epauth/views.py

@@ -116,6 +116,11 @@ def get_access_token_from_request(request, scopes=None):
     """
     Get an access token from the request using MSAL token cache.
     """
+
+    # Check if auth via Access Token
+    if request.headers.get("Authorization"):
+        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
+
     if scopes is None:
         scopes = s.MS_ENTRA_SCOPES
 

epdb/legacy_api.py

@@ -820,6 +820,7 @@ class CreateCompound(Schema):
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
+    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -831,6 +832,25 @@ def create_package_compound(
     try:
         p = get_package_for_write(request.user, package_uuid)
         # inchi is not used atm
+
+        if c.pesLink is not None:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, c.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
+
+            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
+        else:
             c = Compound.create(
                 p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
             )
@@ -1854,6 +1874,7 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
+    pesLink: str | None = None
 
 
 @router.post(
@@ -1865,14 +1886,43 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
+        if n.pesLink:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, c.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
+
+            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
+
+            node = Node()
+            node.stereo_removed = False
+            node.pathway = pw
+            node.depth = 0
+
+            node.default_node_label = c.default_structure
+            node.save()
+
+            node.node_labels.add(c.default_structure)
+            node.save()
+        else:
             if n.nodeDepth is not None and n.nodeDepth.strip() != "":
                 node_depth = int(n.nodeDepth)
             else:
                 node_depth = -1
 
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
-        return redirect(n.url)
+        return redirect(node.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}