🌲 VoSeq is a database to store voucher and sequence data
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README.rst

VoSeq

BuildStatus CoverageStatus Python versions Join the chat at https://gitter.im/VoSeq/VoSeq

Contents

Full documentation.

The new VoSeq is here

We have rebuilt VoSeq from scratch. We decided to migrate from PHP to Python by using the framework Django. We also moved from MySQL to PostgreSQL.

You can still download the old VoSeq v1.7.4 from here. But be aware that we will not be doing major maintenance of that code.

More details about the migration can be found in our discussion list.

VoSeq 2.0.0 is the future! Here is a test installation of the new VoSeq (v2.0) http://try.voseq.com/

New Features

Query suggestions for simple taxon searches:

https://raw.githubusercontent.com/VoSeq/VoSeq/master/imgs/simple_search_suggestion.png

Quick install of VoSeq using Vagrant (Recommended)

Vagrant allows setting up virtual machines that automatically installs all dependencies and sets up configuration from a recipe contained in the Vagrant file.

You need both Vagrant and VirtualBox installed in your computer or server.

Assuming that you have installed [GIT](https://git-scm.com/downloads), you need to get a copy of VoSeq into your hard-disk. From a console or terminal type the following command:

git clone https://github.com/VoSeq/VoSeq.git

Just go to the VoSeq's directory:

cd VoSeq

And execute the following command:

vagrant up

If the installation of packages gets interrupted you can relaunch the process with the following command:

vagrant reload --provision

Once the process has finished, you will have a new Ubuntu virtual machine with VoSeq installed. To enter this virtual machine:

vagrant ssh

Then you just need to run the following commands to set up your database:

cd /vagrant
workon voseq
make migrations

Additionally, you can import your old VoSeq database from a MySQL dump (see Migrate VoSeq database). If you don't import anything your VoSeq installation will be usable, but empty. In such a case, you might want to import test data:

make test_import

Set up an administrator account by using the command make admin (see Administrate the server).

It is necessary to index your imported data:

make index

Since this installation of VoSeq will be running as a deployed application from inside the virtual machine you need to collect the static files in the correct locations:

make collectstatic

Then restart the web server:

sudo supervisorctl restart voseq
sudo service nginx restart

In your host system, open your brower and load this URL: http://33.33.33.10 to see your fresh installation of VoSeq.

Installation instructions

These instructions assume that your libraries are up to date and that you have Python, pip, Java 7+ and virtual environments installed. Python3 is recommended.

Step 1: get VoSeq. Clone or download VoSeq to your preferred directory. We recommend cloning VoSeq as it will be easier to do software upgrades with on single command:

  • To clone VoSeq:
git clone https://github.com/VoSeq/VoSeq.git
  • To upgrade VoSeq to newer versions:
cd /path/to/VoSeq
git pull origin master

Step 2: create a virtual environment and install dependencies. To ensure that all the dependencies will work without conflict, it is best to install them within a virtual environment.

mkvirtualenv -p /usr/bin/python3 voseq_environment
cd /path/to/VoSeq
workon voseq_environment
pip install -r requirements/testing.txt

Exit the virtual environment for now to continue from the shell:

deactivate

Step 3: download and install elasticsearch. Elasticsearch is needed to enable the advanced search tool and auto suggestions. By default, the elasticsearch is enabled. You can disable it in the config.json file by using the key:value "ELASTICSEARCH": "false". In such case, only the general search will work.

Use elasticsearch versions 1.7.3 or below. The newer versions 2.0+ currently do not work with VoSeq. For elasticsearch, java needs to be installed. Mac users can download and install elasticsearch from here: http://www.elasticsearch.org/overview/elkdownloads/. In Linux, you can do:

wget https://download.elastic.co/elasticsearch/elasticsearch/elasticsearch-1.5.2.deb
sudo dpkg -i elasticsearch-1.5.2.deb

The bin directory of elasticsearch should be added automatically to your PATH. If not, add the following line to your .profile (Linux) or .bash_profile (macOSX) file:

export PATH="$PATH:/path/to/elasticsearch/bin/"

