Support the Uniprot mapping REST API (#28)

src/naming_conventions.jl

@@ -99,3 +99,53 @@ function query_uniprot_accession(id)
     end
     return nothing
 end
+
+"""
+    jobID = GPCRAnalysis.map_uniprot_submit(ids, from, to="UniProtKB")
+
+Submit a list of `ids` to the Uniprot ID mapping service, to convert from ID convention `from` to `to`.
+The jobID can be used to check the status (`map_uniprot_status`) and retrieve the results (`map_uniprot_retrieve`).
+
+# Examples
+```jldoctest`
+julia> jobID = GPCRAnalysis.map_uniprot_submit(["ENSMUSG00000067064", "ENSMUSG00000057464"], "Ensembl");
+```
+"""
+function map_uniprot_submit(ids::AbstractString, from::AbstractString, to::AbstractString="UniProtKB")
+    resp = HTTP.post("https://rest.uniprot.org/idmapping/run", [],
+                     Dict("from" => from, "to" => "UniProtKB", "ids" => ids))
+    if resp.status == 200
+        return JSON3.read(String(resp.body))["jobId"]
+    end
+    return nothing
+end
+map_uniprot_submit(ids::AbstractVector, from::AbstractString) = map_uniprot_submit(join(ids, ','), from)
+
+"""
+    status = GPCRAnalysis.map_uniprot_status(jobId)
+
+Check the status of a Uniprot ID mapping job. Returns `true` if the results are
+ready. Otherwise, returns the status object.
+"""
+function map_uniprot_status(jobId)
+    resp = HTTP.get("https://rest.uniprot.org/idmapping/status/$jobId", ["Accept" => "application/json"])
+    if resp.status == 200
+        status = JSON3.read(String(HTTP.decode(resp)))
+        haskey(status, "results") && return true
+        return status
+    end
+    return nothing
+end
+
+"""
+    result = GPCRAnalysis.map_uniprot_retrieve(jobId)
+
+Retrieve the results of a Uniprot ID mapping job.
+"""
+function map_uniprot_retrieve(jobId)
+    resp = HTTP.get("https://rest.uniprot.org/idmapping/stream/$jobId", ["Accept" => "application/json"])
+    if resp.status == 200
+        return JSON3.read(String(HTTP.decode(resp)))
+    end
+    return nothing
+end

test/runtests.jl

@@ -296,6 +296,18 @@ using Test
     if !isdefined(@__MODULE__, :skip_download) || !skip_download
         @testset "Uniprot" begin
             @test query_uniprot_accession("T2R38_MOUSE") == "Q7TQA6"
+
+            jobID = GPCRAnalysis.map_uniprot_submit(["ENSMUSG00000067064", "ENSMUSG00000057464"], "Ensembl")
+            tstart = time()
+            sleep(1)
+            status = false
+            while status != true && time() < tstart + 20
+                sleep(1)
+                status = GPCRAnalysis.map_uniprot_status(jobID)
+            end
+            results = GPCRAnalysis.map_uniprot_retrieve(jobID)[:results]
+            resultsdict = Dict(obj["from"] => obj["to"] for obj in results)
+            @test resultsdict["ENSMUSG00000067064"] == "Q8VGU4"
         end
 
         @testset "EBI and NCBI" begin