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jebus:develop jebus:develop-bayer jebus:fix/ketcher_submission jebus:fix/issue204 jebus:hotfix/login jebus:refactor/html_formatting jebus:fix/missing_nav_links jebus:feat/package_pred jebus:fix/frontpage_predict jebus:fix/search jebus:feature/leftovers jebus:enhancement/licenses jebus:feature/frontend_update jebus:fix/xss jebus:enhancement/dataset jebus:feature/engineered_pathways jebus:feature/tenants jebus:feature/manager_tests jebus:feature/normalization_rules jebus:main
jebus:beta_2025-11-12 jebus:pre_frontpage_update jebus:beta_2025-10-15 jebus:beta_2025-09-18 jebus:beta_2025-09-04 jebus:beta_2025-09-02 jebus:beta_2025-08-25 jebus:beta_#1
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compare: jebus:86b456748b1c39455f143281540d9307b45b8184
Branches Tags
jebus:develop-bayer jebus:develop jebus:fix/ketcher_submission jebus:fix/issue204 jebus:hotfix/login jebus:refactor/html_formatting jebus:fix/missing_nav_links jebus:feat/package_pred jebus:fix/frontpage_predict jebus:fix/search jebus:feature/leftovers jebus:enhancement/licenses jebus:feature/frontend_update jebus:fix/xss jebus:enhancement/dataset jebus:feature/engineered_pathways jebus:feature/tenants jebus:feature/manager_tests jebus:feature/normalization_rules jebus:main
jebus:beta_2025-11-12 jebus:pre_frontpage_update jebus:beta_2025-10-15 jebus:beta_2025-09-18 jebus:beta_2025-09-04 jebus:beta_2025-09-02 jebus:beta_2025-08-25 jebus:beta_#1

3 Commits
develop-ba ... 86b456748b

Author SHA1 Message Date
Tim Lorsbach
86b456748b Show Pack Classification 2026-04-14 12:00:17 +02:00
Tim Lorsbach
9afa122abe Initial bayer app 2026-04-14 12:00:17 +02:00
Tim Lorsbach
fb073438db adjusted migration 2026-04-14 12:00:17 +02:00
70 changed files with 349 additions and 2756 deletions
Expand all files Collapse all files

6
Dockerfile
View File

@ -30,21 +30,17 @@ RUN mkdir -p -m 0700 /root/.ssh \
&& ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts && 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: # 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 \ RUN --mount=type=ssh \
uv sync --locked --extra ms-login --extra pepper-plugin uv sync --locked --extra ms-login --extra pepper-plugin
# Now copy source and do a final sync to install the project itself # Now copy source and do a final sync to install the project itself
# Ensure .dockerignore is reasonable # Ensure .dockerignore is reasonable
COPY bb4g bb4g
COPY biotransformer biotransformer
COPY bayer bayer
COPY bridge bridge COPY bridge bridge
COPY envipath envipath COPY envipath envipath
COPY epapi epapi COPY epapi epapi
COPY epauth epauth COPY epauth epauth
COPY epdb epdb COPY epdb epdb
COPY epiuclid epiuclid
COPY fixtures fixtures COPY fixtures fixtures
COPY migration migration COPY migration migration
COPY pepper pepper COPY pepper pepper

16
bayer/admin.py
View File

@ -1,19 +1,3 @@
from django.contrib import admin from django.contrib import admin
# Register your models here. # 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)

39
bayer/epdb_hooks.py
View File

@ -1,39 +0,0 @@
import logging
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",
)

41
bayer/migrations/0003_pescompound_pesstructure_package_data_pool.py
View File

@ -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'),
),
]

145
bayer/models.py
View File

@ -1,21 +1,16 @@
from typing import List from typing import List
import urllib.parse
import nh3
from django.conf import settings as s 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.db.models import QuerySet
from django.urls import reverse
from epdb.models import ( from epdb.models import (
EnviPathModel, EnviPathModel,
Compound,
CompoundStructure,
ParallelRule, ParallelRule,
SequentialRule, SequentialRule,
SimpleAmbitRule, SimpleAmbitRule,
SimpleRDKitRule, SimpleRDKitRule,
) )
from utilities.chem import FormatConverter
class Package(EnviPathModel): class Package(EnviPathModel):
@ -34,9 +29,6 @@ class Package(EnviPathModel):
default=Classification.RESTRICTED, default=Classification.RESTRICTED,
) )
data_pool = models.ForeignKey("epdb.Group", on_delete=models.SET_NULL, blank=True, null=True,
verbose_name="Data pool", default=None)
def delete(self, *args, **kwargs): def delete(self, *args, **kwargs):
# explicitly handle related Rules # explicitly handle related Rules
for r in self.rules.all(): for r in self.rules.all():
@ -101,136 +93,3 @@ class Package(EnviPathModel):
class Meta: class Meta:
db_table = "epdb_package" 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,
mol_file: 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.mol_file = mol_file
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)}"
}

9
bayer/templates/actions/collections/new_pes.html
View File

@ -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 %}

0
bayer/tests/__init__.py → bayer/templates/actions/objects/compound.html
View File

8
bayer/templates/actions/objects/pathway_add_pes.html
View File

@ -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>

175
bayer/templates/modals/collections/new_package_modal.html
View File

@ -1,175 +0,0 @@
{% load static %}
<dialog
id="new_package_modal"
class="modal"
x-data="{
isSubmitting: false,
packageClassification: null,
reset() {
this.isSubmitting = false;
this.packageClassification = null;
},
setFormData(data) {
this.formData = data;
},
get isSecret() {
return this.packageClassification === '20';
},
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 Package</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_package_form"
accept-charset="UTF-8"
action=""
method="post"
>
{% csrf_token %}
<!-- Name -->
<div class="form-control mb-3">
<label class="label" for="package-name">
<span class="label-text">Name</span>
</label>
<input
id="package-name"
class="input input-bordered w-full"
name="package-name"
placeholder="Name"
required
/>
</div>
<!-- Description -->
<div class="form-control mb-3">
<label class="label" for="package-description">
<span class="label-text">Description</span>
</label>
<input
id="package-description"
type="text"
class="input input-bordered w-full"
placeholder="Description..."
name="package-description"
/>
</div>
<!-- Classification Level -->
<div class="form-control mb-3">
<label class="label" for="package-classification">
<span class="label-text">Package Classification</span>
</label>
<select
id="package-classification"
name="package-classification"
class="select select-bordered w-full"
x-model="packageClassification"
required
>
<option value="null" disabled selected>Select Classification</option>
<option value="0">Internal</option>
<option value="10">Restricted</option>
<option value="20">Secret</option>
</select>
</div>
<!-- Secret Groups -->
<div class="form-control mb-3" x-show="isSecret" x-cloak>
<label class="label" for="package-data-pool">
<span class="label-text">Data Pool for SECRET Package</span>
</label>
<p>Only users with this role can be granted access to this package</p>
<select
id="package-data-pool"
name="package-data-pool"
class="select select-bordered w-full"
>
<option value="" disabled selected>Select Data Pool</option>
{% for obj in meta.secret_groups %}
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endfor %}
</select>
</div>
</form>
</div>
<!-- Footer -->
<div class="modal-action">
<button
type="button"
class="btn"
onclick="this.closest('dialog').close()"
:disabled="isSubmitting"
>
Cancel
</button>
<button
type="button"
class="btn btn-primary"
@click="submit('new_package_form')"
:disabled="isSubmitting || !selectedType || loadingSchemas"
>
<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>

