unipept 0.3.4 → 0.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d8b67a44cab159e17675e6cab96d9fb04e458dc3
-  data.tar.gz: 515cd4c0592854704f26a410fe8d024aa411d56c
+  metadata.gz: 912794c26e712f70f1db0cb0946d87479a1c4dae
+  data.tar.gz: 44adc715b0704425d542ca0450c4e523df0f19d2
 SHA512:
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-  data.tar.gz: b5a17c748755f7dfba4e8598290818e1ac2bf9d6dcdd6d32cd2df363635fe7b1be3911a90e1a476e97ae002a303e1ec06abe2b81eb362e517b50a4460e7a1bd0
+  metadata.gz: e7dea9e6717f0f3b18510ae53b21c040412c4d25db3525fdd13baa660df72c24c44a6f9f5981301f3fc0352768821826acb082712652d9d2fb4d30b51f22527e
+  data.tar.gz: 911afafcbb596b5d66e86c3cdec7ab4022622f635ff0edad85fbfce587949708feb85a2f33b51e0bfdfd4cddb1bb246905bd1dbf40d25db2f181383163030ecc

data/VERSION

@@ -1 +1 @@
-0.3.4
+0.3.5

data/bin/unipept

@@ -94,11 +94,13 @@ class ApiRunner < Cri::CommandRunner
 
             # wait till it's our turn to write
             batch_order.wait(i) do
-              if ! printed_header
-                write_to_output formatter.header(sub_result)
-                printed_header = true
+              if ! sub_result.empty?
+                if ! printed_header
+                  write_to_output formatter.header(sub_result)
+                  printed_header = true
+                end
+                write_to_output formatter.format(sub_result)
               end
-              write_to_output formatter.format(sub_result)
             end
           else
             path = File.expand_path(File.join(Dir.home, "unipept.log"))
@@ -143,7 +145,7 @@ class ApiRunner < Cri::CommandRunner
   def download_xml(result)
     if options[:xml]
       File.open(options[:xml] + ".xml", "wb") do |f|
-        f.write Faraday.get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=#{result.first.map{|h| h['taxon_id'] }.join(",")}&retmode=xml").body
+        f.write Typhoeus.get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=#{result.first.map{|h| h['taxon_id'] }.join(",")}&retmode=xml").response_body
       end
     end
   end
@@ -195,7 +197,7 @@ class Pept2prot < ApiRunner
       FileUtils.mkdir_p(options[:xml])
       result.first.each do |prot|
         File.open(options[:xml] + "/#{prot['uniprot_id']}.xml", "wb") do |f|
-          f.write Faraday.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").body
+          f.write Typhoeus.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").response_body
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.3.4
+  version: 0.3.5
 platform: ruby
 authors:
 - Toon Willems