jebus/enviPy-bayer
1
0
Fork 0
forked from enviPath/enviPy
Code Issues Pull Requests Actions Releases Activity

[Feature] Leftovers after Release (#303)

Browse Source 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#303
This commit is contained in:
jebus
2026-01-22 10:26:38 +13:00
parent f905bf21cf
commit ab0b5a5186
16 changed files with 465 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
epapi/v1/endpoints/settings.py Normal file
View File

@ -0,0 +1,23 @@
from django.conf import settings as s
from ninja import Router
from ninja_extra.pagination import paginate
from epdb.logic import SettingManager
from ..pagination import EnhancedPageNumberPagination
from ..schemas import SettingOutSchema
router = Router()
@router.get("/settings/", response=EnhancedPageNumberPagination.Output[SettingOutSchema])
@paginate(
EnhancedPageNumberPagination,
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
)
def list_all_pathways(request):
"""
List all pathways from reviewed packages.
"""
user = request.user
return SettingManager.get_all_settings(user)

14
epapi/v1/router.py
View File

@ -1,7 +1,18 @@
from ninja import Router
from ninja.security import SessionAuth
from .auth import BearerTokenAuth
from .endpoints import packages, scenarios, compounds, rules, reactions, pathways, models, structure
from .endpoints import (
compounds,
models,
packages,
pathways,
reactions,
rules,
scenarios,
settings,
structure,
)
# Main router with authentication
router = Router(
@ -20,3 +31,4 @@ router.add_router("", reactions.router)
router.add_router("", pathways.router)
router.add_router("", models.router)
router.add_router("", structure.router)
router.add_router("", settings.router)

7
epapi/v1/schemas.py
View File

@ -102,3 +102,10 @@ class PackageOutSchema(Schema):
@staticmethod
def resolve_review_status(obj):
return "reviewed" if obj.reviewed else "unreviewed"
class SettingOutSchema(Schema):
uuid: UUID
url: str = ""
name: str
description: str

4
epdb/admin.py
View File

@ -28,7 +28,7 @@ Package = s.GET_PACKAGE_MODEL()
class UserAdmin(admin.ModelAdmin):
list_display = ["username", "email", "is_active"]
list_display = ["username", "email", "is_active", "is_staff", "is_superuser"]
class UserPackagePermissionAdmin(admin.ModelAdmin):
@ -48,7 +48,7 @@ class JobLogAdmin(admin.ModelAdmin):
class EPAdmin(admin.ModelAdmin):
search_fields = ["name", "description"]
search_fields = ["name", "description", "url", "uuid"]
list_display = ["name", "url", "created"]
ordering = ["-created"]

78
epdb/legacy_api.py
View File

@ -18,6 +18,8 @@ from .models import (
Edge,
EnviFormer,
EPModel,
Group,
GroupPackagePermission,
MLRelativeReasoning,
Node,
PackageBasedModel,
@ -204,6 +206,82 @@ def get_user(request, user_uuid):
}
########
# Group #
########
class GroupMember(Schema):
id: str = Field(None, alias="url")
identifier: str
name: str
class GroupWrapper(Schema):
group: List[SimpleGroup]
class GroupSchema(Schema):
description: str
id: str = Field(None, alias="url")
identifier: str = "group"
members: List[GroupMember] = Field([], alias="members")
name: str = Field(None, alias="name")
ownerid: str = Field(None, alias="owner.url")
ownername: str = Field(None, alias="owner.name")
packages: List["SimplePackage"] = Field([], alias="packages")
readers: List[GroupMember] = Field([], alias="readers")
writers: List[GroupMember] = Field([], alias="writers")
@staticmethod
def resolve_members(obj: Group):
res = []
for member in obj.user_member.all():
res.append(GroupMember(id=member.url, identifier="usermember", name=member.username))
for member in obj.group_member.all():
res.append(GroupMember(id=member.url, identifier="groupmember", name=member.name))
return res
@staticmethod
def resolve_packages(obj: Group):
return Package.objects.filter(
id__in=[
GroupPackagePermission.objects.filter(group=obj).values_list(
"package_id", flat=True
)
]
)
@staticmethod
def resolve_readers(obj: Group):
return GroupSchema.resolve_members(obj)
@staticmethod
def resolve_writers(obj: Group):
return [GroupMember(id=obj.owner.url, identifier="usermember", name=obj.owner.username)]
@router.get("/group", response={200: GroupWrapper, 403: Error})
def get_groups(request):
return {"group": GroupManager.get_groups(request.user)}
@router.get("/group/{uuid:group_uuid}", response={200: GroupSchema, 403: Error})
def get_group(request, group_uuid):
try:
g = GroupManager.get_group_by_id(request.user, group_uuid)
return g
except ValueError:
return 403, {
"message": f"Getting Group with id {group_uuid} failed due to insufficient rights!"
}
##########
# Search #
##########
class Search(Schema):
packages: List[str] = Field(alias="packages[]")
search: str

