rbbt-sources 3.1.24 → 3.1.25

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ee81561a5637519bf4b371909860a44e33fc7843
-  data.tar.gz: d8f3a3d3f9cc8fccdcdc5897b989dc54f2baf620
+  metadata.gz: fa13e63d187140be8064c0533e8b9524225f8724
+  data.tar.gz: a70178b12d875a65cc5610225f92019f87ebfedb
 SHA512:
-  metadata.gz: b68626b2660b886ce6518b260958aa37e3669dbbb264b114fac8d0a1b2e32fc2fc3227105f4323a2374a314291d47a762e22911f736b3b2341f7fa559ae99610
-  data.tar.gz: 1cf79e4bcab2d3decd2856f8d28ec8d2b92d96e151364c6e0e3930550cd9ae1ae1f8e1c8724694e34b2b6e149aeff2bbaceb034f970837f7f89c450c8d715912
+  metadata.gz: a4615a66fba18980e359ae82f27bdfaa5e7719b7c5d506b6179746f95e9ffb62b0a1140128d0bb9615cf58b280fd8bd0da904c8e44018fff63420c99cd473dda
+  data.tar.gz: d513bb462a3fe9fc48f8d61fde185d6f095e9ea1e6110b222e43fdd443ceffb6fb45199039498c815724d1759816c2bf16e043d3161a8e128227ed5f12922f3e

data/lib/rbbt/sources/pubmed.rb

@@ -227,7 +227,9 @@ module PubMed
     result_files = FileCache.cache_online_elements(pmids, 'pubmed-{ID}.xml') do |ids|
       result = {}
       values = []
-      Misc.divide(ids, (ids.length / 20) + 1).each do |list|
+      chunks = Misc.divide(ids, (ids.length / 20) + 1)
+      bar = Log::ProgressBar.new_bar(chunks.length, :desc => "Downloading articles from PubMed")
+      chunks.each do |list|
         begin
           Misc.try3times do
             url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" 
@@ -240,8 +242,12 @@ module PubMed
 
             values += xml.scan(/(<PubmedArticle>.*?<\/PubmedArticle>)/smu).flatten
           end
-        rescue
+        rescue Aborted
+          raise $!
+        rescue Exception
           Log.exception $!
+        ensure
+          bar.tick
         end
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.24
+  version: 3.1.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-07 00:00:00.000000000 Z
+date: 2017-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util