diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml index 8ef3cea2d..266633635 100644 --- a/.github/workflows/pre-commit.yaml +++ b/.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 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 303fa1b57..7d6045e05 100644 --- a/.pre-commit-config.yaml +++ b/.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] diff --git a/Dockerfile b/Dockerfile index f9d8052dc..f5655514d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.8-alpine3.19 as builder +FROM python:3.12.3-alpine3.19 as builder LABEL maintainer="serve@scilifelab.se" 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/ diff --git a/apps/controller.py b/apps/controller.py index 2e405bfe9..74ce0ae0e 100644 --- a/apps/controller.py +++ b/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"])) diff --git a/apps/helpers.py b/apps/helpers.py index 8ce274830..6c4803b85 100644 --- a/apps/helpers.py +++ b/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: diff --git a/apps/views.py b/apps/views.py index 4b592c718..d822eb441 100644 --- a/apps/views.py +++ b/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) diff --git a/collections_module/migrations/0001_initial.py b/collections_module/migrations/0001_initial.py index b149c73e5..a56c4ae28 100644 --- a/collections_module/migrations/0001_initial.py +++ b/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): diff --git a/common/forms.py b/common/forms.py index b5cb2dc10..d55d964d9 100644 --- a/common/forms.py +++ b/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, diff --git a/common/migrations/0001_initial.py b/common/migrations/0001_initial.py index 51492b31a..05cd958db 100644 --- a/common/migrations/0001_initial.py +++ b/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): diff --git a/common/migrations/0002_emailverificationtable.py b/common/migrations/0002_emailverificationtable.py index f6a795375..5cbf987f0 100644 --- a/common/migrations/0002_emailverificationtable.py +++ b/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): diff --git a/common/tasks.py b/common/tasks.py index 623299ced..7be42567f 100644 --- a/common/tasks.py +++ b/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", { diff --git a/common/views.py b/common/views.py index 0dcc26827..cc78da74f 100644 --- a/common/views.py +++ b/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 diff --git a/cypress/e2e/ui-tests/test-brute-force-login-attempts.cy.js b/cypress/e2e/ui-tests/test-brute-force-login-attempts.cy.js index 62a71c208..2d984222c 100644 --- a/cypress/e2e/ui-tests/test-brute-force-login-attempts.cy.js +++ b/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 diff --git a/docker-compose.yaml b/docker-compose.yaml index 173fe2dba..499545f9b 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,5 +1,3 @@ -version: '3' - services: db: container_name: db diff --git a/fixtures/apps_fixtures.json b/fixtures/apps_fixtures.json index 39310bcb6..2a10a45ae 100644 --- a/fixtures/apps_fixtures.json +++ b/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": { diff --git a/manage.py b/manage.py index 6e9b2fc4e..9ad565ba4 100755 --- a/manage.py +++ b/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: diff --git a/monitor/dash_demo.py b/monitor/dash_demo.py index f63e9890a..05e9b1572 100644 --- a/monitor/dash_demo.py +++ b/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 diff --git a/news/views.py b/news/views.py index bc7cf222e..81c310cd6 100644 --- a/news/views.py +++ b/news/views.py @@ -1,10 +1,13 @@ +from typing import Any + import markdown +from 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= ">=3.2,<5.1" +django-mptt = ">=0.13,<0.17" +django-nyt = ">=1.4,<1.5" django-sekizai = ">=0.10" -markdown = ">=3.3,<3.4" +markdown = ">=3.4,<3.7" pillow = "*" +pymdown-extensions = ">=10.5,<10.6" sorl-thumbnail = ">=12.8,<13" [package.extras] -docs = ["bleach (>=6,<7)", "django (>=3.1.13)", "sphinx (>=6,<8)", "sphinx-rtd-theme (==1.2.0)"] +docs = ["sphinx (>=6,<8)", "sphinx-rtd-theme (==2.0.0)"] [[package]] name = "wrapt" @@ -3977,26 +3883,11 @@ files = [ idna = ">=2.0" multidict = ">=4.0" -[[package]] -name = "zipp" -version = "3.18.1" -description = "Backport of pathlib-compatible object wrapper for zip files" -optional = false -python-versions = ">=3.8" -files = [ - {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] - [extras] linters = ["black", "flake8", "isort", "mypy"] tests = ["hypothesis", "moto", "pytest", "pytest-cov", "pytest-django", "pytest-xdist"] [metadata] lock-version = "2.0" -python-versions = "^3.8.10" -content-hash = "926725cf6a1580a0bf6d0c028804ea28d57ac04101a0fc9dd24d912975e647da" +python-versions = "^3.10.0" +content-hash = "302cd2db53228e09bfa677d5e4149fdfc4afb20ca005ffae17a4683a32f826ab" diff --git a/projects/models.py b/projects/models.py index 64d803d9c..1ccd0ca65 100644 --- a/projects/models.py +++ b/projects/models.py @@ -160,7 +160,9 @@ def create_project(self, name, owner, description, status="active", project_temp key = self.generate_passkey() letters = string.ascii_lowercase secret = self.generate_passkey(40) - slug = slugify(name) + slug = slugify(name[:47]) + if len(slug) < 3: + slug = "".join(random.choice(letters) for i in range(3)) slug_extension = "".join(random.choice(letters) for i in range(3)) slug = "{}-{}".format(slugify(slug), slug_extension) diff --git a/projects/urls.py b/projects/urls.py index 6af75800c..21496c44f 100644 --- a/projects/urls.py +++ b/projects/urls.py @@ -49,11 +49,6 @@ UpdatePatternView.as_view(), name="update_pattern", ), - path( - "/project/publish/", - views.publish_project, - name="publish_project", - ), path( "/project/access/grant/", GrantAccessToProjectView.as_view(), diff --git a/projects/views.py b/projects/views.py index 5af8b9933..52379ae50 100644 --- a/projects/views.py +++ b/projects/views.py @@ -159,15 +159,17 @@ def change_description(request, project_slug): description = request.POST.get("description", "") if description != "": project.description = description - project.save() + else: + project.description = None + project.save() - log = ProjectLog( - project=project, - module="PR", - headline="Project description", - description="Changed description for project", - ) - log.save() + log = ProjectLog( + project=project, + module="PR", + headline="Project description", + description="Changed description for project", + ) + log.save() return HttpResponseRedirect( reverse( @@ -633,58 +635,3 @@ def delete(request, project_slug): delete_project.delay(project.pk) return HttpResponseRedirect(next_page, {"message": "Deleted project successfully."}) - - -@login_required -@permission_required_or_403("can_view_project", (Project, "slug", "project_slug")) -def publish_project(request, project_slug): - owner = User.objects.filter(username=request.user).first() - project = Project.objects.filter(owner=owner, slug=project_slug).first() - - if request.method == "POST": - gh_form = PublishProjectToGitHub(request.POST) - - if gh_form.is_valid(): - user_name = gh_form.cleaned_data["user_name"] - user_password = gh_form.cleaned_data["user_password"] - - user_password_bytes = user_password.encode("ascii") - base64_bytes = base64.b64encode(user_password_bytes) - user_password_encoded = base64_bytes.decode("ascii") - - url = "http://{}-file-controller/project/{}/push/{}/{}".format( - project_slug, - project_slug[:-4], - user_name, - user_password_encoded, - ) - try: - response = r.get(url) - - if response.status_code == 200 or response.status_code == 203: - payload = response.json() - - if payload["status"] == "OK": - clone_url = payload["clone_url"] - if clone_url: - project.clone_url = clone_url - project.save() - - log = ProjectLog( - project=project, - module="PR", - headline="GitHub repository", - description=("Published project files" " to a GitHub repository {url}").format( - url=project.clone_url - ), - ) - log.save() - except Exception as e: - logger.error("Failed to get response from {} with error: {}".format(url, e)) - - return HttpResponseRedirect( - reverse( - "projects:settings", - kwargs={"project_slug": project_slug}, - ) - ) diff --git a/pyproject.toml b/pyproject.toml index 445fd45d5..8609df636 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,23 +13,24 @@ authors = ["Team Whale ",] homepage = "https://serve.scilifelab.se" repository = "https://github.com/ScilifelabDataCentre/stackn" keywords = ["machine learning", "life science", "research", "django", "python"] +packages = [] [tool.poetry.dependencies] -python = "^3.8.10" +python = "^3.10.0" -django = "==4.2.7" -django-celery-beat = "==2.5.0" +django = "==5.0.2" +django-celery-beat = "==2.6.0" django-compressor = "==4.4" django-cors-headers = "==4.3.1" django-extensions = "==3.2.3" -django-filter = "==23.3" +django-filter = "==24.2" django-tagulous = "==1.3.3" django-guardian = "==2.4.0" -djangorestframework = "==3.14.0" -django-crispy-forms = "==2.0" +djangorestframework = "== 3.15.1" +django-crispy-forms = "==2.1" # django-wiki -wiki = "==0.10" +wiki = "==0.11.1" # Other Python and project-related libraries @@ -45,12 +46,11 @@ minio = "==7.1.17" celery = "==5.3.4" uvicorn = "==0.20.0" flask-cors = "==4.0.0" -tomli = "==2.0.1" Pillow = "10.2.0" flatten-json = "==0.1.13" PyYAML = "==6.0.1" -Markdown = ">=3.3,<3.4" +Markdown = ">=3.4,<3.6" # Logging django-structlog = "^7.1.0" @@ -60,7 +60,8 @@ colorlog = "^6.8.2" black = { version = "==23.3.0", optional = true } isort = { version = "==5.12.0", optional = true } flake8 = { version = "==6.0.0", optional = true } -mypy = { version = "==1.4.1", optional = true } +mypy = { version = "==1.10.0", optional = true } +#django-stubs = { version = "==5.0.0", optional = true } hypothesis = { version = "==6.86.1", optional = true } moto = { version = "==4.*", extras = ["ec2", "s3", "all"], optional = true } pytest = { version = "~8.0.1", optional = true } @@ -90,7 +91,7 @@ profile = 'black' [tool.black] line-length = 120 -target-version = ['py38'] +target-version = ['py311'] include = '\.pyi?$' extend-exclude = ''' /( @@ -104,25 +105,90 @@ extend-exclude = ''' [tool.mypy] strict = false -python_version = "3.8" -ignore_missing_imports = true +python_version = "3.12" +disallow_subclassing_any = false +ignore_missing_imports = false warn_return_any = true +untyped_calls_exclude = ["apps.helpers","projects.models"] exclude = ["venv", ".venv", "examples"] +#plugins = ["mypy_django_plugin.main"] + +#[tool.django-stubs] +#django_settings_module = "studio.settings" + +[[tool.mypy.overrides]] +module = "studio.*" +strict = true +disallow_subclassing_any = false +disallow_untyped_decorators = false +follow_imports_for_stubs = false + +[[tool.mypy.overrides]] +module = "*.models" +strict = false +check_untyped_defs = false +disallow_incomplete_defs = false +disallow_subclassing_any = false +disallow_untyped_decorators = false +disallow_untyped_defs = false + +[[tool.mypy.overrides]] +module = [ + "*.tests.*", + "*.tests", + "conftest", + "cypress.*" +] +check_untyped_defs = false +disallow_incomplete_defs = false +disallow_subclassing_any = false +disallow_untyped_calls = false +disallow_untyped_decorators = false +disallow_untyped_defs = false [[tool.mypy.overrides]] module = "*.migrations.*" ignore_errors = true +# A temporary section to ease the transition of mypy into the codebase +[[tool.mypy.overrides]] +module = [ + "api.*", + "apps.*", + "collections_module.*", + "common.*", + "customtags.*", + "models.*", + "monitor.*", + "news.*", + "portal.*", + "projects.*", + "scripts.*", +] +strict = false +check_untyped_defs = false +disallow_incomplete_defs = false +disallow_subclassing_any = false +disallow_untyped_calls = false +disallow_untyped_decorators = false +disallow_untyped_defs = false +no_implicit_reexport = false + [[tool.mypy.overrides]] module = [ + "boto3.*", + "colorlog.*", "django.*", + "django_structlog.*", "rest_framework.*", "flatten_json.*", "guardian.*", + "hypothesis.*", "django_filters.*", "rest_framework_nested.*", "tagulous.*", "minio.*", + "moto.*", "celery.*", "dash.*", "dash_core_components.*", @@ -130,10 +196,12 @@ module = [ "django_plotly_dash.*", "dash_bootstrap_components.*", "markdown.*", + "pytest.*", "pytz.*", "requests.*", "s3fs.*", "setuptools.*", + "structlog.*", "yaml.*", ] ignore_missing_imports = true diff --git a/studio/celery.py b/studio/celery.py index 1097b65c2..6bbac233d 100644 --- a/studio/celery.py +++ b/studio/celery.py @@ -16,7 +16,7 @@ @setup_logging.connect -def config_loggers(*args, **kwargs): +def config_loggers(*args: object, **kwargs: object) -> None: logger_config = settings.LOGGING dictConfig(logger_config) diff --git a/studio/helpers.py b/studio/helpers.py index 64928b684..c19f15ca6 100644 --- a/studio/helpers.py +++ b/studio/helpers.py @@ -6,7 +6,7 @@ from common.models import EmailVerificationTable -def do_delete_account(user_id): +def do_delete_account(user_id: int) -> bool: """ Deletes a user account. Sets user.is_active = False and userprofile.deleted_on to now. @@ -29,7 +29,7 @@ def do_delete_account(user_id): return user_account_deleted -def do_pause_account(user_id): +def do_pause_account(user_id: int) -> bool: """ Sets a user account to pause (on hold). Sets user.is_active = False and deletes the user verification token if it exists. diff --git a/studio/middleware.py b/studio/middleware.py index b0cec85a8..401e7264b 100644 --- a/studio/middleware.py +++ b/studio/middleware.py @@ -1,6 +1,9 @@ import logging import sys import traceback +from typing import Any, Callable + +from django.http import HttpRequest, HttpResponse from studio.utils import get_logger @@ -12,14 +15,14 @@ class ExceptionLoggingMiddleware: This middleware provides logging of exception in requests. """ - def __init__(self, get_response): + def __init__(self, get_response: Callable[[HttpRequest], Any]): self.get_response = get_response - def __call__(self, request): + def __call__(self, request: HttpRequest) -> HttpResponse: response = self.get_response(request) return response - def process_exception(self, request, exception): + def process_exception(self, request: HttpRequest, exception: Exception) -> None: """ Processes exceptions during handling of a http request. Logs them with ERROR level. diff --git a/studio/migrations/apps/0001_initial.py b/studio/migrations/apps/0001_initial.py index d386594c8..3d8fee336 100644 --- a/studio/migrations/apps/0001_initial.py +++ b/studio/migrations/apps/0001_initial.py @@ -1,8 +1,8 @@ # Generated by Django 4.2.5 on 2023-11-16 08:07 -from django.db import migrations, models import django.db.models.deletion import tagulous.models.models +from django.db import migrations, models class Migration(migrations.Migration): diff --git a/studio/migrations/apps/0002_initial.py b/studio/migrations/apps/0002_initial.py index 7255e80a9..ea26d718d 100644 --- a/studio/migrations/apps/0002_initial.py +++ b/studio/migrations/apps/0002_initial.py @@ -1,9 +1,9 @@ # Generated by Django 4.2.5 on 2023-11-16 08:07 -from django.conf import settings -from django.db import migrations, models import django.db.models.deletion import tagulous.models.fields +from django.conf import settings +from django.db import migrations, models class Migration(migrations.Migration): diff --git a/studio/migrations/models/0001_initial.py b/studio/migrations/models/0001_initial.py index 12db5195b..eafcdc77d 100644 --- a/studio/migrations/models/0001_initial.py +++ b/studio/migrations/models/0001_initial.py @@ -1,10 +1,10 @@ # Generated by Django 4.2.5 on 2023-11-16 08:07 -from django.db import migrations, models import django.db.models.deletion import django.db.models.manager import tagulous.models.fields import tagulous.models.models +from django.db import migrations, models class Migration(migrations.Migration): diff --git a/studio/migrations/portal/0001_initial.py b/studio/migrations/portal/0001_initial.py index 35089d371..c5a7bf597 100644 --- a/studio/migrations/portal/0001_initial.py +++ b/studio/migrations/portal/0001_initial.py @@ -1,7 +1,7 @@ # Generated by Django 4.2.5 on 2023-11-16 08:07 -from django.db import migrations, models import django.db.models.deletion +from django.db import migrations, models class Migration(migrations.Migration): diff --git a/studio/migrations/projects/0001_initial.py b/studio/migrations/projects/0001_initial.py index 377de0f17..9de409fe9 100644 --- a/studio/migrations/projects/0001_initial.py +++ b/studio/migrations/projects/0001_initial.py @@ -1,8 +1,9 @@ # 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 + import projects.models diff --git a/studio/migrations/projects/0002_project_project_template.py b/studio/migrations/projects/0002_project_project_template.py index 8a6ed94b4..5661af68b 100644 --- a/studio/migrations/projects/0002_project_project_template.py +++ b/studio/migrations/projects/0002_project_project_template.py @@ -1,7 +1,7 @@ # Generated by Django 4.2.7 on 2024-02-23 13:16 -from django.db import migrations, models import django.db.models.deletion +from django.db import migrations, models class Migration(migrations.Migration): diff --git a/studio/settings.py b/studio/settings.py index 8ed9d3ce7..9facb24b7 100644 --- a/studio/settings.py +++ b/studio/settings.py @@ -278,9 +278,6 @@ USE_I18N = True -USE_L10N = True - -USE_TZ = True # Media Files for Studio apps MEDIA_URL = "/media/" diff --git a/studio/singleton.py b/studio/singleton.py index b4818557b..75a637327 100644 --- a/studio/singleton.py +++ b/studio/singleton.py @@ -1,4 +1,4 @@ -from typing import Dict +from typing import Any, Dict, Type class Singleton(type): @@ -7,9 +7,9 @@ class Singleton(type): Usage: ClassName(metaclass=Singleton) """ - _instances: Dict[type, object] = {} + _instances: Dict[Type[type], object] = {} - def __call__(cls, *args, **kwargs): + def __call__(cls: Any, *args: Any, **kwargs: Any) -> Any: if cls not in cls._instances: cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs) return cls._instances[cls] diff --git a/studio/system_version.py b/studio/system_version.py index 45dbd9097..9133b59e6 100644 --- a/studio/system_version.py +++ b/studio/system_version.py @@ -3,10 +3,9 @@ This singleton class would be appropriate to add to a cache and kept in memory. """ -# Using tomli library. When python>=3.11 then can instead use importlib.metadata import pathlib - -import tomli +import tomllib +from typing import Any from .singleton import Singleton from .utils import get_logger @@ -25,50 +24,50 @@ class SystemVersion(metaclass=Singleton): __pyproject_is_parsed = False __init_counter = 0 - def __init__(self, *args, **kwargs): + def __init__(self, *args: Any, **kwargs: Any): self.__init_counter += 1 self.__set_values_from_toml() - def get_version_text(self): + def get_version_text(self) -> str: """Gets a formatted text of the deployed system in format (v0.0.0).""" if self.__build_date == "" or self.__gitref == "": return "unset" return f"{self.__build_date} ({self.__gitref})" - def get_build_date(self): + def get_build_date(self) -> str | None: """Gets the deployed system build date.""" return self.__build_date - def get_gitref(self): + def get_gitref(self) -> str | None: """Gets the deployed system git reference, e.g. develop or v1.0.0.""" return self.__gitref - def get_imagetag(self): + def get_imagetag(self) -> str | None: """Gets the deployed image tag as e.g. main-20230912""" return self.__imagetag - def get_debug_info(self): + def get_debug_info(self) -> str: debug_info = f"toml has been parsed:{self.__pyproject_is_parsed}, init:{self.__init_counter}" return debug_info - def get_init_counter(self): + def get_init_counter(self) -> int: return self.__init_counter - def get_pyproject_is_parsed(self): + def get_pyproject_is_parsed(self) -> bool: return self.__pyproject_is_parsed - def __set_values_from_toml(self): + def __set_values_from_toml(self) -> None: err_message = "" try: proj_path = pathlib.Path(__file__).parents[1] / "pyproject.toml" with open(proj_path, "rb") as f: - toml_dict = tomli.load(f) + toml_dict = tomllib.load(f) self.__build_date = toml_dict["tool"].get("serve").get("build-date") self.__gitref = toml_dict["tool"].get("serve").get("gitref") self.__imagetag = toml_dict["tool"].get("serve").get("imagetag") self.__pyproject_is_parsed = True return - except tomli.TOMLDecodeError: + except tomllib.TOMLDecodeError: logger.error("Unable to parse pyproject.toml file. The toml file is invalid.") err_message = "parsing error" except Exception as e: diff --git a/studio/utils.py b/studio/utils.py index e936a4638..701c43aa2 100644 --- a/studio/utils.py +++ b/studio/utils.py @@ -1,11 +1,11 @@ import logging -from typing import List +from typing import Any, List import structlog from django.conf import settings -def get_logger(name: str): +def get_logger(name: str) -> Any: """ Get different loggers depending on the value of DEBUG. When DEBUG = True, then we return the standard logger, @@ -17,7 +17,7 @@ def get_logger(name: str): return structlog.getLogger(name) -def add_loggers(logging: dict, installed_apps: List[str]) -> dict: +def add_loggers(logging: dict[str, Any], installed_apps: List[str]) -> dict[str, Any]: """ Helper function to add loggers to each installed app """ diff --git a/studio/version.py b/studio/version.py index 2fcd28325..20fb981d8 100644 --- a/studio/version.py +++ b/studio/version.py @@ -1,5 +1,8 @@ +from typing import Any, List, Tuple + + class Version: - def __init__(self, version="v0.0.0"): + def __init__(self, version: str = "v0.0.0"): numbers = version[1:].split(".") self.major = int(numbers[0]) self.minor = int(numbers[1]) @@ -9,7 +12,7 @@ def __init__(self, version="v0.0.0"): # Release a new version # Default is new minor version - def release(self, release_type="minor"): + def release(self, release_type: str = "minor") -> Tuple[bool, str]: if release_type == "minor": self.minor = self.minor + 1 self.patch = 0 @@ -26,7 +29,7 @@ def release(self, release_type="minor"): # Implement comparison operators to allow for sorting # of models - def __gt__(self, other): + def __gt__(self, other: "Version") -> bool: if self.major > other.major: return True elif other.major > self.major: @@ -44,20 +47,20 @@ def __gt__(self, other): return False - def __eq__(self, other): + def __eq__(self, other: Any) -> bool: if self.major == other.major and self.minor == other.minor and self.patch == other.minor: return True return False - def __lt__(self, other): + def __lt__(self, other: "Version") -> bool: if other.__gt__(self) or self.__eq__(other): return False return True - def release_types(self): + def release_types(self) -> list[str]: return ["major", "minor", "patch"] - def __str__(self): - return "v{}.{}.{}".format(self.major, self.minor, self.patch) + def __str__(self) -> str: + return f"v{self.major}.{self.minor}.{self.patch}" diff --git a/studio/views.py b/studio/views.py index 749e2e613..ed75eeeae 100644 --- a/studio/views.py +++ b/studio/views.py @@ -1,4 +1,5 @@ import json +from typing import Any, cast import requests from django.conf import settings @@ -23,6 +24,7 @@ from apps.models import AppInstance from common.models import UserProfile +from models.models import Model from projects.models import Project from studio.utils import get_logger @@ -32,7 +34,7 @@ @receiver(pre_save, sender=User) -def set_new_user_inactive(sender, instance, **kwargs): +def set_new_user_inactive(sender: Model, instance: User, **kwargs: dict[str, Any]) -> None: if instance._state.adding and settings.INACTIVE_USERS and not instance.is_superuser: logger.info("Creating Inactive User") instance.is_active = False @@ -43,12 +45,12 @@ def set_new_user_inactive(sender, instance, **kwargs): # Since this is a production feature, it will only work if DEBUG is set to False -def handle_page_not_found(request, exception): +def handle_page_not_found(request: Response, exception: Exception) -> HttpResponseRedirect: return HttpResponseRedirect("/") class AccessPermission(BasePermission): - def has_permission(self, request, view): + def has_permission(self, request: Response, view: object) -> bool: """ Should simply return, or raise a 403 response. """ @@ -60,12 +62,12 @@ def has_permission(self, request, view): except: # noqa: E722 project_slug = request.GET.get("project") project = Project.objects.get(slug=project_slug) - return request.user.has_perm("can_view_project", project) + return cast(bool, request.user.has_perm("can_view_project", project)) if app_instance.access == "private": - return app_instance.owner == request.user + return cast(bool, app_instance.owner == request.user) elif app_instance.access == "project": - return request.user.has_perm("can_view_project", project) + return cast(bool, request.user.has_perm("can_view_project", project)) else: return True @@ -80,7 +82,7 @@ class ModifiedSessionAuthentication(SessionAuthentication): header can be retrieved and the response code is automatically set to 401 in case of unauthenticated requests. """ - def authenticate_header(self, request): + def authenticate_header(self, request: Response) -> str: return "Session" @@ -88,7 +90,7 @@ class AuthView(APIView): authentication_classes = [ModifiedSessionAuthentication, TokenAuthentication] permission_classes = [IsAuthenticated, AccessPermission] - def get(self, request, format=None): + def get(self, request: Response, format: str | None = None) -> Response: content = { "user": str(request.user), "auth": str(request.auth), @@ -97,7 +99,7 @@ def get(self, request, format=None): @login_required -def profile(request): +def profile(request: Response) -> Response: # Get the user profile try: # Note that not all users have a user profile object @@ -114,7 +116,7 @@ def profile(request): @login_required -def delete_account(request): +def delete_account(request: Response) -> Response: """ Renders a form that allows a user to delete their user account. Verifies that the user does not own any Serve projects. @@ -134,7 +136,7 @@ def delete_account(request): @login_required -def delete_account_post_handler(request, user_id): +def delete_account_post_handler(request: Response, user_id: int) -> Response: """ Handles a POST action request by a user to delete their account. """ @@ -184,12 +186,12 @@ def delete_account_post_handler(request, user_id): return HttpResponse("Unable to delete user account.", status=500) -def account_deleted(request, user_id): +def account_deleted(request: Response, user_id: int) -> Response: """Renders a view shown to users at the end of deletion of their account.""" return render(request, "user/account_deleted.html", {"user_id": user_id}) -def __get_university_name(request, code): +def __get_university_name(request: Response, code: str) -> str: """Gets the university name by making an API call. :param request: The request object. :param str code: The university code. @@ -204,6 +206,6 @@ def __get_university_name(request, code): if response.status_code == 200: data = response.json()["data"] - return data["name"] + return cast(str, data["name"]) else: raise Exception("API did not return status 200") diff --git a/templates/403.html b/templates/403.html index 017c42d65..b865c1784 100644 --- a/templates/403.html +++ b/templates/403.html @@ -5,17 +5,17 @@ {% load static %} {% block content %} -

FORBIDDEN 403

-

You don't have access to that site! Contact project admin to grant you access.

+

Access to page forbidden. Error 403.

+

You don't have access to this project! Log in or ask the project owner to grant you access.

Is this your project? {% if request.user.is_authenticated %} - Sign out + Sign out {% else %} - - Log in + + Log in {% endif %}

diff --git a/templates/apps/create.html b/templates/apps/create.html index 305e2c84a..a32c9a32f 100644 --- a/templates/apps/create.html +++ b/templates/apps/create.html @@ -222,7 +222,7 @@

Create {{ app.name }}

{{ vals.meta_title }}
{% for subkey, subval in vals.items %} - {% if subval.type != "boolean" and subkey == "image" or subkey == "port" or subkey == "userid"%} + {% if subval.type != "boolean" and subkey == "image" or subkey == "port" or subkey == "userid" or subkey == "proxyheartbeatrate" or subkey == "proxyheartbeattimeout" or subkey == "proxycontainerwaittime" %}
{% else %}
@@ -286,7 +286,7 @@
{{ vals.meta_title }}
{% endif %} {% if subval.type == "number" %} - {% if subkey == "port" or subkey == "userid" %} + {% if subkey == "port" or subkey == "userid" or subkey == "proxyheartbeatrate" or subkey == "proxyheartbeattimeout" or subkey == "proxycontainerwaittime" %} {% if subkey == "port" %} @@ -299,10 +299,34 @@
{{ vals.meta_title }}
- +
Please add a valid User ID between 999 and 1010!
+ {% elif subkey == "proxyheartbeatrate" and request.user.is_superuser %} + + + + +
+ Please add a number, needs to be above 1. +
+ {% elif subkey == "proxyheartbeattimeout" and request.user.is_superuser %} + + + + +
+ Please add a number. Cannot be lower than 0 except for '-1' to set no timeout. +
+ {% elif subkey == "proxycontainerwaittime" and request.user.is_superuser %} + + + + +
+ Please add a number, needs to be above 20000. +
{% endif %} {% else %} @@ -359,7 +383,7 @@
{{ vals.meta_title }}
- + {# In the custom app creation form, make the path a required field if a persistent volumet is selected #} {% if app.slug == "customapp" %}