.. _analyzing-databases-with-the-codeql-cli:

Analyzing databases with the CodeQL CLI
=======================================

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

CodeQL analyses produce :ref:`interpreted results
<interpret-query-results>` that can be displayed as alerts or paths in source code.
For information about writing queries to run with ``database analyze``, see
":doc:`Using custom queries with the CodeQL CLI <using-custom-queries-with-the-codeql-cli>`."

.. include:: ../reusables/advanced-query-execution.rst

Before starting an analysis you must:

- :doc:`Set up the CodeQL CLI <getting-started-with-the-codeql-cli>` so that it can find the queries
  and libraries included in the CodeQL repository.
- :doc:`Create a CodeQL database <creating-codeql-databases>` for the source
  code you want to analyze.


Running ``codeql database analyze``
------------------------------------

When you run ``database analyze``, it:

#. 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, :ref:`SARIF
  <sarif-file>`, and graph formats. For more information about CSV and SARIF,
  see `Results <#results>`__. To find out which other results formats are
  supported, see the `database analyze reference
  <../manual/database-analyze>`__.

- ``--output``: the output path of the results file generated during analysis.

You can also specify:

- ``<queries>``: the queries to run over your database. You can
  list one or more individual query files, specify a directory that will be
  searched recursively for query files, or name a query suite that defines a
  particular set of queries. If omitted, the default query suite for the language
  of the database being analyzed will be usedFor more information, see the
  :ref:`examples <database-analyze-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 <https://docs.github.com/en/code-security/secure-coding/using-codeql-code-scanning-with-your-existing-ci-system/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 ":ref:`Including query help for custom CodeQL queries in SARIF files  <including-query-help-for-custom-codeql-queries-in-sarif-files>`."

- .. include:: ../reusables/threads-query-execution.rst


.. pull-quote::

   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 ":doc:`Upgrading CodeQL databases
   <upgrading-codeql-databases>`."

For full details of all the options you can use when analyzing databases, see
the `database analyze reference documentation <../manual/database-analyze>`__.

.. _database-analyze-examples:

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 ":doc:`Using custom queries with the CodeQL CLI <using-custom-queries-with-the-codeql-cli>`."

Running a CodeQL pack
~~~~~~~~~~~~~~~~~~~~~

.. include:: ../reusables/beta-note-package-management.rst

To run an existing CodeQL query pack from the GitHub Container registry, you need to download it first::

   codeql pack download microsoft/coding-standards@1.0.0

Afterwards, you can run the pack on a specific database::

   codeql database analyze <database> microsoft/coding-standards@1.0.0 <scope>/<other-pack> --format=sarifv2.1.0 --output=query-results.sarif

The ``analyze`` command above runs the default suite from ``microsoft/coding-standards v1.0.0`` and the latest version of ``scope/other-pack`` on the specified database.
For further information about default suites, see ":ref:`Publishing and using CodeQL packs <publishing-and-using-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 <https://docs.github.com/en/code-security/secure-coding/configuring-codeql-cli-in-your-ci-system#analyzing-a-codeql-database>`__
or `Code scanning API <https://docs.github.com/en/rest/reference/code-scanning>`__ 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 ":ref:`About QL packs <standard-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 <https://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 ":doc:`Creating
CodeQL query suites <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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. include:: ../reusables/beta-note-package-management.rst

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 <https://docs.github.com/en/code-security/secure-coding/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-codeql-query-packs/>`_" or "`Downloading and using CodeQL query packs in your CI system <https://docs.github.com/en/code-security/secure-coding/using-codeql-code-scanning-with-your-existing-ci-system/configuring-codeql-cli-in-your-ci-system#downloading-and-using-codeql-query-packs>`_."


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.

.. pull-quote::

   Important

   You shouldn't specify the root of a :doc:`QL pack
   <about-ql-packs>` 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: 

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 <https://docs.github.com/en/code-security/code-scanning/using-codeql-code-scanning-with-your-existing-ci-system/configuring-codeql-cli-in-your-ci-system#analyzing-a-codeql-database>`__
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 ":ref:`Query help files <query-help-files>`" 
and ":doc:`Testing query help files <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 :doc:`SARIF output <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:

.. list-table::
   :header-rows: 1
   :widths: 20 40 40

   * - 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.

Further reading
---------------

- ":ref:`Analyzing your projects in CodeQL for VS Code <analyzing-your-projects>`"
