adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

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

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

.gitea/workflows/build-image.yaml

@@ -1,62 +0,0 @@
-name: Build Docker Image
-
-# Trigger when a PR to main/develop is completed.
-on:
-  pull_request:
-    branches:
-      - main
-      - develop
-    types:
-      - closed
-
-jobs:
-  build-and-push:
-    if: ${{ github.event.pull_request.merged == true }}
-    runs-on: ubuntu-latest
-    steps:
-      # Fetch the repository content for the Docker build context.
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      # Enable Buildx for BuildKit features (incl. SSH mount support).
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      # Authenticate against the container registry before pushing images.
-      - name: Log in to container registry
-        uses: docker/login-action@v3
-        with:
-          registry: git.envipath.com
-          username: ${{ secrets.CI_REGISTRY_USER }}
-          password: ${{ secrets.CI_REGISTRY_PASSWORD }}
-
-      # Generate image tags/labels:
-      # - PRs targeting main get "latest" and "main-sha"
-      # - PRs targeting develop get "dev" and "dev-sha"
-      - name: Extract metadata
-        id: meta
-        uses: docker/metadata-action@v5
-        with:
-          images: git.envipath.com/envipath/envipy
-          tags: |
-            type=raw,value=latest,enable=${{ github.event.pull_request.base.ref == 'main' }}
-            type=sha,prefix=main-,enable=${{ github.event.pull_request.base.ref == 'main' }}
-            type=raw,value=dev,enable=${{ github.event.pull_request.base.ref == 'develop' }}
-            type=sha,prefix=dev-,enable=${{ github.event.pull_request.base.ref == 'develop' }}
-
-      # Load SSH key so Docker can pull private git+ssh dependencies during build.
-      - name: Setup SSH for private git dependencies
-        uses: webfactory/ssh-agent@v0.9.0
-        with:
-          ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
-
-      # Build and push the production image; forward SSH agent without registry cache reuse.
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: Dockerfile
-          push: true
-          ssh: default
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
       - id: trailing-whitespace
         exclude: epiuclid/schemas/
       - id: end-of-file-fixer
-        exclude: ^epiuclid/schemas/|^static/js/ketcher3/
+        exclude: epiuclid/schemas/
       - id: check-yaml
       - id: check-added-large-files
-        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/|^static/js/ketcher3/
+        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3

Dockerfile

@@ -60,10 +60,6 @@ COPY tests tests
 COPY utilities utilities
 COPY manage.py .
 
-# Used to run migrations etc
-COPY entrypoint.sh entrypoint.sh
-RUN chmod +x entrypoint.sh
-
 # Install frontend deps
 COPY package.json pnpm-lock.yaml pnpm-workspace.yaml ./
 
@@ -85,7 +81,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxext6 \
     libfontconfig1 \
     nano \
-    openjdk-21-jre-headless \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django
@@ -107,5 +102,4 @@ USER django
 
 EXPOSE 8000
 
-ENTRYPOINT ["/app/entrypoint.sh"]
-CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "8"]
+CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "3"]

bayer/migrations/0004_package_shareable.py

@@ -1,18 +0,0 @@
-# Generated by Django 6.0.3 on 2026-09-08 08:54
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0003_pescompound_pesstructure_package_data_pool'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='package',
-            name='shareable',
-            field=models.BooleanField(default=True, verbose_name='Shareable'),
-        ),
-    ]

bayer/models.py

@@ -23,7 +23,6 @@ class Package(EnviPathModel):
     license = models.ForeignKey(
         "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
     )
-    shareable = models.BooleanField(verbose_name="Shareable", default=True)
 
     class Classification(models.IntegerChoices):
         INTERNAL = 0, "Internal"

bayer/templates/modals/collections/new_package_modal.html

@@ -5,11 +5,11 @@
   class="modal"
   x-data="{
     isSubmitting: false,
-    packageClassification: '',
+    packageClassification: null,
 
     reset() {
       this.isSubmitting = false;
-      this.packageClassification = '';
+      this.packageClassification = null;
     },
 
     setFormData(data) {
@@ -114,7 +114,7 @@
             x-model="packageClassification"
             required
           >
-            <option value="" disabled>Select Classification</option>
+            <option value="null" disabled selected>Select Classification</option>
             <option value="0">Internal</option>
             <option value="10">Restricted</option>
             <option value="20">Secret</option>
@@ -131,9 +131,8 @@
             id="package-data-pool"
             name="package-data-pool"
             class="select select-bordered w-full"
-            :required="isSecret"
           >
-            <option value="" disabled>Select Data Pool</option>
+            <option value="" disabled selected>Select Data Pool</option>
               {% for obj in meta.secret_groups %}
                 <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
               {% endfor %}

bayer/templates/objects/package.html

@@ -4,7 +4,6 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_package_modal.html" %}
-    {% include "modals/objects/view_package_permissions_modal.html" %}
     {% include "modals/objects/edit_package_permissions_modal.html" %}
     {% include "modals/objects/publish_package_modal.html" %}
     {% include "modals/objects/set_license_modal.html" %}

bayer/views.py

@@ -1,40 +1,19 @@
 import base64
-import logging
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
+from django.http import HttpResponse, HttpResponseBadRequest
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
-from epdb.models import Pathway, Node, Group
+from epdb.models import Pathway, Node
 from epdb.views import _anonymous_or_real, error
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
 
 
-logger = logging.getLogger(__name__)
-
-
-def has_secret_group(user):
-    """
-    Determines if the specified user belongs to any secret group.
-
-    This function checks whether the given user is a member of any group
-    that is marked as secret.
-
-    Args:
-        user: The user for whom the check is performed.
-
-    Returns:
-        bool: True if the user belongs to at least one secret group,
-        False otherwise.
-    """
-    return Group.objects.filter(secret=True, user_member=user).exists()
-
-
 @package_permission_required()
 def create_pes(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -55,43 +34,29 @@ def create_pes(request, package_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link, current_user)
+                pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 @package_permission_required()
@@ -115,39 +80,25 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link, current_user)
+                pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Failed to fetch this PES",
-                    "Either the PES-ID is incorrect, or you're missing sufficient permissions to access this (potentially secret) item. In case you're missing permissions you can request the entitlement cs.u.enviPath_secret_data_user_group on go/idnow to gain access."
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
-            node_qs = Node.objects.filter(
-                pathway=current_pathway,
-                default_node_label=pes.default_structure
-            )
-
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
             if node_qs.exists():
                 return redirect(current_pathway.url)
 
@@ -165,91 +116,58 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
-def get_application_token(prod: bool) -> str:
-    scope = f"{s.PROD_PES_SCOPE if prod else s.NON_PROD_PES_SCOPE}/.default"
+def fetch_pes(request, pes_url) -> dict:
+    from epauth.views import get_access_token_from_request
+    token = get_access_token_from_request(request)
 
-    url = f"https://login.microsoftonline.com/{s.MS_ENTRA_TENANT_ID}/oauth2/v2.0/token"
-    data = {
-        "grant_type": "client_credentials",
-        "client_id": s.MS_ENTRA_CLIENT_ID,
-        "client_secret": s.MS_ENTRA_CLIENT_SECRET,
-        "scope": scope,
-    }
+    if token is None:
+        token = pes_url.split('/')[-1] == 'dummy'
 
-    try:
-        response = requests.post(url, data=data)
-        response.raise_for_status()
-        return response.json()["access_token"]
-    except requests.exceptions.HTTPError as e:
-        logger.error(f"Could not fetch application token: {e}")
-        raise ValueError(f"Could not fetch application token!")
+    if token:
+        for k, v in s.PES_API_MAPPING.items():
+            if pes_url.startswith(k):
+                pes_id = pes_url.split('/')[-1]
 
-
-def fetch_pes(request, pes_url, user) -> dict:
-
-    for k, v in s.PES_API_MAPPING.items():
-        if pes_url.startswith(k):
-
-            prod = "cropkey-np" not in pes_url
-
-            pes_id = pes_url.split('/')[-1]
-
-            if pes_id == 'dummy':
-                import json
-                res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
-                res_data["pes_url"] = pes_url
-                return res_data
-            else:
-                headers = {
-                    "accept": "*/*",
-                    "authorization": "Bearer " + get_application_token(prod),
-                }
-
-                # Restrict request if user is not part of any secret group
-                if not has_secret_group(user):
-                    headers["app-classification-level-restriction"] = "restrict-pes-secret-structure-access"
-
-
-                params = {"pes_reg_entity_corporate_id": pes_id}
-
-                res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
-
-                try:
-                    res.raise_for_status()
-                    pes_data = res.json()
-
-                    # Handle missing response
-                    if "detail" in pes_data and "The following PES Reg Entities Corporate Ids could not be found" in pes_data["detail"]:
-                        raise ValueError(f"PES with id {pes_id} not found")
-
-                    # Ensure we have a entity
-                    if len(pes_data) == 0:
-                        raise ValueError(f"PES with id {pes_id} not found")
-
-                    res_data = pes_data[0]
+                if pes_id == 'dummy':
+                    import json
+                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                     res_data["pes_url"] = pes_url
                     return res_data
+                else:
+                    headers = {"Authorization": f"Bearer {token['access_token']}"}
+                    params = {"pes_reg_entity_corporate_id": pes_id}
 
-                except requests.exceptions.HTTPError as e:
-                    raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
 
-    raise ValueError(f"Unknown URL {pes_url}")
+                    try:
+                        res.raise_for_status()
+                        pes_data = res.json()
+
+                        if len(pes_data) == 0:
+                            raise ValueError(f"PES with id {pes_id} not found")
+
+                        res_data = pes_data[0]
+                        res_data["pes_url"] = pes_url
+                        return res_data
+
+                    except requests.exceptions.HTTPError as e:
+                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+        else:
+            raise ValueError(f"Unknown URL {pes_url}")
+    else:
+        raise ValueError("Could not fetch access token from request.")
 
 
 def visualize_pes(request):
     pes_link = request.GET.get('pesLink')
 
     if pes_link:
-        pes_data = fetch_pes(request, pes_link, request.user)
+        pes_data = fetch_pes(request, pes_link)
 
         representations = pes_data.get('representations')
 

bridge/contracts.py

@@ -1,5 +1,4 @@
 import enum
-from typing import Any, Dict
 from abc import ABC, abstractmethod
 
 from envipy_additional_information import EnviPyModel
@@ -70,12 +69,6 @@ class Plugin(ABC):
 
 
 class Property(Plugin):
-    def parameters(self) -> Dict[str, Any]:
-        """
-        Returns the parameters of the PropertyPlugin.
-        """
-        return {}
-
     @classmethod
     @abstractmethod
     def requires_rule_packages(cls) -> bool:
@@ -307,12 +300,6 @@ class Classifier(Plugin):
         """
         pass
 
-    def parameters(self) -> Dict[str, Any]:
-        """
-        Returns the parameters of the ClassifierPlugin.
-        """
-        return {}
-
     @abstractmethod
     def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
         """

entrypoint.sh

@@ -1,9 +0,0 @@
-#!/bin/bash
-set -e
-
-if [ "${SKIP_DJANGO_SETUP:-false}" != "true" ]; then
-  python manage.py migrate --no-input
-  python manage.py collectstatic --no-input
-fi
-
-exec "$@"

envipath/settings.py

@@ -357,7 +357,6 @@ DEFAULT_MODEL_PARAMS = {
 DEFAULT_MAX_NUMBER_OF_NODES = 9999
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
-BATCH_PREDICT_MAX_COMPOUNDS = 150
 
 # Loading Plugins
 PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
@@ -445,8 +444,6 @@ if MS_ENTRA_ENABLED:
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
     MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
     MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
-    NON_PROD_PES_SCOPE = os.environ.get("NON_PROD_PES_SCOPE")
-    PROD_PES_SCOPE = os.environ.get("PROD_PES_SCOPE")
 
 # Site ID 10 -> beta.envipath.org
 MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

epapi/v1/endpoints/additional_information.py

@@ -9,8 +9,8 @@ from envipy_additional_information import registry
 from envipy_additional_information.groups import GroupEnum
 from epapi.utils.schema_transformers import build_rjsf_output
 from epapi.utils.validation_errors import handle_validation_error
-from epdb.models import AdditionalInformation, Scenario, Node
-from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
+from epdb.models import AdditionalInformation
+from ..dal import get_scenario_for_read, get_scenario_for_write
 
 logger = logging.getLogger(__name__)
 
@@ -58,61 +58,6 @@ def list_scenario_info(request, scenario_uuid: UUID):
     return result
 
 
-@router.post("/information/{model_name}/")
-def add_object_info(request, model_name: str, payload: Dict[str, Any] = Body(...)):
-    from epdb.views import EPDBURLParser
-
-    cls = registry.get_model(model_name.lower())
-    if not cls:
-        raise HttpError(404, f"Unknown model: {model_name}")
-
-    try:
-        instance = cls(**payload)  # Pydantic validates
-    except ValidationError as e:
-        handle_validation_error(e)
-
-    if "attach_obj_url" in payload:
-        url_parser = EPDBURLParser(payload["attach_obj_url"])
-
-        if url_parser.contains_package_url():
-            package = get_package_for_write(request.user, url_parser.get_objects()[0].uuid)
-            attach_obj = url_parser.get_object()
-
-            if "scenario_uuid" in payload:
-                scenario = get_scenario_for_read(request.user, payload["scenario_uuid"])
-            else:
-                scenario = Scenario.create(
-                    package,
-                    name=f"Scenario {Scenario.objects.filter(package=package).count() + 1}",
-                    description="no description",
-                    scenario_date=None,
-                    scenario_type=None,
-                    additional_information=[],
-                )
-
-            if isinstance(attach_obj, Node):
-                ai = add_info_to_node(package, instance, scenario, attach_obj)
-            else:
-                raise HttpError(404, f"Bad request - Not implemented for {type(attach_obj)}!")
-
-            return {"status": "created", "uuid": ai.uuid}
-
-    raise HttpError(404, "Bad request!")
-
-
-def add_info_to_node(package, add_inf, scenario, node):
-    ai = AdditionalInformation.create(
-        package,
-        add_inf,
-        scenario=scenario,
-        content_object=node,
-    )
-
-    node.pathway.scenarios.add(scenario)
-
-    return ai
-
-
 @router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
 def add_scenario_info(
     request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)

epapi/v1/interfaces/iuclid/projections.py

@@ -56,7 +56,7 @@ def get_pathway_for_iuclid_export(user, pathway_uuid: UUID) -> PathwayExportDTO:
 
         ai_for_node = []
         scenario_entries: list[PathwayScenarioDTO] = []
-        for scenario in sorted(node.get_scenarios(), key=lambda item: item.pk):
+        for scenario in sorted(node.scenarios.all(), key=lambda item: item.pk):
             ai_for_scenario = list(scenario.get_additional_information(direct_only=True))
             ai_for_node.extend(ai_for_scenario)
             scenario_entries.append(

epauth/views.py

@@ -1,5 +1,3 @@
-import logging
-
 import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
@@ -9,9 +7,6 @@ from django.shortcuts import redirect
 
 from epdb.logic import UserManager, GroupManager
 from epdb.models import Group
-from epdb.views import get_remote_address, error
-
-auth_log = logging.getLogger("auth")
 
 
 def get_msal_app_with_cache(request):
@@ -35,9 +30,6 @@ def get_msal_app_with_cache(request):
 
 
 def entra_login(request):
-
-    auth_log.info(f"Login request from {get_remote_address(request)}")
-
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
@@ -62,28 +54,14 @@ def entra_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    if "error" in result:
-        auth_log.error(f"Login attempt by {get_remote_address(request)} failed due to {result['error']}")
-        return redirect("/")
-
     # Save the token cache to session
     if cache.has_state_changed:
         request.session["msal_token_cache"] = cache.serialize()
 
     claims = result["id_token_claims"]
 
-    if claims.get("roles") is None or claims.get("roles") == [] or "envipath_registered_user" not in claims.get("roles"):
-        auth_log.error(f"Login attempt by {get_remote_address(request)} failed due to missing role")
-        return error(
-            request,
-            "Login Failed",
-            "Request access to role 1230/MON/APPS/Envipath/Envipath_Prod on go/idnow",
-            403,
-        )
-
     user_name = claims.get("name")
-    # preferred_username is a fallback for 2nd CWID
-    user_email = claims.get("emailaddress", claims.get("email", claims.get("preferred_username")))
+    user_email = claims.get("emailaddress", claims.get("email"))
     user_oid = claims.get("oid")
 
     if not all([user_name, user_email, user_oid]):
@@ -92,7 +70,6 @@ def entra_callback(request):
     # Get implementing class
     User = get_user_model()
 
-    registered = False
     if User.objects.filter(uuid=user_oid).exists():
         u = User.objects.get(uuid=user_oid)
 
@@ -101,11 +78,8 @@ def entra_callback(request):
             u.save()
 
     else:
-        auth_log.info(f"Registering {user_name} with OID {user_oid}")
         u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
-        registered = True
 
-    auth_log.info(f"User {user_name} {'(admin) ' if u.is_superuser else ''}with OID {user_oid} successfully logged in as {u.username} from {get_remote_address(request)}")
     login(request, u)
 
     # EDIT START
@@ -128,37 +102,10 @@ def entra_callback(request):
         else:
             g = Group.objects.get(uuid=id)
 
-    sync_groups = list(s.ENTRA_GROUPS.keys()) + list(s.ENTRA_SECRET_GROUPS.keys())
-    user_groups = claims.get("groups", [])
-
-    for uuid in sync_groups:
-        if uuid in user_groups:
-            g = Group.objects.get(uuid=uuid)
-            if not g.user_member.contains(u):
-                g.user_member.add(u)
-                auth_log.info(f"Login Group Sync: Adding {u.username} to Group {g.name} ({ uuid })")
-        else:
-            g = Group.objects.get(uuid=uuid)
-            # Do not remove users from All enviPath Users
-            if g.user_member.contains(u) and g.name != 'All enviPath Users':
-                g.user_member.remove(u)
-                auth_log.info(f"Login Group Sync: Removing {u.username} from Group {g.name} ({ uuid })")
-
-    # Ensure people are part of All enviPath Users -> they have to as, envipath_registered_user is granted
-    all_envipath_users = Group.objects.get(name="All enviPath Users")
-    if not all_envipath_users.user_member.contains(u):
-        all_envipath_users.user_member.add(u)
-
-    if registered:
-        # #72 make package secret if user is part of a secret group
-        for id, name in s.ENTRA_SECRET_GROUPS.items():
-            group = Group.objects.get(uuid=id)
-            if group.user_member.contains(u):
-                # User is eligible for secrete
-                pack = u.default_package
-                pack.data_pool = group
-                pack.classification_level = pack.Classification.SECRET
-                pack.save()
+    for group_uuid in claims.get("groups", []):
+        if Group.objects.filter(uuid=group_uuid).exists():
+            g = Group.objects.get(uuid=group_uuid)
+            g.user_member.add(u)
 
     # EDIT END
 

epdb/admin.py

@@ -11,7 +11,6 @@ from .models import (
     CompoundStructure,
     Edge,
     EnviFormer,
-    EnzymeLink,
     ExternalDatabase,
     ExternalIdentifier,
     Group,
@@ -213,10 +212,6 @@ class CompoundStructureAdmin(EPAdmin):
     pass
 
 
-class EnzymeLinkAdmin(EPAdmin):
-    pass
-
-
 class SimpleAmbitRuleAdmin(EPAdmin):
     pass
 
@@ -271,7 +266,6 @@ admin.site.register(License, LicenseAdmin)
 admin.site.register(ClassifierPluginModel, ClassifierPluginModelAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
-admin.site.register(EnzymeLink, EnzymeLinkAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
 admin.site.register(ParallelRule, ParallelRuleAdmin)
 admin.site.register(Reaction, ReactionAdmin)

epdb/legacy_api.py

@@ -1,4 +1,3 @@
-import logging
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
@@ -10,6 +9,7 @@ from django.contrib.auth import get_user_model
 from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
+from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
 from ninja.security import HttpBearer
 
@@ -45,12 +45,9 @@ from .models import (
     User,
     UserPackagePermission,
 )
-from .views import delete_with_log, get_remote_address
 
 Package = s.GET_PACKAGE_MODEL()
 
-auth_log = logging.getLogger("auth")
-
 
 def get_cached_jwks(tenant_id: str, force=False) -> Dict:
     """Get JWKS using Django cache"""
@@ -72,10 +69,6 @@ def get_cached_jwks(tenant_id: str, force=False) -> Dict:
     return jwks
 
 
-def get_package_for_read(user, package_uuid):
-    return PackageManager.get_package_by_id(user, package_uuid)
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -122,22 +115,15 @@ def validate_token(token: str) -> dict:
 class MSBearerTokenAuth(HttpBearer):
 
     def authenticate(self, request, token):
-
-        auth_log.info(f"Authentication request by {get_remote_address(request)}")
-
         if token is None:
             return None
 
         claims = validate_token(token)
 
         if not User.objects.filter(uuid=claims['oid']).exists():
-            auth_log.info(f"Authentication request by {get_remote_address(request)} failed!")
             return None
 
-        user = User.objects.get(uuid=claims['oid'])
-        request.user = user
-        auth_log.info(
-            f"User {user.username} {'(admin) ' if user.is_superuser else ''}with OID {user.uuid} successfully logged in as {user.username} from {get_remote_address(request)}")
+        request.user = User.objects.get(uuid=claims['oid'])
         return request.user
 
 
@@ -571,10 +557,7 @@ def update_package(request, package_uuid, pack: Form[UpdatePackage]):
 
         if pack.hiddenMethod:
             if pack.hiddenMethod == "DELETE":
-                if PackageManager.administrable(request.user, p):
-                    delete_with_log(request, p)
-                else:
-                    raise ValueError("You do not have the rights to delete this Package!")
+                p.delete()
 
         elif pack.packageDescription is not None:
             description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -611,7 +594,7 @@ def delete_package(request, package_uuid):
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
         if PackageManager.administrable(request.user, p):
-            delete_with_log(request, p)
+            p.delete()
             return redirect(f"{s.SERVER_URL}/package")
         else:
             raise ValueError("You do not have the rights to delete this Package!")
@@ -889,7 +872,7 @@ def create_package_compound(
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, c.pesLink, request.user)
+                pes_data = fetch_pes(request, c.pesLink)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
 
@@ -897,11 +880,12 @@ def create_package_compound(
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
-
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                    return 400, {"Cannot create PESs for non-secret packages."}
 
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
 
             c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
         else:
@@ -1720,7 +1704,7 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, Any]] = []
+    proposed: List[Dict[str, str]] = []
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
     pesLink: str | None = Field(None, alias="pes_link")
@@ -1892,7 +1876,7 @@ def delete_pathway(request, package_uuid, pathway_uuid):
         p = get_package_for_write(request.user, package_uuid)
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-        delete_with_log(request, pw)
+        pw.delete()
         return redirect(f"{p.url}/pathway")
 
     except ValueError:
@@ -1990,7 +1974,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 
 class CreateNode(Schema):
-    nodeAsSmiles: str | None = None
+    nodeAsSmiles: str
     nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
@@ -2014,7 +1998,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, n.pesLink, request.user)
+                pes_data = fetch_pes(request, n.pesLink)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
 
@@ -2022,10 +2006,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
+                    return 400, "Cannot create PESs for non-secret packages."
 
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
 
             c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
 
@@ -2070,7 +2058,7 @@ def delete_node(request, package_uuid, pathway_uuid, node_uuid):
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
         n = Node.objects.get(pathway=pw, uuid=node_uuid)
-        delete_with_log(request, n)
+        n.delete()
         return redirect(f"{pw.url}/node")
 
     except ValueError:
@@ -2230,7 +2218,7 @@ def delete_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
         e = Edge.objects.get(pathway=pw, uuid=edge_uuid)
-        delete_with_log(request, e)
+        e.delete()
         return redirect(f"{pw.url}/edge")
 
     except ValueError:
@@ -2434,42 +2422,3 @@ def predict(request, np: Form[NonPersistent]):
         return 403, {
             "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
         }
-
-
-##########
-# Export #
-##########
-class PackageExportInSchema(Schema):
-    package_uuid: str
-    additional_information_types: List[str] | None = None
-
-
-@router.get("/export", response={200: Any, 403: Error})
-def export(request, q: Query[PackageExportInSchema]):
-    try:
-        p = get_package_for_read(request.user, q.package_uuid)
-
-        from envipy_additional_information import registry
-        from utilities.misc import PathwayExporter
-
-        ai_types = []
-        if q.additional_information_types is not None:
-            for ai_type in q.additional_information_types:
-                if registry.get_model(ai_type) is None:
-                    return 400, {
-                        "message": f"Exporting Package with id {q.package_uuid} failed as {ai_type} is not a valid additional information type!"
-                    }
-                ai_types.append(ai_type)
-
-        exporter = PathwayExporter(p, add_infs_to_export=ai_types)
-        res = exporter.do_export()
-
-        filename = f"{p.get_name().replace(' ', '_')}_{p.uuid}.tsv"
-        response = HttpResponse(res, content_type="text/csv")
-        response["Content-Disposition"] = f'attachment; filename="{filename}"'
-
-        return response
-    except ValueError:
-        return 403, {
-            "message": f"Exporting Package with id {q.package_uuid} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -35,7 +35,6 @@ from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter, PackageImporter
 
 logger = logging.getLogger(__name__)
-auth_log = logging.getLogger("auth")
 
 Package = s.GET_PACKAGE_MODEL()
 
@@ -46,7 +45,7 @@ class EPDBURLParser:
     MODEL_PATTERNS = {
         "epdb.User": re.compile(rf"^.*/user/{UUID_PATTERN}"),
         "epdb.Group": re.compile(rf"^.*/group/{UUID_PATTERN}"),
-        s.EPDB_PACKAGE_MODEL: re.compile(rf"^.*/package/{UUID_PATTERN}"),
+        "epdb.Package": re.compile(rf"^.*/package/{UUID_PATTERN}"),
         "epdb.Compound": re.compile(rf"^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}"),
         "epdb.CompoundStructure": re.compile(
             rf"^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}/structure/{UUID_PATTERN}"
@@ -96,7 +95,7 @@ class EPDBURLParser:
 
     def contains_package_url(self):
         return (
-            bool(self.MODEL_PATTERNS[s.EPDB_PACKAGE_MODEL].findall(self.url))
+            bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
             and not self.is_package_url()
         )
 
@@ -124,7 +123,7 @@ class EPDBURLParser:
             "epdb.EPModel",
             "epdb.Pathway",
             # 1st level
-            s.EPDB_PACKAGE_MODEL,
+            "epdb.Package",
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -146,7 +145,7 @@ class EPDBURLParser:
 
         hierarchy_order = [
             # 1st level
-            s.EPDB_PACKAGE_MODEL,
+            "epdb.Package",
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -211,7 +210,7 @@ class UserManager(object):
         # Create package
         package_name = f"{u.username}{'’' if u.username[-1] in 'sxzß' else 's'} Package"
         package_description = "This package was generated during registration."
-        p = PackageManager.create_package(u, package_name, package_description, shareable=False)
+        p = PackageManager.create_package(u, package_name, package_description)
         u.default_package = p
         u.save()
 
@@ -317,19 +316,13 @@ class GroupManager(object):
         if isinstance(member, Group):
             if add_or_remove == "add":
                 group.group_member.add(member)
-                auth_log.info(f"{caller.username} ({caller.url}) adds {member.name} ({member.url}) to {group.name} ({group.url})")
             else:
                 group.group_member.remove(member)
-                auth_log.info(
-                    f"{caller.username} ({caller.url}) removes {member.name} ({member.url}) from {group.name} ({group.url})")
         else:
             if add_or_remove == "add":
                 group.user_member.add(member)
-                auth_log.info(f"{caller.username} ({caller.url}) adds {member.username} ({member.url}) to {group.name} ({group.url})")
             else:
                 group.user_member.remove(member)
-                auth_log.info(
-                    f"{caller.username} ({caller.url}) removes {member.username} ({member.url}) from {group.name} ({group.url})")
 
         group.save()
 
