Analyzing your code with CodeQL queries

About analyzing databases with the CodeQL CLI

To analyze a codebase, you run queries against a CodeQL database extracted from the code. CodeQL analyses produce results that can be uploaded to GitHub Enterprise Cloud to generate code scanning alerts.

Prerequisites

Before starting an analysis you must:

• Set up the CodeQL CLI to run commands locally.
• Create a CodeQL database for the source code you want to analyze.

The simplest way to run codeql database analyze is using the standard queries included in the CodeQL CLI bundle.

Running codeql database analyze

When you run database analyze, it:

1. Optionally downloads any referenced CodeQL packages that are not available locally.
2. Executes one or more query files, by running them over a CodeQL database.
3. Interprets the results, based on certain query metadata, so that alerts can be displayed in the correct location in the source code.
4. Reports the results of any diagnostic and summary queries to standard output.

You can analyze a database by running the following command:

codeql database analyze <database> --format=<format> --output=<output> <query-specifiers>...

codeql database analyze <database> --format=<format> \
    --sarif-category=<language-specifier> --output=<output> \
    <packs,queries>

You must specify <database>, --format, and --output. You can specify additional options depending on what analysis you want to do.

For full details of all the options you can use when analyzing databases, see "database analyze."

Basic example of analyzing a CodeQL database

This example analyzes a CodeQL database stored at /codeql-dbs/example-repo and saves the results as a SARIF file: /temp/example-repo-js.sarif. It uses --sarif-category to include extra information in the SARIF file that identifies the results as JavaScript. This is essential when you have more than one CodeQL database to analyze for a single commit in a repository.

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

> Running queries.
> Compiling query plan for /codeql-home/codeql/qlpacks/codeql-javascript/AngularJS/DisablingSce.ql.
...
> Shutting down query evaluator.
> Interpreting results.

Adding file coverage information to your results for monitoring

You can optionally submit file coverage information to GitHub Enterprise Cloud for display on the tool status page for code scanning. For more information about file coverage information, see "About the tool status page for code scanning."

To include file coverage information with your code scanning results, add the --sarif-add-baseline-file-info flag to the codeql database analyze invocation in your CI system, for example:

$ codeql database analyze /codeql-dbs/example-repo \
    javascript-code-scanning.qls --sarif-category=javascript-typescript \
    --sarif-add-baseline-file-info \ --format=sarif-latest \
    --output=/temp/example-repo-js.sarif

Examples of running database analyses

The following examples show how to run database analyze using CodeQL packs, and how to use a local checkout of the CodeQL repository. These examples assume your CodeQL databases have been created in a directory that is a sibling of your local copies of the CodeQL repository.

Running a CodeQL query pack

To run an existing CodeQL query pack from the GitHub Container registry, you can specify one or more pack names:

codeql database analyze <database> microsoft/coding-standards@1.0.0 github/security-queries --format=sarifv2.1.0 --output=query-results.sarif --download

This command runs the default query suite of two CodeQL query packs: microsoft/coding-standards version 1.0.0 and the latest version of github/security-queries on the specified database. For further information about default suites, see "Publishing and using CodeQL packs."

The --download flag is optional. Using it will ensure the query pack is downloaded if it isn’t yet available locally.

Running a single query

To run a single query over a CodeQL database for a JavaScript codebase, you could use the following command from the directory containing your database:

codeql database analyze --download <javascript-database> codeql/javascript-queries:Declarations/UnusedVariable.ql --format=csv --output=js-analysis/js-results.csv

This command runs a simple query that finds potential bugs related to unused variables, imports, functions, or classes—it is one of the JavaScript queries included in the CodeQL repository. You could run more than one query by specifying a space-separated list of similar paths.

The analysis generates a CSV file (js-results.csv) in a new directory (js-analysis).

Alternatively, if you have the CodeQL repository checked out, you can execute the same queries by specifying the path to the query directly:

codeql database analyze <javascript-database> ../ql/javascript/ql/src/Declarations/UnusedVariable.ql --format=csv --output=js-analysis/js-results.csv

You can also run your own custom queries with the database analyze command. For more information about preparing your queries to use with the CodeQL CLI, see "Using custom queries with the CodeQL CLI."

Running all queries in a directory

You can run all the queries located in a directory by providing the directory path, rather than listing all the individual query files. Paths are searched recursively, so any queries contained in subfolders will also be executed.

For example, to execute all Python queries contained in the Functions directory in the codeql/python-queries query pack you would run:

codeql database analyze <python-database> codeql/python-queries:Functions --format=sarif-latest --output=python-analysis/python-results.sarif --download

Alternatively, if you have the CodeQL repository checked out, you can execute the same queries by specifying the path to the directory directly:

codeql database analyze <python-database> ../ql/python/ql/src/Functions/ --format=sarif-latest --output=python-analysis/python-results.sarif

When the analysis has finished, a SARIF results file is generated. Specifying --format=sarif-latest ensures that the results are formatted according to the most recent SARIF specification supported by CodeQL.