174
bayer/templates/modals/collections/new_pes_modal.html
View File

@ -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>

174
bayer/templates/modals/objects/add_pathway_pes_node_modal.html
View File

@ -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>

19
bayer/templates/objects/compound_structure_viz.html
View File

@ -1,19 +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">{{ compound_structure.pes_link }}</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 %}

19
bayer/templates/objects/compound_viz.html
View File

@ -1,19 +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">{{ compound.default_structure.pes_link }}</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 %}

19
bayer/templates/objects/node_viz.html
View File

@ -1,19 +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">{{ node.default_node_label.pes_link }}</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 %}

4
bayer/templates/objects/package.html
View File

@ -1,5 +1,5 @@
{% extends "framework_modern.html" %} {% extends "framework_modern.html" %}
{% load static %}
{% block content %} {% block content %}
{% block action_modals %} {% block action_modals %}
@ -16,7 +16,7 @@
<div class="card bg-base-100"> <div class="card bg-base-100">
<div class="card-body"> <div class="card-body">
<div class="flex items-center justify-between"> <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 id="actionsButton" class="dropdown dropdown-e nd hidden">
<div tabindex="0" role="button" class="btn btn-ghost btn-sm"> <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
<svg <svg

154
bayer/templates/static/login.html
View File

@ -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 %}

0
bayer/tests/pes/__init__.py
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174
bayer/tests/pes/test_pes.py
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File diff suppressed because one or more lines are too long

19
bayer/urls.py
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@ -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",
),
]

156
bayer/views.py
View File

@ -1,155 +1,3 @@
import base64 from django.shortcuts import render
import requests # Create your views here.
from django.conf import settings as s
from django.core.exceptions import BadRequest
from django.http import HttpResponse
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
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:
raise BadRequest("Cannot create PESs for internal packages.")
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 BadRequest(f"Could not fetch PES data for {pes_link}")
classification = pes_data.get("classificationLevel", "")
if "secret" == classification.lower():
data_pools = pes_data.get("dataPools")
if data_pools:
if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
return BadRequest(
f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
return redirect(pes.url)
else:
return BadRequest("Please provide a PES link.")
else:
pass
@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:
raise BadRequest("Cannot create PESs for internal packages.")
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 BadRequest(f"Could not fetch PES data for {pes_link}")
classification = pes_data.get("classificationLevel", "")
if "secret" == classification.lower():
data_pools = pes_data.get("dataPools")
if data_pools:
if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
return BadRequest(
f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
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 BadRequest("Please provide a PES link.")
else:
pass
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:
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")

183
bb4g/__init__.py
View File

@ -1,183 +0,0 @@
import json
import math
from datetime import datetime
from typing import List
import enum
import requests
from django.conf import settings as s
from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
from envipy_additional_information import register
from bridge.contracts import Classifier # noqa: I001
from bridge.dto import (
BuildResult,
EnviPyDTO,
EvaluationResult,
RunResult,
TransformationProductPrediction,
) # noqa: I001
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
retries = 0
while not started and retries < 5:
res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
if res.status_code == 200:
started = True
elif res.status_code in [500, 502]:
retries += 1
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,
}
resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
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
return result

10
bridge/contracts.py
View File

@ -254,15 +254,7 @@ class Classifier(Plugin):
def parse_config(cls, data: dict | None = None) -> EnviPyModel | None: def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
if cls.Config is None: if cls.Config is None:
return 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 @classmethod
def create(cls, data: dict | None = None): def create(cls, data: dict | None = None):

44
docker-compose.dev.yml
View File

@ -1,54 +1,26 @@
services: services:
db: db:
image: postgres:18 image: postgres:18
container_name: eppostgres container_name: envipath-postgres
environment: environment:
POSTGRES_USER: ${POSTGRES_USER} POSTGRES_USER: postgres
POSTGRES_PASSWORD: ${POSTGRES_PASSWORD} POSTGRES_PASSWORD: postgres
POSTGRES_DB: ${POSTGRES_DB} POSTGRES_DB: envipath
ports: ports:
- "5432:5432" - "5432:5432"
volumes: volumes:
- ep_bayer_postgres_data:/var/lib/postgresql - postgres_data:/var/lib/postgresql
healthcheck: healthcheck:
test: [ "CMD-SHELL", "pg_isready -U postgres" ] test: ["CMD-SHELL", "pg_isready -U postgres"]
interval: 5s interval: 5s
timeout: 5s timeout: 5s
retries: 5 retries: 5
redis: redis:
image: redis:7-alpine image: redis:7-alpine
container_name: epredis container_name: envipath-redis
ports: ports:
- "6379:6379" - "6379:6379"
volumes:
- ep_bayer_redis_data:/data
biotransformer3:
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: envipath/envipy-bayer:1.0
container_name: epcelery
env_file:
- .env.dev
command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
volumes:
- ep_bayer_data:/opt/enviPy/
volumes: volumes:
ep_bayer_postgres_data: postgres_data:
ep_bayer_redis_data:
ep_bayer_data:

18
docker-compose.yml
View File

@ -7,7 +7,7 @@ services:
POSTGRES_PASSWORD: ${POSTGRES_PASSWORD} POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
POSTGRES_DB: ${POSTGRES_DB} POSTGRES_DB: ${POSTGRES_DB}
volumes: volumes:
- ep_bayer_postgres_data:/var/lib/postgresql - ep_postgres_data:/var/lib/postgresql
healthcheck: healthcheck:
test: [ "CMD-SHELL", "pg_isready -U postgres" ] test: [ "CMD-SHELL", "pg_isready -U postgres" ]
interval: 5s interval: 5s
@ -18,14 +18,14 @@ services:
image: redis:7-alpine image: redis:7-alpine
container_name: epredis container_name: epredis
volumes: volumes:
- ep_bayer_redis_data:/data - ep_redis_data:/data
biotransformer3: biotransformer3:
image: envipath/biotransformer3:1.0 image: envipath/biotransformer3:1.0
container_name: epbiotransformer3 container_name: epbiotransformer3
web: web:
image: envipath/envipy-bayer:1.0 image: envipath/envipy:1.0
container_name: epdjango container_name: epdjango
ports: ports:
- "127.0.0.1:8000:8000" - "127.0.0.1:8000:8000"
@ -33,18 +33,18 @@ services:
- .env - .env
command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3 command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
volumes: volumes:
- ep_bayer_data:/opt/enviPy/ - ep_data:/opt/enviPy/
celery_worker: celery_worker:
image: envipath/envipy-bayer:1.0 image: envipath/envipy:1.0
container_name: epcelery container_name: epcelery
env_file: env_file:
- .env - .env
command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
volumes: volumes:
- ep_bayer_data:/opt/enviPy/ - ep_data:/opt/enviPy/
volumes: volumes:
ep_bayer_postgres_data: ep_postgres_data:
ep_bayer_redis_data: ep_redis_data:
ep_bayer_data: ep_data:

53
envipath/settings.py
View File

@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
For the full list of settings and their values, see For the full list of settings and their values, see
https://docs.djangoproject.com/en/4.2/ref/settings/ https://docs.djangoproject.com/en/4.2/ref/settings/
""" """
import json
import os import os
from pathlib import Path from pathlib import Path
@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
# Build paths inside the project like this: BASE_DIR / 'subdir'. # Build paths inside the project like this: BASE_DIR / 'subdir'.
BASE_DIR = Path(__file__).resolve().parent.parent BASE_DIR = Path(__file__).resolve().parent.parent
ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev") ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
print(f"Loading env from {ENV_PATH}") print(f"Loading env from {ENV_PATH}")
load_dotenv(ENV_PATH, override=False) load_dotenv(ENV_PATH, override=False)
@ -143,12 +143,6 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
"TEMPLATE": os.environ["TEMPLATE_DB"], "TEMPLATE": os.environ["TEMPLATE_DB"],
} }
CACHES = {
"default": {
"BACKEND": "django.core.cache.backends.locmem.LocMemCache",
"LOCATION": "unique-snowflake",
}
}
# Password validation # Password validation
# https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@ -448,46 +442,3 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
if BIOTRANSFORMER_ENABLED: if BIOTRANSFORMER_ENABLED:
BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None) BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
# PES
PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
if PES_API_MAPPING:
import json
PES_API_MAPPING = json.loads(PES_API_MAPPING)
else:
PES_API_MAPPING = {}
# Entra Groups
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")

3
envipath/urls.py
View File

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

23
epapi/v1/endpoints/groups.py
View File

@ -1,23 +0,0 @@
from django.conf import settings as s
from ninja import Router
from ninja_extra.pagination import paginate
from epdb.logic import GroupManager
from ..pagination import EnhancedPageNumberPagination
from ..schemas import GroupOutSchema
router = Router()
@router.get("/groups/", response=EnhancedPageNumberPagination.Output[GroupOutSchema])
@paginate(
EnhancedPageNumberPagination,
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
)
def list_all_groups(request):
"""
List all groups the user has access to.
"""
user = request.user
return GroupManager.get_groups(user)

4
epapi/v1/endpoints/settings.py
View File

@ -15,9 +15,9 @@ router = Router()
EnhancedPageNumberPagination, EnhancedPageNumberPagination,
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE, page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
) )
def list_all_settings(request): def list_all_pathways(request):
""" """
List all settings the user has access to. List all pathways from reviewed packages.
""" """
user = request.user user = request.user
return SettingManager.get_all_settings(user) return SettingManager.get_all_settings(user)

4
epapi/v1/router.py
View File

@ -1,7 +1,6 @@
from ninja import Router from ninja import Router
from ninja.security import SessionAuth from ninja.security import SessionAuth
from envipath import settings as s
from .auth import BearerTokenAuth from .auth import BearerTokenAuth
from .endpoints import ( from .endpoints import (
packages, packages,
@ -14,8 +13,8 @@ from .endpoints import (
structure, structure,
additional_information, additional_information,
settings, settings,
groups,
) )
from envipath import settings as s
# Main router with authentication # Main router with authentication
router = Router( router = Router(
@ -36,7 +35,6 @@ router.add_router("", models.router)
router.add_router("", structure.router) router.add_router("", structure.router)
router.add_router("", additional_information.router) router.add_router("", additional_information.router)
router.add_router("", settings.router) router.add_router("", settings.router)
router.add_router("", groups.router)
if s.IUCLID_EXPORT_ENABLED: if s.IUCLID_EXPORT_ENABLED:
from epiuclid.api import router as iuclid_router from epiuclid.api import router as iuclid_router

7
epapi/v1/schemas.py
View File

@ -126,10 +126,3 @@ class SettingOutSchema(Schema):
url: str = "" url: str = ""
name: str name: str
description: str description: str
class GroupOutSchema(Schema):
uuid: UUID
url: str = ""
name: str
description: str

1
epauth/urls.py
View File

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

132
epauth/views.py
View File

@ -1,32 +1,10 @@
import msal import msal
from django.conf import settings as s from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.contrib.auth import login from django.contrib.auth import login
from django.http import HttpResponse
from django.shortcuts import redirect 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): def entra_login(request):
@ -45,7 +23,11 @@ def entra_login(request):
def entra_callback(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) flow = request.session.pop("msal_auth_flow", None)
if not flow: if not flow:
@ -54,18 +36,11 @@ def entra_callback(request):
# Acquire token using the flow and callback request # Acquire token using the flow and callback request
result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET) 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"] 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 # Get implementing class
User = get_user_model() User = get_user_model()
@ -82,89 +57,4 @@ def entra_callback(request):
login(request, u) 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')

112
epdb/admin.py
View File

@ -1,8 +1,5 @@
import logging
from django.conf import settings as s from django.conf import settings as s
from django.contrib import admin from django.contrib import admin
from django.contrib import messages
from .models import ( from .models import (
AdditionalInformation, AdditionalInformation,
@ -32,8 +29,6 @@ from .models import (
Package = s.GET_PACKAGE_MODEL() Package = s.GET_PACKAGE_MODEL()
logger = logging.getLogger(__name__)
class AdditionalInformationAdmin(admin.ModelAdmin): class AdditionalInformationAdmin(admin.ModelAdmin):
pass pass
@ -50,113 +45,6 @@ class UserAdmin(admin.ModelAdmin):
"date_joined", "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): class UserPackagePermissionAdmin(admin.ModelAdmin):
pass pass

