Merge pull request #76 from ncbo/develop

Merge Develop to Master, release v5.29.0
ontoportal · Mar 14, 2024 · b9c5799 · b9c5799
2 parents cd6a42a + 11c434e
commit b9c5799
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diff --git a/Gemfile b/Gemfile
@@ -10,7 +10,6 @@ gem 'ffi'
 gem "google-apis-analytics_v3"
 
 gem 'google-analytics-data'
-gem 'mail', '2.6.6'
 gem 'multi_json'
 gem 'oj', '~> 3.0'
 gem 'parseconfig'
@@ -25,15 +24,16 @@ gem 'sys-proctable'
 gem 'cube-ruby', require: 'cube'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
 
 group :test do
   gem 'email_spec'
   gem 'minitest', '< 5.0'
   gem 'simplecov'
   gem 'simplecov-cobertura' # for codecov.io
   gem 'test-unit-minitest'
+  gem 'webrick'
 end
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
-  branch: master
+  revision: f00c8f812c4a1f5eaacb4a59b708d0b228dcd41a
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: fe0783c542479ed0a12da5663ef28e1673e80eba
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 0003905c5d101f4df17e35784c0d15d2f5d42110
-  branch: master
+  revision: a973d62ca8be3a6cd86677d9bed24f361f580882
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -46,8 +46,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
-  branch: master
+  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -85,13 +85,14 @@ GEM
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
+    date (3.3.4)
     declarative (0.0.20)
     docile (1.4.0)
     domain_name (0.6.20240107)
-    email_spec (2.1.1)
+    email_spec (2.2.2)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
-      mail (~> 2.6)
+      mail (~> 2.7)
     faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
@@ -108,51 +109,47 @@ GEM
       googleapis-common-protos-types (>= 1.11.0, < 2.a)
       googleauth (~> 1.9)
       grpc (~> 1.59)
-    google-analytics-data (0.5.0)
+    google-analytics-data (0.6.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.11.2)
+    google-analytics-data-v1beta (0.12.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-apis-analytics_v3 (0.14.0)
-      google-apis-core (>= 0.12.0, < 2.a)
-    google-apis-core (0.13.0)
+    google-apis-analytics_v3 (0.15.0)
+      google-apis-core (>= 0.14.0, < 2.a)
+    google-apis-core (0.14.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
       httpclient (>= 2.8.1, < 3.a)
       mini_mime (~> 1.0)
       representable (~> 3.0)
       retriable (>= 2.0, < 4.a)
       rexml
-    google-cloud-core (1.6.1)
+    google-cloud-core (1.7.0)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
-    google-cloud-errors (1.3.1)
-    google-protobuf (3.25.2)
-    google-protobuf (3.25.2-x86_64-darwin)
-    google-protobuf (3.25.2-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 (1.12.0)
+    google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3)
+    google-protobuf (3.25.3-x86_64-linux)
+    googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
-    googleauth (1.10.0)
+      googleapis-common-protos-types (~> 1.7)
+      grpc (~> 1.41)
+    googleapis-common-protos-types (1.13.0)
+      google-protobuf (~> 3.18)
+    googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.61.0)
-      google-protobuf (~> 3.25)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.61.0-x86_64-darwin)
+    grpc (1.62.0)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.61.0-x86_64-linux)
+    grpc (1.62.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
@@ -164,25 +161,38 @@ GEM
       concurrent-ruby (~> 1.0)
     json (2.7.1)
     json_pure (2.7.1)
-    jwt (2.7.1)
+    jwt (2.8.1)
+      base64
     launchy (2.5.2)
       addressable (~> 2.8)
-    libxml-ruby (5.0.2)
+    libxml-ruby (5.0.3)
     logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    mail (2.6.6)
-      mime-types (>= 1.16, < 4)
+    mail (2.8.1)
+      mini_mime (>= 0.1.1)
+      net-imap
+      net-pop
+      net-smtp
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0206)
+    mime-types-data (3.2024.0305)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
+    net-imap (0.4.10)
+      date
+      net-protocol
+    net-pop (0.1.2)
+      net-protocol
+    net-protocol (0.2.2)
+      timeout
+    net-smtp (0.4.0.1)
+      net-protocol
     netrc (0.11.0)
     oj (3.16.3)
       bigdecimal (>= 3.0)
@@ -196,15 +206,15 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.4)
-    rack (3.0.9)
+    rack (3.0.9.1)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (13.1.0)
     rdf (1.0.8)
       addressable (>= 2.2)
     redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.20.0)
+    redis-client (0.21.0)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)
@@ -244,16 +254,17 @@ GEM
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
+    timeout (0.4.1)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webrick (1.8.1)
 
