[Feature] Legacy API (#224)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#224

epdb/legacy_api.py

@@ -1,18 +1,21 @@
 from typing import Any, Dict, List, Optional
 
+import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse
 from django.shortcuts import redirect
-from ninja import Field, Form, Router, Schema
+from ninja import Field, Form, Router, Schema, Query
 
 from utilities.chem import FormatConverter
+from utilities.misc import PackageExporter
 
-from .logic import PackageManager, SettingManager, UserManager
+from .logic import GroupManager, PackageManager, SettingManager, UserManager
 from .models import (
     Compound,
     CompoundStructure,
     Edge,
+    EPModel,
     Node,
     Pathway,
     Reaction,
@@ -21,6 +24,7 @@ from .models import (
     SimpleAmbitRule,
     User,
     UserPackagePermission,
+    ParallelRule,
 )
 
 Package = s.GET_PACKAGE_MODEL()
@@ -121,6 +125,10 @@ class SimpleEdge(SimpleObject):
     identifier: str = "edge"
 
 
+class SimpleModel(SimpleObject):
+    identifier: str = "relative-reasoning"
+
+
 ################
 # Login/Logout #
 ################
@@ -169,9 +177,13 @@ class UserSchema(Schema):
         return SettingManager.get_all_settings(obj)
 
 
+class Me(Schema):
+    whoami: str | None = None
+
+
 @router.get("/user", response={200: UserWrapper, 403: Error})
-def get_users(request, whoami: str = None):
+def get_users(request, me: Query[Me]):
-    if whoami:
+    if me.whoami:
         return {"user": [request.user]}
     else:
         return {"user": User.objects.all()}
@@ -253,67 +265,110 @@ def get_packages(request):
     }
 
 
-@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema, 403: Error})
+class GetPackage(Schema):
-def get_package(request, package_uuid):
+    exportAsJson: str | None = None
+
+
+@router.get("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 403: Error})
+def get_package(request, package_uuid, gp: Query[GetPackage]):
     try:
-        return PackageManager.get_package_by_id(request.user, package_uuid)
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if gp.exportAsJson and gp.exportAsJson.strip() == "true":
+            return PackageExporter(p).do_export()
+
+        return p
     except ValueError:
         return 403, {
             "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
         }
 
 
+class CreatePackage(Schema):
+    packageName: str
+    packageDescription: str | None = None
+
+
 @router.post("/package")
 def create_packages(
-    request, packageName: Form[str], packageDescription: Optional[str] = Form(None)
+    request,
+    p: Form[CreatePackage],
 ):
     try:
-        if packageName.strip() == "":
+        if p.packageName.strip() == "":
             raise ValueError("Package name cannot be empty!")
 
-        new_pacakge = PackageManager.create_package(request.user, packageName, packageDescription)
+        new_pacakge = PackageManager.create_package(
+            request.user, p.packageName, p.packageDescription
+        )
         return redirect(new_pacakge.url)
     except ValueError as e:
         return 400, {"message": str(e)}
 
 
+class UpdatePackage(Schema):
+    packageDescription: str | None = None
+    hiddenMethod: str | None = None
+    permissions: str | None = None
+    ppsURI: str | None = None
+    read: str | None = None
+    write: str | None = None
+
+
 @router.post("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 400: Error})
-def update_package(
+def update_package(request, package_uuid, pack: Form[UpdatePackage]):
-    request,
-    package_uuid,
-    packageDescription: Optional[str] = Form(None),
-    hiddenMethod: Optional[str] = Form(None),
-    exportAsJson: Optional[str] = Form(None),
-    permissions: Optional[str] = Form(None),
-    ppsURI: Optional[str] = Form(None),
-    read: Optional[str] = Form(None),
-    write: Optional[str] = Form(None),
-):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        if hiddenMethod:
+        if pack.hiddenMethod:
-            if hiddenMethod == "DELETE":
+            if pack.hiddenMethod == "DELETE":
                 p.delete()
 
-        elif packageDescription and packageDescription.strip() != "":
+        elif pack.packageDescription is not None:
-            p.description = packageDescription
+            description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
-            p.save()
-            return
-        elif exportAsJson == "true":
-            pack_json = PackageManager.export_package(
-                p, include_models=False, include_external_identifiers=False
-            )
-            return pack_json
-        elif all([permissions, ppsURI, read]):
-            PackageManager.update_permissions
-        elif all([permissions, ppsURI, write]):
-            pass
 
+            if description:
+                p.description = description
+                p.save()
+                return HttpResponse(status=200)
+            else:
+                raise ValueError("Package description cannot be empty!")
+        elif all([pack.permissions, pack.ppsURI, pack.read]):
+            if "group" in pack.ppsURI:
+                grantee = GroupManager.get_group_lp(pack.ppsURI)
+            else:
+                grantee = UserManager.get_user_lp(pack.ppsURI)
+
+            PackageManager.grant_read(request.user, p, grantee)
+            return HttpResponse(status=200)
+        elif all([pack.permissions, pack.ppsURI, pack.write]):
+            if "group" in pack.ppsURI:
+                grantee = GroupManager.get_group_lp(pack.ppsURI)
+            else:
+                grantee = UserManager.get_user_lp(pack.ppsURI)
+
+            PackageManager.grant_write(request.user, p, grantee)
+            return HttpResponse(status=200)
     except ValueError as e:
         return 400, {"message": str(e)}
 
 
+@router.delete("/package/{uuid:package_uuid}")
+def delete_package(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.administrable(request.user, p):
+            p.delete()
+            return redirect(f"{s.SERVER_URL}/package")
+        else:
+            raise ValueError("You do not have the rights to delete this Package!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Package with id {package_uuid} failed due to insufficient rights!"
+        }
+
+
 ################################
 # Compound / CompoundStructure #
 ################################
@@ -511,6 +566,83 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
         }
 
 
+class CreateCompound(Schema):
+    compoundSmiles: str
+    compoundName: str | None = None
+    compoundDescription: str | None = None
+    inchi: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/compound")
+def create_package_compound(
+    request,
+    package_uuid,
+    c: Form[CreateCompound],
+):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        # inchi is not used atm
+        c = Compound.create(
+            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+        )
+        return redirect(c.url)
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
+@router.delete("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}")
+def delete_compound(request, package_uuid, compound_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            c = Compound.objects.get(package=p, uuid=compound_uuid)
+            c.delete()
+            return redirect(f"{p.url}/compound")
+        else:
+            raise ValueError("You do not have the rights to delete this Compound!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Compound with id {compound_uuid} failed due to insufficient rights!"
+        }
+
+
+@router.delete(
+    "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
+)
+def delete_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            c = Compound.objects.get(package=p, uuid=compound_uuid)
+            cs = CompoundStructure.objects.get(compound=c, uuid=structure_uuid)
+
+            # Check if we have to delete the compound as no structure is left
+            if len(cs.compound.structures.all()) == 1:
+                # This will delete the structure as well
+                c.delete()
+                return redirect(p.url + "/compound")
+            else:
+                if cs.normalized_structure:
+                    c.delete()
+                    return redirect(p.url + "/compound")
+                else:
+                    if c.default_structure == cs:
+                        cs.delete()
+                        c.default_structure = c.structures.all().first()
+                        return redirect(c.url + "/structure")
+                    else:
+                        cs.delete()
+                        return redirect(c.url + "/structure")
+        else:
+            raise ValueError("You do not have the rights to delete this CompoundStructure!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting CompoundStructure with id {compound_uuid} failed due to insufficient rights!"
+        }
+
+
 #########
 # Rules #
 #########
@@ -674,6 +806,73 @@ def _get_package_rule(request, package_uuid, rule_uuid):
 
 
 # POST
+class CreateSimpleRule(Schema):
+    smirks: str
+    name: str | None = None
+    description: str | None = None
+    reactantFilterSmarts: str | None = None
+    productFilterSmarts: str | None = None
+    immediate: str | None = None
+    rdkitrule: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/simple-rule")
+def create_package_simple_rule(
+    request,
+    package_uuid,
+    r: Form[CreateSimpleRule],
+):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if r.rdkitrule and r.rdkitrule.strip() == "true":
+            raise ValueError("Not yet implemented!")
+        else:
+            sr = SimpleAmbitRule.create(
+                p, r.name, r.description, r.smirks, r.reactantFilterSmarts, r.productFilterSmarts
+            )
+
+        return redirect(sr.url)
+
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
+class CreateParallelRule(Schema):
+    simpleRules: str
+    name: str | None = None
+    description: str | None = None
+    reactantFilterSmarts: str | None = None
+    productFilterSmarts: str | None = None
+    immediate: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/parallel-rule")
+def create_package_parallel_rule(
+    request,
+    package_uuid,
+    r: Form[CreateParallelRule],
+):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        srs = SimpleRule.objects.filter(package=p, url__in=r.simpleRules)
+
+        if srs.count() != len(r.simpleRules):
+            raise ValueError(
+                f"Not all SimpleRules could be found in Package with id {package_uuid}!"
+            )
+
+        sr = ParallelRule.create(
+            p, list(srs), r.name, r.description, r.reactantFilterSmarts, r.productFilterSmarts
+        )
+
+        return redirect(sr.url)
+
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
 @router.post(
     "/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}", response={200: str | Any, 403: Error}
 )
@@ -723,6 +922,41 @@ def _post_package_rule(request, package_uuid, rule_uuid, compound: Form[str]):
         }
 
 
+@router.delete("/package/{uuid:package_uuid}/rule/{uuid:rule_uuid}")
+def delete_rule(request, package_uuid, rule_uuid):
+    return _delete_rule(request, package_uuid, rule_uuid)
+
+
+@router.delete(
+    "/package/{uuid:package_uuid}/simple-rule/{uuid:rule_uuid}",
+)
+def delete_simple_rule(request, package_uuid, rule_uuid):
+    return _delete_rule(request, package_uuid, rule_uuid)
+
+
+@router.delete(
+    "/package/{uuid:package_uuid}/parallel-rule/{uuid:rule_uuid}",
+)
+def delete_parallel_rule(request, package_uuid, rule_uuid):
+    return _delete_rule(request, package_uuid, rule_uuid)
+
+
+def _delete_rule(request, package_uuid, rule_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            r = Rule.objects.get(package=p, uuid=rule_uuid)
+            r.delete()
+            return redirect(f"{p.url}/rule")
+        else:
+            raise ValueError("You do not have the rights to delete this Rule!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Rule with id {rule_uuid} failed due to insufficient rights!"
+        }
+
+
 ############
 # Reaction #
 ############
@@ -811,6 +1045,82 @@ def get_package_reaction(request, package_uuid, reaction_uuid):
         }
 
 
+class CreateReaction(Schema):
+    reactionName: str | None = None
+    reactionDescription: str | None = None
+    smirks: str | None = None
+    educt: str | None = None
+    product: str | None = None
+    rule: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/reaction")
+def create_package_reaction(
+    request,
+    package_uuid,
+    r: Form[CreateReaction],
+):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if r.smirks is None and (r.educt is None or r.product is None):
+            raise ValueError("Either SMIRKS or educt/product must be provided")
+
+        if r.smirks is not None and (r.educt is not None and r.product is not None):
+            raise ValueError("SMIRKS and educt/product provided!")
+
+        rule = None
+        if r.rule:
+            try:
+                rule = Rule.objects.get(package=p, url=r.rule)
+            except Rule.DoesNotExist:
+                raise ValueError(f"Rule with id {r.rule} does not exist!")
+
+        if r.educt is not None:
+            try:
+                educt_cs = CompoundStructure.objects.get(compound__package=p, url=r.educt)
+            except CompoundStructure.DoesNotExist:
+                raise ValueError(f"Compound with id {r.educt} does not exist!")
+
+            try:
+                product_cs = CompoundStructure.objects.get(compound__package=p, url=r.product)
+            except CompoundStructure.DoesNotExist:
+                raise ValueError(f"Compound with id {r.product} does not exist!")
+
+            new_r = Reaction.create(
+                p, r.reactionName, r.reactionDescription, [educt_cs], [product_cs], rule
+            )
+        else:
+            educts = r.smirks.split(">>")[0].split("\\.")
+            products = r.smirks.split(">>")[1].split("\\.")
+
+            new_r = Reaction.create(
+                p, r.reactionName, r.reactionDescription, educts, products, rule
+            )
+
+        return redirect(new_r.url)
+
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
+@router.delete("/package/{uuid:package_uuid}/reaction/{uuid:reaction_uuid}")
+def delete_reaction(request, package_uuid, reaction_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            r = Reaction.objects.get(package=p, uuid=reaction_uuid)
+            r.delete()
+            return redirect(f"{p.url}/reaction")
+        else:
+            raise ValueError("You do not have the rights to delete this Reaction!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Reaction with id {reaction_uuid} failed due to insufficient rights!"
+        }
+
+
 ############
 # Scenario #
 ############
@@ -825,7 +1135,7 @@ class ScenarioSchema(Schema):
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
-    linkedTo: List[Dict[str, str]] = Field({}, alias="linked_to")
+    linkedTo: List[Dict[str, str]] = Field([], alias="linked_to")
     name: str = Field(None, alias="name")
     pathways: List["SimplePathway"] = Field([], alias="related_pathways")
     relatedScenarios: List[Dict[str, str]] = Field([], alias="related_scenarios")
@@ -876,6 +1186,38 @@ def get_package_scenario(request, package_uuid, scenario_uuid):
         }
 
 
+@router.delete("/package/{uuid:package_uuid}/scenario")
+def delete_scenarios(request, package_uuid, scenario_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            scens = Scenario.objects.filter(package=p)
+            scens.delete()
+            return redirect(f"{p.url}/scenario")
+        else:
+            raise ValueError("You do not have the rights to delete Scenarios!")
+    except ValueError:
+        return 403, {"message": "Deleting Scenarios failed due to insufficient rights!"}
+
+
+@router.delete("/package/{uuid:package_uuid}/scenario/{uuid:scenario_uuid}")
+def delete_scenario(request, package_uuid, scenario_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            scen = Scenario.objects.get(package=p, uuid=scenario_uuid)
+            scen.delete()
+            return redirect(f"{p.url}/scenario")
+        else:
+            raise ValueError("You do not have the rights to delete this Scenario!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Scenario with id {scenario_uuid} failed due to insufficient rights!"
+        }
+
+
 ###########
 # Pathway #
 ###########
@@ -1015,46 +1357,67 @@ def get_package_pathway(request, package_uuid, pathway_uuid):
         }
 
 
+class CreatePathway(Schema):
+    smilesinput: str
+    name: str | None = None
+    description: str | None = None
+    rootOnly: str | None = None
+    selectedSetting: str | None = None
+
+
 @router.post("/package/{uuid:package_uuid}/pathway")
 def create_pathway(
     request,
     package_uuid,
-    smilesinput: Form[str],
+    pw: Form[CreatePathway],
-    name: Optional[str] = Form(None),
-    description: Optional[str] = Form(None),
-    rootOnly: Optional[str] = Form(None),
-    selectedSetting: Optional[str] = Form(None),
 ):
     try:
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
-        stand_smiles = FormatConverter.standardize(smilesinput.strip())
+        stand_smiles = FormatConverter.standardize(pw.smilesinput.strip())
 
-        pw = Pathway.create(p, stand_smiles, name=name, description=description)
+        new_pw = Pathway.create(p, stand_smiles, name=pw.name, description=pw.description)
 
         pw_mode = "predict"
-        if rootOnly and rootOnly == "true":
+        if pw.rootOnly and pw.rootOnly.strip() == "true":
             pw_mode = "build"
 
-        pw.kv.update({"mode": pw_mode})
+        new_pw.kv.update({"mode": pw_mode})
-        pw.save()
+        new_pw.save()
 
         if pw_mode == "predict":
             setting = request.user.prediction_settings()
 
-            if selectedSetting:
+            if pw.selectedSetting:
-                setting = SettingManager.get_setting_by_url(request.user, selectedSetting)
+                setting = SettingManager.get_setting_by_url(request.user, pw.selectedSetting)
 
-            pw.setting = setting
+            new_pw.setting = setting
-            pw.save()
+            new_pw.save()
 
-            from .tasks import predict
+            from .tasks import dispatch, predict
 
-            predict.delay(pw.pk, setting.pk, limit=-1)
+            dispatch(request.user, predict, new_pw.pk, setting.pk, limit=-1)
 
-        return redirect(pw.url)
+        return redirect(new_pw.url)
     except ValueError as e:
-        print(e)
+        return 400, {"message": str(e)}
+
+
+@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
+def delete_pathway(request, package_uuid, pathway_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            pw.delete()
+            return redirect(f"{p.url}/pathway")
+        else:
+            raise ValueError("You do not have the rights to delete this pathway!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
+        }
 
 
 ########
@@ -1145,6 +1508,52 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         }
 
 
+class CreateNode(Schema):
+    nodeAsSmiles: str
+    nodeName: str | None = None
+    nodeReason: str | None = None
+    nodeDepth: str | None = None
+
+
+@router.post(
+    "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
+    response={200: str | Any, 403: Error},
+)
+def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+
+        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)
+
+        return redirect(n.url)
+    except ValueError:
+        return 403, {"message": "Adding node failed!"}
+
+
+@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node/{uuid:node_uuid}")
+def delete_node(request, package_uuid, pathway_uuid, node_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            n = Node.objects.get(pathway=pw, uuid=node_uuid)
+            n.delete()
+            return redirect(f"{pw.url}/node")
+        else:
+            raise ValueError("You do not have the rights to delete this Node!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Node with id {node_uuid} failed due to insufficient rights!"
+        }
+
+
 ########
 # Edge #
 ########
@@ -1208,6 +1617,200 @@ def get_package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
         }
 
 
+class CreateEdge(Schema):
+    edgeAsSmirks: str | None = None
+    educts: str | None = None  # Node URIs comma sep
+    products: str | None = None  # Node URIs comma sep
+    multistep: str | None = None
+    edgeReason: str | None = None
+
+
+@router.post(
+    "/package/{uuid:package_uuid}/üathway/{uuid:pathway_uuid}/edge",
+    response={200: str | Any, 403: Error},
+)
+def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+
+        if e.edgeAsSmirks is None and (e.educts is None or e.products is None):
+            raise ValueError("Either SMIRKS or educt/product must be provided")
+
+        if e.edgeAsSmirks is not None and (e.educts is not None and e.products is not None):
+            raise ValueError("SMIRKS and educt/product provided!")
+
+        educts = []
+        products = []
+
+        if e.edgeAsSmirks:
+            for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
+                educts.append(Node.objects.get(pathway=pw, default_node_label__smiles=ed))
+
+            for pr in e.edgeAsSmirks.split(">>")[1].split("\\."):
+                products.append(Node.objects.get(pathway=pw, default_node_label__smiles=pr))
+        else:
+            for ed in e.educts.split(","):
+                educts.append(Node.objects.get(pathway=pw, url=ed.strip()))
+
+            for pr in e.products.split(","):
+                products.append(Node.objects.get(pathway=pw, url=pr.strip()))
+
+        new_e = Edge.create(
+            pathway=pw,
+            start_nodes=educts,
+            end_nodes=products,
+            rule=None,
+            name=e.name,
+            description=e.edgeReason,
+        )
+
+        return redirect(new_e.url)
+    except ValueError:
+        return 403, {"message": "Adding node failed!"}
+
+
+@router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
+def delete_edge(request, package_uuid, pathway_uuid, edge_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            e = Edge.objects.get(pathway=pw, uuid=edge_uuid)
+            e.delete()
+            return redirect(f"{pw.url}/edge")
+        else:
+            raise ValueError("You do not have the rights to delete this Edge!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Edge with id {edge_uuid} failed due to insufficient rights!"
+        }
+
+
+#########
+# Model #
+#########
+class ModelWrapper(Schema):
+    relative_reasoning: List["SimpleModel"] = Field(..., alias="relative-reasoning")
+
+
+class ModelSchema(Schema):
+    aliases: List[str] = Field([], alias="aliases")
+    description: str = Field(None, alias="description")
+    evalPackages: List["SimplePackage"] = Field([])
+    id: str = Field(None, alias="url")
+    identifier: str = "relative-reasoning"
+    #   "info" : {
+    #       "Accuracy (Single-Gen)" : "0.5932962678936605" ,
+    #       "Area under PR-Curve (Single-Gen)" : "0.5654653182134282" ,
+    #       "Area under ROC-Curve (Single-Gen)" : "0.8178302405034772" ,
+    #       "Precision (Single-Gen)" : "0.6978730822873083" ,
+    #       "Probability Threshold" : "0.5" ,
+    #       "Recall/Sensitivity (Single-Gen)" : "0.4484149210261006"
+    #     } ,
+    name: str = Field(None, alias="name")
+    pathwayPackages: List["SimplePackage"] = Field([])
+    reviewStatus: str = Field(None, alias="review_status")
+    rulePackages: List["SimplePackage"] = Field([])
+    scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
+    status: str
+    statusMessage: str
+    threshold: str
+    type: str
+
+
+@router.get("/model", response={200: ModelWrapper, 403: Error})
+def get_models(request):
+    pass
+
+
+@router.get("/package/{uuid:package_uuid}/model", response={200: ModelWrapper, 403: Error})
+def get_package_models(request, package_uuid, model_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        return EPModel.objects.filter(package=p)
+    except ValueError:
+        return 403, {
+            "message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
+        }
+
+
+class Classify(Schema):
+    smiles: str | None = None
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/model/{uuid:model_uuid}",
+    response={200: ModelSchema | Any, 403: Error, 400: Error},
+)
+def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+        mod = EPModel.objects.get(package=p, uuid=model_uuid)
+
+        if c.smiles:
+            if c.smiles == "":
+                return 400, {"message": "Received empty SMILES"}
+
+            try:
+                stand_smiles = FormatConverter.standardize(c.smiles)
+            except ValueError:
+                return 400, {"message": f'"{c.smiles}" is not a valid SMILES'}
+
+            from epdb.tasks import dispatch_eager, predict_simple
+
+            pred_res = dispatch_eager(request.user, predict_simple, mod.pk, stand_smiles)
+
+            result = []
+
+            for pr in pred_res:
+                if len(pr) > 0:
+                    products = []
+                    for prod_set in pr.product_sets:
+                        products.append(tuple([x for x in prod_set]))
+
+                    res = {
+                        "probability": pr.probability,
+                        "products": list(set(products)),
+                    }
+
+                    if pr.rule:
+                        res["id"] = pr.rule.url
+                        res["identifier"] = pr.rule.get_rule_identifier()
+                        res["name"] = pr.rule.name
+                        res["reviewStatus"] = (
+                            "reviewed" if pr.rule.package.reviewed else "unreviewed"
+                        )
+
+                    result.append(res)
+
+            return result
+
+        return mod
+    except ValueError:
+        return 403, {
+            "message": f"Getting Reaction with id {model_uuid} failed due to insufficient rights!"
+        }
+
+
+@router.delete("/package/{uuid:package_uuid}/model/{uuid:model_uuid}")
+def delete_model(request, package_uuid, model_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.user, package_uuid)
+
+        if PackageManager.writable(request.user, p):
+            m = EPModel.objects.get(package=p, uuid=model_uuid)
+            m.delete()
+            return redirect(f"{p.url}/model")
+        else:
+            raise ValueError("You do not have the rights to delete this Model!")
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Model with id {model_uuid} failed due to insufficient rights!"
+        }
+
+
 ###########
 # Setting #
 ###########

epdb/logic.py

@@ -579,6 +579,14 @@ class PackageManager(object):
         else:
             _ = perm_cls.objects.update_or_create(defaults={"permission": new_perm}, **data)
 
+    @staticmethod
+    def grant_read(caller: User, package: Package, grantee: Union[User, Group]):
+        PackageManager.update_permissions(caller, package, grantee, Permission.READ[0])
+
+    @staticmethod
+    def grant_write(caller: User, package: Package, grantee: Union[User, Group]):
+        PackageManager.update_permissions(caller, package, grantee, Permission.WRITE[0])
+
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
@@ -595,7 +603,6 @@ class PackageManager(object):
             CompoundStructure,
             Edge,
             Node,
-            Package,
             ParallelRule,
             Pathway,
             Reaction,

epdb/models.py

@@ -1079,6 +1079,10 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     def apply(self, *args, **kwargs):
         pass
 
