GeneNetwork REST server
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README.md

GnServer

GeneNetwork server (GnServer) serves data and functionality over a network interface. GnServer can fetch and upload data via a REST API. GnServer can execute remote commands.

GnServer is implemented in the highly parallel and robust Elixir programming language on top of the Erlang VM.

The API documentation can be found here Note: GnServer is a work in progress (YMMV).

Install via GNU Guix

Elixir and packages should soon come with a general genenetwork2 install. For now use the checked out GN2 repositories and install Elixir with

env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i elixir

After setting the GUIX locale (to avoid UTF-8 errors) install with mix

export GUIX_LOCPATH=$HOME/.guix-profile/lib/locale
export LC_ALL=en_US.UTF-8
mix hex.info
mix deps.get
mix test

which will probably render a database error. To start the database use the credentials for your system, e.g., "mysql://gn2:mysql_password@localhost/db_webqtl_s"

mysql -p -u gn2
use db_webqtl_s;
show tables;

Should show the tables as listed on GeneNetwork.

To start the server

iex -S mix

and the following should get you a reply

curl http://localhost:8880/hey
{"I am":"genenetwork"}

Install via Hex

If available in Hex, the package can be installed by providing:

  1. Add gn_server to your list of dependencies in mix.exs:

    def deps do [{:gn_server, "~> 0.0.1"}] end

  2. Ensure gn_server is started before your application:

    def application do [applications: [:gn_server]] end

Configure the service

A configuration file can be passed in. By default it uses the test database with

iex -S mix run -c ./config/config.exs

and

curl http://localhost:8880/hey
{"I am":"genenetwork"}

To change the configuration, copy the confix.exs file and pass it in on the command line, e.g.

cp ./config/config.exs ~/my_config.exs
iex -S mix run -c ~/my_config.exs

Benchmarking

brew install sysbench Create user sbstest with dba grants from the workbench Create a sbtest database from the workbench sysbench --test=oltp --oltp-table-size=1000000 --mysql-db=sbtest --mysql-user=sbtest --mysql-password=sbtest --mysql-table-engine=myisam prepare sysbench --test=oltp --oltp-table-size=1000000 --mysql-db=sbtest --mysql-user=sbtest --mysql-password=sbtest --max-time=60 --oltp-read-only=on --max-requests=0 --num-threads=4 --mysql-table-engine=myisam run

sysbench 0.4.12: multi-threaded system evaluation benchmark

No DB drivers specified, using mysql Running the test with following options: Number of threads: 4

Doing OLTP test.
Running mixed OLTP test
Doing read-only test
Using Special distribution (12 iterations,  1 pct of values are returned in 75 pct cases)
Using "LOCK TABLES READ" for starting transactions
Using auto_inc on the id column
Threads started!
Time limit exceeded, exiting...
(last message repeated 3 times)
Done.

OLTP test statistics:
    queries performed:
        read:                            916370
        write:                           0
        other:                           130910
        total:                           1047280
    transactions:                        65455  (1090.91 per sec.)
    deadlocks:                           0      (0.00 per sec.)
    read/write requests:                 916370 (15272.74 per sec.)
    other operations:                    130910 (2181.82 per sec.)

Test execution summary:
    total time:                          60.0004s
    total number of events:              65455
    total time taken by event execution: 239.5199
    per-request statistics:
         min:                                  1.74ms
         avg:                                  3.66ms
         max:                                145.89ms
         approx.  95 percentile:               5.07ms

Threads fairness:
    events (avg/stddev):           16363.7500/85.88
    execution time (avg/stddev):   59.8800/0.00

License

The source code is released under the Affero General Public License 3 (AGPLv3). See LICENSE.txt.

More information

For more information visit http://www.genenetwork.org/

Contact

IRC on #genenetwork on irc.freenode.net.

Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, Memphis TN, USA.