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[Feature] Leftovers after Release (#303)

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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
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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):