forked from enviPath/enviPy
First Issues / Improvements detected in Beta (#36)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#36
This commit is contained in:
@ -21,6 +21,7 @@ class UserManager(object):
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return bool(re.findall(UserManager.user_pattern, url))
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@staticmethod
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@transaction.atomic
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def create_user(username, email, password, set_setting=True, add_to_group=True, *args, **kwargs):
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# avoid circular import :S
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from .tasks import send_registration_mail
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@ -59,19 +60,24 @@ class UserManager(object):
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def get_user(user_url):
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pass
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@staticmethod
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def get_user_by_id(user, user_uuid: str):
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if user.uuid != user_uuid and not user.is_superuser:
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raise ValueError("Getting user failed!")
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return get_user_model().objects.get(uuid=user_uuid)
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@staticmethod
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def get_user_lp(user_url: str):
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uuid = user_url.strip().split('/')[-1]
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return get_user_model().objects.get(uuid=uuid)
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@staticmethod
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def get_users_lp():
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return get_user_model().objects.all()
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@staticmethod
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def get_users():
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return []
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@staticmethod
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def get_user_lp(user_url: str):
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uuid = user_url.strip().split('/')[-1]
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return get_user_model().objects.get(uuid=uuid)
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raise ValueError("")
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@staticmethod
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def writable(current_user, user):
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@ -102,6 +108,10 @@ class GroupManager(object):
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uuid = group_url.strip().split('/')[-1]
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return Group.objects.get(uuid=uuid)
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@staticmethod
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def get_groups_lp():
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return Group.objects.all()
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@staticmethod
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def get_group_by_url(user, group_url):
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return GroupManager.get_group_by_id(user, group_url.split('/')[-1])
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@ -173,6 +183,30 @@ class PackageManager(object):
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return True
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return False
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@staticmethod
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def has_package_permission(user: 'User', package: Union[str, 'Package'], permission: str):
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if isinstance(package, str):
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package = Package.objects.get(uuid=package)
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groups = GroupManager.get_groups(user)
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perms = {
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'all': ['all'],
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'write': ['all', 'write'],
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'read': ['all', 'write', 'read']
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}
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valid_perms = perms.get(permission)
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if UserPackagePermission.objects.filter(package=package, user=user, permission__in=valid_perms).exists() or \
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GroupPackagePermission.objects.filter(package=package, group__in=groups,
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permission__in=valid_perms).exists() or \
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user.is_superuser:
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return True
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return False
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@staticmethod
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def get_package_lp(package_url):
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match = re.findall(PackageManager.package_pattern, package_url)
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@ -701,8 +735,9 @@ class SettingManager(object):
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@staticmethod
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def get_all_settings(user):
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sp = UserSettingPermission.objects.filter(user=user).values('setting').distinct()
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return Setting.objects.filter(id__in=sp)
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sp = UserSettingPermission.objects.filter(user=user).values('setting')
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return (Setting.objects.filter(id__in=sp) | Setting.objects.filter(public=True) | Setting.objects.filter(
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global_default=True)).distinct()
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@staticmethod
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@transaction.atomic
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232
epdb/views.py
232
epdb/views.py
@ -1,6 +1,5 @@
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import json
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import logging
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from functools import wraps
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from typing import List, Dict, Any
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from django.conf import settings as s
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@ -10,6 +9,7 @@ from django.shortcuts import render, redirect
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from django.views.decorators.csrf import csrf_exempt
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from utilities.chem import FormatConverter, IndigoUtils
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from utilities.decorators import package_permission_required
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from .logic import GroupManager, PackageManager, UserManager, SettingManager, SearchManager
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from .models import Package, GroupPackagePermission, Group, CompoundStructure, Compound, Reaction, Rule, Pathway, Node, \
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EPModel, EnviFormer, MLRelativeReasoning, RuleBaseRelativeReasoning, Scenario, SimpleAmbitRule, APIToken, \
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@ -24,6 +24,20 @@ def log_post_params(request):
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logger.debug(f"{k}\t{v}")
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def error(request, message: str, detail: str, code: int = 400):
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context = get_base_context(request)
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error_context = {
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'error_message': message,
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'error_detail': detail,
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}
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if request.headers.get('Accept') == 'application/json':
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return JsonResponse(error_context, status=500)
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context.update(**error_context)
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return render(request, "errors/error.html", context, status=code)
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def login(request):
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current_user = _anonymous_or_real(request)
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context = get_base_context(request)
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@ -55,8 +69,11 @@ def login(request):
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except get_user_model().DoesNotExist:
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context['message'] = "Login failed!"
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return render(request, 'login.html', context)
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user = authenticate(username=email, password=password)
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try:
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user = authenticate(username=email, password=password)
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except Exception as e:
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context['message'] = "Login failed!"
