diff --git a/README.md b/README.md
index fbfc315..db45956 100644
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@ Create a lab content directory like
And then request your page anywhere like this:
-https://labs.usegalaxy.org.au/export/?content_root=https://raw.githubusercontent.com/my-username/my-labs-repo/my-lab/base.yml
+https://labs.usegalaxy.org.au/?content_root=https://raw.githubusercontent.com/my-username/my-labs-repo/my-lab/base.yml
To get a webpage like
-[this](https://labs.usegalaxy.org.au/export/?content_root=https://raw.githubusercontent.com/neoformit/galaxy-labs-engine/dev/app/labs/content/simple/main.yml).
+[this](https://labs.usegalaxy.org.au/?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-labs-engine/dev/app/labs/content/simple/main.yml).
diff --git a/ansible/dev.yml b/ansible/dev.yml
index f001565..eaa735b 100644
--- a/ansible/dev.yml
+++ b/ansible/dev.yml
@@ -5,7 +5,7 @@
vars_files:
- group_vars/VAULT
- group_vars/webservers.yml
- - host_vars/labs.neoformit.com.yml
+ - host_vars/dev-labs.gvl.org.au.yml
roles:
- role: geerlingguy.docker
tags: init
diff --git a/ansible/prod.yml b/ansible/prod.yml
index 53dffea..e7d4d2c 100644
--- a/ansible/prod.yml
+++ b/ansible/prod.yml
@@ -3,7 +3,10 @@
remote_user: ubuntu
become: true
vars_files:
- - group_vars/secrets.yml
+ - group_vars/VAULT
- group_vars/webservers.yml
+ - host_vars/labs.usegalaxy.org.au.yml
roles:
+ - role: geerlingguy.docker
+ tags: init
- galaxy_labs_engine
diff --git a/ansible/roles/galaxy_labs_engine/tasks/main.yml b/ansible/roles/galaxy_labs_engine/tasks/main.yml
index 32f7ec7..fcd22fb 100644
--- a/ansible/roles/galaxy_labs_engine/tasks/main.yml
+++ b/ansible/roles/galaxy_labs_engine/tasks/main.yml
@@ -7,7 +7,7 @@
- name: clone git repository for galaxy-labs-engine
ansible.builtin.git:
repo: https://github.com/neoformit/galaxy-labs-engine.git
- branch: "{{ git_branch }}"
+ version: "{{ git_branch }}"
dest: "{{ project_root }}"
clone: yes
force: yes
@@ -50,14 +50,6 @@
loop: "{{ labs_engine.files }}"
tags: config
-- name: Django create django_cache table with 'manage.py createcachetable'
- shell: >
- docker compose --profile prod run --rm labs-engine
- python manage.py createcachetable
- args:
- chdir: "{{ config_root }}"
- tags: django
-
- name: update media file ownership
file: dest={{ django_root }}/app/media owner=www-data group=www-data mode=u=rwX,g=rwX,o=rwX recurse=yes
tags:
@@ -75,6 +67,7 @@
tags:
- permissions
- update
+ ignore_errors: yes
- name: update sqlite3 database directory permissions
file:
@@ -86,6 +79,14 @@
- permissions
- update
+- name: Django create django_cache table with 'manage.py createcachetable'
+ shell: >
+ docker compose --profile prod run --rm labs-engine
+ python manage.py createcachetable
+ args:
+ chdir: "{{ config_root }}"
+ tags: django
+
- name: Django run migrations
shell: >
docker compose --profile prod run --rm
@@ -100,12 +101,11 @@
- name: Django collect static files
shell: >
- docker compose --profile prod run --rm
+ docker compose --profile prod run --rm --user root
labs-engine
python manage.py collectstatic --noinput
args:
chdir: "{{ config_root }}"
- when: git.changed
tags: always
- name: Django ensure superuser login
diff --git a/ansible/roles/galaxy_labs_engine/templates/nginx.conf.j2 b/ansible/roles/galaxy_labs_engine/templates/nginx.conf.j2
index d582108..d77dc27 100644
--- a/ansible/roles/galaxy_labs_engine/templates/nginx.conf.j2
+++ b/ansible/roles/galaxy_labs_engine/templates/nginx.conf.j2
@@ -74,7 +74,7 @@ server {
# Redirect all other traffic to HTTPS, but not the challenge
location / {
- if ($host = labs.neoformit.com) {
+ if ($host = {{ inventory_hostname }}) {
return 301 https://$host$request_uri;
}
}
diff --git a/app/app/settings.py b/app/app/settings.py
deleted file mode 100644
index 3a184a4..0000000
--- a/app/app/settings.py
+++ /dev/null
@@ -1,123 +0,0 @@
-"""
-Django settings for app project.
