Merge pull request #20 from BioJulia/fix-eutils-http-body

Bugfix for #19

CHANGELOG.md

@@ -4,7 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.3.1] - 2018-10-5
+### Changes
+- eutils.jl to use the correct http parameter when passing the body to POST
+- tests/eutils.jl to perform efetch with large number of PMID which breaks if incorrect http format is used
+### Removed
+- *.toml files to wait until versioning is ready for new Pkg
+
+## [0.3.0] - 2018-09-21
+### Changed
 - Updated HUMANS.md.
 - Added compatibility with Julia 1.0
 

src/eutils.jl

@@ -92,7 +92,7 @@ Parameters: db, id, WebEnv.
 function epost(ctx::AbstractDict=empty_context(); params...)
     params = process_parameters(params, ctx)
     body = HTTP.escapeuri(params)
-    res = HTTP.request("POST", string(baseURL, "epost.fcgi"), query=body)
+    res = HTTP.request("POST", string(baseURL, "epost.fcgi"), body=body)
     set_context!(ctx, res)
     return res
 end
@@ -107,7 +107,7 @@ Parameters: db, id, query_key, WebEnv, retstart, retmax, retmode, version.
 function esummary(ctx::AbstractDict=empty_context(); params...)
     params = process_parameters(params, ctx)
     body = HTTP.escapeuri(params)
-    return HTTP.request("POST", string(baseURL, "esummary.fcgi"), query=body)
+    return HTTP.request("POST", string(baseURL, "esummary.fcgi"), body=body)
 end
 
 """
@@ -121,7 +121,7 @@ strand, seq_start, seq_stop, complexity.
 function efetch(ctx::AbstractDict=empty_context(); params...)
     params = process_parameters(params, ctx)
     body = HTTP.escapeuri(params)
-    return HTTP.request("POST", string(baseURL, "efetch.fcgi"), query=body, retry_non_idempotent=true)
+    return HTTP.request("POST", string(baseURL, "efetch.fcgi"), body=body, retry_non_idempotent=true)
 end
 
 """
@@ -135,7 +135,7 @@ datetype, reldate, mindate, maxdate.
 function elink(ctx::AbstractDict=empty_context(); params...)
     params = process_parameters(params, ctx)
     body = HTTP.escapeuri(params)
-    return HTTP.request("POST", string(baseURL, "elink.fcgi"), query=body)
+    return HTTP.request("POST", string(baseURL, "elink.fcgi"), body=body)
 end
 
 """

test/eutils.jl

@@ -87,6 +87,30 @@
         @test res.status == 200
         res = efetch(ctx, db="protein", retmode="xml")
         @test res.status == 200
+
+        # esearch then efeth for large number of ids
+        retmax = 1000
+        search_term = """(Asthma[MeSH Major Topic]) 
+                        AND ("1/1/2018"[Date - Publication] :
+                        "3000"[Date - Publication])"""
+        res = esearch(db = "pubmed", term = search_term,
+        retstart = 0, retmax = retmax, tool = "BioJulia")
+
+        #convert xml to dictionary
+        esearch_dict = parse_xml(String(res.body))
+
+        #get the list of ids and perfom a fetch
+        ids = [parse(Int64, id_node) for id_node in esearch_dict["IdList"]["Id"]]
+
+        res = efetch(db = "pubmed", tool = "BioJulia", retmode = "xml", rettype = "null", id = ids)
+        @test res.status == 200
+        @test startswith(Dict(res.headers)["Content-Type"], "text/xml")
+
+        body = parse_xml(String(res.body))
+
+        @test haskey(body, "PubmedArticle")
+        @test length(body["PubmedArticle"]) == retmax
+
     end
 
     @testset "elink" begin