17
epdb/migrations/0015_user_is_reviewer.py Normal file
View File

@ -0,0 +1,17 @@
# Generated by Django 5.2.7 on 2026-01-19 19:26
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
]
operations = [
migrations.AddField(
model_name="user",
name="is_reviewer",
field=models.BooleanField(default=False),
),
]

21
epdb/models.py
View File

@ -72,6 +72,7 @@ class User(AbstractUser):
null=True,
blank=False,
)
is_reviewer = models.BooleanField(default=False)
USERNAME_FIELD = "email"
REQUIRED_FIELDS = ["username"]
@ -1828,8 +1829,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
queue.append(prod)
# We shouldn't lose or make up nodes...
assert len(nodes) == len(self.nodes)
logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
if len(nodes) != len(self.nodes):
logger.debug(f"{self.name}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}")
links = [e.d3_json() for e in self.edges]
@ -1880,6 +1881,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
"source": pseudo_idx,
"target": node_url_to_idx[target],
"app_domain": link.get("app_domain", None),
"multi_step": link["multi_step"],
}
adjusted_links.append(new_link)
@ -2146,6 +2148,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
}
@staticmethod
@transaction.atomic
def create(
pathway: "Pathway",
smiles: str,
@ -2185,8 +2188,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
if data:
rule_ids = defaultdict(list)
for e in Edge.objects.filter(start_nodes__in=[self]):
for r in e.edge_label.rules.all():
rule_ids[str(r.uuid)].append(e.simple_json())
# TODO While the Pathway is being predicted we sometimes
# TODO receive 'NoneType' object has no attribute 'rules'
if e.edge_label:
for r in e.edge_label.rules.all():
rule_ids[str(r.uuid)].append(e.simple_json())
for t in data["assessment"]["transformations"]:
if t["rule"]["uuid"] in rule_ids:
@ -2230,6 +2236,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
"reaction": {"name": self.edge_label.name, "url": self.edge_label.url}
if self.edge_label
else None,
"multi_step": self.edge_label.multi_step if self.edge_label else False,
"reaction_probability": self.kv.get("probability"),
"start_node_urls": [x.url for x in self.start_nodes.all()],
"end_node_urls": [x.url for x in self.end_nodes.all()],
@ -2270,6 +2277,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
return edge_json
@staticmethod
@transaction.atomic
def create(
pathway,
start_nodes: List[Node],
@ -3819,6 +3827,11 @@ class Scenario(EnviPathModel):
yield inst
def related_pathways(self):
return Pathway.objects.filter(
scenarios__in=[self], package__reviewed=True, package=self.package
).distinct()
class UserSettingPermission(Permission):
uuid = models.UUIDField(