+    @abc.abstractmethod
+    def get_rule_identifier(self) -> str:
+        pass
+
     @staticmethod
     def cls_for_type(rule_type: str):
         if rule_type == "SimpleAmbitRule":
@@ -1233,6 +1237,9 @@ class SimpleAmbitRule(SimpleRule):
     def _url(self):
         return "{}/simple-ambit-rule/{}".format(self.package.url, self.uuid)
 
+    def get_rule_identifier(self) -> str:
+        return "simple-rule"
+
     def apply(self, smiles):
         return FormatConverter.apply(smiles, self.smirks)
 
@@ -1278,6 +1285,9 @@ class ParallelRule(Rule):
     def _url(self):
         return "{}/parallel-rule/{}".format(self.package.url, self.uuid)
 
+    def get_rule_identifier(self) -> str:
+        return "parallel-rule"
+
     @cached_property
     def srs(self) -> QuerySet:
         return self.simple_rules.all()
@@ -1309,6 +1319,57 @@ class ParallelRule(Rule):
 
         return res
 
+    @staticmethod
+    @transaction.atomic
+    def create(
+        package: "Package",
+        simple_rules: List["SimpleRule"],
+        name: str = None,
+        description: str = None,
+        reactant_filter_smarts: str = None,
+        product_filter_smarts: str = None,
+    ):
+        if len(simple_rules) == 0:
+            raise ValueError("At least one simple rule is required!")
+
+        for sr in simple_rules:
+            if sr.package != package:
+                raise ValueError(
+                    f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
+                )
+
+        r = ParallelRule()
+        r.package = package
+
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if name is None or name == "":
+            name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
+
+        r.name = name
+        if description is not None and description.strip() != "":
+            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
+            if not FormatConverter.is_valid_smarts(reactant_filter_smarts.strip()):
+                raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
+            else:
+                r.reactant_filter_smarts = reactant_filter_smarts.strip()
+
+        if product_filter_smarts is not None and product_filter_smarts.strip() != "":
+            if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
+                raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
+            else:
+                r.product_filter_smarts = product_filter_smarts.strip()
+
+        r.save()
+
+        for sr in simple_rules:
+            r.simple_rules.add(sr)
+
+        return r
+
 
 class SequentialRule(Rule):
     simple_rules = models.ManyToManyField(
@@ -1318,6 +1379,9 @@ class SequentialRule(Rule):
     def _url(self):
         return "{}/sequential-rule/{}".format(self.compound.url, self.uuid)
 
+    def get_rule_identifier(self) -> str:
+        return "sequential-rule"
+
     @property
     def srs(self):
         return self.simple_rules.all()

epdb/views.py

@@ -907,9 +907,10 @@ def package_model(request, package_uuid, model_uuid):
             if classify:
                 from epdb.tasks import dispatch_eager, predict_simple
 
-                res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
+                pred_res = dispatch_eager(
+                    current_user, predict_simple, current_model.pk, stand_smiles
+                )
 
-                pred_res = current_model.predict(stand_smiles)
                 res = []
 
                 for pr in pred_res:
@@ -1069,9 +1070,7 @@ def package(request, package_uuid):
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
-                    PackageManager.update_permissions(
+                    PackageManager.grant_read(current_user, current_package, g)
-                        current_user, current_package, g, Permission.READ[0]
-                    )
                 return redirect(current_package.url)
             elif hidden == "copy":
                 object_to_copy = request.POST.get("object_to_copy")

templates/objects/model.html

@@ -87,7 +87,7 @@
               data-toggle="collapse"
               data-parent="#model-detail"
               href="#reaction-package"
-              >Rule Packages</a
+              >Data Packages</a
             >
           </h4>
         </div>
@@ -112,7 +112,7 @@
                 data-toggle="collapse"
                 data-parent="#model-detail"
                 href="#eval-package"
-                >Rule Packages</a
+                >Evaluation Packages</a
               >
             </h4>
           </div>

utilities/chem.py

@@ -65,7 +65,7 @@ class PredictionResult(object):
         return iter(self.product_sets)
 
     def __repr__(self):
-        return f"--{self.probability}/{self.rule}--> {self.product_sets}"
+        return f"--{self.probability:.2f}/{self.rule}--> {self.product_sets}"
 
 
 class FormatConverter(object):