@@ -547,7 +540,7 @@ class PackageManager(object):
 
     @staticmethod
     @transaction.atomic
-    def create_package(current_user, name: str, description: str = None, *args, **kwargs):
+    def create_package(current_user, name: str, description: str = None):
         p = Package()
 
         # Clean for potential XSS
@@ -556,9 +549,6 @@ class PackageManager(object):
         if description is not None and description.strip() != "":
             p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if "shareable" in kwargs:
-            p.shareable = kwargs["shareable"]
-
         p.save()
 
         up = UserPackagePermission()
@@ -588,11 +578,9 @@ class PackageManager(object):
         if isinstance(grantee, User):
             perm_cls = UserPackagePermission
             data["user"] = grantee
-            grantee_name = grantee.username
         else:
             perm_cls = GroupPackagePermission
             data["group"] = grantee
-            grantee_name = grantee.name
 
         if new_perm is None:
             qs = perm_cls.objects.filter(**data)
@@ -601,23 +589,11 @@ class PackageManager(object):
             if qs.count() != 0:
                 logger.info(f"Deleting Perm {qs.first()}")
                 qs.delete()
-                auth_log.info(f"{caller.username} ({caller.url}) revokes {grantee_name} ({grantee.url}) all Permissions on {package.name} ({package.url})")
             else:
                 logger.debug(f"No Permission object for {perm_cls} with filter {data} found!")
         else:
-            old_perm = None
-            old_perms_qs = perm_cls.objects.filter(**data)
-
-            if old_perms_qs.exists():
-                old_perm = old_perms_qs.first().permission
-
             _ = perm_cls.objects.update_or_create(defaults={"permission": new_perm}, **data)
 
-            if old_perm is None:
-                auth_log.info(f"{caller.username} ({caller.url}) grants {grantee_name} ({grantee.url}) '{new_perm}' Permissions on {package.name} ({package.url})")
-            else:
-                auth_log.info(f"{caller.username} ({caller.url}) set {grantee_name} ({grantee.url}) Permissions from '{old_perm}' to '{new_perm}' on {package.name} ({package.url})")
-
     @staticmethod
     def grant_read(caller: User, package: Package, grantee: Union[User, Group]):
         PackageManager.update_permissions(caller, package, grantee, Permission.READ[0])
@@ -626,10 +602,6 @@ class PackageManager(object):
     def grant_write(caller: User, package: Package, grantee: Union[User, Group]):
         PackageManager.update_permissions(caller, package, grantee, Permission.WRITE[0])
 
-    @staticmethod
-    def grant_owner(caller: User, package: Package, grantee: Union[User, Group]):
-        PackageManager.update_permissions(caller, package, grantee, Permission.ALL[0])
-
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
@@ -672,11 +644,11 @@ class PackageManager(object):
         # EDIT START
         if data.get("classification"):
             if data["classification"] == "INTERNAL":
-                pack.classification_level = Package.Classification.RESTRICTED
+                pack.classification = Package.Classification.RESTRICTED
             elif data["classification"] == "RESTRICTED":
-                pack.classification_level = Package.Classification.RESTRICTED
+                pack.classification = Package.Classification.RESTRICTED
             elif data["classification"] == "SECRET":
-                pack.classification_level = Package.Classification.SECRET
+                pack.classification = Package.Classification.SECRET
 
                 if not "datapool" in data:
                     raise ValueError("Missing datapool in package")
@@ -828,14 +800,7 @@ class PackageManager(object):
             r.name = rule["name"]
             r.description = rule["description"]
             r.aliases = rule.get("aliases", [])
-
-            if rule.get("smirks") is not None:
-                r.smirks = rule["smirks"]
-            elif rule.get("reactionSmarts") is not None:
-                r.smirks = rule["reactionSmarts"]
-            else:
-                raise ValueError(f"No SMIRKS or reactionSmarts found for rule {rule['id']}")
-
+            r.smirks = rule["smirks"]
             r.reactant_filter_smarts = rule.get("reactantFilterSmarts", None)
             r.product_filter_smarts = rule.get("productFilterSmarts", None)
             r.save()
@@ -1910,51 +1875,12 @@ class SPathway(object):
 
         logger.info("Update done!")
 
-    def compute_bayes_probabilities(self) -> Dict[SEdge, float]:
-        """
-        Computes Bayes-adjusted probabilities for all edges in the pathway
-        by iterating level by level from depth 0 upwards, keyed on educt depth.
-
-        Returns:
-            A dict mapping each SEdge to its Bayes-adjusted probability.
-        """
-        bayes_probs: Dict[SEdge, float] = {}
-
-        # Group edges by their educt depth
-        edges_by_depth: Dict[int, List[SEdge]] = {}
-        for edge in self.edges:
-            d = edge.educts[0].depth
-            edges_by_depth.setdefault(d, []).append(edge)
-
-        for depth in sorted(edges_by_depth.keys()):
-            for edge in edges_by_depth[depth]:
-                if depth == 0:
-                    bayes_probs[edge] = edge.probability
-                else:
-                    predecessor_edges = [e for e in self.edges if edge.educts[0] in e.products]
-
-                    if not predecessor_edges or not all(
-                        e in bayes_probs for e in predecessor_edges
-                    ):
-                        # Predecessor not computed yet (e.g. same-depth product),
-                        # fall back to raw probability
-                        bayes_probs[edge] = edge.probability
-                    else:
-                        predecessor_avg = sum(bayes_probs[e] for e in predecessor_edges) / len(
-                            predecessor_edges
-                        )
-                        bayes_probs[edge] = predecessor_avg * edge.probability
-
-        return bayes_probs
-
     def to_json(self):
         nodes = []
         edges = []
 
         idx_lookup = {}
 
-        bayes_probs = self.compute_bayes_probabilities()
-
         for i, smiles in enumerate(self.smiles_to_node):
             n = self.smiles_to_node[smiles]
             idx_lookup[smiles] = i
@@ -1975,7 +1901,6 @@ class SPathway(object):
 
             if edge.probability:
                 e["probability"] = edge.probability
-                e["multiGenProbability"] = bayes_probs[edge]
 
             edges.append(e)
 

epdb/management/commands/localize_urls.py

@@ -44,25 +44,20 @@ class Command(BaseCommand):
             "EPModel",
             "ApplicabilityDomain",
             "EnzymeLink",
-            "AdditionalInformation",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-
-            update_fields = {"url": Replace(F("url"), Value(options["old"]), Value(options["new"]))}
-            if hasattr(obj_cls, "description"):
-                update_fields["description"] = Replace(
-                    F("description"), Value(options["old"]), Value(options["new"])
-                )
-
+            obj_cls.objects.update(
+                url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
+            )
             if issubclass(obj_cls, EnviPathModel):
-                update_fields["kv"] = Cast(
-                    Replace(
-                        Cast(F("kv"), output_field=TextField()),
-                        Value(options["old"]),
-                        Value(options["new"]),
-                    ),
-                    output_field=JSONField(),
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
                 )
-
-            obj_cls.objects.update(**update_fields)

epdb/management/commands/reaction_rule_mapping.py

@@ -1,97 +0,0 @@
-import logging
-
-from django.core.management.base import BaseCommand
-from django.db import transaction
-from uuid import uuid4
-from epdb.models import Package, ReactionExplanation
-from utilities.chem import FormatConverter
-from django.utils import timezone
-
-
-logger = logging.getLogger(__name__)
-
-
-class Command(BaseCommand):
-    def add_arguments(self, parser):
-        parser.add_argument(
-            "--rule-package",
-            action="append",
-            default=["32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"],
-            type=str,
-            help="UUID to process. Can be specified multiple times.",
-        )
-
-        parser.add_argument(
-            "--reaction-package",
-            action="append",
-            default=[
-                "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1",  # BBD
-                "f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf",  # Sediment
-                "521c547a-fd2a-491c-ad5b-7eaa1577fb65",  # Sludge
-                "5882df9c-dae1-4d80-a40e-db4724271456",  # Soil
-                "87a49584-d937-482c-9c33-25928dcb02a8",  # PFAS
-            ],
-            type=str,
-            help="UUID to process. Can be specified multiple times.",
-        )
-
-        parser.add_argument(
-            "--dry-run",
-            default=False,
-            action="store_true",
-            help="Perform dry run",
-        )
-
-    @transaction.atomic
-    def handle(self, *args, **options):
-        RUN_UUID = uuid4()
-        RUN_START = timezone.now()
-
-        rule_packages = Package.objects.filter(uuid__in=options["rule_package"])
-        reaction_packages = Package.objects.filter(uuid__in=options["reaction_package"])
-
-        rules = []
-        for rule_package in rule_packages:
-            rules.extend(rule_package.get_applicable_rules())
-
-        reactions = []
-        for reaction_package in reaction_packages:
-            reactions.extend(reaction_package.reactions)
-
-        logger.debug(f"Collected {len(rules)} rules and {len(reactions)} reactions.")
-
-        for i, reaction in enumerate(reactions):
-            logger.debug(f"Reaction {i} / {len(reactions)}")
-            for j, rule in enumerate(rules):
-                reactants, products = reaction.smirks().split(">>")
-
-                if len(reactants.split(".")) > 1:
-                    logger.debug(f"Skipping reaction {reaction.uuid} as it has multiple reactants.")
-                    break
-
-                products = products.split(".")
-
-                # Run reaction with rule
-                rule_products = rule.apply(reactants)
-
-                # Check if products match (in both directions if extras are not allowed)
-                for product_set in rule_products:
-                    covered, exact = FormatConverter.smiles_covered_by(
-                        products,
-                        product_set.product_set,
-                        standardize=True,
-                        canonicalize_tautomers=True,
-                        return_exact_match=True,
-                    )
-
-                    if covered and not options["dry-run"]:
-                        logger.debug(f"Reaction {reaction.uuid} explained by rule {rule.uuid}")
-                        re = ReactionExplanation()
-                        re.run_uuid = RUN_UUID
-                        re.run_start = RUN_START
-                        re.reaction = reaction
-                        re.rule = rule
-                        re.exact = exact
-                        re.save()
-                        # Its explained, if there are more sets skip them
-                        break

epdb/migrations/0028_auto_20260812_0902.py

@@ -1,113 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-12 09:02
-
-from django.conf import settings as s
-from django.db import migrations
-from envipy_additional_information import Likelihood, RuleLikelihood
-
-NEW_RULE = {
-    "parent": "bt0005",
-    "name": "bt0005-3667",
-    "description": "vic-unsubstituted Aromatic > vic-Dihydroxyaromatic",
-    "smirks": "[#8:7]([H])-[#6:1]([H])-1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]([H])-1-[#8:8]([H])>>[#8:7]([H])-[#6:1]=1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]=1-[#8:8]([H])",
-    "scenario_name": "bt0005-3667 aerobic likelihood",
-    "scenario_aerobic_likelihood": RuleLikelihood(likelihood=Likelihood.LIKELY),
-}
-
-RULE_FIXES = {
-    "bt0005-4282": "[c:1]([H])1:[c:2]([H]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1>>[c:1]([#8])1:[c:2]([#8]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1",
-    "bt0014-4215": "[c:1]([H])1[c:8][#6,#7;a:7][c:6][c:5][c:4]1[#8;!$([OH]c:[#6,#7;a:7]([OH])):9]([H])>>[#8:9]([H])[c:4]1:[c:5]:[c:6]:[#6,#7;a:7]:[c:8]:[c:1]1[#8]([H])",
-    # "bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([H:3])(=[#1,#6:7]).[#6;A:2]=O",
-    # CN1C=NC2=C1C(=O)N(C)C(=O)N2 not working anymore with bt0063-3938 if change above is applied
-    "bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O",
-    "bt0068-3564": "[#7:4]!@-[#6:2](!@-[#7:1])=[O:5]>>[#7:4]-[#6:2](-[O+0H1])=[O:5].[#7H1:1]",
-    "bt0180-2844": "[H][C:2]([#6:5]([H])([H])([H]))([#1,#6:4])!@-[#6:1]([H])([H])-[#6:3](-[#8-:8])=[O:6]>>[#6:5]([H])([H])([H])\\[#6:2](-[#1,#6:4])=[#6H:1]\\[#6:3](-[#8-:8])=[O:6]",
-    "bt0181-1278": "[#8-:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-[#6:3](-[H])=[#6:5](-Cl)-[#6:6](-[#8-:10])=[O:9]>>[O+0H1:10]-[#6:6](=[O:9])-[#6:5]=[#6:3]-1-[O+0:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-1",
-    "bt0298-3335": "[#6:1][N+:2]#[C:3]>>[#6:1]-[#7H2:2]-[#6:3]=O",
-    "bt0322-3393": "[H:10]\\[#6:6](=[#6:9](/[#6:1]([H])([H])([H]))-[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:5](-[#16:7])=[O:8]>>[H:10]\\[#6:6](-[#6:5](-[#16:7])=[O:8])=[#6:9](\\[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:1]-[#6](-[#8-])=O",
-    "bt0343-2675": "[#8-]-[#6](=O)-[c:1]1[c:6][cH:7][c:8](-[#7H2,#8H1:9])[cH:10][c:11]1>>[#8H][c:1]1[c:6][c:7][c:8]([*:9])[c:10][c:11]1",
-    "bt0350-3319": "[#6:6][#7:3][#6;!R:2]=[#7;!R:1][#6:5]>>[#6:5][#7:1][#6:2]=O.[#6:6][#7:3]",  # Trig before 5 -> all of them shouldn't
-    "bt0374-4081": "[cH:4]1[c:16][c:15][c:14][c:13][c:3]1[#7,#8:2][c:1]1[c:8][c:9][c:10][c:11][c:12]1>>[#7,#8:2]-[c:1]1[c:12][c:11][c:10][c:9][c:8]1[c:13]1[c:14][c:15][c:16][c:4](-[#8])[c:3]1-[#8]",
-    "bt0378-3188": "[#8-:7][c:1]1[c:6]([#7+]([#8-])=O)[c:5][c:4]([#7+:9]([#8-])=O)[c:3][c:2]1([#7+:8]([#8-])=O)>>[#8+0:7]=[#6:1]1-[#6:6]-[#6:5]-[#6:4]([#7+:9]([#8-])=O)-[#6:3]-[#6:2]1([#7+:8]([#8-])=O)",
-    "bt0379-3190": "[#9,#17,#35,#53]-[#6:1](-[H])-1-[#6:5]-,=[#6:6]-[#6:7]-,=[#6:8]-[#6:2](-[H])-1-[#9,#17,#35,#53]>>[#6:6]~1-[#6:7]~[#6:8]-[#6:2]=[#6:1]-[#6:5]~1",
-    "bt0393-3367": "[#6:5]-[#6:1](-[#7:2](-[H])(-[H]))=[S+:3]-[#8-:6]>>[#6:5]-[#6:1](=[#7H1:2])-[S+0:3](=[O])-[#8+0H1:6]",
-}
-
-
-def forward_func(apps, schema_editor):
-    ContentType = apps.get_model("contenttypes", "ContentType")
-
-    pkg_class = s.EPDB_PACKAGE_MODEL
-
-    if len(pkg_class.split(".")) != 2:
-        raise ValueError(
-            f"EPDB_PACKAGE_MODEL must be of the form 'app_label.model_name', got {pkg_class}"
-        )
-
-    app_label, model_name = pkg_class.split(".")
-    Package = apps.get_model(app_label, model_name)
-    SimpleAmbitRule = apps.get_model("epdb", "SimpleAmbitRule")
-    ParallelRule = apps.get_model("epdb", "ParallelRule")
-    Scenario = apps.get_model("epdb", "Scenario")
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-    simple_ambit_rule_ct = ContentType.objects.get_for_model(SimpleAmbitRule)
-
-    if Package.objects.filter(name="EAWAG-BBD").exists():
-        p = Package.objects.get(name="EAWAG-BBD")
-
-        if not SimpleAmbitRule.objects.filter(package=p, name=NEW_RULE["name"]).exists():
-            # Create Missing Rule
-            new_sr = SimpleAmbitRule()
-            new_sr.polymorphic_ctype = simple_ambit_rule_ct
-            new_sr.package = p
-            new_sr.name = NEW_RULE["name"]
-            new_sr.description = NEW_RULE["description"]
-            new_sr.smirks = NEW_RULE["smirks"]
-            new_sr.save()
-
-            new_sr.url = "{}/simple-ambit-rule/{}".format(new_sr.package.url, new_sr.uuid)
-            new_sr.save()
-
-            # Add likelihood
-            new_scen = Scenario()
-            new_scen.package = p
-            new_scen.name = NEW_RULE["scenario_name"]
-            new_scen.save()
-
-            new_scen.url = "{}/scenario/{}".format(new_scen.package.url, new_scen.uuid)
-            new_scen.save()
-
-            ai = NEW_RULE["scenario_aerobic_likelihood"]
-            new_add_inf = AdditionalInformation()
-            new_add_inf.package = p
-            new_add_inf.type = ai.__class__.__name__
-            new_add_inf.data = ai.model_dump(mode="json")
-            new_add_inf.scenario = new_scen
-            new_add_inf.save()
-
-            new_add_inf.url = "{}/additional-information/{}".format(
-                new_add_inf.scenario.url, new_add_inf.uuid
-            )
-            new_add_inf.save()
-
-            # Link Scenario
-            new_sr.scenarios.add(new_scen)
-
-            # Link to bt0005
-            pr = ParallelRule.objects.get(package=p, name="bt0005")
-            pr.simple_rules.add(new_sr)
-
-        # Update others
-        for rule_name, smirks in RULE_FIXES.items():
-            sr = SimpleAmbitRule.objects.get(package=p, name=rule_name)
-            sr.smirks = smirks
-            sr.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0027_alter_compound_aliases_and_more"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0029_reactionexplanation_reaction_explained_by.py