Step 4: download, install and configure PostgreSQL. For macOSX users we recommend to do it by downloading the Postgres.app from http://postgresapp.com. Linux users can use apt-get:

sudo apt-get install postgresql postgresql-contrib postgresql-server-dev-9.3

Create new role by typing:

createuser --interactive

Enter the psql shell, create a password for this user and create a database for VoSeq:

psql
postgres=# ALTER ROLE postgres WITH PASSWORD 'hu8jmn3';
postgres=# create database voseq;

In macOSX if you are using the Postgres.app, it my be enough to run:

psql
user.name=# CREATE DATABASE voseq;

To exit the psql shell:

\q

Next, create a config.json file to keep the database variables:

cd /path/to/Voseq
touch config.json

and write in the following content:

{
"SECRET_KEY": "create_a_secret_key",
"DB_USER": "postgres",
"DB_PASS": "hu8jmn3",
"DB_NAME": "voseq",
"DB_PORT": "5432",
"DB_HOST": "localhost",
"GOOGLE_MAPS_API_KEY": "get_a_google_map_api_key",
"PHOTOS_REPOSITORY": "local",
"ELASTICSEARCH": "true"
}

If you want to host your photos in Flickr you need to change the last parameter of your config.json file to "PHOTOS_REPOSITORY": "flickr".

If you followed the above instructions to the letter, the DB_USER will be "postgres" and the DB_PASS will be "hu8jmn3". It is of recommended to come up with your own password. Instructions to obtain a personal google map browser API key can be found here. You need to create a Google Maps JavaScript API for yourself.

After following these four steps everything should be installed and ready to run. You can now choose to either continue with adding real data migrated from VoSeq 1.x and setting up a publicly available web server, or to first add some test data and test the set-up with a lightweight local server included in the VoSeq package.

Test database for development

You can use test data to populate your PostgreSQL database, useful for development.

First, enter the virtual environment:

workon voseq_environment

Then, create tables for the database:

cd /path/to/Voseq/
make migrations

And import test data for your database:

make test_import

Start a test server

In Linux start elasticsearch as a service, then enter the virtual environment and then start the server:

sudo service elasticsearch start
workon voseq_environment
cd /path/to/Voseq
make serve

In macOSX if you do not have the service command, run elasticsearch in the background and then start the server (*):

elasticsearch -d
cd /path/to/Voseq
make serve

* Note that if you did not check to Start Postgres automatically after login, you first have to go to Applications and start it manually from there by clicking on the Postgres.app. Do this before running the server.

You now have a local webserver running. You can access it by opening this URL in your web browser: http://127.0.0.1:8000/ and try all the buttons to see if they all work! Also notice the debug bar on the right of the screen where you can check if all the configurations are correct.

Migrate VoSeq database

If you have an existing Voseq 1.x database and want to migrate, you need to dump your MySQL database into a XML file:

cd /path/to/Voseq/
mysqldump --xml voseq_database > dump.xml

Then use our script to migrate all your VoSeq data into a PostGreSQL database.

make migrations
python voseq/manage.py migrate_db --dumpfile=dump.xml --settings=voseq.settings.local

If you have used a prefix for your tables in the old VoSeq, you can optionally input this as an argument for the import script:

python voseq/manage.py migrate_db --dumpfile=dump.xml --prefix=voseq_ --settings=voseq.settings.local

It might issue a warning message:

WARNING:: Could not parse dateCreation properly.
WARNING:: Using empty as date for `time_edited` for code Your_Vocher_Code

It means that the creation time for your voucher was probably empty or similar to 0000-00-00. In that case the date of creation for your voucher will be empty. This will not cause any trouble when running VoSeq. You can safely ignore this message.

Create an index for all the data in your database:

make index

If you kept your voucher images in your local computer or server then your need to copy them to the correct location in the VoSeq folders:

cp old_voseq/pictures/* VoSeq/voseq/public_interface/static/.

Now copy the thumbnails of those images:

cp old_voseq/pictures/thumbnails/* VoSeq/voseq/public_interface/static/.

If you have your photos in Flickr, then don't worry you don't need to copy any image file.

Set-up a publicly available web server

To make VoSeq available to multiple users, you will have to set-up a publicly available web server. There are several options to do this, for example using nginx and gunicorn (best performance) or Apache and WSGI (more suitable for hosting multiple websites).

