qa 0.0.2 → 0.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 873698ac06d737a85d38e567cfbc86a237c11726
-  data.tar.gz: aca833c7eaaf7b53e5181f9705828e6bdd64267d
+  metadata.gz: fed80fc0a3c24bbbd3032d4073f7e75aac0aa9c5
+  data.tar.gz: 965f2f9ec8fe396b5d31bfc3fa6d87e2787cd556
 SHA512:
-  metadata.gz: 48ff5de3dabe9ff003cd066d67ded425ac5782ecc5f493d41879832ab0d9bf047118f96b10d091656af0a866e1169e896a86d15958014b15091e1b3f6004d356
-  data.tar.gz: 860a602fc303ec68bdd76f7651a5d193c97ac2656fa281ee83b7c998acb9461d4800f73bd8c8a1d63b53591b446f315cff64854694fbda8e87f93d6b897f3e43
+  metadata.gz: 0c008f809edb88cdea1d9f39c17f938d6d496b9b2e709976789b206cccc9c37bcbe72f30cf585c6f05fce0701fa50337bc6809303863d6d192db0d51652b6b69
+  data.tar.gz: 80c6e14d23838e345affc9723f0d99d56f3c2731a6be9f45d939966ee2d22ea8bcfb80746d1612379cf50837386959aded55bc664dfe88c8169df566b721cb50

data/lib/qa/authorities/local/subauthority.rb

@@ -17,6 +17,10 @@ module Qa::Authorities
       end
     end
 
+    def full_record(id)
+      terms.find { |term| term[:id] == id } || {}
+    end
+
     class << self
       def sub_authorities_path
         config_path = AUTHORITIES_CONFIG[:local_path]

data/lib/qa/authorities/local.rb

@@ -1,6 +1,8 @@
+require 'deprecation'
 module Qa::Authorities
 
   class Local < Qa::Authorities::Base
+    extend Deprecation
 
     class << self
       def sub_authority(name)
@@ -18,16 +20,19 @@ module Qa::Authorities
       end
     end
 
+    delegate :sub_authority, to: self
+
     def search(q, sub_authority)
-      Local.sub_authority(sub_authority).search(q)
+      sub_authority(sub_authority).search(q)
+    end
+
+    def full_record(id, sub_authority)
+      sub_authority(sub_authority).full_record(id)
     end
 
     def get_full_record(id, sub_authority)
-      terms = Local.sub_authority(sub_authority).terms
-      terms.each do |term|
-        return term if term[:id] == id
-      end
-      return {}
+      Deprecation.warn(Local, "get_full_record is deprecated and will be removed in 0.1.0. Use full_record instead", caller)
+      full_record(id, sub_authority)
     end
 
   end

data/lib/qa/version.rb

@@ -1,3 +1,3 @@
 module Qa
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/lib/tasks/mesh.rake

@@ -0,0 +1,26 @@
+require 'benchmark'
+
+namespace :mesh do
+  desc "Import MeSH terms from the file $MESH_FILE, it will update any terms which are already in the database"
+  task :import => :environment do
+    fname = ENV['MESH_FILE']
+    if fname.nil?
+      puts "Need to set $MESH_FILE with path to file to ingest"
+      next  # transfers control out of this block
+    end
+    Benchmark.bm(30) do |bm|
+      bm.report("Importing #{fname}") do
+        m = Qa::Authorities::MeshTools::MeshImporter.new
+        File.open(fname) do |f|
+          m.import_from_file(f)
+        end
+      end
+    end
+  end
+
+  desc "Delete all mesh terms from the database---not implemented"
+  task :clear do
+    puts "Not implemented"
+  end
+
+end

data/spec/internal/Gemfile.lock

@@ -1,9 +1,10 @@
 PATH
   remote: ../../../questioning_authority
   specs:
-    qa (0.0.1)
+    qa (0.0.2)
       activerecord-import (>= 0.4.0)
       curb
+      deprecation
       nokogiri (~> 1.6.0)
       rails (~> 4.0.0)
       rest-client
@@ -51,6 +52,8 @@ GEM
     crack (0.4.1)
       safe_yaml (~> 0.9.0)
     curb (0.8.5)
+    deprecation (0.0.5)
+      activesupport
     diff-lcs (1.2.4)
     erubis (2.7.0)
     execjs (2.0.2)

