Prep configs, added Package Create Modal

.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

@@ -6,23 +6,18 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
-
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    ca-certificates \
+    nodejs \
+    npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Install Node 22 + pnpm
+# Install pnpm
-RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+RUN npm install -g pnpm
-    && apt-get update \
-    && apt-get install -y --no-install-recommends nodejs \
-    && corepack enable \
-    && corepack prepare pnpm@latest --activate \
-    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -35,21 +30,19 @@ RUN mkdir -p -m 0700 /root/.ssh \
     && ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts
 
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
-# docker build --ssh default -t envipath/envipy-bayer:1.0 .
+# docker build --ssh default -t envipath/envipy:1.0 .
 RUN --mount=type=ssh \
     uv sync --locked --extra ms-login --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bb4g bb4g
-COPY biotransformer biotransformer
 COPY bayer bayer
 COPY bridge bridge
+COPY biotransformer biotransformer
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
-COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper

bayer/additional_information/__init__.py

@@ -1,178 +0,0 @@
-import enum
-from typing import Optional
-
-from envipy_additional_information import GroupEnum as G
-from envipy_additional_information import SubcategoryEnum as S
-from envipy_additional_information import (
-    register,
-    register_parser_command,
-    EnviPyModel,
-    # EnviPyModelParser,
-    Interval,
-    UIConfig,
-    IntervalConfig,
-    WidgetType,
-    registry,
-)
-
-
-@register(keyname="compoundlabel", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class CompoundLabel(EnviPyModel):
-    label: str
-
-    class UI:
-        title = "Compound Label"
-        label = UIConfig(widget=WidgetType.TEXT, label="Label", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("compoundlabel")
-class CompoundLabelParser:
-    @staticmethod
-    def from_string(data: str) -> CompoundLabel:
-        return CompoundLabel(label=data)
-
-
-@register(keyname="studywaterstoragecapacity", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class StudyWaterStorageCapacity(EnviPyModel):
-    capacity: str
-
-    class UI:
-        title = "Study Water Storage Capacity"
-        capacity = UIConfig(widget=WidgetType.TEXT, label="Study Water Storage Capacity", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("studywst")
-class StudyWaterStorageCapacityParser:
-    @staticmethod
-    def from_string(data: str) -> StudyWaterStorageCapacity:
-        return StudyWaterStorageCapacity(capacity=data)
-
-
-class ObservationType(enum.Enum):
-    OBSERVED = "observed"
-    APPLIED = "applied"
-    NA = 'NA'
-
-
-@register(keyname="observation", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Observation(EnviPyModel):
-    type: ObservationType
-    min_value: Optional[float] = None
-    max_value: Optional[float] = None
-
-    class UI:
-        title = "Observation"
-        type = UIConfig(widget=WidgetType.SELECT, label="Observed or Applied", order=1)
-        min_value = UIConfig(widget=WidgetType.NUMBER, label="Min Value", order=2)
-        max_value = UIConfig(widget=WidgetType.NUMBER, label="Max Value", order=3)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("observation")
-class ObservationParser:
-    @staticmethod
-    def from_string(data: str) -> Observation:
-        parts = data.split(";")
-
-        observation_type = ObservationType(parts[0])
-        min_value = None
-        if parts[1]:
-            try:
-                min_value = float(parts[1])
-            except ValueError:
-                pass
-
-        max_value = None
-        if parts[2]:
-            try:
-                max_value = float(parts[2])
-            except ValueError:
-                pass
-
-        return Observation(type=observation_type, min_value=min_value, max_value=max_value)
-
-
-@register(keyname="kinetics", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Kinetics(EnviPyModel):
-    dt50: Interval[float]
-    normalized_dt50: bool
-    chi2err: Optional[float] = None
-    t_test: Optional[float] = None
-    swarc: Optional[float] = None
-    visual_fit: Optional[int] = None
-    comment: str
-    source: str
-    kinetic_model: str
-    k1: Optional[float] = None
-    k2: Optional[float] = None
-    g: Optional[float] = None
-    tb: Optional[float] = None
-    alpha: Optional[float] = None
-    beta: Optional[float] = None
-
-    class UI:
-        title = "Kinetics"
-
-        # Field config
-        dt50 = IntervalConfig(label="DT50 Range", order=1, unit="d")
-        normalized_dt50 = UIConfig(widget=WidgetType.CHECKBOX, label="Normalized DT50", order=2)
-        chi2err = UIConfig(widget=WidgetType.NUMBER, label="Chi2err", order=3)
-        t_test = UIConfig(widget=WidgetType.NUMBER, label="T-Test", order=4)
-        swarc = UIConfig(widget=WidgetType.NUMBER, label="SWARC", order=5)
-        visual_fit = UIConfig(widget=WidgetType.NUMBER, label="Visual Fit", order=6)
-        comment = UIConfig(widget=WidgetType.TEXTAREA, label="Comments", order=7)
-        source = UIConfig(widget=WidgetType.TEXT, label="Source", order=8)
-        kinetic_model = UIConfig(widget=WidgetType.SELECT, label="Kinetic Model", order=9)
-        k1 = UIConfig(widget=WidgetType.NUMBER, label="K1", order=10)
-        k2 = UIConfig(widget=WidgetType.NUMBER, label="K2", order=11)
-        g = UIConfig(widget=WidgetType.NUMBER, label="G", order=12)
-        tb = UIConfig(widget=WidgetType.NUMBER, label="TB", order=13)
-        alpha = UIConfig(widget=WidgetType.NUMBER, label="Alpha", order=14)
-        beta = UIConfig(widget=WidgetType.NUMBER, label="Beta", order=15)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("kineticevaluation")
-class KinecticsParser:
-    @staticmethod
-    def from_string(data: str) -> Kinetics:
-        parts = data.split(";")
-        dt50 = registry.get_parser("interval").from_string(parts[0])
-        normalized_dt50 = parts[1] == "true"
-        chi2err = float(parts[2]) if parts[2] else None
-        t_test = float(parts[3]) if parts[3] else None
-        swarc = float(parts[4]) if parts[4] else None
-        visual_fit = int(parts[5]) if parts[5] else None
-        comment = parts[6]
-        source = parts[7]
-        kinetic_model = parts[8]
-        k1 = float(parts[9]) if parts[9] else None
-        k2 = float(parts[10]) if parts[10] else None
-        g = float(parts[11]) if parts[11] else None
-        tb = float(parts[12]) if parts[12] else None
-        alpha = float(parts[13]) if parts[13] else None
-        beta = float(parts[14]) if parts[14] else None
-
-        return Kinetics(
-            dt50=dt50,
-            normalized_dt50=normalized_dt50,
-            chi2err=chi2err,
-            t_test=t_test,
-            swarc=swarc,
-            visual_fit=visual_fit,
-            comment=comment,
-            source=source,
-            kinetic_model=kinetic_model,
-            k1=k1,
-            k2=k2,
-            g=g,
-            tb=tb,
-            alpha=alpha,
-            beta=beta,
-        )
-
-
-if __name__ == '__main__':
-    print(KinecticsParser.from_string("187.0 - 187.0;false;;;;;;;AFO;;;;;;"))

bayer/admin.py

@@ -1,19 +1,3 @@
 from django.contrib import admin
 
 # Register your models here.
-from .models import (
-    PESCompound,
-    PESStructure
-)
-
-
-class PESCompoundAdmin(admin.ModelAdmin):
-    pass
-
-
-class PESStructureAdmin(admin.ModelAdmin):
-    pass
-
-
-admin.site.register(PESCompound, PESCompoundAdmin)
-admin.site.register(PESStructure, PESStructureAdmin)

bayer/epdb_hooks.py

@@ -1,40 +0,0 @@
-import logging
-
-from bayer import additional_information  # noqa: F401
-from epdb.template_registry import register_template
-
-logger = logging.getLogger(__name__)
-
-# PES Create
-register_template(
-    "epdb.actions.collections.compound",
-    "actions/collections/new_pes.html",
-)
-register_template(
-    "modals.collections.compound",
-    "modals/collections/new_pes_modal.html",
-)
-register_template(
-    "epdb.actions.objects.pathway.add",
-    "actions/objects/pathway_add_pes.html",
-)
-register_template(
-    "epdb.modals.objects.pathway.add",
-    "modals/objects/add_pathway_pes_node_modal.html"
-)
-
-# PES Viz
-register_template(
-    "epdb.objects.compound.viz",
-    "objects/compound_viz.html",
-)
-
-register_template(
-    "epdb.objects.compound_structure.viz",
-    "objects/compound_structure_viz.html",
-)
-
-register_template(
-    "epdb.objects.node.viz",
-    "objects/node_viz.html",
-)

bayer/migrations/0003_package_data_pool.py

@@ -0,0 +1,20 @@
+# Generated by Django 6.0.3 on 2026-04-14 19:07
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0002_initial'),
+        ('epdb', '0023_alter_compoundstructure_options_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='package',
+            name='data_pool',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
+        ),
+    ]

bayer/migrations/0003_pescompound_pesstructure_package_data_pool.py

@@ -1,41 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-17 21:22
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0002_initial'),
-        ('epdb', '0023_alter_compoundstructure_options_and_more'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='PESCompound',
-            fields=[
-                ('compound_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compound')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.compound',),
-        ),
-        migrations.CreateModel(
-            name='PESStructure',
-            fields=[
-                ('compoundstructure_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compoundstructure')),
-                ('pes_link', models.URLField(verbose_name='PES Link')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.compoundstructure',),
-        ),
-        migrations.AddField(
-            model_name='package',
-            name='data_pool',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
-        ),
-    ]

bayer/models.py

@@ -1,21 +1,16 @@
 from typing import List
-import urllib.parse
+
-import nh3
 from django.conf import settings as s
-from django.db import models, transaction
+from django.db import models
 from django.db.models import QuerySet
-from django.urls import reverse
 
 from epdb.models import (
     EnviPathModel,
-    Compound,
-    CompoundStructure,
     ParallelRule,
     SequentialRule,
     SimpleAmbitRule,
     SimpleRDKitRule,
 )
-from utilities.chem import FormatConverter
 
 
 class Package(EnviPathModel):
@@ -101,137 +96,3 @@ class Package(EnviPathModel):
 