168
epdb/legacy_api.py
View File

@ -1,20 +1,17 @@
from collections import defaultdict from collections import defaultdict
from typing import Any, Dict, List, Optional from typing import Any, Dict, List, Optional
import jwt
import nh3 import nh3
import requests
from django.conf import settings as s from django.conf import settings as s
from django.contrib.auth import get_user_model from django.contrib.auth import get_user_model
from django.core.cache import cache
from django.http import HttpResponse, JsonResponse from django.http import HttpResponse, JsonResponse
from django.shortcuts import redirect from django.shortcuts import redirect
from jwt import InvalidIssuerError
from ninja import Field, Form, Query, Router, Schema 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.chem import FormatConverter
from utilities.misc import PackageExporter from utilities.misc import PackageExporter
from .logic import ( from .logic import (
EPDBURLParser, EPDBURLParser,
GroupManager, GroupManager,
@ -49,26 +46,6 @@ from .models import (
Package = s.GET_PACKAGE_MODEL() 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): def get_package_for_write(user, package_uuid):
p = PackageManager.get_package_by_id(user, package_uuid) p = PackageManager.get_package_by_id(user, package_uuid)
if not PackageManager.writable(user, p): if not PackageManager.writable(user, p):
@ -82,52 +59,7 @@ def _anonymous_or_real(request):
return get_user_model().objects.get(username="anonymous") 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): class Error(Schema):
@ -221,6 +153,21 @@ class SimpleModel(SimpleObject):
identifier: str = "relative-reasoning" 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 # # User #
@ -820,7 +767,6 @@ class CreateCompound(Schema):
compoundName: str | None = None compoundName: str | None = None
compoundDescription: str | None = None compoundDescription: str | None = None
inchi: str | None = None inchi: str | None = None
pesLink: str | None = None
@router.post("/package/{uuid:package_uuid}/compound") @router.post("/package/{uuid:package_uuid}/compound")
@ -832,28 +778,9 @@ def create_package_compound(
try: try:
p = get_package_for_write(request.user, package_uuid) p = get_package_for_write(request.user, package_uuid)
# inchi is not used atm # inchi is not used atm
c = Compound.create(
if c.pesLink is not None: p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
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():
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, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
)
return redirect(c.url) return redirect(c.url)
except ValueError as e: except ValueError as e:
return 400, {"message": str(e)} return 400, {"message": str(e)}
@ -1874,7 +1801,6 @@ class CreateNode(Schema):
nodeName: str | None = None nodeName: str | None = None
nodeReason: str | None = None nodeReason: str | None = None
nodeDepth: str | None = None nodeDepth: str | None = None
pesLink: str | None = None
@router.post( @router.post(
@ -1886,43 +1812,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
p = get_package_for_write(request.user, package_uuid) p = get_package_for_write(request.user, package_uuid)
pw = Pathway.objects.get(package=p, uuid=pathway_uuid) pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
if n.pesLink: if n.nodeDepth is not None and n.nodeDepth.strip() != "":
from bayer.views import fetch_pes node_depth = int(n.nodeDepth)
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():
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)
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: else:
if n.nodeDepth is not None and n.nodeDepth.strip() != "": node_depth = -1
node_depth = int(n.nodeDepth)
else:
node_depth = -1
node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason) n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
return redirect(node.url) return redirect(n.url)
except ValueError: except ValueError:
return 403, {"message": "Adding node failed!"} return 403, {"message": "Adding node failed!"}
@ -2032,16 +1929,13 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
educts = [] educts = []
products = [] products = []
subclasses = CompoundStructure.__subclasses__()
if e.edgeAsSmirks: if e.edgeAsSmirks:
for ed in e.edgeAsSmirks.split(">>")[0].split("\\."): for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
stand_ed = FormatConverter.standardize(ed, remove_stereo=True) stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
educts.append( educts.append(
Node.objects.get( Node.objects.get(
pathway=pw, 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__package=p, smiles=stand_ed
).compound.default_structure, ).compound.default_structure,
) )
@ -2052,8 +1946,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
products.append( products.append(
Node.objects.get( Node.objects.get(
pathway=pw, 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__package=p, smiles=stand_pr
).compound.default_structure, ).compound.default_structure,
) )
@ -2074,12 +1967,9 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
description=e.edgeReason, description=e.edgeReason,
) )
# Update depths as sideeffect of above operation
pw.update_depths()
return redirect(new_e.url) return redirect(new_e.url)
except ValueError: 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}") @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

188
epdb/logic.py
View File

@ -7,7 +7,6 @@ import nh3
from django.conf import settings as s from django.conf import settings as s
from django.contrib.auth import get_user_model from django.contrib.auth import get_user_model
from django.db import transaction from django.db import transaction
from django.db.models import QuerySet
from pydantic import ValidationError from pydantic import ValidationError
from epdb.models import ( from epdb.models import (
@ -265,12 +264,8 @@ class GroupManager(object):
return bool(re.findall(GroupManager.group_pattern, url)) return bool(re.findall(GroupManager.group_pattern, url))
@staticmethod @staticmethod
def create_group(current_user, name, description, *args, **kwargs): def create_group(current_user, name, description):
g = Group() g = Group()
if "uuid" in kwargs:
g.uuid = kwargs["uuid"]
# Clean for potential XSS # Clean for potential XSS
g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip() g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
g.description = nh3.clean(description, 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 @staticmethod
def readable(user, package): 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 @staticmethod
def writable(user, package): 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 @staticmethod
def administrable(user, package): 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 @staticmethod
def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str): 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) 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"]} perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
valid_perms = perms.get(permission) valid_perms = perms.get(permission)
@ -415,7 +437,6 @@ class PackageManager(object):
try: try:
p = Package.objects.get(uuid=package_id) p = Package.objects.get(uuid=package_id)
if PackageManager.readable(user, p): if PackageManager.readable(user, p):
p = PackageManager.check_package_classification(user, p)
return p return p
else: else:
# FIXME: use custom exception to be translatable to 403 in API # FIXME: use custom exception to be translatable to 403 in API
@ -425,37 +446,6 @@ class PackageManager(object):
except Package.DoesNotExist: except Package.DoesNotExist:
raise ValueError("Package with ID {} does not exist!".format(package_id)) 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 @staticmethod
def get_all_readable_packages(user, include_reviewed=False): def get_all_readable_packages(user, include_reviewed=False):
# UserPermission only exists if at least read is granted... # 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 # remove package if user is owner and package is reviewed e.g. admin
qs = qs.filter(reviewed=False) 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 @staticmethod
def get_all_writeable_packages(user): def get_all_writeable_packages(user):
@ -530,13 +514,11 @@ class PackageManager(object):
qs = qs.filter(reviewed=False) 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 @staticmethod
@transaction.atomic @transaction.atomic
@ -641,25 +623,6 @@ class PackageManager(object):
else: else:
pack.reviewed = False 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.description = data["description"]
pack.save() pack.save()
@ -745,13 +708,7 @@ class PackageManager(object):
default_structure = None default_structure = None
for structure in compound["structures"]: for structure in compound["structures"]:
if structure.get("pesLink"): struc = CompoundStructure()
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.object_url = Command.get_id(structure, keep_ids)
struc.compound = comp struc.compound = comp
struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4() struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@ -759,10 +716,6 @@ class PackageManager(object):
struc.description = structure["description"] struc.description = structure["description"]
struc.aliases = structure.get("aliases", []) struc.aliases = structure.get("aliases", [])
struc.smiles = structure["smiles"] struc.smiles = structure["smiles"]
if structure.get("molfile"):
struc.molfile = structure["molfile"]
struc.save() struc.save()
for scen in structure["scenarios"]: for scen in structure["scenarios"]:
@ -1065,9 +1018,52 @@ class PackageManager(object):
print("Fixing Node depths...") print("Fixing Node depths...")
total_pws = Pathway.objects.filter(package=pack).count() total_pws = Pathway.objects.filter(package=pack).count()
for p, pw in enumerate(Pathway.objects.filter(package=pack)): 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") print(f"{p + 1}/{total_pws} fixed.", end="\r")
return pack return pack