@@ -1,63 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-13 09:58
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0028_auto_20260812_0902"),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name="ReactionExplanation",
-            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"
-                    ),
-                ),
-                ("run_uuid", models.UUIDField()),
-                ("run_start", models.DateTimeField()),
-                ("exact", models.BooleanField(default=False)),
-                (
-                    "reaction",
-                    models.ForeignKey(
-                        on_delete=django.db.models.deletion.CASCADE, to="epdb.reaction"
-                    ),
-                ),
-                (
-                    "rule",
-                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
-                ),
-            ],
-            options={
-                "abstract": False,
-            },
-        ),
-        migrations.AddField(
-            model_name="reaction",
-            name="explained_by",
-            field=models.ManyToManyField(
-                related_name="explained_reactions",
-                through="epdb.ReactionExplanation",
-                to="epdb.rule",
-            ),
-        ),
-    ]

epdb/migrations/0030_auto_20260814_0741.py

@@ -1,37 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-14 07:41
-
-from django.db import migrations
-
-
-def forward_func(apps, schema_editor):
-    ContentType = apps.get_model("contenttypes", "ContentType")
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    models = {}
-
-    for c in ContentType.objects.all():
-        try:
-            models[(c.app_label, c.model)] = apps.get_model(c.app_label, c.model)
-        except Exception:
-            pass
-
-    for ai in AdditionalInformation.objects.all():
-        if ai.url is None:
-            if ai.content_type is None:
-                ai.url = "{}/additional-information/{}".format(ai.scenario.url, ai.uuid)
-            else:
-                model = models[(ai.content_type.app_label, ai.content_type.model)]
-                obj = model.objects.get(pk=ai.object_id)
-                ai.url = "{}/additional-information/{}".format(obj.url, ai.uuid)
-
-            ai.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0029_reactionexplanation_reaction_explained_by"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/models.py

@@ -859,15 +859,9 @@ class Compound(
     @property
     def related_reactions(self):
         return (
-            (
-                Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
-                | Reaction.objects.filter(
-                    package=self.package, products__in=[self.default_structure]
-                )
-            )
-            .distinct()
-            .order_by("name")
-        )
+            Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
+            | Reaction.objects.filter(package=self.package, products__in=[self.default_structure])
+        ).order_by("name")
 
     @property
     def related_nodes(self):
@@ -937,10 +931,8 @@ class Compound(
             found_structure = qs.first()
             found_compound = found_structure.compound
 
-            # We've only found the standardized one, create the very structure
-            _ = found_compound.add_structure(
-                smiles, molfile=molfile, name=name, description=description
-            )
+            # We've only found the normalized one, create the very structure
+            new_structure = found_compound.add_structure(smiles, molfile=molfile, name=name, description=description)
 
             if name:
                 found_compound.add_alias(name)
@@ -1274,15 +1266,14 @@ class CompoundStructure(
         if name is not None:
             cs.name = name
 
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
+        if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.compound = compound
         cs.smiles = smiles
+        cs.compound = compound
 
-        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
-        if molfile is not None:
+        # Check if molfile is present and valid
+        if molfile is not None and molfile.strip() != "":
             cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
@@ -1658,9 +1649,6 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         # Deduplication check
         query = ParallelRule.objects.annotate(
             srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@@ -1672,19 +1660,15 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(
-                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
-                )
-
-            found_rule = existing_rule_qs.first()
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
+                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+            return existing_rule_qs.first()
 
         r = ParallelRule()
         r.package = package
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1741,14 +1725,6 @@ class SequentialRuleOrdering(models.Model):
     order_index = models.IntegerField(null=False, blank=False)
 
 
-class ReactionExplanation(TimeStampedModel):
-    run_uuid = models.UUIDField(null=False, blank=False)
-    run_start = models.DateTimeField(null=False, blank=False)
-    reaction = models.ForeignKey("epdb.Reaction", on_delete=models.CASCADE)
-    rule = models.ForeignKey("epdb.Rule", on_delete=models.CASCADE)
-    exact = models.BooleanField(default=False)
-
-
 class Reaction(
     EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin, AdditionalInformationMixin
 ):
@@ -1774,12 +1750,6 @@ class Reaction(
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
-    explained_by = models.ManyToManyField(
-        "epdb.Rule",
-        through="ReactionExplanation",
-        related_name="explained_reactions",
-    )
-
     def _url(self):
         return "{}/reaction/{}".format(self.package.url, self.uuid)
 
@@ -1794,6 +1764,7 @@ class Reaction(
         rules: Union[Rule | List[Rule]] = None,
         multi_step: bool = False,
     ):
+
         # Clean for potential XSS
         if name is not None and name.strip() != "":
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1863,10 +1834,8 @@ class Reaction(
         r = Reaction()
         r.package = package
 
-        if name is None or name == "":
-            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
-
-        r.name = name
+        if name is not None:
+            r.name = name
 
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -2193,7 +2162,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
 
             row += [cs.smiles, cs.get_name(), n.depth]
 
-            edges = self.edges.filter(end_nodes=n)
+            edges = self.edges.filter(end_nodes__in=[n])
             if len(edges):
                 for e in edges:
                     _row = row.copy()
@@ -2486,7 +2455,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "name": self.get_name(),
             "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
-            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.get_scenarios()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2495,7 +2464,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.get_proposed_info(),
+            "proposed": self.is_proposed_intermediate(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2584,15 +2553,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return data
 
-    def simple_json(self, include_description=False):
-        res = super().simple_json()
-        name = res.get("name", None)
-        if name == "no name":
-            res["name"] = self.default_node_label.get_name()
-
-        return res
-
-    def get_proposed_info(self):
+    def is_proposed_intermediate(self):
         collected = defaultdict(dict)
         for ai in self.additional_information.filter(
             type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
@@ -2605,7 +2566,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
                 collected[str(ai.scenario.uuid)]["proposed"] = True
 
             if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level.value
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
 
             if ai.type == "TransformationProductImportance":
                 collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
@@ -2614,14 +2575,13 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return list(collected.values())
 
-    def get_scenarios(self):
-        qs = self.scenarios.all()
-        qs |= Scenario.objects.filter(
-            id__in=self.additional_information.filter(scenario__isnull=False)
-            .values_list("scenario", flat=True)
-            .distinct()
-        )
-        return qs.distinct()
+    def simple_json(self, include_description=False):
+        res = super().simple_json()
+        name = res.get("name", None)
+        if name == "no name":
+            res["name"] = self.default_node_label.get_name()
+
+        return res
 
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
@@ -2878,58 +2838,6 @@ class PackageBasedModel(EPModel):
 
         return res
 
-    def parameters(self):
-        params = {
-            "Model Evaluation Threshold": f"{self.threshold:.2f}",
-            "Multi Gen Evaluation": "Yes" if self.multigen_eval else "No",
-        }
-
-        if self.app_domain:
-            params["Applicability Domain Num Neighbors"] = f"{self.app_domain.num_neighbours:.2f}"
-            params["Applicability Domain Reliability Threshold"] = (
-                f"{self.app_domain.reliability_threshold:.2f}"
-            )
-            params["Applicability Domain Local Compatibility Threshold"] = (
-                f"{self.app_domain.local_compatibilty_threshold:.2f}"
-            )
-
-        return params
-
-    def statistics(self):
-        from sklearn.metrics import auc
-
-        recall = list(self.eval_results["average_recall_per_threshold"].values())
-        precision = list(self.eval_results["average_precision_per_threshold"].values())
-        mg_recall = list(
-            self.eval_results.get("multigen_average_recall_per_threshold", {}).values()
-        )
-        mg_precision = list(
-            self.eval_results.get("multigen_average_precision_per_threshold", {}).values()
-        )
-
-        return {
-            "accuracy": [
-                self.eval_results["average_accuracy"],
-                self.eval_results.get("multigen_average_accuracy"),
-            ],
-            "precision": [
-                self.eval_results["average_precision_per_threshold"][f"{self.threshold:.2f}"],
-                self.eval_results.get("multigen_average_precision_per_threshold", {}).get(
-                    f"{self.threshold:.2f}"
-                ),
-            ],
-            "recall": [
-                self.eval_results["average_recall_per_threshold"][f"{self.threshold:.2f}"],
-                self.eval_results.get("multigen_average_recall_per_threshold", {}).get(
-                    f"{self.threshold:.2f}"
-                ),
-            ],
-            "Area under PR Curve": [
-                auc(recall, precision),
-                auc(mg_recall, mg_precision) if self.multigen_eval else None,
-            ],
-        }
-
     @cached_property
     def applicable_rules(self) -> List["Rule"]:
         """
@@ -3086,14 +2994,7 @@ class PackageBasedModel(EPModel):
 
             prec, rec = dict(), dict()
 
-            thresholds = list(np.arange(0, 1.05, 0.05))
-
-            # Add specific threshold set during object creation if not already present
-            if np.float64(threshold) not in thresholds:
-                thresholds.append(np.float64(threshold))
-                thresholds.sort()
-
-            for t in thresholds:
+            for t in np.arange(0, 1.05, 0.05):
                 temp_thresholded = (y_pred_filtered >= t).astype(int)
                 prec[f"{t:.2f}"] = precision_score(
                     y_test_filtered, temp_thresholded, zero_division=0
@@ -3103,12 +3004,7 @@ class PackageBasedModel(EPModel):
             return acc, prec, rec
 
         def evaluate_mg(model, pathways: Union[QuerySet["Pathway"] | List["Pathway"]], threshold):
-            thresholds = list(np.arange(0, 1.05, 0.05))
-
-            # Add specific threshold set during object creation if not already present
-            if np.float64(threshold) not in thresholds:
-                thresholds.append(np.float64(threshold))
-                thresholds.sort()
+            thresholds = np.arange(0.1, 1.1, 0.1)
 
             precision = {f"{t:.2f}": [] for t in thresholds}
             recall = {f"{t:.2f}": [] for t in thresholds}
@@ -3134,7 +3030,7 @@ class PackageBasedModel(EPModel):
 
             s = Setting()
             s.model = mod
-            s.model_threshold = 0.0
+            s.model_threshold = thresholds.min()
             s.max_depth = 10
             s.max_nodes = 50
 
