content/code-security/codeql-cli/codeql-cli-manual/database-index-files.md

---
title: database index-files
versions: # DO NOT MANUALLY EDIT. CHANGES WILL BE OVERWRITTEN BY A 🤖
  fpt: '*'
  ghec: '*'
  ghes: '*'
topics:
  - Code Security
  - Code scanning
  - CodeQL
type: reference
product: '{% data reusables.gated-features.codeql %}'
autogenerated: codeql-cli
intro: '[Plumbing] Index standalone files with a given CodeQL extractor.'
redirect_from:
  - /code-security/codeql-cli/manual/database-index-files
---

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{% data reusables.codeql-cli.man-pages-version-note %}

## Synopsis

```shell copy
codeql database index-files --language=<lang> [--threads=<num>] [--ram=<MB>] [--extractor-option=<extractor-option-name=value>] <options>... -- <database>
```

## Description

\[Plumbing] Index standalone files with a given CodeQL extractor.

This command selects a set of files under the specified working
directory, and applies the given extractor to them. By default, all
files are selected. Typical invocations will specify options to restrict
the set of included files.

The `--include`, `--exclude`, and `--prune` options all take glob
patterns, which can use the following wildcard characters:

* A single "?" matches any character other than a forward/backward
  slash;
* A single "\*" matches any number of characters other than a
  forward/backward slash;
* The pattern "\*\*" matches zero or more complete directory
  components.

## Options

### Primary Options

#### `<database>`

\[Mandatory] Path to the CodeQL database under construction. This must
have been prepared for extraction with [codeql database init](/code-security/codeql-cli/codeql-cli-manual/database-init).

#### `-l, --language=<lang>`

\[Mandatory] The extractor that should be used to index matching files.

#### `-j, --threads=<num>`

Ask the extractor to use this many threads. This option is passed to the
extractor as a suggestion. If the CODEQL\_THREADS environment variable is
set, the environment variable value takes precedence over this option.

You can pass 0 to use one thread per core on the machine, or -_N_ to
leave _N_ cores unused (except still use at least one thread).

#### `-M, --ram=<MB>`

Ask the extractor to use this much memory. This option is passed to the
extractor as a suggestion. If the CODEQL\_RAM environment variable is
set, the environment variable value takes precedence over this option.

#### `--working-dir=<dir>`

\[Advanced] The directory in which the specified command should be
executed. If this argument is not provided, the command is executed in
the value of `--source-root` passed to [codeql database create](/code-security/codeql-cli/codeql-cli-manual/database-create), if one exists. If no `--source-root` argument is provided, the command is executed in the
current working directory.

### Options to control extractor behavior

#### `-O, --extractor-option=<extractor-option-name=value>`

Set options for CodeQL extractors. `extractor-option-name` should be of
the form extractor\_name.group1.group2.option\_name or
group1.group2.option\_name. If `extractor_option_name` starts with an
extractor name, the indicated extractor must declare the option
group1.group2.option\_name. Otherwise, any extractor that declares the
option group1.group2.option\_name will have the option set. `value` can
be any string that does not contain a newline.

You can use this command-line option repeatedly to set multiple
extractor options. If you provide multiple values for the same extractor
option, the behavior depends on the type that the extractor option
expects. String options will use the last value provided. Array options
will use all the values provided, in order. Extractor options specified
using this command-line option are processed after extractor options
given via `--extractor-options-file`.

When passed to [codeql database init](/code-security/codeql-cli/codeql-cli-manual/database-init) or `codeql database begin-tracing`, the options will only be
applied to the indirect tracing environment. If your workflow also makes
calls to
[codeql database trace-command](/code-security/codeql-cli/codeql-cli-manual/database-trace-command) then the options also need to be passed there if desired.

See <https://codeql.github.com/docs/codeql-cli/extractor-options> for
more information on CodeQL extractor options, including how to list the
options declared by each extractor.

#### `--extractor-options-file=<extractor-options-bundle-file>`

Specify extractor option bundle files. An extractor option bundle file
is a JSON file (extension `.json`) or YAML file (extension `.yaml` or
`.yml`) that sets extractor options. The file must have the top-level
map key 'extractor' and, under it, extractor names as second-level map
keys. Further levels of maps represent nested extractor groups, and
string and array options are map entries with string and array values.

