setvariable variable="
             $template += $_.Name
             $template += "]"
             $template += $_.Value
             echo "$template"
         }

# Use `codeql database finalize` to complete database creation after the build is done.
- task: CmdLine@2
   displayName: Finalize CodeQL database
   inputs:
      script: 'codeql database finalize /codeql-dbs/example-repo'

# Analyze the database and upload the results.
- task: CmdLine@2
   displayName: Analyze CodeQL database
   inputs:
      script: 'codeql database analyze /codeql-dbs/example-repo csharp-code-scanning.qls --sarif-category=csharp --format=sarif-latest --output=/temp/example-repo-csharp.sarif'

- task: CmdLine@2
   displayName: Upload CodeQL results
   inputs:
      script: 'echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
    --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
    --sarif=/temp/example-repo-csharp.sarif --github-auth-stdin'

Multiple languages using autobuild (C++, Python)

This example is not strictly possible with the CodeQL runner. Only one language (the compiled language with the most files) will be analyzed.

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages cpp,python \
    --github-url https://github.com --github-auth-stdin

# Source the script generated by the init step to set up the environment to monitor the build.
. codeql-runner/codeql-env.sh

# Run the autobuilder for the language with the most files.
codeql-runner-linux autobuild

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo
    --github-url https://github.com --github-auth-stdin
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

# Create multiple databases using `--db-cluster`.
# Run autobuild by omitting `--command`.
codeql database create /codeql-dbs/example-repo-multi \
    --db-cluster --language cpp,python \
    --no-run-unnecessary-builds \
    --source-root .

# Analyze each database in turn and upload the results.
for language in cpp python; do
  codeql database analyze "/codeql-dbs/example-repo-multi/$language"  \
      "$language-code-scanning.qls" --sarif-category="$language"
      --format=sarif-latest --output="/temp/example-repo-$language.sarif"

  echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
      --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
      --sarif="/temp/example-repo-$language.sarif" --github-auth-stdin
done

Multiple languages using a custom build command (C++, Python)

Runner:

echo "$TOKEN" | codeql-runner-linux init --repository my-org/example-repo \
    --languages cpp,python \
    --github-url https://github.com --github-auth-stdin

# Source the script generated by the init step to set up the environment to monitor the build.
. codeql-runner/codeql-env.sh

# Run a custom build command.
make

echo "$TOKEN" | codeql-runner-linux analyze --repository my-org/example-repo
    --github-url https://github.com --github-auth-stdin
    --commit deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 --ref refs/heads/main

CLI:

# Create multiple databases using `--db-cluster`.
codeql database create /codeql-dbs/example-repo-multi \
    --db-cluster --language cpp,python \
    --command make --no-run-unnecessary-builds \
    --source-root .

# Analyze each database in turn and upload the results.
for language in cpp python; do
  codeql database analyze "/codeql-dbs/example-repo-multi/$language"  \
      "$language-code-scanning.qls" --sarif-category="$language"
      --format=sarif-latest --output="/temp/example-repo-$language.sarif"

  echo "$TOKEN" | codeql github upload-results --repository=my-org/example-repo \
      --ref=refs/heads/main --commit=deb275d2d5fe9a522a0b7bd8b6b6a1c939552718 \
      --sarif="/temp/example-repo-$language.sarif" --github-auth-stdin
done