include pid on extended metadata attribute for import via JSON #2044

seek4science · Nov 6, 2024 · 3bc526c · 3bc526c
1 parent 1277919
commit 3bc526c
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Showing 6 changed files with 16 additions and 2 deletions.
diff --git a/lib/seek/extended_metadata_type/emt_extractor.rb b/lib/seek/extended_metadata_type/emt_extractor.rb
@@ -63,7 +63,8 @@ def self.create_extended_metadata_type_from_json(data)
             sample_attribute_type: sample_attribute_type,
             sample_controlled_vocab: sample_controlled_vocab,
             linked_extended_metadata_type: linked_extended_metadata_type,
-            required: attr['required'].present? ? attr['required'] : false
+            required: attr['required'].present? ? attr['required'] : false,
+            pid: attr['pid'].present? ? attr['pid'] : nil
           )
         end
         emt

diff --git a/lib/seek/extended_metadata_type/extended_metadata_type_schema.json b/lib/seek/extended_metadata_type/extended_metadata_type_schema.json
@@ -36,6 +36,9 @@
               },
               "pos": {
                 "type": "integer"
+              },
+              "pid": {
+                "type": "string"
               }
             },
             "required": ["title", "type"],
@@ -69,6 +72,9 @@
               },
               "pos": {
                 "type": "integer"
+              },
+              "pid": {
+                "type": "string"
               }
             },
             "required": ["title", "type", "ID"],

diff --git a/test/fixtures/files/extended_metadata_type/valid_emt_with_cv_with_ontologies.json b/test/fixtures/files/extended_metadata_type/valid_emt_with_cv_with_ontologies.json
@@ -9,6 +9,7 @@
       "type": "Controlled Vocabulary",
       "required": true,
       "pos": 1,
+      "pid": "http://edamontology.org/topic_0003",
       "ID": "CV_TOPICS_ID"
     }
   ]

diff --git a/test/fixtures/files/extended_metadata_type/valid_emt_with_linked_emt.json b/test/fixtures/files/extended_metadata_type/valid_emt_with_linked_emt.json
@@ -9,6 +9,7 @@
       "description": null,
       "type": "Linked Extended Metadata",
       "required": false,
+      "pid": "https://somevocab.org/father",
       "ID": "PERSON_EMT_ID"
     },
     {

diff --git a/test/fixtures/files/extended_metadata_type/valid_simple_emt.json b/test/fixtures/files/extended_metadata_type/valid_simple_emt.json
@@ -12,7 +12,8 @@
       "title": "last_name",
       "label": "last name",
       "description": null,
-      "type": "String"
+      "type": "String",
+      "pid": "http://schema.org/family_name"
     }
   ]
 }
diff --git a/test/unit/extended_metadatas/emt_extractor_test.rb b/test/unit/extended_metadatas/emt_extractor_test.rb
@@ -19,6 +19,7 @@ class EmtExtractorTest < ActiveSupport::TestCase
     assert_equal 'first_name', attr1.title
     assert_equal SampleAttributeType.find_by(title: 'String'), attr1.sample_attribute_type
     assert_equal true, attr1.required
+    assert_nil attr1.pid
 
     attr2 = emt.extended_metadata_attributes.second
     assert_not_nil attr2
@@ -27,6 +28,7 @@ class EmtExtractorTest < ActiveSupport::TestCase
     assert_nil attr2.description
     assert_equal SampleAttributeType.find_by(title: 'String'), attr2.sample_attribute_type
     assert_equal false, attr2.required
+    assert_equal "http://schema.org/family_name", attr2.pid
 
   end
 
@@ -50,6 +52,7 @@ class EmtExtractorTest < ActiveSupport::TestCase
     assert_nil dad_attr.description
     assert_equal SampleAttributeType.find_by(title: 'Linked Extended Metadata'), dad_attr.sample_attribute_type
     refute dad_attr.required
+    assert_equal "https://somevocab.org/father", dad_attr.pid
 
     mom_attr = emt.extended_metadata_attributes.second
     assert_not_nil mom_attr
@@ -85,6 +88,7 @@ class EmtExtractorTest < ActiveSupport::TestCase
     assert_equal "Topics, used for annotating. Describes the domain, field of interest, of study, application, work, data, or technology. Initially seeded from the EDAM ontology.", topics_attr.description
     assert_equal SampleAttributeType.find_by(title: 'Controlled Vocabulary'), topics_attr.sample_attribute_type
     assert topics_attr.required
+    assert_equal 'http://edamontology.org/topic_0003', topics_attr.pid
 
     assert_equal topic_cv, topics_attr.sample_controlled_vocab
     assert_equal 4, topics_attr.sample_controlled_vocab.sample_controlled_vocab_terms.count