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return render(request, 'login.html', context)
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if user is not None:
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login(request, user)
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@ -68,15 +85,23 @@ def login(request):
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elif is_register:
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username = request.POST.get('username')
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email = request.POST.get('email')
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password = request.POST.get('password')
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rpassword = request.POST.get('rpassword')
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password = request.POST.get('password', '').strip()
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rpassword = request.POST.get('rpassword', '').strip()
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if password != rpassword:
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pass
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if password != rpassword or password == '':
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context['message'] = "Registration failed, provided passwords differ!"
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return render(request, 'login.html', context)
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u = UserManager.create_user(username, email, password)
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try:
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u = UserManager.create_user(username, email, password)
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except Exception:
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context['message'] = "Registration failed! Couldn't create User Account."
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return render(request, 'login.html', context)
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context['message'] = "Your account has been created! An admin will activate it soon!"
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if s.ADMIN_APPROVAL_REQUIRED:
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context['message'] = "Your account has been created! An admin will activate it soon!"
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else:
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context['message'] = "Account has been created! You'll receive a mail to activate your account shortly."
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return render(request, 'login.html', context)
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@ -92,25 +117,11 @@ def logout(request):
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return HttpResponseBadRequest()
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def catch_exceptions(view_func):
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@wraps(view_func)
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def _wrapped_view(request, *args, **kwargs):
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try:
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return view_func(request, *args, **kwargs)
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except Exception as e:
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# Optionally return JSON or plain HttpResponse
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if request.headers.get('Accept') == 'application/json':
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return JsonResponse(
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{'error': 'Internal server error. Please try again later.'},
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status=500
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)
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else:
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return render(request, 'errors/error.html', get_base_context(request))
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return _wrapped_view
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def editable(request, user):
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if user.is_superuser:
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return True
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url = request.build_absolute_uri(request.path)
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if PackageManager.is_package_url(url):
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_package = PackageManager.get_package_lp(request.build_absolute_uri())
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@ -129,11 +140,13 @@ def editable(request, user):
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return False
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def get_base_context(request) -> Dict[str, Any]:
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def get_base_context(request, for_user=None) -> Dict[str, Any]:
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current_user = _anonymous_or_real(request)
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can_edit = editable(request, current_user)
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if for_user:
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current_user = for_user
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ctx = {
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'title': 'enviPath',
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'meta': {
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@ -183,8 +196,6 @@ def breadcrumbs(first_level_object=None, second_level_namespace=None, second_lev
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return bread
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# @catch_exceptions
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def index(request):
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context = get_base_context(request)
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context['title'] = 'enviPath - Home'
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@ -269,6 +280,9 @@ def compounds(request):
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default_package = current_user.default_package
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return package_compounds(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def rules(request):
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if request.method == 'GET':
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@ -305,6 +319,9 @@ def rules(request):
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default_package = current_user.default_package
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return package_rules(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def reactions(request):
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if request.method == 'GET':
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@ -341,6 +358,9 @@ def reactions(request):
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default_package = current_user.default_package
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return package_reactions(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def pathways(request):
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if request.method == 'GET':
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@ -378,6 +398,9 @@ def pathways(request):
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default_package = current_user.default_package
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return package_pathways(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def scenarios(request):
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if request.method == 'GET':
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@ -408,11 +431,14 @@ def scenarios(request):
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context['reviewed_objects'] = reviewed_scenario_qs
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return render(request, 'collections/objects_list.html', context)
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# TODO
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# elif request.method == 'POST':
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# # delegate to default package
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# default_package = request.user.default_package
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# return package_scenarios(request, default_package.uuid)
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elif request.method == 'POST':
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# delegate to default package
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default_package = request.user.default_package
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return package_scenarios(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def models(request):
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@ -459,6 +485,9 @@ def models(request):
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default_package = current_user.default_package
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return package_models(request, default_package.uuid)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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def search(request):
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current_user = _anonymous_or_real(request)
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@ -504,7 +533,11 @@ def search(request):
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return render(request, 'search.html', context)
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else:
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return HttpResponseNotAllowed(['GET'])
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@package_permission_required()
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def package_models(request, package_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -587,10 +620,15 @@ def package_models(request, package_uuid):
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mod = RuleBaseRelativeReasoning()
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mod.save()
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else:
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return error(request, 'Invalid model type.', f'Model type "{model_type}" is not supported."')
