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

...

epdb/exceptions.py

@@ -1,2 +1,2 @@
 class InvalidSMILESException(Exception):
-    pass
+    pass

epdb/legacy_api.py

@@ -1687,13 +1687,13 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
-    idreact: str = Field(None, alias="node_label_id")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="smiles")
+    smiles: str = Field(None, alias="default_node_label.smiles")
     pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod

epdb/management/commands/bootstrap.py

@@ -99,15 +99,11 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner, all_envipath_user_group):
+    def import_package(self, data, owner):
-        p = PackageManager.import_legacy_package(
+        return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
-        PackageManager.grant_read(owner, p, all_envipath_user_group)
-
-        return p
-
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -202,7 +198,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin, g)
+            imported_package = self.import_package(package_data, admin)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0027_alter_compound_aliases_and_more.py

@@ -1,150 +0,0 @@
-# Generated by Django 6.0.3 on 2026-07-01 20:59
-
-import django.contrib.postgres.fields
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0026_auto_20260602_1718"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="compound",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="default_structure",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                related_name="compound_default_structure",
-                to="epdb.compoundstructure",
-                verbose_name="Default Structure",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="edge_label",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                to="epdb.reaction",
-                verbose_name="Edge label",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="medline_references",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(),
-                blank=True,
-                null=True,
-                verbose_name="Medline References",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="rules",
-            field=models.ManyToManyField(
-                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-    ]

epdb/models.py

@@ -637,7 +637,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -660,9 +660,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -862,7 +860,7 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package", smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
             raise InvalidSMILESException("SMILES is required")
@@ -1660,15 +1658,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -2262,12 +2255,10 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         depth_map[0] = list()
         processed = set()
 
-        data_driven_root_nodes = (
+        data_driven_root_nodes = self.node_set.all().annotate(
-            self.node_set.all()
+            prod_cnt=Count('edge_products'),
-            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
+            educt_cnt=Count('edge_educts')
-            .filter(prod_cnt=0, educt_cnt__gt=0)
+        ).filter(prod_cnt=0, educt_cnt__gt=0).distinct()
-            .distinct()
-        )
 
         # Eval QuerySet
         root_nodes_by_depth = list(self.root_nodes)
@@ -2360,12 +2351,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
+                self.default_node_label.molfile if self.default_node_label.molfile is not None and self.default_node_label.molfile.strip() else self.default_node_label.smiles,
-                if self.default_node_label.molfile is not None
+                width=40, height=40
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
             ),
             "image_type": "svg",
             "name": self.get_name(),
@@ -2419,10 +2406,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     @property
     def as_svg(self):
-        if (
+        if self.default_node_label.molfile is not None and self.default_node_label.molfile.strip() != "":
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
             return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 

epdb/views.py

@@ -785,7 +785,6 @@ def models(request):
             {"Home": s.SERVER_URL},
             {"Model": s.SERVER_URL + "/model"},
         ]
-
         context["entity_type"] = "model"
         context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
@@ -810,7 +809,7 @@ def models(request):
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -943,12 +942,13 @@ def package_models(request, package_uuid):
                 "requires_data_packages": True,
             },
         }
+
         if s.ENVIFORMER_PRESENT:
             context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1124,10 +1124,8 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
+                # Sort data by prob desc
-                        res["pred"] = sorted(
+                res["pred"] = sorted(res["pred"], key=lambda x: x["probability"], reverse=True)
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
 
                 return JsonResponse(res, safe=False)
 
@@ -1232,7 +1230,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -2368,13 +2368,10 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-
         try:
             current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        except InvalidSMILESException:
+        except InvalidSMILESException as e:
-            return error(
+            return error(request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid")
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
 
         return redirect(current_pathway.url)
 

migration/views.py

@@ -81,7 +81,6 @@ def migration(request):
         "bt0416-4269",
         "bt0432-4254",
         "bt0337-4117",
-        "bt0322-3393",
     ]
 
     if request.method == "GET":

static/js/pw.js

@@ -1,14 +1,18 @@
 console.log("loaded pw.js")
 
+
 function findPaths(source_idx, target_idx, links) {
     const resultLinks = new Set();
     const visited = new Set();
+
     // Helper function for depth-first search
     function dfs(current) {
         if (current === target_idx) {
             return;
         }
+
         visited.add(current);
+
         links.forEach(link => {
             if (
                 link.target.id === current &&
@@ -19,13 +23,18 @@ function findPaths(source_idx, target_idx, links) {
                 dfs(link.source.id);
             }
         });
+
         visited.delete(current);
     }
+
     // Start DFS
     dfs(source_idx);
+
     return Array.from(resultLinks); // Convert Set to Array for result
 }
 