     class Meta:
         db_table = "epdb_package"
-
-
-class PESCompound(Compound):
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
-    ) -> "Compound":
-
-        pes_url = pes_data["pes_url"]
-
-        # Check if we find a direct match for a given pes_link
-        if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
-            # Due to normalization we might end up in having multiple structures
-            # All of them point to the same compound -> pick any
-            return PESStructure.objects.filter(pes_link=pes_url, compound__package=package).first().compound
-
-        # Generate Compound
-        c = PESCompound()
-        c.package = package
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if name is None or name == "":
-            name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
-
-        c.name = name
-
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
-            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        c.save()
-
-        molfile = pes_data.get("representativeStructures", [{}])[0].get("ctab")
-
-        if molfile is None:
-            raise ValueError("PES data does not contain a valid mol file!")
-
-        smiles = FormatConverter.to_smiles(FormatConverter.from_molfile(molfile))
-
-        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
-
-        is_standardized = standardized_smiles == smiles
-
-        if not is_standardized:
-            _ = PESStructure.create(
-                c,
-                pes_url,
-                molfile,
-                standardized_smiles,
-                name="Normalized structure of {}".format(name),
-                description="{} (in its normalized form)".format(description),
-                normalized_structure=True,
-            )
-
-
-        cs = PESStructure.create(
-            c,
-            pes_url,
-            molfile,
-            smiles,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized
-        )
-
-        c.default_structure = cs
-        c.save()
-
-        return c
-
-
-class PESStructure(CompoundStructure):
-    pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
-
-    @staticmethod
-    @transaction.atomic
-    def create(
-            compound: Compound,
-            pes_link: str,
-            molfile: str,
-            smiles: str,
-            name: str = None,
-            description: str = None,
-            *args,
-            **kwargs
-    ):
-        if compound.pk is None:
-            raise ValueError("Unpersisted Compound! Persist compound first!")
-
-        cs = PESStructure()
-        # Clean for potential XSS
-        if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        if description is not None:
-            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
-
-        cs.smiles = smiles
-        cs.molfile = molfile
-        cs.pes_link = pes_link
-        cs.compound = compound
-
-        if "normalized_structure" in kwargs:
-            cs.normalized_structure = kwargs["normalized_structure"]
-
-        cs.save()
-
-        return cs
-
-    @transaction.atomic
-    def add_structure(
-        self,
-        smiles: str,
-        name: str = None,
-        description: str = None,
-        default_structure: bool = False,
-        *args,
-        **kwargs,
-    ) -> "CompoundStructure":
-        raise ValueError("Not supported!")
-
-    def d3_json(self):
-        return {
-            "is_pes": True,
-            "pes_link": self.pes_link,
-            # Will overwrite image from Node
-            "image": f"{reverse('depict_pes')}?pesLink={urllib.parse.quote(self.pes_link)}",
-            "image_type": "png",
-        }

bayer/templates/actions/collections/new_pes.html

@@ -1,9 +0,0 @@
-{% if meta.can_edit %}
-    <button
-      type="button"
-      class="btn btn-primary btn-sm"
-      onclick="document.getElementById('new_pes_modal').showModal(); return false;"
-    >
-      New PES
-    </button>
-{% endif %}

bayer/templates/actions/objects/pathway_add_pes.html

@@ -1,8 +0,0 @@
-<li>
-  <a
-    class="button"
-    onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-plus"></i> Add PES</a
-  >
-</li>

bayer/templates/modals/collections/new_package_modal.html

@@ -9,7 +9,11 @@
 
     reset() {
       this.isSubmitting = false;
-      this.packageClassification = null;
+      this.selectedType = '';
+      this.buildAppDomain = false;
+      this.requiresRulePackages = false;
+      this.requiresDataPackages = false;
+      this.additional_parameters = null;
     },
 
     setFormData(data) {
@@ -133,8 +137,10 @@
             class="select select-bordered w-full"
           >
             <option value="" disabled selected>Select Data Pool</option>
-              {% for obj in meta.secret_groups %}
+              {% for obj in meta.available_groups %}
+                {% if obj.secret %}
                   <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
+                {% endif %}
               {% endfor %}
           </select>
         </div>

bayer/templates/modals/collections/new_pes_modal.html

@@ -1,174 +0,0 @@
-{% load static %}
-
-<dialog
-  id="new_pes_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    pesLink: null,
-    pesVizHtml: '',
-
-    reset() {
-      this.isSubmitting = false;
-    },
-
-    get isPESSet() {
-      console.log(this.pesLink);
-      return this.pesLink !== null;
-    },
-
-    updatePesViz() {
-      if (!this.isPESSet) {
-        this.pesVizHtml = '';
-        return;
-      }
-
-      const img = new Image();
-      img.src = '{% url 'depict_pes' %}?pesLink=' + encodeURIComponent(this.pesLink);
-      img.style.width = '100%';
-      img.style.height = '100%';
-      img.style.objectFit = 'cover';
-
-      img.onload = () => {
-        this.pesVizHtml = img.outerHTML;
-      };
-
-      img.onerror = () => {
-        this.pesVizHtml = `
-          <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
-          </div>`;
-      };
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-  <!-- Header -->
-  <h3 class="text-lg font-bold">New PES</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-pes-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'create pes' meta.current_package.uuid %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="compound-name"
-            class="input input-bordered w-full"
-            name="compound-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pes-link">
-            <span class="label-text">Link to PES</span>
-          </label>
-          <input
-            id="pes-link"
-            name="pes-link"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
-            x-model="pesLink"
-            @input="updatePesViz()"
-            required
-          />
-        </div>
-
-        <div id="pes-viz" class="mb-3" x-html="pesVizHtml"></div>
-
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-pes-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

@@ -1,174 +0,0 @@
-{% load static %}
-
-<dialog
-  id="add_pathway_pes_node_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    pesLink: null,
-    pesVizHtml: '',
-
-    reset() {
-      this.isSubmitting = false;
-    },
-
-    get isPESSet() {
-      console.log(this.pesLink);
-      return this.pesLink !== null;
-    },
-
-    updatePesViz() {
-      if (!this.isPESSet) {
-        this.pesVizHtml = '';
-        return;
-      }
-
-      const img = new Image();
-      img.src = '{% url 'depict_pes' %}?pesLink=' + encodeURIComponent(this.pesLink);
-      img.style.width = '100%';
-      img.style.height = '100%';
-      img.style.objectFit = 'cover';
-
-      img.onload = () => {
-        this.pesVizHtml = img.outerHTML;
-      };
-
-      img.onerror = () => {
-        this.pesVizHtml = `
-          <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
-          </div>`;
-      };
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-  <!-- Header -->
-  <h3 class="text-lg font-bold">New PES</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-pes-node-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'create pes node' current_object.package.uuid current_object.uuid  %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="compound-name"
-            class="input input-bordered w-full"
-            name="compound-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pes-link">
-            <span class="label-text">Link to PES</span>
-          </label>
-          <input
-            id="pes-link"
-            name="pes-link"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
-            x-model="pesLink"
-            @input="updatePesViz()"
-            required
-          />
-        </div>
-
-        <div id="pes-viz" class="mb-3" x-html="pesVizHtml"></div>
-
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-pes-node-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/objects/compound_structure_viz.html

@@ -1,23 +0,0 @@
-{% if compound_structure.pes_link %}
-  <!-- PES -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
-      </p>
-    </div>
-  </div>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/compound_viz.html

@@ -1,23 +0,0 @@
-{% if compound.default_structure.pes_link %}
-  <!-- PES -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-      </p>
-    </div>
-  </div>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ compound.default_structure.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/node_viz.html

@@ -1,23 +0,0 @@
-{% if node.default_node_label.pes_link %}
-  <!-- PES -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
-      </p>
-    </div>
-  </div>
-
-  <!-- Image Representation -->
-  <div class="collapse-arrow bg-base-200 collapse">
-    <input type="checkbox" checked />
-    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
-    <div class="collapse-content">
-      <div class="flex justify-center">
-        <img src='{% url 'depict_pes' %}?pesLink={{ node.default_node_label.pes_link|urlencode }}'/>
-      </div>
-    </div>
-  </div>
-{% endif %}

bayer/templates/objects/package.html

@@ -1,10 +1,9 @@
 {% extends "framework_modern.html" %}
-{% load static %}
+
 {% block content %}
 
   {% 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" %}
@@ -17,7 +16,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ package.name }} {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}<img src="{% static 'images/restricted_mid.png' %}" width="100">{% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}<img src="{% static 'images/secret_mid.png' %}" width="60">{% endif %}</h2>
+          <h2 class="card-title text-2xl">{{ package.name }} - ({{ package.get_classification_level_display }})</h2>
           <div id="actionsButton" class="dropdown dropdown-e nd hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg

bayer/templates/static/login.html

@@ -1,154 +0,0 @@
-{% extends "static/login_base.html" %}
-{% load static %}
-{% block title %}enviPath - Sign In{% endblock %}
-
-{% block extra_styles %}
-  <style>
-    /* Tab styling */
-    .tab-content {
-      display: none;
-    }
-    .tab-content.active {
-      display: block;
-    }
-    input[type="radio"].tab-radio {
-      display: none;
-    }
-    .tab-label {
-      cursor: pointer;
-      padding: 0.75rem 1.5rem;
-      border-bottom: 2px solid transparent;
-      transition: all 0.3s ease;
-    }
-    .tab-label:hover {
-      background-color: rgba(0, 0, 0, 0.05);
-    }
-    input[type="radio"].tab-radio:checked + .tab-label {
-      border-bottom-color: #3b82f6;
-      font-weight: 600;
-    }
-  </style>
-{% endblock %}
-
-{% block content %}
-  <div>
-  <img src="{% static 'images/bayer-logo.svg' %}">
-
-  </div>
-  <div class="flex flex-col space-y-4 ...">
-    <div><p></p></div>
-  <div><p></p></div>
-
-  </div>
-
-  <!-- Tab Navigation -->
-  <div class="border-base-300 mb-6 border-b" hidden>
-    <div class="flex justify-start">
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-sso"
-        class="tab-radio"
-        checked
-      />
-      <label for="tab-sso" class="tab-label">SSO</label>
-
-      <input
-        type="radio"
-        name="auth-tab"
-        id="tab-signin"
-        class="tab-radio"
-      />
-      <label for="tab-signin" class="tab-label">Local User</label>
-    </div>
-  </div>
-
-  <!-- SSO Tab -->
-  <div id="content-sso" class="tab-content active">
-      <button role="link" onclick="window.location.href='/entra/login'" name="sso" class="btn btn-primary w-full">
-        Login with Microsoft
-      </button>
-  </div>
-
-  <!-- Sign In Tab -->
-  <div id="content-signin" class="tab-content">
-    <form method="post" action="{% url 'login' %}" class="space-y-4">
-      {% csrf_token %}
-      <input type="hidden" name="login" value="true" />
-
-      <div class="form-control">
-        <label class="label" for="username">
-          <span class="label-text">Account</span>
-        </label>
-        <input
-          type="text"
-          id="username"
-          name="username"
-          placeholder="Username or Email"
-          class="input input-bordered w-full"
-          required
-          autocomplete="username"
-        />
-      </div>
-
-      <div class="form-control">
-        <label class="label" for="passwordinput">
-          <span class="label-text">Password</span>
-        </label>
-        <input
-          type="password"
-          id="passwordinput"
-          name="password"
-          placeholder="••••••••"
-          class="input input-bordered w-full"
-          required
-          autocomplete="current-password"
-        />
-      </div>
-
-      <div class="text-right">
-        <a href="{% url 'password_reset' %}" class="link link-primary text-sm"
-          >Forgot password?</a
-        >
-      </div>
-
-      <input type="hidden" name="next" value="{{ next }}" />
-
-      <button type="submit" name="signin" class="btn btn-primary w-full">
-        Sign In
-      </button>
-    </form>
-  </div>
-
-{% endblock %}
-
-{% block extra_scripts %}
-  <script>
-    // Tab switching functionality
-    document.querySelectorAll('input[name="auth-tab"]').forEach((radio) => {
-      radio.addEventListener("change", function () {
-        // Hide all content
-        document.querySelectorAll(".tab-content").forEach((content) => {
-          content.classList.remove("active");
-        });
-
-        // Show selected content
-        const contentId = "content-" + this.id.replace("tab-", "");
-        document.getElementById(contentId).classList.add("active");
-      });
-    });
-
-    // Check for hash in URL to auto-select tab
-    window.addEventListener("DOMContentLoaded", function () {
-      const hash = window.location.hash.substring(1); // Remove the # symbol
-      if (hash === "signup" || hash === "signin") {
-        const tabRadio = document.getElementById("tab-" + hash);
-        if (tabRadio) {
-          tabRadio.checked = true;
-          // Trigger change event to show correct content
-          tabRadio.dispatchEvent(new Event("change"));
-        }
-      }
-    });
-  </script>
-{% endblock %}

bayer/urls.py

@@ -1,19 +0,0 @@
-from django.urls import re_path
-
-from . import views as v
-
-UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
-
-urlpatterns = [
-    re_path(r"^depict_pes$", v.visualize_pes, name="depict_pes"),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pes$",
-        v.create_pes,
-        name="create pes",
-    ),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/pes$",
-        v.create_pes_node,
-        name="create pes node",
-    ),
-]

bayer/views.py

@@ -1,225 +1,3 @@
-import base64
+from django.shortcuts import render
 
-import requests
+# Create your views here.
-from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
-from django.shortcuts import redirect
-
-from bayer.models import PESCompound
-from epdb.logic import PackageManager
-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()
-
-
-@package_permission_required()
-def create_pes(request, package_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                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}"
-                )
-
-            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."
-                    )
-
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if (current_package.data_pool.name not in s.DATA_POOL_MAPPING
-                            or s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools):
-
-                        if current_package.data_pool.name not in s.DATA_POOL_MAPPING:
-                            detail = f"Data pool {current_package.data_pool.name} not found in Mapping."
-                        else:
-                            detail = f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data"
-
-                        return error(
-                            request,
-                            "Invalid PES data",
-                            detail
-                        )
-
-            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."
-            )
-    else:
-        return HttpResponseNotAllowed(["POST"])
-
-
-@package_permission_required()
-def create_pes_node(request, package_uuid, pathway_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                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}"
-                )
-
-            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."
-                    )
-
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if (current_package.data_pool.name not in s.DATA_POOL_MAPPING
-                            or s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools):
-
-                        if current_package.data_pool.name not in s.DATA_POOL_MAPPING:
-                            detail = f"Data pool {current_package.data_pool.name} not found in Mapping."
-                        else:
-                            detail = f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data"
-
-                        return error(
-                            request,
-                            "Invalid PES data",
-                            detail
-                        )
-
-            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
-            )
-
-            if node_qs.exists():
-                return redirect(current_pathway.url)
-
-            n = Node()
-            n.stereo_removed = False
-            n.pathway = current_pathway
-            n.depth = 0
-
-            n.default_node_label = pes.default_structure
-            n.save()
-
-            n.node_labels.add(pes.default_structure)
-            n.save()
-
-            return redirect(current_pathway.url)
-
-        else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
-    else:
-        return HttpResponseNotAllowed(["POST"])
-
-
-def fetch_pes(request, pes_url) -> dict:
-    from epauth.views import get_access_token_from_request
-    token = get_access_token_from_request(request)
-
-    if token is None:
-        token = pes_url.split('/')[-1] == 'dummy'
-
-    if token:
-        for k, v in s.PES_API_MAPPING.items():
-            if pes_url.startswith(k):
-                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 = {"Authorization": f"Bearer {token['access_token']}"}
-                    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()
-
-                        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)
-
-        representations = pes_data.get('representations')
-
-        for rep in representations:
-            if rep.get('type') == 'color':
-                image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
-                return HttpResponse(image_data, content_type="image/png")

bb4g/__init__.py

@@ -1,198 +0,0 @@
-import enum
-import json
-import logging
-import math
-from datetime import datetime
-from typing import List
-
-import requests
-from django.conf import settings as s
-from envipy_additional_information import register, EnviPyModel, UIConfig, WidgetType
-
-from bridge.contracts import Classifier  # noqa: I001
-from bridge.dto import (
-    BuildResult,
-    EnviPyDTO,
-    EvaluationResult,
-    RunResult,
-    TransformationProductPrediction,
-)  # noqa: I001
-
-logger = logging.getLogger("epdb")
-
-
-class SamplingAlgorithm(enum.Enum):
-    EXACT = "exact"
-
-
-@register("bb4gconfig")
-class BB4GConfig(EnviPyModel):
-    sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
-    cutoff: int = -5
-
-    class UI:
-        title = "BB4G Configuration"
-        sampling_algorithm = UIConfig(
-            widget=WidgetType.SELECT,
-            label="BB4G Sampling Algorithm",
-            order=1,
-            placeholder="If unset defaults to 'exact'"
-        )
-        cutoff = UIConfig(
-            widget=WidgetType.NUMBER,
-            label="BB4G Cutoff",
-            order=2,
-            placeholder="If unset defaults to -5"
-        )
-
-
-# Once stable these will be exposed by enviPy-plugins lib
-class BB4G(Classifier):
-    Config = BB4GConfig
-
-    def __init__(self, config: BB4GConfig | None = None):
-        super().__init__(config)
-        self.url = f"{s.BB4G_URL}"
-
-        self.token = self.acquire_token()
-        self.header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-    def acquire_token(self):
-        BB4G_TENANT_ID = s.BB4G_TENANT_ID
-        BB4G_CLIENT_ID = s.BB4G_CLIENT_ID
-        BB4G_CLIENT_SECRET = s.BB4G_CLIENT_SECRET
-        BB4G_SCOPE = s.BB4G_SCOPE
-
-        BB4G_TOKEN_URL = f"https://login.microsoftonline.com/{BB4G_TENANT_ID}/oauth2/v2.0/token"
-
-        payload = {
-            "client_id": BB4G_CLIENT_ID,
-            "client_secret": BB4G_CLIENT_SECRET,
-            "scope": BB4G_SCOPE,
-            "grant_type": "client_credentials"
-        }
-
-        # No Proxy required, URL is whitelisted
-        res = requests.post(BB4G_TOKEN_URL, data=payload)
-
-        res.raise_for_status()
-
-        return res.json()["access_token"]
-
-    def start(self):
-        header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-        started = False
-
-        while not started:
-            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
-            logger.info(f"Starting BB4G: {res.status_code}")
-            if res.status_code == 200:
-                started = True
-            elif res.status_code in [500, 502]:
-                import time
-                time.sleep(5)
-            else:
-                raise ValueError(f"Unexpected status code: {res.status_code}")
-
-    @classmethod
-    def requires_rule_packages(cls) -> bool:
-        return False
-
-    @classmethod
-    def requires_data_packages(cls) -> bool:
-        return False
-
-    @classmethod
-    def identifier(cls) -> str:
-        return "bb4g"
-
-    @classmethod
-    def name(cls) -> str:
-        return "BB4G Template Free Model"
-
-    @classmethod
-    def display(cls) -> str:
-        return "BB4G Template Free Model"
-
-    def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
-        return
-
-    def run(self, eP: EnviPyDTO, *args, **kwargs) -> RunResult:
-
-        # Ensure Service is running
-        self.start()
-
-        smiles = [c.smiles for c in eP.get_compounds()]
-        preds = self._post(smiles)
-
-        results = []
-
-        for substrate in preds.keys():
-            results.append(
-                TransformationProductPrediction(
-                    substrate=substrate,
-                    products=preds[substrate],
-                )
-            )
-
-        return RunResult(
-            producer=eP.get_context().url,
-            description=f"Generated at {datetime.now()}",
-            result=results,
-        )
-
-    def evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
-        pass
-
-    def build_and_evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
-        pass
-
-    def _post(self, smiles: List[str]) -> dict[str, dict[str, float]]:
-        header = {
-            "Authorization": f"Bearer {self.token}",
-            "Content-Type": "application/json",
-        }
-
-        result = {}
-
-        for smi in smiles:
-            data = {
-                "smiles": smi,
-                "sampling_alg": self.config.sampling_algorithm.value,
-                "cutoff": self.config.cutoff,
-            }
-
-            retries = 0
-            while retries < 100:
-                resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
-                                     proxies=s.PROXIES or None)
-
-                if resp.status_code == 418:
-                    retries += 1
-                    logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
-                    import time
-                    time.sleep(3)
-                    continue
-
-                resp.raise_for_status()
-
-                for substrate, predictions in resp.json().items():
-                    preds = {}
-
-                    for pred in predictions:
-                        prod = pred["prediction"]
-                        prob = math.exp(pred["log_likelihood"])
-                        preds[prod] = prob
-
-                    result[substrate] = preds
-
-                break
-
-        return result

bridge/contracts.py

@@ -254,14 +254,7 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-
+        return cls.Config(**(data or {}))
-        # remove empty strings a.k.a unset params to not overwrite defaults
-        cpy = {}
-        if data is not None:
-            for k, v in data.items():
-                if v != "":
-                    cpy[k] = v
-        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

docker-compose.dev.yml

@@ -25,14 +25,25 @@ services:
       - ep_bayer_redis_data:/data
 
   biotransformer3:
-    image: git.envipath.com/envipath/biotransformer3:1.0
+    image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
+#  web:
+#    image: envipath/envipy-bayer:1.0
+#    container_name: epdjango
+#    ports:
+#      - "127.0.0.1:8000:8000"
+#    env_file:
+#      - .env
+#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
+#    volumes:
+#      - ep_bayer_data:/opt/enviPy/
+
   celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.2
+    image: envipath/envipy-bayer:1.0
     container_name: epcelery
     env_file:
-      - .env
+      - .env.dev
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
       - ep_bayer_data:/opt/enviPy/

envipath/settings.py

@@ -143,12 +143,6 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
         "TEMPLATE": os.environ["TEMPLATE_DB"],
     }
 
-CACHES = {
-    "default": {
-        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
-        "LOCATION": "unique-snowflake",
-    }
-}
 
 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@@ -275,12 +269,6 @@ LOGGING = {
             "filename": os.path.join(LOG_DIR, "debug.log"),
             "formatter": "simple",
         },
-        "auth_file": {
-            "level": "INFO",  # Or higher
-            "class": "logging.FileHandler",
-            "filename": os.path.join(LOG_DIR, "auth.log"),
-            "formatter": "simple",
-        }
     },
     "loggers": {
         # For everything under epdb/ loaded via getlogger(__name__)
@@ -301,11 +289,6 @@ LOGGING = {
             "propagate": True,
             "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
-        "auth": {
-            "handlers": ["auth_file"],
-            "propagate": True,
-            "level": os.environ.get("LOG_LEVEL", "INFO"),
-        }
     },
 }
 