54
epdb/migrations/0023_alter_compoundstructure_options_and_more.py
View File

@ -1,54 +0,0 @@
# Generated by Django 6.0.3 on 2026-04-21 11:43
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
]
operations = [
migrations.AlterModelOptions(
name="compoundstructure",
options={},
),
migrations.AlterModelOptions(
name="epmodel",
options={},
),
migrations.AlterModelOptions(
name="parallelrule",
options={},
),
migrations.AlterModelOptions(
name="rule",
options={},
),
migrations.AlterModelOptions(
name="sequentialrule",
options={},
),
migrations.AlterModelOptions(
name="simpleambitrule",
options={},
),
migrations.AlterModelOptions(
name="simplerdkitrule",
options={},
),
migrations.AlterModelOptions(
name="simplerule",
options={},
),
migrations.AddField(
model_name="compoundstructure",
name="molfile",
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
),
migrations.AddField(
model_name="group",
name="secret",
field=models.BooleanField(default=False, verbose_name="Secret Group"),
),
]

17
epdb/migrations/0024_user_contacted.py
View File

@ -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),
),
]

56
epdb/migrations/0025_auto_20260511_2025.py
View File

@ -1,56 +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,
}
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),
]

89
epdb/models.py
View File

@ -75,7 +75,6 @@ class User(AbstractUser):
blank=False, blank=False,
) )
is_reviewer = models.BooleanField(default=False) is_reviewer = models.BooleanField(default=False)
contacted = models.BooleanField(null=True, blank=True)
USERNAME_FIELD = "email" USERNAME_FIELD = "email"
REQUIRED_FIELDS = ["username"] REQUIRED_FIELDS = ["username"]
@ -204,7 +203,6 @@ class Group(TimeStampedModel):
name = models.TextField(blank=False, null=False, verbose_name="Group name") name = models.TextField(blank=False, null=False, verbose_name="Group name")
owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE) owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
public = models.BooleanField(verbose_name="Public Group", default=False) public = models.BooleanField(verbose_name="Public Group", default=False)
secret = models.BooleanField(verbose_name="Secret Group", default=False)
description = models.TextField( description = models.TextField(
blank=False, null=False, verbose_name="Descriptions", default="no description" blank=False, null=False, verbose_name="Descriptions", default="no description"
) )
@ -868,25 +866,18 @@ class Compound(
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True) 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 # Check if we find a direct match for a given SMILES
if qs.exists(): if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
return qs.first().compound return CompoundStructure.objects.get(smiles=smiles, compound__package=package).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 # Check if we can find the standardized one
if qs.exists(): if CompoundStructure.objects.filter(
smiles=standardized_smiles, compound__package=package
).exists():
# TODO should we add a structure? # TODO should we add a structure?
return qs.first().compound return CompoundStructure.objects.get(
smiles=standardized_smiles, compound__package=package
).compound
# Generate Compound # Generate Compound
c = Compound() c = Compound()
@ -1121,7 +1112,6 @@ class CompoundStructure(
canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES") 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") inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
normalized_structure = models.BooleanField(null=False, blank=False, default=False) normalized_structure = models.BooleanField(null=False, blank=False, default=False)
molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
external_identifiers = GenericRelation("ExternalIdentifier") external_identifiers = GenericRelation("ExternalIdentifier")
@ -1218,9 +1208,6 @@ class CompoundStructure(
return dict(hls) return dict(hls)
def d3_json(self):
return {}
class EnzymeLink(EnviPathModel, KEGGIdentifierMixin): class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True) rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@ -2186,56 +2173,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
): ):
return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description) 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()
for n in self.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:
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:
for e in self.edges:
if n in e.start_nodes.all():
for p in e.end_nodes.all():
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:
n.depth = depth
n.save()
class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin): class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
pathway = models.ForeignKey( pathway = models.ForeignKey(
@ -2277,11 +2214,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
if isinstance(ai.get(), PropertyPrediction): if isinstance(ai.get(), PropertyPrediction):
predicted_properties[ai.get().__class__.__name__].append(ai.data) 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, "depth": self.depth,
"stereo_removed": self.stereo_removed, "stereo_removed": self.stereo_removed,
"url": self.url, "url": self.url,
@ -2290,7 +2223,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"image_svg": IndigoUtils.mol_to_svg( "image_svg": IndigoUtils.mol_to_svg(
self.default_node_label.smiles, width=40, height=40 self.default_node_label.smiles, width=40, height=40
), ),
"image_type": "svg",
"name": self.get_name(), "name": self.get_name(),
"smiles": self.default_node_label.smiles, "smiles": self.default_node_label.smiles,
"scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()], "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@ -2303,11 +2235,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"predicted_properties": predicted_properties, "predicted_properties": predicted_properties,
"is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False), "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
"timeseries": self.get_timeseries_data(), "timeseries": self.get_timeseries_data(),
**structure_data,
} }
return res
@staticmethod @staticmethod
@transaction.atomic @transaction.atomic
def create( def create(

50
epdb/views.py
View File

@ -388,9 +388,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
"debug": s.DEBUG, "debug": s.DEBUG,
"external_databases": ExternalDatabase.get_databases(), "external_databases": ExternalDatabase.get_databases(),
"site_id": s.MATOMO_SITE_ID, "site_id": s.MATOMO_SITE_ID,
# EDIT START
"secret_groups": Group.objects.filter(secret=True),
# EDIT END
}, },
} }
@ -590,38 +587,10 @@ def packages(request):
"package-description", s.DEFAULT_VALUES["description"] "package-description", s.DEFAULT_VALUES["description"]
) )
# EDIT START
data_pool = None
package_classification = request.POST.get("package-classification")
classification = Package.Classification(int(package_classification))
# For SECRET we'll need a data pool which will be an additional perm check later
if classification == Package.Classification.SECRET:
package_data_pool = request.POST.get("package-data-pool")
if package_data_pool is None:
return error(request, "Invalid data pool.", "Data Pool is required!")
data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
if data_pool is None:
return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
if not data_pool.secret:
return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
created_package = PackageManager.create_package( created_package = PackageManager.create_package(
current_user, package_name, package_description current_user, package_name, package_description
) )
created_package.classification_level = classification
# Set previously determined data pool
if classification == Package.Classification.SECRET:
created_package.data_pool = data_pool
created_package.save()
# EDIT END
return redirect(created_package.url) return redirect(created_package.url)
elif request.method == "OPTIONS": elif request.method == "OPTIONS":
@ -937,14 +906,12 @@ def package_models(request, package_uuid):
"requires_rule_packages": True, "requires_rule_packages": True,
"requires_data_packages": True, "requires_data_packages": True,
}, },
} "EnviFormer": {
if s.ENVIFORMER_PRESENT:
context["model_types"]["EnviFormer"] = {
"type": "enviformer", "type": "enviformer",
"requires_rule_packages": False, "requires_rule_packages": False,
"requires_data_packages": True, "requires_data_packages": True,
}, },
}
if s.FLAGS.get("PLUGINS", False): if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items(): for k, v in s.CLASSIFIER_PLUGINS.items():
@ -2539,9 +2506,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
substrate_nodes, product_nodes, name=edge_name, description=edge_description 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) return redirect(current_pathway.url)
else: else:
@ -2882,15 +2846,9 @@ def groups(request):
{"Group": s.SERVER_URL + "/group"}, {"Group": s.SERVER_URL + "/group"},
] ]
# Context for paginated template context["objects"] = Group.objects.all()
context["entity_type"] = "group"
context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/groups/"
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
context["list_title"] = "groups"
context["list_mode"] = "combined"
return render(request, "collections/groups_paginated.html", context)
return render(request, "collections/objects_list.html", context)
elif request.method == "POST": elif request.method == "POST":
group_name = request.POST.get("group-name") group_name = request.POST.get("group-name")
group_description = request.POST.get("group-description", s.DEFAULT_VALUES["description"]) group_description = request.POST.get("group-description", s.DEFAULT_VALUES["description"])

