+ View the full section.yml schema documentation
+ here.
+
@@ -76,7 +84,8 @@
section_1.yml
and
section_2.yml
- for examples of how to structure this content in YAML format.
+ for examples of how to structure this content in YAML format, or check out the full
+ sections schema definition to see exactly how this YAML should be structured.
@@ -95,15 +104,15 @@
- Build your Galaxy Lab's info, tools and workflows by editing the YAML and HTML files.
- Custom CSS and JavaScript are possible too.
+ Build on your Galaxy Lab content by editing the downloaded YAML
+ and MD/HTML files. Custom CSS and JavaScript are possible too.
+ Try to keep the content as concise and modular as possible, and
+ think about what essential resources your users should know about.
+ Critical Tools, Workflows and tutorials are a great place to start.
Request the site with the content_root GET parameter pointing to your remote content:
@@ -171,12 +180,22 @@
data-bs-target="#infoModal"
>Try one now!
+
+
+ Try to make all Markdown/HTML content as modular as possible by using
+ variables defined in the base.yml and
+ server.yml files. This means that content will be rendered
+ differently on each Galaxy server, depending on what's in that
+ server's server.yml file!
+
+ A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
+ Learn more
+.
+
+ You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy.
+ Just look for the "Upload data" button at the top of the tool panel.
+
+ We recommend subsampling large data sets to test tools and workflows.
+ A useful tool is
+ seqtk_seq,
+ setting the parameter at "Sample fraction of sequences"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/app/labs/templates/labs/snippets/imports.html b/app/labs/templates/labs/snippets/imports.html
index 895b508..781e6bc 100644
--- a/app/labs/templates/labs/snippets/imports.html
+++ b/app/labs/templates/labs/snippets/imports.html
@@ -4,6 +4,11 @@
+
+
+
+
+
diff --git a/app/labs/urls.py b/app/labs/urls.py
index cef54bb..cd41c45 100644
--- a/app/labs/urls.py
+++ b/app/labs/urls.py
@@ -6,5 +6,7 @@
urlpatterns = [
path('', views.export_lab, name="lab_export"),
+ path('bootstrap', views.BootstrapLab.as_view(), name="lab_bootstrap"),
+ path('schema', views.schema, name="lab_schema"),
path('lab/feedback/', api.lab_feedback, name="lab_feedback"),
]
diff --git a/app/labs/validators.py b/app/labs/validators.py
new file mode 100644
index 0000000..d75f339
--- /dev/null
+++ b/app/labs/validators.py
@@ -0,0 +1,13 @@
+"""Custom validators for model/form fields."""
+
+import re
+from django.core.exceptions import ValidationError
+
+
+def validate_github_username(value):
+ if not re.match(r'^[a-zA-Z0-9]([a-zA-Z0-9-]{0,37}[a-zA-Z0-9])?$', value):
+ raise ValidationError(
+ "Invalid GitHub username. It must be 1-39 characters long, contain"
+ " only letters, numbers, or single hyphens, and cannot start or"
+ " end with a hyphen."
+ )
diff --git a/app/labs/views.py b/app/labs/views.py
index d75e177..95f5ff9 100644
--- a/app/labs/views.py
+++ b/app/labs/views.py
@@ -1,16 +1,22 @@
"""Views for home app."""
import logging
+import os
from django.conf import settings
+from django.http import HttpResponse
from django.shortcuts import render
+from django.views.static import serve
from django.template import (
RequestContext,
Template,
)
from django.template.loader import render_to_string
+from django.utils.text import slugify
+from django.views import View
from utils.exceptions import LabBuildError
from .cache import LabCache
+from .forms import LabBootstrapForm
from .lab_export import ExportLabContext
logger = logging.getLogger('django')
@@ -67,6 +73,56 @@ def export_lab(request):
return response
+def schema(request):
+ """Render the schema page."""
+ return render(request, 'labs/schema.html')
+
+
+class BootstrapLab(View):
+ """Generate new lab content from submitted form data."""
+
+ form = LabBootstrapForm
+
+ def get(self, request):
+ form = self.form()
+ return render(request, 'labs/bootstrap.html', {
+ 'form': form,
+ })
+
+ def post(self, request):
+ form = self.form(request.POST, request.FILES)
+ if form.is_valid():
+ zipfile_path = form.bootstrap_lab()
+ return self.force_download(
+ request,
+ zipfile_path,
+ slugify(form.cleaned_data['lab_name']) + '.zip',
+ )
+ return render(request, 'labs/bootstrap.html', {
+ 'form': form,
+ }, status=400)
+
+ def force_download(self, request, fpath, fname=None):
+ fname = fname or fpath.name
+ if settings.DEBUG:
+ logger.debug('Returning Django static serve (DEBUG mode)')
+ logger.debug('Serving file %s' % fpath)
+ response = serve(
+ request,
+ os.path.basename(fpath),
+ os.path.dirname(fpath)
+ )
+ response['Content-Disposition'] = "attachment; filename=%s" % fname
+ return response
+
+ logger.debug('Serving file via Nginx X-Accel-Redirect: %s' % fpath)
+ response = HttpResponse()
+ response['Content-Type'] = ''
+ response['Content-Disposition'] = "attachment; filename=%s" % fname
+ response['X-Accel-Redirect'] = settings.INSTALLER_BASE_URL + fname
+ return response
+
+
def report_exception_response(request, exc, title=None):
"""Report an exception to the user."""
return render(request, 'generic.html', {
diff --git a/app/utils/webforms.py b/app/utils/webforms.py
new file mode 100644
index 0000000..30041aa
--- /dev/null
+++ b/app/utils/webforms.py
@@ -0,0 +1,83 @@
+"""Utilities for Django forms."""
+
+import logging
+from django import forms
+from django.utils.safestring import mark_safe
+
+logger = logging.getLogger('django')
+
+
+class SubmitDelaySpamFilterMixin(forms.Form):
+ """Enforce a submit delay to prevent spam/bot submissions."""
+
+ SUBMIT_DELAY_MINIMUM_SECONDS = 3.0
+
+ submit_delay_seconds = forms.FloatField(
+ min_value=SUBMIT_DELAY_MINIMUM_SECONDS, required=False)
+
+ submit_delay_field_html = """
+
+ """
+
+
+class HoneypotSpamFilterMixin(forms.Form):
+ """Include a honeypot field to catch spam/bot submissions."""
+
+ DELAY_DISABLE_MS = 1000
+ HONEYPOT_FIELD_NAME = 'institution_hp'
+ institution_hp = forms.CharField(
+ required=False,
+ widget=forms.HiddenInput()
+ )
+ honeypot_field_html = f"""
+
+ """
+
+ def clean_institution_hp(self):
+ """Check honeypot field."""
+ value = self.cleaned_data.get(self.HONEYPOT_FIELD_NAME)
+ if value:
+ logger.warning('Honeypot field was filled in.')
+ raise forms.ValidationError('This value is incorrect.')
+ return value
+
+
+class SpamFilterFormMixin(
+ SubmitDelaySpamFilterMixin,
+ HoneypotSpamFilterMixin,
+):
+ """A base form with multiple levels of spam filtering/prevention."""
+
+ INTERNAL_FIELDS = (
+ 'submit_delay_seconds',
+ 'institution_hp',
+ 'captcha',
+ )
+ antispam_html = mark_safe(
+ HoneypotSpamFilterMixin.honeypot_field_html
+ + SubmitDelaySpamFilterMixin.submit_delay_field_html)
diff --git a/requirements.txt b/requirements.txt
index 2d9a4b3..840d6e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,3 +11,5 @@ django_light
requests==2.*
requests_mock==1.*
sentry-sdk==2.*
+django-crispy-forms==2.*
+crispy-bootstrap5==2024.*