Merge branch 'main' of https://github.com/artbio/ansible-galaxy into main

Author: drosofff

.github/workflows/molecule.yml

@@ -22,9 +22,9 @@ jobs:
           - ubuntu:20.04
           - ubuntu:22.04
         galaxy-version:
-          - '21.01'
           - '22.01'
           - '22.05'
+          - '23.0'
           - 'dev'
         exclude:
           # wheels often don't exist in the combination of old package versions in older galaxy releases for newer

.github/workflows/release.yml

@@ -5,7 +5,7 @@
 # See: https://github.com/marketplace/actions/publish-ansible-role-to-galaxy
 # See: https://github.com/ansible/galaxy/issues/46
 
-name: Release
+name: Release (by Tag Push)
 
 'on':
   push:
@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the codebase.
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python 3.
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: '3.x'
 

.github/workflows/slugger.yml

@@ -16,50 +16,57 @@ name: "Automatic Regular Releases"
 on:
   workflow_dispatch:
   schedule:
-    - cron:  '0 0 * * 1'
+    - cron: '0 0 * * 1'
 
 jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
     steps:
       - name: Check out the codebase.
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python 3.
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: '3.x'
 
       - name: Install Ansible.
-        run: pip3 install ansible-base
+        run: pip3 install six ansible-base
 
       - name: Check for changes
         run: |
-          MOST_RECENT_TAG=$(git describe --tags --abbrev=0)
-          CHANGES=$(git diff ${MOST_RECENT_TAG} --name-only | wc -l)
-          echo "Found ${CHANGES} files"
-          git diff ${MOST_RECENT_TAG} --name-only
+          LATEST_TAG=$(git describe --tags --abbrev=0)
+          echo "The last released tag was ${LATEST_TAG}"
+          CHANGES=$(git diff ${LATEST_TAG} --name-only | wc -l)
+          echo "Found ${CHANGES} changed files"
+          git diff ${LATEST_TAG} --name-only
           echo "changed_files=${CHANGES}" >> $GITHUB_ENV
 
       - name: Create a new git tag
         run: |
-          MOST_RECENT_TAG=$(git describe --tags --abbrev=0)
-          major_minor=$(echo "$MOST_RECENT_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\1/')
-          patch=$(echo "$MOST_RECENT_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\2/')
+          LATEST_TAG=$(git describe --tags --abbrev=0)
+          major_minor=$(echo "$LATEST_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\1/')
+          patch=$(echo "$LATEST_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\2/')
           newpatch=$(echo "$patch + 1" | bc)
           NEW_TAG="${major_minor}${newpatch}"
-          echo "$MOST_RECENT_TAG -> $NEW_TAG"
+          echo "$LATEST_TAG -> $NEW_TAG"
 
           git config user.name github-actions
           git config user.email [email protected]
           git tag "$NEW_TAG"
           git push --tags
+          echo "Creating new tag $NEW_TAG" >> $GITHUB_STEP_SUMMARY
         if: env.changed_files > 0
 
-      # We have to do this step as GHA prevents triggering it's own actions, to prevent runaway loops.
+      # We have to do this step as GHA prevents triggering it's own actions, to
+      # prevent runaway loops.
       - name: Trigger a new import on Galaxy.
-        run: ansible-galaxy role import --api-key ${{ secrets.GALAXY_API_KEY }} $(echo ${{ github.repository }} | cut -d/ -f1) $(echo ${{ github.repository }} | cut -d/ -f2) --branch main
+        run: |
+          org=$(echo ${{ github.repository }} | cut -d/ -f1)
+          repo=$(echo ${{ github.repository }} | cut -d/ -f2)
+          key=${{ secrets.GALAXY_API_KEY }}
+          ansible-galaxy role import --api-key $key $org $repo --branch main
         if: env.changed_files > 0

README.md

@@ -105,6 +105,44 @@ 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_subdomain_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 feature, you need to create the following directory structure under files/ (customizable with the `galaxy_themes_ansible_file_path` variable):
+
+~~~bash
+files/galaxy/static
+├──<subdomain-name-1>
+│   ├── static
+│   │   ├── dist (optional)
+│   │   │   └── some-image.png 
+│   │   ├── images (optional)
+│   │   │   └── more-content.jpg
+│   │   └── welcome.html (optional, galaxyproject.org will be displayed otherwise.)
+│   └── themes 
+│       └── <subdomain-name-1>.yml           
+├── <subdomain-name-2>                            
+│   ├── static
+│   │   ├── dist (optional)
+│   │   │   ├── another-static-image.svg
+│   │   │   └── more-static-content-2.svg
+│   │   └── welcome.html (optional)
+│   └── themes
+│       └── <subdomain-name-2>.yml
+... (and many more subdomains)
+~~~
+
+Where 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 +541,4 @@ 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 +23,10 @@ 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
+galaxy_auto_brand: no # automatically sets the subdomain name as brand
 
 
 # Control whether to output verbose task diffs (e.g. when performing a git update) when running Ansible with --diff.
@@ -107,13 +111,19 @@ galaxy_dirs:
   - "{{ galaxy_tool_data_path }}"
   - "{{ galaxy_log_dir }}"
 