 PLATFORMS
   ruby
-  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -263,7 +274,6 @@ DEPENDENCIES
   goo!
   google-analytics-data
   google-apis-analytics_v3
-  mail (= 2.6.6)
   minitest (< 5.0)
   multi_json
   ncbo_annotator!
@@ -281,6 +291,7 @@ DEPENDENCIES
   sparql-client!
   sys-proctable
   test-unit-minitest
+  webrick
 
 BUNDLED WITH
    2.4.22
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -63,9 +63,9 @@ services:
       GOO_BACKEND_NAME: ag
       GOO_PORT: 10035
       GOO_HOST: agraph-ut
-      GOO_PATH_QUERY: /repositories/bioportal_test
-      GOO_PATH_DATA: /repositories/bioportal_test/statements
-      GOO_PATH_UPDATE: /repositories/bioportal_test/statements
+      GOO_PATH_QUERY: /repositories/ontoportal_test
+      GOO_PATH_DATA: /repositories/ontoportal_test/statements
+      GOO_PATH_UPDATE: /repositories/ontoportal_test/statements
     profiles:
       - agraph
     depends_on:
@@ -93,7 +93,7 @@ services:
       - 4store
 
   solr-ut:
-    image: ontoportal/solr-ut:0.0.2
+    image: ontoportal/solr-ut:0.1.0
     healthcheck:
       test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"]
       start_period: 3s
@@ -112,7 +112,7 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.1
+    image: franzinc/agraph:v8.1.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
@@ -122,12 +122,12 @@ services:
     #  - 10035:10035
     command: >
        bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start
-       ; agtool repos create bioportal_test
+       ; agtool repos create --supersede ontoportal_test
        ; agtool users add anonymous
-       ; agtool users grant anonymous root:bioportal_test:rw
+       ; agtool users grant anonymous root:ontoportal_test:rw
        ; tail -f /agraph/data/agraph.log"
     healthcheck:
-      test: ["CMD-SHELL", "agtool storage-report bioportal_test || exit 1"]
+      test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"]
       start_period: 30s #AllegroGraph can take a loooooong time to start
       interval: 20s
       timeout: 10s

diff --git a/lib/ncbo_cron/ontology_analytics.rb b/lib/ncbo_cron/ontology_analytics.rb
@@ -158,15 +158,15 @@ def merge_and_fill_missing_data(ga4_data)
           ua_ga4_intersecting_month = Date.parse(GA4_START_DATE).month.to_s
 
           # add up hits for June of 2023 (the only intersecting month between UA and GA4)
-          ua_data.each do |acronym, _|
-            if ga4_data.has_key?(acronym)
-              if ga4_data[acronym][ua_ga4_intersecting_year].has_key?(ua_ga4_intersecting_month)
-                ua_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] +=
-                    ga4_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month]
-                # delete data for June of 2023 from ga4_data to avoid overwriting when merging
-                ga4_data[acronym][ua_ga4_intersecting_year].delete(ua_ga4_intersecting_month)
-              end
-            end
+          ua_data.each do |acronym|
+            next unless ga4_data.key?(acronym)
+            next unless ga4_data[acronym].key?(ua_ga4_intersecting_year)
+            next unless ga4_data[acronym][ua_ga4_intersecting_year].key?(ua_ga4_intersecting_month)
+
+            ua_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] +=
+              ga4_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month]
+            # delete data for June of 2023 from ga4_data to avoid overwriting when merging
+            ga4_data[acronym][ua_ga4_intersecting_year].delete(ua_ga4_intersecting_month)
           end
         end