= The Elixir Cross Referencer
:doctype: book
:pp: {plus}{plus}
:toc:
:toc-placement!:

image::https://travis-ci.com/bootlin/elixir.svg?branch=master[Build Status,link=https://travis-ci.com/bootlin/elixir]

Elixir is a source code cross-referencer inspired by
https://en.wikipedia.org/wiki/LXR_Cross_Referencer[LXR]. It's written
in Python and its main purpose is to index every release of a C or C{pp}
project (like the Linux kernel) while keeping a minimal footprint.

It uses Git as a source-code file store and Berkeley DB for cross-reference
data. Internally, it indexes Git _blobs_ rather than trees of files to avoid
duplicating work and data. It has a straightforward data structure
(reminiscent of older LXR releases) to keep queries simple and fast.

You can see it in action on https://elixir.bootlin.com/

NOTE: this documentation applies to version 1.0 of Elixir.

toc::[]

= Requirements

* Python >= 3.6
* The Jinja2 and Pygments (>= 2.2) Python libraries
* Berkeley DB (and its Python binding)
* Exuberant Ctags
* Perl (for non-greedy regexes and automated testing)
* Falcon and `mod_wsgi` (for the REST API)

= Architecture

Elixir has the following architecture:

 .---------------.----------------.
 | CGI interface | REST interface |
 |---------------|----------------.
 | Query command | Update command |
 |---------------|----------------|
 |          Shell script          |
 '--------------------------------'

The shell script (`script.sh`) is the lower layer and provides commands
to interact with Git and other Unix utilities. The Python commands use
the shell script's services to provide access to the annotated source
code and identifier lists (`query.py`) or to create and update the
databases (`update.py`). Finally, the CGI interface (`web.py`) and
the REST interface (`api.py`) use the query interface to generate HTML
pages and to answer REST queries, respectively.

When installing the system, you should test each layer manually and make
sure it works correctly before moving on to the next one.

== Database design

`./update.py` stores a bidirectionnal mapping between git object hashes ("blobs") and a sequential key.
The goal of indexing such hashes is to reduce their storage footprint (20 bytes for a SHA-1 hash
versus 4 bytes for a 32 bit integer).

A detailed diagram of the databases will be provided. Until then, just use the Source, Luke.

= Manual Installation

== Install Dependences

____
For RedHat/CentOS
____

----
yum install python36-jinja2 python36-pygments python36-bsddb3 python3-falcon global-ctags git httpd
----

____
For Debian
____

----
sudo apt install python3 python3-jinja2 python3-pygments python3-bsddb3 python3-falcon python3-pytest exuberant-ctags perl git apache2 libapache2-mod-wsgi-py3
----

To enable the REST API, follow the installation instructions on https://github.com/GrahamDumpleton/mod_wsgi[`mod_wsgi`]
and connect it to the apache installation as detailed in https://github.com/GrahamDumpleton/mod_wsgi#connecting-into-apache-installation.

To know which packages to install, you can also read the Docker files in the `docker/` directory
to know what packages Elixir needs in your favorite distribution.

== Special dependencies

=== Device Tree and Kconfig Source syntax highlighting

The service on https://elixir.bootlin.com relies on a modified version of https://pygments.org/[Pygments],
to enable syntax highlighting on Device Tree Source (DTS) files and on all Kconfig files.

The changes have been sent upstream and should appear in future distributions.

In the meantime, you can either rebuild this package from its source on
https://github.com/MaximeChretien/pygments/tree/dev[GitHub], or download this
https://bootlin.com/pub/elixir/Pygments-2.6.1.elixir-py3-none-any.whl[binary module]
and install it as follows:

----
sudo pip3-install Pygments-2.6.1.elixir-py3-none-any.whl
----

== Download Elixir Project

----
git clone https://github.com/bootlin/elixir.git /usr/local/elixir/
----

== Create Directory

----
mkdir -p /path/elixir-data/linux/repo
mkdir -p /path/elixir-data/linux/data
----

== Set environment variables

Two environment variables are used to tell Elixir where to find the project's
local git repository and its databases:

* `LXR_REPO_DIR` (the git repository directory for your project)
* `LXR_DATA_DIR` (the database directory for your project)

Now open `/etc/profile` and append the following content.

----
export LXR_REPO_DIR=/path/elixir-data/linux/repo
export LXR_DATA_DIR=/path/elixir-data/linux/data
----

And then run `source /etc/profile`.

== Clone Kernel source code

First clone the master tree released by Linus Torvalds:

----
cd /pathy/elixir-data/linux
git clone https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git repo
----

Then, you should also declare a `stable` remote branch corresponding to the `stable` tree, to get all release updates:

----
cd repo
git remote add stable git://git.kernel.org/pub/scm/linux/kernel/git/stable/linux-stable.git
git fetch stable
----

Feel free to add more remote branches in this way, as Elixir will consider tags from all remote branches.

