[Bugfix] Added Missing Paper in Cite Modal (#87 )

Fixes #77 Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#87
[Feature] Move Login exempt urls to settings (#86 )
2025-09-05 08:21:46 +12:00 · 2025-09-05 08:04:20 +12:00 · 2025-09-05 07:59:14 +12:00 · 2025-09-05 06:50:16 +12:00
9 changed files with 211 additions and 8 deletions
--- a/envipath/settings.py
+++ b/envipath/settings.py
@ -43,6 +43,7 @@ INSTALLED_APPS = [
    'django.contrib.staticfiles',
    # 3rd party
    'django_extensions',
+    'oauth2_provider',
    # Custom
    'epdb',
    'migration',
@ -60,8 +61,13 @@ MIDDLEWARE = [
    'django.contrib.auth.middleware.AuthenticationMiddleware',
    'django.contrib.messages.middleware.MessageMiddleware',
    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+    'oauth2_provider.middleware.OAuth2TokenMiddleware',
 ]

+OAUTH2_PROVIDER = {
+    "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
+}
+
 if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
    MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')

@ -335,3 +341,9 @@ FLAGS = {
    'ENVIFORMER': ENVIFORMER_PRESENT,
    'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
 }
+
+LOGIN_EXEMPT_URLS = [
+    '/api/legacy/',
+    '/o/token/',
+    '/o/userinfo/',
+]
--- a/envipath/urls.py
+++ b/envipath/urls.py
@ -25,4 +25,5 @@ urlpatterns = [
    path("admin/", admin.site.urls),
    path("api/v1/", api_v1.urls),
    path("api/legacy/", api_legacy.urls),
+    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
--- a/epdb/middleware/login_required_middleware.py
+++ b/epdb/middleware/login_required_middleware.py
@ -1,6 +1,7 @@
 from django.conf import settings
 from django.shortcuts import redirect
 from django.urls import reverse
+from urllib.parse import quote

 class LoginRequiredMiddleware:
    def __init__(self, get_response):
@ -10,12 +11,14 @@ class LoginRequiredMiddleware:
                               reverse('logout'),
                               reverse('admin:login'),
                               reverse('admin:index'),
-                               '/api/legacy/'
                           ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])

    def __call__(self, request):
        if not request.user.is_authenticated:
            path = request.path_info
            if not any(path.startswith(url) for url in self.exempt_urls):
+                if request.method == 'GET':
+                    if request.get_full_path() and request.get_full_path() != '/':
+                        return redirect(f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}")
                return redirect(settings.LOGIN_URL)
        return self.get_response(request)
--- a/epdb/urls.py
+++ b/epdb/urls.py
@ -76,5 +76,7 @@ urlpatterns = [
    re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
    re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),

-    re_path(r'^depict$', v.depict, name='depict')
+    re_path(r'^depict$', v.depict, name='depict'),
+
+    path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
 ]
--- a/epdb/views.py
+++ b/epdb/views.py
@ -8,6 +8,7 @@ from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, Http
 from django.shortcuts import render, redirect
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
+from oauth2_provider.decorators import protected_resource

 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
@ -46,6 +47,7 @@ def login(request):

    if request.method == 'GET':
        context['title'] = 'enviPath'
+        context['next'] = request.GET.get('next', '')
        return render(request, 'login.html', context)

    elif request.method == 'POST':
@ -59,7 +61,7 @@ def login(request):
            username = request.POST.get('username')
            password = request.POST.get('password')

-            # Get email for username and check if account is active
+            # Get email for username and check if the account is active
            try:
                temp_user = get_user_model().objects.get(username=username)

@ -79,6 +81,10 @@ def login(request):

