Merge pull request #20 from usegalaxy-au/boilerplate-generator

Boilerplate generator

.gitignore

@@ -2,6 +2,7 @@
 *.sqlite3
 app/app/static/
 app/app/media/
+temp/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

app/app/settings/base.py

@@ -42,6 +42,7 @@
 STATIC_ROOT = BASE_DIR / 'app/static'
 MEDIA_ROOT = BASE_DIR / 'app/media'
 LOG_ROOT = ensure_dir(BASE_DIR / 'app/logs')
+TEMP_DIR = ensure_dir(BASE_DIR / 'app/temp')
 DEFAULT_EXPORTED_LAB_CONTENT_ROOT = (
     f'http://{HOSTNAME}/static/labs/content/docs/base.yml')
 
@@ -97,8 +98,13 @@
     'django.contrib.messages',
     'django.contrib.staticfiles',
     'labs',
+    'crispy_forms',
+    "crispy_bootstrap5",
 ]
 
+CRISPY_ALLOWED_TEMPLATE_PACKS = "bootstrap5"
+CRISPY_TEMPLATE_PACK = "bootstrap5"
+
 MIDDLEWARE = [
     'django.middleware.security.SecurityMiddleware',
     'django.contrib.sessions.middleware.SessionMiddleware',

app/labs/bootstrap.py

@@ -0,0 +1,116 @@
+"""Render a new lab from form data."""
+
+import random
+import shutil
+import string
+import time
+import zipfile
+from django.conf import settings
+from django.template.loader import render_to_string
+from django.utils.text import slugify
+from pathlib import Path
+
+HOURS_72 = 3 * 24 * 60 * 60
+ALPHANUMERIC = string.ascii_letters + string.digits
+TEMPLATE_DIR = Path('labs/bootstrap')
+TEMPLATES_TO_RENDER = [
+    'base.yml',
+    'intro.md',
+    'conclusion.md',
+    'footer.md',
+    'section-1.yml',
+    'README.md',
+    'custom.css',
+    'CONTRIBUTORS',
+]
+GALAXY_SERVERS = {
+    '': 'usegalaxy.org',
+    'Europe': 'usegalaxy.eu',
+    'Australia': 'usegalaxy.org.au',
+}
+
+
+def random_string(length):
+    return ''.join(random.choices(ALPHANUMERIC, k=length))
+
+
+def lab(form_data):
+    """Render a new lab from form data."""
+    clean_dir(settings.TEMP_DIR)
+    output_dir = settings.TEMP_DIR / random_string(6)
+    form_data['logo_filename'] = create_logo(form_data, output_dir)
+    render_templates(form_data, output_dir)
+    render_server_yml(form_data, output_dir)
+    zipfile_path = output_dir.with_suffix('.zip')
+    root_dir = Path(slugify(form_data['lab_name']))
+    with zipfile.ZipFile(zipfile_path, 'w') as zf:
+        for path in output_dir.rglob('*'):
+            zf.write(path, root_dir / path.relative_to(output_dir))
+    return zipfile_path
+
+
+def render_templates(data, output_dir):
+    for template in TEMPLATES_TO_RENDER:
+        subdir = None
+        if template.endswith('.md') and 'README' not in template:
+            subdir = 'templates'
+        elif template.endswith('css'):
+            subdir = 'static'
+        elif template == 'section-1.yml':
+            subdir = 'sections'
+        render_file(
+            data,
+            template,
+            output_dir,
+            subdir=subdir,
+        )
+
+
+def render_file(data, template, output_dir, subdir=None, filename=None):
+    outfile_relpath = filename or template
+    if subdir:
+        outfile_relpath = Path(subdir) / outfile_relpath
+    path = output_dir / outfile_relpath
+    path.parent.mkdir(parents=True, exist_ok=True)
+    content = render_to_string(TEMPLATE_DIR / template, data)
+    path.write_text(content)
+    return path
+
+
+def render_server_yml(data, output_dir):
+    """Create a YAML file for each Galaxy server."""
+    for site_name, root_domain in GALAXY_SERVERS.items():
+        data['site_name'] = site_name
+        data['galaxy_base_url'] = (
+            'https://'
+            + data['subdomain']
+            + '.'
+            + root_domain
+        )
+        data['root_domain'] = root_domain
+        render_file(
+            data,
+            'server.yml',
+            output_dir,
+            filename=f'{root_domain}.yml',
+        )
+
+
+def create_logo(data, output_dir):
+    """Copy the uploaded logo to the output directory."""
+    logo_file = data.get(
+        'logo'
+    ) or settings.BASE_DIR / 'labs/example_labs/docs/static/flask.svg'
+    logo_dest_path = output_dir / 'static' / logo_file.name
+    logo_dest_path.parent.mkdir(parents=True, exist_ok=True)
+    with logo_file.open('rb') as src, logo_dest_path.open('wb') as dest:
+        shutil.copyfileobj(src, dest)
+    return logo_dest_path.name
+
+
+def clean_dir(directory):
+    """Delete directories that were created more than 7 days ago."""
+    for path in directory.iterdir():
+        if path.is_dir() and path.stat().st_ctime < time.time() - HOURS_72:
+            shutil.rmtree(path)
+    return directory

