TermSet minor test updates, _repr_html_, name field (#967)

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Enhancements
 - Added `target_tables` attribute to `DynamicTable` to allow users to specify the target table of any predefined
 `DynamicTableRegion` columns of a `DynamicTable` subclass. @rly [#971](https://github.com/hdmf-dev/hdmf/pull/971)
+- Updated `TermSet` to include `_repr_html_` for easy to read notebook representation. @mavaylon1 [967](https://github.com/hdmf-dev/hdmf/pull/967)
 
 ### Bug fixes
 - Updated custom class generation to handle specs with fixed values and required names. @rly [#800](https://github.com/hdmf-dev/hdmf/pull/800)

src/hdmf/term_set.py

@@ -53,11 +53,43 @@ def __init__(self,
             self.expanded_termset_path = self.__enum_expander()
             self.view = SchemaView(self.expanded_termset_path)
 
+        self.name = self.view.schema.name
         self.sources = self.view.schema.prefixes
 
     def __repr__(self):
-        re = "class: %s\n" % str(self.__class__)
-        re += "term_schema_path: %s\n" % self.term_schema_path
+        terms = list(self.view_set.keys())
+
+        re = "Schema Path: %s\n" % self.term_schema_path
+        re += "Sources: " + ", ".join(list(self.sources.keys()))+"\n"
+        re += "Terms: \n"
+        if len(terms) > 4:
+            re += "   - %s\n" % terms[0]
+            re += "   - %s\n" % terms[1]
+            re += "   - %s\n" % terms[2]
+            re += "   ... ... \n"
+            re += "   - %s\n" % terms[-1]
+        else:
+            for term in terms:
+                re += "   - %s\n" % term
+        re += "Number of terms: %s" % len(terms)
+        return re
+
+    def _repr_html_(self):
+        terms = list(self.view_set.keys())
+
+        re = "<b>" + "Schema Path: " + "</b>" + self.term_schema_path + "<br>"
+        re += "<b>" + "Sources: " + "</b>" + ", ".join(list(self.sources.keys())) + "<br>"
+        re += "<b> Terms: </b>"
+        if len(terms) > 4:
+            re += "<li> %s </li>" % terms[0]
+            re += "<li> %s </li>" % terms[1]
+            re += "<li> %s </li>" % terms[2]
+            re += "... ..."
+            re += "<li> %s </li>" % terms[-1]
+        else:
+            for term in terms:
+                re += "<li> %s </li>" % term
+        re += "<i> Number of terms:</i> %s" % len(terms)
         return re
 
     def __perm_value_key_info(self, perm_values_dict: dict, key: str):

tests/unit/example_test_term_set.yaml

@@ -22,3 +22,6 @@ enums:
       Myrmecophaga tridactyla:
         description: the species is an anteater
         meaning: NCBI_TAXON:71006
+      Ailuropoda melanoleuca:
+        description: the species is a panda
+        meaning: NCBI_TAXON:9646

tests/unit/example_test_term_set2.yaml

@@ -0,0 +1,21 @@
+id: termset/species_example2
+name: Species
+version: 0.0.1
+prefixes:
+  NCBI_TAXON: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
+imports:
+  - linkml:types
+default_range: string
+
+enums:
+  Species:
+    permissible_values:
+      Homo sapiens:
+        description: the species is human
+        meaning: NCBI_TAXON:9606
+      Mus musculus:
+        description: the species is a house mouse
+        meaning: NCBI_TAXON:10090
+      Ursus arctos horribilis:
+        description: the species is a grizzly bear
+        meaning: NCBI_TAXON:116960

tests/unit/test_term_set.py

@@ -26,11 +26,41 @@ def setUp(self):
 
     def test_termset_setup(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        self.assertEqual(termset.name, 'Species')
         self.assertEqual(list(termset.sources), ['NCBI_TAXON'])
 
+    def test_repr_short(self):
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set2.yaml')
+        output = ('Schema Path: tests/unit/example_test_term_set2.yaml\nSources: NCBI_TAXON\nTerms: \n'
+                  '   - Homo sapiens\n   - Mus musculus\n   - Ursus arctos horribilis\nNumber of terms: 3')
+        self.assertEqual(repr(termset), output)
+
+    def test_repr_html_short(self):
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set2.yaml')
+        output = ('<b>Schema Path: </b>tests/unit/example_test_term_set2.yaml<br><b>Sources:'
+                  ' </b>NCBI_TAXON<br><b> Terms: </b><li> Homo sapiens </li><li> Mus musculus'
+                  ' </li><li> Ursus arctos horribilis </li><i> Number of terms:</i> 3')
+        self.assertEqual(termset._repr_html_(), output)
+
+    def test_repr_long(self):
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        output = ('Schema Path: tests/unit/example_test_term_set.yaml\nSources: NCBI_TAXON\nTerms: \n'
+                  '   - Homo sapiens\n   - Mus musculus\n   - Ursus arctos horribilis\n   ... ... \n'
+                  '   - Ailuropoda melanoleuca\nNumber of terms: 5')
+        self.assertEqual(repr(termset), output)
+
+    def test_repr_html_long(self):
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        output = ('<b>Schema Path: </b>tests/unit/example_test_term_set.yaml<br><b>Sources:'
+                  ' </b>NCBI_TAXON<br><b> Terms: </b><li> Homo sapiens </li><li> Mus musculus'
+                  ' </li><li> Ursus arctos horribilis </li>... ...<li> Ailuropoda melanoleuca'
+                  ' </li><i> Number of terms:</i> 5')
+        self.assertEqual(termset._repr_html_(), output)
+
     def test_view_set(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
-        expected = ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis', 'Myrmecophaga tridactyla']
+        expected = ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis', 'Myrmecophaga tridactyla',
+                    'Ailuropoda melanoleuca']
         self.assertEqual(list(termset.view_set), expected)
         self.assertIsInstance(termset.view, SchemaView)
 
@@ -46,7 +76,10 @@ def test_get_item(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset['Homo sapiens'].id, 'NCBI_TAXON:9606')
         self.assertEqual(termset['Homo sapiens'].description, 'the species is human')
-        self.assertEqual(termset['Homo sapiens'].meaning, 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')
+        self.assertEqual(
+            termset['Homo sapiens'].meaning,
+            'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
+        )
 
     def test_get_item_key_error(self):
         termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')