Instructions for how to do this will follow later, but the DigitalOcean tutorials may be of use for now:

Apache and WSGI

Nginx and Gunicorn

Administrate the server

Optionally if you want to add items/vouchers to your database interactively, you need to create an administration account. Run the following command and provide the requested information:

make admin

Create a database index for the simple and advanced search functions. This will speed up the data retrieval. You need to run it once as soon as you deploy VoSeq to the server:

make index

Some features of VoSeq need to be run periodically

You can setup cronjobs to execute some commands once a day or every 2 hours depending on your needs.

If you remove or add data to VoSeq quite rarely (once a day) you might want to sync the database index with your real data. In this way, new vouchers or sequences will be found by VoSeq's search tools.

To update your database index every 24 hours (at 3:00 am) set the following cronjob:

crontab -e

Add the following line, save and exit:

0 3 * * * /path/to/python /path/to/voseq/manage.py update_index --age=24 --remove --settings=voseq.settings.production

If you add and delete data several times a day then you might want to update your database index more often. Let us try every three hours:

0 */3 * * * /path/to/python /path/to/voseq/manage.py update_index --age=3 --remove --settings=voseq.settings.production

If you installed VoSeq using Vagrant, then your cronjob command with the correct paths should be this:

0 */3 * * * /home/vagrant/.virtualenvs/voseq/bin/python /vagrant/voseq/manage.py update_index --settings=voseq.settings.production

Update some voucher and gene statistics for your installation of VoSeq:

make stats

Deployment of VoSeq

VoSeq comes with a very simple server software (from Django) that you can use for development and testing purposes. This is the server that starts up when you use the command make serve.

However, the Django developers warn that you will need to do some extra configuration if you want VoSeq to start serving data to the users of your lab from your institution server or commercial servers:

  • To serve statics files such as stylesheet and javascript files, you need to choose a folder in your sever to be the root folder for such files. Open the file VoSeq_repo/voseq/voseq/settings/production.py and change this line so that it points to your server's folder:
STATIC_ROOT = "/var/www/VoSeq/static/"
  • Do something similar for being able to serve voucher images from your local server:
MEDIA_ROOT = "/var/www/VoSeq/media/"

You might want to leave it with the default values. It should work (# TODO test).

  • If you have installed VoSeq in a commercial server and already bought an Internet domain, you need to add it to the production.py file. Change the following line:
ALLOWED_HOSTS = [
    '192.168.0.106',  # Your Domain or IP address
]

If you don't have a domain like (myawesomedomain.com) then just replace the IP address for the one of your server.

Before starting up VoSeq, you will need to gather all the static files in the folders you just specified so they will be available for your users. Use the following command:

python voseq/manage.py collectstatic --settings=voseq.settings.production

Then start VoSeq using the production configuration file:

python voseq/manage.py runserver --settings=voseq.settings.production

Upgrade VoSeq's software

If you cloned the VoSeq software you can easily get the new changes by typing the following commands in a computer terminal or console:

cd /path/to/VoSeq
git pull origin master

Do the updates to the database structure:

workon voseq_environment
make migrations

Rebuild the index and start the test server:

make index
make serve

Database backups

You might want to do periodical backups of your VoSeq database. You can follow these instrucctions for backup data from postgreSQL databases: https://wiki.postgresql.org/wiki/Automated_Backup_on_Linux

Flickr Plugin

VoSeq is able to host all the specimen photos in Flickr. If you have a free account you can host up to 200 photos. The Pro account allows you hosting unlimited number of photos for a yearly fee (25 USD).

You need to get API keys from Flickr and place them in the config.json configuration file of VoSeq:

  • Create and account in Flickr (if you don't own one already)

  • Follow the instructions to get an API key and Secret key.

  • After submitting you will get your Key and Secret. Write down those keys.

  • Using a text editor software, edit the file config.json by copying your keys in it.

    • For example [these are not real keys and will not work if you use them]:
    "FLICKR_API_KEY": "2d7f59f9aaa2d5c0a2782d7f5d9083a6",
    "FLICKR_API_SECRET": "ef0def0f3d5f3f15f1"
    • Save and exit.

Thus, every picture that you upload into your VoSeq installation will be uploaded into your Flickr account.

Lineages

GenBank fasta files have the optional field Lineages. You can add lineages in the form:

LINEAGES = {
# superfamily: lineage from domain Eukaryota to suborder Ditrysia "Papilionoidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ", "Hesperioidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ", "Hedyloidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",

}

by editing the file voseq/create_dataset/utils.py.