Remove Fingerprint calculation from migration

This comments out the initial calculation of Fingerprint records from
the migrations in this PR. A following commit will add a rake task that
will focus on this work.

A side effect of this work is that we need to change the fixtures used
for our test suite, to match the state the migrations will produce. This
in turn causes some tests to change, because some tests will require
additional setup work.

More complex tests now have code comments to indicate this sort of
sequencing.

db/migrate/20241211195504_add_fingerprint_to_terms.rb

@@ -3,9 +3,9 @@ def up
     add_reference :terms, :fingerprint, foreign_key: true
 
     # Seed the relationship between Terms and Fingerprints
-    Term.all.each do |t|
-      t.save
-    end
+    # Term.all.each do |t|
+    #   t.save
+    # end
   end
 
   def down

test/fixtures/terms.yml

@@ -12,48 +12,36 @@
 
 cool:
   phrase: Super cool search
-  fingerprint: cool
 
 cool_cluster:
   phrase: Super. Cool. Search.
-  fingerprint: cool
 
 hi:
   phrase: hello world
-  fingerprint: hi
 
 pmid_38908367:
   phrase: 'TERT activation targets DNA methylation and multiple aging hallmarks. Shim HS, et al. Cell. 2024. PMID: 38908367'
-  fingerprint: pmid_38908367
 
 lcsh:
   phrase: 'Geology -- Massachusetts'
-  fingerprint: lcsh
 
 issn_1075_8623:
   phrase: 1075-8623
-  fingerprint: issn_1075_8623
 
 doi:
   phrase: '10.1016/j.physio.2010.12.004'
-  fingerprint: doi
 
 isbn_9781319145446:
   phrase: 'Sadava, D. E., D. M. Hillis, et al. Life The Science of Biology. 11th ed. W. H. Freeman, 2016. ISBN: 9781319145446'
-  fingerprint: isbn_9781319145446
 
 journal_nature_medicine:
   phrase: 'nature medicine'
-  fingerprint: journal_nature_medicine
 
 suggested_resource_jstor:
   phrase: 'jstor'
-  fingerprint: suggested_resource_jstor
 
 multiple_detections:
   phrase: 'Environmental and Health Impacts of Air Pollution: A Review. Frontiers in Public Health. PMID: 32154200. DOI: 10.3389/fpubh.2020.00014'
-  fingerprint: multiple_detections
 
 citation:
   phrase: "A. Altun, "Understanding hypertext in the context of reading on the web: Language learners' experience," Current Issues in Education, vol. 6, no. 12, July, 2005. [Online serial]. Available: http://cie.ed.asu.edu/volume6/number12/. [Accessed Dec. 2, 2007]."
-  fingerprint: citation

test/models/fingerprint_test.rb

@@ -21,17 +21,23 @@ class FingerprintTest < ActiveSupport::TestCase
   end
 
   test 'deleting a Fingerprint does not delete its Term, which is still valid' do
+    # Setup
+    target_term = Term.last
+    target_term.save
+    target_term.reload
+    target = target_term.fingerprint
+
+    # Initial condition
     term_count = Term.count
     fingerprint_count = Fingerprint.count
 
-    target = Fingerprint.last
-    target_term = target.terms.last
-
     assert_operator 0, :<, target.terms.count
 
+    # Change
     target.destroy
     target_term.reload
 
+    # Verify impact
     assert_equal term_count, Term.count
     assert_equal fingerprint_count - 1, Fingerprint.count
     assert_nil target_term.fingerprint_value

test/models/term_test.rb

@@ -97,9 +97,12 @@ class TermTest < ActiveSupport::TestCase
   end
 
   test 'destroying a Term will delete its Fingerprint if no cluster exists' do
+    term = terms('hi')
+    term.save
+    term.reload
+
     term_pre_count = Term.count
     fingerprints_pre_count = Fingerprint.count
-    term = terms('hi')
 
     assert_equal 1, term.fingerprint.terms.count
 
@@ -110,16 +113,25 @@ class TermTest < ActiveSupport::TestCase
   end
 
   test 'destroying a Term will not delete its Fingerprint if other terms exist in that cluster' do
+    # Setup
+    term = terms('cool')
+    term_cluster = terms('cool_cluster')
+    term.save
+    term_cluster.save
+    term.reload
+
+    # Initial conditions
     term_pre_count = Term.count
     fingerprints_pre_count = Fingerprint.count
-    term = terms('cool')
     fingerprint = term.fingerprint
     cluster_size = fingerprint.terms.count
 