+
+
 function predictFromNode(url) {
     fetch("", {
         method: "POST",
@@ -653,34 +662,36 @@ function draw(pathway, elem) {
             return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
         })
         .attr("fill", "none")
-        .on("click", function(event, d) {
+	.on("click", function(event, d) {
           const wasHighlighted = d3.select(this).classed("highlighted");
-	      d3.selectAll("path").classed("highlighted", false);
+
+	  d3.selectAll("path").classed("highlighted", false);
+
           if (!wasHighlighted) {
-            const toHighlight = [];
+              const toHighlight = [];
-            toHighlight.push(d.el);
+              toHighlight.push(d.el);
 
-            if (d.source.pseudo || d.target.pseudo) {
+              if (d.source.pseudo || d.target.pseudo) {
-              if (d.target.pseudo) {
+                  if (d.target.pseudo) {
-                d3.selectAll("path").each(e => {
+                      d3.selectAll("path").each(e => {
-                  if (e !== undefined && e.source.id === d.target.id) {
+                          if (e !== undefined && e.source.id === d.target.id) {
-                    toHighlight.push(e.el);
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  } else {
+                      d3.selectAll("path").each(e => {
+                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                              toHighlight.push(e.el);
+                          }
+                      });
                   }
-                });
-              } else {
-                d3.selectAll("path").each(e => {
-                  if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
-                    toHighlight.push(e.el);
-                  }
-                });
               }
-            }
 
-            for (const e of toHighlight) {
+              for (const e of toHighlight) {
-              d3.select(e).classed("highlighted", true);
+                  d3.select(e).classed("highlighted", true);
-            }
+              }
           }
-        });
+      })
 
     // add element to links array
     link.each(function (d) {
@@ -697,41 +708,44 @@ function draw(pathway, elem) {
         .call(d3.drag()
             .on("start", dragstarted)
             .on("drag", dragged)
-            .on("end", dragended)
+            .on("end", dragended))
-        )
         .on("click", function (event, d) {
-          const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
-          d3.selectAll('circle.highlighted').classed('highlighted', false);
-          d3.selectAll("path").classed("inedge", false);
-          d3.selectAll("path").classed("outedge", false);
 
-          if (!wasHighlighted) {
+            d3.selectAll('circle.highlighted').classed('highlighted', false);
-            d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
+            d3.selectAll("path").classed("inedge", false);
-            const inEdges = findPaths(d.id, 3, links);
+            d3.selectAll("path").classed("outedge", false);
-            const outEdges = []
+
-            // Colorize out edges green
+            if (!wasHighlighted) {
-            for (const l of links) {
+                d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-              if (l.source.id === d.id) {
+
-                outEdges.push(l);
+                const inEdges = findPaths(d.id, 3, links);
-                if (l.target.pseudo) {
+                const outEdges = []
-                  for (const l2 of links) {
+
-                    if (l.target.id === l2.source.id) {
+                // Colorize out edges green
-                      outEdges.push(l2);
+                for (const l of links) {
+                    if (l.source.id === d.id) {
+                        outEdges.push(l);
+                        if (l.target.pseudo) {
+                            for (const l2 of links) {
+                                if (l.target.id === l2.source.id) {
+                                    outEdges.push(l2);
+                                }
+                            }
+                        }
                     }
-                  }
                 }
-              }
+
+                for (const e of inEdges) {
+                    d3.select(e.el).classed("inedge", true);
+                }
+                for (const e of outEdges) {
+                    d3.select(e.el).classed("outedge", true);
+                }
             }
 
-            for (const e of inEdges) {
-              d3.select(e.el).classed("inedge", true);
-            }
 
