Themes

README.md

@@ -105,6 +105,40 @@ The handler should "listen" to the topic `"restart galaxy"`.
 
 [gravity]: https://github.com/galaxyproject/gravity
 
+From release 22.01 Galaxy can serve different static content per host (e.g. subdomain) and you can set [themes][themes] per host.
+By setting `galaxy_manage_static: yes` you enable the creation of static directories and configuration per host and by setting `galaxy_manage_themes: yes` the role will append your themes_config.yml file specified under `galaxy_themes_conf_path` to your themes files after coping them over to your galaxy server and create the respective configuration.
+In order to use this features, you need to create the following directory structure under files/ (cusomizable with the `galaxy_themes_ansible_ansible_file_path` variable):
+~~~bash
+files/galaxy/static
+├──<subdomain-name-1>
+│   ├── static
+│   │   ├── dist (optional)
+│   │   │   └── some-image.png 
+│   │   ├── images (optional)
+│   │   │   └── more-content.jpg
+│   │   └── welcome.html
+│   └── themes 
+│       └── <subdomain-name-1>.yml           
+├── <subdomain-name-2>                            
+│   ├── static
+│   │   ├── dist (optional)
+│   │   │   ├── another-static-image.svg
+│   │   │   └── more-static-content-2.svg
+│   │   └── welcome.html
+│   └── themes
+│       └── <subdomain-name-1>.yml
+... (and many more subdomains)
+~~~
+Were the <subdomain-name-1> should exactly match your subdomain's name. The subdirectories `static` and `themes` are mandatory, as well as the correctly named theme file (if you enabled `galaxy_manage_themes`), while all subdirectories in `static` are optional.  
+Which subdirectories and files are copied is managed by the `static_galaxy_themes_keys` variable.
+
+Also make sure that you set `galaxy_themes_welcome_url_prefix`, so your welcome pages are templated correctly.
+
+It is mandatory to set the variables under `galaxy_themes_subdomains` as shown in the example in [defaults/main.yml](defaults/main.yml). If you enabled the `galaxy_manage_host_filters` variable, you can also specify the tool sections that should be shown for each individual subdomain.
+
+
+
+[themes]: https://training.galaxyproject.org/training-material/topics/admin/tutorials/customization/tutorial.html
 **New options for Galaxy 18.01 and later**
 
 - `galaxy_config_style` (default: `yaml`): The type of Galaxy configuration file to write, `yaml` for the YAML format supported by uWSGI or `ini-paste` for the traditional PasteDeploy-style INI file
@@ -503,3 +537,4 @@ This role was written and contributed to by the following people:
 - [John Chilton](https://github.com/jmchilton)
 - [Nate Coraor](https://github.com/natefoo)
 - [Helena Rasche](https://github.com/hexylena)
+- [Mira Kuntz](https://github.com/mira-miracoli)

defaults/main.yml

@@ -23,6 +23,9 @@ galaxy_manage_gravity: "{{ false if __galaxy_major_version is version('22.05', '
 galaxy_manage_systemd: no # For Galaxy
 galaxy_manage_systemd_reports: no # For Reports
 galaxy_manage_cleanup: no
+galaxy_manage_themes: no
+galaxy_manage_subdomain_static: no
+galaxy_manage_host_filters: no
 
 
 # Control whether to output verbose task diffs (e.g. when performing a git update) when running Ansible with --diff.
@@ -295,6 +298,50 @@ galaxy_app_config_default:
   # Everything else
   visualization_plugins_directory: "config/plugins/visualizations"
 
+  # Static and themes configuration, will only be added if galaxy_manage_themes
+  enable_static: "{{ galaxy_manage_subdomain_static }}"
+  static_dir_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/'
+    {% endfor %}
+    {% endif %} }
+  static_images_dir_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/images'
+    {% endfor %}
+    {% endif %} }
+  static_welcome_html_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/welcome.html'
+    {% endfor %}
+    {% endif %} }
+  static_scripts_dir_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/scripts'
+    {% endfor %}
+    {% endif %} }
+  static_favicon_dir_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/favicon.ico'
+    {% endfor %}
+    {% endif %} }
+  static_robots_txt_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/robots.txt'
+    {% endfor %}
+    {% endif %} }
+  themes_dir_by_host: >
+    { {% if galaxy_manage_themes %}
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name  }}.{{ galaxy_themes_instance_domain}}': {{ subdomain.name }}.yml
+    {% endfor %}
+    {% endif %} }
 # Need to set galaxy_config_default[galaxy_app_config_section] dynamically but Ansible/Jinja2 does not make this easy
 galaxy_config_default: "{{ {} | combine({galaxy_app_config_section: galaxy_app_config_default}) }}"
 galaxy_config_merged: "{{ galaxy_config_default | combine(galaxy_config | default({}), recursive=True) }}"
@@ -425,3 +472,64 @@ galaxy_systemd_env: []
 