8
pepper/__init__.py
View File

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

5
pepper/impl/pepper.py
View File

@ -187,9 +187,8 @@ class Pepper:
groups = [group for group in dataset.group_by("structure_id")] groups = [group for group in dataset.group_by("structure_id")]
# Unless explicitly set compute everything serial # 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]) delayed(compute_bayes_per_group)(group[1])
for group in dataset.group_by("structure_id") for group in dataset.group_by("structure_id")
) )

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static/images/bayer-logo.svg
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@ -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
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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
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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>
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107
static/js/pw.js
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@ -605,36 +605,7 @@ function draw(pathway, elem) {
// Check if target is pseudo and draw marker only if not pseudo // Check if target is pseudo and draw marker only if not pseudo
.attr("class", d => d.target.pseudo ? "link_no_arrow" : "link") .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
.attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)') .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
.on("click", function(event, d) {
const wasHighlighted = d3.select(this).classed("highlighted");
d3.selectAll("line").classed("highlighted", false);
if (!wasHighlighted) {
const toHighlight = [];
toHighlight.push(d.el);
if (d.source.pseudo || d.target.pseudo) {
if (d.target.pseudo) {
d3.selectAll("line").each(e => {
if (e !== undefined && e.source.id === d.target.id) {
toHighlight.push(e.el);
}
});
} else {
d3.selectAll("line").each(e => {
if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
toHighlight.push(e.el);
}
});
}
}
for (const e of toHighlight) {
d3.select(e).classed("highlighted", true);
}
}
})
// add element to links array // add element to links array
link.each(function (d) { link.each(function (d) {
@ -653,13 +624,7 @@ function draw(pathway, elem) {
.on("drag", dragged) .on("drag", dragged)
.on("end", dragended)) .on("end", dragended))
.on("click", function (event, d) { .on("click", function (event, d) {
const wasHighlighted = d3.select(this).select("circle").classed("highlighted"); d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
d3.selectAll('circle.highlighted').classed('highlighted', false);
if (!wasHighlighted) {
d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
}
}) })
// Kreise für die Knoten hinzufügen // Kreise für die Knoten hinzufügen
@ -672,56 +637,44 @@ function draw(pathway, elem) {
node.filter(d => !d.pseudo).each(function (d, i) { node.filter(d => !d.pseudo).each(function (d, i) {
const g = d3.select(this); const g = d3.select(this);
if (d.image_type === "svg") { // Parse the SVG string
// Parse the SVG string const parser = new DOMParser();
const parser = new DOMParser(); const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml"); const svgElem = svgDoc.documentElement;
const svgElem = svgDoc.documentElement;
// Create a unique prefix per node // Create a unique prefix per node
const prefix = `node-${i}-`; const prefix = `node-${i}-`;
// Rename all IDs and fix <use> references // Rename all IDs and fix <use> references
svgElem.querySelectorAll("[id]").forEach(el => { svgElem.querySelectorAll('[id]').forEach(el => {
const oldId = el.id; const oldId = el.id;
const newId = prefix + oldId; const newId = prefix + oldId;
el.id = newId; el.id = newId;
const XLINK_NS = "http://www.w3.org/1999/xlink"; const XLINK_NS = "http://www.w3.org/1999/xlink";
// Update <use> elements that reference this old ID // Update <use> elements that reference this old ID
const uses = Array.from(svgElem.querySelectorAll("use")).filter( const uses = Array.from(svgElem.querySelectorAll('use')).filter(
u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}` u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
); );
uses.forEach(u => { uses.forEach(u => {
u.setAttributeNS(XLINK_NS, "href", `#${newId}`); u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
});
}); });
});
g.node().appendChild(svgElem); g.node().appendChild(svgElem);
const vb = svgElem.viewBox.baseVal; const vb = svgElem.viewBox.baseVal;
const svgWidth = vb.width || 40; const svgWidth = vb.width || 40;
const svgHeight = vb.height || 40; const svgHeight = vb.height || 40;
const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight); const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
g.select("svg")
.attr("width", svgWidth * scale)
.attr("height", svgHeight * scale)
.attr("x", -svgWidth * scale / 2)
.attr("y", -svgHeight * scale / 2);
} else {
// We have a image type different than svg
// include it via img url
g.append("svg:image")
.attr("xlink:href", d.image)
.attr("width", 40)
.attr("height", 40)
.attr("x", -20)
.attr("y", -20);
}
g.select("svg")
.attr("width", svgWidth * scale)
.attr("height", svgHeight * scale)
.attr("x", -svgWidth * scale / 2)
.attr("y", -svgHeight * scale / 2);
}); });
// add element to nodes array // add element to nodes array

8
templates/actions/collections/group.html
View File

@ -0,0 +1,8 @@
<li>
<a
role="button"
onclick="document.getElementById('new_group_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Group</a
>
</li>

27
templates/actions/objects/pathway.html
View File

@ -1,5 +1,3 @@
{% load envipytags %}
{% if meta.can_edit %} {% if meta.can_edit %}
<li> <li>
<a <a
@ -17,12 +15,7 @@
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
> >
</li> </li>
{% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %} <li role="separator" class="divider"></li>
{% for tpl in action_button_templates %}
{% include tpl %}
{% endfor %}
<li role="separator" class="divider h-px"></li>
{% endif %} {% endif %}
<li> <li>
<a <a
@ -74,7 +67,7 @@
Rules</a Rules</a
> >
</li> </li>
<li role="separator" class="divider h-px"></li> <li role="separator" class="divider"></li>
<li> <li>
<a <a
class="button" class="button"
@ -99,16 +92,11 @@
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
> >
</li> </li>
<li role="separator" class="divider h-px"></li> <li role="separator" class="divider"></li>
<li> <li>
<a <a
class="button" class="button"
onclick=" onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
const modal = document.getElementById('delete_pathway_node_modal');
modal.showModal();
window.dispatchEvent(new Event('modal-opened'));
return false;
"
> >
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
> >
@ -116,12 +104,7 @@
<li> <li>
<a <a
class="button" class="button"
onclick=" onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
const modal = document.getElementById('delete_pathway_edge_modal');
modal.showModal();
window.dispatchEvent(new Event('modal-opened'));
return false;
"
> >
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
> >

