Merge 0fe960c into dc400a7

.rubocop.yml

@@ -10,25 +10,17 @@ Style/ClassAndModuleChildren:
   Enabled: false
 
 # disable for now
-Style/AccessorMethodName:
-  Enabled: false
 Style/ClassVars:
   Enabled: false
 Style/Documentation:
   Enabled: false
-Style/IfUnlessModifier:
-  Enabled: false
 Style/RescueModifier:
   Enabled: false
 Metrics/AbcSize:
   Enabled: false
 Metrics/ClassLength:
   Enabled: false
-Metrics/CyclomaticComplexity:
-  Enabled: false
 Metrics/LineLength:
   Enabled: false
 Metrics/MethodLength:
   Enabled: false
-Metrics/PerceivedComplexity:
-  Enabled: false

README.md

@@ -23,8 +23,8 @@ The Unipept CLI is available as a *gem*. This means it can easily be installed w
 
 ```bash
 $ gem install unipept
-Successfully installed unipept-0.7.1
-Parsing documentation for unipept-0.7.1
+Successfully installed unipept-0.8.0
+Parsing documentation for unipept-0.8.0
 Done installing documentation for unipept after 0 seconds
 1 gem installed
 ```
@@ -33,7 +33,7 @@ After successful installation, the unipept command should be available:
 
 ```bash
 $ unipept -v
-0.7.1
+0.8.0
 ```
 
 The help can be accessed by running `unipept -h`.

VERSION

@@ -1 +1 @@
-0.7.1
+0.8.0

lib/commands/peptfilter.rb

@@ -33,9 +33,7 @@ class Peptfilter
           end
 
           pept = pept.chomp
-          if Peptfilter.filter(pept, minlen, maxlen, lacks, contains)
-            puts pept
-          end
+          puts pept if Peptfilter.filter(pept, minlen, maxlen, lacks, contains)
         end
       end
     end

lib/commands/unipept/api_runner.rb

@@ -1,3 +1,5 @@
+require_relative '../../retryable_typhoeus'
+
 module Unipept
   class Commands::ApiRunner < Cri::CommandRunner
     attr_reader :configuration
@@ -21,13 +23,13 @@ def initialize(args, opts, cmd)
     # - the host
     # - the user agent
     def set_configuration
-      @host = get_host
+      @host = host
       @user_agent = 'Unipept CLI - unipept ' + Unipept::VERSION
     end
 
     # Returns the host. If a value is defined by both an option and the config
     # file, the value of the option is used.
-    def get_host
+    def host
       # find host in opts first
       host = options[:host] ? options[:host] : @configuration['host']
 
@@ -117,15 +119,27 @@ def run
       batch_order = Unipept::BatchOrder.new
 
       batch_iterator.iterate(input_iterator) do |input_slice, batch_id, fasta_mapper|
-        request = Typhoeus::Request.new(
+        request = ::RetryableTyphoeus::Request.new(
           @url,
           method: :post,
           body: construct_request_body(input_slice),
           accept_encoding: 'gzip',
           headers: { 'User-Agent' => @user_agent }
         )
 
-        request.on_complete do |resp|
+        # Failure callback: retry if retries not exceeded
+        request.on_failure do |resp|
+          if resp.request.retries <= 0
+            block = handle_response(resp, batch_id, fasta_mapper)
+            batch_order.wait(batch_id, &block)
+          else
+            resp.request.retries -= 1
+            hydra.queue_front resp.request
+          end
+        end
+
+        # Success callback
+        request.on_success do |resp|
           block = handle_response(resp, batch_id, fasta_mapper)
           batch_order.wait(batch_id, &block)
         end

lib/commands/unipept/config.rb

@@ -1,9 +1,7 @@
 module Unipept
   class Commands::Config < Cri::CommandRunner
     def run
-      if arguments.size == 0 || arguments.size > 2
-        abort command.help
-      end
+      abort command.help if arguments.size == 0 || arguments.size > 2
 
       key, value = *arguments
 

lib/commands/uniprot.rb

@@ -62,9 +62,7 @@ def self.get_uniprot_entry(accession, format)
       else
         # other format has been specified, just download and output
         resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{accession}.#{format}")
-        if resp.success?
-          resp.response_body
-        end
+        resp.response_body if resp.success?
       end
     end
   end

