miga-base 0.2.3.0 → 0.2.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 08a4a7fe880fa3b6653122e96d4e25fc39832020
-  data.tar.gz: 9a154fe5ec29b9b4bcb56cf01f11eb9a5ce77e3a
+  metadata.gz: 8204affac00281361567c3a597321dd3ab5a5145
+  data.tar.gz: 62fbd4daf6698b317e9f76b89b352b7bf33d3b54
 SHA512:
-  metadata.gz: 19b8971dca597bc26a30cefc6b4c9973774a54cfd104ca5f45c8cea844205a01f58370556457426621009e7c7bfbc1c3f28afad93ff76fe818514b392b1fcaa0
-  data.tar.gz: ed05189ab71cbe8f8721dd7b584441cc3bf338a2746be46a08aeb1550545a9261c5d86f4d7133f99c5b6d4237fe975353832d7516400cbd1e3c037aef8d6bf38
+  metadata.gz: f1d1b5e052e91e176529a6cec60736f2c21bca0591ba4b184485e59f6d906204ae34c1dba0464f1d5b1d01ed691e599cf15f63b3e1760f89c222187030a2a830
+  data.tar.gz: 1611ac19a30c23bb7fd79c7acc2d1b0559b03ae3d179dd8881c10d0a828ba447f4546e1ce18b9907a277260656bcb85120054e739395922a505e93f9a84efe70

data/lib/miga/project_result.rb

@@ -11,7 +11,7 @@ module MiGA::ProjectResult
     # Internal alias for all add_result_*_distances.
     def add_result_distances(base)
       return nil unless result_files_exist?(base, %w[.Rdata .log .txt])
-      r = Result.new(base + ".json")
+      r = MiGA::Result.new(base + ".json")
       r.add_file(:rdata, "miga-project.Rdata")
       r.add_file(:matrix, "miga-project.txt")
       r.add_file(:log, "miga-project.log")
@@ -41,7 +41,7 @@ module MiGA::ProjectResult
     end
 
     def add_result_iter_clades(base)
-      r = Result.new(base + ".json")
+      r = MiGA::Result.new(base + ".json")
       r.add_file(:report,	"miga-project.pdf")
       r.add_file(:class_table,	"miga-project.class.tsv")
       r.add_file(:class_tree,	"miga-project.class.nwk")
@@ -52,7 +52,7 @@ module MiGA::ProjectResult
 
     def add_result_ogs(base)
       return nil unless result_files_exist?(base, %w[.ogs .stats])
-      r = Result.new(base + ".json")
+      r = MiGA::Result.new(base + ".json")
       r.add_file(:ogs, "miga-project.ogs")
       r.add_file(:stats, "miga-project.stats")
       r.add_file(:rbm, "miga-project.rbm")

data/lib/miga/remote_dataset.rb

@@ -63,16 +63,22 @@ class MiGA::RemoteDataset < MiGA::MiGA
         @@UNIVERSE[universe][:dbs][db][:map_to]
       url = sprintf @@UNIVERSE[universe][:url],
         db, ids.join(","), format, map_to
-      response = RestClient::Request.execute(:method=>:get,  :url=>url,
-        :timeout=>600)
-      raise "Unable to reach #{universe} client, error code "+
+      response = RestClient::Request.execute(method: :get, url:url, timeout:600)
+      raise "Unable to reach #{universe} client, error code " +
         "#{response.code}." unless response.code == 200
       doc = response.to_s
     when :net
-      url = sprintf @@UNIVERSE[universe][:url],
-        db, ids.join(","), format, map_to
+      url = sprintf @@UNIVERSE[universe][:url],db,ids.join(","),format,map_to
       doc = ""
-      open(url) { |f| doc = f.read }
+      @timeout_try = 0
+      begin
+        open(url) { |f| doc = f.read }
+      rescue Net::ReadTimeout
+        @timeout_try += 1
+        if @timeout_try > 3 ; raise Net::ReadTimeout
+        else ; retry
+        end
+      end
     end
     unless file.nil?
       ofh = File.open(file, "w")

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.2, 3, 0]
+  VERSION = [0.2, 3, 1]
   
   ##
   # Nickname for the current major.minor version.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.2.3.0
+  version: 0.2.3.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R