2
templates/collections/compounds_paginated.html
View File

@ -5,7 +5,7 @@
{% block action_button %} {% block action_button %}
<div class="flex items-center gap-2"> <div class="flex items-center gap-2">
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<button <button
type="button" type="button"
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

21
templates/collections/groups_paginated.html
View File

@ -1,21 +0,0 @@
{% extends "collections/paginated_base.html" %}
{% block page_title %}Groups{% endblock %}
{% block action_button %}
<button
type="button"
class="btn btn-primary btn-sm"
onclick="document.getElementById('new_group_modal').showModal(); return false;"
>
New Group
</button>
{% endblock action_button %}
{% block action_modals %}
{% include "modals/collections/new_group_modal.html" %}
{% endblock action_modals %}
{% block description %}
<p>Users can team up in groups to share packages.</p>
{% endblock description %}

18
templates/collections/models_paginated.html
View File

@ -3,16 +3,14 @@
{% block page_title %}Models{% endblock %} {% block page_title %}Models{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
{% if meta.enabled_features.MODEL_BUILDING %} <button
<button type="button"
type="button" class="btn btn-primary btn-sm"
class="btn btn-primary btn-sm" onclick="document.getElementById('new_model_modal').showModal(); return false;"
onclick="document.getElementById('new_model_modal').showModal(); return false;" >
> New Model
New Model </button>
</button>
{% endif %}
{% endif %} {% endif %}
{% endblock action_button %} {% endblock action_button %}

2
templates/collections/packages_paginated.html
View File

@ -3,6 +3,7 @@
{% block page_title %}Packages{% endblock %} {% block page_title %}Packages{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit %}
<div class="flex items-center gap-2"> <div class="flex items-center gap-2">
<button <button
type="button" type="button"
@ -70,6 +71,7 @@
</ul> </ul>
</div> </div>
</div> </div>
{% endif %}
{% endblock action_button %} {% endblock action_button %}
{% block action_modals %} {% block action_modals %}

2
templates/collections/pathways_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Pathways{% endblock %} {% block page_title %}Pathways{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<div class="flex items-center gap-2"> <div class="flex items-center gap-2">
<a <a
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

2
templates/collections/reactions_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Reactions{% endblock %} {% block page_title %}Reactions{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<button <button
type="button" type="button"
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

2
templates/collections/rules_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Rules{% endblock %} {% block page_title %}Rules{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<button <button
type="button" type="button"
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

2
templates/collections/scenarios_paginated.html
View File

@ -11,7 +11,7 @@
{% endblock action_modals %} {% endblock action_modals %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<button <button
type="button" type="button"
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

2
templates/collections/structures_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}{{ page_title|default:"Structures" }}{% endblock %} {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
{% block action_button %} {% block action_button %}
{% if meta.can_edit or not meta.url_contains_package %} {% if meta.can_edit %}
<button <button
type="button" type="button"
class="btn btn-primary btn-sm" class="btn btn-primary btn-sm"

12
templates/components/navbar.html
View File

@ -35,7 +35,6 @@
<use href="{% static "/images/logo-name.svg" %}#ep-logo-name" /> <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
</svg> </svg>
</a> </a>
<img src="{% static 'images/bayer-logo.svg' %}" width="40">
</div> </div>
{% if not public_mode %} {% if not public_mode %}
@ -89,23 +88,12 @@
>Scenario</a >Scenario</a
> >
</li> </li>
<hr/>
<li>
<a href="{{ meta.server_url }}/group" id="scenarioLink"
>Group</a
>
</li>
</ul> </ul>
</div> </div>
</div> </div>
{% endif %} {% endif %}
<div class="navbar-end"> <div class="navbar-end">
{% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}
<img src="{% static 'images/restricted_mid.png' %}" width="200">
{% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
<img src="{% static 'images/secret_mid.png' %}" width="120">
{% endif %}
{% if not public_mode %} {% if not public_mode %}
<a id="search-trigger" role="button" class="cursor-pointer"> <a id="search-trigger" role="button" class="cursor-pointer">
<div <div

4
templates/modals/collections/new_prediction_setting_modal.html
View File

@ -203,11 +203,11 @@
id="model-based-prediction-setting-threshold" id="model-based-prediction-setting-threshold"
name="model-based-prediction-setting-threshold" name="model-based-prediction-setting-threshold"
class="input input-bordered w-full" class="input input-bordered w-full"
value="0.25" placeholder="0.25"
type="number" type="number"
min="0" min="0"
max="1" max="1"
step="any" step="0.05"
/> />
</div> </div>

19
templates/modals/objects/delete_pathway_edge_modal.html
View File

@ -4,25 +4,6 @@
id="delete_pathway_edge_modal" id="delete_pathway_edge_modal"
class="modal" class="modal"
x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })" x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
@modal-opened.window="
const links = d3.selectAll('line.highlighted');
console.log(links);
if (!links.empty()) {
const el = links.node();
const selectElement = document.getElementById('delete_pathway_edge_edges');
console.log(el);
console.log(el.__data__);
for (let option of selectElement.options) {
if (option.value === el.__data__.url) {
option.selected = true;
break;
}
}
selectElement.dispatchEvent(new Event('change'));
}
"
@close="reset()" @close="reset()"
> >
<div class="modal-box"> <div class="modal-box">

16
templates/modals/objects/delete_pathway_node_modal.html
View File

@ -4,22 +4,6 @@
id="delete_pathway_node_modal" id="delete_pathway_node_modal"
class="modal" class="modal"
x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })" x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
@modal-opened.window="
const el = d3.select('circle.highlighted').node();
if (el !== null) {
const selectElement = document.getElementById('delete_pathway_node_nodes');
for (let option of selectElement.options) {
if (option.value === el.__data__.url) {
option.selected = true;
break;
}
}
selectElement.dispatchEvent(new Event('change'));
}
"
@close="reset()" @close="reset()"
> >
<div class="modal-box"> <div class="modal-box">

7
templates/objects/compound.html
View File

@ -1,5 +1,4 @@
{% extends "framework_modern.html" %} {% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %} {% block content %}
@ -83,12 +82,6 @@
<div class="collapse-content">{{ compound.description }}</div> <div class="collapse-content">{{ compound.description }}</div>
</div> </div>
<!-- Extension Slot for Viz -->
{% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation --> <!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse"> <div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked /> <input type="checkbox" checked />