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return redirect(mod.url)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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@package_permission_required()
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def package_model(request, package_uuid, model_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -641,9 +679,10 @@ def package_model(request, package_uuid, model_uuid):
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return HttpResponseBadRequest()
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else:
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return HttpResponseBadRequest()
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return HttpResponseNotAllowed(['GET', 'POST'])
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@package_permission_required()
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def package(request, package_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -751,10 +790,10 @@ def package(request, package_uuid):
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return HttpResponseBadRequest()
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else:
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return HttpResponseBadRequest()
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return HttpResponseNotAllowed(['GET', 'POST'])
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# https://envipath.org/package/<id>/compound
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@package_permission_required()
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def package_compounds(request, package_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -797,8 +836,11 @@ def package_compounds(request, package_uuid):
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return redirect(c.url)
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else:
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return HttpResponseNotAllowed(['GET', 'POST'])
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# https://envipath.org/package/<id>/compound/<id>
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@package_permission_required()
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def package_compound(request, package_uuid, compound_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -838,11 +880,12 @@ def package_compound(request, package_uuid, compound_uuid):
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return redirect(current_compound.url)
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else:
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return HttpResponseBadRequest()
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else:
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return HttpResponseBadRequest()
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return HttpResponseNotAllowed(['GET', 'POST'])
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# https://envipath.org/package/<uuid>/compound/<uuid>/structure
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@package_permission_required()
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def package_compound_structures(request, package_uuid, compound_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -878,10 +921,10 @@ def package_compound_structures(request, package_uuid, compound_uuid):
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return redirect(cs.url)
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|
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else:
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return HttpResponseBadRequest()
|
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return HttpResponseNotAllowed(['GET', 'POST'])
|
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|
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|
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# https://envipath.org/package/<id>/compound/<id>/structure/<id>
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@package_permission_required()
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def package_compound_structure(request, package_uuid, compound_uuid, structure_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -899,8 +942,11 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
|
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return render(request, 'objects/compound_structure.html', context)
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|
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else:
|
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return HttpResponseNotAllowed(['GET', ])
|
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|
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# https://envipath.org/package/<id>/rule
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|
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@package_permission_required()
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def package_rules(request, package_uuid):
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -965,10 +1011,10 @@ def package_rules(request, package_uuid):
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return redirect(r.url)
|
||||
|
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else:
|
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return HttpResponseBadRequest()
|
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return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/rule/<id>
|
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@package_permission_required()
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def package_rule(request, package_uuid, rule_uuid):
|
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current_user = _anonymous_or_real(request)
|
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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@ -1012,10 +1058,10 @@ def package_rule(request, package_uuid, rule_uuid):
|
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return HttpResponseBadRequest()
|
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|
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else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/reaction
|
||||
@package_permission_required()
|
||||
def package_reactions(request, package_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1063,10 +1109,10 @@ def package_reactions(request, package_uuid):
|
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return redirect(r.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/reaction/<id>
|
||||
@package_permission_required()
|
||||
def package_reaction(request, package_uuid, reaction_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1108,10 +1154,10 @@ def package_reaction(request, package_uuid, reaction_uuid):
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway
|
||||
@package_permission_required()
|
||||
def package_pathways(request, package_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1154,13 +1200,22 @@ def package_pathways(request, package_uuid):
|
||||
pw_mode = request.POST.get('predict', 'predict')
|
||||
smiles = request.POST.get('smiles')
|
||||
|
||||
if smiles is None or smiles == '':
|
||||
return HttpResponseBadRequest()
|
||||
if smiles is None or smiles.strip() == '':
|
||||
return error(request, "Pathway prediction failed!",
|
||||
"Pathway prediction failed due to missing or empty SMILES")
|
||||
|
||||
stand_smiles = FormatConverter.standardize(smiles)
|
||||
smiles = smiles.strip()
|
||||
|
||||
if pw_mode not in ['predict', 'build', 'incremental']:
|
||||
return HttpResponseBadRequest()
|
||||
try:
|
||||
stand_smiles = FormatConverter.standardize(smiles)
|
||||
except ValueError:
|
||||
return error(request, "Pathway prediction failed!",
|
||||
f'Pathway prediction failed as standardization of SMILES "{smiles}" failed!')