@@ -3158,17 +3054,14 @@ class PackageBasedModel(EPModel):
             for t in thresholds:
                 for true, pred in zip(pathways, pred_pathways):
                     acc, pre, rec = multigen_eval(true, pred, t)
-
-                    if f"{t:.2f}" == f"{threshold:.2f}":
-                        mg_acc += acc
-
+                    if abs(t - threshold) < 0.01:
+                        mg_acc = acc
                     precision[f"{t:.2f}"].append(pre)
                     recall[f"{t:.2f}"].append(rec)
 
-            avg_mg_acc = mg_acc / len(root_compounds)
             precision = {k: sum(v) / len(v) if len(v) > 0 else 0 for k, v in precision.items()}
             recall = {k: sum(v) / len(v) if len(v) > 0 else 0 for k, v in recall.items()}
-            return avg_mg_acc, precision, recall
+            return mg_acc, precision, recall
 
         # If there are eval packages perform single generation evaluation on them instead of random splits
         if self.eval_packages.count() > 0:
@@ -4300,9 +4193,6 @@ class ClassifierPluginModel(PackageBasedModel):
         instance = impl(conf)
         return instance
 
-    def parameters(self):
-        return self.instance().parameters()
-
     def build_dataset(self):
         """
         Required by general model contract but actual implementation resides in plugin.
@@ -4523,9 +4413,6 @@ class PropertyPluginModel(PackageBasedModel):
         instance = impl()
         return instance
 
-    def parameters(self):
-        return self.instance().parameters()
-
     def build_dataset(self):
         """
         Required by general model contract but actual implementation resides in plugin.

epdb/tasks.py

@@ -477,7 +477,8 @@ def batch_predict(
             limit=None,
             setting_overrides={
                 "max_nodes": num_tps,
-                "model_threshold": 0.0,
+                "max_depth": num_tps,
+                "model_threshold": 0.001,
             },
         )
 

epdb/views.py

@@ -61,7 +61,6 @@ from .models import (
 )
 
 logger = logging.getLogger(__name__)
-auth_log = logging.getLogger("auth")
 
 Package = s.GET_PACKAGE_MODEL()
 
@@ -72,18 +71,6 @@ def log_post_params(request):
             logger.debug(f"{k}\t{v}")
 
 
-def get_remote_address(request):
-    remote_address = ""
-
-    if request is not None:
-        remote_address = request.META.get("HTTP_X_FORWARDED_FOR")
-
-        if not remote_address:
-            remote_address = request.META.get("REMOTE_ADDR", "")
-
-    return remote_address
-
-
 def get_error_handler_context(request, for_user=None) -> Dict[str, Any]:
     current_user = _anonymous_or_real(request)
 
@@ -160,20 +147,6 @@ def handler500(request):
     return render(request, "errors/error.html", context, status=500)
 
 
-def delete_with_log(request, obj):
-    caller = request.user
-    obj_type = obj.__class__.__name__
-
-    try:
-        obj.delete()
-        auth_log.info(f"{caller.username} ({caller.url}) deleted {obj_type}: {obj.name} ({obj.url})")
-    except Exception as e:
-        logger.info(f"Tried to delete {obj_type}: {obj.name} ({obj.url}) but deletion failed! Exception {e}")
-        auth_log.info(
-            f"{caller.username} ({caller.url}) tried to delete {obj_type}: {obj.name} ({obj.url}) but deletion failed!")
-        raise e
-
-
 def login(request):
     context = get_base_context(request)
 
@@ -232,18 +205,11 @@ def login(request):
         if user is not None:
             login(request, user)
 
-            if user.is_superuser:
-                auth_log.error(f"admin ({user.username}) login attempt by {get_remote_address(request)} successful")
-
             if next := request.POST.get("next"):
                 return redirect(next)
 
             return redirect(reverse("index"))
         else:
-            if _user := User.objects.get(email=email):
-                if _user.is_superuser:
-                    auth_log.error(f"admin ({_user.username}) login attempt by {get_remote_address(request)} failed")
-
             context["message"] = "Login failed!"
             return render(request, "static/login.html", context)
     else:
@@ -424,7 +390,7 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
             # EDIT START
-            "secret_groups": Group.objects.filter(secret=True, user_member=current_user),
+            "secret_groups": Group.objects.filter(secret=True),
             # EDIT END
         },
     }
@@ -560,7 +526,6 @@ def batch_predict_pathway(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Batch Predict Pathway"
     context["meta"]["current_package"] = context["meta"]["user"].default_package
-    context["batch_predict_max_compounds"] = s.BATCH_PREDICT_MAX_COMPOUNDS
 
     return render(request, "batch_predict_pathway.html", context)
 
@@ -1145,23 +1110,19 @@ def package_model(request, package_uuid, model_uuid):
                 for pr in pred_res:
                     if len(pr) > 0:
                         products = []
-
                         for prod_set in pr.product_sets:
                             logger.debug(f"Checking {prod_set}")
                             products.append(tuple([x for x in prod_set]))
 
-                        products = list(set(products))
-
-                        for prod in products:
-                            res["pred"].append(
-                                {
-                                    "products": list(prod),
-                                    "probability": pr.probability,
-                                    "btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
-                                    if pr.rule is not None
-                                    else None,
-                                }
-                            )
+                        res["pred"].append(
+                            {
+                                "products": list(set(products)),
+                                "probability": pr.probability,
+                                "btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
+                                if pr.rule is not None
+                                else None,
+                            }
+                        )
 
                         # Sort data by prob desc
                         res["pred"] = sorted(
@@ -1320,8 +1281,7 @@ def package(request, package_uuid):
                         "You cannot delete the default package. If you want to delete this package you have to set another default package first.",
                     )
 
-                delete_with_log(request, current_package)
-
+                logger.debug(current_package.delete())
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
@@ -1988,24 +1948,9 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reaction_smiles = request.POST.get("reaction-smiles")
-
-        if reaction_smiles is None or reaction_smiles.strip() == "":
-            return error(
-                request,
-                "Reaction SMILES is empty / missing",
-                "No reaction SMILES provided. Please provide a SMILES for the reaction.",
-            )
-
-        if not FormatConverter.is_valid_smirks(reaction_smiles):
-            return error(
-                request,
-                "Reaction SMILES is invalid",
-                f"The provided reactions SMILES {reaction_smiles} is invalid",
-            )
-
-        educts = reaction_smiles.split(">>")[0].split(".")
-        products = reaction_smiles.split(">>")[1].split(".")
+        reactions_smirks = request.POST.get("reaction-smirks")
+        educts = reactions_smirks.split(">>")[0].split(".")
+        products = reactions_smirks.split(">>")[1].split(".")
 
         r = Reaction.create(
             current_package,
@@ -2312,7 +2257,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
     elif request.method == "POST":
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_pathway)
+                current_pathway.delete()
                 return redirect(current_package.url + "/pathway")
             else:
                 return HttpResponseBadRequest()
@@ -2434,8 +2379,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
 
-        node_smiles = request.POST.get("node-smiles")
-        node_molfile = request.POST.get("node-molfile")
+        node_smiles = request.POST.get("node-smiles").strip()
+        node_molfile = request.POST.get("node-molfile").strip()
 
         try:
             current_pathway.add_node(
@@ -2530,7 +2475,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
                 # pre_delete signal will take care of edge deletion
-                delete_with_log(request, current_node)
+                current_node.delete()
 
                 return redirect(current_pathway.url)
             else:
@@ -2684,7 +2629,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_edge)
+                current_edge.delete()
                 return redirect(current_pathway.url)
 
         if "selected-scenarios" in request.POST:
@@ -3046,7 +2991,7 @@ def group(request, group_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_group)
+                current_group.delete()
                 return redirect(s.SERVER_URL + "/group")
             else:
                 return HttpResponseBadRequest()

epiuclid/serializers/pathway_mapper.py

@@ -120,6 +120,13 @@ class PathwayMapper:
             )
             bundle.reference_substances.append(ref_sub)
 
+            sub = IUCLIDSubstanceData(
+                uuid=sub_uuid,
+                name=compound.name,
+                reference_substance_uuid=ref_sub_uuid,
+            )
+            bundle.substances.append(sub)
+
         if not export.compounds:
             return bundle
 
@@ -138,16 +145,6 @@ class PathwayMapper:
         if not root_compound_pks:
             return bundle
 
-        for root_pk in root_compound_pks:
-            root_sub_uuid, root_ref_uuid = seen_compounds[root_pk]
-            bundle.substances.append(
-                IUCLIDSubstanceData(
-                    uuid=root_sub_uuid,
-                    name=compound_names[root_pk],
-                    reference_substance_uuid=root_ref_uuid,
-                )
-            )
-
         edge_templates: list[tuple[UUID, frozenset[int], tuple[int, ...], tuple[UUID, ...]]] = []
         for edge in sorted(export.edges, key=lambda item: str(item.edge_uuid)):
             parent_compound_pks = sorted(
@@ -351,8 +348,7 @@ class PathwayMapper:
 
         props = SoilPropertiesData()
 
-        for ai_obj in ai_list:
-            ai = ai_obj.get()
+        for ai in ai_list:
             if isinstance(ai, SoilTexture1) and props.soil_type is None:
                 props.soil_type = ai.type.value
             elif isinstance(ai, SoilTexture2):

epiuclid/tests/test_api.py

@@ -70,7 +70,8 @@ class IUCLIDExportAPITest(TestCase):
             names = zf.namelist()
             self.assertIn("manifest.xml", names)
             i6d_files = [n for n in names if n.endswith(".i6d")]
-            self.assertEqual(len(i6d_files), 4)
+            # 2 substances + 2 ref substances + 1 ESR = 5 i6d files
+            self.assertEqual(len(i6d_files), 5)
 
     def test_anonymous_returns_401(self):
         self.client.logout()

epiuclid/tests/test_i6z.py

@@ -7,11 +7,6 @@ from uuid import uuid4
 
 from django.test import SimpleTestCase, tag
 
-from epapi.v1.interfaces.iuclid.dto import (
-    PathwayCompoundDTO,
-    PathwayEdgeDTO,
-    PathwayExportDTO,
-)
 from epiuclid.serializers.i6z import I6ZSerializer
 from epiuclid.serializers.pathway_mapper import (
     IUCLIDDocumentBundle,
@@ -19,24 +14,9 @@ from epiuclid.serializers.pathway_mapper import (
     IUCLIDReferenceSubstanceData,
     IUCLIDSubstanceData,
     IUCLIDTransformationProductEntry,
-    PathwayMapper,
 )
 
 
-def _unlinked_documents(manifest_xml: str) -> list[tuple[str | None, str]]:
-    ns = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
-    root = ET.fromstring(manifest_xml)
-    base = root.findtext(f"{{{ns}}}base-document-uuid")
-    linked_targets: set[str | None] = {base}
-    docs: dict[str, str | None] = {}
-    for doc in root.findall(f".//{{{ns}}}document"):
-        uuid = doc.findtext(f"{{{ns}}}uuid")
-        docs[uuid] = doc.findtext(f"{{{ns}}}type")
-        for link in doc.findall(f"{{{ns}}}links/{{{ns}}}link"):
-            linked_targets.add(link.findtext(f"{{{ns}}}ref-uuid"))
-    return [(doc_type, uuid) for uuid, doc_type in docs.items() if uuid not in linked_targets]
-
-
 def _make_bundle() -> IUCLIDDocumentBundle:
     ref_uuid = uuid4()
     sub_uuid = uuid4()
@@ -217,29 +197,3 @@ class I6ZSerializerTest(SimpleTestCase):
             }
             self.assertIn(parent_ref_key, reference_links)
             self.assertIn(product_ref_key, reference_links)
-
-    def test_multi_compound_pathway_has_no_unlinked_documents(self):
-        compounds = [
-            PathwayCompoundDTO(pk=1, name="Root", smiles="c1ccccc1"),
-            PathwayCompoundDTO(pk=2, name="P1", smiles="CCO"),
-            PathwayCompoundDTO(pk=3, name="P2", smiles="CCN"),
-            PathwayCompoundDTO(pk=4, name="P3", smiles="CCC"),
-        ]
-        export = PathwayExportDTO(
-            pathway_uuid=uuid4(),
-            pathway_name="Regression Pathway",
-            compounds=compounds,
-            edges=[
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[2]),
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[3]),
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[2], end_compound_pks=[4]),
-            ],
-            root_compound_pks=[1],
-        )
-        bundle = PathwayMapper().map(export)
-        data = I6ZSerializer().serialize(bundle)
-
-        with zipfile.ZipFile(io.BytesIO(data)) as zf:
-            manifest_xml = zf.read("manifest.xml").decode("utf-8")
-
-        self.assertEqual(_unlinked_documents(manifest_xml), [])

epiuclid/tests/test_pathway_mapper.py

@@ -31,7 +31,7 @@ class PathwayMapperTest(SimpleTestCase):
         )
         bundle = PathwayMapper().map(export)
 
-        self.assertEqual(len(bundle.substances), 1)
+        self.assertEqual(len(bundle.substances), 2)
         self.assertEqual(len(bundle.reference_substances), 2)
         self.assertEqual(len(bundle.endpoint_study_records), 1)
 
@@ -49,7 +49,8 @@ class PathwayMapperTest(SimpleTestCase):
         )
         bundle = PathwayMapper().map(export)
 
-        self.assertEqual(len(bundle.substances), 1)
+        # 2 unique compounds -> 2 substances, 2 ref substances
+        self.assertEqual(len(bundle.substances), 2)
         self.assertEqual(len(bundle.reference_substances), 2)
         # One endpoint study record per pathway
         self.assertEqual(len(bundle.endpoint_study_records), 1)

static/js/api/additional-information.js

@@ -186,40 +186,6 @@ window.AdditionalInformationApi = {
     return this._handleResponse(response, "createItem");
   },
 
