gn_list_resolver 3.0.1 → 3.0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,5 +1,9 @@
 # ``gn_list_resolver`` CHANGELOG
 
+## 3.0.1.1
+
+* @dimus - refactoring, GnListResolver.run returns stats
+
 ## 3.0.1
 
 * @dimus - fixes #31 bug: prevent csv row to get  squashed

data/README.md

@@ -63,6 +63,12 @@ cat my_list.csv | crossmap -i my_list.csv -s
 
 ### Usage as Ruby Library (API description)
 
+#### Changing default url for gnindex API
+
+Default URL for API is `http://index-api.globalnames.org/api/graphql`
+
+if you want to change it, set an environment variable `GN_RESOLVER_URL`
+
 #### `GnListResolver.run`
 
 Compares an input list to a data source from [GN Resolver][resolver] and
@@ -94,9 +100,6 @@ from original data. Otherwise all original data is preserved. If there is no
 : (array) empty array by default. If `alt_headers` are not empty they are used
 instead of the headers supplied with the file
 
-``resolver_url``
-: URL to globalnames' resolver. Default is ``http://resolver.globalnames.org``
-
 #### `GnListResolver.logger=`
 
 Allows to set logger to a custom logger (default is `STDERR`)

data/gn_list_resolver.gemspec

@@ -12,7 +12,7 @@ Gem::Specification.new do |gem|
   gem.name          = "gn_list_resolver"
   gem.version       = GnListResolver::VERSION
   gem.license       = "MIT"
-  gem.authors       = ["Dmitry Mozzherin"]
+  gem.authors       = ["Dmitry Mozzherin", "Alexander Myltsev"]
   gem.email         = ["dmozzherin@gmail.com"]
 
   gem.summary       = "Resolves a list of scientific names to names from " \

data/lib/gn_list_resolver.rb

@@ -8,6 +8,10 @@ require "logger"
 require "logger/colors"
 require "biodiversity"
 require "gn_uuid"
+require "graphql/client"
+require "graphql/client/http"
+require "gn_list_resolver/constants"
+require "gn_list_resolver/graphql"
 require "gn_list_resolver/errors"
 require "gn_list_resolver/version"
 require "gn_list_resolver/reader"
@@ -21,10 +25,6 @@ require "gn_list_resolver/stats"
 
 # Namespace module for resolving lists with GN sources
 module GnListResolver
-  INPUT_MODE = "r:utf-8"
-  OUTPUT_MODE = "w:utf-8"
-  MATCH_TYPE_EMPTY = "EmptyMatch"
-
   class << self
     attr_writer :logger
 
@@ -36,7 +36,7 @@ module GnListResolver
       writer = create_writer(reader, output_io, opts)
       resolver = create_resolver(writer, opts)
       block_given? ? resolver.resolve(data, &Proc.new) : resolver.resolve(data)
-      opts.output
+      resolver.stats
     end
 
     def logger
@@ -54,7 +54,7 @@ module GnListResolver
     private
 
     def create_resolver(writer, opts)
-      Resolver.new(writer, opts.data_source_id, opts.resolver_url, opts.stats)
+      Resolver.new(writer, opts.data_source_id, opts.stats)
     end
 
     def create_writer(reader, output_io, opts)
@@ -67,12 +67,7 @@ module GnListResolver
     end
 
     def opts_struct(opts)
-      # resolver_url = "http://gnresolver.globalnames.org/api/graphql".freeze
-      # resolver_url = "http://localhost:8888/api/graphql".freeze
-      # resolver_url = "http://localhost:8080/api/graphql".freeze
-      resolver_url = "http://index-api.globalnames.org/api/graphql"
-      OpenStruct.new({ stats: Stats.new, alt_headers: [],
-                       resolver_url: resolver_url }.merge(opts))
+      OpenStruct.new({ stats: Stats.new, alt_headers: [] }.merge(opts))
     end
 
     def io(input, output)

data/lib/gn_list_resolver/constants.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Namespace module for resolving lists with GN sources
+module GnListResolver
+  INPUT_MODE = "r:utf-8"
+  OUTPUT_MODE = "w:utf-8"
+  MATCH_TYPE_EMPTY = "EmptyMatch"
+  RESOLVER_URL = ENV["GN_RESOLVER_URL"] ||
+                 "http://index-api.globalnames.org/api/graphql"
+end