Extractor option bundle files are read in the order they are specified.
If different extractor option bundle files specify the same extractor
option, the behavior depends on the type that the extractor option
expects. String options will use the last value provided. Array options
will use all the values provided, in order. Extractor options specified
using this command-line option are processed before extractor options
given via `--extractor-option`.

When passed to [codeql database init](/code-security/codeql-cli/codeql-cli-manual/database-init) or `codeql database begin-tracing`, the options will only be
applied to the indirect tracing environment. If your workflow also makes
calls to
[codeql database trace-command](/code-security/codeql-cli/codeql-cli-manual/database-trace-command) then the options also need to be passed there if desired.

See <https://codeql.github.com/docs/codeql-cli/extractor-options> for
more information on CodeQL extractor options, including how to list the
options declared by each extractor.

### Options for limiting the set of indexed files

#### `--include-extension=<.ext>`

Include all files in the search directory tree that have the given
extension. Typically, you should include the dot before the extension.
For example, passing `--include-extension .xml` will include all files
with the ".xml" extension. This option is incompatible with negated
`--include` options.

#### `--include=<glob>`

Include all files and directories in the search directory tree that
match the given glob, using each file and directory's relative path
from the search directory. If the glob begins with a `!` character, the
matching files and directories would instead be excluded.

`--include` options are processed in order, with later options
overriding earlier ones. For example,
`--include ** --include !sub/*.ts --include sub/main.*` would include
`sub/main.ts` (because it is included by `sub/main.*`), exclude
`sub/index.ts` (because it is excluded by `!sub/*.ts`), and include
`sub/test.js` (because it is included by `**` without being subsequently
excluded.)

#### `--also-match=<glob>`

Require all results to also match the given glob, using each file and
directory's relative path from the search directory. This option has
the same structure and the same interpretation as `--include` but
specifies a separate sequence of globs that are applied in conjunction
with `--include`.

#### `--exclude=<glob>`

Exclude all files and directories that match the given glob, using each
file and directory's relative path from the search directory. This
option overrides all include options. This option is incompatible with
negated `--include` options.

#### `--prune=<glob>`

Exclude all files and directories that match the given glob, using each
file and directory's relative path from the search directory. This
option overrides all include options. This option is incompatible with
negated `--include` options.

#### `--size-limit=<bytes>`

Exclude all files whose size exceeds the given limit. The size limit is
in bytes, or in kibibytes (KiB) with the "k" suffix, in mebibytes
(MiB) with the "m" suffix, and in gibibytes (GiB) with the "g"
suffix. This option overrides all include options.

#### `--total-size-limit=<bytes>`

Make the command exit with an error if the combined size of all resolved
files would exceed the given limit. The size limit is in bytes, or in
kibibytes (KiB) with the "k" suffix, in mebibytes (MiB) with the "m"
suffix, and in gibibytes (GiB) with the "g" suffix.

#### `--[no-]follow-symlinks`

Follow any symbolic links to their targets.

#### `--[no-]find-any`

Find at most one match (as opposed to all matches).

Available since `v2.11.3`.

### Common options

#### `-h, --help`

Show this help text.

#### `-J=<opt>`

\[Advanced] Give option to the JVM running the command.

(Beware that options containing spaces will not be handled correctly.)

#### `-v, --verbose`

Incrementally increase the number of progress messages printed.

#### `-q, --quiet`

Incrementally decrease the number of progress messages printed.

#### `--verbosity=<level>`

\[Advanced] Explicitly set the verbosity level to one of errors,
warnings, progress, progress+, progress++, progress+++. Overrides `-v`
and `-q`.

#### `--logdir=<dir>`

\[Advanced] Write detailed logs to one or more files in the given
directory, with generated names that include timestamps and the name of
the running subcommand.

(To write a log file with a name you have full control over, instead
give `--log-to-stderr` and redirect stderr as desired.)

#### `--common-caches=<dir>`

\[Advanced] Controls the location of cached data on disk that will
persist between several runs of the CLI, such as downloaded QL packs and
compiled query plans. If not set explicitly, this defaults to a
directory named `.codeql` in the user's home directory; it will be
created if it doesn't already exist.

Available since `v2.15.2`.