wip

bayer/models.py

@@ -1,11 +1,15 @@
 from typing import List
-
+import urllib.parse
+import nh3
 from django.conf import settings as s
-from django.db import models
+from django.db import models, transaction
 from django.db.models import QuerySet
+from django.urls import reverse
 
 from epdb.models import (
     EnviPathModel,
+    Compound,
+    CompoundStructure,
     ParallelRule,
     SequentialRule,
     SimpleAmbitRule,
@@ -95,4 +99,70 @@ class Package(EnviPathModel):
         return rules
 
     class Meta:
-        db_table = "epdb_package"
+        db_table = "epdb_package"
+
+
+class PESCompound(Compound):
+
+    @staticmethod
+    @transaction.atomic
+    def create(
+        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
+    ) -> "Compound":
+
+        pes_url = pes_data["pes_url"]
+
+        # Check if we find a direct match for a given pes_link
+        if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
+            return PESStructure.objects.get(pes_link=pes_url, compound__package=package).compound
+
+        # Generate Compound
+        c = PESCompound()
+        c.package = package
+
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if name is None or name == "":
+            name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
+
+        c.name = name
+
+        # We have a default here only set the value if it carries some payload
+        if description is not None and description.strip() != "":
+            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        c.save()
+
+        is_standardized = standardized_smiles == smiles
+
+        if not is_standardized:
+            _ = CompoundStructure.create(
+                c,
+                standardized_smiles,
+                name="Normalized structure of {}".format(name),
+                description="{} (in its normalized form)".format(description),
+                normalized_structure=True,
+            )
+
+        cs = CompoundStructure.create(
+            c, smiles, name=name, description=description, normalized_structure=is_standardized
+        )
+
+        c.default_structure = cs
+        c.save()
+
+        return c
+
+
+class PESStructure(CompoundStructure):
+    pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
+
+    def d3_json(self):
+        return {
+            "is_pes": True,
+            "pes_link": self.pes_link,
+            # Will overwrite image from Node
+            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
+        }