Merge branch 'develop'

Gemfile

@@ -33,5 +33,5 @@ group :development do
 end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: daea7822af9e5ca1961d6873a758735133a1b2db
-  branch: master
+  revision: 6db93bb3d5095a5fe0d017e572c5a04caa34ebc6
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ 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)
@@ -181,11 +181,7 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  aarch64-linux
-  arm64-darwin-22
   x86_64-darwin-18
-  x86_64-darwin-21
-  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 4)

lib/ontologies_linked_data/models/slice.rb

@@ -13,12 +13,25 @@ class Slice < LinkedData::Models::Base
 
     def self.validate_acronym(inst, attr)
       inst.bring(attr) if inst.bring?(attr)
-      value = inst.send(attr)
-      acronym_regex = /\A[-_a-z]+\Z/
-      if (acronym_regex.match value).nil?
-        return [:acronym_value_validator,"The acronym value #{value} is invalid"]
+      acronym = inst.send(attr)
+
+      return [] if acronym.nil?
+
+      errors = []
+
+      if acronym.match(/\A[^a-z^A-Z]{1}/)
+        errors << [:start_with_letter, "`acronym` must start with a letter"]
+      end
+
+      if acronym.match(/[^-0-9a-zA-Z]/)
+        errors << [:special_characters, "`acronym` must only contain the folowing characters: -, letters, and numbers"]
+      end
+
+      if acronym.match(/.{17,}/)
+        errors << [:length, "`acronym` must be sixteen characters or less"]
       end
-      return [:acronym_value_validator, nil]
+
+      return errors.flatten
     end
 
     def self.synchronize_groups_to_slices
@@ -31,7 +44,7 @@ def self.synchronize_groups_to_slices
           slice.save if slice.valid?
         else
           slice = self.new({
-            acronym: g.acronym.downcase.gsub(" ", "_"),
+            acronym: g.acronym.downcase.gsub(" ", "-"),
             name: g.name,
             description: g.description,
             ontologies: g.ontologies

lib/ontologies_linked_data/monkeypatches/object.rb

@@ -101,6 +101,7 @@ def to_flex_hash(options = {}, &block)
         hash, modified = embed_goo_objects_just_values(hash, k, v, options, &block)
       rescue Exception => e
         puts "Bad data found in submission: #{hash}"
+        puts "#{e.class}: #{e.message}\n#{e.backtrace.join("\n")}"
         raise e
       end
 

lib/ontologies_linked_data/parser/owlapi.rb

@@ -13,7 +13,7 @@ class RDFFileNotGeneratedException < Parser::ParserException
 
     class OWLAPICommand
       def initialize(input_file, output_repo, opts = {})
-        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.4.1.jar"
+        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.4.2.jar"
         @input_file = input_file
         @output_repo = output_repo
         @master_file = opts[:master_file]

test/models/test_slice.rb

@@ -54,7 +54,7 @@ def test_slice_lifecycle
     s = LinkedData::Models::Slice.new({
       :name => "Test Slice",
       :description => "This is a test slice",
-      :acronym => "test_slice",
+      :acronym => "test-slice",
       :ontologies => @@onts[3..-1]
     })
 
@@ -70,6 +70,27 @@ def test_synchronization
     assert slices.map {|s| s.acronym}.include?(@@group_acronym)
   end
 
+  def test_slice_acronym_validity
+    s = LinkedData::Models::Slice.new({
+                                        :name => "Test Slice",
+                                        :description => "This is a test slice",
+                                        :acronym => "test_slice",
+                                        :ontologies => @@onts[3..-1]
+                                      })
+
+    refute s.valid?
+
+    s = LinkedData::Models::Slice.new({
+                                        :name => "Test Slice",
+                                        :description => "This is a test slice",
+                                        :acronym => "test-slice",
+                                        :ontologies => @@onts[3..-1]
+                                      })
+
+    assert s.valid?
+
+  end
+
   private
 
   def self._create_group