-            for (const e of outEdges) {
+        })
-              d3.select(e.el).classed("outedge", true);
-            }
-          }
-        });
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")

templates/modals/objects/delete_pathway_edge_modal.html

@@ -6,6 +6,7 @@
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
   @modal-opened.window="
    const links = d3.selectAll('path.highlighted');
+
    if (!links.empty()) {
         const el = links.node();
         const selectElement = document.getElementById('delete_pathway_edge_edges');
@@ -17,7 +18,9 @@
                 break;
             }
         }
+
         selectElement.dispatchEvent(new Event('change'));
+
    }
   "
   @close="reset()"

templates/modals/objects/delete_pathway_node_modal.html

@@ -6,14 +6,17 @@
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
   @modal-opened.window="
    const el = d3.select('circle.highlighted').node();
+
    if (el !== null) {
     const selectElement = document.getElementById('delete_pathway_node_nodes');
+
     for (let option of selectElement.options) {
         if (option.value === el.__data__.url) {
             option.selected = true;
             break;
         }
     }
+
     selectElement.dispatchEvent(new Event('change'));
    }
   "

templates/objects/group.html

@@ -56,10 +56,8 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a
+                <a href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
-                href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}"
+                  >{{ um.username }}
-                class="hover:bg-base-300"
-                >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >
             </li>

templates/objects/pathway.html

@@ -77,10 +77,12 @@
       stroke: red;
       stroke-width: 3px;
     }
+
     .outedge {
       stroke: green;
       stroke-width: 3px;
     }
+
   </style>
   <script src="{% static 'js/pw.js' %}"></script>
 
@@ -120,7 +122,7 @@
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
       </div>
-      <div class="collapse-content">
+      <div class="collapse-content ">
         <div class="bg-base-100 mb-2 rounded-lg p-2">
           <div class="navbar bg-base-100 rounded-lg">
             <div class="flex-1">

templates/predict_pathway.html

@@ -212,8 +212,6 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-
-        // Set text depending on mode
         if (document.getElementById("predict-submit-button").innerText === "Build") {
           button.textContent = "Building...";
         } else {

tests/test_compound_model.py

@@ -1,7 +1,5 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
-
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -35,13 +33,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -98,7 +96,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(
                 self.package,
                 smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",

tests/test_reaction_model.py

@@ -1,7 +1,6 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
@@ -164,7 +163,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_model_views.py

@@ -46,14 +46,6 @@ class ModelViewTest(TestCase):
         )
 
         expected = [
-            {
-                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
-                "probability": 0.75,
-                "btrule": {
-                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
-                    "name": "bt0001-3568",
-                },
-            },
             {
                 "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
@@ -70,6 +62,14 @@ class ModelViewTest(TestCase):
                     "name": "bt0243-4301",
                 },
             },
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
         ]
 
         actual = response.json()["pred"]

utilities/misc.py

@@ -6,15 +6,12 @@ import logging
 import uuid
 from collections import defaultdict
 from datetime import datetime
-from typing import Any, Dict, List, Optional, TYPE_CHECKING
+from typing import Any, Dict, List, TYPE_CHECKING
 
 from django.conf import settings as s
 from django.db import transaction
-from ninja import Schema
-from pydantic import HttpUrl
 
 from epdb.models import (
-    AdditionalInformation,
     Compound,
     CompoundStructure,
     Edge,
@@ -31,6 +28,7 @@ from epdb.models import (
     Rule,
     RuleBasedRelativeReasoning,
     Scenario,
+    SequentialRule,
     Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
@@ -45,235 +43,408 @@ if TYPE_CHECKING:
     from epdb.logic import SPathway
 