@@ -354,7 +337,7 @@ DEFAULT_MODEL_PARAMS = {
     "num_chains": 10,
 }
 
-DEFAULT_MAX_NUMBER_OF_NODES = 9999
+DEFAULT_MAX_NUMBER_OF_NODES = 50
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
 
@@ -468,39 +451,5 @@ if PES_API_MAPPING:
 else:
     PES_API_MAPPING = {}
 
-# Entra Groups
+# AD Group Mapping
-ENTRA_GROUPS = os.environ.get("ENTRA_GROUPS", None)
-if ENTRA_GROUPS:
-    import json
-    ENTRA_GROUPS = json.loads(ENTRA_GROUPS)
-else:
-    ENTRA_GROUPS = {}
 
-ENTRA_SECRET_GROUPS = os.environ.get("ENTRA_SECRET_GROUPS", None)
-if ENTRA_SECRET_GROUPS:
-    import json
-    ENTRA_SECRET_GROUPS = json.loads(ENTRA_SECRET_GROUPS)
-else:
-    ENTRA_SECRET_GROUPS = {}
-
-# PES Data Pools vs Entra Mapping
-DATA_POOL_MAPPING = os.environ.get("DATA_POOL_MAPPING", None)
-if DATA_POOL_MAPPING:
-    import json
-    DATA_POOL_MAPPING = json.loads(DATA_POOL_MAPPING)
-else:
-    DATA_POOL_MAPPING = {}
-
-PROXIES = {}
-if os.environ.get("HTTP_PROXY"):
-    PROXIES["http"] = os.environ.get("HTTP_PROXY")
-    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
-
-# BB4g
-BB4G_URL = os.environ.get("BB4G_URL")
-BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
-BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
-BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
-BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
-
-os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

envipath/urls.py

@@ -40,9 +40,6 @@ if "migration" in s.INSTALLED_APPS:
 if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
-if s.TENANT != "public":
-    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
-
 # Custom error handlers
 handler400 = "epdb.views.handler400"
 handler403 = "epdb.views.handler403"

epapi/tests/v1/test_api_permissions.py

@@ -117,28 +117,25 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
+            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
+            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
+            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
+            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
+            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access,
+            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
-            "CCCCCC",
-            name="No Access Compound",
-            description="Test compound",
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
+            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            name=f"Reviewed Compound {idx:03d}",
+            f"Reviewed Compound {idx:03d}",
-            description="Compound for pagination tests",
+            "Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            name=f"Draft Compound {idx:03d}",
+            f"Draft Compound {idx:03d}",
-            description="Compound for pagination tests",
+            "Compound for pagination tests",
         )
 
 

epapi/v1/endpoints/joblogs.py

@@ -1,26 +0,0 @@
-from django.conf import settings as s
-from ninja import Router
-from ninja_extra.pagination import paginate
-
-from epdb.models import JobLog
-from ..pagination import EnhancedPageNumberPagination
-from ..schemas import JobLogOutSchema
-
-router = Router()
-
-
-@router.get("/joblog/", response=EnhancedPageNumberPagination.Output[JobLogOutSchema])
-@paginate(
-    EnhancedPageNumberPagination,
-    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
-)
-def list_all_joblogs(request):
-    """
-    List all JobLogs from reviewed packages.
-    """
-    current_user = request.user
-
-    if current_user.is_superuser:
-        return JobLog.objects.all().order_by("-created")
-    else:
-        return JobLog.objects.filter(user=current_user).order_by("-created")

epapi/v1/router.py

@@ -15,7 +15,6 @@ from .endpoints import (
     additional_information,
     settings,
     groups,
-    joblogs,
 )
 
 # Main router with authentication
@@ -38,7 +37,6 @@ router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
 router.add_router("", groups.router)
-router.add_router("", joblogs.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -1,10 +1,7 @@
-from datetime import datetime
+from ninja import FilterSchema, FilterLookup, Schema
 from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
-from django.urls import reverse
-from ninja import Field, FilterSchema, FilterLookup, Schema
-
 
 # Filter schema for query parameters
 class ReviewStatusFilter(FilterSchema):
@@ -136,23 +133,3 @@ class GroupOutSchema(Schema):
     url: str = ""
     name: str
     description: str
-
-
-class SimpleUserOutSchema(Schema):
-    uuid: UUID
-    url: str
-    name: str = Field(alias="username")
-
-
-class JobLogOutSchema(Schema):
-    user: SimpleUserOutSchema
-    id: UUID = Field(alias="task_id")
-    url: str
-    name: str = Field(alias="job_name")
-    created: datetime = Field(alias="created")
-    status: str = Field(alias="status")
-    done: Optional[datetime] = Field(None, alias="done_at")
-
-    @staticmethod
-    def resolve_url(obj):
-        return reverse("job detail", kwargs={"job_uuid": obj.task_id})

epauth/urls.py

@@ -5,5 +5,4 @@ from . import views
 urlpatterns = [
     path("entra/login/", views.entra_login, name="entra_login"),
     path("auth/redirect/", views.entra_callback, name="entra_callback"),
-    path("auth/token/", views.get_token, name="get_token"),
 ]

epauth/views.py

@@ -1,32 +1,10 @@
 import msal
 from django.conf import settings as s
-from django.contrib.auth import get_user_model
 from django.contrib.auth import login
-from django.http import HttpResponse
 from django.shortcuts import redirect
+from django.contrib.auth import get_user_model
 
-from epdb.logic import UserManager, GroupManager
+from epdb.logic import UserManager
-from epdb.models import Group
-
-
-def get_msal_app_with_cache(request):
-    """
-    Create MSAL app with session-based token cache.
-    """
-    cache = msal.SerializableTokenCache()
-
-    # Load cache from session if it exists
-    if request.session.get("msal_token_cache"):
-        cache.deserialize(request.session["msal_token_cache"])
-
-    msal_app = msal.ConfidentialClientApplication(
-        client_id=s.MS_ENTRA_CLIENT_ID,
-        client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY,
-        token_cache=cache,
-    )
-
-    return msal_app, cache
 
 
 def entra_login(request):
@@ -45,7 +23,11 @@ def entra_login(request):
 
 
 def entra_callback(request):
-    msal_app, cache = get_msal_app_with_cache(request)
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY,
+    )
 
     flow = request.session.pop("msal_auth_flow", None)
     if not flow:
@@ -54,18 +36,11 @@ def entra_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    # Save the token cache to session
-    if cache.has_state_changed:
-        request.session["msal_token_cache"] = cache.serialize()
-
     claims = result["id_token_claims"]
 
-    user_name = claims.get("name")
+    user_name = claims["name"]
-    user_email = claims.get("emailaddress", claims.get("email"))
+    user_email = claims["emailaddress"]
-    user_oid = claims.get("oid")
+    user_oid = claims["oid"]
-
-    if not all([user_name, user_email, user_oid]):
-        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
@@ -82,89 +57,4 @@ def entra_callback(request):
 
     login(request, u)
 
-    # EDIT START
+    return redirect("/")  # Handle errors
-
-    # Ensure groups exists in eP
-    for id, name in s.ENTRA_SECRET_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-        # Ensure its secret
-        g.secret = True
-        g.save()
-
-    for id, name in s.ENTRA_GROUPS.items():
-        if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
-                                          uuid=id)
-        else:
-            g = Group.objects.get(uuid=id)
-
-    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
-
-    return redirect(s.SERVER_URL)  # Handle errors
-
-
-def get_access_token_from_request(request, scopes=None):
-    """
-    Get an access token from the request using MSAL token cache.
-    """
-
-    # Check if auth via Access Token
-    if request.headers.get("Authorization"):
-        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
-
-    if scopes is None:
-        scopes = s.MS_ENTRA_SCOPES
-
-    # Get user from request (must be authenticated)
-    if not request.user.is_authenticated:
-        return None
-
-    # Create MSAL app with persistent cache
-    msal_app, cache = get_msal_app_with_cache(request)
-
-    # Try to get accounts from cache
-    accounts = msal_app.get_accounts()
-
-    if not accounts:
-        return None
-
-    # Find the account that matches the current user
-    user_account = None
-    for account in accounts:
-        if account.get("local_account_id") == str(request.user.uuid):
-            user_account = account
-            break
-
-    # If no matching account found, use the first available account
-    if not user_account and accounts:
-        user_account = accounts[0]
-
-    if not user_account:
-        return None
-
-    # Try to acquire token silently from cache
-    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
-
-    # Save cache changes back to session
-    if cache.has_state_changed:
-        request.session["msal_token_cache"] = cache.serialize()
-
-    if result and "access_token" in result:
-        return result
-
-    return None
-
-
-def get_token(request):
-    token = get_access_token_from_request(request)
-    msg = f"{token}"
-    return HttpResponse(msg, content_type='text/plain')

epdb/admin.py

@@ -1,8 +1,5 @@
-import logging
-
 from django.conf import settings as s
 from django.contrib import admin
-from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -32,8 +29,6 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
-logger = logging.getLogger(__name__)
-
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -50,113 +45,6 @@ class UserAdmin(admin.ModelAdmin):
         "date_joined",
     ]
 
-    actions = ["send_welcome_mail", "send_affiliation_mail"]
-
-    @admin.action(description="Send welcome mail")
-    def send_welcome_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Hello {username},
-
-Your account has been successfully activated.
-
-To log in, please visit
-https://envipath.org/password_reset/
-and request a new password.
-
-If you have any questions or feedback, feel free to visit our community forum at
-https://community.envipath.org/.
-You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
-
-Best regards,
-
-The enviPath Team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active:
-                logger.info(f"{user.username} already active - not sending mail again")
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Your enviPath Account Is Now Active",
-                    tpl.format(username=user.username),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.is_active = True
-                user.password = "ASDF"
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
-    @admin.action(description="Send affiliation mail")
-    def send_affiliation_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Dear {username},
-
-Thank you for your interest in enviPath!
-
-Please note that the public enviPath system is intended for non-commercial use only.
-We see that you registered using the email address {email}.
-If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
-
-If you would like us to update your account, simply reply to this email and let us know which address we should use.
-We will then change it in our system, and you will receive a password reset email at the new address.
-
-If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
-To book a meeting, please visit https://envipath.com/book
-
-If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
-
-Best regards,
-
-enviPath team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active or user.contacted:
-                logger.info(
-                    f"{user.username} already active or already contacted - not sending mail again"
-                )
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Regarding your enviPath registration",
-                    tpl.format(username=user.username, email=user.email),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.contacted = True
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} affiliation mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass

epdb/exceptions.py

@@ -1,10 +0,0 @@
-class InvalidSMILESException(Exception):
-    pass
-
-
-class InvalidMolfileException(Exception):
-    pass
-
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -1,17 +1,13 @@
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
-import jwt
 import nh3
-import requests
 from django.conf import settings as s
 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
+from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
@@ -50,26 +46,6 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
-def get_cached_jwks(tenant_id: str, force=False) -> Dict:
-    """Get JWKS using Django cache"""
-    cache_key = f"jwks_{tenant_id}"
-
-    jwks = cache.get(cache_key)
-
-    if jwks is None or force:
-        # Cache miss, fetch new keys
-        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
-        response = requests.get(jwks_uri)
-        response.raise_for_status()
-
-        jwks = response.json()
-
-        # Cache for 1 hour (3600 seconds)
-        cache.set(cache_key, jwks, 3600)
-
-    return jwks
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -83,52 +59,7 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-def validate_token(token: str) -> dict:
+router = Router(auth=SessionAuth(csrf=False))
-    TENANT_ID = s.MS_ENTRA_TENANT_ID
-    CLIENT_ID = s.MS_ENTRA_CLIENT_ID
-
-    jwks = get_cached_jwks(TENANT_ID)
-
-    header = jwt.get_unverified_header(token)
-
-    public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
-        next(k for k in jwks["keys"] if k["kid"] == header["kid"])
-    )
-
-    # Handle V1 and V2 tokens
-    try:
-        claims = jwt.decode(
-            token,
-            public_key,
-            algorithms=["RS256"],
-            audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-            issuer=[
-                f"https://sts.windows.net/{TENANT_ID}/",
-                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
-            ]
-        )
-    except Exception as e:
-        raise ValueError(f"Token verification failed! - {e}")
-
-    return claims
-
-
-class MSBearerTokenAuth(HttpBearer):
-
-    def authenticate(self, request, token):
-        if token is None:
-            return None
-
-        claims = validate_token(token)
-
-        if not User.objects.filter(uuid=claims['oid']).exists():
-            return None
-
-        request.user = User.objects.get(uuid=claims['oid'])
-        return request.user
-
-
-router = Router(auth=MSBearerTokenAuth())
 
 
 class Error(Schema):
@@ -222,6 +153,21 @@ class SimpleModel(SimpleObject):
     identifier: str = "relative-reasoning"
 
 
+################
+# Login/Logout #
+################
+@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
+def login(request, loginusername: Form[str], loginpassword: Form[str]):
+    from django.contrib.auth import authenticate, login
+
+    email = User.objects.get(username=loginusername).email
+    user = authenticate(username=email, password=loginpassword)
+    if user:
+        login(request, user)
+        return user
+    else:
+        return 403, {"message": "Invalid username and/or password"}
+
 
 ########
 # User #
@@ -440,50 +386,23 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        readers = []
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.READ[0]
+            ).values_list("user", flat=True)
+        ).distinct()
 
-        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+        return [{u.id: u.get_name()} for u in users]
-
-        users = User.objects.filter(id__in=user_ids).distinct()
-
-        for u in users:
-            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
-            "group", flat=True
-        )
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        writers = []
+        users = User.objects.filter(
-
+            id__in=UserPackagePermission.objects.filter(
-        user_ids = UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.WRITE[0]
-            package=obj,
-            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
             ).values_list("user", flat=True)
+        ).distinct()
 
-        users = User.objects.filter(id__in=user_ids).distinct()
+        return [{u.id: u.get_name()} for u in users]
-
-        for u in users:
-            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(
-            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
-        ).values_list("group", flat=True)
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -634,14 +553,9 @@ class CompoundSchema(Schema):
     reviewStatus: str = Field(False, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     structures: List["CompoundStructureSchema"] = []
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
-    def resolve_pes_link(obj: Compound):
+    def resolve_review_status(obj: CompoundStructure):
-        return getattr(obj.default_structure, "pes_link", None)
-
-    @staticmethod
-    def resolve_review_status(obj: Compound):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -715,7 +629,6 @@ class CompoundStructureSchema(Schema):
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smiles: str = Field(None, alias="smiles")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_review_status(obj: CompoundStructure):
@@ -851,11 +764,9 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
-    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
-    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -867,36 +778,8 @@ def create_package_compound(
     try:
         p = get_package_for_write(request.user, package_uuid)
         # inchi is not used atm
-
-        if c.pesLink is not None:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-
-                if p.classification_level != Package.Classification.SECRET:
-                    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:
         c = Compound.create(
-                p,
+            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
-                c.compoundSmiles,
-                molfile=c.compoundMolFile,
-                name=c.compoundName,
-                description=c.compoundDescription,
-                inchi=c.inchi
         )
         return redirect(c.url)
     except ValueError as e:
@@ -916,27 +799,6 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
-class CreateCompoundStructure(Schema):
-    smiles: str
-    name: str | None = None
-    description: str | None = None
-    inchi: str | None = None
-    molfile: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
-def create_package_compound_structure(
-    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
-):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-        c = Compound.objects.get(package=p, uuid=compound_uuid)
-        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
-        return redirect(cs.url)
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1463,7 +1325,6 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
-    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1607,7 +1468,6 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
-        if request.POST.get("adInfoTypes[]"):
         url_parser = EPDBURLParser(request.POST.get("attach_obj"))
         attach_obj = url_parser.get_object()
 
@@ -1631,33 +1491,6 @@ def create_package_additional_information(request, package_uuid):
                 content_object=attach_obj,
             )
 
-        elif request.POST.get("ais"):
-            import json
-
-            parsed_ais = json.loads(request.POST.get("ais"))
-
-            for ai_type, ais in parsed_ais.items():
-                for ai in ais:
-                    attach_obj = None
-                    if ai.get("related"):
-                        url_parser = EPDBURLParser(ai.get("related").get("url"))
-                        attach_obj = url_parser.get_object()
-
-                        if not hasattr(attach_obj, "additional_information"):
-                            raise ValueError("Can't attach additional information to this object!")
-
-                        if not attach_obj.url.startswith(p.url):
-                            raise ValueError(
-                                "Additional Information can only be set to objects stored in the same package!"
-                            )
-
-                    AdditionalInformation.create(
-                        p,
-                        AdditionalInformation.from_dict(ai_type, ai),
-                        scenario=scenario,
-                        content_object=attach_obj,
-                    )
-
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
     except ValueError:
@@ -1700,15 +1533,13 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
-    idreact: str = Field(None, alias="node_label_id")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, str]] = []
+    proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="smiles")
+    smiles: str = Field(None, alias="default_node_label.smiles")
-    pseudo: bool = Field(False, alias="pseudo")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1721,10 +1552,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1848,29 +1693,6 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
-@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
-def update_pathway(request, package_uuid, pathway_uuid):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-
-        if request.POST.get("scenario"):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
-
-            pw.scenarios.add(scen)
-            pw.save()
-
-            return redirect(f"{pw.url}")
-
-        else:
-            return 400, {"message": "No scenario specified!"}
-
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
-        }
-
-
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1976,78 +1798,28 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
-    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 400: Error, 403: Error},
+    response={200: str | Any, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        # TODO Code Dup from bayer.views
-
-        if n.pesLink:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, n.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-
-                if p.classification_level != Package.Classification.SECRET:
-                    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, n.nodeName, n.nodeReason)
-
-            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
-            if node_qs.exists():
-                return redirect(pw.url)
-
-            node = Node()
-            node.stereo_removed = False
-            node.pathway = pw
-            node.depth = 0
-
-            node.default_node_label = c.default_structure
-            node.save()
-
-            node.node_labels.add(c.default_structure)
-            node.save()
-        else:
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
             node_depth = int(n.nodeDepth)
         else:
             node_depth = -1
 
-            node = Node.create(
+        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
-                pw,
-                n.nodeAsSmiles,
-                node_depth,
-                molfile=n.nodeAsMolFile,
-                name=n.nodeName,
-                description=n.nodeReason,
-            )
 
-        return redirect(node.url)
+        return redirect(n.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -2157,16 +1929,13 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
-        subclasses = CompoundStructure.__subclasses__()
-
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -2177,8 +1946,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -2190,10 +1958,6 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
-        multi_step = False
-        if e.multistep and e.multistep.strip() == "true":
-            multi_step = True
-
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -2201,15 +1965,11 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
-            multi_step=multi_step,
         )
 
-        # Update depths as sideeffect of above operation
-        pw.update_depths()
-
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding Edge failed!"}
+        return 403, {"message": "Adding node failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
@@ -2400,26 +2160,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@router.post("/util", response={200: Any, 403: Error})
-def predict(request, np: Form[NonPersistent]):
-    try:
-        from epdb.logic import SPathway
-
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
-        spw.predict()
-        return spw.to_json()
-    except ValueError:
-        return 403, {
-            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -7,7 +7,6 @@ import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
-from django.db.models import QuerySet
 from pydantic import ValidationError
 
 from epdb.models import (
@@ -265,12 +264,8 @@ class GroupManager(object):
         return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
-    def create_group(current_user, name, description, *args, **kwargs):
+    def create_group(current_user, name, description):
         g = Group()
-
-        if "uuid" in kwargs:
-            g.uuid = kwargs["uuid"]
-
         # Clean for potential XSS
         g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -346,17 +341,52 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        return (
+        if (
-            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
+            UserPackagePermission.objects.filter(package=package, user=user).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package, group__in=GroupManager.get_groups(user)
             )
+            or package.reviewed is True
+            or user.is_superuser
+        ):
+            return True
+
+        return False
 
     @staticmethod
     def writable(user, package):
-        return PackageManager.has_package_permission(user, package, "write")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.WRITE[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.WRITE[0],
+            ).exists()
+            or UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def administrable(user, package):
-        return PackageManager.has_package_permission(user, package, "all")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.ALL[0],
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -365,14 +395,6 @@ class PackageManager(object):
 
         groups = GroupManager.get_groups(user)
 
-        # EDIT START
-
-        if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
-                return False
-
-        # EDIT END
-
         perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
 
         valid_perms = perms.get(permission)
@@ -415,7 +437,6 @@ class PackageManager(object):
         try:
             p = Package.objects.get(uuid=package_id)
             if PackageManager.readable(user, p):
-                p = PackageManager.check_package_classification(user, p)
                 return p
             else:
                 # FIXME: use custom exception to be translatable to 403 in API
@@ -425,37 +446,6 @@ class PackageManager(object):
         except Package.DoesNotExist:
             raise ValueError("Package with ID {} does not exist!".format(package_id))
 
-    # EDIT START
-
-    @staticmethod
-    def check_package_classification(user, pack: Package):
-        if pack.classification_level == Package.Classification.SECRET:
-            if pack.data_pool.user_member.filter(id=user.id).exists():
-                return pack
-
-            raise ValueError("Package is secret and not accessible to user!")
-
-        else:
-            return pack
-
-
-    @staticmethod
-    def check_package_classifications(user, package_qs: QuerySet[Package]):
-        non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
-        secret = package_qs.filter(classification_level=Package.Classification.SECRET)
-
-        # TODO we should be able to do via the db
-        accessible_secret = []
-
-        for s_package in secret:
-            if s_package.data_pool.user_member.filter(id=user.id).exists():
-                accessible_secret.append(s_package.pk)
-
-        # Cannot combine a unique query with a non-unique query -> we have to call distinct
-        return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
-
-    # EDIT END
-
     @staticmethod
     def get_all_readable_packages(user, include_reviewed=False):
         # UserPermission only exists if at least read is granted...
@@ -480,13 +470,7 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
-
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
-        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -530,13 +514,11 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
 