app/labs/forms.py

@@ -1,14 +1,30 @@
 """User facing forms for making support requests (help/tools/data)."""
 
 import logging
+from crispy_forms.helper import FormHelper
+from crispy_forms.layout import Layout, HTML, Submit
 from django import forms
 from django.conf import settings
 from django.core.mail import EmailMultiAlternatives
+from django.core.validators import FileExtensionValidator
 from utils.mail import retry_send_mail
+from utils.webforms import SpamFilterFormMixin
+
+from . import bootstrap, validators
 
 logger = logging.getLogger('django')
 
 MAIL_APPEND_TEXT = f"Sent from {settings.HOSTNAME}"
+IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'gif', 'webp', 'svg']
+INTRO_MD = 'Welcome to the Galaxy {{ site_name }} {{ lab_name }}!'
+CONCLUSION_MD = ('Thanks for checking out the Galaxy {{ site_name }}'
+                 ' {{ lab_name }}!')
+FOOTER_MD = f"""
+<footer class="text-center">
+    This page was generated by the
+    <a href="{settings.HOSTNAME}/bootstrap">Galaxy Labs Engine</a>.
+</footer>
+"""
 
 
 def dispatch_form_mail(
@@ -80,3 +96,99 @@ def dispatch(self, subject=None):
                 + data['message']
             )
         )
+
+
+class LabBootstrapForm(SpamFilterFormMixin, forms.Form):
+    """Form to bootstrap a new lab."""
+
+    lab_name = forms.CharField(
+        label="Lab name",
+        widget=forms.TextInput(attrs={
+            'placeholder': "e.g. Genome Lab",
+            'autocomplete': 'off',
+        }),
+    )
+    subdomain = forms.CharField(
+        label="Galaxy Lab Subdomain",
+        widget=forms.TextInput(attrs={
+            'placeholder': "e.g. genome",
+            'autocomplete': 'off',
+        }),
+        help_text=(
+            "The subdomain that the lab will be served under. i.e."
+            " &lt;subdomain&gt;.usegalaxy.org"
+        ),
+    )
+    github_username = forms.CharField(
+        label="GitHub Username",
+        widget=forms.TextInput(attrs={
+            'autocomplete': 'off',
+        }),
+        help_text=(
+            '(Optional) Your GitHub username to add to the list of'
+            ' contributors.'
+        ),
+        validators=[validators.validate_github_username],
+        required=False,
+    )
+    logo = forms.FileField(
+        label="Lab logo",
+        help_text=("(Optional) Upload a custom logo to be displayed in the Lab"
+                   " header. Try to make it square and less than 100KB"
+                   " - SVG format is highly recommended."),
+        required=False,
+        allow_empty_file=False,
+        validators=[
+            FileExtensionValidator(
+                allowed_extensions=IMAGE_EXTENSIONS,
+            ),
+        ],
+        widget=forms.FileInput(attrs={
+            'accept': ','.join(f"image/{ext}" for ext in IMAGE_EXTENSIONS),
+        }),
+    )
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.helper = FormHelper()
+        self.helper.layout = Layout(
+            'lab_name',
+            'subdomain',
+            'github_username',
+            'logo',
+            HTML(self.antispam_html),
+            Submit('submit', 'Build'),
+        )
+
+    def clean_subdomain(self):
+        """Validate the subdomain."""
+        subdomain = self.cleaned_data['subdomain'].lower().strip()
+        if not subdomain.isalnum():
+            raise forms.ValidationError("Subdomain must be alphanumeric.")
+        return subdomain
+
+    def clean_lab_name(self):
+        """Validate the lab name."""
+        lab_name = self.cleaned_data['lab_name'].title().strip()
+        if not lab_name.replace(' ', '').isalnum():
+            raise forms.ValidationError("Lab name cannot be empty.")
+        return lab_name
+
+    def clean_github_username(self):
+        username = self.cleaned_data.get('github_username')
+        return username.strip() if username else None
+
+    def bootstrap_lab(self):
+        data = self.cleaned_data
+        data.update({
+            'intro_md': INTRO_MD,  # TODO: Render from user-input
+            'conclusion_md': CONCLUSION_MD,
+            'footer_md': FOOTER_MD,
+            'root_domain': 'usegalaxy.org',
+            'galaxy_base_url': (
+                f"https://{data['subdomain']}.usegalaxy.org"),
+            'section_paths': [
+                'sections/section-1.yml',  # TODO: Auto-render from user input
+            ],
+        })
+        return bootstrap.lab(data)

app/labs/static/labs/content/docs/section_1.yml

@@ -43,11 +43,11 @@ tabs:
 
   - id: workflows
     title: Workflows
-    heading_md: |
+    heading_md: >
       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](https://galaxyproject.org/learn/advanced-workflow/).
+      <a href="https://galaxyproject.org/learn/advanced-workflow">Learn more</a>.
     content:
       - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
         button_tip: Import to Galaxy AU

app/labs/static/labs/content/docs/templates/intro.html

@@ -13,13 +13,21 @@
       </a>
     </li>
     <li>
-      See a full working example of an exported Galaxy Lab page
+      See a full working example of a Galaxy Lab page
       <a href="/?content_root={{ EXAMPLE_LABS.FULL.RAW_URL }}">here</a>.
     </li>
     <li>
       See a minimal working example of a lab page
       <a href="/?content_root={{ EXAMPLE_LABS.SIMPLE.RAW_URL }}">here</a>.
     </li>
+    <li>
+      Start a new Lab page in 30 seconds
+      <a href="/bootstrap">here</a>.
+    </li>
+    <li>
+      View the full <code>section.yml</code> schema documentation
+      <a href="/schema">here</a>.
+    </li>
   </ul>
 
   <p>
@@ -76,7 +84,8 @@ <h2 class="accordion-header" id="headingOne">
                 <a href="{{ EXAMPLE_LABS.DOCS.WEB_DIR_ROOT }}/section_1.yml" target="_blank">section_1.yml</a>
                 and
                 <a href="{{ EXAMPLE_LABS.DOCS.WEB_DIR_ROOT }}/section_2.yml" target="_blank">section_2.yml</a>
-                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
+                <a href="/schema">sections schema definition</a> to see exactly how this YAML should be structured.
               </li>
             </ul>
           </p>
@@ -95,15 +104,15 @@ <h2 class="accordion-header" id="headingTwo">
           <p>
             <ol>
               <li>
-                Copy our
-                <a href="{{ EXAMPLE_LABS.DOCS.WEB_DIR_URL }}" target="_blank">
-                  example content
-                </a>
-                directory to your own github repository.
+                Generate a new content folder using our
+                <a href="/bootstrap">Lab Generator</a>.
               </li>
               <li>
-                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.
               </li>
               <li>
                 Request the site with the <code>content_root</code> GET parameter pointing to your remote content:
@@ -171,12 +180,22 @@ <h2 class="accordion-header" id="headingThree">
               data-bs-target="#infoModal"
             >Try one now!</a>
           </p>
+
+          <p class="alert alert-info">
+            Try to make all Markdown/HTML content as modular as possible by using
+            variables defined in the <code>base.yml</code> and
+            <code>server.yml</code> files. This means that content will be rendered
+            differently on each Galaxy server, depending on what's in that
+            server's <code>server.yml</code> file!
+          </p>
         </div>
       </div>
     </div>
   </div>
 </section>
 
+<!-- Modals -->
+
 <div class="modal fade" id="infoModal" tabindex="-1">
   <div class="modal-dialog modal-lg">
     <div class="modal-content">
@@ -206,6 +225,7 @@ <h5 class="modal-title">Galaxy {{ site_name }}</h5>
 
 
 <script>
+  // Some fancy JavaScript to add "View on GitHub" overlay to each section
   function addHoverInfo(id, relpath) {
     const exportInfoButton = $(`
       <a

app/labs/static/labs/content/simple/base.yml

@@ -1,6 +1,6 @@
 # Default spec for an exported lab landing page
 
-# You can test with: /?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-labs-engine/dev/app/labs/content/docs/base.yml
+# You can test with: /?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-labs-engine/dev/app/labs/content/simple/base.yml
 
 site_name: Archaeology
 lab_name: Archaeology Lab