data/spec/internal/log/development.log

@@ -6548,3 +6548,499 @@ Completed 400 Bad Request in 0ms (ActiveRecord: 0.0ms)
    (0.1ms)  rollback transaction
    (0.1ms)  begin transaction
    (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.6ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.3ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.2ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.2ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.2ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.2ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.2ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.0ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+  ActiveRecord::SchemaMigration Load (0.2ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.2ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+  ActiveRecord::SchemaMigration Load (0.1ms)  SELECT "schema_migrations".* FROM "schema_migrations"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  select sqlite_version(*)
+  Class Create Many Without Validations Or Callbacks (0.4ms)  INSERT INTO "qa_subject_mesh_terms" ("term_id","term","term_lower","synonyms") VALUES ('D008288','Malaria','malaria','Marsh Fever|Plasmodium Infections|Remittent Fever|Infections, Plasmodium|Paludism|Fever, Marsh|Fever, Remittent|Infection, Plasmodium|Plasmodium Infection'),('D000001','Calcimycin','calcimycin','A-23187|A23187|Antibiotic A23187|A 23187|A23187, Antibiotic'),('D005260','Female','female','Females'),('D005261','Female Urogenital Diseases and Pregnancy Complications','female urogenital diseases and pregnancy complications',''),('D010272','Parasitic Diseases','parasitic diseases','Disease, Parasitic|Diseases, Parasitic|Parasitic Disease'),('D011528','Protozoan Infections','protozoan infections','Histomoniasis|Infections, Protozoan|Histomoniases|Infection, Protozoan|Protozoan Infection'),('D062310','Tropical Diseases','tropical diseases','Disease, Tropical|Diseases, Tropical|Tropical Disease'),('D013568','Pathological Conditions, Signs and Symptoms','pathological conditions, signs and symptoms','Symptoms and General Pathology'),('D001583','Benzoxazoles','benzoxazoles',''),('D006574','Heterocyclic Compounds, 2-Ring','heterocyclic compounds, 2-ring','2-Ring Heterocyclic Compounds|Compounds, 2-Ring Heterocyclic|Heterocyclic Compounds, 2 Ring'),('D006571','Heterocyclic Compounds','heterocyclic compounds','Compounds, Heterocyclic')
+  Class Create Many Without Validations Or Callbacks (0.2ms)  INSERT INTO "qa_mesh_trees" ("term_id","tree_number") VALUES ('D008288','C03.752.530'),('D008288','C23.996.660'),('D000001','D03.438.221.173'),('D005261','C13'),('D010272','C03'),('D011528','C03.752'),('D062310','C03.883'),('D062310','C23.996'),('D013568','C23'),('D001583','D03.438.221'),('D006574','D03.438'),('D006571','D03')
+  Qa::SubjectMeshTerm Load (0.1ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" WHERE "qa_subject_mesh_terms"."term_lower" = 'malaria'
+  Qa::SubjectMeshTerm Load (0.1ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" WHERE "qa_subject_mesh_terms"."term" = 'Malaria'
+  Qa::SubjectMeshTerm Load (0.1ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" WHERE "qa_subject_mesh_terms"."term_id" = 'D008288'
+  Qa::SubjectMeshTerm Load (0.3ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms"
+   (1.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+  SQL (0.6ms)  INSERT INTO "qa_subject_mesh_terms" ("term", "term_id", "term_lower") VALUES (?, ?, ?)  [["term", "Mr Plow"], ["term_id", "1"], ["term_lower", "mr plow"]]
+   (1.5ms)  commit transaction
+   (0.1ms)  begin transaction
+  SQL (0.3ms)  INSERT INTO "qa_subject_mesh_terms" ("term", "term_id", "term_lower") VALUES (?, ?, ?)  [["term", "Mr Snow"], ["term_id", "2"], ["term_lower", "mr snow"]]
+   (1.4ms)  commit transaction
+   (0.1ms)  begin transaction
+  SQL (0.3ms)  INSERT INTO "qa_subject_mesh_terms" ("term", "term_id", "term_lower") VALUES (?, ?, ?)  [["term", "Mrs Fields"], ["term_id", "3"], ["term_lower", "mrs fields"]]
+   (1.4ms)  commit transaction
+   (0.1ms)  begin transaction
+  Qa::SubjectMeshTerm Load (0.2ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" WHERE (term_lower LIKE 'mr%') LIMIT 10
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+  Qa::SubjectMeshTerm Load (0.2ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" WHERE "qa_subject_mesh_terms"."term_id" = '2' ORDER BY "qa_subject_mesh_terms"."id" ASC LIMIT 1
+   (0.1ms)  rollback transaction
+  SQL (1.6ms)  DELETE FROM "qa_subject_mesh_terms"
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.0ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.0ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"foo", "vocab"=>"loc"}
+Completed 200 OK in 5ms (Views: 0.2ms | ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"Tibetan", "vocab"=>"tgnlang"}
+Completed 200 OK in 48ms (Views: 0.2ms | ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"foo", "vocab"=>"loc", "sub_authority"=>"relators"}
+Completed 200 OK in 4ms (Views: 0.2ms | ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"Blues", "vocab"=>"lcsh"}
+Completed 200 OK in 5ms (Views: 0.6ms | ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"foo", "vocab"=>"bar"}
+Filter chain halted as :check_authority rendered or redirected
+Completed 400 Bad Request in 2ms (ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>nil}
+Filter chain halted as :check_vocab_param rendered or redirected
+Completed 400 Bad Request in 0ms (ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"q"=>"foo", "vocab"=>"loc", "sub_authority"=>"foo"}
+Filter chain halted as :check_sub_authority rendered or redirected
+Completed 400 Bad Request in 0ms (ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+Processing by Qa::TermsController#index as HTML
+  Parameters: {"vocab"=>nil}
+Filter chain halted as :check_vocab_param rendered or redirected
+Completed 400 Bad Request in 0ms (ActiveRecord: 0.0ms)
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.2ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+  SQL (0.4ms)  INSERT INTO "qa_subject_mesh_terms" ("term", "term_id") VALUES (?, ?)  [["term", "Glyphon"], ["term_id", "ABCDEFG"]]
+   (1.4ms)  commit transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  SAVEPOINT active_record_1
+  SQL (0.4ms)  INSERT INTO "qa_subject_mesh_terms" ("synonyms", "term_id") VALUES (?, ?)  [["synonyms", "b|c"], ["term_id", "a"]]
+   (0.0ms)  RELEASE SAVEPOINT active_record_1
+   (0.9ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  SAVEPOINT active_record_1
+  SQL (0.4ms)  INSERT INTO "qa_mesh_trees" ("term_id", "tree_number") VALUES (?, ?)  [["term_id", "ABCDEFG"], ["tree_number", "D1.2.3.4"]]
+   (0.0ms)  RELEASE SAVEPOINT active_record_1
+  Qa::SubjectMeshTerm Load (0.1ms)  SELECT "qa_subject_mesh_terms".* FROM "qa_subject_mesh_terms" INNER JOIN qa_mesh_trees ON qa_subject_mesh_terms.term_id = qa_mesh_trees.term_id WHERE (qa_mesh_trees.tree_number = 'D1.2.3.4')
+   (0.8ms)  rollback transaction
+   (0.1ms)  begin transaction
+  Qa::MeshTree Load (0.2ms)  SELECT "qa_mesh_trees".* FROM "qa_mesh_trees" WHERE "qa_mesh_trees"."term_id" = 'ABCDEFG'
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+  SQL (2.2ms)  DELETE FROM "qa_subject_mesh_terms" WHERE "qa_subject_mesh_terms"."id" = ?  [["id", 180]]
+   (1.6ms)  commit transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction
+   (0.1ms)  begin transaction
+   (0.1ms)  rollback transaction

data/spec/lib/authorities_local_spec.rb

@@ -12,9 +12,17 @@ describe Qa::Authorities::Local do
       Qa::Authorities::Local.sub_authorities.should include "authority_B"
     end    
 
+    describe "the class" do
+      subject { Qa::Authorities::Local }
+      it "should return a sub_authority" do
+        expect { subject.sub_authority('authority_Z')}.to raise_error ArgumentError, "Invalid sub-authority 'authority_Z'"
+        expect(subject.sub_authority('authority_A')).to be_kind_of Qa::Authorities::Subauthority
+      end
+    end
+
     it "should return a sub_authority" do
-      expect { Qa::Authorities::Local.sub_authority('authority_Z')}.to raise_error ArgumentError, "Invalid sub-authority 'authority_Z'"
-      expect(Qa::Authorities::Local.sub_authority('authority_A')).to be_kind_of Qa::Authorities::Subauthority
+      expect { subject.sub_authority('authority_Z')}.to raise_error ArgumentError, "Invalid sub-authority 'authority_Z'"
+      expect(subject.sub_authority('authority_A')).to be_kind_of Qa::Authorities::Subauthority
     end
   end
 
@@ -78,14 +86,14 @@ describe Qa::Authorities::Local do
       let(:id) { "A2" }
       let(:expected) { { 'id' => "A2", 'term' => "Term A2", 'active' => false } }
       it "should return the full term record" do
-        record = authorities.get_full_record(id, "authority_A")
+        record = authorities.full_record(id, "authority_A")
         expect(record).to be_a HashWithIndifferentAccess
         expect(record).to eq(expected)
       end
     end
     context "source is a list" do
       it "should be indifferent access" do
-        record = authorities.get_full_record('Term C1', "authority_C")
+        record = authorities.full_record('Term C1', "authority_C")
         expect(record).to be_a HashWithIndifferentAccess
       end
     end
@@ -94,7 +102,15 @@ describe Qa::Authorities::Local do
       let(:id) { "NonID" }
       let(:expected) { {} }
       it "should return an empty hash" do
-        expect(authorities.get_full_record(id, "authority_A")).to eq(expected)
+        expect(authorities.full_record(id, "authority_A")).to eq(expected)
+      end
+    end
+
+    context "on a sub-authority" do
+      it "should return the full term record" do
+        record = authorities.sub_authority('authority_A').full_record('A2')
+        expect(record).to be_a HashWithIndifferentAccess
+        expect(record).to eq('id' => "A2", 'term' => "Term A2", 'active' => false)
       end
     end
 

data/spec/lib/tasks/mesh.rake_spec.rb

@@ -0,0 +1,43 @@
+require 'spec_helper'
+require 'rake'
+require 'stringio'
+
+describe "mesh rake tasks" do
+  before do
+    @rake = Rake::Application.new
+    Rake.application = @rake
+    Rake.application.rake_require "mesh", ["#{Rails.root}/lib/tasks", "#{Rails.root}/../../lib/tasks"], []
+    Rake::Task.define_task(:environment)  # rspec has loaded rails
+  end
+
+  describe "mesh:import" do
+    before do
+      @task_name = "mesh:import"
+      @output = StringIO.new
+      $stdout = @output
+    end
+    after :all do
+      $stdout = STDOUT
+    end
+    it "should have 'environment' as a prereq" do
+      @rake[@task_name].prerequisites.should include("environment")
+    end
+    it "should require $MESH_FILE to be set" do
+      old_mesh_file = ENV.delete('MESH_FILE')
+      @rake[@task_name].invoke
+      @output.seek(0)
+      @output.read.should =~ /Need to set \$MESH_FILE with path to file to ingest/
+      ENV['MESH_FILE'] = old_mesh_file
+    end
+    it "should create or update all records in the config file" do
+      ENV['MESH_FILE'] = "dummy"
+      input = StringIO.new("*NEWRECORD\nUI = 5\nMH = test\n")
+      File.should_receive(:open).with("dummy").and_yield(input)
+      @rake[@task_name].invoke
+      term = Qa::SubjectMeshTerm.find_by_term_id(5)
+      term.should_not be_nil
+      term.term.should == "test"
+      ENV['MESH_FILE'] = nil
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: qa
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - Stephen Anderson
@@ -15,7 +15,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-07 00:00:00.000000000 Z
+date: 2013-11-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -87,6 +87,20 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.4.0
+- !ruby/object:Gem::Dependency
+  name: deprecation
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
@@ -226,6 +240,7 @@ files:
 - lib/qa/engine.rb
 - lib/qa/version.rb
 - lib/qa.rb
+- lib/tasks/mesh.rake
 - lib/tasks/qa_tasks.rake
 - LICENSE
 - Rakefile
@@ -293,6 +308,7 @@ files:
 - spec/lib/authorities_oclcts_spec.rb
 - spec/lib/authorities_tgnlang_spec.rb
 - spec/lib/mesh_data_parser_spec.rb
+- spec/lib/tasks/mesh.rake_spec.rb
 - spec/models/subject_mesh_term_spec.rb
 - spec/spec_helper.rb
 - spec/support/lib/generators/test_app_generator.rb
@@ -384,6 +400,7 @@ test_files:
 - spec/lib/authorities_oclcts_spec.rb
 - spec/lib/authorities_tgnlang_spec.rb
 - spec/lib/mesh_data_parser_spec.rb
+- spec/lib/tasks/mesh.rake_spec.rb
 - spec/models/subject_mesh_term_spec.rb
 - spec/spec_helper.rb
 - spec/support/lib/generators/test_app_generator.rb