== First Test

----
cd /usr/local/elixir/
./script.sh list-tags
----

== Create Database

----
./update.py
----

____
Generating the full database can take a long time: it takes about 15 hours on a Xeon E3-1245 v5 to index 1800 tags in the Linux kernel. For that reason, you may want to tweak the script (for example, by limiting the number of tags with a "head") in order to test the update and query commands. You can even create a new Git repository and just create one tag instead of using the official kernel repository which is very large.
____

== Second Test

Verify that the queries work:

 $ ./query.py v4.10 ident raw_spin_unlock_irq
 $ ./query.py v4.10 file /kernel/sched/clock.c

NOTE: `v4.10` can be replaced with any other tag.

== Configure httpd

The CGI interface (`web.py`) is meant to be called from your web
server. Since it includes support for indexing multiple projects,
it expects a different variable (`LXR_PROJ_DIR`) which points to a
directory with a specific structure:

* `<LXR_PROJ_DIR>`
 ** `<project 1>`
  *** `data`
  *** `repo`
 ** `<project 2>`
  *** `data`
  *** `repo`
 ** `<project 3>`
  *** `data`
  *** `repo`

It will then generate the other two variables upon calling the query
command.

Now open `/etc/httpd/conf.d/elixir.conf` and write the following content.
Note: If using apache2 (Ubuntu/Debian) instead of httpd (RedHat/Centos),
the default config file to edit is: `/etc/apache2/sites-enabled/000-default.conf`

----
HttpProtocolOptions Unsafe
# Required for HTTP
<Directory /usr/local/elixir/http/>
    Options +ExecCGI
    AllowOverride None
    Require all granted
    SetEnv PYTHONIOENCODING utf-8
    SetEnv LXR_PROJ_DIR /path/elixir-data
</Directory>

# Required for the REST API
<Directory /usr/local/elixir/api/>
    SetHandler wsgi-script
    Require all granted
    SetEnv PYTHONIOENCODING utf-8
    SetEnv LXR_PROJ_DIR /path/elixir-data
</Directory>

AddHandler cgi-script .py
#Listen 80
<VirtualHost *:80>
    ServerName xxx
    DocumentRoot /usr/local/elixir/http

    # To enable REST api after installing mod_wsgi: Fill path and uncomment:
    #WSGIScriptAlias /api /usr/local/elixir/api/api.py

    AllowEncodedSlashes On

    RewriteEngine on
    RewriteRule "^/$" "/linux/latest/source" [R]
    RewriteRule "^/(?!api).*/(source|ident|search)" "/web.py" [PT]
</VirtualHost>
----

cgi and rewrite support has been enabled by default in RHEL/CentOS, but you should enable it manually if your distribution is Debian/Ubuntu.

----
a2enmod cgi rewrite
----

Finally, start the httpd server.

----
systemctl start httpd
----

== Configure lighthttpd

Here's a sample configuration for lighthttpd:

----
server.document-root = server_root + "/elixir/http"
url.redirect = ( "^/$" => "/linux/latest/source" )
url.rewrite  = ( "^/.*/(source|ident|search)" =>  "/web.py/$1")
setenv.add-environment = ( "PYTHONIOENCODING" => "utf-8",
    "LXR_PROJ_DIR" => "/path/to/elixir-data" )
----

= REST API usage

After configuring httpd, you can test the API usage:

== ident query

Send a get request to `/api/ident/<Project>/<Ident>?version=<version>`.
For example:

 curl http://127.0.0.1/api/ident/barebox/cdev?version=latest

The response body is of the following structure:

----
{
    "definitions":
        [{"path": "commands/loadb.c", "line": 71, "type": "variable"}, ...],
    "references":
        [{"path": "arch/arm/boards/cm-fx6/board.c", "line": "64,64,71,72,75", "type": null}, ...]
}
----

= Maintenance and enhancements

== Using a cache to improve performance

At Bootlin, we're using the https://varnish-cache.org/[Varnish http cache]
as a front-end to reduce the load on the server running the Elixir code.

 .-------------.           .---------------.           .-----------------------.
 | Http client | --------> | Varnish cache | --------> | Apache running Elixir |
 '-------------'           '---------------'           '-----------------------'

== Keeping Elixir databases up to date

To keep your Elixir databases up to date and index new versions that are released,
we're proposing to use a script like `utils/update-elixir-data` which is called
through a daily cron job.

== Keeping git repository disk usage under control

As you keep updating your git repositories, you may notice that some can become
considerably bigger than they originally were. This seems to happen when a `gc.log`
file appears in a big repository, apparently causing git's garbage collector (`git gc`)
to fail, and therefore causing the repository to consume disk space at a fast
pace every time new objects are fetched.

When this happens, you can save disk space by packing git directories as follows:

----
cd <bare-repo>
git prune
rm gc.log
git gc --aggressive
----

Actually, a second pass with the above commands will save even more space.

To process multiple git repositories in a loop, you may use the
`utils/pack-repositories` that we are providing, run from the directory
where all repositories are found.

= Building Docker images

Docker files are provided in the `docker/` directory. To generate your own
Docker image for indexing the sources of a project (for example for the Musl
project which is much faster to index that Linux), download the `Dockerfile`
file for your target distribution and run:

 $ docker build -t elixir --build-arg GIT_REPO_URL=git://git.musl-libc.org/musl --build-arg PROJECT=musl .

