Merge branch 'develop'

ncbo · Jan 12, 2024 · 75436fe · 75436fe
2 parents 657149d + db2b330
commit 75436fe
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Showing 5 changed files with 267 additions and 283 deletions.
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -30,20 +30,19 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.5)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
-    base64 (0.1.1)
+    base64 (0.2.0)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20240107)
     eventmachine (1.2.7)
-    faraday (2.7.11)
+    faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
@@ -53,13 +52,13 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json_pure (2.6.3)
+    json_pure (2.7.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     method_source (1.0.0)
-    mime-types (3.5.1)
+    mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2023.1205)
     minitest (4.7.5)
     multi_json (1.15.0)
     mustermann (3.0.0)
@@ -69,20 +68,21 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     rack (2.2.8)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-post-body-to-params (0.1.8)
       activesupport (>= 2.3)
-    rack-protection (3.1.0)
+    rack-protection (3.2.0)
+      base64 (>= 0.1.0)
       rack (~> 2.2, >= 2.2.4)
     rake (13.1.0)
     rdf (1.0.8)
       addressable (>= 2.2)
     redis (5.0.8)
       redis-client (>= 0.17.0)
-    redis-client (0.18.0)
+    redis-client (0.19.1)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -103,10 +103,10 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
-    sinatra (3.1.0)
+    sinatra (3.2.0)
       mustermann (~> 3.0)
       rack (~> 2.2, >= 2.2.4)
-      rack-protection (= 3.1.0)
+      rack-protection (= 3.2.0)
       tilt (~> 2.0)
     systemu (2.6.5)
     thin (1.8.2)
@@ -116,15 +116,11 @@ GEM
     thread_safe (0.3.6)
     tilt (2.3.0)
     tzinfo (0.3.62)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   ruby
-  x86_64-darwin-16
   x86_64-linux
 
 DEPENDENCIES
@@ -144,4 +140,4 @@ DEPENDENCIES
   uuid
 
 BUNDLED WITH
-   2.3.15
+   2.3.22
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -21,15 +21,13 @@ services:
       retries: 5
 
   agraph-ut:
-    #image: franzinc/agraph:v7.3.1
-    image: ontoportal/agraph:v7.3.1-patch1
+    image: franzinc/agraph:v8.0.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
       - AGRAPH_SUPER_PASSWORD=xyzzy
     shm_size: 1g
     ports:
-      #      - 10035:10035
       - 10000-10035:10000-10035
     volumes:
       - agdata:/agraph/data
@@ -41,8 +39,8 @@ services:
         ; agtool users grant anonymous root:ontoportal_test:rw
         ; tail -f /agraph/data/agraph.log"
     # healthcheck:
-    #   test: ["CMD-SHELL", "curl -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1"]
-    #   start_period: 10s
+    #   test: ["CMD-SHELL", "curl -m 1 -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1"]
+    #   start_period: 60s
     #   interval: 10s
     #   timeout: 5s
     #   retries: 5

diff --git a/rakelib/docker_based_test.rake b/rakelib/docker_based_test.rake
@@ -3,6 +3,11 @@
 desc 'Run unit tests with docker based backend'
 namespace :test do
   namespace :docker do
+    desc "clean docker images and volumes"
+
+    task :clean do
+      system("docker compose down --volumes")
+    end
     task :up do
       system("docker compose up -d") || abort("Unable to start docker containers")
     end
@@ -19,19 +24,22 @@ namespace :test do
       ENV["GOO_PATH_UPDATE"]="/repositories/ontoportal_test/statements"
       ENV["COMPOSE_PROFILES"]="ag"
       Rake::Task["test:docker:up"].invoke
+
       # AG takes some time to start and create databases/accounts
       # TODO: replace system curl command with native ruby code
-      unless system("curl -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1")
-        printf("waiting for AllegroGraph container to initialize")
-        sec = 0
-        until system("curl -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1") do
-          sleep(1)
-          printf(".")
-          sec += 1
-          abort("  AllegroGraph container hasn't initialized properly") if sec > 30
-        end
+      printf("waiting for AllegroGraph container to initialize")
+      sec = 0
+      until system("curl -m 3 -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1")
+        sleep(1)
+        printf(".")
+        sec += 1
+        next unless sec > 60
+
+        puts
+        Rake::Task["test:docker:down"].invoke
+        abort("\nAborted; can't initialise AllegroGraph container")
       end
-      puts
+    puts
       system("docker compose ps") # TODO: remove after GH actions troubleshooting is complete
       Rake::Task["test"].invoke
       Rake::Task["test:docker:down"].invoke

diff --git a/test/test_chunks_write.rb b/test/test_chunks_write.rb
@@ -85,16 +85,16 @@ def test_reentrant_queries
       sleep(1.5)
       count_queries = 0
       tq = Thread.new {
-       5.times do
-         oq = "SELECT (count(?s) as ?c) WHERE { ?s a ?o }"
-         Goo.sparql_query_client.query(oq).each do |sol|
-           assert sol[:c].object > 0
-         end
-         count_queries += 1
-       end
+        5.times do
+          oq = "SELECT (count(?s) as ?c) WHERE { ?s a ?o }"
+          Goo.sparql_query_client.query(oq).each do |sol|
+            assert_operator 0, :<, sol[:c].object
+          end
+          count_queries += 1
+        end
       }
       tq.join
-      assert tput.alive?
+      assert_predicate tput, :alive?
       assert_equal 5, count_queries
       tput.join
 
@@ -110,13 +110,13 @@ def test_reentrant_queries
       sleep(1.5)
       count_queries = 0
       tq = Thread.new {
-       5.times do
-         oq = "SELECT (count(?s) as ?c) WHERE { ?s a ?o }"
-         Goo.sparql_query_client.query(oq).each do |sol|
-           assert sol[:c].object > 0
-         end
-         count_queries += 1
-       end
+        5.times do
+          oq = "SELECT (count(?s) as ?c) WHERE { ?s a ?o }"
+          Goo.sparql_query_client.query(oq).each do |sol|
+            assert_operator 0, :<, sol[:c].object
+          end
+          count_queries += 1
+        end
       }
       tq.join
       assert tdelete.alive?
@@ -144,7 +144,7 @@ def test_query_flood
           50.times do |j|
             oq = "SELECT (count(?s) as ?c) WHERE { ?s a ?o }"
             Goo.sparql_query_client.query(oq).each do |sol|
-              assert sol[:c].object > 0
+              assert_operator 0, :<, sol[:c].object
             end
           end
         }
@@ -158,13 +158,15 @@ def test_query_flood
             sleep(1.2)
           end
         }
+      end
 
-        threads.each do |t|
-          t.join
-        end
-        tput.join
+      threads.each do |t|
+        t.join
+      end
+      tput.join
 
-        assert log_status.map { |x| x[:outstanding] }.max > 0
+      if Goo.sparql_backend_name.downcase == BACKEND_4STORE
+        assert_operator 0, :<, log_status.map { |x| x[:outstanding] }.max
         assert_equal 16, log_status.map { |x| x[:running] }.max
       end
     end
@@ -182,6 +184,5 @@ def self.params_for_backend(method, graph_name, ntriples_file_path = nil)
       end
       params
     end
-
   end
 end