7
templates/objects/compound_structure.html
View File

@ -1,5 +1,4 @@
{% extends "framework_modern.html" %} {% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %} {% block content %}
@ -51,12 +50,6 @@
</div> </div>
</div> </div>
<!-- Extension Slot for Viz -->
{% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation --> <!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse"> <div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked /> <input type="checkbox" checked />

7
templates/objects/node.html
View File

@ -1,5 +1,4 @@
{% extends "framework_modern.html" %} {% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %} {% block content %}
@ -55,12 +54,6 @@
</div> </div>
</div> </div>
{% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation --> <!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse"> <div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked /> <input type="checkbox" checked />

12
templates/objects/pathway.html
View File

@ -1,7 +1,5 @@
{% extends "framework_modern.html" %} {% extends "framework_modern.html" %}
{% load static %} {% load static %}
{% load envipytags %}
{% block content %} {% block content %}
<script src="https://d3js.org/d3.v7.min.js"></script> <script src="https://d3js.org/d3.v7.min.js"></script>
<style> <style>
@ -78,10 +76,6 @@
{% block action_modals %} {% block action_modals %}
{% include "modals/objects/add_pathway_node_modal.html" %} {% include "modals/objects/add_pathway_node_modal.html" %}
{% include "modals/objects/add_pathway_edge_modal.html" %} {% include "modals/objects/add_pathway_edge_modal.html" %}
{% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
{% for tpl in add_templates %}
{% include tpl %}
{% endfor %}
{% include "modals/objects/download_pathway_csv_modal.html" %} {% include "modals/objects/download_pathway_csv_modal.html" %}
{% include "modals/objects/download_pathway_image_modal.html" %} {% include "modals/objects/download_pathway_image_modal.html" %}
{% include "modals/objects/identify_missing_rules_modal.html" %} {% include "modals/objects/identify_missing_rules_modal.html" %}
@ -106,12 +100,12 @@
</div> </div>
<!-- Graphical Representation --> <!-- Graphical Representation -->
<div class="collapse-arrow bg-base-200 collapse overflow-y-auto"> <div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked /> <input type="checkbox" checked />
<div class="collapse-title text-xl font-medium"> <div class="collapse-title text-xl font-medium">
Graphical Representation Graphical Representation
</div> </div>
<div class="collapse-content "> <div class="collapse-content">
<div class="bg-base-100 mb-2 rounded-lg p-2"> <div class="bg-base-100 mb-2 rounded-lg p-2">
<div class="navbar bg-base-100 rounded-lg"> <div class="navbar bg-base-100 rounded-lg">
<div class="flex-1"> <div class="flex-1">
@ -140,7 +134,7 @@
</div> </div>
<ul <ul
tabindex="0" tabindex="0"
class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2" class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
> >
{% include "actions/objects/pathway.html" %} {% include "actions/objects/pathway.html" %}
</ul> </ul>

17
utilities/chem.py
View File

@ -88,10 +88,6 @@ class FormatConverter(object):
def from_smiles(smiles): def from_smiles(smiles):
return Chem.MolFromSmiles(smiles) return Chem.MolFromSmiles(smiles)
@staticmethod
def from_molfile(molfile: str):
return Chem.MolFromMolBlock(molfile)
@staticmethod @staticmethod
def to_smiles(mol, canonical=False): def to_smiles(mol, canonical=False):
return Chem.MolToSmiles(mol, canonical=canonical) return Chem.MolToSmiles(mol, canonical=canonical)
@ -175,17 +171,12 @@ class FormatConverter(object):
try: try:
Chem.Kekulize(mol) Chem.Kekulize(mol)
except Exception: except Exception:
mol = Chem.Mol(mol.ToBinary()) mc = Chem.Mol(mol.ToBinary())
if not mol.GetNumConformers(): if not mc.GetNumConformers():
Chem.rdDepictor.Compute2DCoords(mol) Chem.rdDepictor.Compute2DCoords(mc)
drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size) pass
opts = drawer.drawOptions()
opts.clearBackground = False
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
return drawer.GetDrawingText()
@staticmethod @staticmethod
def normalize(smiles): def normalize(smiles):

17
utilities/legacy.py
View File

@ -64,7 +64,7 @@
import logging import logging
from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel from envipy_additional_information import HalfLife, HalfLifeWS
from envipy_additional_information.information import Interval from envipy_additional_information.information import Interval
from envipy_additional_information.parsers import ( from envipy_additional_information.parsers import (
AcidityParser, AcidityParser,
@ -473,12 +473,17 @@ def build_additional_information_from_request(request, type_):
comment = get_parameter_or_empty_string(request, "comment") comment = get_parameter_or_empty_string(request, "comment")
source = get_parameter_or_empty_string(request, "source") source = get_parameter_or_empty_string(request, "source")
# first_order = get_parameter_or_empty_string(request, "firstOrder") first_order = get_parameter_or_empty_string(request, "firstOrder")
model = get_parameter_or_empty_string(request, "model") model = get_parameter_or_empty_string(request, "model")
fit = get_parameter_or_empty_string(request, "fit") fit = get_parameter_or_empty_string(request, "fit")
if model: if first_order != "":
model = HalfLifeModel(model.upper()) if model != "":
raise ValueError("not both, model and firstOrder can be set!")
if first_order == "true":
model = "SFO"
else:
logger.info("firstOrder is set to false which is not meaningful")
return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source) return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
@ -503,10 +508,6 @@ def build_additional_information_from_request(request, type_):
comment_ws = get_parameter_or_empty_string(request, "comment_ws") comment_ws = get_parameter_or_empty_string(request, "comment_ws")
source_ws = get_parameter_or_empty_string(request, "source_ws") source_ws = get_parameter_or_empty_string(request, "source_ws")
model_ws = get_parameter_or_empty_string(request, "model_ws") model_ws = get_parameter_or_empty_string(request, "model_ws")
if model_ws:
model_ws = HalfLifeModel(model_ws.upper())
fit_ws = get_parameter_or_empty_string(request, "fit_ws") fit_ws = get_parameter_or_empty_string(request, "fit_ws")
dt50_total = IntervalParser.from_string(hl_ws_total) dt50_total = IntervalParser.from_string(hl_ws_total)

180
uv.lock generated
View File

@ -17,7 +17,7 @@ wheels = [
[[package]] [[package]]
name = "aiohttp" name = "aiohttp"
version = "3.13.5" version = "3.13.3"
source = { registry = "https://pypi.org/simple" } source = { registry = "https://pypi.org/simple" }
dependencies = [ dependencies = [
{ name = "aiohappyeyeballs" }, { name = "aiohappyeyeballs" },
@ -28,76 +28,76 @@ dependencies = [
{ name = "propcache" }, { name = "propcache" },
{ name = "yarl" }, { name = "yarl" },
] ]
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