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Cleanup (#52)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#52
This commit is contained in:
jebus
2025-08-22 06:36:22 +12:00
parent ec387cc12e
commit 6e6b394289
42 changed files with 222 additions and 368 deletions
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79
epdb/views.py
View File

@ -4,6 +4,9 @@ from typing import List, Dict, Any
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.db.models import F, Value
from django.db.models.fields import CharField
from django.db.models.functions import Concat
from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
from django.shortcuts import render, redirect
from django.views.decorators.csrf import csrf_exempt
@ -436,8 +439,16 @@ def scenarios(request):
if request.GET.get('all'):
return JsonResponse({
"objects": [
{"name": pw.name, "url": pw.url, "reviewed": True}
for pw in reviewed_scenario_qs
{"name": s.name, "url": s.full_url, "reviewed": True}
for s in reviewed_scenario_qs.annotate(
full_url=Concat(
Value(s.SERVER_URL + '/package/'),
F("package__uuid"),
Value("/scenario/"),
F("uuid"),
output_field=CharField(),
)
)
]
})
@ -517,6 +528,7 @@ def search(request):
packages = PackageManager.get_reviewed_packages()
search_result = SearchManager.search(packages, searchterm, mode)
return JsonResponse(search_result, safe=False)
context = get_base_context(request)
@ -542,6 +554,7 @@ def search(request):
packages = PackageManager.get_reviewed_packages()
context['search_result'] = SearchManager.search(packages, searchterm, mode)
context['search_result']['searchterm'] = searchterm
return render(request, 'search.html', context)
@ -706,7 +719,7 @@ def package_model(request, package_uuid, model_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-model':
if hidden == 'delete':
current_model.delete()
return redirect(current_package.url + '/model')
else:
@ -757,7 +770,7 @@ def package(request, package_uuid):
logger.debug(f"{k}\t{v}")
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-package':
if hidden == 'delete':
logger.debug(current_package.delete())
return redirect(s.SERVER_URL + '/package')
else:
@ -897,7 +910,7 @@ def package_compound(request, package_uuid, compound_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-compound':
if hidden == 'delete':
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
@ -940,6 +953,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
context['meta']['current_package'] = current_package
context['object_type'] = 'structure'
context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure')
reviewed_compound_structure_qs = CompoundStructure.objects.none()
unreviewed_compound_structure_qs = CompoundStructure.objects.none()
@ -979,15 +993,38 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
context['title'] = f'enviPath - {current_package.name} - {current_compound.name} - {current_structure.name}'
context['meta']['current_package'] = current_package
context['object_type'] = 'compound'
context['object_type'] = 'structure'
context['compound_structure'] = current_structure
context['current_object'] = current_structure
context['breadcrumbs'] = breadcrumbs(current_package, 'compound', current_compound, 'structure', current_structure)
return render(request, 'objects/compound_structure.html', context)
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete':
# Check if we have to delete the compound as no structure is left
if len(current_structure.compound.structures.all()) == 1:
# This will delete the structure as well
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
if current_structure.normalized_structure:
current_compound.delete()
return redirect(current_package.url + '/compound')
else:
if current_compound.default_structure == current_structure:
current_structure.delete()
current_compound.default_structure = current_compound.structures.all().first()
return redirect(current_compound.url + '/structure')
else:
current_structure.delete()
return redirect(current_compound.url + '/structure')
else:
return HttpResponseBadRequest()
selected_scenarios = request.POST.getlist('selected-scenarios')
if selected_scenarios:
@ -1109,7 +1146,7 @@ def package_rule(request, package_uuid, rule_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-rule':
if hidden == 'delete':
current_rule.delete()
return redirect(current_package.url + '/rule')
else:
@ -1212,7 +1249,7 @@ def package_reaction(request, package_uuid, reaction_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-reaction':
if hidden == 'delete':
current_reaction.delete()
return redirect(current_package.url + '/reaction')
else:
@ -1281,8 +1318,8 @@ def package_pathways(request, package_uuid):
log_post_params(request)
name = request.POST.get('name', 'Pathway ' + str(Pathway.objects.filter(package=current_package).count()))
description = request.POST.get('description', s.DEFAULT_VALUES['description'])
name = request.POST.get('name')
description = request.POST.get('description')
pw_mode = request.POST.get('predict', 'predict')
smiles = request.POST.get('smiles')
@ -1303,7 +1340,14 @@ def package_pathways(request, package_uuid):
return error(request, "Pathway prediction failed!",
f'Pathway prediction failed as received mode "{pw_mode}" is none of {modes}')
prediction_setting = request.POST.get('prediction-setting', None)
if prediction_setting:
prediction_setting = SettingManager.get_setting_by_url(current_user, prediction_setting)
else:
prediction_setting = current_user.prediction_settings()
pw = Pathway.create(current_package, stand_smiles, name=name, description=description)
# set mode
pw.kv.update({'mode': pw_mode})
pw.save()
@ -1316,12 +1360,11 @@ def package_pathways(request, package_uuid):
if pw_mode == 'incremental':
limit = 1
pred_setting = current_user.prediction_settings()
pw.setting = pred_setting
pw.setting = prediction_setting
pw.save()
from .tasks import predict
predict.delay(pw.pk, pred_setting.pk, limit=limit)
predict.delay(pw.pk, prediction_setting.pk, limit=limit)
return redirect(pw.url)
@ -1371,7 +1414,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
elif request.method == 'POST':
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-pathway':
if hidden == 'delete':
current_pathway.delete()
return redirect(current_package.url + '/pathway')
else:
@ -1514,7 +1557,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-node':
if hidden == 'delete':
# pre_delete signal will take care of edge deletion
current_node.delete()
@ -1616,7 +1659,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
'title'] = f'enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}'
context['meta']['current_package'] = current_package
context['object_type'] = 'reaction'
context['object_type'] = 'edge'
context['breadcrumbs'] = breadcrumbs(current_package, 'pathway', current_pathway, 'edge', current_edge)
context['edge'] = current_edge
context['current_object'] = current_edge
@ -1628,7 +1671,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-edge':
if hidden == 'delete':
current_edge.delete()
return redirect(current_pathway.url)
@ -1896,7 +1939,7 @@ def group(request, group_uuid):
log_post_params(request)
if hidden := request.POST.get('hidden', None):
if hidden == 'delete-group':
if hidden == 'delete':
current_group.delete()
return redirect(s.SERVER_URL + '/group')
else: