Merge remote-tracking branch 'origin/develop' into feature/frontend_update

envipath/settings.py

@@ -135,6 +135,7 @@ USE_TZ = True
 
 DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
 
+EMAIL_SUBJECT_PREFIX = "[enviPath] "
 if DEBUG:
     EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
 else:
@@ -144,6 +145,8 @@ else:
     EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
     EMAIL_HOST_PASSWORD = os.environ["EMAIL_HOST_PASSWORD"]
     EMAIL_PORT = 587
+    DEFAULT_FROM_EMAIL = os.environ["DEFAULT_FROM_EMAIL"]
+    SERVER_EMAIL = os.environ["SERVER_EMAIL"]
 
 AUTH_USER_MODEL = "epdb.User"
 ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") == "True"

epdb/admin.py

@@ -7,6 +7,7 @@ from .models import (
     GroupPackagePermission,
     Package,
     MLRelativeReasoning,
+    EnviFormer,
     Compound,
     CompoundStructure,
     SimpleAmbitRule,
@@ -50,6 +51,10 @@ class MLRelativeReasoningAdmin(EPAdmin):
     pass
 
 
+class EnviFormerAdmin(EPAdmin):
+    pass
+
+
 class CompoundAdmin(EPAdmin):
     pass
 
@@ -104,6 +109,7 @@ admin.site.register(Group, GroupAdmin)
 admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
 admin.site.register(Package, PackageAdmin)
 admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
+admin.site.register(EnviFormer, EnviFormerAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)

epdb/logic.py

@@ -26,6 +26,7 @@ from epdb.models import (
     Compound,
     Reaction,
     CompoundStructure,
+    EnzymeLink,
 )
 from utilities.chem import FormatConverter
 from utilities.misc import PackageImporter, PackageExporter
@@ -617,6 +618,8 @@ class PackageManager(object):
         parent_mapping = {}
         # Mapping old scen_id to old_obj_id
         scen_mapping = defaultdict(list)
+        # Enzymelink Mapping rule_id to enzymelink objects
+        enzyme_mapping = defaultdict(list)
 
         # Store Scenarios
         for scenario in data["scenarios"]:
@@ -648,9 +651,7 @@ class PackageManager(object):
                 # Broken eP Data
                 if name == "initialmasssediment" and addinf_data == "missing data":
                     continue
-
+                if name == "columnheight" and addinf_data == "(2)-(2.5);(6)-(8)":
-                # TODO Enzymes arent ready yet
-                if name == "enzyme":
                     continue
 
                 try:
@@ -740,6 +741,9 @@ class PackageManager(object):
             for scen in rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
         print("Par: ", len(par_rules))
         print("Seq: ", len(seq_rules))
 
@@ -757,6 +761,9 @@ class PackageManager(object):
             for scen in par_rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in par_rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
             for simple_rule in par_rule["simpleRules"]:
                 if simple_rule["id"] in mapping:
                     r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule["id"]]))
@@ -777,6 +784,9 @@ class PackageManager(object):
             for scen in seq_rule["scenarios"]:
                 scen_mapping[scen["id"]].append(r)
 
+            for enzyme_link in seq_rule.get("enzymeLinks", []):
+                enzyme_mapping[r.uuid].append(enzyme_link)
+
             for i, simple_rule in enumerate(seq_rule["simpleRules"]):
                 sro = SequentialRuleOrdering()
                 sro.simple_rule = simple_rule
@@ -910,6 +920,39 @@ class PackageManager(object):
 
         print("Scenarios linked...")
 
+        # Import Enzyme Links
+        for rule_uuid, enzyme_links in enzyme_mapping.items():
+            r = Rule.objects.get(uuid=rule_uuid)
+            for enzyme in enzyme_links:
+                e = EnzymeLink()
+                e.uuid = UUID(enzyme["id"].split("/")[-1]) if keep_ids else uuid4()
+                e.rule = r
+                e.name = enzyme["name"]
+                e.ec_number = enzyme["ecNumber"]
+                e.classification_level = enzyme["classificationLevel"]
+                e.linking_method = enzyme["linkingMethod"]
+                e.save()
+
+                for reaction in enzyme["reactionLinkEvidence"]:
+                    reaction = Reaction.objects.get(uuid=mapping[reaction["id"]])
+                    e.reaction_evidence.add(reaction)
+
+                for edge in enzyme["edgeLinkEvidence"]:
+                    edge = Edge.objects.get(uuid=mapping[edge["id"]])
+                    e.reaction_evidence.add(edge)
+
+                for evidence in enzyme["linkEvidence"]:
+                    matches = re.findall(r">(R[0-9]+)<", evidence["evidence"])
+                    if not matches or len(matches) != 1:
+                        logger.warning(f"Could not find reaction id in {evidence['evidence']}")
+                        continue
+
+                    e.add_kegg_reaction_id(matches[0])
+
+                e.save()
+
+        print("Enzyme links imported...")
+
         print("Import statistics:")
         print("Package {} stored".format(pack.url))
         print("Imported {} compounds".format(Compound.objects.filter(package=pack).count()))

epdb/management/commands/create_ml_models.py

@@ -7,10 +7,11 @@ from epdb.models import MLRelativeReasoning, EnviFormer, Package
 
 class Command(BaseCommand):
     """This command can be run with
-    `python manage.py create_ml_models [model_names] -d [data_packages] OPTIONAL: -e [eval_packages]`
+    `python manage.py create_ml_models [model_names] -d [data_packages] FOR MLRR ONLY: -r [rule_packages]
-    For example, to train both EnviFormer and MLRelativeReasoning on BBD and SOIL and evaluate them on SLUDGE
+                                        OPTIONAL: -e [eval_packages] -t threshold`
-    the below command would be used:
+    For example, to train both EnviFormer and MLRelativeReasoning on BBD and SOIL and evaluate them on SLUDGE with a
-    `python manage.py create_ml_models enviformer mlrr -d bbd soil -e sludge
+    threshold of 0.6, the below command would be used:
+    `python manage.py create_ml_models enviformer mlrr -d bbd soil -e sludge -t 0.6
     """
 
     def add_arguments(self, parser):
@@ -34,6 +35,13 @@ class Command(BaseCommand):
             help="Rule Packages mandatory for MLRR",
             default=[],
         )
+        parser.add_argument(
+            "-t",
+            "--threshold",
+            type=float,
+            help="Model prediction threshold",
+            default=0.5,
+        )
 
     @transaction.atomic
     def handle(self, *args, **options):
@@ -67,7 +75,11 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(f"Creating models: {options['model_names']}")
+        print(f"Creating models: {options['model_names']}\n"
+              f"Data packages: {options['data_packages']}\n"
+              f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
+              f"Eval Packages: {options['eval_packages']}\n"
+              f"Threshold: {options['threshold']:.2f}")
         data_packages = decode_packages(options["data_packages"])
         eval_packages = decode_packages(options["eval_packages"])
         rule_packages = decode_packages(options["rule_packages"])
@@ -78,9 +90,10 @@ class Command(BaseCommand):
                     pack,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=0.5,
+                    threshold=options['threshold'],
-                    name="EnviFormer - T0.5",
+                    name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
-                    description="EnviFormer transformer",
+                    description=f"EnviFormer transformer trained on {options['data_packages']} "
+                                f"evaluated on {options['eval_packages']}.",
                 )
             elif model_name == "mlrr":
                 model = MLRelativeReasoning.create(
@@ -88,9 +101,10 @@ class Command(BaseCommand):
                     rule_packages=rule_packages,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=0.5,
+                    threshold=options['threshold'],
-                    name="ECC - BBD - T0.5",
+                    name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
-                    description="ML Relative Reasoning",
+                    description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
+                                f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",
                 )
             else:
                 raise ValueError(f"Cannot create model of type {model_name}, unknown model type")
@@ -100,6 +114,6 @@ class Command(BaseCommand):
             print(f"Training {model_name}")
             model.build_model()
             print(f"Evaluating {model_name}")
-            model.evaluate_model()
+            model.evaluate_model(False, eval_packages=eval_packages)
             print(f"Saving {model_name}")
             model.save()

epdb/management/commands/dump_enviformer.py

@@ -0,0 +1,59 @@
+import json
+import os
+import tarfile
+from tempfile import TemporaryDirectory
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import EnviFormer
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "model",
+            type=str,
+            help="Model UUID of the Model to Dump",
+        )
+        parser.add_argument("--output", type=str)
+
+    def package_dict_and_folder(self, dict_data, folder_path, output_path):
+        with TemporaryDirectory() as tmpdir:
+            dict_filename = os.path.join(tmpdir, "data.json")
+
+            with open(dict_filename, "w", encoding="utf-8") as f:
+                json.dump(dict_data, f, indent=2)
+
+            with tarfile.open(output_path, "w:gz") as tar:
+                tar.add(dict_filename, arcname="data.json")
+                tar.add(folder_path, arcname=os.path.basename(folder_path))
+
+            os.remove(dict_filename)
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        output = options["output"]
+
+        if os.path.exists(output):
+            raise ValueError(f"Output file {output} already exists")
+
+        model = EnviFormer.objects.get(uuid=options["model"])
+
+        data = {
+            "uuid": str(model.uuid),
+            "name": model.name,
+            "description": model.description,
+            "kv": model.kv,
+            "data_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "eval_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "threshold": model.threshold,
+            "eval_results": model.eval_results,
+            "multigen_eval": model.multigen_eval,
+            "model_status": model.model_status,
+        }
+
+        model_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid))
+
+        self.package_dict_and_folder(data, model_folder, output)

