Feature/sckan 226 (#202)

* SCKAN-226 feat: Update ingestion script

* SCKAN-226 chore: Refactor add_destination to match with add_vias

* SCKAN-226 feat: Enforce reference_uri uniqueness

* SCKAN-226 feat: Update ingestion logic

* SCKAN-226 feat: WIP - Update neurondm script

* SCKAN-226 feat: WIP - Undo validation neurondm script

* SCKAN-226 feat: Use predicates in partial order processing

* SCKAN-226 feat: Merge vias that differ only on from_entities

* SCKAN-226 feat: Merge destinations

* SCKAN-226 feat: Merge destinations by from_entities

* SCKAN-226 feat: Merge origins

* SCKAN-226 feat: Update ingestion script

* SCKAN-226 feat: Test both region and layer on entity identification

* SCKAN-226 feat: Update ingestion script

* SCKAN-226 feat: Update default state on ingestion creation

* SCKAN-226 feat: Add forward connection ingestion

* SCKAN-226 feat: WIP - Update validation and add logging service

* SCKAN-226 feat: Make ingestion atomic; Update logging service

* SCKAN-226 fix: Update forward connection check

* SCKAN-226 refactor: Use update_or_create instead of custom method

* SCKAN-226 feat: Add new transition draft to exported for ingestion

* SCKAN-226 feat: Remove unnecessary transition

* SCKAN-248 fix: Update journey tests

* SCKAN-248 feat: Add tests to neurondm processing

* SCKAN-248 feat: WIP - Ignore partial order mismatches

* Revert "SCKAN-226 feat: Remove unnecessary transition"

This reverts commit d29ac5a.

* SCKAN-226 feat: Use .update and .create instead of .update_or_create

* SCKAN-226 refactor: Use .get_or_create instead of filter

* SCKAN-226 refactor: Remove __exact from filter

* SCKAN-226 refactor: Add has_changes check

* SCKAN-226 feat: Ingest inconsistent populations but flag them with warnings

* SCKAN-248 feat: Add invalid state; Update ingestion accordingly

* SCKAN-248 feat: Optimize upstream algorithm

* SCKAN-248 chore: Remove TODO annotation

* SCKAN-248 feat: Add note on step 3 even if state was invalid

* SCKAN-248 feat: Allow transition to invalid from any state

* SCKAN-248 fix: Update process connection algorithm and jump test

* SCKAN-248 feat: Update process connection algorithm and multiple axioms test

* SCKAN-248 feat: Add partial order vs axioms validation

* SCKAN-248 fix: Update has_changes logic

* SCKAN-248 feat: Update notes

* SCKAN-248 feat: Remove deprecated method

backend/composer/enums.py

@@ -61,6 +61,7 @@ class CSState(models.TextChoices):
     CONNECTION_MISSING = "connection_missing"
     NPO_APPROVED = "npo_approved"
     EXPORTED = "exported"
+    INVALID = "invalid"
 
 
 class NoteType(models.TextChoices):

backend/composer/management/commands/ingest_statements.py

@@ -5,5 +5,13 @@
 class Command(BaseCommand):
     help = "Ingests Statements from neurondm pyp package"
 
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--update_upstream',
+            action='store_true',
+            help='Set this flag to update upstream statements.',
+        )
+
     def handle(self, *args, **options):
-        ingest_statements()
+        update_upstream = options['update_upstream']
+        ingest_statements(update_upstream)

backend/composer/migrations/0033_alter_connectivitystatement_reference_uri.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.1.4 on 2024-01-05 15:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("composer", "0032_alter_connectivitystatement_projection"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="reference_uri",
+            field=models.URLField(blank=True, null=True, unique=True),
+        ),
+    ]

backend/composer/models.py

@@ -413,7 +413,7 @@ class ConnectivityStatement(models.Model):
     )
     apinatomy_model = models.CharField(max_length=200, null=True, blank=True)
     additional_information = models.TextField(null=True, blank=True)
-    reference_uri = models.URLField(null=True, blank=True)
+    reference_uri = models.URLField(null=True, blank=True, unique=True)
     functional_circuit_role = models.ForeignKey(
         FunctionalCircuitRole,
         on_delete=models.DO_NOTHING,
@@ -443,6 +443,7 @@ def __str__(self):
             CSState.REJECTED,
             CSState.NPO_APPROVED,
             CSState.EXPORTED,
+            CSState.INVALID
         ],
         permission=lambda instance, user: ConnectivityStatementService.has_permission_to_transition_to_compose_now(
             instance, user
@@ -500,6 +501,26 @@ def npo_approved(self, *args, **kwargs):
     def exported(self, *args, **kwargs):
         ...
 
+    @transition(
+        field=state,
+        source=[
+            CSState.DRAFT,
+            CSState.COMPOSE_NOW,
+            CSState.CURATED,
+            CSState.EXCLUDED,
+            CSState.REJECTED,
+            CSState.TO_BE_REVIEWED,
+            CSState.CONNECTION_MISSING,
+            CSState.NPO_APPROVED,
+            CSState.EXPORTED,
+        ],
+        target=CSState.INVALID,
+        permission=lambda instance, user: ConnectivityStatementService.has_permission_to_transition_to_invalid(
+            instance, user
+        ), )
+    def invalid(self, *args, **kwargs):
+        ...
+
     @property
     def export_id(self):
         return f"CPR:{self.id:06d}"
@@ -590,7 +611,7 @@ class Destination(AbstractConnectionLayer):
         choices=DestinationType.choices,
         default=DestinationType.UNKNOWN
     )
-    
+
     objects = DestinationManager()
 
     class Meta:
@@ -604,7 +625,7 @@ class Meta:
 
 class Via(AbstractConnectionLayer):
     anatomical_entities = models.ManyToManyField(AnatomicalEntity, blank=True, related_name='via_connection_layers')
-    
+
     objects = ViaManager()
 
     type = models.CharField(