adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

utilities/misc.py

@@ -12,6 +12,7 @@ from django.conf import settings as s
 from ninja import Schema
 from pydantic import HttpUrl, ValidationError
 
+from bayer.models import PESCompound, PESStructure
 from epdb.exceptions import PackageImportException
 from epdb.models import (
     AdditionalInformation,
@@ -34,7 +35,7 @@ logger = logging.getLogger(__name__)
 Package = s.GET_PACKAGE_MODEL()
 
 if TYPE_CHECKING:
-    from epdb.logic import SPathway
+    from epdb.logic import SPathway, GroupManager
 
 
 class LicenseExportSchema(Schema):
@@ -56,6 +57,9 @@ class RefExportSchema(Schema):
         return str(value)
 
 
+class RefGroupExportSchema(RefExportSchema): ...
+
+
 class RefCompoundExportSchema(RefExportSchema): ...
 
 
@@ -105,6 +109,26 @@ class CompoundStructureExportSchema(RefCompoundStructureExportSchema):
     scenarios: List[RefScenarioExportSchema]
 
 
+class PESCompoundExportSchema(RefCompoundExportSchema):
+    name: str
+    description: str
+    aliases: List[str]
+    default_structure: RefCompoundStructureExportSchema
+    structures: List["PESCompoundStructureExportSchema"]
+    scenarios: List[RefScenarioExportSchema]
+
+
+class PESCompoundStructureExportSchema(RefCompoundStructureExportSchema):
+    name: str
+    description: str
+    aliases: List[str]
+    smiles: str
+    molfile: Optional[str]
+    normalized_structure: bool
+    scenarios: List[RefScenarioExportSchema]
+    pes_link: HttpUrl
+
+
 ############
 # Reaction #
 ############
@@ -227,7 +251,9 @@ class PackageExportSchema(Schema):
     uuid: str
     reviewed: bool
     license: LicenseExportSchema | None = None
-    compounds: List[CompoundExportSchema]
+    classification_level: str = "Internal"
+    data_pool: RefGroupExportSchema | None = None
+    compounds: List[CompoundExportSchema | PESCompoundExportSchema]
     reactions: List[ReactionExportSchema]
     simple_rules: List[RuleExportSchema]
     composite_rules: List[ParallelRuleExportSchema]
@@ -240,14 +266,30 @@ class PackageExportSchema(Schema):
         value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
         return str(value)
 
+    @staticmethod
+    def resolve_classification_level(obj):
+        if isinstance(obj, dict):
+            return obj["classification_level"]
+        return obj.Classification(obj.classification_level).name
+
+
     @staticmethod
     def resolve_compounds(obj):
         res = []
         if isinstance(obj, dict):
             for c in obj.get("compounds", []):
-                res.append(CompoundExportSchema.model_validate(c))
-            return res
-        return obj.compounds.all()
+                is_pes = any([cs.get("pes_link", None) is not None for cs in c.get("structures", [])])
+                if is_pes:
+                    res.append(PESCompoundExportSchema.model_validate(c))
+                else:
+                    res.append(CompoundExportSchema.model_validate(c))
+        else:
+            for c in obj.compounds.all():
+                if isinstance(c, PESCompound):
+                    res.append(PESCompoundExportSchema.from_orm(c))
+                else:
+                    res.append(CompoundExportSchema.from_orm(c))
+        return res
 
     @staticmethod
     def resolve_simple_rules(obj):
@@ -311,12 +353,18 @@ class PackageImporter:
         return self._import_package_from_json()
 
     def _import_compounds(
-        self,
-        package: Package,
-        compounds: List[CompoundExportSchema],
+            self,
+            package: Package,
+            compounds: List[CompoundExportSchema | PESCompoundExportSchema],
     ):
         for c in compounds:
-            new_c = Compound()
+
+            if isinstance(c, PESCompoundExportSchema):
+                c_cls = PESCompound
+            else:
+                c_cls = Compound
+
+            new_c = c_cls()
             new_c.uuid = str(uuid.uuid4()) if not self.preserve_uuids else c.uuid
             new_c.package = package
             new_c.name = c.name
@@ -327,7 +375,13 @@ class PackageImporter:
             self._cache[c.uuid] = new_c
 
             for cs in c.structures:
-                new_cs = CompoundStructure()
+
+                if isinstance(cs, PESCompoundStructureExportSchema):
+                    cs_cls = PESStructure
+                else:
+                    cs_cls = CompoundStructure
+
+                new_cs = cs_cls()
                 new_cs.uuid = str(uuid.uuid4()) if not self.preserve_uuids else cs.uuid
                 new_cs.compound = new_c
                 new_cs.name = cs.name
@@ -336,6 +390,9 @@ class PackageImporter:
                 new_cs.smiles = cs.smiles
                 new_cs.molfile = cs.molfile
 
+                if cs_cls == PESStructure:
+                    new_cs.pes_link = cs.pes_link
+
                 new_cs.normalized_structure = cs.normalized_structure
                 new_cs.save()
 
@@ -514,6 +571,7 @@ class PackageImporter:
             package_uuid = parsed.uuid
 
         package_license = License.objects.get(link=parsed.license.link) if parsed.license else None
+        package_classification_level = Package.Classification[parsed.classification_level.upper()]
 
         package = Package()
         package.uuid = package_uuid
@@ -521,6 +579,10 @@ class PackageImporter:
         package.description = parsed.description
         package.reviewed = False
         package.license = package_license
+        package.classification_level = package_classification_level
+
+        if package_classification_level == Package.Classification.SECRET:
+            package.data_pool = Group.objects.get(uuid=parsed.data_pool.uuid)
 
         package.save()