 
-class LicenseExportSchema(Schema):
-    cc_string: str
-    link: HttpUrl
-    image_link: HttpUrl
-
-
-##############
-# RefSchemas #
-##############
-class RefExportSchema(Schema):
-    uuid: str
-    url: str
-
-    @staticmethod
-    def resolve_uuid(obj):
-        value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
-        return str(value)
-
-
-class RefCompoundExportSchema(RefExportSchema): ...
-
-
-class RefCompoundStructureExportSchema(RefExportSchema): ...
-
-
-class RefReactionExportSchema(RefExportSchema): ...
-
-
-class RefRuleExportSchema(RefExportSchema): ...
-
-
-class RefNodeExportSchema(RefExportSchema): ...
-
-
-class RefEdgeExportSchema(RefExportSchema): ...
-
-
-class RefPathwayExportSchema(RefExportSchema): ...
-
-
-class RefScenarioExportSchema(RefExportSchema): ...
-
-
-############
-# Compound #
-############
-class CompoundExportSchema(RefCompoundExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    default_structure: RefCompoundStructureExportSchema
-    structures: List["CompoundStructureExportSchema"]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class CompoundStructureExportSchema(RefCompoundStructureExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    smiles: str
-    molfile: Optional[str]
-    normalized_structure: bool
-    scenarios: List[RefScenarioExportSchema]
-
-
-############
-# Reaction #
-############
-class ReactionExportSchema(RefReactionExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    educts: List[RefCompoundStructureExportSchema]
-    products: List[RefCompoundStructureExportSchema]
-    rules: List[RefRuleExportSchema]
-    multi_step: bool
-    medline_references: List[str] | None
-    scenarios: List[RefScenarioExportSchema]
-
-
-#########
-# Rules #
-#########
-class RuleExportSchema(RefRuleExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    smirks: str
-    reactant_filter_smarts: Optional[str]
-    product_filter_smarts: Optional[str]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class ParallelRuleExportSchema(RefRuleExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    simple_rules: List[RefRuleExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-###########################
-# Pathway / Nodes / Edges #
-###########################
-class NodeExportSchema(RefNodeExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    default_node_label: RefCompoundStructureExportSchema
-    node_labels: List[RefCompoundStructureExportSchema]
-    depth: int
-    stereo_removed: bool
-    scenarios: List[RefScenarioExportSchema]
-
-
-class EdgeExportSchema(RefEdgeExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    edge_label: RefReactionExportSchema
-    start_nodes: List[RefNodeExportSchema]
-    end_nodes: List[RefNodeExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class PathwayExportSchema(RefPathwayExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    predicted: bool
-    nodes: List[NodeExportSchema]
-    edges: List[EdgeExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class ScenarioExportSchema(RefScenarioExportSchema):
-    name: str
-    description: str
-    scenario_date: str
-    scenario_type: str
-
-
-class AdditionalInformationExportSchema(RefExportSchema):
-    type: str
-    data: dict
-    scenario: RefScenarioExportSchema | None = None
-    attach_object: RefExportSchema | None = None
-
-    @staticmethod
-    def resolve_attach_object(obj):
-        if isinstance(obj, dict):
-            if obj.get("attach_object") is None:
-                return None
-            return RefExportSchema.model_validate(obj["attach_object"])
-        return obj.content_object
-
-
-###########
-# Package #
-###########
-class PackageExportSchema(Schema):
-    name: str
-    description: str
-    uuid: str
-    reviewed: bool
-    license: LicenseExportSchema | None
-    compounds: List[CompoundExportSchema]
-    reactions: List[ReactionExportSchema]
-    simple_rules: List[RuleExportSchema]
-    composite_rules: List[ParallelRuleExportSchema]
-    pathways: List[PathwayExportSchema]
-    scenarios: List[ScenarioExportSchema]
-    additional_information: List[AdditionalInformationExportSchema]
-
-    @staticmethod
-    def resolve_uuid(obj):
-        value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
-        return str(value)
-
-    @staticmethod
-    def resolve_simple_rules(obj):
-        if isinstance(obj, dict):
-            result = []
-            for r in obj.get("simple_rules", []):
-                result.append(RuleExportSchema.model_validate(r))
-            return result
-        return SimpleAmbitRule.objects.filter(package=obj)
-
-    @staticmethod
-    def resolve_composite_rules(obj):
-        if isinstance(obj, dict):
-            result = []
-            for r in obj.get("composite_rules", []):
-                result.append(ParallelRuleExportSchema.model_validate(r))
-            return result
-        return ParallelRule.objects.filter(package=obj)
-
-    @staticmethod
-    def resolve_additional_information(obj):
-        if isinstance(obj, dict):
-            result = []
-            for ai in obj.get("additional_information", []):
-                result.append(AdditionalInformationExportSchema.model_validate(ai))
-            return result
-        return AdditionalInformation.objects.filter(package=obj)
-
-
 class PackageExporter:
-    def __init__(self, package: Package):
+    def __init__(
+        self,
+        package: Package,
+        include_models: bool = False,
+        include_external_identifiers: bool = True,
+    ):
         self._raw_package = package
+        self.include_modes = include_models
+        self.include_external_identifiers = include_external_identifiers
 
     def do_export(self):
-        return PackageExporter._export_package_as_json(self._raw_package)
+        return PackageExporter._export_package_as_json(
+            self._raw_package, self.include_modes, self.include_external_identifiers
+        )
 
     @staticmethod
-    def _export_package_as_json(package: Package) -> Dict[str, Any]:
+    def _export_package_as_json(
+        package: Package, include_models: bool = False, include_external_identifiers: bool = True
+    ) -> Dict[str, Any]:
         """
         Dumps a Package and all its related objects as JSON.
 
