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Fetch taxonomic and functional information for UniProt id's #20

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merged 4 commits into from
Jun 14, 2023
Merged

Fetch taxonomic and functional information for UniProt id's #20

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8c59588
uniprot endpoint
tibvdm May 15, 2023
f40a035
fix linting
tibvdm May 15, 2023
8bd30a4
same format as peptinfo
tibvdm May 15, 2023
03c0762
rename interpro field to ipr
tibvdm Jun 9, 2023
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26 changes: 24 additions & 2 deletions app/controllers/api/api_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
class Api::ApiController < ApplicationController
respond_to :json

before_action :set_headers, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree]
before_action :set_params, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree]
before_action :set_headers, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree protinfo]
before_action :set_params, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree protinfo]
before_action :set_query, only: %i[pept2taxa pept2lca peptinfo taxonomy]
before_action :set_sequences, only: %i[pept2prot]

Expand Down Expand Up @@ -270,6 +270,28 @@ def taxonomy
respond_with(@result)
end

# Returns the taxonomic and functional information for given uniprot id's
# param[input]: Array, required, List of input uniprot id's
def protinfo
@result = {}

UniprotEntry
.includes(:taxon, :ec_numbers, :go_terms, :interpro_entries)
.where(uniprot_accession_number: @input_order)
.find_in_batches do |batch|
batch.each do |uniprot_id|
@result[uniprot_id.uniprot_accession_number] = {
taxon: uniprot_id.taxon,
ec: uniprot_id.ec_numbers.map { |ec| { ec_number: ec.code } },
go: uniprot_id.go_terms.map { |go| { go_term: go.code } },
ipr: uniprot_id.interpro_entries.map { |interpro| { code: interpro.code } }
}
end
end

respond_with(@result)
end

private

# log all api calls to stathat
Expand Down
13 changes: 13 additions & 0 deletions app/views/api/api/protinfo.json.jbuilder
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
json.array! @input_order do |uniprot_id|
if @result.key? uniprot_id
json.protein uniprot_id

json.ec @result[uniprot_id][:ec]
json.go @result[uniprot_id][:go]
json.ipr @result[uniprot_id][:ipr]

json.taxon_id @result[uniprot_id][:taxon][:id]
json.taxon_name @result[uniprot_id][:taxon][:name]
json.taxon_rank @result[uniprot_id][:taxon][:rank]
end
end
2 changes: 2 additions & 0 deletions config/routes.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
match 'peptinfo' => 'api#peptinfo', via: %i[get post]
match 'taxonomy' => 'api#taxonomy', via: %i[get post]
match 'messages' => 'api#messages', via: %i[get post]
match 'protinfo' => 'api#protinfo', via: %i[get post]
end

namespace :api, path: 'api/v2' do
Expand All @@ -49,5 +50,6 @@
match 'peptinfo' => 'api#peptinfo', via: %i[get post]
match 'taxonomy' => 'api#taxonomy', via: %i[get post]
match 'messages' => 'api#messages', via: %i[get post]
match 'protinfo' => 'api#protinfo', via: %i[get post]
end
end
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