Module: MiGA::RemoteDataset::Base

Included in:

MiGA::RemoteDataset

Defined in:

lib/miga/remote_dataset/base.rb

Constant Summary

@@_EUTILS =

'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'

@@_EBI_API =

'https://www.ebi.ac.uk/Tools'

@@_GTDB_API =

'https://api.gtdb.ecogenomic.org'

@@_NCBI_API_KEY =

lambda { |url|
  ENV['NCBI_API_KEY'].nil? ? url : "#{url}&api_key=#{ENV['NCBI_API_KEY']}"
}

@@UNIVERSE =

Structure of the different database Universes or containers. The structure is a Hash with universe names as keys as Symbol and values being a Hash with supported keys as Symbol:

• :dbs => Hash with keys being the database name and the values a Hash of properties such as stage, format, map_to, and getter.

• url => Pattern of the URL where the data can be obtained, where %1$s is the name of the database, %2$s is the IDs, and %3$s is format. Additional parameters can be passed to certain functions using the extra option.

• method => Method used to query the URL. Only :rest and :net are currently supported.

• api_key => A lambda function that takes a URL as input and returns the URL to be downloaded with an API Key (if available).

• map_to_universe => Universe where results map to. Currently unsupported.

{
  web: {
    dbs: {
      assembly: { stage: :assembly, format: :fasta },
      assembly_gz: { stage: :assembly, format: :fasta_gz },
      text: { stage: :metadata, format: :text }
    },
    url: '%2$s',
    method: :net
  },
  ebi: {
    dbs: { embl: { stage: :assembly, format: :fasta } },
    url: "#{@@_EBI_API}/dbfetch/dbfetch/%1$s/%2$s/%3$s",
    method: :rest
  },
  gtdb: {
    dbs: {
      # This is a dummy entry plugged directly to +ncbi_asm_rest+
      assembly: { stage: :assembly, format: :fasta_gz, getter: :ncbi_asm },
      # The 'taxon' namespace actually returns a list of genomes (+format+)
      taxon: {
        stage: :metadata, format: :genomes, map_to: [:assembly],
        extra: ['sp_reps_only=false']
      },
      # The 'genome' namespace actually returns the taxonomy (+format+)
      genome: { stage: :metadata, format: 'taxon-history' }
    },
    url: "#{@@_GTDB_API}/%1$s/%2$s/%3$s?%4$s",
    method: :rest,
    map_to_universe: :ncbi,
    headers: 'accept: application/json' # < TODO not currently supported
  },
  ncbi: {
    dbs: {
      nuccore: { stage: :assembly, format: :fasta, getter: :ncbi_gb },
      assembly: { stage: :assembly, format: :fasta_gz, getter: :ncbi_asm },
      taxonomy: { stage: :metadata, format: :xml }
    },
    url: "#{@@_EUTILS}efetch.fcgi?db=%1$s&id=%2$s&rettype=%3$s&retmode=text",
    method: :rest,
    api_key: @@_NCBI_API_KEY
  },
  ncbi_map: {
    dbs: {
      nuccore: {
        stage: :metadata, map_to: [:biosample, :assembly], format: :json
      },
      biosample: { stage: :metadata, map_to: [:assembly], format: :json }
    },
    url: "#{@@_EUTILS}elink.fcgi?dbfrom=%1$s&id=%2$s&db=%4$s&retmode=%3$s",
    method: :net,
    map_to_universe: :ncbi,
    api_key: @@_NCBI_API_KEY
  },
  ncbi_summary: {
    dbs: { assembly: { stage: :metadata, format: :json } },
    url: "#{@@_EUTILS}esummary.fcgi?db=%1$s&id=%2$s&retmode=%3$s",
    method: :rest,
    api_key: @@_NCBI_API_KEY
  },
  ncbi_search: {
    dbs: { assembly: { stage: :metadata, format: :json } },
    url: "#{@@_EUTILS}esearch.fcgi?db=%1$s&term=%2$s&retmode=%3$s",
    method: :rest,
    api_key: @@_NCBI_API_KEY
  }
}