Analyzing databases with the CodeQL CLI¶

To analyze a codebase, you run queries against a CodeQL database extracted from the code.

CodeQL analyses produce interpreted results that can be displayed as alerts or paths in source code. For information about writing queries to run with database analyze, see “Using custom queries with the CodeQL CLI.”

Other query-running commands

Queries run with database analyze have strict metadata requirements. You can also execute queries using the following plumbing-level subcommands:

database run-queries, which outputs non-interpreted results in an intermediate binary format called BQRS.

query run, which will output BQRS files, or print results tables directly to the command line. Viewing results directly in the command line may be useful for iterative query development using the CLI.

Queries run with these commands don’t have the same metadata requirements. However, to save human-readable data you have to process each BQRS results file using the bqrs decode plumbing subcommand. Therefore, for most use cases it’s easiest to use database analyze to directly generate interpreted results.

Before starting an analysis you must:

Set up the CodeQL CLI so that it can find the queries and libraries included in the CodeQL repository.
Create a CodeQL database for the source code you want to analyze.

Running `codeql database analyze`¶

When you run database analyze, it:

Optionally downloads any referenced CodeQL packages that are not available locally.
Executes one or more query files, by running them over a CodeQL database.
Interprets the results, based on certain query metadata, so that alerts can be displayed in the correct location in the source code.
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> <queries>

You must specify:

<database>: the path to the CodeQL database you want to analyze.
--format: the format of the results file generated during analysis. A number of different formats are supported, including CSV, SARIF, and graph formats. For more information about CSV and SARIF, see Results. To find out which other results formats are supported, see the database analyze reference.
--output: the output path of the results file generated during analysis.

You can also specify:

...<query-specifications>: a list of queries to run over your database. This is a list of arguments. Where each argument can be:
- a path to a query file
- a path to a directory containing query files
- a path to a query suite file
- the name of a CodeQL query pack If omitted, the default query suite for the language of the database being analyzed will be used. For more information, see the examples below.
--sarif-category: an identifying category for the results. Used when you want to upload more than one set of results for a commit. For example, when you use github upload-results to send results for more than one language to the GitHub code scanning API. For more information about this use case, see Configuring CodeQL CLI in your CI system in the GitHub documentation.
--sarif-add-query-help: (supported in version 2.7.1 onwards) adds any custom query help written in markdown to SARIF files (v2.1.0 or later) generated by the analysis. Query help stored in .qhelp files must be converted to .md before running the analysis. For further information, see “Including query help for custom CodeQL queries in SARIF files.”
--download: a boolean flag that will allow the CLI to download any referenced CodeQL packages that are not available locally. If this flag is missing and a referenced CodeQL package is not available locally, the command will fail.
--threads: optionally, the number of threads to use when running queries. The default option is 1. You can specify more threads to speed up query execution. Specifying 0 matches the number of threads to the number of logical processors.

Upgrading databases

If the CodeQL queries you want to use are newer than the extractor used to create the database, then you may see a message telling you that your database needs to be upgraded when you run database analyze. You can quickly upgrade a database by running the database upgrade command. For more information, see “Upgrading CodeQL databases.”

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

Examples¶

The following examples assume your CodeQL databases have been created in a directory that is a sibling of your local copies of the CodeQL and CodeQL for Go repositories.

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 <javascript-database> ../ql/javascript/ql/src/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).

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 a CodeQL pack¶

Note

The CodeQL package management functionality, including CodeQL packs, is currently available as a beta release and is subject to change. During the beta release, CodeQL packs are available only using GitHub Packages - the GitHub Container registry. To use this beta functionality, install version 2.6.0 or higher of the CodeQL CLI bundle from: https://github.com/github/codeql-action/releases.

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

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

The analyze command above runs the default suite from microsoft/coding-standards v1.0.0 and the latest version of github/security-queries on the specified database. For further information about default suites, see “Publishing and using CodeQL packs”.

For more information about CodeQL packs, see About CodeQL Packs.