Then you can use your new container as follows (you get the container id from the output of `docker build`):

 $ docker run <container-id>

You can the open the below URL in a browser on your host: http://172.17.0.2/musl/latest/source
(change the container IP address if you don't get the default one)

= Hardware requirements

Performance requirements depend mostly on the amount of traffic that you get
on your Elixir service. However, a fast server also helps for the initial
indexing of the projects.

SSD storage is strongly recommended because of the frequent access to
git repositories.

At Bootlin, here are a few details about the server we're using:

* As of July 2019, our Elixir service consumes 17 GB of data (supporting all projects),
or for the Linux kernel alone (version 5.2 being the latest), 12 GB for indexing data,
and 2 GB for the git repository.
* We're using an LXD instance with 8 GB of RAM on a cloud server with 8 CPU cores
running at 3.1 GHz.

= Contributing to Elixir

== Supporting a new project

Elixir has a very simple modular architecture that allows to support
new source code projects by just adding a new file to the Elixir sources.

Elixir's assumptions:

* Project sources have to be available in a git repository
* All project releases are associated to a given git tag. Elixir
only considers such tags.

First make an installation of Elixir by following the above instructions.
See the `projects` subdirectory for projects that are already supported.

Once Elixir works for at least one project, it's time to clone the git
repository for the project you want to support:

 cd /srv/git
 git clone --bare https://github.com/zephyrproject-rtos/zephyr

After doing this, you may also reference and fetch remote branches for this project,
for example corresponding to the `stable` tree for the Linux kernel (see the
instructions for Linux earlier in this document).

Now, in your `LXR_PROJ_DIR` directory, create a new directory for the
new project:

 cd $LXR_PROJ_DIR
 mkdir -p zephyr/data
 ln -s /srv/git/zephyr.git repo
 export LXR_DATA_DIR=$LXR_PROJ_DIR/data
 export LXR_REPO_DIR=$LXR_PROJ_DIR/repo

Now, go back to the Elixir sources and test that tags are correctly
extracted:

 ./script.sh list-tags

Depending on how you want to show the available versions on the Elixir pages,
you may have to apply substitutions to each tag string, for example to add
a `v` prefix if missing, for consistency with how other project versions are
shown. You may also decide to ignore specific tags. All this can be done
by redefining the default `list_tags()` function in a new `project/<projectname>.sh`
file. Here's an example (`projects/zephyr.sh` file):

 list_tags()
 {
     echo "$tags" |
     grep -v '^zephyr-v'
 }

Note that `<project_name>` *must* match the name of the directory that
you created under `LXR_PROJ_DIR`.

The next step is to make sure that versions are classified as you wish
in the version menu. This classification work is done through the
`list_tags_h()` function which generates the output of the `./scripts.sh list-tags -h`
command. Here's what you get for the Linux project:

 v4 v4.16 v4.16
 v4 v4.16 v4.16-rc7
 v4 v4.16 v4.16-rc6
 v4 v4.16 v4.16-rc5
 v4 v4.16 v4.16-rc4
 v4 v4.16 v4.16-rc3
 v4 v4.16 v4.16-rc2
 v4 v4.16 v4.16-rc1
 ...

The first column is the top level menu entry for versions.
The second one is the next level menu entry, and
the third one is the actual version that can be selected by the menu.
Note that this third entry must correspond to the exact
name of the tag in git.

If the default behavior is not what you want, you will have
to customize the `list_tags_h` function.

You should also make sure that Elixir properly identifies
the most recent versions:

 ./script.sh get-latest

If needed, customize the `get_latest()` function.

You are now ready to generate Elixir's database for your
new project:

 ./update.py

You can then check that Elixir works through your http server.

== Coding style

If you wish to contribute to Elixir's Python code, please
follow the https://www.python.org/dev/peps/pep-0008/[official coding style for Python].

== How to send patches

The best way to share your contributions with us is to https://github.com/bootlin/elixir/pulls[file a pull
request on GitHub].

= Automated testing

Elixir includes a simple test suite in `t/`.  To run it,
from the top-level Elixir directory, run:

 prove

The test suite uses code extracted from Linux v5.4 in `t/tree`.

== Licensing of code in `t/tree`

The copied code is licensed as described in the https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/plain/COPYING[COPYING] file included with
Linux.  All the files copied carry SPDX license identifiers of `GPL-2.0+` or
`GPL-2.0-or-later`.  Per https://www.gnu.org/licenses/gpl-faq.en.html#AllCompatibility[GNU's compatibility table], GPL 2.0+ code can be used
under GPLv3 provided the combination is under GPLv3.  Moreover, https://www.gnu.org/licenses/license-list.en.html#AGPLv3.0[GNU's overview
of AGPLv3] indicates that its terms "effectively consist of the terms of GPLv3"
plus the network-use paragraph.  Therefore, the developers have a good-faith
belief that licensing these files under AGPLv3 is authorized.  (See also https://github.com/Freemius/wordpress-sdk/issues/166#issuecomment-310561976[this
issue comment] for another example of a similar situation.)