            if user is not None:
                login(request, user)
+
+                if next := request.POST.get('next'):
+                    return redirect(next)
+
                return redirect(s.SERVER_URL)
            else:
                context['message'] = "Login failed!"
@ -2213,3 +2219,16 @@ def depict(request):
        return HttpResponse(IndigoUtils.smirks_to_svg(smirks, query_smirks), content_type='image/svg+xml')
    else:
        return HttpResponseBadRequest()
+
+
+@protected_resource()
+def userinfo(request):
+    user = request.resource_owner
+    res = {
+        "sub": str(user.uuid),
+        "email": user.email,
+        "username": user.username,
+        "name": user.get_full_name() or user.username,
+        "email_verified": user.is_active,
+    }
+    return JsonResponse(res)
--- a/pyproject.toml
+++ b/pyproject.toml
@ -10,6 +10,7 @@ dependencies = [
    "django-extensions>=4.1",
    "django-model-utils>=5.0.0",
    "django-ninja>=1.4.1",
+    "django-oauth-toolkit>=3.0.1",
    "django-polymorphic>=4.1.0",
    "enviformer",
    "envipy-additional-information",
--- a/templates/login.html
+++ b/templates/login.html
@ -124,6 +124,7 @@
                                        </button>
                                    </div>
                                </div>
+                                <input type="hidden" name="next" value="{{ next }}" />
                            </fieldset>
                        </form>
                    </div>
--- a/templates/modals/cite_modal.html
+++ b/templates/modals/cite_modal.html
@ -3,13 +3,25 @@
    <div class="modal-dialog modal-lg">
        <div class="modal-content">
            <div class="modal-header">
-                <h4>How to cite enviPath</h4>
+                <h3>How to cite enviPath</h3>
            </div>
            <div class="modal-body">
-                <p>
-                    enviPath–The environmental contaminant biotransformation pathway resource. J Wicker, T Lorsbach, M
-                    Gütlein, E Schmid, D Latino, S Kramer, K Fenner. Nucleic Acids Research, gkv1229
-                </p>
+                <ol class="list-group list-group-numbered">
+                    <li class="list-group-item">
+                        Hafner, J., Lorsbach, T., Schmidt, S. <em>et al.</em>
+                        <cite>Advancements in biotransformation pathway prediction: enhancements, datasets, and novel
+                            functionalities in enviPath.</cite>
+                        <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank">J Cheminform 16, 93
+                            (2024)</a>
+                    </li>
+                    <li class="list-group-item">
+                        Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., Fenner, K.
+                        <cite>enviPath - The environmental contaminant biotransformation pathway resource</cite>
+                        <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank">
+                            Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D502-D508
+                        </a>
+                    </li>
+                </ol>
            </div>
            <div class="modal-footer">
                <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
--- a/uv.lock
+++ b/uv.lock
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    { name = "django-ninja" },
+    { name = "django-oauth-toolkit" },
    { name = "django-polymorphic" },
    { name = "enviformer" },
    { name = "envipy-additional-information" },
@ -424,6 +544,7 @@ requires-dist = [
    { name = "django-extensions", specifier = ">=4.1" },
    { name = "django-model-utils", specifier = ">=5.0.0" },
    { name = "django-ninja", specifier = ">=1.4.1" },
+    { name = "django-oauth-toolkit", specifier = ">=3.0.1" },
    { name = "django-polymorphic", specifier = ">=4.1.0" },
    { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.0" },
    { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?rev=v0.1.4" },
@ -625,6 +746,19 @@ wheels = [
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 ]

+[[package]]
+name = "jwcrypto"
+version = "1.5.6"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "cryptography" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/e1/db/870e5d5fb311b0bcf049630b5ba3abca2d339fd5e13ba175b4c13b456d08/jwcrypto-1.5.6.tar.gz", hash = "sha256:771a87762a0c081ae6166958a954f80848820b2ab066937dc8b8379d65b1b039", size = 87168 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/cd/58/4a1880ea64032185e9ae9f63940c9327c6952d5584ea544a8f66972f2fda/jwcrypto-1.5.6-py3-none-any.whl", hash = "sha256:150d2b0ebbdb8f40b77f543fb44ffd2baeff48788be71f67f03566692fd55789", size = 92520 },
+]
+
 [[package]]
 name = "kombu"
 version = "5.5.3"
@ -1042,6 +1176,15 @@ wheels = [
    { url = "https://files.pythonhosted.org/packages/9e/4e/0d0c945463719429b7bd21dece907ad0bde437a2ff12b9b12fee94722ab0/nvidia_nvtx_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl", hash = "sha256:6574241a3ec5fdc9334353ab8c479fe75841dbe8f4532a8fc97ce63503330ba1", size = 89265 },
 ]

+[[package]]
+name = "oauthlib"
+version = "3.3.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/0b/5f/19930f824ffeb0ad4372da4812c50edbd1434f678c90c2733e1188edfc63/oauthlib-3.3.1.tar.gz", hash = "sha256:0f0f8aa759826a193cf66c12ea1af1637f87b9b4622d46e866952bb022e538c9", size = 185918 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/be/9c/92789c596b8df838baa98fa71844d84283302f7604ed565dafe5a6b5041a/oauthlib-3.3.1-py3-none-any.whl", hash = "sha256:88119c938d2b8fb88561af5f6ee0eec8cc8d552b7bb1f712743136eb7523b7a1", size = 160065 },
+]
+
 [[package]]
 name = "packaging"
 version = "25.0"
@ -1284,6 +1427,15 @@ wheels = [
    { url = "https://files.pythonhosted.org/packages/08/50/d13ea0a054189ae1bc21af1d85b6f8bb9bbc5572991055d70ad9006fe2d6/psycopg2_binary-2.9.10-cp313-cp313-win_amd64.whl", hash = "sha256:27422aa5f11fbcd9b18da48373eb67081243662f9b46e6fd07c3eb46e4535142", size = 2569224 },
 ]

+[[package]]
+name = "pycparser"
+version = "2.22"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/1d/b2/31537cf4b1ca988837256c910a668b553fceb8f069bedc4b1c826024b52c/pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6", size = 172736 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/13/a3/a812df4e2dd5696d1f351d58b8fe16a405b234ad2886a0dab9183fb78109/pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc", size = 117552 },
+]
+
 [[package]]
 name = "pydantic"
 version = "2.11.7"
Author	SHA1	Message	Date
jebus	a16035677c	[Bugfix] Added Missing Paper in Cite Modal (#87 ) Fixes #77 Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#87	2025-09-05 08:21:46 +12:00
jebus	498a53ab3d	[Feature] Move Login exempt urls to settings (#86 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#86	2025-09-05 08:04:20 +12:00
jebus	aa3b53e94b	[Bugfix] Login required exempts auth for SSO Flow (#85 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#85	2025-09-05 07:59:14 +12:00
jebus	3c8f0e80cb	[Feature] OAuth2 Provider (#84 ) Fixes #74 Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#84	2025-09-05 06:50:16 +12:00