Running query suites¶

To run a query suite over 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> cpp-code-scanning.qls --format=sarifv2.1.0 --output=cpp-results.sarif

The analysis generates a file in the v2.1.0 SARIF 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 Analyzing a CodeQL database or Code scanning API in the GitHub documentation.

CodeQL query suites are .qls files that use directives to select queries to run based on certain metadata properties. The standard QL 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 “About QL packs.”

The standard query suites are stored at the following paths in the CodeQL repository:

ql/<language>/ql/src/codeql-suites/<language>-code-scanning.qls

and at the following path in the CodeQL for Go repository:

ql/src/codeql-suites/go-code-scanning.qls

The repository also includes the query suites used by LGTM.com. These are stored alongside the query suites for code scanning with names of the form: <language>-lgtm.qls.

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

Diagnostic and summary information¶

When you create a CodeQL database, the extractor stores diagnostic data in the database. The code scanning query suites include additional queries to report on this diagnostic data and calculate summary metrics. When the database analyze command completes, the CLI generates the results file and reports any diagnostic and summary data to standard output. If you choose to generate SARIF output, the additional data is also included in the SARIF file.

If the analysis found fewer results for standard queries than you expected, review the results of the diagnostic and summary queries to check whether the CodeQL database is likely to be a good representation of the codebase that you want to analyze.

Integrating a CodeQL pack into a code scanning workflow in GitHub¶

Note

The CodeQL package management functionality, including CodeQL packs, is currently available as a beta release and is subject to change. During the beta release, CodeQL packs are available only using GitHub Packages - the GitHub Container registry. To use this beta functionality, install version 2.6.0 or higher of the CodeQL CLI bundle from: https://github.com/github/codeql-action/releases.

You can use CodeQL query packs in your code scanning setup. This allows you to select query packs published by various sources and use them to analyze your code. For more information, see “Using CodeQL query packs in the CodeQL action” or “Downloading and using CodeQL query packs in your CI system.”

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.

Important

You shouldn’t specify the root of a QL pack when executing database analyze as it contains some special queries that aren’t designed to be used with the command. Rather, to run a wide range of useful queries, run one of the LGTM.com query suites.

For example, to execute all Python queries contained in the Functions directory you would run:

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

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.

Including query help for custom CodeQL queries in SARIF files¶

If you use the CodeQL CLI to to run code scanning analyses on third party CI/CD systems, you can include the query help for your custom queries in SARIF files generated during an analysis. After uploading the SARIF file to GitHub, the query help is shown in the code scanning UI for any alerts generated by the custom queries.

From CodeQL CLI 2.7.1 onwards, you can include markdown-rendered query help in SARIF files by providing the --sarif-add-query-help option when running codeql database analyze. For more information, see Configuring CodeQL CLI in your CI system in the GitHub documentation.

You can write query help for custom queries directly in a markdown file and save it alongside the corresponding query. Alternatively, for consistency with the standard CodeQL queries, you can write query help in the .qhelp format. Query help written in .qhelp files can’t be included in SARIF files, and they can’t be processed by code scanning so must be converted to markdown before running the analysis. For more information, see “Query help files” and “Testing query help files.”

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 SARIF output.

If you choose to generate results in CSV format, then each line in the output file corresponds to an alert. Each line is a comma-separated list with the following information:

Property	Description	Example
Name	Name of the query that identified the result.	`Inefficient regular expression`
Description	Description of the query.	`A regular expression that requires exponential time to match certain inputs can be a performance bottleneck, and may be vulnerable to denial-of-service attacks.`
Severity	Severity of the query.	`error`
Message	Alert message.	`This part of the regular expression may cause exponential backtracking on strings containing many repetitions of '\\\\'.`
Path	Path of the file containing the alert.	`/vendor/codemirror/markdown.js`
Start line	Line of the file where the code that triggered the alert begins.	`617`
Start column	Column of the start line that marks the start of the alert code. Not included when equal to 1.	`32`
End line	Line of the file where the code that triggered the alert ends. Not included when the same value as the start line.	`64`
End column	Where available, the column of the end line that marks the end of the alert code. Otherwise the end line is repeated.	`617`

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.