-
-Generated by 'django-admin startproject' using Django 5.0.7.
-
-For more information on this file, see
-https://docs.djangoproject.com/en/5.0/topics/settings/
-
-For the full list of settings and their values, see
-https://docs.djangoproject.com/en/5.0/ref/settings/
-"""
-
-from pathlib import Path
-
-# Build paths inside the project like this: BASE_DIR / 'subdir'.
-BASE_DIR = Path(__file__).resolve().parent.parent
-
-
-# Quick-start development settings - unsuitable for production
-# See https://docs.djangoproject.com/en/5.0/howto/deployment/checklist/
-
-# SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = 'django-insecure-g33bcvq6_*x)*(7h)-%^pn#&qa1neoiyx1z)z4rn(4@h@)xw%k'
-
-# SECURITY WARNING: don't run with debug turned on in production!
-DEBUG = True
-
-ALLOWED_HOSTS = []
-
-
-# Application definition
-
-INSTALLED_APPS = [
- 'django.contrib.admin',
- 'django.contrib.auth',
- 'django.contrib.contenttypes',
- 'django.contrib.sessions',
- 'django.contrib.messages',
- 'django.contrib.staticfiles',
-]
-
-MIDDLEWARE = [
- 'django.middleware.security.SecurityMiddleware',
- 'django.contrib.sessions.middleware.SessionMiddleware',
- 'django.middleware.common.CommonMiddleware',
- 'django.middleware.csrf.CsrfViewMiddleware',
- 'django.contrib.auth.middleware.AuthenticationMiddleware',
- 'django.contrib.messages.middleware.MessageMiddleware',
- 'django.middleware.clickjacking.XFrameOptionsMiddleware',
-]
-
-ROOT_URLCONF = 'app.urls'
-
-TEMPLATES = [
- {
- 'BACKEND': 'django.template.backends.django.DjangoTemplates',
- 'DIRS': [],
- 'APP_DIRS': True,
- 'OPTIONS': {
- 'context_processors': [
- 'django.template.context_processors.debug',
- 'django.template.context_processors.request',
- 'django.contrib.auth.context_processors.auth',
- 'django.contrib.messages.context_processors.messages',
- ],
- },
- },
-]
-
-WSGI_APPLICATION = 'app.wsgi.application'
-
-
-# Database
-# https://docs.djangoproject.com/en/5.0/ref/settings/#databases
-
-DATABASES = {
- 'default': {
- 'ENGINE': 'django.db.backends.sqlite3',
- 'NAME': BASE_DIR / 'db.sqlite3',
- }
-}
-
-
-# Password validation
-# https://docs.djangoproject.com/en/5.0/ref/settings/#auth-password-validators
-
-AUTH_PASSWORD_VALIDATORS = [
- {
- 'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',
- },
- {
- 'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
- },
- {
- 'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
- },
- {
- 'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
- },
-]
-
-
-# Internationalization
-# https://docs.djangoproject.com/en/5.0/topics/i18n/
-
-LANGUAGE_CODE = 'en-us'
-
-TIME_ZONE = 'UTC'
-
-USE_I18N = True
-
-USE_TZ = True
-
-
-# Static files (CSS, JavaScript, Images)
-# https://docs.djangoproject.com/en/5.0/howto/static-files/
-
-STATIC_URL = 'static/'
-
-# Default primary key field type
-# https://docs.djangoproject.com/en/5.0/ref/settings/#default-auto-field
-
-DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
diff --git a/app/app/settings/base.py b/app/app/settings/base.py
index a97b56f..3ed2bf5 100644
--- a/app/app/settings/base.py
+++ b/app/app/settings/base.py
@@ -44,9 +44,40 @@
LOG_ROOT = ensure_dir(BASE_DIR / 'app/logs')
DEFAULT_EXPORTED_LAB_CONTENT_ROOT = (
f'http://{HOSTNAME}/static/labs/content/docs/base.yml')
-GITHUB_CONTENT_ROOT_BASE_URL = (
- "https://raw.githubusercontent.com/neoformit"
- "/galaxy-labs-engine/dev/app/labs/content")
+
+CODEX_REPO = 'galaxyproject/galaxy_codex'
+CODEX_GITHUB_URL = f'https://github.com/{CODEX_REPO}'
+LABS_ENGINE_GITHUB_REPO = 'usegalaxy-au/galaxy-labs-engine'
+LABS_ENGINE_GITHUB_URL = f'https://github.com/{LABS_ENGINE_GITHUB_REPO}'
+EXAMPLE_LABS = {
+ 'FULL': {
+ 'RAW_URL': (
