fix: resolve migration failure when merging several diverging issues

After migrations were on hold for a while, merging back several issues with migrations caused a migration error. This was caused by sligtly wrong order of procedures (possibly as a result of an automatic merge) but also an oversight on my part - as the compound identifiers are loaded from compounds_manual.csv during LHS data loading I didn't think to test with RHS data, but evidently this partly touches the same models and filled the tables with incompatible data types. This patch should resolve these issues without a data loss.

viewer/migrations/0074_auto_20241018_1028.py

@@ -19,66 +19,28 @@ def temporary_name(apps, schema_editor):
     def reverse_temporary_name(apps, schema_editor):
         pass
 
-    def relink_type(apps, schema_editor):
-        CompoundIdentifier = apps.get_model('viewer', 'CompoundIdentifier')
-        CompoundIdentifierType = apps.get_model('viewer', 'CompoundIdentifierType')
-
-        for idf in CompoundIdentifier.objects.all():
-            idf.type = CompoundIdentifierType.objects.get(name=idf.name_type)
-            idf.save()
 
-    def reverse_relink_type(apps, schema_editor):
-        pass
-
-    # with my edits:
+    # this contains some edits, the automatically constructed
+    # migration was not in the correct order, so I had to move things
+    # around to preserve data
     operations = [
-        # migrations.RunPython(lambda apps, schema_editor: print('first migration')),
-        # migrations.AlterField(
-        #     model_name='compoundidentifiertype',
-        #     name='name',
-        #     field=models.TextField(unique=True),
-        # ),
-        # add new foreign key field to CompoundIdentifier
-        # migrations.RunPython(lambda apps, schema_editor: print('second migration')),
-        # migrations.AddField(
-        #     model_name='compoundidentifier',
-        #     name='name_type',
-        #     field=models.ForeignKey(null=True, to_field='name', on_delete=django.db.models.deletion.CASCADE, to='viewer.compoundidentifiertype'),
-        # ),
         migrations.AddField(
             model_name='compoundidentifier',
             name='name_type',
             field=models.TextField(null=True),
         ),
-        # populate values in new field
-        migrations.RunPython(lambda apps, schema_editor: print('third migration, data')),
         migrations.RunPython(temporary_name, reverse_temporary_name),
-
-        # continue with the original migration, remove field, set the new pk
-        migrations.RunPython(lambda apps, schema_editor: print('fourth migration')),
         migrations.RemoveField(
             model_name='compoundidentifier',
             name='type',
         ),
-        migrations.RunPython(lambda apps, schema_editor: print('fifth migration')),
         migrations.RemoveField(
             model_name='compoundidentifiertype',
             name='id',
         ),
-        # migrations.AlterField(
-        #     model_name='compoundidentifier',
-        #     name='name',
-        #     field=models.TextField(),
-        # ),
-        migrations.RunPython(lambda apps, schema_editor: print('6th migration')),
         migrations.AlterField(
             model_name='compoundidentifiertype',
             name='name',
             field=models.TextField(primary_key=True, serialize=False),
         ),
-        # migrations.RemoveField(
-        #     model_name='compoundidentifiertype',
-        #     name='id',
-        # ),
-
     ]

viewer/migrations/0075_remove_compoundidentifier_type.py

@@ -22,11 +22,6 @@ def reverse_relink_type(apps, schema_editor):
         pass
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0075')),
-        # migrations.RemoveField(
-        #     model_name='compoundidentifier',
-        #     name='type',
-        # ),
         migrations.AddField(
             model_name='compoundidentifier',
             name='type',

viewer/migrations/0076_compoundidentifier_type.py

@@ -11,18 +11,6 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        # migrations.AddField(
-        #     model_name='compoundidentifier',
-        #     name='type',
-        #     field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='viewer.compoundidentifiertype'),
-        # ),
-        # continuing the migration tweak that started in 0074
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0076')),
-        # migrations.RenameField(
-        #     model_name='compoundidentifier',
-        #     old_name='name_type',
-        #     new_name='type',
-        # ),
         migrations.RemoveField(
             model_name='compoundidentifier',
             name='name_type',

viewer/migrations/0077_alter_compoundidentifier_type.py

@@ -11,7 +11,6 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0077')),
         migrations.AlterField(
             model_name='compoundidentifier',
             name='type',

viewer/migrations/0078_compoundidentifier_unique_compoundidentifier.py

@@ -10,7 +10,6 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0078')),
         migrations.AddConstraint(
             model_name='compoundidentifier',
             constraint=models.UniqueConstraint(fields=('type', 'compound', 'name'), name='unique_compoundidentifier'),

viewer/migrations/0079_auto_20241023_1439.py

@@ -10,27 +10,6 @@ class Migration(migrations.Migration):
         ('viewer', '0078_compoundidentifier_unique_compoundidentifier'),
     ]
 
-    # def temporary_name(apps, schema_editor):
-    #     Compound = apps.get_model('viewer', 'Compound')
-
-    #     for compound in Compound.objects.all():
-    #         compound.id_current_identifier = compound.type.name
-    #         compound.save()
-
-    # def reverse_temporary_name(apps, schema_editor):
-    #     pass
-
-    # def relink_type(apps, schema_editor):
-    #     CompoundIdentifier = apps.get_model('viewer', 'CompoundIdentifier')
-    #     CompoundIdentifierType = apps.get_model('viewer', 'CompoundIdentifierType')
-
-    #     for idf in CompoundIdentifier.objects.all():
-    #         idf.type = CompoundIdentifierType.objects.get(name=idf.name_type)
-    #         idf.save()
-
-    # def reverse_relink_type(apps, schema_editor):
-    #     pass
-
 
     def move_contents(apps, schema_editor):
         Compound = apps.get_model('viewer', 'Compound')
@@ -45,18 +24,11 @@ def reverse_move_contents(apps, schema_editor):
 
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0079, first')),
         migrations.RemoveField(
             model_name='compound',
             name='all_identifiers',
         ),
 
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0079, second')),
-        # migrations.AddField(
-        #     model_name='compoundid',
-        #     name='name_current_identifier',
-        #     field=models.TextField(null=True),
-        # ),
         migrations.RunPython(move_contents, reverse_move_contents),
         migrations.RemoveField(
             model_name='compound',

viewer/migrations/0080_alter_compoundidentifier_compound.py

@@ -11,7 +11,6 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0080')),
         migrations.AlterField(
             model_name='compoundidentifier',
             name='compound',

viewer/migrations/0081_alter_compound_current_identifier.py

@@ -11,7 +11,6 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
-        migrations.RunPython(lambda apps, schema_editor: print('migration 0081')),
         migrations.AlterField(
             model_name='compound',
             name='current_identifier',