Merge branch 'develop'

ncbo · Dec 15, 2023 · 1170a94 · 1170a94
2 parents 4f4361e + c72bbfe
commit 1170a94
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Showing 2 changed files with 23 additions and 22 deletions.
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: daea7822af9e5ca1961d6873a758735133a1b2db
+  revision: 657149d6b33813253fa7440252f69c04e0631190
   branch: master
   specs:
     goo (0.0.2)
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: a7ad210e846a390f203457be2459719214d142fe
+  revision: 7783784f9d2ceada9be706cf6c084d272ae653e8
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -52,18 +52,18 @@ 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)
-    bcrypt (3.1.19)
+    bcrypt (3.1.20)
+    bigdecimal (3.1.5)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
-    date (3.3.3)
+    date (3.3.4)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
@@ -93,10 +93,10 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
-    json_pure (2.6.3)
-    libxml-ruby (4.1.1)
-    logger (1.5.3)
+    json (2.7.1)
+    json_pure (2.7.1)
+    libxml-ruby (4.1.2)
+    logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -107,31 +107,32 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2023.1205)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.8)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
     net-smtp (0.4.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.1)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     rack (3.0.8)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -140,7 +141,7 @@ GEM
       addressable (>= 2.2)
     redis (5.0.8)
       redis-client (>= 0.17.0)
-    redis-client (0.18.0)
+    redis-client (0.19.0)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -165,11 +166,8 @@ GEM
     simplecov_json_formatter (0.1.4)
     systemu (2.6.5)
     thread_safe (0.3.6)
-    timeout (0.4.0)
+    timeout (0.4.1)
     tzinfo (0.3.62)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
 

diff --git a/lib/ncbo_annotator.rb b/lib/ncbo_annotator.rb
@@ -3,7 +3,7 @@
 # require 'sparql_http'
 # require 'ontologies_linked_data'
 # require_relative 'dictionary/generator'
-
+require 'uri'
 require 'zlib'
 require 'redis'
 require 'ontologies_linked_data'
@@ -723,6 +723,9 @@ def mappings_for_class_ids(class_ids)
       end
 
       def hierarchy_query(class_ids)
+        # mdorf, 12/14/2023: AllegroGraph throws a MalformedQuery exception
+        # if an ID is not of the proper URI format
+        class_ids.select! { |id| id =~ URI::regexp }
         filter_ids = class_ids.map { |id| "?id = <#{id}>" } .join " || "
         query = <<eos
 SELECT DISTINCT ?id ?parent ?graph WHERE { GRAPH ?graph { ?id <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent . }