Merge branch 'staging' into main

.github/workflows/pre-commit.yaml

@@ -20,11 +20,11 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pre-commit==3.3.3
+        python -m pip install --upgrade pre-commit==3.7.1
 
     - name: Run pre-commit
       run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -48,7 +48,8 @@ repos:
 
 # static type checking
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.7.0
+  rev: v1.10.0
   hooks:
   - id: mypy
+    args: [--config-file, pyproject.toml]
     additional_dependencies: [types-requests==2.25.9]

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-alpine3.19 as builder
+FROM python:3.12.3-alpine3.19 as builder
 
 LABEL maintainer="[email protected]"
 WORKDIR /app
@@ -32,7 +32,7 @@ RUN apk add --update --no-cache \
     curl
 
 # Install Poetry, change configs and install packages.
-RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.0 python3 - \
+RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.2 python3 - \
     && /root/.local/bin/poetry self add poetry-plugin-export \
     && /root/.local/bin/poetry config virtualenvs.create false \
     && /root/.local/bin/poetry config installer.max-workers 10 \
@@ -43,7 +43,7 @@ RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.0 python3 -
 
 FROM bitnami/kubectl:1.28.6 as kubectl
 FROM alpine/helm:3.14.0 as helm
-FROM python:3.8-alpine3.19 as runtime
+FROM python:3.12.3-alpine3.19 as runtime
 
 ARG DISABLE_EXTRAS=false
 
@@ -55,9 +55,9 @@ RUN apk add --update --no-cache \
     jpeg-dev \
     openjpeg-dev \
     libpng-dev \
-    && rm -rf /usr/local/lib/python3.8/site-packages/
+    && rm -rf /usr/local/lib/python3.12/site-packages/
 
-COPY --from=builder /usr/local/lib/python3.8/site-packages/ /usr/local/lib/python3.8/site-packages/
+COPY --from=builder /usr/local/lib/python3.12/site-packages/ /usr/local/lib/python3.12/site-packages/
 COPY --from=builder /usr/local/bin/ /usr/local/bin/
 COPY --from=kubectl /opt/bitnami/kubectl/bin/kubectl /usr/local/bin/
 COPY --from=helm /usr/bin/helm /usr/local/bin/

apps/controller.py

@@ -60,11 +60,59 @@ def deploy(options):
             try:
                 port = int(options["appconfig"]["port"])
             except Exception:
-                logger.error("Userid not a number.", exc_info=True)
+                logger.error("Port not a number.", exc_info=True)
                 return json.dumps({"status": "failed", "reason": "Port not an integer."})
             if port > 9999 or port < 3000:
                 logger.info("Port outside of allowed range.")
                 return json.dumps({"status": "failed", "reason": "Port outside of allowed range."})
+        # check if valid proxyheartbeatrate
+        if "proxyheartbeatrate" in options["appconfig"]:
+            try:
+                proxyheartbeatrate = int(options["appconfig"]["proxyheartbeatrate"])
+            except Exception:
+                logger.error("Proxy heartbeat rate not a number.", exc_info=True)
+                return json.dumps({"status": "failed", "reason": "Proxyheartbeatrate not an integer."})
+            if proxyheartbeatrate < 1:
+                logger.info("Heartbeat rate outside of allowed range, must be at least 1.")
+                return json.dumps(
+                    {"status": "failed", "reason": "Heartbeat rate outside of allowed range, must be at least 1."}
+                )
+        else:
+            options["appconfig"]["proxyheartbeatrate"] = "10000"
+        # check if valid proxyheartbeattimeout
+        if "proxyheartbeattimeout" in options["appconfig"]:
+            try:
+                proxyheartbeattimeout = int(options["appconfig"]["proxyheartbeattimeout"])
+            except Exception:
+                logger.error("Proxy heartbeat timeout not a number.", exc_info=True)
+                return json.dumps({"status": "failed", "reason": "Proxyheartbeattimeout not an integer."})
+            if proxyheartbeattimeout < -1 or proxyheartbeattimeout == 0:
+                logger.info("Heartbeat timeout outside of allowed range, cannot be lower than 0 except for -1.")
+                return json.dumps(
+                    {
+                        "status": "failed",
+                        "reason": "Heartbeat timeout outside of allowed range, , cannot be lower than 0 except for -1.",
+                    }
+                )
+        else:
+            options["appconfig"]["proxyheartbeattimeout"] = "60000"
+        # check if valid proxycontainerwaittime
+        if "proxycontainerwaittime" in options["appconfig"]:
+            try:
+                proxycontainerwaittime = int(options["appconfig"]["proxycontainerwaittime"])
+            except Exception:
+                logger.error("Proxy container wait time not a number.", exc_info=True)
+                return json.dumps({"status": "failed", "reason": "Proxycontainerwaittime not an integer."})
+            if proxycontainerwaittime < 20000:
+                logger.info("Proxy container wait time outside of allowed range, must be at least 20000.")
+                return json.dumps(
+                    {
+                        "status": "failed",
+                        "reason": "Proxycontainerwaittime outside of allowed range, must be at least 20000.",
+                    }
+                )
+        else:
+            options["appconfig"]["proxycontainerwaittime"] = "30000"
 
     # Save helm values file for internal reference
     unique_filename = "charts/values/{}-{}.yaml".format(str(uuid.uuid4()), str(options["app_name"]))

apps/helpers.py

@@ -216,6 +216,12 @@ def create_app_instance(user, project, app, app_settings, data=[], wait=False):
                     )
         if "userid" not in app_instance.parameters["appconfig"]:
             app_instance.parameters["appconfig"]["userid"] = "1000"
+        if "proxyheartbeatrate" not in app_instance.parameters["appconfig"]:
+            app_instance.parameters["appconfig"]["proxyheartbeatrate"] = "10000"
+        if "proxyheartbeattimeout" not in app_instance.parameters["appconfig"]:
+            app_instance.parameters["appconfig"]["proxyheartbeattimeout"] = "60000"
+        if "proxycontainerwaittime" not in app_instance.parameters["appconfig"]:
+            app_instance.parameters["appconfig"]["proxycontainerwaittime"] = "30000"
     app_instance.save()
     # Saving ReleaseName, status and setting up dependencies
     if rel_name_obj:

apps/views.py

@@ -215,8 +215,11 @@ def get(self, request, project, ai_id):
         existing_userid = None
         existing_path = None
         existing_source_code_url = appinstance.source_code_url
+        existing_proxyheartbeatrate = None
+        existing_proxyheartbeattimeout = None
+        existing_proxycontainerwaittime = None
 
-        # Settings for custom app
+        # Settings for custom app and shinyproxy
         if "appconfig" in appinstance.parameters:
             appconfig = appinstance.parameters["appconfig"]
             existing_userid = appconfig.get("userid", None)
@@ -227,6 +230,9 @@ def get(self, request, project, ai_id):
 
                 if not created_by_admin:
                     existing_path = existing_path.replace("/home/", "", 1)
+            existing_proxyheartbeatrate = appconfig.get("proxyheartbeatrate", None)
+            existing_proxyheartbeattimeout = appconfig.get("proxyheartbeattimeout", None)
+            existing_proxycontainerwaittime = appconfig.get("proxycontainerwaittime", None)
 
         app = appinstance.app
         do_display_description_field = app.category.name is not None and app.category.name.lower() == "serve"
@@ -271,6 +277,9 @@ def filter_func():
             "existing_app_release_name": existing_app_release_name,
             "existing_userid": existing_userid,
             "existing_source_code_url": existing_source_code_url,
+            "existing_proxyheartbeatrate": existing_proxyheartbeatrate,
+            "existing_proxyheartbeattimeout": existing_proxyheartbeattimeout,
+            "existing_proxycontainerwaittime": existing_proxycontainerwaittime,
         }
 
         return render(request, template, context)

collections_module/migrations/0001_initial.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.7 on 2024-03-20 15:02
 
+import django.db.models.deletion
 from django.conf import settings
 from django.db import migrations, models
-import django.db.models.deletion
 
 
 class Migration(migrations.Migration):

common/forms.py

@@ -32,7 +32,7 @@
 EMAIL_ALLOW_REGEX = re.compile(
     (
         r"^(?:(?!\b(?:student|stud)\b\.)[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)*?"  # Subdomain part
-        + f"({('|').join([l[0] for l in UNIVERSITIES if l[0] != 'other'])}"
+        + f"({('|').join([u[0] for u in UNIVERSITIES if u[0] != 'other'])}"
         + r")\.se"  # End of the domain
     ),
     re.IGNORECASE,

common/migrations/0001_initial.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.5 on 2023-11-16 08:07
 
+import django.db.models.deletion
 from django.conf import settings
 from django.db import migrations, models
-import django.db.models.deletion
 
 
 class Migration(migrations.Migration):

common/migrations/0002_emailverificationtable.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.5 on 2023-11-24 13:27
 
+import django.db.models.deletion
 from django.conf import settings
 from django.db import migrations, models
-import django.db.models.deletion
 
 
 class Migration(migrations.Migration):

common/tasks.py

@@ -19,7 +19,7 @@
 
 
 @app.task
-def handle_deleted_users():
+def handle_deleted_users() -> None:
     """
     Handles deleted user accounts.
 
@@ -65,7 +65,7 @@ def handle_deleted_users():
 
 
 @app.task
-def alert_pause_dormant_users():
+def alert_pause_dormant_users() -> None:
     """
     Handles dormant user accounts.
     The term dormant is used rather than inactive because of the overuse of the term inactive.
@@ -152,8 +152,7 @@ def alert_pause_dormant_users():
 
 
 @app.task(ignore_result=True)
-def send_email_task(subject, message, html_message, recipient_list):
-    logger.info("Sending email to %s", recipient_list)
+def send_email_task(subject: str, message: str, html_message: str | None, recipient_list: list[str]) -> None:
     send_mail(
         subject,
         message,
@@ -164,7 +163,7 @@ def send_email_task(subject, message, html_message, recipient_list):
     )
 
 
-def send_verification_email_task(email, token):
+def send_verification_email_task(email: str, token: str) -> None:
     html_message = render_to_string(
         "registration/verify_email.html",
         {

common/views.py

@@ -1,5 +1,6 @@
 from django.conf import settings
 from django.contrib import messages
+from django.contrib.auth import authenticate, login, logout
 from django.core.mail import send_mail
 from django.db import transaction
 from django.http.response import HttpResponseRedirect
@@ -21,8 +22,6 @@ class RegistrationCompleteView(TemplateView):
 
 
 # Sign Up View
-
-
 class SignUpView(CreateView):
     """
     View for user registration

cypress/e2e/ui-tests/test-brute-force-login-attempts.cy.js

@@ -37,7 +37,8 @@ describe("Test brute force login attempts are blocked", () => {
 
         // Sign out before logging in again
         cy.log("Sign out before logging in again")
-        cy.visit("accounts/logout/")
+        cy.get('button.btn-profile').click()
+        cy.get('li.btn-group').find('button').contains("Sign out").click()
         cy.get("title").should("have.text", "Logout | SciLifeLab Serve (beta)")
 
         // Repeatedly perform failing login attempts

docker-compose.yaml

@@ -1,5 +1,3 @@
-version: '3'
-
 services:
   db:
     container_name: db

fixtures/apps_fixtures.json

@@ -688,7 +688,7 @@
   {
     "fields": {
       "category": "serve",
-      "chart": "ghcr.io/scilifelabdatacentre/serve-charts/shinyproxy:1.0.0",
+      "chart": "ghcr.io/scilifelabdatacentre/serve-charts/shinyproxy:1.1.0",
       "created_on": "2023-08-25T21:34:37.815Z",
       "description": "",
       "logo": "shinyapp-logo.svg",
@@ -708,6 +708,21 @@
             "default": "3838",
             "title": "Port",
             "type": "number"
+          },
+          "proxyheartbeatrate": {
+            "default": "10000",
+            "title": "Proxy heartbeat rate",
+            "type": "number"
+          },
+          "proxyheartbeattimeout": {
+            "default": "60000",
+            "title": "Proxy heartbeat timeout",
+            "type": "number"
+          },
+          "proxycontainerwaittime": {
+            "default": "30000",
+            "title": "Proxy container wait time",
+            "type": "number"
           }
         },
         "default_values": {

manage.py

@@ -4,7 +4,7 @@
 import sys
 
 
-def main():
+def main() -> None:
     """Run administrative tasks."""
     os.environ.setdefault("DJANGO_SETTINGS_MODULE", "studio.settings")
     try:

monitor/dash_demo.py

@@ -1,7 +1,7 @@
 import dash_bootstrap_components as dbc
 import dash_core_components as dcc
 import dash_html_components as html
-import requests  # type: ignore
+import requests
 from dash.dependencies import Input, Output
 from dash.exceptions import PreventUpdate
 from django_plotly_dash import DjangoDash

news/views.py

@@ -1,10 +1,13 @@
+from typing import Any
+
 import markdown
+from django.http import HttpRequest, HttpResponse
 from django.shortcuts import render
 
 from .models import NewsObject
 
 
-def news(request):
+def news(request: HttpRequest) -> HttpResponse:
     news_objects = NewsObject.objects.all().order_by("-created_on")
     for news in news_objects:
         news.body_html = markdown.markdown(news.body)