-    /**
-   * Create new additional information and attach it to an object.
-
-   * @param {string} modelName - Name/type of the additional information model
-   * @param {Object} data - Data for the new item
-   * @param {string} attachObjectUrl - UUID of the object this data should be attached to
-   * @param {string} scenarioUuid - UUID of the scenario
-   * @returns {Promise<{status: string, uuid: string}>}
-   */
-  async createItemOnNonScenarioObject(modelName, data, attachObjectUrl, scenarioUuid) {
-    const sanitizedData = this.sanitizePayload(data);
-    this._log("createItemOnNonScenarioObject", { modelName, data: sanitizedData, attachObjectUrl, scenarioUuid });
-
-    sanitizedData.attach_obj_url = attachObjectUrl;
-    if (scenarioUuid) {
-      sanitizedData.scenario_uuid = scenarioUuid;
-    }
-
-
-    // Normalize model name to lowercase
-    const normalizedName = modelName.toLowerCase();
-
-    const response = await fetch(
-      `/api/v1/information/${normalizedName}/`,
-      {
-        method: "POST",
-        headers: this._buildHeaders(),
-        body: JSON.stringify(sanitizedData),
-      },
-    );
-
-    return this._handleResponse(response, "createItemOnNonScenarioObject");
-  },
-
   /**
    * Delete additional information from a scenario
    * @param {string} scenarioUuid - UUID of the scenario

static/js/ketcher2/DEVNOTES.md

@@ -0,0 +1,57 @@
+## Prerequisites
+
+   Stable [Node.js](https://nodejs.org) version
+
+## Build instructions
+
+    npm install
+    npm start
+
+For production build:
+
+    npm run build
+   
+You could also build only the style with command
+
+    npm run style
+
+## Indigo Service
+
+Ketcher uses Indigo Service for server operations.
+You can use `--api-path` parameter to start with it:
+
+    npm start -- --api-path=<server-url>
+For production build:
+
+    npm run build -- --api-path=<server-url>
+
+You can find the instruction for service installation
+[here](http://lifescience.opensource.epam.com/indigo/service/index.html).
+
+## Tests instructions
+
+You can start tests for input/output `.mol`-files and render.
+
+    npm test
+
+Tests are started for all structures in `test/fixtures` directory.
+
+To start the tests separately:
+
+    npm run test-io
+    npm run test-render
+
+#### Parameters
+
+You can use following parameters to start the tests:
+ - `--fixtures` - for the choice of a specific directory with molecules
+ - `--headless` - for start of the browser in headless mode
+
+```
+npm run test-render -- --fixtures=fixtures/super --headless
+```
+
+If you have added new structures for testing to the `test/fixtures` directory 
+you have to generate `svg` from them for correct render-test with:
+
+    npm run generate-svg    

static/js/ketcher2/LICENSE

@@ -0,0 +1,184 @@
+                               Apache License
+                         Version 2.0, January 2004
+                      http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+    "License" shall mean the terms and conditions for use, reproduction,
+    and distribution as defined by Sections 1 through 9 of this document.
+    "Licensor" shall mean the copyright owner or entity authorized by
+    the copyright owner that is granting the License.
+    "Legal Entity" shall mean the union of the acting entity and all
+    other entities that control, are controlled by, or are under common
+    control with that entity. For the purposes of this definition,
+    "control" means (i) the power, direct or indirect, to cause the
+    direction or management of such entity, whether by contract or
+    otherwise, or (ii) ownership of fifty percent (50%) or more of the
+    outstanding shares, or (iii) beneficial ownership of such entity.
+    "You" (or "Your") shall mean an individual or Legal Entity
+    exercising permissions granted by this License.
+    "Source" form shall mean the preferred form for making modifications,
+    including but not limited to software source code, documentation
+    source, and configuration files.
+    "Object" form shall mean any form resulting from mechanical
+    transformation or translation of a Source form, including but
+    not limited to compiled object code, generated documentation,
+    and conversions to other media types.
+    "Work" shall mean the work of authorship, whether in Source or
+    Object form, made available under the License, as indicated by a
+    copyright notice that is included in or attached to the work
+    (an example is provided in the Appendix below).
+    "Derivative Works" shall mean any work, whether in Source or Object
+    form, that is based on (or derived from) the Work and for which the
+    editorial revisions, annotations, elaborations, or other modifications
+    represent, as a whole, an original work of authorship. For the purposes
+    of this License, Derivative Works shall not include works that remain
+    separable from, or merely link (or bind by name) to the interfaces of,
+    the Work and Derivative Works thereof.
+    "Contribution" shall mean any work of authorship, including
+    the original version of the Work and any modifications or additions
+    to that Work or Derivative Works thereof, that is intentionally
+    submitted to Licensor for inclusion in the Work by the copyright owner
+    or by an individual or Legal Entity authorized to submit on behalf of
+    the copyright owner. For the purposes of this definition, "submitted"
+    means any form of electronic, verbal, or written communication sent
+    to the Licensor or its representatives, including but not limited to
+    communication on electronic mailing lists, source code control systems,
+    and issue tracking systems that are managed by, or on behalf of, the
+    Licensor for the purpose of discussing and improving the Work, but
+    excluding communication that is conspicuously marked or otherwise
+    designated in writing by the copyright owner as "Not a Contribution."
+    "Contributor" shall mean Licensor and any individual or Legal Entity
+    on behalf of whom a Contribution has been received by Licensor and
+    subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+    this License, each Contributor hereby grants to You a perpetual,
+    worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+    copyright license to reproduce, prepare Derivative Works of,
+    publicly display, publicly perform, sublicense, and distribute the
+    Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
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+    worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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+
+ 4. Redistribution. You may reproduce and distribute copies of the
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+    meet the following conditions:
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+        Derivative Works a copy of this License; and
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+    (c) You must retain, in the Source form of any Derivative Works
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+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
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+ 6. Trademarks. This License does not grant permission to use the trade
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+
+ 8. Limitation of Liability. In no event and under no legal theory,
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+    unless required by applicable law (such as deliberate and grossly
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+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+    To apply the Apache License to your work, attach the following
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+
+ Copyright 2017 EPAM Systems
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
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+ See the License for the specific language governing permissions and
+ limitations under the License.

static/js/ketcher2/LICENSE-history

@@ -0,0 +1,5 @@
+ Ketcher version 1 was released under GNU Affero General Public License v3.0
+ Ketcher version 2 was re-licensed under Apache License, Version 2.
+
+ Current version is distributed by the terms of the Apache License, Version 2.
+ which is included in the file LICENSE, found at the root of the Ketcher source tree.

static/js/ketcher2/NOTICE

@@ -0,0 +1,19 @@
+ Ketcher
+ Copyright (C) 2017 EPAM Systems
+ This product includes software developed at EPAM Systems, Inc.
+
+ In addition, this product contains dependencies on files licensed under:
+
+ The FreeBSD Documentation License https://www.freebsd.org/copyright/freebsd-doc-license.html
+ The MIT License https://opensource.org/licenses/MIT
+ X11 License http://www.xfree86.org/3.3.6/COPYRIGHT2.html
+ Academic Free License https://opensource.org/licenses/AFL-3.0
+ Apache License, Version 1.0 http://www.apache.org/licenses/LICENSE-1.0
+ Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0
+ The 2-Clause BSD License https://opensource.org/licenses/BSD-2-Clause
+ The 3-Clause BSD License https://opensource.org/licenses/BSD-3-Clause
+ ISC License (ISC) https://opensource.org/licenses/ISC
+ GNU Lesser General Public License version 2.1 https://opensource.org/licenses/LGPL-2.1
+ The Mozilla Public License https://opensource.org/licenses/MPL-1.0
+ Public Domain https://wiki.creativecommons.org/wiki/Public_domain
+ Unlicense http://unlicense.org/

static/js/ketcher2/README.md

@@ -0,0 +1,35 @@
+# EPAM Ketcher projects
+Copyright (c) 2017 EPAM Systems, Inc
+
+Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.
+
+## KEY FEATURES
+* Fast 2D structure representation that satisfies common chemical drawing standards
+* 3D structure visualization
+* Draw and edit structures using major tools: Atom Tool, Bond Tool, and Template Tool
+* Template library (including custom and user's templates)
+* Add atom and bond basic properties and query features, add aliases and Generic groups
+* Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
+* Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) and Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout) 
+* Aromatize/De-aromatize Tool
+* Calculate CIP Descriptors Tool
+* Structure Check Tool
+* MW and Structure Parameters Calculate Tool 
+* Stereochemistry support during editing, loading, and saving chemical structures
+* Storing history of actions, with the ability to rollback to previous state
+* Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
+* Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group) 
+* Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping) 
+* Flip/Rotate Tool
+* Zoom in/out, hotkeys, cut/copy/paste
+* OCR - ability to recognize structures at pictures (image files) and reproduce them
+* Copy and paste between different chemical editors
+* Settings support (Rendering, Displaying, Debugging)
+* Use of SVG to achieve best quality in-browser chemical structure rendering
+* Languages: JavaScript with third-party libraries
+
+## Build instructions
+Please read [DEVNOTES.md](DEVNOTES.md) for details.
+
+## License
+Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.