-        # EDIT START
+    @staticmethod
-        qs = PackageManager.check_package_classifications(user, qs)
+    def get_packages():
-        # EDIT END
+        return Package.objects.all()
-
-        return qs
 
     @staticmethod
     @transaction.atomic
@@ -641,25 +623,6 @@ class PackageManager(object):
         else:
             pack.reviewed = False
 
-        # EDIT START
-        if data.get("classification"):
-            if data["classification"] == "INTERNAL":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "RESTRICTED":
-                pack.classification = Package.Classification.RESTRICTED
-            elif data["classification"] == "SECRET":
-                pack.classification = Package.Classification.SECRET
-
-                if not "datapool" in data:
-                    raise ValueError("Missing datapool in package")
-
-                g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
-                pack.data_pool = g
-            else:
-                raise ValueError(f"Invalid classification {data['classification']}")
-
-        # EDIT END
-
         pack.description = data["description"]
         pack.save()
 
@@ -745,13 +708,7 @@ class PackageManager(object):
             default_structure = None
 
             for structure in compound["structures"]:
-                if structure.get("pesLink"):
-                    from bayer.models import PESStructure
-                    struc = PESStructure()
-                    struc.pes_link = structure["pesLink"]
-                else:
                 struc = CompoundStructure()
-
                 # struc.object_url = Command.get_id(structure, keep_ids)
                 struc.compound = comp
                 struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@@ -759,10 +716,6 @@ class PackageManager(object):
                 struc.description = structure["description"]
                 struc.aliases = structure.get("aliases", [])
                 struc.smiles = structure["smiles"]
-
-                if structure.get("molfile"):
-                    struc.molfile = structure["molfile"]
-
                 struc.save()
 
                 for scen in structure["scenarios"]:
@@ -1065,9 +1018,52 @@ class PackageManager(object):
 
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
-
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            pw.update_depths()
+            in_count = defaultdict(lambda: 0)
+            out_count = defaultdict(lambda: 0)
+
+            for e in pw.edges:
+                # TODO check if this will remain
+                for react in e.start_nodes.all():
+                    out_count[str(react.uuid)] += 1
+
+                for prod in e.end_nodes.all():
+                    in_count[str(prod.uuid)] += 1
+
+            root_nodes = []
+            for n in pw.nodes:
+                num_parents = in_count[str(n.uuid)]
+                if num_parents == 0:
+                    # must be a root node or unconnected node
+                    if n.depth != 0:
+                        n.depth = 0
+                        n.save()
+
+                    # Only root node may have children
+                    if out_count[str(n.uuid)] > 0:
+                        root_nodes.append(n)
+
+            levels = [root_nodes]
+            seen = set()
+            # Do a bfs to determine depths starting with level 0 a.k.a. root nodes
+            for i, level_nodes in enumerate(levels):
+                new_level = []
+                for n in level_nodes:
+                    for e in n.out_edges.all():
+                        for prod in e.end_nodes.all():
+                            if str(prod.uuid) not in seen:
+                                old_depth = prod.depth
+                                if old_depth != i + 1:
+                                    prod.depth = i + 1
+                                    prod.save()
+
+                                new_level.append(prod)
+
+                    seen.add(str(n.uuid))
+
+                if new_level:
+                    levels.append(new_level)
+
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack
@@ -1078,8 +1074,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1896,12 +1894,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

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

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -1,54 +1,50 @@
-# Generated by Django 6.0.3 on 2026-04-21 11:43
+# Generated by Django 6.0.3 on 2026-04-14 19:07
 
 from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
+
     dependencies = [
-        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
+        ('epdb', '0022_alter_classifierpluginmodel_data_packages_and_more'),
     ]
 
     operations = [
         migrations.AlterModelOptions(
-            name="compoundstructure",
+            name='compoundstructure',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="epmodel",
+            name='epmodel',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="parallelrule",
+            name='parallelrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="rule",
+            name='rule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="sequentialrule",
+            name='sequentialrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simpleambitrule",
+            name='simpleambitrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simplerdkitrule",
+            name='simplerdkitrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simplerule",
+            name='simplerule',
             options={},
         ),
         migrations.AddField(
-            model_name="compoundstructure",
+            model_name='group',
-            name="molfile",
+            name='secret',
-            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
+            field=models.BooleanField(default=False, verbose_name='Secret Group'),
-        ),
-        migrations.AddField(
-            model_name="group",
-            name="secret",
-            field=models.BooleanField(default=False, verbose_name="Secret Group"),
         ),
     ]

epdb/migrations/0024_user_contacted.py

@@ -1,17 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-21 19:56
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0023_alter_compoundstructure_options_and_more"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="user",
-            name="contacted",
-            field=models.BooleanField(blank=True, null=True),
-        ),
-    ]

epdb/migrations/0025_auto_20260511_2025.py

@@ -1,57 +0,0 @@
-# Generated by Django 6.0.3 on 2026-05-11 20:25
-
-from django.db import migrations
-from envipy_additional_information import HalfLife, HalfLifeModel, HalfLifeWS
-
-MAPPING = {
-    "": HalfLifeModel.OTHER,
-    "HS-SFO": HalfLifeModel.HS_SFO,
-    "FOMC": HalfLifeModel.FOMC,
-    "FOTC": HalfLifeModel.DFOP,
-    "FMOC": HalfLifeModel.FOMC,
-    "DFOP": HalfLifeModel.DFOP,
-    "SFO + SFO": HalfLifeModel.SFO_SFO,
-    "FOMC-SFO": HalfLifeModel.FOMC_SFO,
-    "first order kinetics": HalfLifeModel.SFO,
-    "SFO²": HalfLifeModel.SFO,
-    "HS": HalfLifeModel.HS,
-    "top down": HalfLifeModel.OTHER,
-    "SFO": HalfLifeModel.SFO,
-    "First Order": HalfLifeModel.SFO,
-    "SFO/SFO": HalfLifeModel.SFO_SFO,
-    "FOMC + SFO": HalfLifeModel.FOMC_SFO,
-    "true": HalfLifeModel.SFO,
-    "SFO-SFO": HalfLifeModel.SFO_SFO,
-    "DFOP-SFO": HalfLifeModel.DFOP_SFO,
-    "other": HalfLifeModel.OTHER,
-}
-
-
-def forward_func(apps, schema_editor):
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    hls = AdditionalInformation.objects.filter(type="HalfLife")
-
-    for hl in hls:
-        data = hl.data
-        data["model"] = MAPPING[data["model"]].value
-        hl.data = HalfLife(**data).model_dump(mode="json")
-        hl.save()
-
-    hlws = AdditionalInformation.objects.filter(type="HalfLifeWS")
-
-    for hl in hlws:
-        data = hl.data
-        data["model"] = MAPPING[data["model"]].value
-        hl.data = HalfLifeWS(**data).model_dump(mode="json")
-        hl.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0024_user_contacted"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0026_auto_20260602_1718.py

@@ -1,48 +0,0 @@
-# Generated by Django 6.0.3 on 2026-06-02 17:18
-
-from django.db import migrations
-from envipy_additional_information import DOI
-
-
-def forward_func(apps, schema_editor):
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    refs = AdditionalInformation.objects.filter(type="Reference")
-
-    remaining = []
-
-    for ref in refs:
-        r = ref.data["reference"]
-        try:
-            # PubMed IDs are plain ints, try parsing
-            _ = int(r)
-            # Nothing to do
-        except ValueError:
-            DOMAINS = [
-                "http://dx.doi.org/",
-                "https://dx.doi.org/",
-                "http://doi.org/",
-                "https://doi.org/",
-            ]
-            for d in DOMAINS:
-                r = r.replace(d, "")
-
-            if r.startswith("10."):
-                ref.type = DOI.__name__
-                ref.data = {"doi": r}
-                ref.save()
-            else:
-                remaining.append(ref)
-
-    if len(remaining) > 0:
-        raise ValueError(f"Could not parse {len(remaining)} references")
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0025_auto_20260511_2025"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0027_alter_compound_aliases_and_more.py

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

epdb/models.py

@@ -31,10 +31,6 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import (
-    InvalidMolfileException,
-    InvalidSMILESException,
-)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -79,7 +75,6 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
-    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -580,10 +575,6 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
-    def contains_pes(self):
-        from bayer.models import PESStructure
-        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
-            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #
@@ -640,7 +631,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -663,9 +654,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -791,19 +780,12 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.SET_NULL,
+        on_delete=models.CASCADE,
         null=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
-    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
-        for struct in self.structures.all():
-            if struct.smiles == smiles:
-                return struct
-
-        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
-
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -872,79 +854,40 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
+        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
-        smiles: str,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
-        *args,
-        **kwargs,
     ) -> "Compound":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles.strip() == "":
-            raise InvalidSMILESException("SMILES is required")
+            raise ValueError("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise InvalidSMILESException("Given SMILES is invalid")
+            raise ValueError("Given SMILES is invalid")
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
-        subclasses = CompoundStructure.__subclasses__()
-
-        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
-
         # Check if we find a direct match for a given SMILES
-        if qs.exists():
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            found_structure = qs.first()
+            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
-            found_compound = found_structure.compound
-
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
-
-        qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
-        if qs.exists():
+        if CompoundStructure.objects.filter(
-            found_structure = qs.first()
+            smiles=standardized_smiles, compound__package=package
-            found_compound = found_structure.compound
+        ).exists():
-
+            # TODO should we add a structure?
-            # We've only found the standardized one, create the very structure
+            return CompoundStructure.objects.get(
-            _ = found_compound.add_structure(
+                smiles=standardized_smiles, compound__package=package
-                smiles, molfile=molfile, name=name, description=description
+            ).compound
-            )
-
-            if name:
-                found_compound.add_alias(name)
-
-            return found_compound
 
         # Generate Compound
         c = Compound()
         c.package = package
 
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -968,12 +911,7 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c,
+            c, smiles, name=name, description=description, normalized_structure=is_standardized
-            smiles,
-            molfile=molfile,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized,
         )
 
         c.default_structure = cs
@@ -986,22 +924,11 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
-        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -1021,28 +948,16 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
+        if CompoundStructure.objects.filter(
-            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
+            smiles__in=smiles, compound__package=self.package
-
+        ).exists():
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
-            return found_cs
 
         cs = CompoundStructure.create(
-            self,
+            self, smiles, name=name, description=description, normalized_structure=is_standardized
-            smiles,
-            name=name,
-            molfile=molfile,
-            description=description,
-            normalized_structure=is_standardized,
         )
 
         if default_structure:
@@ -1198,7 +1113,6 @@ class CompoundStructure(
     canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
     inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
-    molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
@@ -1223,61 +1137,24 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound,
+        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
-        smiles: str,
-        molfile: str = None,
-        name: str = None,
-        description: str = None,
-        *args,
-        **kwargs,
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
-        # Clean for potential XSS
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
-
-            if name:
-                found_cs.add_alias(name)
-
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
-            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-
+        # Clean for potential XSS
         if name is not None:
-            cs.name = name
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        # We have a default here only set the value if it carries some payload
+        if description is not None:
-        if description is not None and description.strip() != "":
             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:
-            cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
@@ -1296,8 +1173,6 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
-        if self.molfile is not None and self.molfile.strip() != "":
-            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1334,9 +1209,6 @@ class CompoundStructure(
 
         return dict(hls)
 