epdb/management/commands/load_enviformer.py

@@ -0,0 +1,81 @@
+import json
+import os
+import shutil
+import tarfile
+from tempfile import TemporaryDirectory
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import EnviFormer, Package
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "input",
+            type=str,
+            help=".tar.gz file containing the Model dump.",
+        )
+        parser.add_argument(
+            "package",
+            type=str,
+            help="Package UUID where the Model should be loaded to.",
+        )
+
+    def read_dict_and_folder_from_archive(self, archive_path, extract_to="extracted_folder"):
+        with tarfile.open(archive_path, "r:gz") as tar:
+            tar.extractall(extract_to)
+
+            dict_path = os.path.join(extract_to, "data.json")
+
+            if not os.path.exists(dict_path):
+                raise FileNotFoundError("data.json not found in the archive.")
+
+            with open(dict_path, "r", encoding="utf-8") as f:
+                data_dict = json.load(f)
+
+            extracted_items = os.listdir(extract_to)
+            folders = [item for item in extracted_items if item != "data.json"]
+            folder_path = os.path.join(extract_to, folders[0]) if folders else None
+
+        return data_dict, folder_path
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        if not os.path.exists(options["input"]):
+            raise ValueError(f"Input file {options['input']} does not exist.")
+
+        target_package = Package.objects.get(uuid=options["package"])
+
+        with TemporaryDirectory() as tmpdir:
+            data, folder = self.read_dict_and_folder_from_archive(options["input"], tmpdir)
+
+            model = EnviFormer()
+            model.package = target_package
+            # model.uuid = data["uuid"]
+            model.name = data["name"]
+            model.description = data["description"]
+            model.kv = data["kv"]
+            model.threshold = float(data["threshold"])
+            model.eval_results = data["eval_results"]
+            model.multigen_eval = data["multigen_eval"]
+            model.model_status = data["model_status"]
+            model.save()
+
+            for p_uuid in data["data_packages_uuids"]:
+                p = Package.objects.get(uuid=p_uuid)
+                model.data_packages.add(p)
+
+            for p_uuid in data["eval_packages_uuids"]:
+                p = Package.objects.get(uuid=p_uuid)
+                model.eval_packages.add(p)
+
+            target_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid))
+
+            shutil.copytree(folder, target_folder)
+            os.rename(
+                os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{data['uuid']}.ckpt"),
+                os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{model.uuid}.ckpt"),
+            )

epdb/management/commands/localize_urls.py

@@ -1,8 +1,10 @@
 from django.apps import apps
 from django.core.management.base import BaseCommand
 
-from django.db.models import F, Value
+from django.db.models import F, Value, TextField, JSONField
-from django.db.models.functions import Replace
+from django.db.models.functions import Replace, Cast
+
+from epdb.models import EnviPathModel
 
 
 class Command(BaseCommand):
@@ -41,6 +43,7 @@ class Command(BaseCommand):
             "RuleBasedRelativeReasoning",
             "EnviFormer",
             "ApplicabilityDomain",
+            "EnzymeLink",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
@@ -48,3 +51,14 @@ class Command(BaseCommand):
             obj_cls.objects.update(
                 url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
             )
+            if issubclass(obj_cls, EnviPathModel):
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
+                )

epdb/management/commands/update_job_logs.py

@@ -0,0 +1,38 @@
+from datetime import date, timedelta
+
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import JobLog
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--cleanup",
+            type=int,
+            default=None,
+            help="Remove all logs older than this number of days. Default is None, which does not remove any logs.",
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        if options["cleanup"] is not None:
+            cleanup_dt = date.today() - timedelta(days=options["cleanup"])
+            print(JobLog.objects.filter(created__lt=cleanup_dt).delete())
+
+        logs = JobLog.objects.filter(status="INITIAL")
+        print(f"Found {logs.count()} logs to update")
+        updated = 0
+        for log in logs:
+            res = log.check_for_update()
+            if res:
+                updated += 1
+
+        print(f"Updated {updated} logs")
+
+        from django.db.models import Count
+
+        qs = JobLog.objects.values("status").annotate(total=Count("status"))
+        for r in qs:
+            print(r["status"], r["total"])

epdb/migrations/0008_enzymelink.py

@@ -0,0 +1,64 @@
+# Generated by Django 5.2.7 on 2025-10-10 06:58
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="EnzymeLink",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "uuid",
+                    models.UUIDField(
+                        default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
+                    ),
+                ),
+                ("name", models.TextField(default="no name", verbose_name="Name")),
+                (
+                    "description",
+                    models.TextField(default="no description", verbose_name="Descriptions"),
+                ),
+                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
+                ("kv", models.JSONField(blank=True, default=dict, null=True)),
+                ("ec_number", models.TextField(verbose_name="EC Number")),
+                ("classification_level", models.IntegerField(verbose_name="Classification Level")),
+                ("linking_method", models.TextField(verbose_name="Linking Method")),
+                ("edge_evidence", models.ManyToManyField(to="epdb.edge")),
+                ("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
+                (
+                    "rule",
+                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

epdb/migrations/0009_joblog.py

@@ -0,0 +1,66 @@
+# Generated by Django 5.2.7 on 2025-10-27 09:39
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0008_enzymelink"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="JobLog",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                ("task_id", models.UUIDField(unique=True)),
+                ("job_name", models.TextField()),
+                (
+                    "status",
+                    models.CharField(
+                        choices=[
+                            ("INITIAL", "Initial"),
+                            ("SUCCESS", "Success"),
+                            ("FAILURE", "Failure"),
+                            ("REVOKED", "Revoked"),
+                            ("IGNORED", "Ignored"),
+                        ],
+                        default="INITIAL",
+                        max_length=20,
+                    ),
+                ),
+                ("done_at", models.DateTimeField(blank=True, default=None, null=True)),
+                ("task_result", models.TextField(blank=True, default=None, null=True)),
+                (
+                    "user",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

epdb/models.py

@@ -310,7 +310,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="ChEBI"),
-                    "placeholder": "ChEBI ID without prefix e.g. 12345",
+                    "placeholder": "ChEBI ID without prefix e.g. 10576",
                 },
             ],
             "structure": [
@@ -328,7 +328,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="ChEBI"),
-                    "placeholder": "ChEBI ID without prefix e.g. 12345",
+                    "placeholder": "ChEBI ID without prefix e.g. 10576",
                 },
             ],
             "reaction": [
@@ -342,7 +342,7 @@ class ExternalDatabase(TimeStampedModel):
                 },
                 {
                     "database": ExternalDatabase.objects.get(name="UniProt"),
-                    "placeholder": "Query ID for UniPro e.g. rhea:12345",
+                    "placeholder": "Query ID for UniProt e.g. rhea:12345",
                 },
             ],
         }
@@ -477,7 +477,7 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
         return self.add_external_identifier("CAS", cas_number)
 
     def get_pubchem_identifiers(self):
-        return self.get_external_identifier("PubChem Compound") or self.get_external_identifier(
+        return self.get_external_identifier("PubChem Compound") | self.get_external_identifier(
             "PubChem Substance"
         )
 
@@ -494,6 +494,20 @@ class ChemicalIdentifierMixin(ExternalIdentifierMixin):
         return self.get_external_identifier("CAS")
 
 
+class KEGGIdentifierMixin(ExternalIdentifierMixin):
+    @property
+    def kegg_reaction_links(self):
+        return self.get_external_identifier("KEGG Reaction")
+
+    def add_kegg_reaction_id(self, kegg_id):
+        return self.add_external_identifier(
+            "KEGG Reaction", kegg_id, f"https://www.genome.jp/entry/{kegg_id}"
+        )
+
+    class Meta:
+        abstract = True
+
+
 class ReactionIdentifierMixin(ExternalIdentifierMixin):
     class Meta:
         abstract = True
@@ -1014,6 +1028,26 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
         return self.compound.default_structure == self
 
 
+class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
+    rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
+    ec_number = models.TextField(blank=False, null=False, verbose_name="EC Number")
+    classification_level = models.IntegerField(
+        blank=False, null=False, verbose_name="Classification Level"
+    )
+    linking_method = models.TextField(blank=False, null=False, verbose_name="Linking Method")
+
+    reaction_evidence = models.ManyToManyField("epdb.Reaction")
+    edge_evidence = models.ManyToManyField("epdb.Edge")
+
+    external_identifiers = GenericRelation("ExternalIdentifier")
+
+    def _url(self):
+        return "{}/enzymelink/{}".format(self.rule.url, self.uuid)
+
+    def get_group(self) -> str:
+        return ".".join(self.ec_number.split(".")[:3]) + ".-"
+
+
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
         "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
@@ -1095,6 +1129,18 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
 
         return new_rule
 
+    def enzymelinks(self):
+        return self.enzymelink_set.all()
+
+    def get_grouped_enzymelinks(self):
+        res = defaultdict(list)
+
+        for el in self.enzymelinks():
+            key = ".".join(el.ec_number.split(".")[:3]) + ".-"
+            res[key].append(el)
+
+        return dict(res)
+
 
 class SimpleRule(Rule):
     pass
@@ -1437,6 +1483,16 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
             id__in=Edge.objects.filter(edge_label=self).values("pathway_id")
         ).order_by("name")
 
+    def get_related_enzymes(self):
+        res = []
+        edges = Edge.objects.filter(edge_label=self)
+        for e in edges:
+            for scen in e.scenarios.all():
+                for ai in scen.additional_information.keys():
+                    if ai == "Enzyme":
+                        res.extend(scen.additional_information[ai])
+        return res
+
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
@@ -2169,10 +2225,18 @@ class PackageBasedModel(EPModel):
         self.model_status = self.BUILT_NOT_EVALUATED
         self.save()
 
-    def evaluate_model(self):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
+        if multigen:
+            self.multigen_eval = multigen
+            self.save()
+
+        if eval_packages is not None:
+            for p in eval_packages:
+                self.eval_packages.add(p)
+
         self.model_status = self.EVALUATING
         self.save()
 
@@ -2469,7 +2533,6 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
         package: "Package",
         rule_packages: List["Package"],
         data_packages: List["Package"],
-        eval_packages: List["Package"],
         threshold: float = 0.5,
         min_count: int = 10,
         max_count: int = 0,
@@ -2518,10 +2581,6 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
             for p in rule_packages:
                 rbrr.data_packages.add(p)
 
-        if eval_packages:
-            for p in eval_packages:
-                rbrr.eval_packages.add(p)
-
         rbrr.save()
 
         return rbrr
@@ -2576,7 +2635,6 @@ class MLRelativeReasoning(PackageBasedModel):
         package: "Package",
         rule_packages: List["Package"],
         data_packages: List["Package"],
-        eval_packages: List["Package"],
         threshold: float = 0.5,
         name: "str" = None,
         description: str = None,
@@ -2616,10 +2674,6 @@ class MLRelativeReasoning(PackageBasedModel):
             for p in rule_packages:
                 mlrr.data_packages.add(p)
 
-        if eval_packages:
-            for p in eval_packages:
-                mlrr.eval_packages.add(p)
-
         if build_app_domain:
             ad = ApplicabilityDomain.create(
                 mlrr,
@@ -2939,7 +2993,6 @@ class EnviFormer(PackageBasedModel):
     def create(
         package: "Package",
         data_packages: List["Package"],
-        eval_packages: List["Package"],
         threshold: float = 0.5,
         name: "str" = None,
         description: str = None,
@@ -2972,10 +3025,6 @@ class EnviFormer(PackageBasedModel):
         for p in data_packages:
             mod.data_packages.add(p)
 
-        if eval_packages:
-            for p in eval_packages:
-                mod.eval_packages.add(p)
-
         # if build_app_domain:
         #     ad = ApplicabilityDomain.create(mod, app_domain_num_neighbours, app_domain_reliability_threshold,
         #                                     app_domain_local_compatibility_threshold)
@@ -2989,7 +3038,8 @@ class EnviFormer(PackageBasedModel):
         from enviformer import load
 
         ckpt = os.path.join(s.MODEL_DIR, "enviformer", str(self.uuid), f"{self.uuid}.ckpt")
-        return load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt)
+        mod = load(device=s.ENVIFORMER_DEVICE, ckpt_path=ckpt)
+        return mod
 
     def predict(self, smiles) -> List["PredictionResult"]:
         return self.predict_batch([smiles])[0]
@@ -3003,8 +3053,12 @@ class EnviFormer(PackageBasedModel):
             for smiles in smiles_list
         ]
         logger.info(f"Submitting {canon_smiles} to {self.name}")
+        start = datetime.now()
         products_list = self.model.predict_batch(canon_smiles)
-        logger.info(f"Got results {products_list}")
+        end = datetime.now()
+        logger.info(
+            f"Prediction took {(end - start).total_seconds():.2f} seconds. Got results {products_list}"
+        )
 
         results = []
         for products in products_list:
@@ -3031,6 +3085,7 @@ class EnviFormer(PackageBasedModel):
 
         start = datetime.now()
         # Standardise reactions for the training data, EnviFormer ignores stereochemistry currently
+        co2 = {"C(=O)=O", "O=C=O"}
         ds = []
         for reaction in self._get_reactions():
             educts = ".".join(
@@ -3045,7 +3100,8 @@ class EnviFormer(PackageBasedModel):
                     for smile in reaction.products.all()
                 ]
             )
-            ds.append(f"{educts}>>{products}")
+            if products not in co2:
+                ds.append(f"{educts}>>{products}")
 
         end = datetime.now()
         logger.debug(f"build_dataset took {(end - start).total_seconds()} seconds")
@@ -3081,10 +3137,18 @@ class EnviFormer(PackageBasedModel):
         args = {"clz": "EnviFormer"}
         return args
 
-    def evaluate_model(self):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
+        if multigen:
+            self.multigen_eval = multigen
+            self.save()
+
+        if eval_packages is not None:
+            for p in eval_packages:
+                self.eval_packages.add(p)
+
         self.model_status = self.EVALUATING
         self.save()
 
@@ -3241,7 +3305,7 @@ class EnviFormer(PackageBasedModel):
 
             ds = self.load_dataset()
             n_splits = 20
-            shuff = ShuffleSplit(n_splits=n_splits, test_size=0.25, random_state=42)
+            shuff = ShuffleSplit(n_splits=n_splits, test_size=0.1, random_state=42)
 
             # Single gen eval is done in one loop of train then evaluate rather than storing all n_splits trained models
             # this helps reduce the memory footprint.
@@ -3309,7 +3373,7 @@ class EnviFormer(PackageBasedModel):
                 # Compute splits of the collected pathway and evaluate. Like single gen we train and evaluate in each
                 # iteration instead of storing all trained models.
                 for split_id, (train, test) in enumerate(
-                    ShuffleSplit(n_splits=n_splits, test_size=0.25, random_state=42).split(pathways)
+                    ShuffleSplit(n_splits=n_splits, test_size=0.1, random_state=42).split(pathways)
                 ):
                     train_pathways = [pathways[i] for i in train]
                     test_pathways = [pathways[i] for i in test]
@@ -3608,3 +3672,53 @@ class Setting(EnviPathModel):
             self.public = True
         self.global_default = True
         self.save()
+
+
+class JobLogStatus(models.TextChoices):
+    INITIAL = "INITIAL", "Initial"
+    SUCCESS = "SUCCESS", "Success"
+    FAILURE = "FAILURE", "Failure"
+    REVOKED = "REVOKED", "Revoked"
+    IGNORED = "IGNORED", "Ignored"
+
+
+class JobLog(TimeStampedModel):
+    user = models.ForeignKey("epdb.User", models.CASCADE)
+    task_id = models.UUIDField(unique=True)
+    job_name = models.TextField(null=False, blank=False)
+    status = models.CharField(
+        max_length=20,
+        choices=JobLogStatus.choices,
+        default=JobLogStatus.INITIAL,
+    )
+
+    done_at = models.DateTimeField(null=True, blank=True, default=None)
+    task_result = models.TextField(null=True, blank=True, default=None)
+
+    def check_for_update(self):
+        async_res = self.get_result()
+        new_status = async_res.state
+
+        TERMINAL_STATES = [
+            "SUCCESS",
+            "FAILURE",
+            "REVOKED",
+            "IGNORED",
+        ]
+
+        if new_status != self.status and new_status in TERMINAL_STATES:
+            self.status = new_status
+            self.done_at = async_res.date_done
+
+            if new_status == "SUCCESS":
+                self.task_result = async_res.result
+
+            self.save()
+
+            return True
+        return False
+
+    def get_result(self):
+        from celery.result import AsyncResult
+
+        return AsyncResult(str(self.task_id))

epdb/tasks.py

@@ -1,12 +1,56 @@
 import logging
-from typing import Optional
+from datetime import datetime
+from typing import Callable, Optional
+from uuid import uuid4
 
 from celery import shared_task
-from epdb.models import Pathway, Node, EPModel, Setting
+from celery.utils.functional import LRUCache
-from epdb.logic import SPathway
 
+from epdb.logic import SPathway
+from epdb.models import EPModel, JobLog, Node, Package, Pathway, Setting, User
 
 logger = logging.getLogger(__name__)
+ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
+
+
+def get_ml_model(model_pk: int):
+    if model_pk not in ML_CACHE:
+        ML_CACHE[model_pk] = EPModel.objects.get(id=model_pk)
+    return ML_CACHE[model_pk]
+
+
+def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
+    try:
+        x = job(*args, **kwargs)
+        log = JobLog()
+        log.user = user
+        log.task_id = uuid4()
+        log.job_name = job.__name__
+        log.status = "SUCCESS"
+        log.done_at = datetime.now()
+        log.task_result = str(x) if x else None
+        log.save()
+
+        return x
+    except Exception as e:
+        logger.exception(e)
+        raise e
+
+
+def dispatch(user: "User", job: Callable, *args, **kwargs):
+    try:
+        x = job.delay(*args, **kwargs)
+        log = JobLog()
+        log.user = user
+        log.task_id = x.task_id
+        log.job_name = job.__name__
+        log.status = "INITIAL"
+        log.save()
+
+        return x.result
+    except Exception as e:
+        logger.exception(e)
+        raise e
 
 
 @shared_task(queue="background")
@@ -16,7 +60,7 @@ def mul(a, b):
 
 @shared_task(queue="predict")
 def predict_simple(model_pk: int, smiles: str):
-    mod = EPModel.objects.get(id=model_pk)
+    mod = get_ml_model(model_pk)
     res = mod.predict(smiles)
     return res
 
@@ -26,17 +70,55 @@ def send_registration_mail(user_pk: int):
     pass
 
 
-@shared_task(queue="model")
+@shared_task(bind=True, queue="model")
-def build_model(model_pk: int):
+def build_model(self, model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
-    mod.build_dataset()
+
-    mod.build_model()
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=mod.url)
+
+    try:
+        mod.build_dataset()
+        mod.build_model()
+    except Exception as e:
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=mod.url
+            )
+
+        raise e
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=mod.url)
+
+    return mod.url
 
 
-@shared_task(queue="model")
+@shared_task(bind=True, queue="model")
-def evaluate_model(model_pk: int):
+def evaluate_model(self, model_pk: int, multigen: bool, package_pks: Optional[list] = None):
+    packages = None
+
+    if package_pks:
+        packages = Package.objects.filter(pk__in=package_pks)
+
     mod = EPModel.objects.get(id=model_pk)
-    mod.evaluate_model()
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=mod.url)
+
+    try:
+        mod.evaluate_model(multigen, eval_packages=packages)
+    except Exception as e:
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=mod.url
+            )
+
+        raise e
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=mod.url)
+
+    return mod.url
 
 
 @shared_task(queue="model")
@@ -45,16 +127,26 @@ def retrain(model_pk: int):
     mod.retrain()
 
 
-@shared_task(queue="predict")
+@shared_task(bind=True, queue="predict")
 def predict(
-    pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None
+    self,
+    pw_pk: int,
+    pred_setting_pk: int,
+    limit: Optional[int] = None,
+    node_pk: Optional[int] = None,
 ) -> Pathway:
     pw = Pathway.objects.get(id=pw_pk)
     setting = Setting.objects.get(id=pred_setting_pk)
+    # If the setting has a model add/restore it from the cache
+    if setting.model is not None:
+        setting.model = get_ml_model(setting.model.pk)
 
     pw.kv.update(**{"status": "running"})
     pw.save()
 
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=pw.url)
+
     try:
         # regular prediction
         if limit is not None:
@@ -79,7 +171,18 @@ def predict(
     except Exception as e:
         pw.kv.update({"status": "failed"})
         pw.save()
+
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=pw.url
+            )
+
         raise e
 
     pw.kv.update(**{"status": "completed"})
     pw.save()
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=pw.url)
+
+    return pw.url

epdb/templatetags/envipytags.py

@@ -1,8 +1,21 @@
 from django import template
+from pydantic import AnyHttpUrl, ValidationError
+from pydantic.type_adapter import TypeAdapter
 
 register = template.Library()
 
+url_adapter = TypeAdapter(AnyHttpUrl)
+
 
 @register.filter
 def classname(obj):
     return obj.__class__.__name__
+
+
+@register.filter
+def is_url(value):
+    try:
+        url_adapter.validate_python(value)
+        return True
+    except ValidationError:
+        return False

epdb/urls.py

@@ -1,5 +1,5 @@
-from django.urls import path, re_path
 from django.contrib.auth import views as auth_views
+from django.urls import path, re_path
 
 from . import views as v
 
@@ -88,20 +88,36 @@ urlpatterns = [
         v.package_rule,
         name="package rule detail",
     ),
-    re_path(
+    # re_path(
-        rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
+    #     rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
-        v.package_rule,
+    #     v.package_rule,
-        name="package rule detail",
+    #     name="package rule detail",
-    ),
+    # ),
     re_path(
         rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$",
         v.package_rule,
         name="package rule detail",
     ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    # EnzymeLinks
     re_path(
-        rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
-        v.package_rule,
+        v.package_rule_enzymelink,
-        name="package rule detail",
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
     ),
     # Reaction
     re_path(
@@ -174,15 +190,16 @@ urlpatterns = [
     re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
     re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
     re_path(r"^depict$", v.depict, name="depict"),
+    re_path(r"^jobs", v.jobs, name="jobs"),
     # OAuth Stuff
     path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
     # Static Pages
-    re_path(r"^terms$", v.terms_of_use, name="terms_of_use"),
+    re_path(r"^terms$", v.static_terms_of_use, name="terms_of_use"),
-    re_path(r"^privacy$", v.privacy_policy, name="privacy_policy"),
+    re_path(r"^privacy$", v.static_privacy_policy, name="privacy_policy"),
-    re_path(r"^cookie-policy$", v.cookie_policy, name="cookie_policy"),
+    re_path(r"^cookie-policy$", v.static_cookie_policy, name="cookie_policy"),
-    re_path(r"^about$", v.about_us, name="about_us"),
+    re_path(r"^about$", v.static_about_us, name="about_us"),
-    re_path(r"^contact$", v.contact_support, name="contact_support"),
+    re_path(r"^contact$", v.static_contact_support, name="contact_support"),
-    re_path(r"^jobs$", v.jobs, name="jobs"),
+    re_path(r"^jobs$", v.static_jobs, name="jobs"),
-    re_path(r"^cite$", v.cite, name="cite"),
+    re_path(r"^cite$", v.static_cite, name="cite"),
-    re_path(r"^legal$", v.legal, name="legal"),
+    re_path(r"^legal$", v.static_legal, name="legal"),
 ]

epdb/views.py

@@ -46,6 +46,8 @@ from .models import (
     Edge,
     ExternalDatabase,
     ExternalIdentifier,
+    EnzymeLink,
+    JobLog,
 )
 
 logger = logging.getLogger(__name__)
@@ -756,8 +758,8 @@ def package_models(request, package_uuid):
         context["unreviewed_objects"] = unreviewed_model_qs
 
         context["model_types"] = {
-            "ML Relative Reasoning": "ml-relative-reasoning",
+            "ML Relative Reasoning": "mlrr",
-            "Rule Based Relative Reasoning": "rule-based-relative-reasoning",
+            "Rule Based Relative Reasoning": "rbrr",
         }
 
         if s.FLAGS.get("ENVIFORMER", False):
@@ -777,69 +779,67 @@ def package_models(request, package_uuid):
 
         model_type = request.POST.get("model-type")
 
+        # Generic fields for ML and Rule Based
+        rule_packages = request.POST.getlist("model-rule-packages")
+        data_packages = request.POST.getlist("model-data-packages")
+
+        # Generic params
+        params = {
+            "package": current_package,
+            "name": name,
+            "description": description,
+            "data_packages": [
+                PackageManager.get_package_by_url(current_user, p) for p in data_packages
+            ],
+        }
+
         if model_type == "enviformer":
-            threshold = float(request.POST.get(f"{model_type}-threshold", 0.5))
+            threshold = float(request.POST.get("model-threshold", 0.5))
+            params["threshold"] = threshold
 
-            mod = EnviFormer.create(current_package, name, description, threshold)
+            mod = EnviFormer.create(**params)
+        elif model_type == "mlrr":
+            # ML Specific
+            threshold = float(request.POST.get("model-threshold", 0.5))
+            # TODO handle additional fingerprinter
+            # fingerprinter = request.POST.get("model-fingerprinter")
 
-        elif model_type == "ml-relative-reasoning" or model_type == "rule-based-relative-reasoning":
+            params["rule_packages"] = [
-            # Generic fields for ML and Rule Based
+                PackageManager.get_package_by_url(current_user, p) for p in rule_packages
-            rule_packages = request.POST.getlist("package-based-relative-reasoning-rule-packages")
+            ]
-            data_packages = request.POST.getlist("package-based-relative-reasoning-data-packages")
-            eval_packages = request.POST.getlist(
-                "package-based-relative-reasoning-evaluation-packages", []
-            )
 
-            # Generic params
+            # App Domain related parameters
-            params = {
+            build_ad = request.POST.get("build-app-domain", False) == "on"
-                "package": current_package,
+            num_neighbors = request.POST.get("num-neighbors", 5)
-                "name": name,
+            reliability_threshold = request.POST.get("reliability-threshold", 0.5)
-                "description": description,
+            local_compatibility_threshold = request.POST.get("local-compatibility-threshold", 0.5)
-                "rule_packages": [
-                    PackageManager.get_package_by_url(current_user, p) for p in rule_packages
-                ],
-                "data_packages": [
-                    PackageManager.get_package_by_url(current_user, p) for p in data_packages
-                ],
-                "eval_packages": [
-                    PackageManager.get_package_by_url(current_user, p) for p in eval_packages
-                ],
-            }
 
-            if model_type == "ml-relative-reasoning":
+            params["threshold"] = threshold
-                # ML Specific
+            # params['fingerprinter'] = fingerprinter
-                threshold = float(request.POST.get(f"{model_type}-threshold", 0.5))
+            params["build_app_domain"] = build_ad
-                # TODO handle additional fingerprinter
+            params["app_domain_num_neighbours"] = num_neighbors
-                # fingerprinter = request.POST.get(f"{model_type}-fingerprinter")
+            params["app_domain_reliability_threshold"] = reliability_threshold
+            params["app_domain_local_compatibility_threshold"] = local_compatibility_threshold
 
-                # App Domain related parameters
+            mod = MLRelativeReasoning.create(**params)
-                build_ad = request.POST.get("build-app-domain", False) == "on"
+        elif model_type == "rbrr":
-                num_neighbors = request.POST.get("num-neighbors", 5)
+            params["rule_packages"] = [
-                reliability_threshold = request.POST.get("reliability-threshold", 0.5)
+                PackageManager.get_package_by_url(current_user, p) for p in rule_packages
-                local_compatibility_threshold = request.POST.get(
+            ]
-                    "local-compatibility-threshold", 0.5
-                )
 
-                params["threshold"] = threshold
+            mod = RuleBasedRelativeReasoning.create(**params)
-                # params['fingerprinter'] = fingerprinter
+        elif s.FLAGS.get("PLUGINS", False) and model_type in s.CLASSIFIER_PLUGINS.values():
-                params["build_app_domain"] = build_ad
+            pass
-                params["app_domain_num_neighbours"] = num_neighbors
-                params["app_domain_reliability_threshold"] = reliability_threshold
-                params["app_domain_local_compatibility_threshold"] = local_compatibility_threshold
-
-                mod = MLRelativeReasoning.create(**params)
-            else:
-                mod = RuleBasedRelativeReasoning.create(**params)
-
-            from .tasks import build_model
-
-            build_model.delay(mod.pk)
         else:
             return error(
                 request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
             )
-        return redirect(mod.url)
 
+        from .tasks import dispatch, build_model
+
+        dispatch(current_user, build_model, mod.pk)
+
+        return redirect(mod.url)
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -867,6 +867,10 @@ def package_model(request, package_uuid, model_uuid):
                 return JsonResponse({"error": f'"{smiles}" is not a valid SMILES'}, status=400)
 
             if classify:
+                from epdb.tasks import dispatch_eager, predict_simple
+
+                res = dispatch_eager(current_user, predict_simple, current_model.pk, stand_smiles)
+
                 pred_res = current_model.predict(stand_smiles)
                 res = []
 
@@ -911,9 +915,25 @@ def package_model(request, package_uuid, model_uuid):
                 current_model.delete()
                 return redirect(current_package.url + "/model")
             elif hidden == "evaluate":
-                from .tasks import evaluate_model
+                from .tasks import dispatch, evaluate_model
+
+                eval_type = request.POST.get("model-evaluation-type")
+
+                if eval_type not in ["sg", "mg"]:
+                    return error(
+                        request,
+                        "Invalid evaluation type",
+                        f'Evaluation type "{eval_type}" is not supported. Only "sg" and "mg" are supported.',
+                    )
+
+                multigen = eval_type == "mg"
+
+                eval_packages = request.POST.getlist("model-evaluation-packages")
+                eval_package_ids = [
+                    PackageManager.get_package_by_url(current_user, p).id for p in eval_packages
+                ]
+                dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
 
-                evaluate_model.delay(current_model.pk)
                 return redirect(current_model.url)
             else:
                 return HttpResponseBadRequest()
@@ -1253,7 +1273,16 @@ def package_compound_structures(request, package_uuid, compound_uuid):
         structure_smiles = request.POST.get("structure-smiles")
         structure_description = request.POST.get("structure-description")
 
-        cs = current_compound.add_structure(structure_smiles, structure_name, structure_description)
+        try:
+            cs = current_compound.add_structure(
+                structure_smiles, structure_name, structure_description
+            )
+        except ValueError:
+            return error(
+                request,
+                "Adding structure failed!",
+                "The structure could not be added as normalized structures don't match!",
+            )
 
         return redirect(cs.url)
 
@@ -1456,12 +1485,20 @@ def package_rule(request, package_uuid, rule_uuid):
                 logger.info(
                     f"Rule {current_rule.uuid} returned multiple product sets on {smiles}, picking the first one."
                 )
-
+            # Some Rules are touching unrelated areas which might result in ~ indicating
-            smirks = f"{stand_smiles}>>{'.'.join(sorted(res[0]))}"
+            # any bond (-, =, #). For drawing we need a concrete bond. -> use single bond
+            product_smiles = [x.replace("~", "-") for x in res[0]]
+            smirks = f"{stand_smiles}>>{'.'.join(sorted(product_smiles))}"
             # Usually the functional groups are a mapping of fg -> count
             # As we are doing it on the fly here fake a high count to ensure that its properly highlighted
-            educt_functional_groups = {x: 1000 for x in current_rule.reactants_smarts}
+
-            product_functional_groups = {x: 1000 for x in current_rule.products_smarts}
+            if isinstance(current_rule, SimpleAmbitRule):
+                educt_functional_groups = {current_rule.reactants_smarts: 1000}
+                product_functional_groups = {current_rule.products_smarts: 1000}
+            else:
+                educt_functional_groups = {x: 1000 for x in current_rule.reactants_smarts}
+                product_functional_groups = {x: 1000 for x in current_rule.products_smarts}
+
             return HttpResponse(
                 IndigoUtils.smirks_to_svg(
                     smirks,
@@ -1531,6 +1568,32 @@ def package_rule(request, package_uuid, rule_uuid):
         return HttpResponseNotAllowed(["GET", "POST"])
 
 
+@package_permission_required()
+def package_rule_enzymelink(request, package_uuid, rule_uuid, enzymelink_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+    current_rule = Rule.objects.get(package=current_package, uuid=rule_uuid)
+    current_enzymelink = EnzymeLink.objects.get(rule=current_rule, uuid=enzymelink_uuid)
+
+    if request.method == "GET":
+        context = get_base_context(request)
+
+        context["title"] = f"enviPath - {current_package.name} - {current_rule.name}"
+
+        context["meta"]["current_package"] = current_package
+        context["object_type"] = "enzyme"
+        context["breadcrumbs"] = breadcrumbs(
+            current_package, "rule", current_rule, "enzymelink", current_enzymelink
+        )
+
+        context["enzymelink"] = current_enzymelink
+        context["current_object"] = current_enzymelink
+
+        return render(request, "objects/enzymelink.html", context)
+
+    return HttpResponseNotAllowed(["GET"])
+
+
 @package_permission_required()
 def package_reactions(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -1768,9 +1831,9 @@ def package_pathways(request, package_uuid):
             pw.setting = prediction_setting
             pw.save()
 
-            from .tasks import predict
+            from .tasks import dispatch, predict
 
-            predict.delay(pw.pk, prediction_setting.pk, limit=limit)
+            dispatch(current_user, predict, pw.pk, prediction_setting.pk, limit=limit)
 
         return redirect(pw.url)
 
@@ -1889,10 +1952,16 @@ def package_pathway(request, package_uuid, pathway_uuid):
         if node_url:
             n = current_pathway.get_node(node_url)
 
-            from .tasks import predict
+            from .tasks import dispatch, predict
+
+            dispatch(
+                current_user,
+                predict,
+                current_pathway.pk,
+                current_pathway.setting.pk,
+                node_pk=n.pk,
+            )
 
-            # Dont delay?
-            predict(current_pathway.pk, current_pathway.setting.pk, node_pk=n.pk)
             return JsonResponse({"success": current_pathway.url})
 
         return HttpResponseBadRequest()
@@ -1969,9 +2038,42 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
     if request.method == "GET":
         is_image_request = request.GET.get("image")
+        is_highlight_request = request.GET.get("highlight", False)
+        is_highlight_reactivity = request.GET.get("highlightReactivity", False)
         if is_image_request:
             if is_image_request == "svg":
-                svg_data = current_node.as_svg
+                # TODO optimize this chain
+                if is_highlight_request:
+                    # User functional groups covered by the model training data
+                    fgs = {}
+                    if current_pathway.setting:
+                        if current_pathway.setting.model:
+                            if current_pathway.setting.model.app_domain:
+                                fgs = current_pathway.setting.model.app_domain.functional_groups
+
+                    svg_data = IndigoUtils.mol_to_svg(
+                        current_node.default_node_label.smiles, functional_groups=fgs
+                    )
+                elif is_highlight_reactivity:
+                    # Use reactant smarts to show all reaction sites
+                    # set a high count to obtain a strong color
+                    ad_data = current_node.get_app_domain_assessment_data()
+                    fgs = {}
+                    for t in ad_data.get("assessment", {}).get("transformations", []):
+                        r = Rule.objects.get(url=t["rule"]["url"])
+
+                        if isinstance(r, SimpleAmbitRule):
+                            fgs[r.reactants_smarts] = 1000
+                        else:
+                            for sr in r.srs:
+                                fgs[sr.reactants_smarts] = 1000
+
+                    svg_data = IndigoUtils.mol_to_svg(
+                        current_node.default_node_label.smiles, functional_groups=fgs
+                    )
+                else:
+                    svg_data = current_node.as_svg
+
                 return HttpResponse(svg_data, content_type="image/svg+xml")
 
         context = get_base_context(request)
@@ -2631,6 +2733,24 @@ def setting(request, setting_uuid):
     pass
 
 
+def jobs(request):
+    current_user = _anonymous_or_real(request)
+    context = get_base_context(request)
+
+    if request.method == "GET":
+        context["object_type"] = "joblog"
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Jobs": s.SERVER_URL + "/jobs"},
+        ]
+        if current_user.is_superuser:
+            context["jobs"] = JobLog.objects.all().order_by("-created")
+        else:
+            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+
+        return render(request, "collections/joblog.html", context)
+
+
 ###########
 # KETCHER #
 ###########
@@ -2705,49 +2825,49 @@ def userinfo(request):
 
 
 # Static Pages
-def terms_of_use(request):
+def static_terms_of_use(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Terms of Use"
     return render(request, "static/terms_of_use.html", context)
 
 
-def privacy_policy(request):
+def static_privacy_policy(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Privacy Policy"
     return render(request, "static/privacy_policy.html", context)
 
 
-def cookie_policy(request):
+def static_cookie_policy(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Cookie Policy"
     return render(request, "static/cookie_policy.html", context)
 
 
-def about_us(request):
+def static_about_us(request):
     context = get_base_context(request)
     context["title"] = "enviPath - About Us"
     return render(request, "static/about_us.html", context)
 
 
-def contact_support(request):
+def static_contact_support(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Contact & Support"
     return render(request, "static/contact.html", context)
 
 
-def jobs(request):
+def static_jobs(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Jobs & Careers"
     return render(request, "static/jobs.html", context)
 
 
-def cite(request):
+def static_cite(request):
     context = get_base_context(request)
     context["title"] = "enviPath - How to Cite"
     return render(request, "static/cite.html", context)
 
 
-def legal(request):
+def static_legal(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Legal Information"
     return render(request, "static/legal.html", context)

pyproject.toml

@@ -13,7 +13,7 @@ dependencies = [
     "django-oauth-toolkit>=3.0.1",
     "django-polymorphic>=4.1.0",
     "django-stubs>=5.2.4",
-    #"enviformer",
+    "enviformer",
     "envipy-additional-information",
     "envipy-ambit>=0.1.0",
     "envipy-plugins",
@@ -31,9 +31,9 @@ dependencies = [
 ]
 
 [tool.uv.sources]
-#enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
 envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
-envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.4"}
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7"}
 envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
 
 [dependency-groups]
@@ -45,6 +45,8 @@ dev = [
 [project.optional-dependencies]
 ms-login = ["msal>=1.33.0"]
 dev = [
+    "celery-stubs==0.1.3",
+    "django-stubs>=5.2.4",
     "poethepoet>=0.37.0",
     "pre-commit>=4.3.0",
     "ruff>=0.13.3",

static/js/pps.js

@@ -646,8 +646,8 @@ function handleAssessmentResponse(depict_url, data) {
     var reactivityCentersImgSrc = null;
 
     if (data['assessment']['node'] !== undefined) {
-        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>";
+        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlight=true'>";
-        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>"
+        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlightReactivity=true'>"
     } else {
         functionalGroupsImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">";
         reactivityCentersImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">"

static/js/pw.js

@@ -444,6 +444,13 @@ function serializeSVG(svgElement) {
         line.setAttribute("fill", style.fill);
     });
 
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
+        const style = getComputedStyle(line);
+        line.setAttribute("stroke", style.stroke);
+        line.setAttribute("stroke-width", style.strokeWidth);
+        line.setAttribute("fill", style.fill);
+    });
+
     const serializer = new XMLSerializer();
     let svgString = serializer.serializeToString(svgElement);
 
@@ -455,7 +462,26 @@ function serializeSVG(svgElement) {
     return svgString;
 }
 
+function shrinkSVG(svgSelector) {
+
+    const svg = d3.select(svgSelector);
+    const node = svg.node();
+
+    // Compute bounding box of everything inside the SVG
+    const bbox = node.getBBox();
+
+    const padding = 10;
+    svg.attr("viewBox",
+        `${bbox.x - padding} ${bbox.y - padding} ${bbox.width + 2 * padding} ${bbox.height + 2 * padding}`
+    )
+        .attr("width", bbox.width + 2 * padding)
+        .attr("height", bbox.height + 2 * padding);
+
+    return bbox;
+}
+
 function downloadSVG(svgElement, filename = 'chart.svg') {
+    shrinkSVG("#" + svgElement.id);
     const svgString = serializeSVG(svgElement);
     const blob = new Blob([svgString], {type: 'image/svg+xml;charset=utf-8'});
     const url = URL.createObjectURL(blob);

templates/collections/joblog.html

@@ -0,0 +1,71 @@
+{% extends "framework.html" %}
+{% load static %}
+{% load envipytags %}
+{% block content %}
+
+    <div class="panel-group" id="reviewListAccordion">
+        <div class="panel panel-default">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                Jobs
+            </div>
+            <div class="panel-body">
+                <p>
+                    Job Logs Desc
+                </p>
+
+            </div>
+
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
+                        Jobs
+                    </a>
+                </h4>
+            </div>
+            <div id="jobs"
+                 class="panel-collapse collapse in">
+                <div class="panel-body list-group-item" id="job-content">
+                    <table class="table table-bordered table-hover">
+                        <tr style="background-color: rgba(0, 0, 0, 0.08);">
+                            <th scope="col">ID</th>
+                            <th scope="col">Name</th>
+                            <th scope="col">Status</th>
+                            <th scope="col">Queued</th>
+                            <th scope="col">Done</th>
+                            <th scope="col">Result</th>
+                        </tr>
+                        <tbody>
+                        {% for job in jobs %}
+                            <tr>
+                                <td>{{ job.task_id }}</td>
+                                <td>{{ job.job_name }}</td>
+                                <td>{{ job.status }}</td>
+                                <td>{{ job.created }}</td>
+                                <td>{{ job.done_at }}</td>
+                                {% if job.task_result and job.task_result|is_url == True %}
+                                    <td><a href="{{ job.task_result }}">Result</a></td>
+                                {% elif job.task_result %}
+                                    <td>{{ job.task_result|slice:"40" }}...</td>
+                                {% else %}
+                                    <td>Empty</td>
+                                {% endif %}
+                            </tr>
+                        {% endfor %}
+                        </tbody>
+                    </table>
+                </div>
+            </div>
+
+            <!-- Unreviewable objects such as User / Group / Setting -->
+            <ul class='list-group'>
+                {% for obj in objects %}
+                    {% if object_type == 'user' %}
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
+                    {% else %}
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                    {% endif %}
+                {% endfor %}
+            </ul>
+        </div>
+    </div>
+{% endblock content %}

templates/framework.html

@@ -242,21 +242,23 @@
     <div class="row">
         <div class="col-lg-12">
             <ul class="nav nav-pills nav-justified">
-                <li><a href="http://eawag.ch" target="_blank">
-                    <img id="image-ealogo"
-                         height="60"
-                         src='{% static "/images/ealogo.gif" %}'
-                         alt="Eawag"/>
-                </a>
-                </li>
                 <li>
                     <a href="http://ml.auckland.ac.nz" target="_blank">
-                        <img id="image-uoalogo"
+                        <img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
-                             height="60"
-                             src='{% static "/images/uoa.png" %}'
                              alt="The Univserity of Auckland"/>
                     </a>
                 </li>
+                <li>
+                    <a href="https://eawag.ch" target="_blank">
+                        <img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
+                    </a>
+                </li>
+                <li>
+                    <a href="https://www.uzh.ch/" target="_blank">
+                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
+                             alt="University of Zurich"/>
+                    </a>
+                </li>
             </ul>
         </div>
     </div>

templates/modals/collections/new_model_modal.html

@@ -18,113 +18,117 @@
                         prediction. You just need to set a name and the packages
                         you want the object to be based on. There are multiple types of models available.
                         For additional information have a look at our
-                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki &gt;&gt;</a>
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
+                            &gt;&gt;</a>
                     </div>
+                    <!-- Name -->
                     <label for="model-name">Name</label>
                     <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
+
+                    <!-- Description -->
                     <label for="model-description">Description</label>
                     <input id="model-description" name="model-description" class="form-control"
                            placeholder="Description"/>
+
+                    <!-- Model Type -->
                     <label for="model-type">Model Type</label>
                     <select id="model-type" name="model-type" class="form-control" data-width='100%'>
                         <option disabled selected>Select Model Type</option>
                         {% for k, v in model_types.items %}
-                        <option value="{{ v }}">{{ k }}</option>
+                            <option value="{{ v }}">{{ k }}</option>
                         {% endfor %}
                     </select>
-                    <!-- ML and Rule Based Based Form-->
+
-                    <div id="package-based-relative-reasoning-specific-form">
+                    <!-- Rule Packages -->
-                        <!-- Rule Packages -->
+                    <div id="rule-packages" class="ep-model-param mlrr rbrr">
-                        <label for="package-based-relative-reasoning-rule-packages">Rule Packages</label>
+                        <label for="model-rule-packages">Rule Packages</label>
-                        <select id="package-based-relative-reasoning-rule-packages" name="package-based-relative-reasoning-rule-packages"
+                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
+                                class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
-                            {% if obj.reviewed %}
+                                {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
-                            {% endif %}
+                                {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
-                            {% if not obj.reviewed %}
+                                {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
-                            {% endif %}
+                                {% endif %}
                             {% endfor %}
                         </select>
-                        <!-- Data Packages -->
-                        <label for="package-based-relative-reasoning-data-packages" >Data Packages</label>
-                        <select id="package-based-relative-reasoning-data-packages" name="package-based-relative-reasoning-data-packages"
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
-                            <option disabled>Reviewed Packages</option>
-                            {% for obj in meta.readable_packages %}
-                            {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
-                            {% endif %}
-                            {% endfor %}
-
-                            <option disabled>Unreviewed Packages</option>
-                            {% for obj in meta.readable_packages %}
-                            {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
-                            {% endif %}
-                            {% endfor %}
-                        </select>
-
-                        <div id="ml-relative-reasoning-specific-form">
-                            <!-- Fingerprinter -->
-                            <label for="ml-relative-reasoning-fingerprinter">Fingerprinter</label>
-                            <select id="ml-relative-reasoning-fingerprinter" name="ml-relative-reasoning-fingerprinter"
-                                    class="form-control">
-                                <option value="MACCS" selected>MACCS Fingerprinter</option>
-                            </select>
-                            {% if meta.enabled_features.PLUGINS and additional_descriptors %}
-                                <!-- Property Plugins go here -->
-                                <label for="ml-relative-reasoning-additional-fingerprinter">Additional Fingerprinter /
-                                    Descriptors</label>
-                                <select id="ml-relative-reasoning-additional-fingerprinter"
-                                        name="ml-relative-reasoning-additional-fingerprinter" class="form-control">
-                                    <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
-                                    {% for k, v in additional_descriptors.items %}
-                                        <option value="{{ v }}">{{ k }}</option>
-                                    {% endfor %}
-                                </select>
-                            {% endif %}
-
-                            <label for="ml-relative-reasoning-threshold">Threshold</label>
-                            <input type="number" min="0" max="1" step="0.05" value="0.5"
-                                   id="ml-relative-reasoning-threshold"
-                                   name="ml-relative-reasoning-threshold" class="form-control">
-                        </div>
-                    {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
-                        <!-- Build AD? -->
-                        <div class="checkbox">
-                            <label>
-                                <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
-                                Applicability Domain?
-                            </label>
-                        </div>
-                        <div id="ad-params" style="display:none">
-                            <!-- Num Neighbors -->
-                            <label for="num-neighbors">Number of Neighbors</label>
-                            <input id="num-neighbors" name="num-neighbors" type="number" class="form-control" value="5"
-                                   step="1" min="0" max="10">
-                            <!-- Local Compatibility -->
-                            <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                            <input id="local-compatibility-threshold" name="local-compatibility-threshold" type="number"
-                                   class="form-control" value="0.5" step="0.01" min="0" max="1">
-                            <!-- Reliability -->
-                            <label for="reliability-threshold">Reliability Threshold</label>
-                            <input id="reliability-threshold" name="reliability-threshold" type="number"
-                                   class="form-control" value="0.5" step="0.01" min="0" max="1">
-                        </div>
-                    {% endif %}
                     </div>
-                    <!-- EnviFormer-->
+
-                    <div id="enviformer-specific-form">
+                    <!-- Data Packages -->
-                        <label for="enviformer-threshold">Threshold</label>
+                    <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
-                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="enviformer-threshold"
+                        <label for="model-data-packages">Data Packages</label>
-                               name="enviformer-threshold" class="form-control">
+                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
+                                class="form-control" multiple data-width='100%'>
+                            <option disabled>Reviewed Packages</option>
+                            {% for obj in meta.readable_packages %}
+                                {% if obj.reviewed %}
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                {% endif %}
+                            {% endfor %}
+
+                            <option disabled>Unreviewed Packages</option>
+                            {% for obj in meta.readable_packages %}
+                                {% if not obj.reviewed %}
+                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                {% endif %}
+                            {% endfor %}
+                        </select>
+                    </div>
+
+                    <!-- Fingerprinter -->
+                    <div id="fingerprinter" class="ep-model-param mlrr">
+                        <label for="model-fingerprinter">Fingerprinter</label>
+                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
+                                class="form-control" multiple data-width='100%'>
+                            <option value="MACCS" selected>MACCS Fingerprinter</option>
+                            {% if meta.enabled_features.PLUGINS and additional_descriptors %}
+                                <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
+                                {% for k, v in additional_descriptors.items %}
+                                    <option value="{{ v }}">{{ k }}</option>
+                                {% endfor %}
+                            {% endif %}
+                        </select>
+                    </div>
+
+                    <!-- Threshold -->
+                    <div id="threshold" class="ep-model-param mlrr enviformer">
+                        <label for="model-threshold">Threshold</label>
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
+                               name="model-threshold" class="form-control">
+                    </div>
+
+                    <div id="appdomain" class="ep-model-param mlrr">
+                        {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
+                            <!-- Build AD? -->
+                            <div class="checkbox">
+                                <label>
+                                    <input type="checkbox" id="build-app-domain" name="build-app-domain">Also build an
+                                    Applicability Domain?
+                                </label>
+                            </div>
+                            <div id="ad-params" style="display:none">
+                                <!-- Num Neighbors -->
+                                <label for="num-neighbors">Number of Neighbors</label>
+                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
+                                       value="5"
+                                       step="1" min="0" max="10">
+                                <!-- Local Compatibility -->
+                                <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
+                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
+                                       type="number"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
+                                <!-- Reliability -->
+                                <label for="reliability-threshold">Reliability Threshold</label>
+                                <input id="reliability-threshold" name="reliability-threshold" type="number"
+                                       class="form-control" value="0.5" step="0.01" min="0" max="1">
+                            </div>
+                        {% endif %}
                     </div>
                 </form>
             </div>
@@ -137,53 +141,47 @@
 </div>
 
 <script>
-$(function() {
+    $(function () {
-    // Initially hide all "specific" forms
+        // Built in Model Types
-    $("div[id$='-specific-form']").each( function() {
+        var nativeModelTypes = [
-        $(this).hide();
+            "mlrr",
-    });
+            "rbrr",
+            "enviformer",
+        ]
 
-    $('#model-type').selectpicker();
+        // Initially hide all "specific" forms
-    $("#ml-relative-reasoning-fingerprinter").selectpicker();
+        $(".ep-model-param").each(function () {
-    $("#package-based-relative-reasoning-rule-packages").selectpicker();
-    $("#package-based-relative-reasoning-data-packages").selectpicker();
-    $("#package-based-relative-reasoning-evaluation-packages").selectpicker();
-    if ($('#ml-relative-reasoning-additional-fingerprinter').length > 0) {
-        $("#ml-relative-reasoning-additional-fingerprinter").selectpicker();
-    }
-
-    $("#build-app-domain").change(function () {
-        if ($(this).is(":checked")) {
-            $('#ad-params').show();
-        } else {
-            $('#ad-params').hide();
-        }
-    });
-
-    // On change hide all and show only selected
-    $("#model-type").change(function() {
-        $("div[id$='-specific-form']").each( function() {
             $(this).hide();
         });
-        val = $('option:selected', this).val();
 
-        if (val === 'ml-relative-reasoning' || val === 'rule-based-relative-reasoning') {
+        $('#model-type').selectpicker();
-            $("#package-based-relative-reasoning-specific-form").show();
+        $("#model-fingerprinter").selectpicker();
-            if (val === 'ml-relative-reasoning') {
+        $("#model-rule-packages").selectpicker();
-                 $("#ml-relative-reasoning-specific-form").show();
+        $("#model-data-packages").selectpicker();
+
+        $("#build-app-domain").change(function () {
+            if ($(this).is(":checked")) {
+                $('#ad-params').show();
+            } else {
+                $('#ad-params').hide();
             }
-        } else {
+        });
-            $("#" + val + "-specific-form").show();
+
-        }
+        // On change hide all and show only selected
+        $("#model-type").change(function () {
+            $('.ep-model-param').hide();
+            var modelType = $('#model-type').val();
+            if (nativeModelTypes.indexOf(modelType) !== -1) {
+                $('.' + modelType).show();
+            } else {
+                // do nothing
+            }
+        });
+
+        $('#new_model_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+            $('#new_model_form').submit();
+        });
+
     });
-
-    $('#new_model_modal_form_submit').on('click', function(e){
-        e.preventDefault();
-        $('#new_model_form').submit();
-    });
-
-});
-
-
-
 </script>

templates/modals/objects/evaluate_model_modal.html

@@ -17,10 +17,10 @@
                         For evaluation, you need to select the packages you want to use.
                         While the model is evaluating, you can use the model for predictions.
                     </div>
-                    <!-- Evaluation -->
+                    <!-- Evaluation Packages -->
-                    <label for="relative-reasoning-evaluation-packages">Evaluation Packages</label>
+                    <label for="model-evaluation-packages">Evaluation Packages</label>
-                    <select id="relative-reasoning-evaluation-packages" name=relative-reasoning-evaluation-packages"
+                    <select id="model-evaluation-packages" name="model-evaluation-packages" data-actions-box='true'
-                            data-actions-box='true' class="form-control" multiple data-width='100%'>
+                            class="form-control" multiple data-width='100%'>
                         <option disabled>Reviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
@@ -35,7 +35,16 @@
                             {% endif %}
                         {% endfor %}
                     </select>
-                <input type="hidden" name="hidden" value="evaluate">
+
+                    <!-- Eval Type -->
+                    <label for="model-evaluation-type">Evaluation Type</label>
+                    <select id="model-evaluation-type" name="model-evaluation-type" class="form-control">
+                        <option disabled selected>Select evaluation type</option>
+                        <option value="sg">Single Generation</option>
+                        <option value="mg">Multiple Generations</option>
+                    </select>
+
+                    <input type="hidden" name="hidden" value="evaluate">
                 </form>
             </div>
             <div class="modal-footer">
@@ -50,7 +59,7 @@
 
     $(function () {
 
-        $("#relative-reasoning-evaluation-packages").selectpicker();
+        $("#model-evaluation-packages").selectpicker();
 
         $('#evaluate_model_form_submit').on('click', function (e) {
             e.preventDefault();

templates/modals/objects/generic_set_scenario_modal.html

@@ -18,6 +18,7 @@
                     <select id="scenario-select" name="selected-scenarios" data-actions-box='true' class="form-control"
                             multiple data-width='100%'>
                         <option disabled>Select Scenarios</option>
+                        <option value="" hidden></option>
                     </select>
                 </form>
             </div>
@@ -65,7 +66,7 @@
             $('#set_scenario_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
                 if ($('#scenario-select').val().length == 0) {
-                    $('#scenario-select').val([''])
+                    $('#scenario-select').val("")
                 }
                 $('#set_scenario_modal_form').submit();
             });

templates/objects/composite_rule.html

@@ -29,7 +29,7 @@
         </div>
         <div class="panel-body">
             <p>
-                {{ rule.description }}
+                {{ rule.description|safe }}
             </p>
         </div>
 
@@ -87,19 +87,41 @@
             </div>
         {% endif %}
 
-        <!-- EC Numbers -->
+        {% if rule.enzymelinks %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <!-- EC Numbers -->
-            <h4 class="panel-title">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                <h4 class="panel-title">
-                   href="#rule-ec-numbers">EC Numbers</a>
+                    <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
-            </h4>
+                       href="#rule-ec-numbers">EC Numbers</a>
-        </div>
+                </h4>
-        <div id="rule-ec-numbers" class="panel-collapse collapse">
-            <div class="panel-body list-group-item">
-
             </div>
-        </div>
+            <div id="rule-ec-numbers" class="panel-collapse collapse in">
-
+                <div class="panel-body list-group-item">
+                    {% for k, v in rule.get_grouped_enzymelinks.items %}
+                        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                            <h4 class="panel-title">
+                                <a id="{{ k|slugify }}_Link" data-toggle="collapse"
+                                   data-parent="#{{ k|slugify }}_Accordion"
+                                   href="#{{ k|slugify }}">
+                                    {{ k }}
+                                </a>
+                            </h4>
+                        </div>
+                        <div id="{{ k|slugify }}" class="panel-collapse collapse in">
+                            <div class="panel-body list-group-item">
+                                {% for enzyme in v %}
+                                    <a class="list-group-item" href="{{ enzyme.url }}">
+                                        {{ enzyme.ec_number }}
+                                        <div style="position:absolute;bottom:10px;left:100px;">{{ enzyme.name }}</div>
+                                        <div style="float:right;">{{ enzyme.linking_method }}</div>
+                                    </a>
+                                {% endfor %}
+                            </div>
+                        </div>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
     </div>
 </div>
 {% endblock content %}

templates/objects/compound.html

@@ -183,7 +183,7 @@
                 </div>
                 <div id="compound-external-identifier" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
-                        {% if compound.get_pubchem_identifiers %}
+                        {% if compound.get_pubchem_compound_identifiers %}
                             <div class="panel panel-default panel-heading list-group-item"
                                  style="background-color:silver">
                                 <h4 class="panel-title">
@@ -193,12 +193,28 @@
                                 </h4>
                             </div>
                             <div id="compound-pubchem-identifier" class="panel-collapse collapse in">
-                                {% for eid in compound.get_pubchem_identifiers %}
+                                {% for eid in compound.get_pubchem_compound_identifiers %}
                                     <a class="list-group-item"
                                        href="{{ eid.external_url }}">CID{{ eid.identifier_value }}</a>
                                 {% endfor %}
                             </div>
                         {% endif %}
+                        {% if compound.get_pubchem_substance_identifiers %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="compound-pubchem-identifier-link" data-toggle="collapse"
+                                       data-parent="#compound-external-identifier"
+                                       href="#compound-pubchem-identifier">PubChem Substance Identifier</a>
+                                </h4>
+                            </div>
+                            <div id="compound-pubchem-identifier" class="panel-collapse collapse in">
+                                {% for eid in compound.get_pubchem_substance_identifiers %}
+                                    <a class="list-group-item"
+                                       href="{{ eid.external_url }}">SID{{ eid.identifier_value }}</a>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
                         {% if compound.get_chebi_identifiers %}
                             <div class="panel panel-default panel-heading list-group-item"
                                  style="background-color:silver">

templates/objects/enzymelink.html

@@ -0,0 +1,105 @@
+{% extends "framework.html" %}
+
+{% block content %}
+
+    <div class="panel-group" id="enzyme-detail">
+        <div class="panel panel-default">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                {{ enzymelink.ec_number }}
+            </div>
+
+            <!-- Name -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-name-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-name">Enzyme Name</a>
+                </h4>
+            </div>
+            <div id="enzyme-name" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ enzymelink.name }}
+                </div>
+            </div>
+
+            <!-- Linking Method -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-linking-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-linking">Linking Method</a>
+                </h4>
+            </div>
+            <div id="enzyme-linking" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ enzymelink.linking_method }}. &nbsp;<a
+                        href="https://wiki.envipath.org/index.php/Rules#EnzymeLinks" target="#">Learn more &gt;&gt;</a>
+                </div>
+            </div>
+
+            {% if enzymelink.kegg_reaction_links %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-evidence">Linking Evidence</a>
+                    </h4>
+                </div>
+                <div id="enzyme-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for kl in enzymelink.kegg_reaction_links %}
+                            <a class="list-group-item"
+                               href="{{ kl.external_url }}">{{ kl.identifier_value }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if enzymelink.reaction_evidence.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-reaction-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-reaction-evidence">Linking Evidence - enviPath Reactions</a>
+                    </h4>
+                </div>
+                <div id="enzyme-reaction-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in enzymelink.reaction_evidence.all %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if enzymelink.edge_evidence.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-edge-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-edge-evidence">Linking Evidence - enviPath Pathways</a>
+                    </h4>
+                </div>
+                <div id="enzyme-edge-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for e in enzymelink.edge_evidence.all %}
+                            <a class="list-group-item" href="{{ e.pathway.url }}">{{ e.pathway.name }}
+                                <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- External DB Reference -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-external-identifier-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-external-identifier">External DB References</a>
+                </h4>
+            </div>
+            <div id="enzyme-external-identifier" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    <a class="list-group-item"
+                       href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ enzymelink.ec_number }}"
+                       target="_blank"> Brenda entry for {{ enzymelink.ec_number }}</a>
+                </div>
+            </div>
+
+        </div>
+    </div>
+{% endblock content %}

templates/objects/model.html

@@ -117,7 +117,7 @@
                 <!-- End Predict Panel       -->
             {% endif %}
 
-            {% if model.app_domain %}
+            {% if model.ready_for_prediction and model.app_domain %}
                 <!-- App Domain -->
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">

templates/objects/pathway.html

@@ -177,9 +177,6 @@
                 </nav>
                 <div id="vizdiv" >
                     <svg id="pwsvg">
-                        {% if debug %}
-                            <rect width="100%" height="100%" fill="aliceblue"/>
-                        {% endif %}
                         <defs>
                             <marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
                                     orient="auto-start-reverse" markerUnits="userSpaceOnUse">

templates/objects/reaction.html

@@ -124,6 +124,23 @@
                 </div>
             {% endif %}
 
+            {% if reaction.get_related_enzymes %}
+                <!-- EC Numbers -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-ec-numbers">EC Numbers</a>
+                    </h4>
+                </div>
+                <div id="rule-ec-numbers" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for e in reaction.get_related_enzymes %}
+                            <a class="list-group-item" href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ e.ec_number }}">{{ e.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             {% if reaction.related_pathways %}
                 <!-- Pathways -->
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">

templates/objects/simple_rule.html

@@ -201,6 +201,43 @@
                     </div>
                 </div>
             {% endif %}
+
+            {% if rule.enzymelinks %}
+                <!-- EC Numbers -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-ec-numbers">EC Numbers</a>
+                    </h4>
+                </div>
+                <div id="rule-ec-numbers" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for k, v in rule.get_grouped_enzymelinks.items %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="{{ k|slugify }}_Link" data-toggle="collapse"
+                                       data-parent="#{{ k|slugify }}_Accordion"
+                                       href="#{{ k|slugify }}">
+                                        {{ k }}
+                                    </a>
+                                </h4>
+                            </div>
+                            <div id="{{ k|slugify }}" class="panel-collapse collapse in">
+                                <div class="panel-body list-group-item">
+                                    {% for enzyme in v %}
+                                        <a class="list-group-item" href="{{ enzyme.url }}">
+                                            {{ enzyme.ec_number }}
+                                            <div style="position:absolute;bottom:10px;left:100px;">{{ enzyme.name }}</div>
+                                            <div style="float:right;">{{ enzyme.linking_method }}</div>
+                                        </a>
+                                    {% endfor %}
+                                </div>
+                            </div>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
         </div>
     </div>
 {% endblock content %}

tests/test_enviformer.py

@@ -1,7 +1,27 @@
+from collections import defaultdict
+from datetime import datetime
 from tempfile import TemporaryDirectory
 from django.test import TestCase, tag
 from epdb.logic import PackageManager
-from epdb.models import User, EnviFormer, Package
+from epdb.models import User, EnviFormer, Package, Setting
+from epdb.tasks import predict_simple, predict
+
+
+def measure_predict(mod, pathway_pk=None):
+    # Measure and return the prediction time
+    start = datetime.now()
+    if pathway_pk:
+        s = Setting()
+        s.model = mod
+        s.model_threshold = 0.2
+        s.max_depth = 4
+        s.max_nodes = 20
+        s.save()
+        pred_result = predict.delay(pathway_pk, s.pk, limit=s.max_depth)
+    else:
+        pred_result = predict_simple.delay(mod.pk, "C1=CC=C(CSCC2=CC=CC=C2)C=C1")
+    _ = pred_result.get()
+    return round((datetime.now() - start).total_seconds(), 2)
 
 
 @tag("slow")
@@ -28,8 +48,41 @@ class EnviFormerTest(TestCase):
 
                 mod.build_dataset()
                 mod.build_model()
-                mod.multigen_eval = True
+                mod.evaluate_model(True, eval_packages_objs)
-                mod.save()
-                mod.evaluate_model()
 
                 mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
+
+    def test_predict_runtime(self):
+        with TemporaryDirectory() as tmpdir:
+            with self.settings(MODEL_DIR=tmpdir):
+                threshold = float(0.5)
+                data_package_objs = [self.BBD_SUBSET]
+                eval_packages_objs = [self.BBD_SUBSET]
+                mods = []
+                for _ in range(4):
+                    mod = EnviFormer.create(
+                        self.package, data_package_objs, eval_packages_objs, threshold=threshold
+                    )
+                    mod.build_dataset()
+                    mod.build_model()
+                    mods.append(mod)
+
+                # Test prediction time drops after first prediction
+                times = [measure_predict(mods[0]) for _ in range(5)]
+                print(f"First prediction took {times[0]} seconds, subsequent ones took {times[1:]}")
+
+                # Test pathway prediction
+                times = [measure_predict(mods[1], self.BBD_SUBSET.pathways[0].pk) for _ in range(5)]
+                print(
+                    f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}"
+                )
+
+                # Test eviction by performing three prediction with every model, twice.
+                times = defaultdict(list)
+                for _ in range(
+                    2
+                ):  # Eviction should cause the second iteration here to have to reload the models
+                    for mod in mods:
+                        for _ in range(3):
+                            times[mod.pk].append(measure_predict(mod))
+                print(times)

tests/test_model.py

@@ -30,7 +30,6 @@ class ModelTest(TestCase):
                     self.package,
                     rule_package_objs,
                     data_package_objs,
-                    eval_packages_objs,
                     threshold=threshold,
                     name="ECC - BBD - 0.5",
                     description="Created MLRelativeReasoning in Testcase",
@@ -50,9 +49,7 @@ class ModelTest(TestCase):
 
                 mod.build_dataset()
                 mod.build_model()
-                mod.multigen_eval = True
+                mod.evaluate_model(True, eval_packages_objs)
-                mod.save()
-                mod.evaluate_model()
 
                 results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
 

tests/views/test_model_views.py

@@ -6,7 +6,7 @@ from epdb.logic import UserManager
 from epdb.models import Package, User
 
 
-@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class PathwayViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 

tests/views/test_pathway_views.py

@@ -6,7 +6,7 @@ from epdb.logic import UserManager, PackageManager
 from epdb.models import Pathway, Edge
 
 
-@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class PathwayViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 

utilities/chem.py

@@ -729,6 +729,7 @@ class IndigoUtils(object):
         height: int = 0,
         educt_functional_groups: Dict[str, int] = None,
         product_functional_groups: Dict[str, int] = None,
+        debug: bool = False,
     ):
         if educt_functional_groups is None:
             educt_functional_groups = {}
@@ -739,6 +740,11 @@ class IndigoUtils(object):
         i = Indigo()
         renderer = IndigoRenderer(i)
 
+        if debug:
+            i.setOption("render-atom-ids-visible", True)
+            i.setOption("render-bond-ids-visible", False)
+            i.setOption("render-atom-bond-ids-from-one", True)
+
         i.setOption("render-output-format", "svg")
         i.setOption("render-coloring", True)
         i.setOption("render-image-size", width, height)