 # A list of additional python packages to install into galaxy's virtual environment
 galaxy_additional_venv_packages: []
+
+# galaxy themes variables
+galaxy_themes_subdomains: {}
+# - name: assembly
+#   tool_sections:
+#     - "hicexplorer"
+#     - "graph_display_data"
+#     - "peak_calling"
+#     - "assembly"
+#     - "annotation"
+#     - "genome_diversity"
+#     - "multiple_alignments"
+#   extra_tool_labels:
+#     - "proteomics"
+galaxy_themes_static_keys:
+  static_dir: ""
+  static_images_dir: "images/"
+  static_scripts_dir: "scripts/"
+  static_welcome_html: "welcome.html/"
+  static_favicon_dir: "favicon.ico"
+  static_robots_txt: "robots.txt"
+galaxy_themes_conf_path: files/galaxy/config/themes_conf.yml
+galaxy_themes_static_path: "{{ galaxy_root }}/server"
+galaxy_themes_static_dir: "{{ galaxy_root }}/server/static"
+galaxy_themes_welcome_url_prefix: https://usegalaxy-eu.github.io/index-
+galaxy_themes_default_welcome: https://galaxyproject.org
+galaxy_themes_ansible_file_path: files/galaxy/static
+galaxy_themes_instance_domain: usegalaxy.eu
+galaxy_themes_global_host_filters_path: "{{ galaxy_root }}/server/lib/galaxy/tool_util/toolbox/filters/global_host_filters.py"
+galaxy_themes_tool_base_labels:
+  - "file_and_meta_tools"
+  - "general_text_tools"
+  - "genomic_file_manipulation"
+  - "gff"
+  - "common_genomics"
+galaxy_themes_tool_ngs_labels:
+  - "specific_genomics"
+  - "genomics_toolkits"
+
+# These sections will be displayed in the tool panel for every subdomain
+galaxy_themes_tool_base_sections:
+  - "getext"
+  - "send"
+  - "collection_operations"
+  - "textutil"
+  - "convert"
+  - "filter"
+  - "group"
+  - "expression_tools"
+
+# There sections are a collection of general NGS tools and will be used in most but not all subdomains
+galaxy_themes_tool_ngs_sections:
+  - "deeptools"
+  - "bed"
+  - "sambam"
+  - "bxops"
+  - "fastafastq"
+  - "fastq_quality_control"
+  - "picard"
+  - "mapping"
+  - "sambam"

tasks/copy_static_files.yml

@@ -0,0 +1,18 @@
+---
+- name: Copy static files
+  ansible.builtin.copy:
+    src: "{{ item }}"
+    dest: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/{{ object.value }}"
+    mode: '0644'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+  with_fileglob: "{{ galaxy_themes_ansible_file_path }}/{{ subdomain.name }}/static/{{ object.value }}*"
+
+- name: Copy files from dist
+  ansible.builtin.copy:
+    src: "{{ item }}"
+    dest: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/dist/"
+    mode: '0644'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+  with_fileglob: "{{ galaxy_themes_ansible_file_path }}/{{ subdomain.name }}/static/dist/*"

tasks/main.yml

@@ -160,3 +160,32 @@
   when: galaxy_manage_cleanup
   tags:
     - galaxy_manage_cleanup
+
+- name: Include create subdomain static dirs and copy static files
+  ansible.builtin.include_tasks: setup_static_dirs.yml
+  # fail only if enabled but dictionary is empty
+  loop: "{{ galaxy_themes_subdomains if galaxy_themes_subdomains|length or \
+    galaxy_manage_static else [] }}"
+  loop_control:
+    loop_var: subdomain
+  when: galaxy_manage_subdomain_static
+  tags:
+    - galaxy_manage_subdomain_static
+
+- name: Include copy themes files
+  ansible.builtin.include_tasks: themes.yml
+  # fail only if enabled but dictionary is empty
+  loop: "{{ galaxy_themes_subdomains if galaxy_themes_subdomains|length or \
+    galaxy_manage_themes else [] }}"
+  loop_control:
+    loop_var: subdomain
+  when: galaxy_manage_themes
+  tags:
+    - galaxy_manage_themes
+
+- name: Set global host filters
+  ansible.builtin.template:
+    src: "global_host_filters.py.j2"
+    dest: "{{ galaxy_themes_global_host_filters_path }}"
+    mode: 0644
+  when: galaxy_manage_host_filters