-    def d3_json(self):
-        return {}
-
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1495,9 +1367,6 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1509,17 +1378,14 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-
+            return query.first()
-            found_rule = query.first()
-
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
 
         r = SimpleAmbitRule()
         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}"
 
@@ -1652,9 +1518,6 @@ 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)
@@ -1666,19 +1529,15 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(
+                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
-                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
+            return existing_rule_qs.first()
-                )
-
-            found_rule = existing_rule_qs.first()
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
 
         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}"
 
@@ -1747,15 +1606,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1772,12 +1626,8 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = False,
+        multi_step: bool = True,
     ):
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         _educts = []
         _products = []
 
@@ -1832,23 +1682,16 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-
+            return existing_reaction_qs.first()
-            found_reaction = existing_reaction_qs.first()
-
-            if name:
-                found_reaction.add_alias(name)
-
-            return found_reaction
 
         r = Reaction()
         r.package = package
 
-        if name is None or name == "":
+        # Clean for potential XSS
-            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
+        if name is not None and name.strip() != "":
+            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        r.name = name
+        if description is not None and name.strip() != "":
-
-        if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1926,7 +1769,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
 
     @property
     def as_svg(self):
@@ -2039,9 +1882,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
-        for i in queue:
-            processed.add(i)
-
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2082,7 +1922,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
-                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -2092,7 +1931,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
-                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -2100,7 +1938,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
-                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -2111,7 +1948,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
-                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2321,12 +2157,11 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        molfile: str | None = None,
+        name: Optional[str] = None,
-        name: str | None = None,
+        description: Optional[str] = None,
-        description: str | None = None,
+        depth: Optional[int] = 0,
-        depth: int = -1,
     ):
-        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
+        return Node.create(self, smiles, depth, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2339,68 +2174,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
-    def update_depths(self):
-        # Collect number of in and out links per node
-        in_count = defaultdict(lambda: 0)
-        out_count = defaultdict(lambda: 0)
-
-        for e in self.edges:
-            for react in e.start_nodes.all():
-                out_count[str(react.uuid)] += 1
-
-            for prod in e.end_nodes.all():
-                in_count[str(prod.uuid)] += 1
-
-        depth_map = {}
-        depth_map[0] = list()
-        processed = set()
-
-        data_driven_root_nodes = (
-            self.node_set.all()
-            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
-            .filter(prod_cnt=0, educt_cnt__gt=0)
-            .distinct()
-        )
-
-        # Eval QuerySet
-        root_nodes_by_depth = list(self.root_nodes)
-
-        data_driven_root_nodes.update(depth=0)
-        root_nodes = [n for n in data_driven_root_nodes]
-
-        for n in root_nodes_by_depth:
-            if n not in root_nodes:
-                if len(n.edge_products.all()) == 0:
-                    root_nodes.append(n)
-
-        for n in root_nodes:
-            depth_map[0].append(n)
-
-        # At most depth len(nodes) is possible
-        for i in range(self.nodes.count()):
-            level_nodes = depth_map.get(i, [])
-
-            if len(level_nodes) == 0:
-                break
-
-            unique_next_level = set()
-            for n in level_nodes:
-                processed.add(n)
-                for e in self.edges:
-                    if n in e.start_nodes.all():
-                        for p in e.end_nodes.all():
-                            if p not in processed:
-                                unique_next_level.add(p)
-
-            if len(unique_next_level) > 0:
-                depth_map[i + 1] = list(unique_next_level)
-
-        for depth, nodes in depth_map.items():
-            for n in nodes:
-                if n.depth != depth and depth != 0:
-                    n.depth = depth
-                    n.save()
-
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2422,19 +2195,17 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
-        if self.name is None or self.name == "no name":
+        if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
+        return (
-            return self.name
+            self.name
-        else:
+            if non_generic_name
-            if include_suffix:
+            else f"{self.default_node_label.name} (taken from underlying structure)"
-                return f"{self.default_node_label.name} (taken from underlying structure)"
+        )
-            else:
-                return self.default_node_label.name
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2444,27 +2215,16 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        return {
-        # by overwriting keys
-        structure_data = self.default_node_label.d3_json()
-
-        res = {
             "depth": self.depth,
             "stereo_removed": self.stereo_removed,
             "url": self.url,
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
+                self.default_node_label.smiles, width=40, height=40
-                if self.default_node_label.molfile is not None
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
             ),
-            "image_type": "svg",
             "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.scenarios.all()],
             "app_domain": {
@@ -2475,73 +2235,49 @@ 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(),
             "timeseries": self.get_timeseries_data(),
-            **structure_data,
         }
 
-        return res
-
     @staticmethod
     @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        molfile: str | None = None,
+        name: Optional[str] = None,
-        name: str | None = None,
+        description: Optional[str] = None,
-        description: str | None = None,
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(
+        c = Compound.create(pathway.package, smiles, name=name, description=description)
-            pathway.package, smiles, molfile=molfile, name=name, description=description
-        )
 
-        structure = c.get_structure_by_smiles(smiles)
+        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
-
+            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
-        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
-            return Node.objects.get(pathway=pathway, default_node_label=structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = structure
+        n.default_node_label = c.default_structure
         n.save()
 
-        n.node_labels.add(structure)
+        n.node_labels.add(c.default_structure)
         n.save()
 
         return n
 
     @property
     def as_svg(self):
-        if (
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
-            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.type == "OECD301FTimeSeries":
+            if ai.__class__.__name__ == "OECD301FTimeSeries":
-                return ai.get().model_dump(mode="json")
+                return ai.model_dump(mode="json")
 
         return None
 
@@ -2572,35 +2308,13 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_proposed_info(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
-            scenario__isnull=False,
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
-
-            if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
-                    ai.get().importance.value
-                )
-
-        return list(collected.values())
-
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2615,7 +2329,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2680,8 +2393,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        *args,
-        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2711,7 +2422,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=kwargs.get("multi_step", False),
+            multi_step=False,
         )
 
         e.edge_label = r
@@ -2730,19 +2441,17 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
+        return (
-            return self.name
+            self.name
-        else:
+            if non_generic_name
-            if include_suffix:
+            else f"{self.edge_label.name} (taken from underlying reaction)"
-                return f"{self.edge_label.name} (taken from underlying reaction)"
+        )
-            else:
-                return self.edge_label.name
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):
@@ -4721,22 +4430,18 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    @staticmethod
+    def get(self) -> "EnviPyModel":
-    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[ai_type](**ai_data)
+            inst = MAPPING[self.type](**self.data)
         except Exception as e:
-            print(f"Error loading {ai_type}: {e}")
+            print(f"Error loading {self.type}: {e}")
             raise e
 
-        return inst
-
-    def get(self) -> "EnviPyModel":
-        inst = AdditionalInformation.from_dict(self.type, self.data)
         inst.__dict__["uuid"] = str(self.uuid)
+
         return inst
 
     def __str__(self) -> str:

epdb/views.py

@@ -19,7 +19,6 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -389,9 +388,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
-            # EDIT START
-            "secret_groups": Group.objects.filter(secret=True),
-            # EDIT END
         },
     }
 
@@ -786,11 +782,6 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -803,13 +794,11 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
+            "EnviFormer": {
-
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
+            },
         }
 
         if s.FLAGS.get("PLUGINS", False):
@@ -818,9 +807,6 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
-                    "additional_parameters": v.Config.__name__.lower()
-                    if v.Config.__name__ != ""
-                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -829,6 +815,12 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
+        # Context for paginated template
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -942,12 +934,11 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
+            "EnviFormer": {
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
+            },
         }
 
         if s.FLAGS.get("PLUGINS", False):
@@ -1124,11 +1115,6 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
-                        res["pred"] = sorted(
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
-
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1232,7 +1218,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -1415,18 +1403,12 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
-        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
-
         try:
             c = Compound.create(
-                current_package,
+                current_package, compound_smiles, compound_name, compound_description
-                compound_smiles,
-                molfile=compound_molfile,
-                name=compound_name,
-                description=compound_description,
             )
-        except (InvalidSMILESException, InvalidMolfileException) as e:
+        except ValueError as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1552,15 +1534,11 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
-        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles,
+                structure_smiles, structure_name, structure_description
-                molfile=structure_molfile,
-                name=structure_name,
-                description=structure_description,
             )
         except ValueError:
             return error(
@@ -1948,9 +1926,9 @@ 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")
+        reactions_smirks = request.POST.get("reaction-smirks")
-        educts = reaction_smiles.split(">>")[0].split(".")
+        educts = reactions_smirks.split(">>")[0].split(".")
-        products = reaction_smiles.split(">>")[1].split(".")
+        products = reactions_smirks.split(">>")[1].split(".")
 
         r = Reaction.create(
             current_package,
@@ -2131,14 +2109,12 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
-        is_predict_mode = pw_mode in {"predict", "incremental"}
-
         pw = Pathway.create(
             current_package,
-            stand_smiles if is_predict_mode else smiles,
+            stand_smiles,
             name=name,
             description=description,
-            predicted=is_predict_mode,
+            predicted=pw_mode in {"predict", "incremental"},
         )
 
         # set mode
@@ -2379,17 +2355,8 @@ 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_smiles = request.POST.get("node-smiles").strip()
-        node_molfile = request.POST.get("node-molfile")
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-
-        try:
-            current_pathway.add_node(
-                node_smiles, molfile=node_molfile, name=node_name, description=node_description
-            )
-        except InvalidSMILESException:
-            return error(
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
 
         return redirect(current_pathway.url)
 