+ f'https://raw.githubusercontent.com/{CODEX_REPO}/refs/heads/main'
+ '/communities/genome/lab/base.yml'),
+ 'WEB_DIR_URL': (
+ f'{CODEX_GITHUB_URL}/blob/main'
+ '/communities/genome/lab'),
+ },
+ 'DOCS': {
+ 'RAW_URL': (
+ f'https://raw.githubusercontent.com/{LABS_ENGINE_GITHUB_REPO}/refs'
+ '/heads/main/app/labs/static/labs/content/docs/base.yml'),
+ 'WEB_DIR_URL': (
+ f'{LABS_ENGINE_GITHUB_URL}/tree/dev/app/labs/static/labs/content'
+ '/docs'),
+ 'WEB_DIR_ROOT': (
+ f'{LABS_ENGINE_GITHUB_URL}/blob/dev/app/labs/static/labs/content'
+ '/docs'),
+ },
+ 'SIMPLE': {
+ 'RAW_URL': (
+ f'https://raw.githubusercontent.com/{LABS_ENGINE_GITHUB_REPO}'
+ '/refs/heads/main/app/labs/static/labs/content/simple/base.yml'),
+ 'WEB_DIR_URL': (
+ f'{LABS_ENGINE_GITHUB_URL}/blob/dev/app/labs/static/labs/content'
+ '/simple'),
+ },
+}
# Hostnames
ALLOWED_HOSTS = [
diff --git a/app/labs/context_processors.py b/app/labs/context_processors.py
index f8a3580..79792b4 100644
--- a/app/labs/context_processors.py
+++ b/app/labs/context_processors.py
@@ -6,8 +6,5 @@
def settings(request):
"""Include some settings variables."""
return {
- 'title': None, # prevents variable not found templating error
'HOSTNAME': app_settings.HOSTNAME,
- "GITHUB_CONTENT_ROOT_BASE_URL":
- app_settings.GITHUB_CONTENT_ROOT_BASE_URL,
}
diff --git a/app/labs/lab_export.py b/app/labs/lab_export.py
index 05b704c..d72004e 100644
--- a/app/labs/lab_export.py
+++ b/app/labs/lab_export.py
@@ -1,10 +1,10 @@
"""Exported landing pages to be requested by external Galaxy servers.
Example with local YAML:
-http://127.0.0.1:8000/landing/export?content_root=http://127.0.0.1:8000/static/labs/content/genome/main.yml
+http://127.0.0.1:8000/?content_root=http://127.0.0.1:8000/static/labs/content/simple/base.yml
Example URL with remote YAML:
-http://127.0.0.1:8000/landing/export?content_root=https://raw.githubusercontent.com/neoformit/galaxy-labs-engine/dev/app/labs/content/... base.yml # noqa
+http://127.0.0.1:8000/?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-labs-engine/blob/main/app/labs/content/simple/base.yml
"""
@@ -140,12 +140,9 @@ def looks_like_a_webpage(response):
def _validate_url(self, url, expected_type):
"""Validate URL to prevent circular request."""
- if (
- '/lab/export' in url
- and url.split('/')[1, 2] == ['lab', 'export']
- ):
+ if url.strip('/').split('/')[-1] == settings.HOSTNAME:
raise LabBuildError(
- "URL cannot contain '/lab/export'.",
+ "URL cannot match the root URL of this server",
url=url,
source=expected_type,
)
diff --git a/app/labs/static/labs/content/docs/base.yml b/app/labs/static/labs/content/docs/base.yml
index 72ebd31..24be751 100644
--- a/app/labs/static/labs/content/docs/base.yml
+++ b/app/labs/static/labs/content/docs/base.yml
@@ -1,6 +1,6 @@
# Default spec for an exported lab landing page
-# You can test with: /lab/export?content_root=https://raw.githubusercontent.com/neoformit/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/docs/base.yml
site_name: Antarctica
lab_name: Galaxy Lab Pages
diff --git a/app/labs/static/labs/content/docs/templates/intro.html b/app/labs/static/labs/content/docs/templates/intro.html
index 2d3669a..bc38f4e 100644
--- a/app/labs/static/labs/content/docs/templates/intro.html
+++ b/app/labs/static/labs/content/docs/templates/intro.html
@@ -8,24 +8,24 @@
- See the content used to generate this documentation page
-
+
here.
-
See a full working example of an exported Galaxy Lab page
- here.
+ here.
-
See a minimal working example of a lab page
- here.
+ here.
This custom introductory text was pulled down from GitHub and rendered in real time.
Updates to
-
+
this text
on the remote will be reflected on this page. Note that GitHub raw content is
@@ -48,7 +48,7 @@