[Feature] Engineer Pathway (#256)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#256

tests/test_jobs.py

@@ -0,0 +1,95 @@
+from django.conf import settings as s
+from django.test import TestCase, override_settings
+
+from epdb.logic import PackageManager
+from epdb.models import Pathway, User
+
+Package = s.GET_PACKAGE_MODEL()
+
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
+class MultiGenTest(TestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(MultiGenTest, cls).setUpClass()
+        cls.user: "User" = User.objects.get(username="anonymous")
+        cls.package: "Package" = PackageManager.create_package(
+            cls.user, "Anon Test Package", "No Desc"
+        )
+        cls.BBD_SUBSET: "Package" = Package.objects.get(name="Fixtures")
+        # 1,1,1-Trichloroethane (an/aerobic)
+        cls.PW_WITH_INTERMEDIATE_NAME = "1,1,1-Trichloroethane (an/aerobic)"
+        cls.PW_WITHOUT_INTERMEDIATE_NAME = "Caffeine"
+
+    def test_engineer_pathway(self):
+        from epdb.tasks import engineer_pathways
+
+        pw_to_engineer = Pathway.objects.get(name=self.PW_WITH_INTERMEDIATE_NAME)
+        engineered, predicted = engineer_pathways(
+            [pw_to_engineer.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 1)
+        self.assertEqual(len(predicted), 1)
+        eng_pw = Pathway.objects.get(url=engineered[0])
+
+        for n in eng_pw.nodes:
+            if n.kv.get("is_engineered_intermediate"):
+                self.assertEqual(n.default_node_label.smiles, "CCO")
+
+        pw_to_engineer = Pathway.objects.get(name=self.PW_WITHOUT_INTERMEDIATE_NAME)
+        engineered, predicted = engineer_pathways(
+            [pw_to_engineer.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 0)
+        self.assertEqual(len(predicted), 0)
+
+        # Test pathway deduplication in eng pathway process
+        pw1 = Pathway.objects.get(name=self.PW_WITH_INTERMEDIATE_NAME)
+
+        # Add pw1 twice
+        engineered, predicted = engineer_pathways(
+            [pw1.pk, pw1.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 1)
+        self.assertEqual(len(predicted), 1)
+
+        # Check that both pathways contain the intermediate
+        num_intermediates_found = 0
+        for eng in engineered:
+            eng_pw = Pathway.objects.get(url=eng)
+
+            for n in eng_pw.nodes:
+                if n.kv.get("is_engineered_intermediate"):
+                    self.assertEqual(n.default_node_label.smiles, "CCO")
+                    num_intermediates_found += 1
+
+        self.assertEqual(num_intermediates_found, 1)
+
+        # Get a copy to have two pathways with potential intermediates as the fixture
+        # only contains one
+        mapping = {}
+        pw2 = pw1.copy(self.package, mapping=mapping)
+
+        engineered, predicted = engineer_pathways(
+            [pw1.pk, pw2.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 2)
+        self.assertEqual(len(predicted), 2)
+
+        # Check that both pathways contain the intermediate
+        num_intermediates_found = 0
+        for eng in engineered:
+            eng_pw = Pathway.objects.get(url=eng)
+
+            for n in eng_pw.nodes:
+                if n.kv.get("is_engineered_intermediate"):
+                    self.assertEqual(n.default_node_label.smiles, "CCO")
+                    num_intermediates_found += 1
+
+        self.assertEqual(num_intermediates_found, 2)