static/js/ketcher2/doc/help.md

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+**Ketcher** is a tool to draw molecular structures and chemical
+reactions.
+
+# Ketcher Overview
+
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions. Ketcher operates in two modes, the Server mode with most
+functions available and the client mode with limited functions
+available.
+
+**Ketcher** consists of the following elements:
+
+ ![](main.png "Main window")
+
+**Note** : Depending on the screen size, some tools on the _Tool
+palette_ can be displayed in expanded or collapsed forms.
+
+Using the _Tool palette_, you can
+
+  * draw and edit a molecule or reaction by clicking on and dragging
+  atoms, bonds, and other elements provided with the buttons on the
+  _Atoms_ toolbar and _Tool palette_;
+
+  * delete any element of the drawing (atom or bond) by clicking on it
+  with the Erase tool;
+
+  * delete the entire molecule or its fragment by a lasso,
+  rectangular, or fragment selection with the Erase tool;
+
+  * draw special structures (see the following sections);
+
+  * select the entire molecule or its fragment in one of the following
+  ways (click on the button to see the list of available options):
+
+    * in the expanded form
+
+      ![](expanded.png "Expanded tool")
+
+    * in the collapsed form
+
+      ![](collapsed.png "Collapsed tool")
+
+To select one atom or bond, click Lasso or Rectangle Selection tool,
+and then click the atom or bond.
+
+To select the entire structure:
+
+  * Select the Fragment Selection tool and then click the object.
+
+  * Select the Lasso or Rectangle Selection tool, and then drag the
+  mouse to select the object.
+
+  * `Ctrl-click` with the Lasso or Rectangle Selection tool.
+
+To select multiple atoms, bonds, structures, or other objects, do one
+of the following:
+
+  * `Shift-click` with the Lasso or Rectangle Selection tool selects
+  some (connected or not) atoms/bonds.
+
+  * With the Lasso or Rectangle Selection tool click and drag the
+  mouse around the atoms, bonds, or structures that you want to
+  select.
+
+**Note** : `Ctrl+Shift-click` with the Lasso or Rectangle Selection tool
+selects several structures.
+
+You can use the buttons of the _Main_ toolbar:
+
+
+ ![](toolbar.png "Tolbar")
+
+  * **Clear Canvas** (1) button to start drawing a new molecule; this
+  command clears the drawing area;
+
+  * **Open…** (2) and **Save As…** (3) buttons to import a molecule
+  from a molecular file or save it to a supported molecular file
+  format;
+
+  * **Undo** / **Redo** (4), **Cut** (5), **Copy** (6), **Paste** (7),
+  **Zoom In** / **Out** (8), and **Scaling** (9) buttons to perform
+  the corresponding actions;
+
+  * **Layout** button (10) to change the position of the structure to
+  work with it with the most convenience;
+
+  * **Clean Up** button (11) to improve the appearance of the
+  structure by assigning them uniform bond lengths and angles.
+
+  * **Aromatize** / **Dearomatize** buttons (12) to mark aromatic
+  structures (to convert a structure to the Aromatic or Kekule
+  presentation);
+
+  * **Calculate CIP** button (13) to determine R/S and E/Z
+  configurations;
+
+  * **Check Structure** button (14) to check the following properties
+  of the structure:
+
+    ![](check.png "Structure Ckeck")
+
+  * **Calculated Values** button (15) to display some properties of
+  the structure:
+
+    ![](analyse.png "Calculated Values")
+
+  * **Recognize Molecule** button (16) to recognize a structure in the
+  image file and load it to the canvas;
+
+  * **3D Viewer** button (17) to open the structure in the
+  three-dimensional Viewer;
+
+  * **Settings** button (18) to make some settings for molecular
+    files:
+    
+    ![](settings.png "Settings")
+
+  * **Help** button (19) to view Help;
+    
+  * **About** button (20) to display version and copyright information
+  of the program.
+
+**Note** : **Layout,** **Clean Up,** **Aromatize** / **Dearomatize,**
+**Calculate CIP,** **Check Structure,** **Calculated Values,**
+**Recognize Molecule** and **3D View** buttons are active only in the
+Server mode.
+
+# 3D Viewer
+
+The structure appears in a modal window after clicking on the **3D
+Viewer** button:
+
+ ![](miew.png "3D Viewer")
+
+You can perform the following actions:
+
+  * Rotate the structure holding the left mouse button;
+
+  * Zoom In/Out the structure;
+
+Ketcher Settings allow to change the appearance of the structure and background coloring.
+
+"Lines" drawing method, "Bright" atom name coloring
+method and "Light" background coloring are default.
+
+# Drawing Atoms
+
+To draw/edit atoms you can:
+
+  * select an atom in the Atoms toolbar and click inside the drawing
+  area;
+
+  * if the desired atom is absent in the toolbar, click on
+  the ![](periodic-table.png) button to invoke the Periodic Table and
+  click on the desired atom (available options: _Single_ – selection
+  of a single atom, _List_ – choose an atom from the list of selected
+  options (To allow one atom from a list of atoms of your choice at
+  that position), _Not List_ - exclude any atom on your list at that
+  position).
+
+    ![](periodic-dialog.png "Periodic Table")
+
+  * add an atom to the existing molecule by selecting an atom in the
+  _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
+  the cursor; the atom will be added with a single bond; vacant
+  valences will be filled with the corresponding number of hydrogen
+  atoms;
+
+  * change an atom by selecting an atom in the _Atoms_ toolbar and
+  clicking on the atom to be changed; in the case a wrong valence thus
+  appears the atom will be underlined in red;
+
+  * change an atom by clicking on an existing atom with the
+  _Selection_ tool and waiting for a couple of seconds for the text
+  box to appear; type another atom symbol in the text box:
+
+    ![](inline-edit.png "Change Atom")
+
+  * change the charge of an atom by selecting the Charge Plus or
+  Charge Minus tool and clicking consecutively on an atom to
+  increase/decrease its charge
+
+    ![](charge.png "Ions")
+
+  * change an atom or its properties by double-clicking on the atom to
+  invoke the Atom Properties dialog (the dialog also provides atom
+  query features):
+
+    ![](atom-dialog.png "Atom Properties")
+
+  * click on the Periodic Table button, open the Extended table and
+  select a corresponding Generic group or Special Node:
+
+    ![](periodic-dialog-ext.png "Generic Groups")
+
+# Drawing Bonds
+
+To draw/edit bonds you can:
+
+  * Click an arrow on the Bond tool ![](bond.png) in the Tools palette
+  to open the drop-down list with the following bond types:
+
+    ![](bonds.png)
+
+    For the full screen format, the Bond tool from the Tools palette
+    splits into three: _Single Bond,__Single Up Bond,_ and _Any
+    Bond_,which include the corresponding bond types:
+
+    ![](bond-types.png)
+
+  * select a bond type from the drop down list and click inside the
+  drawing area; a bond of the selected type will be drawn;
+
+  * click on an atom in the molecule; a bond of the selected type will
+  be added to the atom at the angle of 120 degrees;
+
+  * add a bond to the existing molecule by clicking on an atom in the
+  molecule and dragging the cursor; in this case you can set the angle
+  manually;
+
+  * change the bond type by clicking on it;
+
+  * use the Chain Tool ![](chain.png) to draw consecutive single
+  bonds;
+
+  * change a bond or its properties by double-clicking on the bond to
+  invoke the Bond Properties dialog:
+
+    ![](bond-dialog.png "Bond Properties")
+
+  * clicking on a drawn stereo bond changes its direction.
+
+  * clicking with the Single Bond tool or Chain tool switches the bond type
+  cyclically: Single-Double-Triple-Single.
+
+# Drawing R-Groups
+
+Use the _R-Group_ toolbox ![](rgroup.png) to draw R-groups in Markush
+structures:
+
+ ![](rgroup-types.png)
+
+Selecting the _R-Group_ _Label_ Tool and clicking on an atom in the
+structure invokes the dialog to select the R-Group label for a current
+atom position in the structure:
+
+ ![](rgroup-dialog.png)
+
+Selecting the R-Group label and clicking **OK** converts the structure
+into a Markush structure with the selected R-Group label:
+
+ ![](rgroup-example1.png)
+
+**Note** : You can choose several R-Group labels simultaneously:
+
+ ![](rgroup-example2.png)
+
+Particular chemical fragments that may be substituted for a given
+R-Group form a set of R-Group members. R-Group members can be any
+structural fragment, including functional groups and single atoms or
+atom lists.
+
+To create a set of R-Group members:
+
+  1. Draw a structure to become an R-Group member.
+
+  2. Select the structure using the _R-Group Fragment Tool_ to invoke
+     the R-Group dialog; in this dialog select the label of the
+     R-Group to assign the fragment to.
+
+  3. Click on **OK** to convert the structure into an R-Group member.
+
+An R-Group attachment point is the atom in an R-Group member fragment
+that attaches the fragment to the initial Markush structure.
+
+Selecting the _Attachment Point Tool_ and clicking on an atom in the
+R-Group fragment converts this atom into an attachment point. If the
+R-Group contains more than one attachment point, you can specify one
+of them as primary and the other as secondary. You can select between
+either the primary or secondary attachment point using the dialog that
+appears after clicking on the atom:
+
+ ![](attpoints-dialog.png)
+
+If there are two attachment points on an R-Group member, there must be
+two corresponding attachments (bonds) to the R-Group atom that has the
+same R-Group label. Clicking on **OK** in the above dialog creates the
+attachment point.
+
+Schematically, the entire process of the R-Group member creation can
+be presented as:
+
+ ![](rgroup-example3.png)
+
+ ![](rgroup-example4.png)
+
+# R-Group Logic
+
+**Ketcher** enables one to add logic when using R-Groups. To access
+the R-Group logic:
+
+  1. Create an R-Group member fragment as described above.
+
+  2. Move the cursor over the entire fragment for the green frame to
+     appear, then click inside the fragment. The following dialog
+     appears:
+
+     ![](rlogic-dialog.png)
+
+  3. Specify **Occurrence** to define how many of an R-Group
+     occurs. If an R-Group atom appears several times in the initial
+     structure, you will specify **Occurrence**">n", n
+     being the number of occurrences; if it appears once, you see
+     "R1 > 0".
+
+  4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
+     clear the checkbox.
+
+  5. Specify the logical **Condition**. Use the R-Group condition **If
+     R(i) Then** to specify whether the presence of an R-Group is
+     dependent on the presence of another R-Group.
+
+
+# Marking S-Groups
+
+To mark S-Groups, use the _S-Group tool_ ![](sgroup.png) and the
+following dialog that appears after selecting a fragment with this
+tool:
+
+ ![](sgroup-dialog.png "S-Group Dialog")
+
+Available S-Group types:
+
+_Generic_
+
+Generic is a pair of brackets without any labels.
+
+_Multiple group_
+
+A Multiple group indicates a number of replications of a fragment or a part of a
+structure in contracted form.
+
+_SRU Polymer_
+
+The Structural Repeating Unit (SRU) brackets enclose the structural
+repeating of a polymer. You have three available patterns:
+head-to-tail (the default), head-to-head, and either/unknown.
+
+_Superatom_
+
+An abbreviated structure (abbreviation) is all or part of a structure
+(molecule or reaction component) that has been abbreviated to a text
+label. Structures that you abbreviate keep their chemical
+significance, but their underlying structure is hidden. The current
+version can't display contracted structures but correctly
+saves/reads them into/from files.
+
+# Data S-Groups
+
+The _Data S-Groups Tool_ ![](sdata.png) is a separate tool for
+comfortable use with the accustomed set of descriptors (like Attached
+Data in **Marvin** Editor).
+
+You can attach data to an atom, a fragment, a single bond, or a
+group. The defined set of _Names_ and _Values_ is introduced for each
+type of selected elements:
+
+ ![](sdata-dialog.png)
+
+  * Select the appropriate S-Group Field Name.
+
+  * Select or type the appropriate Field Value.
+
+  * Labels can be specified as Absolute, Relative or Attached.
+
+# Changing Structure Display
+
+Use the _Flip/Rotate_ tool ![](transform.png) to change the structure
+display:
+
+ ![](transform-types.png)
+
+For the full screen format, the _Flip/Rotate_ tool is split into
+separate buttons:
+
+ ![](rotate.png)
+
+_Rotate Tool_
+
+This tool allows rotating objects.
+  * If some objects are selected, the tool rotates the selected objects.
+  * If no objects are selected, or all objects are selected, the tool rotates the whole canvas
+  * The default rotation step is 15 degrees. 
+  * Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
+
+Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
+Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
+
+_Flip Tool_
+
+This tool flips the objects horizontally or vertically.
+  * If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
+  * If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
+  * If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
+  * If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
+
+# Drawing Reactions
+
+To draw/edit reactions you can
+
+  * draw reagents and products as described above;
+  * use options of the _Reaction Arrow Tool_ ![](reaction.png) to draw an
+  arrow and pluses in the reaction equation and map same atoms in
+  reagents and products.
+
+    ![](reaction-types.png)
+
+**Note** : Reaction Auto-Mapping Tool is available only in the Server
+mode.
+
+# Templates toolbar
+
+You can add templates (rings or other predefined structures) to the
+structure using the _Templates_ toolbar together with the _Custom
+Templates_ button located at the bottom:
+
+ ![](template.png)
+
+To add a ring to the molecule, select a ring from the toolbar and
+click inside the drawing area, or click on an atom or a bond in the
+molecule.
+
+Rules of using templates:
+
+  * Selecting a template and clicking on an atom in the existing
+  structure adds the template to the structure connected with a single
+  bond:
+
+    ![](template-example1.png)
+
+  * Selecting a template and dragging the cursor from an atom in the
+  existing structure adds the template directly to this atom resulting
+  in the fused structure:
+
+    ![](template-example2.png)
+
+  * Dragging the cursor from an atom in the existing structure results
+  in the single bond attachment if the cursor is dragged to more than
+  the bond length; otherwise the fused structure is drawn.
+  * Selecting a template and clicking on a bond in the existing
+  structure created a bond-to-bond fused structure:
+
+    ![](template-example3.png)
+
+  * The bond in the initial structure is replaced with the bond in the
+  template.
+
+  * This procedure doesn't change the length of the bond in the
+  initial structure.
+
+  * Dragging the cursor relative to the initial bond applies the
+  template at the corresponding side of the bond.
+
+**Note** : The added template will be fused by the default attachment
+atom or bond preset in the program.
+
+**Note** : User is able to define the attachment atom and bond by clicking
+the Edit button for template structure.
+
+
+The _Custom Templates_ button ![](template-lib.png)invokes the scrolling
+list of templates available in the program; both built-in and created
+by user:
+
+ ![](template-dialog.png)
+
+
+To create a user template:
+* draw a structure.
+* click the Save as button.
+* click the Save to Templates button.
+* enter a name and define the attachment atom and bond.
+
+# Working with Files
+
+Ketcher supports the following molecular formats that can be entered
+either manually or from files:
+
+  * MDL Molfile or RXN file;
+
+  * Daylight SMILES (Server mode only);
+
+  * Daylight SMARTS (Server mode only);
+
+  * InChi string (Server mode only);
+
+  * CML file (Server mode only).
+
+You can use the **Open…** and **Save As…** buttons of the _Main_
+toolbar to import a molecule from a molecular file or save it to a
+supported molecular file format. The _Open Structure_ dialog enables
+one to either browse for a file (Server mode) or manually input, e.g.,
+the Molfile ctable for the molecule to be imported:
+
+ ![](open.png)
+
+The _Save Structure_ dialog enables one to save the molecular file:
+
+ ![](save.png)
+
+**Note** : In the standalone version only mol/rxn are supported for
+Open and mol/rxn/SMILES for Save.
+
+
+# Hotkeys
+
+You can use keyboard hotkeys (including Numeric keypad) for some
+features/commands of the Editor. To display the hotkeys just place the
+cursor over a toolbar button. If a hotkey is available for the button,
+it will appear in brackets after the description of the button.
+
+| Key | Action |
+| --- | --- |
+| `Esc` | Switching between the Lasso/Rectangle/Fragment Selection tools |
+| `Del` | Delete the selected objects |
+| `0` | Draw Any bond. |
+| `1` | Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types. |
+| `2` | Double / Double Cis/Trans bond |
+| `3` | Draw a triple bond. |
+| `4` | Draw an aromatic bond. |
+| `5` | Charge Plus/Charge Minus |
+| `A` | Draw any atom |
+| `H` | Draw a hydrogen |
+| `C` | Draw a carbon |
+| `N` | Draw a nitrogen |
+| `O` | Draw an oxygen |
+| `S` | Draw a sulfur |
+| `F` | Draw a fluorine |
+| `P` | Draw a phosphorus |
+| `I` | Draw an iodine |
+| `T` | Basic templates. Consecutive pressing switches between different templates |
+| `Shift+t` | Open template library |
+| `Alt+r` | Rotate tool |
+| `Alt+v` | Flip vertically |
+| `Alt+h` | Flip horizontally |
+| `Ctrl+g` | S-Group tool / Data S-Group tool |
+| `Ctrl+d` | Align and select all S-Group data
+| `Ctrl+r` | Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool |
+| `Ctrl+Shift+r`  | R-Group Fragment Tool |
+| `Ctrl+Del` | Clear canvas |
+| `Ctrl+o` | Open |
+| `Ctrl+s` | Save As |
+| `Ctrl+z` | Undo |
+| `Ctrl+Shift+z` | Redo |
+| `Ctrl+x` | Cut selected objects |
+| `Ctrl+c` | Copy selected objects |
+| `Ctrl+v` | Paste selected objects |
+| `+` | Zoom In |
+| `-` | Zoom Out |
+| `Ctrl+l` | Layout |
+| `Ctrl+Shift+l` | Clean Up |
+| `Ctrl+p` | Calculate CIP |
+| `?` | Help |
+
+**Note** : Please, use `Ctrl+V` to paste the selected object in
+Google Chrome and Mozilla Firefox browsers.
+
+**Note 2** : Probably, you have forbidden access to the local storage.
+If you are using IE10 or IE11 and didn't forbid access to local storage 
+intentionally, you can pay attention here: https://stackoverflow.com/a/20848924

