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Refget Reference Implementation Server

The refget reference implementation server is a Perl version of the refget protocol. The server uses a database to store metadata about a set of sequences and uses a local filesystem to store sequences in. The sequences are stored on disk as single line sequences with no whitespace and indexed under their checksum using the first 4 characters of the checksum to generate a directory hierarchy. This is the same mechanism used by htslib to create local sequence caches for CRAM files.

Installing

Pre-requisites

  • GCC
  • Perl 5.14+
  • cpanminus
  • Postgres, MySQL development headers / libraries

Normally all of these pre-requisits can be installed using your package management system such as apt. Install these requiremnets on Alpine Linux you can run the following:

apk update
apk add perl perl-io-socket-ssl perl-dbd-pg perl-dbd-mysql perl-dev g++ make wget curl tar 
curl -L https://cpanmin.us | perl - App::cpanminus

This will install Perl, SSL, Postgres and MySQL DBD drivers, Perl headers and the GCC build toolkit.

Installing Perl dependencies

You can use cpanminus to install all Perl requirements.

cpanm --installdeps .

Database URLs

This section assumes you have already have a database available to communicate with. If not see creating & populating the database.

The system supports setting a database URL held in the variable DATABASE_URL. These are formatted as database://username:password@server:port/database. SQLite is supported by specifying just a database name e.g. sqlite:////database_path.db. (note the 4 slashes)

You can also provide additional arguments through the DBIx::Class (the underlying engine) using URL parameters. These will all be passed onto the underlying engine verbatim and can be used to give additional data to a connection e.g. supporting PostgeSQL schemas.

Supporting PostgreSQL schemas

Using URL parameters you can tell the server to use an alternative schema within your PostgreSQL database. This is done using the on_connect_do key like so

export DATABASE_URL="postgres://user:pass@server:5432/db?on_connect_do=SET search_path TO myschema,otherschema,public"

Running

Configuration

Config file

By default the application expects to find a file called refget-app.json in the root directory. You can alter this by specifying MOJO_CONFIG=path/to/json. Consult the file refget-app.json.example for available configuration variables. This file is used to configure the sequence storage layer.

Environment variables

Note these config variables pre-date the use of a configuration file. In time many of these options will migrate into the config file.

  • MOJO_CONFIG: Control the location of the configuration file
  • DATABASE_URL: Location of the database (see earlier for a description)
  • APP_PID_FILE: If executing using Hypnotoad, set the location of the PID file
  • APP_LOG_FILE: Write logs to this file via Mojo::Log
  • APP_LOG_LEVEL: The level of log to record. Options are debug, info, warn, error, fatal
  • APP_ACCESS_LOG_FILE: Location of the access log file to write using Mojolicous::Plugin::AccessLog
  • APP_ACCESS_LOG_FORMAT: Format of access log to write. Options are common, combined, combinedio or you can specify your own Apache LogFormat string
  • APP_ENABLE_COMPRESSION: Enable on-the-wire gzip compression on responses

Running the server

The following will start an instance of Mojo::Server::Daemon in production mode listening on port 8080 with the database location specified as a URL.

export DATABASE_URL=postgres://username:password@server:port/databasename
export MOJO_CONFIG="refget-app.json"
./bin/app.pl daemon -m production -l http://*:8080

Since this is a Mojolicous application you can use any of the supported servers such as hypnotoad, morbo or any PSGI compatible server. See mojolicous's deployment guide for more information on options.

Creating and populating the database

Creating the database

The server can run off a variety of database types as it uses DBIx::Class as an ORM layer. However we have tested the server with SQLite, MySQL and Postgres. The latest database schemas are located in the schema directory. Pipe the SQL into your target database type and then give the server the database location. Examples about how to do this are given below.