+# Additional directories to create as the Galaxy user, so you don't have to copy the default galaxy_dirs
+galaxy_extra_dirs: []
+
 # Directories to create as the privilege separated user if galaxy_manage_paths is enabled
 galaxy_privsep_dirs:
   - "{{ galaxy_venv_dir }}"
   - "{{ galaxy_server_dir }}"
   - "{{ galaxy_config_dir }}"
   - "{{ galaxy_local_tools_dir }}"
 
+# Additional directories to create as the privilege separated user, so you don't have to copy the default galaxy_dirs
+galaxy_extra_privsep_dirs: []
+
 # Local (relative to playbook) path to local tools
 galaxy_local_tools_src_dir: files/galaxy/tools
 
@@ -182,7 +192,7 @@ _galaxy_tmpclean_command:
 
 galaxy_tmpclean_verbose_statement: "{{ galaxy_tmpclean_verbose | ternary(' -v', '') }}"
 galaxy_tmpclean_log_statement: >-
-  {{ (galaxy_tmpclean_log is not true) | ternary(
+  {{ (galaxy_tmpclean_log != true) | ternary(
       ((galaxy_tmpclean_log is none) | ternary(
           '>/dev/null',
           '>>' ~ galaxy_tmpclean_log
@@ -246,6 +256,7 @@ galaxy_app_config_section: "{{ 'galaxy' if galaxy_config_style in ('yaml', 'yml'
 
 # Galaxy configuration files will be written with these permissions (mode argument to Ansible copy/template module)
 galaxy_config_perms: 0640
+galaxy_config_perms_public: 0644
 
 # The default Galaxy configuration, ensures that Galaxy can find all of the configs if galaxy_config_dir !=
 # galaxy_server_dir
@@ -288,6 +299,64 @@ galaxy_app_config_default:
   # Everything else
   visualization_plugins_directory: "config/plugins/visualizations"
 
+  # Static and themes configuration, will only be added if galaxy_manage_themes
+  static_enabled: "{{ galaxy_manage_subdomain_static }}"
+  static_dir_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/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 %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/static/images',
+    {% 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 %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/static/welcome.html',
+    {% 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 %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/static/scripts',
+    {% 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 %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/static',
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}',
+    {% endfor %}
+    {% endif %} }
+  static_robots_txt_by_host: >
+    { {% if galaxy_manage_subdomain_static %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_static_path }}/static',
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name }}.{{ galaxy_themes_instance_domain}}': '{{ galaxy_themes_static_path }}/static-{{ subdomain.name }}',
+    {% endfor %}
+    {% endif %} }
+  themes_config_file_by_host: >
+    { {% if galaxy_manage_themes %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_conf_file_name }}',
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name  }}.{{ galaxy_themes_instance_domain}}': '{{ subdomain.name }}.yml',
+    {% endfor %}
+    {% endif %} }
+  brand_by_host: >
+    { {% if galaxy_auto_brand %}
+    '{{ galaxy_themes_instance_domain }}': '{{ galaxy_themes_instance_domain }}',
+    {% for subdomain in galaxy_themes_subdomains %}
+    '{{ subdomain.name  }}.{{ galaxy_themes_instance_domain}}': '{{ subdomain.name[0]|upper }}{{ subdomain.name[1:] }}',
+    {% 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) }}"
@@ -313,6 +382,8 @@ galaxy_errordocs_prefix: /error
 # templates to be installed on the managed host.
 galaxy_config_files: []
 galaxy_config_templates: []
+# Like above, except with world readable permissions
+galaxy_config_files_public: []
 
 # Default Gravity configuration
 galaxy_gravity_state_dir: "{{ (galaxy_mutable_data_dir, 'gravity') | path_join }}"
@@ -358,6 +429,9 @@ galaxy_uwsgi_config_default:
 # build separately, but this is not guaranteed to work for all version of Galaxy - using `make` is the safer choice.
 galaxy_client_make_target: client-production-maps
 
+# Build the client even if it is not out of date
+galaxy_client_force_build: false
+
 # If galaxy_client_make_target is null, you can set this to `development` to build the client for development
 galaxy_client_node_env: production
 galaxy_client_build_steps:
@@ -369,10 +443,21 @@ galaxy_client_build_steps:
     - stageLibs
     - plugins
 
+__galaxy_node_version_max:
+  "redhat7": "16.19.1"
+galaxy_node_version_max: >-
+  {{
+    (__galaxy_node_version_max[(ansible_os_family | lower) ~ ansible_distribution_major_version]) | default(galaxy_node_version)
+  }}
+
 #
 # systemd options
 #
 
+__galaxy_gravity_pm: "{{ (galaxy_config_merged.gravity | default({})).process_manager | default('supervisor') }}"
+__galaxy_gravity_instance_name: "{{ (galaxy_config_merged.gravity | default({})).instance_name | default(none) }}"
+galaxy_gravity_wrapper_path: "/usr/local/bin/galaxyctl{{ __galaxy_gravity_instance_name | ternary('-' ~ __galaxy_gravity_instance_name, '') }}"
+
 # Currently `mule` (aka uWSGI) and `gravity` (runs Galaxy 22.01+ under gunicorn) are supported
 galaxy_systemd_mode: "{{ 'mule' if __galaxy_major_version is version('22.05', '<') else 'gravity' }}"
 
@@ -405,3 +490,67 @@ 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_conf_file_name: "{{ galaxy_themes_conf_path | basename }}"
+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_symlinks: true
+galaxy_themes_symlinks_no_log: false # Hides extended logs for the symlink task in static/dist
+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"