data/lib/gn_list_resolver/graphql.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module GnListResolver
+  # GraphQL client for gnindex API
+  class GnGraphQL
+    attr_reader :client, :query
+
+    def initialize
+      http = GraphQL::Client::HTTP.new(RESOLVER_URL)
+      schema = GraphQL::Client.load_schema(http)
+      @client = GraphQL::Client.new(schema: schema, execute: http)
+      @query = <<~GRAPHQL_QUERY
+        query($names: [name!]!, $dataSourceIds: [Int!]) {
+          nameResolver(names: $names, dataSourceIds: $dataSourceIds) {
+            total suppliedId suppliedInput
+            results {
+              name { name }
+              canonicalName { name }
+              synonym
+              matchType { kind score editDistance }
+              taxonId classification { pathRanks }
+              score { value parsingQuality }
+            }
+          }
+        }
+      GRAPHQL_QUERY
+    end
+  end
+end

data/lib/gn_list_resolver/resolver.rb

@@ -1,36 +1,14 @@
 # frozen_string_literal: true
 
-require "graphql/client"
-require "graphql/client/http"
-
 # GnListResolver::test
 module GnListResolver
-  # resolver_url = "http://gnresolver.globalnames.org/api/graphql".freeze
-  # resolver_url = "http://localhost:8888/api/graphql".freeze
-  # resolver_url = "http://localhost:8080/api/graphql".freeze
-  resolver_url = "http://index-api.globalnames.org/api/graphql"
-  HTTP = GraphQL::Client::HTTP.new(resolver_url)
-  SCHEMA = GraphQL::Client.load_schema(HTTP)
-  CLIENT = GraphQL::Client.new(schema: SCHEMA, execute: HTTP)
-  NAME_RESOLVERS_QUERY = CLIENT.parse <<-'GRAPHQL'
-      query($names: [name!]!, $dataSourceIds: [Int!]) {
-        nameResolver(names: $names, dataSourceIds: $dataSourceIds) {
-          total suppliedId suppliedInput
-          results {
-            name { name }
-            canonicalName { name }
-            synonym
-            matchType { kind score editDistance }
-            taxonId classification { pathRanks }
-            score { value parsingQuality }
-          }
-        }
-      }
-    GRAPHQL
-
   # Sends data to GN Resolver and collects results
   class Resolver
-    def initialize(writer, data_source_id, _resolver_url, stats)
+    GRAPHQL = GnGraphQL.new
+    QUERY = GRAPHQL.client.parse(GRAPHQL.query)
+    attr_reader :stats
+
+    def initialize(writer, data_source_id, stats)
       @stats = stats
       @processor = GnListResolver::ResultProcessor.new(writer, @stats)
       @ds_id = data_source_id
@@ -43,7 +21,12 @@ module GnListResolver
       update_stats(data.size)
       block_given? ? process(data, &Proc.new) : process(data)
       wrap_up
-      yield(@stats.stats) if block_given?
+
+      if block_given?
+        yield(@stats.stats)
+      else
+        @stats.stats
+      end
     end
 
     private
@@ -78,7 +61,7 @@ module GnListResolver
       e = [@count, @stats.stats[:total_records]].min
       GnListResolver.log("Resolve #{s}-#{e} out of " \
                          "#{@stats.stats[:total_records]} records at " \
-                         "#{@resolver_url}")
+                         "#{RESOLVER_URL}")
       yield
     end
 
@@ -102,7 +85,7 @@ module GnListResolver
 
     def remote_resolve(names)
       batch_start = Time.now
-      res = CLIENT.query(NAME_RESOLVERS_QUERY, variables: variables(names))
+      res = GRAPHQL.client.query(QUERY, variables: variables(names))
       @processor.process(res.data.name_resolver, @current_data)
       update_batch_times(batch_start)
     end

data/lib/gn_list_resolver/version.rb

@@ -2,7 +2,7 @@
 
 # Namespace module for crossmapping checklists to GN sources
 module GnListResolver
-  VERSION = "3.0.1"
+  VERSION = "3.0.1.1"
 
   def self.version
     VERSION

metadata

@@ -1,14 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: gn_list_resolver
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.0.1.1
 platform: ruby
 authors:
 - Dmitry Mozzherin
+- Alexander Myltsev
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-07-18 00:00:00.000000000 Z
+date: 2017-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -234,7 +235,9 @@ files:
 - lib/gn_list_resolver.rb
 - lib/gn_list_resolver/collector.rb
 - lib/gn_list_resolver/column_collector.rb
+- lib/gn_list_resolver/constants.rb
 - lib/gn_list_resolver/errors.rb
+- lib/gn_list_resolver/graphql.rb
 - lib/gn_list_resolver/reader.rb
 - lib/gn_list_resolver/resolver.rb
 - lib/gn_list_resolver/result_processor.rb