     assert_operator 1, :<, cluster_size
 
+    # Change
     term.destroy
 
+    # Verify impact
     assert_equal term_pre_count - 1, Term.count
     assert_equal fingerprints_pre_count, Fingerprint.count
     assert_equal cluster_size - 1, fingerprint.terms.count
@@ -128,32 +140,23 @@ class TermTest < ActiveSupport::TestCase
   # This test, and maybe the actual dynamic, may need to be refactored. For right now I'm confirming this behavior via
   # the test here.
   test 'a Term without a Fingerprint is valid (but regenerates on next save)' do
-    term_count = Term.count
-    fingerprint_count = Fingerprint.count
-
-    target_fingerprint = fingerprints('hi')
-    target_term = target_fingerprint.terms.last
-
-    assert_operator 0, :<, target_fingerprint.terms.count
-
-    target_fingerprint.destroy
-    target_term.reload
+    target_term = terms('hi')
 
+    assert_nil target_term.fingerprint
     assert_predicate target_term, :valid?
-    assert_equal fingerprint_count - 1, Fingerprint.count
 
     target_term.save
     target_term.reload
 
-    assert_equal term_count, Term.count
-    assert_equal fingerprint_count, Fingerprint.count
+    assert_not_nil target_term.fingerprint
+    assert_predicate target_term, :valid?
   end
 
   test 'deleting a Term without a Fingerprint succeeds without problem' do
     term_count = Term.count
 
     target = fingerprints('hi')
-    target_term = target.terms.last
+    target_term = terms('hi')
 
     target.destroy
     target_term.reload
@@ -355,15 +358,27 @@ class TermTest < ActiveSupport::TestCase
 
   test 'Term.fingerprint_value is a delegate of the Fingerprint method' do
     t = terms('cool')
+    t.save
+    t.reload
+
     tf = t.fingerprint
 
     assert_equal t.fingerprint_value, tf.fingerprint
   end
 
   test 'Term.fingerprint returns nil of there is no fingerprint' do
-    # Terms without fingerprints are a temporary condition, but one that might occur for brief periods
-    target_fingerprint = fingerprints('hi')
-    target_term = target_fingerprint.terms.last
+    # Terms without fingerprints are a legacy condition - fingerprints are generated when saving the term - but one that
+    # we still need to confirm is stable.
+    target_term = terms('hi')
+
+    assert_nil target_term.fingerprint
+
+    target_term.save
+    target_term.reload
+
+    assert_not_nil target_term.fingerprint
+
+    target_fingerprint = target_term.fingerprint
 
     target_fingerprint.destroy
     target_term.reload
@@ -373,13 +388,19 @@ class TermTest < ActiveSupport::TestCase
 
   test 'Term.cluster returns empty array if no related record exists' do
     t = terms('hi')
+    t.save
+    t.reload
 
     assert_equal 1, t.fingerprint.terms.count
     assert_empty t.cluster
   end
 
   test 'Term.cluster returns array of terms if other terms share a fingerprint' do
     t = terms('cool')
+    t.save
+    t2 = terms('cool_cluster')
+    t2.save
+    t.reload
 
     assert_operator 1, :<, t.fingerprint.terms.count
     assert_instance_of Array, t.cluster
@@ -389,16 +410,25 @@ class TermTest < ActiveSupport::TestCase
   end
 
   test 'Term.cluster returns nil if there is no fingerprint' do
-    target_fingerprint = fingerprints('hi')
-    target_term = target_fingerprint.terms.last
+    # Setup
+    target_term = terms('hi')
+
+    # Initial condition
+    assert_nil target_term.cluster
+
+    # Changes
+    target_term.save
+    target_term.reload
+    target_fingerprint = target_term.fingerprint
 
-    # Before we delete the fingerprint, the cluster method returns an array
+    # Verify impact
     assert_instance_of Array, target_term.cluster
 
     # Delete the fingerprint, leave the term - this will only ever be a temporary condition, but one that might exist.
     target_fingerprint.destroy
     target_term.reload
 
-    assert_instance_of NilClass, target_term.cluster
+    # Verify impact
+    assert_nil target_term.cluster
   end
 end