         Args:
             package: The Package instance to dump
+            include_models: Whether to include EPModel objects
+            include_external_identifiers: Whether to include external identifiers
 
         Returns:
             Dict containing the complete package data as JSON-serializable structure
         """
 
-        data = PackageExportSchema.from_orm(package)
+        def serialize_base_object(
+            obj, include_aliases: bool = True, include_scenarios: bool = True
+        ) -> Dict[str, Any]:
+            """Serialize common EnviPathModel fields"""
+            base_dict = {
+                "uuid": str(obj.uuid),
+                "name": obj.name,
+                "description": obj.description,
+                "url": obj.url,
+                "kv": obj.kv,
+            }
 
-        return data.model_dump(mode="json")
+            # Add aliases if the object has them
+            if include_aliases and hasattr(obj, "aliases"):
+                base_dict["aliases"] = obj.aliases
+
+            # Add scenarios if the object has them
+            if include_scenarios and hasattr(obj, "scenarios"):
+                base_dict["scenarios"] = [
+                    {"uuid": str(s.uuid), "url": s.url} for s in obj.scenarios.all()
+                ]
+
+            return base_dict
+
+        def serialize_external_identifiers(obj) -> List[Dict[str, Any]]:
+            """Serialize external identifiers for an object"""
+            if not include_external_identifiers or not hasattr(obj, "external_identifiers"):
+                return []
+
+            identifiers = []
+            for ext_id in obj.external_identifiers.all():
+                identifier_dict = {
+                    "uuid": str(ext_id.uuid),
+                    "database": {
+                        "uuid": str(ext_id.database.uuid),
+                        "name": ext_id.database.name,
+                        "base_url": ext_id.database.base_url,
+                    },
+                    "identifier_value": ext_id.identifier_value,
+                    "url": ext_id.url,
+                    "is_primary": ext_id.is_primary,
+                }
+                identifiers.append(identifier_dict)
+            return identifiers
+
+        # Start with the package itself
+        result = serialize_base_object(package, include_aliases=True, include_scenarios=True)
+        result["reviewed"] = package.reviewed
+
+        # # Add license information
+        # if package.license:
+        #     result['license'] = {
+        #         'uuid': str(package.license.uuid),
+        #         'name': package.license.name,
+        #         'link': package.license.link,
+        #         'image_link': package.license.image_link
+        #     }
+        # else:
+        #     result['license'] = None
+
+        # Initialize collections
+        result.update(
+            {
+                "compounds": [],
+                "structures": [],
+                "rules": {"simple_rules": [], "parallel_rules": [], "sequential_rules": []},
+                "reactions": [],
+                "pathways": [],
+                "nodes": [],
+                "edges": [],
+                "scenarios": [],
+                "models": [],
+            }
+        )
+
+        print(f"Exporting package: {package.name}")
+
+        # Export compounds
+        print("Exporting compounds...")
+        for compound in package.compounds.prefetch_related("default_structure").order_by("url"):
+            compound_dict = serialize_base_object(
+                compound, include_aliases=True, include_scenarios=True
+            )
+
+            if compound.default_structure:
+                compound_dict["default_structure"] = {
+                    "uuid": str(compound.default_structure.uuid),
+                    "url": compound.default_structure.url,
+                }
+            else:
+                compound_dict["default_structure"] = None
+
+            compound_dict["external_identifiers"] = serialize_external_identifiers(compound)
+            result["compounds"].append(compound_dict)
+
+        # Export compound structures
+        print("Exporting compound structures...")
+        compound_structures = (
+            CompoundStructure.objects.filter(compound__package=package)
+            .select_related("compound")
+            .order_by("url")
+        )
+
+        for structure in compound_structures:
+            structure_dict = serialize_base_object(
+                structure, include_aliases=True, include_scenarios=True
+            )
+            structure_dict.update(
+                {
+                    "compound": {
+                        "uuid": str(structure.compound.uuid),
+                        "url": structure.compound.url,
+                    },
+                    "smiles": structure.smiles,
+                    "canonical_smiles": structure.canonical_smiles,
+                    "inchikey": structure.inchikey,
+                    "normalized_structure": structure.normalized_structure,
+                    "external_identifiers": serialize_external_identifiers(structure),
+                }
+            )
+            result["structures"].append(structure_dict)