tasks/setup_static_dirs.yml

@@ -0,0 +1,55 @@
+---
+- name: Create static dirs
+  ansible.builtin.file:
+    state: directory
+    mode: '0755'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+    path: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}"
+
+- name: Move all contents from static to parent directory
+  ansible.builtin.copy: 
+    src: "{{ galaxy_themes_static_dir }}"
+    dest: "{{ galaxy_themes_static_path }}/static-{{ \
+      subdomain.name }}"
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+    directory_mode: true
+  changed_when: false
+
+- name: Remove static dirs
+  ansible.builtin.file:
+    state: absent
+    mode: '0755'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+    path: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/static"
+
+- name: Create welcome.html directory
+  ansible.builtin.file:
+    state: directory
+    mode: '0755'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+    path: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/welcome.html"
+
+- name: Check if iframe for subdomain exists
+  ansible.builtin.uri:
+    url: "{{ galaxy_themes_welcome_url_prefix }}{{ subdomain.name }}.html"
+    return_content: true
+  register: iframe
+  failed_when: false
+
+- name: Template welcome.html for subdomains
+  ansible.builtin.template:
+    src: welcome.html.j2
+    dest: "{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}/welcome.html/index.html"
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+    mode: '0644'
+
+- name: Copy static files
+  ansible.builtin.include_tasks: copy_static_files.yml
+  loop: "{{ galaxy_themes_static_keys | dict2items }}"
+  loop_control:
+    loop_var: object

tasks/themes.yml

@@ -0,0 +1,14 @@
+---
+
+- name: Copy themes files
+  ansible.builtin.copy:
+    src: "{{ galaxy_themes_ansible_file_path }}/{{ subdomain.name }}/themes/{{ subdomain.name }}.yml"
+    dest: "{{ galaxy_config_dir }}"
+    mode: '0644'
+    owner: "{{ __galaxy_privsep_user_name }}"
+    group: "{{ __galaxy_privsep_user_group }}"
+
+- name: Append themes_conf.yml to all files in galaxy/config/themes
+  ansible.builtin.blockinfile:
+    block: "{{ lookup('ansible.builtin.file', galaxy_themes_conf_path) }}"
+    path: "{{ galaxy_config_dir }}/{{ subdomain.name }}.yml"

templates/global_host_filters.py.j2

@@ -0,0 +1,67 @@
+import logging
+log = logging.getLogger( __name__ )
+
+def per_host_tool_labels( context, label ):
+    """
+    This tool section filter results in different labels being displayed based on
+    the fqdn the user is making the request to. This could allow a single Galaxy instance
+    to seem like several different instances hosting different tools based on the fqdn used
+    to access the Galxy. This can be enabled by renaming this file to examples.py and adding
+    the following to the ``app:main`` section of ``galaxy.yml``:
+
+        tool_label_filters = examples:per_host_tool_labels
+    """
+    host = context.trans.request.host
+    subdomain = host.replace('.{{ galaxy_themes_instance_domain }}', '')
+    # Core tools used by all virtual hosts.
+    valid_labels = {{ galaxy_themes_tool_base_labels }}
+    general_ngs_labels = {{ galaxy_themes_tool_ngs_labels }}
+{% if galaxy_themes_subdomains is defined %}
+{% for subsite in galaxy_themes_subdomains %}
+    if "{{ subsite.name }}.{{ galaxy_themes_instance_domain }}" in host:
+        valid_labels += general_ngs_labels
+{% if subsite.extra_tool_labels is defined %}
+        valid_labels += {{ subsite.extra_tool_labels }}
+{% endif %}
+        return label.id in valid_labels
+{% endfor %}
+{% endif %}        
+    return True
+
+BASE_SECTIONS = {{ galaxy_themes_tool_base_sections }}
+
+GENERAL_NGS_SECTIONS = {{ galaxy_themes_tool_ngs_sections }}
+
+DOMAIN_SECTIONS = {
+{% if galaxy_themes_subdomains is defined %}
+{% for subdomain in galaxy_themes_subdomains %}
+{% if subdomain.tool_sections is defined %}
+    '{{ subdomain.name }}': GENERAL_NGS_SECTIONS + {{ subdomain.tool_sections }},
+{% endif %}    
+{% endfor %}
+{% endif %}    
+}
+
+
+def per_host_tool_sections( context, section ):
+    """
+    This tool section filter results in different sections being displayed based on
+    the fqdn the user is making the request to. This could allow a single Galaxy instance
+    to seem like several different instances hosting different tools based on the fqdn used
+    to access the Galxy. This can be enabled by renaming this file to examples.py and adding
+    the following to the ``app:main`` section of ``galaxy.yml``:
+
+        tool_section_filters = examples:per_host_tool_sections
+    """
+    host = context.trans.request.host
+    subdomain = host.replace('.{{ galaxy_themes_instance_domain }}', '')
+
+    # Core tools used by all virtual hosts.
+    # HiCtools mode: published in NAR 2018
+    if host == "{{ galaxy_themes_instance_domain }}":
+        return True
+
+    if subdomain in DOMAIN_SECTIONS:
+        return section.id in DOMAIN_SECTIONS[subdomain] or section.id in BASE_SECTIONS
+    else:
+        return True