SQLite

sqlite3 my-refget.db < schema/Refget-Schema-1.0.0-SQLite.sql

MySQL

mysql --user=username --password=password --port=3306 -e "create database refget"
mysql --user=username --password=password --port=3306 refget < schema/Refget-Schema-1.0.0-MySQL.sql

Populating the dictionaries

The schema needs all of its enumerated dictionaries populated with default values. Run the following command to do this.

export DATABASE_URL=postgres://username:password@server:port/databasename
perl -I lib ./bin/populate-db-dicts.pl

If you want to use different values, then you can manually insert these into those tables i.e. division, mol_type and source. All other enumerated tables are populated as/when required.

Populating it with with sequence metadata and the filesystem with sequences

To load sequences into a database you can use the bin/run.pl script. The arguments are positional and are

  1. FASTA input file
  2. Release number to link to
  3. Molecule type. Must be one of the supported types of protein, cds, cdna, ncrna, dna
  4. Species. Give a species name
  5. A division name. If unsure set to none
  6. Assembly name. Normally set to the default name for an assembly. If one does not exist set it to none
  7. Source. Set to the source input of your sequence (Ensembl, RefSeq, UCSC, INSDC, unknown)
  8. A commit rate (how many times we should commit on our inserts)
  9. A path to the config file. Used to create an appropriate sequence storage layer
export DATABASE_URL=postgres://username:password@server:port/databasename
perl -I lib ./bin/run.pl fasta.file 96 dna homo_sapiens none grch37 Ensembl 1000 path/to/config.json

The script will iterate through the file, loads sequences if it were not already in the database and links additional metadata to the record. Please note this script was originally envisaged to load data from Ensembl resources hence a number of Ensembl conventions are present. These should not affect your usage of the loader code.

Generating Schemas

perl -I lib ./bin/schema.pl

When executed from the root directory, this will create a set of schemas located in the schema directory. Version of schemas are controlled by the $Refget::Schema::VERSION variable located in lib/Refget/Schema.pm.

Sequence Storage Layers

Three types of sequences storage layers exist; File, DBIx and Redis. All storage layers require you to specify the checksum to use for indexing. A sequence storage layer can work with only one checksum and requires the metadata systems to normalise into this single key. Whilst DBIx is the simplest to configure both the file and Redis layers have some advantages such as scalability to numbers of sequences or speed of access. Ultimately it is up to the implementation to understand what is important and to use the appropriate storage layer.

File Storage

File storage creates a htslib like hts-ref storage system, where a directory hierarchy is created. The first two levels are the first and second hex number from the generated HASH e.g. the sequence for 959cb1883fc1ca9ae1394ceb475a356ead1ecceff5824ae7 is held under 95/9c/959cb1883fc1ca9ae1394ceb475a356ead1ecceff5824ae7.

File storage configuration

{
  "seq_store" : "File",
  "seq_store_args" : {
    "root_dir" : "/path/to/storage/area",
    "checksum" : "trunc512"
  }
}

DBIx

DBIx storage uses the same database as where all loaded sequence metadata goes and pushes data into a table called raw_seq, which is indexed by the chosen checksum identifier. This is the simplest storage system to use as it keeps metadata and sequence together.

DBIx configuration

{
  "seq_store" : "DBIx",
  "seq_store_args" : {
    "checksum" : "trunc512"
  }
}

Redis

Redis storage uses the Redis database to store and access data. The code uses Redis' GETRANGE function to retrieve sub-sequences. You configure the instance by passing through parameters meant for the Perl Redis module.

Redis configuration

{
  "seq_store" : "Redis",
  "seq_store_args" : {
    "server" : "127.0.0.1:6379"
  }
}

Supporting additional layers

Additional layers can be supported. They require using the Refget::SeqStore::Base Moose role. This requires you to implement two methods _store(self, checksum, sequence) and _sub_seq(self, checksum, start, length). Once created the new storage layer can be added to the list of allowed layers in Refget::SeqStore::Builder.

Future Developments

  • Better loading code
  • More scripts for loading sequence aliases