62
epdb/views.py
View File

@ -1352,6 +1352,14 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
)
if request.method == "GET":
is_image_request = request.GET.get("image")
if is_image_request:
if is_image_request == "svg":
return HttpResponse(current_structure.as_svg, content_type="image/svg+xml")
else:
return HttpResponseBadRequest("Currently only SVG as image formate supported!")
context = get_base_context(request)
context["title"] = (
f"enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}"
@ -2569,6 +2577,28 @@ def package_scenario(request, package_uuid, scenario_uuid):
return redirect(current_scenario.url)
else:
return HttpResponseBadRequest()
new_scenario_name = request.POST.get("scenario-name")
if new_scenario_name is not None:
new_scenario_name = nh3.clean(new_scenario_name, tags=s.ALLOWED_HTML_TAGS).strip()
if new_scenario_name:
current_scenario.name = new_scenario_name
new_scenario_description = request.POST.get("scenario-description")
if new_scenario_description is not None:
new_scenario_description = nh3.clean(
new_scenario_description, tags=s.ALLOWED_HTML_TAGS
).strip()
if new_scenario_description:
current_scenario.description = new_scenario_description
if any([new_scenario_name, new_scenario_description]):
current_scenario.save()
return redirect(current_scenario.url)
else:
return HttpResponseBadRequest()
else:
@ -2784,10 +2814,17 @@ def settings(request):
context["object_type"] = "setting"
context["breadcrumbs"] = [
{"Home": s.SERVER_URL},
{"Group": s.SERVER_URL + "/setting"},
{"Setting": s.SERVER_URL + "/setting"},
]
context["objects"] = SettingManager.get_all_settings(current_user)
# Context for paginated template
context["entity_type"] = "setting"
context["api_endpoint"] = "/api/v1/settings/"
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
context["list_title"] = "settings"
context["list_mode"] = "combined"
return render(request, "collections/settings_paginated.html", context)
return render(request, "collections/objects_list.html", context)
elif request.method == "POST":
@ -2867,7 +2904,26 @@ def settings(request):
def setting(request, setting_uuid):
pass
current_user = _anonymous_or_real(request)
current_setting = SettingManager.get_setting_by_id(current_user, setting_uuid)
if request.method == "GET":
context = get_base_context(request)
context["title"] = f"enviPath - {current_setting.name}"
context["object_type"] = "setting"
context["breadcrumbs"] = [
{"Home": s.SERVER_URL},
{"Setting": s.SERVER_URL + "/setting"},
{f"{current_setting.name}": current_setting.url},
]
context["setting"] = current_setting
context["current_object"] = current_setting
return render(request, "objects/setting.html", context)
else:
return HttpResponseNotAllowed(["GET"])
def jobs(request):

3
static/js/pw.js
View File

@ -498,7 +498,8 @@ function draw(pathway, elem) {
.enter().append("line")
// Check if target is pseudo and draw marker only if not pseudo
.attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
.attr("marker-end", d => d.target.pseudo ? '' : 'url(#arrow)')
.attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
// add element to links array
link.each(function (d) {

8
templates/actions/objects/scenario.html
View File

@ -1,4 +1,12 @@
{% if meta.can_edit %}
<li>
<a
class="button"
onclick="document.getElementById('edit_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Edit Scenario</a
>
</li>
<li>
<a
class="button"

20
templates/collections/settings_paginated.html Normal file
View File

@ -0,0 +1,20 @@
{% extends "collections/paginated_base.html" %}
{% block page_title %}Settings{% endblock %}
{% block action_button %}
{% endblock action_button %}
{% block action_modals %}
{% endblock action_modals %}
{% block description %}
<p>A setting includes configuration parameters for pathway predictions.</p>
<a
target="_blank"
href="https://wiki.envipath.org/index.php/Setting"
class="link link-primary"
>
Learn more &gt;&gt;
</a>
{% endblock description %}

91
templates/modals/objects/edit_scenario_modal.html Normal file
View File

@ -0,0 +1,91 @@
{% load static %}
<dialog
id="edit_scenario_modal"
class="modal"
x-data="modalForm()"
@close="reset()"
>
<div class="modal-box">
<!-- Header -->
<h3 class="font-bold text-lg">Edit Scenario</h3>
<!-- Close button (X) -->
<form method="dialog">
<button
class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
:disabled="isSubmitting"
>
✕
</button>
</form>
<!-- Body -->
<div class="py-4">
<form
id="edit-scenario-modal-form"
accept-charset="UTF-8"
action=""
method="post"
>
{% csrf_token %}
<div class="form-control mb-3">
<label class="label" for="scenario-name">
<span class="label-text">Name</span>
</label>
<input
id="scenario-name"
class="input input-bordered w-full"
name="scenario-name"
value="{{ scenario.name|safe }}"
required
/>
</div>
<div class="form-control mb-3">
<label class="label" for="scenario-description">
<span class="label-text">Description</span>
</label>
<input
id="scenario-description"
type="text"
class="input input-bordered w-full"
value="{{ scenario.description|safe }}"
name="scenario-description"
/>
</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('edit-scenario-modal-form')"
:disabled="isSubmitting"
>
<span x-show="!isSubmitting">Update</span>
<span
x-show="isSubmitting"
class="loading loading-spinner loading-sm"
></span>
<span x-show="isSubmitting">Updating...</span>
</button>
</div>
</div>
<!-- Backdrop -->
<form method="dialog" class="modal-backdrop">
<button :disabled="isSubmitting">close</button>
</form>
</dialog>

