Merge pull request galaxyproject#16795 from sveinugu/it_inject_entry_…

…point_path

Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf

config/galaxy.yml.interactivetools

@@ -2,18 +2,29 @@ gravity:
   gx_it_proxy:
     enable: true
     port: 4002
+
+  #handlers:
+  #  handler:
+  #    processes: 3
+  #    pools:
+  #      - job-handlers
+  #      - workflow-schedulers
+
 galaxy:
   interactivetools_enable: true
+  interactivetools_map: database/interactivetools_map.sqlite
+
   # outputs_to_working_directory will provide you with a better level of isolation. It is highly recommended to set
   # this parameter with InteractiveTools.
   outputs_to_working_directory: true
-  interactivetools_map: database/interactivetools_map.sqlite
+
   # `galaxy_infrastructure_url` needs to be reachable from IT containers.
-  # For local development you can map arbitrary hostnames. See `job_conf.xml.interactivetools`
+  # For local development you can map arbitrary hostnames. See `job_conf.yml.interactivetools`
   # for an example.
   # In the local development case you should use the `http` protocol (e.g http://localhost:8080) to access
   # your Galaxy, so saving notebooks doesn't fail due to invalid certificates.
   galaxy_infrastructure_url: http://localhost:8080
+
   # Do not set the following 2 options if you are using an upstream proxy server like nginx
   interactivetools_upstream_proxy: false
   interactivetools_proxy_host: localhost:4002

config/job_conf.yml.interactivetools

@@ -0,0 +1,58 @@
+## A sample job config for InteractiveTools using local runner. ##
+
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 4
+
+# Uncomment if dynamic handlers are defined in "gravity:handlers" section in galaxy.yml
+#
+#handling:
+#  assign:
+#    - db-skip-locked
+
+execution:
+  default: docker_dispatch
+  environments:
+    local:
+      runner: local
+
+    docker_local:
+      runner: local
+      docker_enabled: true
+      #docker_volumes: $defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro
+      #docker_volumes_from: parent_container_name
+      #docker_memory: 24G
+      #docker_sudo: false
+      #docker_sudo_cmd: /usr/bin/sudo -extra_param
+      #docker_net: bridge
+      #docker_auto_rm: true
+      #docker_set_user: $UID
+      docker_set_user:
+
+      # InteractiveTools do need real hostnames or URLs to work - simply specifying IPs will not work.
+      # If you develop interactive tools on your 'localhost' and don't have a proper domain name
+      # you need to tell all Docker containers a hostname where Galaxy is running.
+      # This can be done via the add-host parameter during the `docker run` command.
+      # 'localhost' here is an arbitrary hostname that matches the IP address of your
+      # Galaxy host. Make sure this hostname ('localhost') is also set in your galaxy.yml file, e.g.
+      # `galaxy_infrastructure_url: http://localhost:8080`.
+      #docker_run_extra_arguments: add-host localhost:host-gateway
+
+      #docker_cmd: /usr/local/custom_docker/docker
+      #docker_host:
+      #docker_container_id_override: busybox:ubuntu-14.04
+      #docker_default_container_id: busybox:ubuntu-14.04
+      #require_container: true
+      #container_monitor: true
+      #container_monitor_result: file
+      #container_monitor_command: python /path/to/galaxy/lib/galaxy_ext/container_monitor/monitor.py
+      #container_monitor_get_ip_method: null
+      #container_resolvers_config_file: null
+      #container_resolvers:
+
+    docker_dispatch:
+      runner: dynamic
+      type: docker_dispatch
+      docker_destination_id: docker_local
+      default_destination_id: local

config/job_conf.yml.interactivetools.podman

@@ -0,0 +1,38 @@
+## A sample job config for InteractiveTools using local runner, configured for Podman ##
+
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 4
+
+# Uncomment if dynamic handlers are defined in "gravity:handlers" section in galaxy.yml
+#
+#handling:
+#  assign:
+#    - db-skip-locked
+
+execution:
+  default: docker_dispatch
+  environments:
+    local:
+      runner: local
+
+    docker_local:
+      runner: local
+      docker_enabled: true
+
+      docker_set_user:
+
+      # For containers running as root (on the inside)
+      docker_run_extra_arguments: --security-opt label=disable
+      # Should work for containers with non-root user (on the inside)
+      #docker_run_extra_arguments:  --userns=keep-id --security-opt label=disable
+
+      # Change to home directory of the galaxy user, not the directory of the galaxy installation
+      docker_cmd: HOME="/home/galaxy"; podman
+
+    docker_dispatch:
+      runner: dynamic
+      type: docker_dispatch
+      docker_destination_id: docker_local
+      default_destination_id: local

doc/source/admin/galaxy_options.rst

@@ -2023,18 +2023,6 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``interactivetools_shorten_url``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Shorten the uuid portion of the subdomain or path for interactive
-    tools. Especially useful for avoiding the need for wildcard
-    certificates by keeping subdomain under 63 chars
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``retry_interactivetool_metadata_internally``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~