Module: MiGA::RemoteDataset::Base
- Included in:
- MiGA::RemoteDataset
- Defined in:
- lib/miga/remote_dataset/base.rb
Constant Summary collapse
- @@_EUTILS =
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
- @@_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 asstage
,format
,map_to
, andgetter
. -
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$s is format. Additional parameters can be passed to certain functions using theextra
option. -
method
=> Method used to query the URL. Only:rest
and:net
are currently supported. -
api_key
=> A lambda function that takes a URL as input and returns the URL to be downloaded with an API Key (if available). -
map_to_universe
=> Universe where results map to. Currently unsupported.
-
{ web: { dbs: { assembly: {stage: :assembly, format: :fasta}, assembly_gz: {stage: :assembly, format: :fasta_gz}, text: {stage: :metadata, format: :text} }, url: '%2$s', method: :net }, ebi: { dbs: { embl: {stage: :assembly, format: :fasta} }, url: 'https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/%1$s/%2$s/%3$s', method: :rest }, ncbi: { dbs: { nuccore: { stage: :assembly, format: :fasta }, assembly: { stage: :assembly, format: :fasta_gz, getter: :ncbi_asm }, taxonomy: { stage: :metadata, format: :xml } }, url: "#{@@_EUTILS}efetch.fcgi?db=%1$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 } }