15
templates/objects/pathway.html
View File

@ -306,6 +306,21 @@
>
<path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
</marker>
<marker
id="doublearrow"
viewBox="0 0 20 30"
refX="53"
refY="5"
markerWidth="18"
markerHeight="18"
orient="auto-start-reverse"
markerUnits="userSpaceOnUse"
>
<!-- first triangle -->
<path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
<!-- second triangle -->
<path d="M 10 0 L 20 5 L 10 10 Z" fill="#999" />
</marker>
<marker
id="arrow_passes_app_domain"
viewBox="0 0 10 10"

20
templates/objects/scenario.html
View File

@ -3,6 +3,7 @@
{% block content %}
{% block action_modals %}
{% include "modals/objects/edit_scenario_modal.html" %}
{% include "modals/objects/add_additional_information_modal.html" %}
{% include "modals/objects/update_scenario_additional_information_modal.html" %}
{% include "modals/objects/generic_delete_modal.html" %}
@ -160,6 +161,25 @@
</div>
</div>
</div>
<!-- Pathways -->
{% if scenario.related_pathways %}
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">Pathways</div>
<div class="collapse-content">
<ul class="menu bg-base-100 rounded-box">
{% for p in scenario.related_pathways %}
<li>
<a href="{{ p.url }}" class="hover:bg-base-200"
>{{ p.name }} <i>({{ p.package.name }})</i></a
>
</li>
{% endfor %}
</ul>
</div>
</div>
{% endif %}
</div>
<script>

67
templates/objects/setting.html Normal file
View File

@ -0,0 +1,67 @@
{% extends "framework_modern.html" %}
{% block content %}
{% block action_modals %}
{% endblock action_modals %}
<div class="space-y-2 p-4">
<!-- Header Section -->
<div class="card bg-base-100">
<div class="card-body">
<div class="flex items-center justify-between">
<h2 class="card-title text-2xl">{{ setting.name }}</h2>
<div id="actionsButton" class="dropdown dropdown-end hidden">
<div tabindex="0" role="button" class="btn btn-ghost btn-sm">
<svg
xmlns="http://www.w3.org/2000/svg"
width="16"
height="16"
viewBox="0 0 24 24"
fill="none"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
class="lucide lucide-wrench"
>
<path
d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
/>
</svg>
Actions
</div>
<ul
tabindex="-1"
class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
>
{% block actions %}
{% endblock %}
</ul>
</div>
</div>
</div>
</div>
<!-- The actual setting -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />
<div class="collapse-content">
{% with setting_to_render=setting can_be_default=False %}
{% include "objects/setting_template.html" %}
{% endwith %}
</div>
</div>
</div>
<script>
// Show actions button if there are actions
document.addEventListener("DOMContentLoaded", function () {
const actionsButton = document.getElementById("actionsButton");
const actionsList = actionsButton?.querySelector("ul");
if (actionsList && actionsList.children.length > 0) {
actionsButton?.classList.remove("hidden");
}
});
</script>
{% endblock content %}

26
templates/static/login.html
View File

@ -31,6 +31,32 @@
{% endblock %}
{% block content %}
<div class="card bg-base-200 mb-6 ">
<div class="card-body">
<h3 class="card-title">Welcome to the new enviPath!</h3>
<p class="mb-4 text-sm">
Rebuilt from the ground up for faster predictions, greater stability,
and powerful scalability. Explore a decade of research on a modern,
reliable platform.<br />
The old system is still accessible but will be shut down at a later
date. If you want to back up your data, download it from the
<a
href="https://legacy.envipath.org"
class="link link-primary"
target="_blank"
>old system</a
>
or contact us via the
<a
href="https://community.envipath.org/"
class="link link-primary"
target="_blank"
>community forum</a
>
for assistance.
</p>
</div>
</div>
<!-- Tab Navigation -->
<div class="border-base-300 mb-6 border-b">
<div class="flex justify-start">