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https://github.com/bootlin/elixir

The Elixir Cross Referencer
https://github.com/bootlin/elixir

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The Elixir Cross Referencer

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README 

        
= The Elixir Cross Referencer

:doctype: book

:pp: {plus}{plus}

:toc:

:toc-placement!:



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/



link:CHANGELOG.adoc[Changelog]



toc::[]



= Requirements



* Python >= 3.8

* Git >= 1.9

* The Jinja2 and Pygments (>= 2.7) 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



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 web interface (`web.py`) and

uses 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.



= Manual Installation



== Install Dependencies



____

For Debian

____



----

sudo apt install python3-pip python3-venv libdb-dev python3-dev build-essential universal-ctags perl git apache2 libapache2-mod-wsgi-py3 libjansson4

----



== Download Elixir Project



----

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

----



== Create a virtualenv for Elixir



----

python -m venv /usr/local/elixir/venv

. /usr/local/elixir/venv/bin/activate

pip install -r /usr/local/elixir/requirements.txt

----



== Create directories for project data



----

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 --bare 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



----

. ./venv/bin/activate

./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:



 $ python3 -m utils.query ident v4.10 raw_spin_unlock_irq C

 $ python3 -m utils.query file v4.10 /kernel/sched/clock.c



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

NOTE: Don't forget to activate the virtual environment!



== 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:



* ``

 ** ``

  *** `data`

  *** `repo`

 ** ``

  *** `data`

  *** `repo`

 ** ``

  *** `data`

  *** `repo`



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

command.



Now replace `/etc/apache2/sites-enabled/000-default.conf` with `docker/000-default.conf`.

Note: If using httpd (RedHat/Centos) instead of apache2 (Ubuntu/Debian),

the default config file to edit is `/etc/httpd/conf.d/elixir.conf`.



Finally, start the httpd server.



----

systemctl restart apache2

----



== Configure SELinux policy



When running systemd with SELinux enabled, httpd server can only visit limited directories.

If your /path/elixir-data/ is not one of these allowed directories, you will be responded with 500 status code.



To allow httpd server to visit /path/elixir-data/, run following codes:

----

chcon -R -t httpd_sys_rw_content_t /path/elixir-data/

----



To check if it takes effect, run the following codes:

----

ls -Z /path/elixir-data/

----



In case you want to check SELinux log related with httpd, run the following codes:

----

audit2why -a | grep httpd | less

----



== Configure systemd log directory



By default, the error log of elixir will be put in /tmp/elixir-errors.

However, systemd enables PrivateTmp by default.

And, the final error directory will be like /tmp/systemd-private-xxxxx-httpd.service-xxxx/tmp/elixir-errors.

If you want to disable it, configure httpd.service with the following attribute:

----

PrivateTmp=false

----



== Configuration for other servers



Other HTTP servers (like nginx or lighthttpd) may not support WSGI and may require a separate WSGI server, like uWSGI.



Information about how to configure uWSGI with Lighthttpd can be found here:

https://redmine.lighttpd.net/projects/lighttpd/wiki/HowToPythonWSGI#Python-WSGI-apps-via-uwsgi-SCGI-FastCGI-or-HTTP-using-the-uWSGI-server



Pull requests with example uWSGI configuration for Elixir are welcome.



= REST API usage



After configuring httpd, you can test the API usage:



== ident query



Send a get request to `/api/ident//?version=&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 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 `index /srv/elixir-data --all` 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 (by default the number of CPUs on your system).



= Building Docker images



Dockerfiles are provided in the `docker/` directory.

To build the image, run the following commands:



 # git clone https://github.com/bootlin/elixir.git ./elixir

 # docker build -t elixir --build-arg ELIXIR_VERSION=`git rev-parse --short HEAD` -f ./elixir/docker/Dockerfile ./elixir



ELIXIR_VER build argument is optional. Since .git directory is not copied into Docker image by default,

the option is used to pass a version string to Elixir.



You can then run the image using `docker run`.

Here we mount a host directory as Elixir data:



 # mkdir ./elixir-data

 # docker run -v ./elixir-data/:/srv/elixir-data -d --name elixir-container elixir



The Docker image does not contain any repositories.

To index a repository, you can use the `index-repository` script.

For example, to add the https://musl.libc.org/[musl] repository, run:



 # docker exec -it elixir-container index /srv/elixir-data musl



Or, to run indexing in a separate container:



 # docker run -v ./elixir-data/:/srv/elixir-data \

    --entrypoint index elixir /srv/elixir-data musl



You can also use `index /srv/elixir-data --all` to start indexing all officially supported repositories.



After indexing is done, Elixir should be available under the following URL on your host:

http://172.17.0.2/musl/latest/source



If 172.17.0.2 does not answer, you can check the IP address of the container by running:



 # docker inspect elixir-container | grep IPAddress



== Automatic repository updates



The Docker image does not automatically update repositories by itself.

You can, for example, start `index /srv/elixir-data --all` in the container (or in a separate container, with Elixir data volume/directory mounted)

from cron on the host to periodically update repositories.



== Using Docker image as a development server



You can easily use the Docker image as a development server by following the steps above, but mounting Elixir source directory from the host

into `/usr/local/elixir/` in the container when running `docker run elixir`.



Changes in the code made on the host should be automatically reflected in the container.

You can use `apache2ctl` to restart Apache.

Error logs are available in `/var/log/apache2/error.log` within the container.



= 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/.sh`

file. Here's an example (`projects/zephyr.sh` file):



 list_tags()

 {

     echo "$tags" |

     grep -v '^zephyr-v'

 }



Note that `` *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-tags | head



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



If you want to enable support for `compatible` properties in Devicetree files,

add `dts_comp_support=1` at the beginning of `projects/.sh`.



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.)



= License



Elixir is copyright (c) 2017--2020 its contributors.  It is licensed AGPLv3.

See the `COPYING` file included with Elixir for details.