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README.adoc

The Elixir Cross Referencer

Build Status

Elixir is a source code cross-referencer inspired by LXR. It’s written in Python and its main purpose is to index every release of a C or C++ 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 2.0 of Elixir.

Requirements

  • Python >= 3.6

  • Git >= 1.9

  • The Jinja2 and Pygments (>= 2.2) Python libraries

  • Berkeley DB (and its Python binding)

  • Universal 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-pip python36-pytest python36-jinja2 python36-bsddb3 python36-falcon git httpd perl perl-autodie jansson libyaml rh-python36-mod_wsgi

For Debian

sudo apt install python3 python3-jinja2 python3-bsddb3 python3-falcon python3-pytest universal-ctags perl git apache2 libapache2-mod-wsgi-py3 libjansson4

To enable the REST API, follow the installation instructions on 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 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 GitHub, or download this binary module and install it as follows:

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

Kconfig identifiers support

The service on https://elixir.bootlin.com relies on a modified version of Universal-ctags, to enable indexing of Kconfig identifiers.

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 GitHub, or download this deb binary package or rpm binary package and install it as follows:

sudo dpkg -i universal-ctags_0+git20200526-0ubuntu1_amd64.deb
or
sudo rpm -iv universal-ctags-0+git~20e934e3-1.6.x86_64.rpm

Then tell apt to hold this package and block future updates of the normal package:

sudo apt-mark hold universal-ctags

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 /path/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

Then, you can also declare an history remote branch corresponding to the old Linux versions not present in the other repos, to get all the old version still available:

cd repo
git remote add history https://github.com/bootlin/linux-history.git
git fetch history --tags

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 <number of threads (default 10 | min 5)>

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 C
$ ./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|acp).*/(source|ident|search)" "/web.py" [PT]
    RewriteRule "^/acp" "/autocomplete.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  = ( "^/(?!api|acp).*/(source|ident|search)" =>  "/web.py/$1")
url.rewrite  = ( "^/acp" =>  "/autocomplete.py")
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>&family=<family>. For example:

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

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 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.

You can set $ELIXIR_THREADS if you want to change the number of threads used by update.py for indexing (default is 10 and minimum is 5).

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 projects/<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.

If you want to enable support for compatible properties in Devicetree files, add dts_comp_support=1 at the beginning of projects/<projectname>.sh.

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

./update.py <number of threads (default 10 | min 5)>

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 official coding style for Python.

How to send patches

The best way to share your contributions with us is to 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 COPYING file included with Linux. All the files copied carry SPDX license identifiers of GPL-2.0+ or GPL-2.0-or-later. Per GNU’s compatibility table, GPL 2.0+ code can be used under GPLv3 provided the combination is under GPLv3. Moreover, 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 this issue comment for another example of a similar situation.)

License

Elixir is copyright (c) 2017—​2020 its contributors. It is licensed AGPLv3. See the COPYING file included with Elixir for details.
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