Running a subset of queries in a CodeQL pack

If you are using CodeQL CLI v2.8.1 or later, you can include a path at the end of a pack specification to run a subset of queries inside the pack. This applies to any command that locates or runs queries within a pack.

The complete way to specify a set of queries is in the form scope/name@range:path, where:

• scope/name is the qualified name of a CodeQL pack.

• range is a semver range.

• path is a file system path to a single query, a directory containing queries, or a query suite file.

When you specify a scope/name, the range and path are optional. If you omit a range then the latest version of the specified pack is used. If you omit a path then the default query suite of the specified pack is used.

The path can be one of a \*.ql query file, a directory containing one or more queries, or a .qls query suite file. If you omit a pack name, then you must provide a path, which will be interpreted relative to the working directory of the current process.

If you specify a scope/name and path, then the path cannot be absolute. It is considered relative to the root of the CodeQL pack.

To analyze a database using all queries in the experimental/Security folder within the codeql/cpp-queries CodeQL pack you can use:

codeql database analyze --format=sarif-latest --output=results <db> \
    codeql/cpp-queries:experimental/Security

To run the RedundantNullCheckParam.ql query in the codeql/cpp-queries CodeQL pack use:

codeql database analyze --format=sarif-latest --output=results <db> \
    'codeql/cpp-queries:experimental/Likely Bugs/RedundantNullCheckParam.ql'

To analyze your database using the cpp-security-and-quality.qls query suite from a version of the codeql/cpp-queries CodeQL pack that is >= 0.0.3 and < 0.1.0 (the highest compatible version will be chosen) you can use:

codeql database analyze --format=sarif-latest --output=results <db> \
   'codeql/cpp-queries@~0.0.3:codeql-suites/cpp-security-and-quality.qls'

If you need to reference a query file, directory, or suite whose path contains a literal @ or :, you can prefix the query specification with path: like so:

codeql database analyze --format=sarif-latest --output=results <db> \
    path:C:/Users/ci/workspace@2/security/query.ql

For more information about CodeQL packs, see Customizing analysis with CodeQL packs.

Running query suites

To run a query suite on a CodeQL database for a C/C++ codebase, you could use the following command from the directory containing your database:

codeql database analyze <cpp-database> codeql/cpp-queries:codeql-suites/cpp-code-scanning.qls --format=sarifv2.1.0 --output=cpp-results.sarif --download

This command downloads the codeql/cpp-queries CodeQL query pack, runs the analysis, and generates a file in the SARIF version 2.1.0 format that is supported by all versions of GitHub. This file can be uploaded to GitHub by executing codeql github upload-results or the code scanning API. For more information, see "Uploading CodeQL analysis results to GitHub" or "REST API endpoints for code scanning".

CodeQL query suites are .qls files that use directives to select queries to run based on certain metadata properties. The standard CodeQL packs have metadata that specify the location of the query suites used by code scanning, so the CodeQL CLI knows where to find these suite files automatically, and you don’t have to specify the full path on the command line. For more information, see "Creating CodeQL query suites."

For information about creating custom query suites, see "Creating CodeQL query suites."

Including model packs to add potential sources of tainted data

You can configure threat models in a code scanning analysis. For more information, see "Threat models for Java and Kotlin" and "Threat models for C#" in the CodeQL documentation.

$ codeql database analyze /codeql-dbs/my-company --format=sarif-latest \
  --threat-model=local \
  --output=/temp/my-company.sarif codeql/java-queries

In this example, the relevant queries in the standard query pack codeql/java-queries will use the local threat model as well as the default threat model for remote dataflow sources. You should use the local threat model if you consider data from local sources (for example: file systems, command-line arguments, databases, and environment variables) to be potential sources of tainted data for your codebase.

Results

You can save analysis results in a number of different formats, including SARIF and CSV.

The SARIF format is designed to represent the output of a broad range of static analysis tools. For more information, see "CodeQL CLI SARIF output."

For more information about what the results look like in CSV format, see "CodeQL CLI CSV output."

Results files can be integrated into your own code-review or debugging infrastructure. For example, SARIF file output can be used to highlight alerts in the correct location in your source code using a SARIF viewer plugin for your IDE.

Viewing log and diagnostic information

When you analyze a CodeQL database using a code scanning query suite, in addition to generating detailed information about alerts, the CLI reports diagnostic data from the database generation step and summary metrics. If you choose to generate SARIF output, the additional data is also included in the SARIF file. For repositories with few alerts, you may find this information useful for determining if there are genuinely few problems in the code, or if there were errors generating the CodeQL database. For more detailed output from codeql database analyze, use the --verbose option.

For more information about the type of diagnostic information available, see "Viewing code scanning logs".

You can choose to export and upload diagnostic information to GitHub Enterprise Cloud even if a CodeQL analysis fails. For more information, see "Uploading CodeQL analysis results to GitHub."

Next steps

• To learn how to upload your CodeQL analysis results to GitHub Enterprise Cloud, see "Uploading CodeQL analysis results to GitHub."