|
||||
|
||||
modes = ['predict', 'build', 'incremental']
|
||||
if pw_mode not in modes:
|
||||
return error(request, "Pathway prediction failed!",
|
||||
f'Pathway prediction failed as received mode "{pw_mode}" is none of {modes}')
|
||||
|
||||
pw = Pathway.create(current_package, stand_smiles, name=name, description=description)
|
||||
# set mode
|
||||
@ -1185,10 +1240,10 @@ def package_pathways(request, package_uuid):
|
||||
return redirect(pw.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway/<id>
|
||||
@package_permission_required()
|
||||
def package_pathway(request, package_uuid, pathway_uuid):
|
||||
current_user: User = _anonymous_or_real(request)
|
||||
current_package: Package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1257,10 +1312,10 @@ def package_pathway(request, package_uuid, pathway_uuid):
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway/<id>/node
|
||||
@package_permission_required()
|
||||
def package_pathway_nodes(request, package_uuid, pathway_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1313,10 +1368,10 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
|
||||
return redirect(current_pathway.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway/<id>/node/<id>
|
||||
@package_permission_required()
|
||||
def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1361,10 +1416,10 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
|
||||
return redirect(current_pathway.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway/<id>/edge
|
||||
@package_permission_required()
|
||||
def package_pathway_edges(request, package_uuid, pathway_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1422,10 +1477,10 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
|
||||
return redirect(current_pathway.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/pathway/<id>/edge/<id>
|
||||
@package_permission_required()
|
||||
def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1440,7 +1495,8 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
|
||||
return HttpResponse(svg_data, content_type="image/svg+xml")
|
||||
|
||||
context = get_base_context(request)
|
||||
context['title'] = f'enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}'
|
||||
context[
|
||||
'title'] = f'enviPath - {current_package.name} - {current_pathway.name} - {current_edge.edge_label.name}'
|
||||
|
||||
context['meta']['current_package'] = current_package
|
||||
context['object_type'] = 'reaction'
|
||||
@ -1460,10 +1516,10 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
|
||||
return redirect(current_pathway.url)
|
||||
|
||||
else:
|
||||
return HttpResponseBadRequest()
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
# https://envipath.org/package/<id>/scenario
|
||||
@package_permission_required()
|
||||
def package_scenarios(request, package_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1497,8 +1553,11 @@ def package_scenarios(request, package_uuid):
|
||||
|
||||
return render(request, 'collections/objects_list.html', context)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', ])
|
||||
|
||||
# https://envipath.org/package/<id>/scenario/<id>
|
||||
|
||||
@package_permission_required()
|
||||
def package_scenario(request, package_uuid, scenario_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
@ -1516,6 +1575,9 @@ def package_scenario(request, package_uuid, scenario_uuid):
|
||||
|
||||
return render(request, 'objects/scenario.html', context)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', ])
|
||||
|
||||
|
||||
##############
|
||||
# User/Group #
|
||||
@ -1536,6 +1598,9 @@ def users(request):
|
||||
|
||||
return render(request, 'collections/objects_list.html', context)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET'])
|
||||
|
||||
|
||||
def user(request, user_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
@ -1546,6 +1611,8 @@ def user(request, user_uuid):
|
||||
if str(current_user.uuid) != user_uuid and not current_user.is_superuser:
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
user = UserManager.get_user_by_id(current_user, user_uuid)
|
||||
|
||||
context = get_base_context(request)
|
||||
context['title'] = f'enviPath - User'
|
||||
|
||||
@ -1556,7 +1623,7 @@ def user(request, user_uuid):
|
||||
{current_user.username: current_user.url}
|
||||
]
|
||||
|
||||
context['user'] = current_user
|
||||
context['user'] = user
|
||||
|
||||
model_qs = EPModel.objects.none()
|
||||
for p in PackageManager.get_all_readable_packages(current_user, include_reviewed=True):
|
||||
@ -1637,6 +1704,9 @@ def user(request, user_uuid):
|
||||
|
||||
return HttpResponseBadRequest()
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
def groups(request):
|
||||
current_user = _anonymous_or_real(request)
|
||||
@ -1663,6 +1733,9 @@ def groups(request):
|
||||
|
||||
return redirect(g.url)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
def group(request, group_uuid):
|
||||
current_user = _anonymous_or_real(request)
|
||||
@ -1681,9 +1754,8 @@ def group(request, group_uuid):
|
||||
|
||||
context['group'] = current_group
|
||||
|
||||
# TODO use managers
|
||||
context['users'] = get_user_model().objects.exclude(id__in=current_group.user_member.all())
|
||||
context['groups'] = Group.objects.exclude(id__in=current_group.group_member.all()).exclude(id=current_group.pk)
|
||||
context['users'] = UserManager.get_users_lp().exclude(id__in=current_group.user_member.all())
|
||||
context['groups'] = GroupManager.get_groups_lp().exclude(id__in=current_group.group_member.all()).exclude(id=current_group.pk)
|
||||
|
||||
context['packages'] = Package.objects.filter(
|
||||
id__in=GroupPackagePermission.objects.filter(group=current_group).values('package').distinct())
|
||||
@ -1716,6 +1788,9 @@ def group(request, group_uuid):
|
||||
|
||||
return redirect(current_group.url)
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
def settings(request):
|
||||
current_user = _anonymous_or_real(request)
|
||||
@ -1775,6 +1850,9 @@ def settings(request):
|
||||
|
||||
return HttpResponse("Success!")
|
||||
|
||||
else:
|
||||
return HttpResponseNotAllowed(['GET', 'POST'])
|
||||
|
||||
|
||||
def setting(request, setting_uuid):
|
||||
pass
|
||||
|
||||
Reference in New Issue
Block a user