+
+        # Export rules
+        print("Exporting rules...")
+
+        # Simple rules (including SimpleAmbitRule and SimpleRDKitRule)
+        for rule in SimpleRule.objects.filter(package=package).order_by("url"):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+
+            # Add specific fields for SimpleAmbitRule
+            if isinstance(rule, SimpleAmbitRule):
+                rule_dict.update(
+                    {
+                        "rule_type": "SimpleAmbitRule",
+                        "smirks": rule.smirks,
+                        "reactant_filter_smarts": rule.reactant_filter_smarts or "",
+                        "product_filter_smarts": rule.product_filter_smarts or "",
+                    }
+                )
+            elif isinstance(rule, SimpleRDKitRule):
+                rule_dict.update(
+                    {"rule_type": "SimpleRDKitRule", "reaction_smarts": rule.reaction_smarts}
+                )
+            else:
+                rule_dict["rule_type"] = "SimpleRule"
+
+            result["rules"]["simple_rules"].append(rule_dict)
+
+        # Parallel rules
+        for rule in (
+            ParallelRule.objects.filter(package=package)
+            .prefetch_related("simple_rules")
+            .order_by("url")
+        ):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+            rule_dict["rule_type"] = "ParallelRule"
+            rule_dict["simple_rules"] = [
+                {"uuid": str(sr.uuid), "url": sr.url} for sr in rule.simple_rules.all()
+            ]
+            result["rules"]["parallel_rules"].append(rule_dict)
+
+        # Sequential rules
+        for rule in (
+            SequentialRule.objects.filter(package=package)
+            .prefetch_related("simple_rules")
+            .order_by("url")
+        ):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+            rule_dict["rule_type"] = "SequentialRule"
+            rule_dict["simple_rules"] = [
+                {
+                    "uuid": str(sr.uuid),
+                    "url": sr.url,
+                    "order_index": sr.sequentialruleordering_set.get(
+                        sequential_rule=rule
+                    ).order_index,
+                }
+                for sr in rule.simple_rules.all()
+            ]
+            result["rules"]["sequential_rules"].append(rule_dict)
+
+        # Export reactions
+        print("Exporting reactions...")
+        for reaction in package.reactions.prefetch_related("educts", "products", "rules").order_by(
+            "url"
+        ):
+            reaction_dict = serialize_base_object(
+                reaction, include_aliases=True, include_scenarios=True
+            )
+            reaction_dict.update(
+                {
+                    "educts": [{"uuid": str(e.uuid), "url": e.url} for e in reaction.educts.all()],
+                    "products": [
+                        {"uuid": str(p.uuid), "url": p.url} for p in reaction.products.all()
+                    ],
+                    "rules": [{"uuid": str(r.uuid), "url": r.url} for r in reaction.rules.all()],
+                    "multi_step": reaction.multi_step,
+                    "medline_references": reaction.medline_references,
+                    "external_identifiers": serialize_external_identifiers(reaction),
+                }
+            )
+            result["reactions"].append(reaction_dict)
+
+        # Export pathways
+        print("Exporting pathways...")
+        for pathway in package.pathways.order_by("url"):
+            pathway_dict = serialize_base_object(
+                pathway, include_aliases=True, include_scenarios=True
+            )
+
+            # Add setting reference if exists
+            if hasattr(pathway, "setting") and pathway.setting:
+                pathway_dict["setting"] = {
+                    "uuid": str(pathway.setting.uuid),
+                    "url": pathway.setting.url,
+                }
+            else:
+                pathway_dict["setting"] = None
+
+            result["pathways"].append(pathway_dict)
+
+        # Export nodes
+        print("Exporting nodes...")
+        pathway_nodes = (
+            Node.objects.filter(pathway__package=package)
+            .select_related("pathway", "default_node_label")
+            .prefetch_related("node_labels", "out_edges")
+            .order_by("url")
+        )
+
+        for node in pathway_nodes:
+            node_dict = serialize_base_object(node, include_aliases=True, include_scenarios=True)
+            node_dict.update(
+                {
+                    "pathway": {"uuid": str(node.pathway.uuid), "url": node.pathway.url},
+                    "default_node_label": {
+                        "uuid": str(node.default_node_label.uuid),
+                        "url": node.default_node_label.url,
+                    },
+                    "node_labels": [
+                        {"uuid": str(label.uuid), "url": label.url}
+                        for label in node.node_labels.all()
+                    ],
+                    "out_edges": [
+                        {"uuid": str(edge.uuid), "url": edge.url} for edge in node.out_edges.all()
+                    ],
+                    "depth": node.depth,
+                }
+            )
+            result["nodes"].append(node_dict)
+
+        # Export edges
+        print("Exporting edges...")
+        pathway_edges = (
+            Edge.objects.filter(pathway__package=package)
+            .select_related("pathway", "edge_label")
+            .prefetch_related("start_nodes", "end_nodes")
+            .order_by("url")
+        )
+
+        for edge in pathway_edges:
+            edge_dict = serialize_base_object(edge, include_aliases=True, include_scenarios=True)
+            edge_dict.update(
+                {
+                    "pathway": {"uuid": str(edge.pathway.uuid), "url": edge.pathway.url},
+                    "edge_label": {"uuid": str(edge.edge_label.uuid), "url": edge.edge_label.url},
+                    "start_nodes": [
+                        {"uuid": str(node.uuid), "url": node.url} for node in edge.start_nodes.all()
+                    ],
+                    "end_nodes": [
+                        {"uuid": str(node.uuid), "url": node.url} for node in edge.end_nodes.all()
+                    ],
+                }
+            )
+            result["edges"].append(edge_dict)
+
+        # Export scenarios
+        print("Exporting scenarios...")
+        for scenario in package.scenarios.order_by("url"):
+            scenario_dict = serialize_base_object(
+                scenario, include_aliases=False, include_scenarios=False
+            )
+            scenario_dict.update(
+                {
+                    "scenario_date": scenario.scenario_date,
+                    "scenario_type": scenario.scenario_type,
+                    "parent": {"uuid": str(scenario.parent.uuid), "url": scenario.parent.url}
+                    if scenario.parent
+                    else None,
+                    "additional_information": scenario.additional_information,
+                }
+            )
+            result["scenarios"].append(scenario_dict)
+
+        # Export models
+        if include_models:
+            print("Exporting models...")
+            package_models = (
+                package.models.select_related("app_domain")
+                .prefetch_related("rule_packages", "data_packages", "eval_packages")
+                .order_by("url")
+            )
+
+            for model in package_models:
+                model_dict = serialize_base_object(
+                    model, include_aliases=True, include_scenarios=False
+                )
+
+                # Common fields for PackageBasedModel
+                if hasattr(model, "rule_packages"):
+                    model_dict.update(
+                        {
+                            "rule_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.rule_packages.all()
+                            ],
+                            "data_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.data_packages.all()
+                            ],
+                            "eval_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.eval_packages.all()
+                            ],
+                            "threshold": model.threshold,
+                            "eval_results": model.eval_results,
+                            "model_status": model.model_status,
+                        }
+                    )
+
+                    if model.app_domain:
+                        model_dict["app_domain"] = {
+                            "uuid": str(model.app_domain.uuid),
+                            "url": model.app_domain.url,
+                        }
+                    else:
+                        model_dict["app_domain"] = None
+
+                # Specific fields for different model types
+                if isinstance(model, RuleBasedRelativeReasoning):
+                    model_dict.update(
+                        {
+                            "model_type": "RuleBasedRelativeReasoning",
+                            "min_count": model.min_count,
+                            "max_count": model.max_count,
+                        }
+                    )
+                elif isinstance(model, MLRelativeReasoning):
+                    model_dict["model_type"] = "MLRelativeReasoning"
+                elif isinstance(model, EnviFormer):
+                    model_dict["model_type"] = "EnviFormer"
+                else:
+                    model_dict["model_type"] = "EPModel"
+
+                result["models"].append(model_dict)
+
+        print(f"Export completed for package: {package.name}")
+        print(f"- Compounds: {len(result['compounds'])}")
+        print(f"- Structures: {len(result['structures'])}")
+        print(f"- Simple rules: {len(result['rules']['simple_rules'])}")
+        print(f"- Parallel rules: {len(result['rules']['parallel_rules'])}")
+        print(f"- Sequential rules: {len(result['rules']['sequential_rules'])}")
+        print(f"- Reactions: {len(result['reactions'])}")
+        print(f"- Pathways: {len(result['pathways'])}")
+        print(f"- Nodes: {len(result['nodes'])}")
+        print(f"- Edges: {len(result['edges'])}")
+        print(f"- Scenarios: {len(result['scenarios'])}")
+        print(f"- Models: {len(result['models'])}")
+
+        return result
 
 
 class PackageImporter: