Merge branch 'develop'

ncbo · Aug 9, 2023 · 5f2fdc9 · 5f2fdc9
2 parents c4baa22 + dde48c2
commit 5f2fdc9
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diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
@@ -7,6 +7,7 @@ on:
 jobs:
   test:
     strategy:
+      fail-fast: false
       matrix:
         backend: ['api', 'api-agraph'] # api runs tests with 4store backend and api-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest

diff --git a/Gemfile b/Gemfile
@@ -1,9 +1,8 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 3.1'
+gem 'activesupport', '~> 3.0'
 # see https://github.com/ncbo/ontologies_api/issues/69
 gem 'bigdecimal', '1.4.2'
-gem 'faraday', '~> 2.0'
 gem 'json-schema', '~> 2.0'
 gem 'multi_json', '~> 1.0'
 gem 'oj', '~> 3.0'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: e8816b06244c26088ef0596ddc0623562a75a284
+  revision: 59fa167d6e8d2cb55bd0d574d029057f46cbc594
   branch: master
   specs:
     goo (0.0.2)
@@ -53,7 +53,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: d858e2e29e5da84c9741b7508efa235919642e46
+  revision: 0cdb8f84a4d8b19fdcebcaabb2e4968a63809863
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -103,9 +103,9 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.4)
+    addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.4.1)
+    airbrussh (1.4.2)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.24.1)
     bcrypt (3.1.19)
@@ -162,16 +162,15 @@ GEM
     google-cloud-env (1.6.0)
       faraday (>= 0.17.3, < 3.0)
     google-cloud-errors (1.3.1)
-    google-protobuf (3.23.4-aarch64-linux)
-    google-protobuf (3.23.4-arm64-darwin)
-    google-protobuf (3.23.4-x86_64-darwin)
-    google-protobuf (3.23.4-x86_64-linux)
+    google-protobuf (3.24.0-aarch64-linux)
+    google-protobuf (3.24.0-x86_64-darwin)
+    google-protobuf (3.24.0-x86_64-linux)
     googleapis-common-protos (1.4.0)
       google-protobuf (~> 3.14)
       googleapis-common-protos-types (~> 1.2)
       grpc (~> 1.27)
-    googleapis-common-protos-types (1.7.0)
-      google-protobuf (~> 3.14)
+    googleapis-common-protos-types (1.8.0)
+      google-protobuf (~> 3.18)
     googleauth (1.7.0)
       faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
@@ -213,10 +212,10 @@ GEM
       net-smtp
     memoist (0.16.2)
     method_source (1.0.0)
-    mime-types (3.4.1)
+    mime-types (3.5.0)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0218.1)
-    mini_mime (1.1.2)
+    mime-types-data (3.2023.0808)
+    mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
@@ -234,10 +233,10 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-smtp (0.3.3)
       net-protocol
-    net-ssh (7.1.0)
+    net-ssh (7.2.0)
     netrc (0.11.0)
     newrelic_rpm (9.3.1)
-    oj (3.15.0)
+    oj (3.15.1)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
@@ -257,7 +256,7 @@ GEM
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (3.1.0)
+    rack-mini-profiler (3.1.1)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
@@ -283,7 +282,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.5)
+    rexml (3.2.6)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -342,13 +341,12 @@ GEM
 
 PLATFORMS
   aarch64-linux
-  arm64-darwin-22
   x86_64-darwin-18
   x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
-  activesupport (~> 3.1)
+  activesupport (~> 3.0)
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bigdecimal (= 1.4.2)
   capistrano (~> 3)
@@ -357,7 +355,6 @@ DEPENDENCIES
   capistrano-rbenv
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
-  faraday (~> 2.0)
   ffi
   goo!
   haml (~> 5.2.2)

diff --git a/config/environments/test.rb b/config/environments/test.rb
@@ -5,7 +5,7 @@
 GOO_PATH_DATA    = ENV.include?("GOO_PATH_DATA")    ? ENV["GOO_PATH_DATA"]    : "/data/"
 GOO_PATH_QUERY   = ENV.include?("GOO_PATH_QUERY")   ? ENV["GOO_PATH_QUERY"]   : "/sparql/"
 GOO_PATH_UPDATE  = ENV.include?("GOO_PATH_UPDATE")  ? ENV["GOO_PATH_UPDATE"]  : "/update/"
-GOO_PORT         = ENV.include?("GOO_PORT")         ? ENV["GOO_PORT"]         : 9000
+GOO_PORT         = ENV.include?("GOO_PORT")         ? ENV["GOO_PORT"]         : 8080
 MGREP_DICTIONARY_FILE = ENV.include?("MGREP_DICTIONARY_FILE") ? ENV["MGREP_DICTIONARY_FILE"] : "./test/data/dictionary.txt"
 MGREP_HOST       = ENV.include?("MGREP_HOST")       ? ENV["MGREP_HOST"]       : "localhost"
 MGREP_PORT       = ENV.include?("MGREP_PORT")       ? ENV["MGREP_PORT"]       : 55555

diff --git a/controllers/ontology_analytics_controller.rb b/controllers/ontology_analytics_controller.rb
@@ -28,7 +28,11 @@ class OntologyAnalyticsController < ApplicationController
       expires 86400, :public
       ont = Ontology.find(params["acronym"]).first
       error 404, "No ontology exists with the acronym: #{params["acronym"]}" if ont.nil?
-      analytics = ont.analytics
+      year = year_param(params)
+      error 400, "The year you supplied is invalid. Valid years start with 2 and contain 4 digits." if params["year"] && !year
+      month = month_param(params)
+      error 400, "The month you supplied is invalid. Valid months are 1-12." if params["month"] && !month
+      analytics = ont.analytics(year, month)
 
       if params["format"].to_s.downcase.eql?("csv")
         tf = Tempfile.new("analytics-#{params['acronym']}")
@@ -39,7 +43,7 @@ class OntologyAnalyticsController < ApplicationController
         years.each do |year|
           months = analytics[params["acronym"]][year].keys.sort
           months.each do |month|
-            next if now.year == year && now.month <= month || (year == 2013 && month < 10) # we don't have good data going back past Oct 2013
+            next if year && month && (now.year == year.to_i && now.month <= month.to_i || year.to_i == 2013 && month.to_i < 10) # we don't have good data going back past Oct 2013
             visits = analytics[params["acronym"]][year][month]
             month = DateTime.parse("#{year}/#{month}").strftime("%b %Y")
             csv << [month, visits]

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -114,7 +114,8 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v7.3.1
+    #image: franzinc/agraph:v7.3.1
+    image: ontoportal/agraph:v7.3.1-patch1
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test

diff --git a/helpers/application_helper.rb b/helpers/application_helper.rb
@@ -261,9 +261,10 @@ def month_param(params=nil)
         if params["month"]
           month = params["month"].strip
           if %r{(?<month>^(0[1-9]|[1-9]|1[0-2])$)}x === month
-            month.to_i
+            return month.to_i.to_s
           end
         end
+        nil
       end
 
       # validates year for starting with 1 or 2 and containing 4 digits
@@ -272,9 +273,10 @@ def year_param(params=nil)
         if params["year"]
           year = params["year"].strip
           if %r{(?<year>^([1-2]\d{3})$)}x === year
-            year.to_i
+            return year.to_i.to_s
           end
         end
+        nil
       end
 
       ##