lib/retryable_typhoeus.rb

@@ -0,0 +1,21 @@
+# Retryable Typheous
+# Inspiration: https://gist.github.com/kunalmodi/2939288
+# Patches the request and hydra to allow requests to get resend when they fail
+
+module RetryableTyphoeus
+  require 'typhoeus'
+
+  include Typhoeus
+
+  DEFAULT_RETRIES = 10
+
+  class Request < Typhoeus::Request
+    attr_accessor :retries
+
+    def initialize(base_url, options = {})
+      @retries = (options.delete(:retries) || DEFAULT_RETRIES)
+
+      super
+    end
+  end
+end

test/commands/unipept/test_api_runner.rb

@@ -22,14 +22,14 @@ def test_config_host
       runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
       runner.options.delete(:host)
       runner.configuration['host'] = 'http://config_host'
-      host = runner.get_host
+      host = runner.host
       assert_equal('http://config_host', host)
     end
 
     def test_param_host
       runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
       runner.configuration.delete('host')
-      host = runner.get_host
+      host = runner.host
       assert_equal('http://param_host', host)
     end
 
@@ -39,7 +39,7 @@ def test_no_host
       runner.options.delete(:host)
       _out, err = capture_io_while do
         assert_raises SystemExit do
-          runner.get_host
+          runner.host
         end
       end
       assert(err.start_with? 'WARNING: no host has been set')
@@ -48,19 +48,19 @@ def test_no_host
     def test_host_priority
       runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
       runner.configuration['host'] = 'http://config_host'
-      host = runner.get_host
+      host = runner.host
       assert_equal('http://param_host', host)
     end
 
     def test_http_host
       runner = new_runner('test', { host: 'param_host' }, %w(a b c))
-      host = runner.get_host
+      host = runner.host
       assert_equal('http://param_host', host)
     end
 
     def test_https_host
       runner = new_runner('test', { host: 'https://param_host' }, %w(a b c))
-      host = runner.get_host
+      host = runner.host
       assert_equal('https://param_host', host)
     end
 

test/test_formatters.rb

@@ -38,15 +38,15 @@ def formatter
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.get_object))
+      assert_equal('', formatter.header(TestObject.test_object))
     end
 
     def test_type
       assert_equal('', formatter.type)
     end
 
     def test_format
-      assert_equal(TestObject.get_object, formatter.format(TestObject.get_object))
+      assert_equal(TestObject.test_object, formatter.format(TestObject.test_object))
     end
   end
 
@@ -56,15 +56,15 @@ def formatter
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.get_object))
+      assert_equal('', formatter.header(TestObject.test_object))
     end
 
     def test_type
       assert_equal('json', formatter.type)
     end
 
     def test_format
-      assert_equal(TestObject.as_json, formatter.format(TestObject.get_object))
+      assert_equal(TestObject.as_json, formatter.format(TestObject.test_object))
     end
   end
 
@@ -75,7 +75,7 @@ def formatter
 
     def test_header
       fasta = [['peptide', '>test']]
-      object = [TestObject.get_object, TestObject.get_object]
+      object = [TestObject.test_object, TestObject.test_object]
       assert_equal(TestObject.as_csv_header, formatter.header(object))
       assert_equal('fasta_header,' + TestObject.as_csv_header, formatter.header(object, fasta))
     end
@@ -85,14 +85,14 @@ def test_type
     end
 
     def test_format
-      object = [TestObject.get_object, TestObject.get_object]
+      object = [TestObject.test_object, TestObject.test_object]
       csv = [TestObject.as_csv, TestObject.as_csv, ''].join("\n")
       assert_equal(csv, formatter.format(object))
     end
 
     def test_format_with_fasta
       fasta = [['>test', '5']]
-      object = [TestObject.get_object, TestObject.get_object]
+      object = [TestObject.test_object, TestObject.test_object]
       csv = ['>test,' + TestObject.as_csv, '>test,' + TestObject.as_csv, ''].join("\n")
       assert_equal(csv, formatter.format(object, fasta))
     end
@@ -104,20 +104,20 @@ def formatter
     end
 
     def test_header
-      assert_equal('', formatter.header(TestObject.get_object))
+      assert_equal('', formatter.header(TestObject.test_object))
     end
 
     def test_type
       assert_equal('xml', formatter.type)
     end
 
     def test_format
-      assert_equal(TestObject.as_xml, formatter.format(TestObject.get_object))
+      assert_equal(TestObject.as_xml, formatter.format(TestObject.test_object))
     end
   end
 
   class TestObject
-    def self.get_object
+    def self.test_object
       JSON.parse('{"integer": 5, "string": "string", "list": ["a", 2, false]}')
     end