Merge branch 'main' of https://github.com/usegalaxy-au/galaxy-labs-en…

…gine
usegalaxy-au · Sep 28, 2024 · 8c9ff0e · 8c9ff0e
2 parents 6a8b561 + afd780e
commit 8c9ff0e
Show file tree

Hide file tree

Showing 15 changed files with 80 additions and 172 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git 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
@@ -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
@@ -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
@@ -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