@@ -2497,26 +2464,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
+        return HttpResponseBadRequest()
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.name = new_node_name
-
-            if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(
-                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
-                ).strip()
-                current_node.description = new_node_description
-
-            current_node.save()
-
-            return redirect(current_node.url)
-
-        return error(request, "Node update failed!", "No changes were made to the node")
-
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -2586,9 +2534,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
-        # Update depths as sideeffect of above operation
-        current_pathway.update_depths()
-
         return redirect(current_pathway.url)
 
     else:
@@ -3048,15 +2993,9 @@ def settings(request):
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         # min 2, max s.DEFAULT_MAX_NUMBER_OF_NODES
-        temp_max_nodes = request.POST.get("prediction-setting-max-nodes")
-        if temp_max_nodes is None or temp_max_nodes == "" or int(temp_max_nodes) == -1:
-            temp_max_nodes = s.DEFAULT_MAX_NUMBER_OF_NODES
-        else:
-            temp_max_nodes = int(request.POST.get("prediction-setting-max-nodes", 1))
-
         max_nodes = min(
             max(
-                temp_max_nodes,
+                int(request.POST.get("prediction-setting-max-nodes", 1)),
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -3077,7 +3016,6 @@ def settings(request):
 
             model_uuid = model_url.split("/")[-1]
             params["model"] = EPModel.objects.get(uuid=model_uuid)
-            # TODO Check if removed if request contains "" or not at all
             params["model_threshold"] = request.POST.get(
                 "model-based-prediction-setting-threshold", s.DEFAULT_MODEL_THRESHOLD
             )
@@ -3167,21 +3105,12 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        # if current_user.is_superuser:
+        if current_user.is_superuser:
-        #     context["jobs"] = JobLog.objects.all().order_by("-created")
+            context["jobs"] = JobLog.objects.all().order_by("-created")
-        # else:
+        else:
-        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        # Context for paginated template
+        return render(request, "collections/joblog.html", context)
-        context["entity_type"] = "joblog"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "joblog"
-        context["list_mode"] = "combined"
-
-        return render(request, "collections/joblog_paginated.html", context)
-
-        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

migration/views.py

@@ -65,25 +65,6 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
-    accepted_diffs = [
-        "bt0055-3469.1",
-        "bt0056-2685",
-        "bt0193-4263",
-        "bt0231-1871.1",
-        "bt0242-3803",
-        "bt0254-4224.1",
-        "bt0254-4224.2",
-        "bt0291-1129",
-        "bt0337-3543",
-        "bt0391-4285",
-        "bt0402-3576",
-        "bt0404-3928",
-        "bt0416-4269",
-        "bt0432-4254",
-        "bt0337-4117",
-        "bt0322-3393",
-    ]
-
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -128,11 +109,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res or r.name in accepted_diffs,
+                        "status": res,
                     }
                 )
 
-                if res or r.name in accepted_diffs:
+                if res:
                     success += 1
                 else:
                     error += 1
@@ -154,16 +135,7 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
-            if r["name"] in accepted_diffs:
-                r["status"] = True
 
-        migration_status["results"] = sorted(
-            migration_status["results"], key=lambda x: (x["status"], x["name"])
-        )
-
-        num_success = sum([int(x["status"]) for x in migration_status["results"]])
-        migration_status["success"] = num_success
-        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

package.json

@@ -21,11 +21,5 @@
     "django",
     "tailwindcss",
     "daisyui"
-  ],
-  "pnpm": {
-    "onlyBuiltDependencies": [
-      "@parcel/watcher",
-      "@tailwindcss/oxide"
   ]
 }
-}

pepper/__init__.py

@@ -46,7 +46,7 @@ class PepperPrediction(PropertyPrediction):
 
         import matplotlib.patches as mpatches
         import numpy as np
-        from matplotlib.figure import Figure
+        from matplotlib import pyplot as plt
         from scipy import stats
 
         """
@@ -101,8 +101,7 @@ class PepperPrediction(PropertyPrediction):
         mask_red = x > vp
 
         # Plot
-        fig = Figure(figsize=(9, 5.5))
+        fig, ax = plt.subplots(figsize=(9, 5.5))
-        ax = fig.subplots()
         ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
 
         if np.any(mask_green):
@@ -147,12 +146,13 @@ class PepperPrediction(PropertyPrediction):
         ]
         ax.legend(handles=patches, frameon=True)
 
-        fig.tight_layout()
+        plt.tight_layout()
 
         # --- Export to SVG string ---
         buf = io.StringIO()
         fig.savefig(buf, format="svg", bbox_inches="tight")
         svg = buf.getvalue()
+        plt.close(fig)
         buf.close()
 
         return svg

pepper/impl/pepper.py

@@ -187,9 +187,8 @@ class Pepper:
         groups = [group for group in dataset.group_by("structure_id")]
 
         # Unless explicitly set compute everything serial
-        n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
+        if os.environ.get("N_PEPPER_THREADS", 1) > 1:
-        if n_threads > 1:
+            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
-            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

pnpm-workspace.yaml

@@ -1,5 +1,3 @@
-allowBuilds:
-  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
   - '@tailwindcss/oxide'

static/css/input.css

@@ -34,12 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-select.select[multiple] {
-  display: block;
-  white-space: normal;
-}
-
-p a {
-  @apply underline;
-}

static/images/bayer-logo.svg

@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<svg version="1.1" id="Layer_2" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
-	 viewBox="0 0 76 76" style="enable-background:new 0 0 76 76;" xml:space="preserve">
-<style type="text/css">
-	.st0{fill:#10384F;}
-	.st1{fill:#89D329;}
-	.st2{fill:#00BCFF;}
-</style>
-<g id="Bayer_Cross_1_">
-	<path class="st0" d="M35.9,11.3h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9h-4.4V11.3z M35.9,15.5h4.5c0.6,0,1-0.4,1-1
-		c0-0.6-0.4-1-1-1h-4.5V15.5z M43,12.3c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2h-7.3V7.3l7.2,0c1.7,0,3.1,1.4,3.1,3.1
-		C43.7,11.1,43.4,11.8,43,12.3z M44.7,30.3H42l-0.8-1.8h-5.9l-0.8,1.8h-2.7L37,19.8h2.4L44.7,30.3z M38.2,22.5l-1.8,3.8H40
-		L38.2,22.5z M41.8,32.6h3l-5.3,6.8v3.7h-2.5v-3.7l-5.3-6.8h3l3.6,4.8L41.8,32.6z M55.7,32.6v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3
-		h-9.5V32.6H55.7z M63.4,39.1h-1.9v4h-2.5V32.6h6.4c1.8,0,3.2,1.5,3.2,3.3c0,1.5-1,2.7-2.3,3.1l3.1,4.1h-3L63.4,39.1z M65.2,34.8
-		h-3.6v2h3.6c0.6,0,1-0.5,1-1C66.2,35.3,65.7,34.8,65.2,34.8z M32.8,43.1h-2.7l-0.8-1.8h-5.9l-0.8,1.8h-2.7l5.3-10.5h2.4L32.8,43.1z
-		 M26.3,35.3l-1.8,3.8h3.7L26.3,35.3z M10.4,36.6h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9l-4.4,0V36.6z M10.4,40.8h4.5
-		c0.6,0,1-0.4,1-1c0-0.6-0.4-1-1-1h-4.5V40.8z M17.5,37.6c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2H7.9V32.6h7.2
-		c1.7,0,3.1,1.4,3.1,3.1C18.2,36.4,17.9,37.1,17.5,37.6z M43,45.3v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3h-9.5V45.3H43z M41.2,61.6
-		c0-0.6-0.4-1-1-1h-4.3v2h4.3C40.8,62.6,41.2,62.2,41.2,61.6z M33.4,68.9V58.4h7c1.8,0,3.2,1.5,3.2,3.3c0,1.4-0.8,2.5-2,3l3.2,4.2
-		h-3l-3-4h-2.9v4H33.4z"/>
-	<path class="st1" d="M76.1,35.6C74.9,15.8,58.4,0,38.2,0C18,0,1.5,15.8,0.3,35.6c0,0.8,0.1,1.6,0.2,2.4c0.8,6.6,3.3,12.7,7.1,17.8
-		c6.9,9.4,18,15.5,30.6,15.5c-17.6,0-32-13.7-33.2-30.9c-0.1-0.8-0.1-1.6-0.1-2.4c0-0.8,0-1.6,0.1-2.4C6.2,18.4,20.6,4.7,38.2,4.7
-		c12.6,0,23.7,6.1,30.6,15.5c3.8,5.1,6.3,11.2,7.1,17.8c0.1,0.8,0.2,1.6,0.2,2.3c0-0.8,0.1-1.6,0.1-2.4
-		C76.2,37.2,76.2,36.4,76.1,35.6"/>
-	<path class="st2" d="M0.3,40.4C1.5,60.2,18,76,38.2,76c20.2,0,36.7-15.8,37.9-35.6c0-0.8-0.1-1.6-0.2-2.4
-		c-0.8-6.6-3.3-12.7-7.1-17.8c-6.9-9.4-18-15.5-30.6-15.5c17.6,0,32,13.7,33.2,30.9c0.1,0.8,0.1,1.6,0.1,2.4c0,0.8,0,1.6-0.1,2.4
-		c-1.2,17.3-15.6,30.9-33.2,30.9c-12.6,0-23.7-6.1-30.6-15.5C3.8,50.7,1.3,44.6,0.5,38c-0.1-0.8-0.2-1.6-0.2-2.3
-		c0,0.8-0.1,1.6-0.1,2.4C0.2,38.8,0.2,39.6,0.3,40.4"/>
-</g>
-</svg>

static/js/alpine/components/widgets.js

@@ -59,9 +59,6 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
-    get isRequired() {
-      return (this.schema.required || []).indexOf(this.fieldName) > -1
-    }
   });
 
   // Text widget
@@ -296,34 +293,6 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
-    // PubMed link widget
-  Alpine.data(
-    "doiWidget",
-    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
-      ...baseWidget(
-        fieldName,
-        data,
-        schema,
-        uiSchema,
-        mode,
-        debugErrors,
-        context,
-      ),
-
-      get value() {
-        return this.data[this.fieldName] || "";
-      },
-      set value(v) {
-        this.data[this.fieldName] = v;
-      },
-      get doiUrl() {
-        return this.value
-          ? `https://dx.doi.org/${this.value}`
-          : null;
-      },
-    }),
-  );
-
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/alpine/pagination.js

@@ -5,126 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    })
-  );
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

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.
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+    the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+    any Contribution intentionally submitted for inclusion in the Work
+    by You to the Licensor shall be under the terms and conditions of
+    this License, without any additional terms or conditions.
+    Notwithstanding the above, nothing herein shall supersede or modify
+    the terms of any separate license agreement you may have executed
+    with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+    names, trademarks, service marks, or product names of the Licensor,
+    except as required for reasonable and customary use in describing the
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+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+    Contributor provides its Contributions) on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+    PARTICULAR PURPOSE. You are solely responsible for determining the
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+
+ 8. Limitation of Liability. In no event and under no legal theory,
+    whether in tort (including negligence), contract, or otherwise,
+    unless required by applicable law (such as deliberate and grossly
+    negligent acts) or agreed to in writing, shall any Contributor be
+    liable to You for damages, including any direct, indirect, special,
+    incidental, or consequential damages of any character arising as a
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+    work stoppage, computer failure or malfunction, or any and all
+    other commercial damages or losses), even if such Contributor
+    has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+    the Work or Derivative Works thereof, You may choose to offer,
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+    on Your own behalf and on Your sole responsibility, not on behalf
+    of any other Contributor, and only if You agree to indemnify,
+    defend, and hold each Contributor harmless for any liability
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+    of your accepting any such warranty or additional liability.
+
+ 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
+    boilerplate notice, with the fields enclosed by brackets "[]"
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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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+ 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.

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

@@ -0,0 +1,570 @@
+**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