static/js/ketcher2/gulpfile.js

@@ -0,0 +1,310 @@
+/****************************************************************************
+ * Copyright 2017 EPAM Systems
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+var gulp = require('gulp');
+var gutil = require('gulp-util');
+var plugins = require('gulp-load-plugins')();
+
+var browserify = require('browserify');
+var source = require('vinyl-source-stream');
+var buffer = require('vinyl-buffer');
+var budo = require('budo');
+var istanbul = require('browserify-babel-istanbul');
+
+var fs = require('fs');
+var cp = require('child_process');
+var del = require('del');
+var minimist = require('minimist');
+var MarkdownIt = require('markdown-it');
+
+var pkg = require('./package.json');
+var options = minimist(process.argv.slice(2), {
+	string: ['dist', 'api-path', 'build-number', 'build-date',
+	         'miew-path'],
+	boolean: ['sgroup-data-special', 'no-generics', 'no-reactions',
+	          'no-sgroup', 'no-rgroup', 'rgroup-label-only'],
+	default: {
+		'dist': 'dist',
+		'api-path': '',
+		'miew-path': '',
+		'build-number': '',
+		'build-date': new Date() // TODO: format me
+	}
+});
+
+var distrib = ['LICENSE', 'demo.html', 'library.sdf', 'library.svg'];
+
+var bundleConfig = {
+	entries: 'script',
+	extensions: ['.js', '.jsx', '.es'],
+	debug: true,
+	standalone: pkg.name,
+	transform: [
+		['exposify', {
+			expose: {'raphael': 'Raphael' }
+		}],
+		['browserify-replace', {
+			replace: [
+				{ from: '__VERSION__', to: pkg.version },
+				{ from: '__API_PATH__', to: options['api-path'] },
+				{ from: '__BUILD_NUMBER__', to: options['build-number'] },
+				{ from: '__BUILD_DATE__', to: options['build-date'] },
+				{ from: '__MIEW_PATH__', to: options['miew-path'] },
+			]
+		}],
+		['babelify', {
+			presets: [
+				["env", {
+					"targets": {
+						"browsers": ["last 2 versions", "safari > 8", "chrome > 52"]
+					},
+					"useBuiltIns": true
+				}],
+				"react"],
+			plugins: ['lodash', 'transform-class-properties', 'transform-object-rest-spread']
+		}]
+	]
+};
+
+var iconfont = null;
+
+gulp.task('script', ['patch-version'], function() {
+	bundleConfig.transform.push(
+		['loose-envify', {
+			NODE_ENV: 'production',
+			global: true
+		}]
+	);
+	return browserify(bundleConfig).bundle()
+		// Don't transform, see: http://git.io/vcJlV
+		.pipe(source(`${pkg.name}.js`)).pipe(buffer())
+		.pipe(plugins.sourcemaps.init({ loadMaps: true }))
+		.pipe(plugins.uglify({
+			compress: {
+				global_defs: {
+					DEBUG: false
+				},
+				dead_code: true
+		}}))
+		.pipe(plugins.header(fs.readFileSync('script/banner.js', 'utf8')))
+		.pipe(plugins.sourcemaps.write('./'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('test-render', function() {
+	return browserify({
+		entries: 'test/render/render-test.js',
+		debug: true,
+		transform: [
+			istanbul,
+			['exposify', {
+				expose: {
+					raphael: 'Raphael',
+					resemblejs: 'resemble'
+				}
+			}]
+		]
+	}).bundle()
+		.pipe(source('render-test.js'))
+		.pipe(plugins.header(fs.readFileSync('script/banner.js', 'utf8')))
+		.pipe(gulp.dest('./test/dist'));
+});
+
+gulp.task('style', ['font'], function () {
+	return gulp.src('style/index.less')
+		.pipe(plugins.sourcemaps.init())
+		.pipe(plugins.rename(pkg.name))
+		.pipe(plugins.less({
+			paths: ['node_modules/normalize.css'],
+			modifyVars: iconfont
+		}))
+	    // don't use less plugins due http://git.io/vqVDy bug
+		.pipe(plugins.autoprefixer({ browsers: ['> 0.5%'] }))
+		.pipe(plugins.cleanCss({compatibility: 'ie8'}))
+		.pipe(plugins.sourcemaps.write('./'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('html', ['patch-version'], function () {
+	var hbs = plugins.hb()
+	    .partials('template/menu/*.hbs')
+	    .partials('template/dialog/*.hbs')
+	    .data(Object.assign({ pkg: pkg }, options));
+	return gulp.src('template/index.hbs')
+		.pipe(hbs)
+		.pipe(plugins.rename('ketcher.html'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('doc', function () {
+	return gulp.src('doc/*.{png, jpg, gif}')
+		.pipe(gulp.dest(options.dist + '/doc'));
+});
+
+gulp.task('help', ['doc'], function () {
+	return gulp.src('doc/help.md')
+		.pipe(plugins.tap(markdownify()))
+		.pipe(gulp.dest(options.dist + '/doc'));
+});
+
+gulp.task('font', function (cb) {
+	return iconfont ? cb() : gulp.src(['icons/*.svg'])
+		.pipe(plugins.iconfont({
+			fontName: pkg.name,
+			formats: ['ttf', 'svg', 'eot', 'woff'],
+			timestamp: options['build-date'],
+			normalize: true
+		}))
+		.on('glyphs', function(glyphs) {
+			iconfont = glyphReduce(glyphs);
+		})
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('images', function () {
+	return gulp.src('images/*')
+		.pipe(gulp.dest(options.dist + '/images'));
+});
+
+gulp.task('copy', ['images'], function () {
+	return gulp.src(['raphael'].map(require.resolve)
+	                .concat(distrib))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('patch-version', function (cb) {
+	if (pkg.rev)
+		return cb();
+	cp.exec('git rev-list ' + pkg.version + '..HEAD --count', function (err, stdout, stderr) {
+		if (err && stderr.toString().search('path not in') > 0) {
+			cb(new Error('Could not fetch revision. ' +
+			             'Please git tag the package version.'));
+		}
+		else if (!err && stdout > 0) {
+			pkg.rev =  stdout.toString().trim();
+			pkg.version += ('+r' + pkg.rev);
+		}
+		cb();
+	});
+});
+
+gulp.task('lint', function () {
+	return gulp.src('script/**')
+		.pipe(plugins.eslint())
+		.pipe(plugins.eslint.format())
+		.pipe(plugins.eslint.failAfterError());
+});
+
+gulp.task('check-epam-email', function(cb) {
+	// TODO: should be pre-push and check remote origin
+	try {
+		var email = cp.execSync('git config user.email').toString().trim();
+		if (/@epam.com$/.test(email))
+			cb();
+		else {
+			cb(new Error('Email ' + email + ' is not from EPAM domain.'));
+			gutil.log('To check git project\'s settings run `git config --list`');
+			gutil.log('Could not continue. Bye!');
+		}
+	} catch(e) {};
+});
+
+gulp.task('check-deps-exact', function (cb) {
+	var semver = require('semver'); // TODO: output corrupted packages
+	var allValid = ['dependencies', 'devDependencies'].every(d => {
+		var dep = pkg[d];
+		return Object.keys(dep).every(name => {
+			var ver = dep[name];
+			return (semver.valid(ver) && semver.clean(ver));
+		});
+	});
+	if (!allValid) {
+		cb(new gutil.PluginError('check-deps-exact',
+		                         'All top level dependencies should be installed' +
+		                         'using `npm install --save-exact` command'));
+	} else
+		cb();
+});
+
+gulp.task('clean', function () {
+	return del.sync([options.dist + '/**', pkg.name + '-*.zip']);
+});
+
+gulp.task('archive', ['clean', 'assets', 'code'], function () {
+	var an = pkg.name + '-' + pkg.version;
+	return gulp.src(['**', '!*.map'], { cwd: options.dist })
+		.pipe(plugins.rename(function (path) {
+			path.dirname = an + '/' + path.dirname;
+			return path;
+		}))
+		.pipe(plugins.zip(an + '.zip'))
+		.pipe(gulp.dest('.'));
+});
+
+gulp.task('serve', ['clean', 'style', 'html', 'assets'], function(cb) {
+	var server = budo(`${bundleConfig.entries}:${pkg.name}.js`, {
+		dir: options.dist,
+		browserify: bundleConfig,
+		stream: process.stdout,
+		host: '0.0.0.0',
+		live: true,
+		watchGlob: `${options.dist}/*.{html,css}`,
+		staticOptions: {
+			index: `ketcher.html`
+		}
+	}).on('exit', cb);
+
+	gulp.watch('style/**.less', ['style']);
+	gulp.watch('template/**', ['html']);
+	gulp.watch('doc/**', ['help']);
+	gulp.watch(['gulpfile.js', 'package.json'], function() {
+	server.close();
+		cp.spawn('gulp', process.argv.slice(2), {
+			stdio: 'inherit'
+		});
+		process.exit(0);
+	});
+
+	return server;
+});
+
+function markdownify (options) {
+	var header = '<!DOCTYPE html>';
+	var footer = '';
+	var md = MarkdownIt(Object.assign({
+		html: true,
+		linkify: true,
+		typographer: true
+	}, options));
+	return function process (file) {
+		var data = md.render(file.contents.toString());
+		file.contents = new Buffer(header + data + footer);
+		file.path = gutil.replaceExtension(file.path, '.html');
+	};
+}
+
+function glyphReduce(glyphs) {
+	return glyphs.reduce(function (res, glyph) {
+		res['icon-' + glyph.name] = "'" + glyph.unicode[0] + "'";
+		return res;
+	}, {});
+}
+
+gulp.task('pre-commit', ['lint', 'check-epam-email',
+                         'check-deps-exact']);
+gulp.task('assets', ['copy', 'help']);
+gulp.task('code', ['style', 'script', 'html']);
+gulp.task('build', ['clean', 'code', 'assets']);

static/js/ketcher2/icons/about.svg

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Generated by IcoMoon.io -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   version="1.1"
+   width="1000"
+   height="1000"
+   viewBox="0 0 1000 1000"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="about.svg">
+  <metadata
+     id="metadata11">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <defs
+     id="defs9" />
+  <sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="1280"
+     inkscape:window-height="974"
+     id="namedview7"
+     showgrid="false"
+     inkscape:zoom="0.52678571"
+     inkscape:cx="708.89624"
+     inkscape:cy="375.86441"
+     inkscape:window-x="0"
+     inkscape:window-y="23"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="svg2" />
+  <g
+     id="icomoon-ignore"
+     transform="translate(0,552)" />
+  <path
+     d="m 666.66667,812.5 0,-104.16667 c 0,-11.71875 -9.11459,-20.83333 -20.83334,-20.83333 l -62.5,0 0,-333.33333 c 0,-11.71875 -9.11458,-20.83334 -20.83333,-20.83334 l -208.33333,0 c -11.71875,0 -20.83334,9.11459 -20.83334,20.83334 l 0,104.16666 c 0,11.71875 9.11459,20.83334 20.83334,20.83334 l 62.5,0 0,208.33333 -62.5,0 c -11.71875,0 -20.83334,9.11458 -20.83334,20.83333 l 0,104.16667 c 0,11.71875 9.11459,20.83333 20.83334,20.83333 l 291.66666,0 c 11.71875,0 20.83334,-9.11458 20.83334,-20.83333 z m -83.33334,-583.33333 0,-104.16667 c 0,-11.71875 -9.11458,-20.83333 -20.83333,-20.83333 l -125,0 c -11.71875,0 -20.83333,9.11458 -20.83333,20.83333 l 0,104.16667 C 416.66667,240.88542 425.78125,250 437.5,250 l 125,0 c 11.71875,0 20.83333,-9.11458 20.83333,-20.83333 z M 1000,500 c 0,276.04167 -223.95833,500 -500,500 C 223.95833,1000 0,776.04167 0,500 0,223.95833 223.95833,0 500,0 c 276.04167,0 500,223.95833 500,500 z"
+     id="path5"
+     inkscape:connector-curvature="0" />
+</svg>

static/js/ketcher2/icons/analyse.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" width="1000" height="1000" viewBox="0 0 750 750"><path d="M585.781 276.055l-8.73 15.797H559.59s-24.945 0-31.598 34.921l-7.066 34.922h47.808l-8.73 17.461H518.43l-24.942 122.23c-10.394 52.384-47.812 52.384-47.812 52.384h-54.047l7.07-17.461h17.043s26.61 0 33.676-34.922l24.945-122.23H435.7l8.73-17.462h33.676l7.067-34.922c10.394-52.382 47.808-52.382 47.808-52.382zm0 186.668l-33.676-46.149-12.054 7.485-12.059 7.898 34.508 52.8-57.79 55.708 19.958 19.957 54.047-51.969 37 56.125 12.058-7.898 12.055-7.485-41.574-60.699 57.371-55.293-9.977-9.976-9.976-10.395zm166.297-23.282c-.367 91.606-55.082 174.254-139.273 210.364a113.081 113.081 0 0 1-14.137 38.25c-19.602 35.312-55.742 58.308-96.035 61.113H110.172a118.487 118.487 0 0 1-93.543-60.7 124.736 124.736 0 0 1-4.574-115.16l180.851-356.706a41.618 41.618 0 0 0 5.82-17.461V80.238c-15.167-4.71-25.246-19.058-24.53-34.922C173.78 16.215 196.23.832 225.331.832h162.14a41.57 41.57 0 0 1 48.641 44.066c.91 17.106-11.008 32.23-27.855 35.34v118.489c0 6.234 5.406 12.054 8.316 17.46l7.899 12.473c71.336-30.547 153.21-23.472 218.25 18.856 65.039 42.332 104.66 114.328 105.613 191.925M87.723 644.816c4.988 7.899 13.304 21.204 22.863 21.204h369.18c-111.414-17.891-193.543-113.74-194.149-226.58a228.229 228.229 0 0 1 69.012-163.386l-12.473-22.453a127.586 127.586 0 0 1-17.875-54.875V83.98h-41.574v114.747a133.024 133.024 0 0 1-14.555 56.957L86.472 614.469a34.522 34.522 0 0 0 0 29.933m430.298-16.629c103.734-1.148 187.007-85.964 186.246-189.703-.762-103.738-85.27-187.328-189.012-186.949-103.738.379-187.64 84.578-187.645 188.32.684 104.54 85.868 188.79 190.41 188.332"/></svg>

static/js/ketcher2/icons/arom.svg

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="1000px"
+   height="1000px"
+   viewBox="0 0 1000 1000"
+   version="1.1"
+   id="svg3017"
+   inkscape:version="0.48.4 r9939"
+   sodipodi:docname="arom.svg">
+  <sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="1280"
+     inkscape:window-height="985"
+     id="namedview3024"
+     showgrid="false"
+     inkscape:zoom="0.788"
+     inkscape:cx="451.14213"
+     inkscape:cy="500.63452"
+     inkscape:window-x="-2"
+     inkscape:window-y="16"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="svg3017" />
+  <metadata
+     id="metadata3028">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <defs
+     id="defs3026" />
+  <path
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static/js/ketcher2/icons/bond-aromatic.svg

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static/js/ketcher2/icons/bond-crossed.svg

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static/js/ketcher2/icons/bond-double.svg

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static/js/ketcher2/icons/bond-doublearomatic.svg

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static/js/ketcher2/icons/bond-down.svg

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static/js/ketcher2/icons/bond-single.svg

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static/js/ketcher2/icons/bond-singlearomatic.svg

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static/js/ketcher2/icons/bond-up.svg

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static/js/ketcher2/icons/bond-updown.svg

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