Support setting container resolvers directly in the app config

doc/source/admin/galaxy_options.rst

@@ -692,6 +692,22 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~
+``container_resolvers``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Rather than specifying a container_resolvers_config_file, the
+    definition of the resolvers to enable can be embedded into
+    Galaxy's config with this option. This has no effect if a
+    container_resolvers_config_file is used.
+    The syntax, available resolvers, and documentation of their
+    options is explained in detail in the documentation:
+    https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+:Default: ``None``
+:Type: seq
+
+
 ~~~~~~~~~~~~~~~~~~
 ``involucro_path``
 ~~~~~~~~~~~~~~~~~~

lib/galaxy/config/__init__.py

@@ -1178,6 +1178,7 @@ class ConfiguresGalaxyMixin:
             library_import_dir=self.config.library_import_dir,
             enable_mulled_containers=self.config.enable_mulled_containers,
             container_resolvers_config_file=self.config.container_resolvers_config_file,
+            container_resolvers_config_dict=self.config.container_resolvers,
             involucro_path=self.config.involucro_path,
             involucro_auto_init=self.config.involucro_auto_init,
             mulled_channels=self.config.mulled_channels,

lib/galaxy/config/sample/galaxy.yml.sample

@@ -442,6 +442,15 @@ galaxy:
   # determined by enable_mulled_containers.
   #container_resolvers_config_file: null
 
+  # Rather than specifying a container_resolvers_config_file, the
+  # definition of the resolvers to enable can be embedded into Galaxy's
+  # config with this option. This has no effect if a
+  # container_resolvers_config_file is used.
+  # The syntax, available resolvers, and documentation of their options
+  # is explained in detail in the documentation:
+  # https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+  #container_resolvers: null
+
   # involucro is a tool used to build Docker or Singularity containers
   # for tools from Conda dependencies referenced in tools as
   # `requirement` s. The following path is the location of involucro on

lib/galaxy/tool_util/deps/containers.py

@@ -195,13 +195,19 @@ class ContainerRegistry:
 
     def __build_container_resolvers(self, app_info):
         conf_file = getattr(app_info, 'container_resolvers_config_file', None)
-        if not conf_file:
-            return self.__default_container_resolvers()
-        if not os.path.exists(conf_file):
-            log.debug("Unable to find config file '%s'", conf_file)
-            return self.__default_container_resolvers()
-        plugin_source = plugin_config.plugin_source_from_path(conf_file)
-        return self._parse_resolver_conf(plugin_source)
+        conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+        plugin_source = None
+        if conf_file and not os.path.exists(conf_file):
+            log.warning(f"Unable to find config file '{conf_file}'")
+        elif conf_file:
+            log.debug("Loading container resolution config from file '{conf_file}'")
+            plugin_source = plugin_config.plugin_source_from_path(conf_file)
+        elif conf_dict:
+            log.debug("Loading container resolution config inline from Galaxy configuration file")
+            plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
+        if plugin_source:
+            return self._parse_resolver_conf(plugin_source)
+        return self.__default_container_resolvers()
 
     def _parse_resolver_conf(self, plugin_source):
         extra_kwds = {

lib/galaxy/tool_util/deps/dependencies.py

@@ -16,6 +16,7 @@ class AppInfo:
         library_import_dir=None,
         enable_mulled_containers=False,
         container_resolvers_config_file=None,
+        container_resolvers_config_dict=None,
         involucro_path=None,
         involucro_auto_init=True,
         mulled_channels=DEFAULT_CHANNELS,
@@ -30,6 +31,7 @@ class AppInfo:
         self.library_import_dir = library_import_dir
         self.enable_mulled_containers = enable_mulled_containers
         self.container_resolvers_config_file = container_resolvers_config_file
+        self.container_resolvers_config_dict = container_resolvers_config_dict
         self.involucro_path = involucro_path
         self.involucro_auto_init = involucro_auto_init
         self.mulled_channels = mulled_channels

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -513,6 +513,20 @@ mapping:
           this is set to None, the default container resolvers loaded is
           determined by enable_mulled_containers.
 
+      container_resolvers:
+        type: seq
+        sequence:
+          - type: any
+        desc: |
+          Rather than specifying a container_resolvers_config_file, the definition of the
+          resolvers to enable can be embedded into Galaxy's config with this option.
+          This has no effect if a container_resolvers_config_file is used.
+
+          The syntax, available resolvers, and documentation of their options is explained in detail in the
+          documentation:
+
+          https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
+
       involucro_path:
         type: str
         default: involucro

test/integration/test_containerized_jobs.py

@@ -183,6 +183,25 @@ class MappingContainerResolverTestCase(integration_util.IntegrationTestCase):
         assert "0.7.15-r1140" in output
 
 
+class InlineContainerConfigurationTestCase(MappingContainerResolverTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls.jobs_directory = cls._test_driver.mkdtemp()
+        config["jobs_directory"] = cls.jobs_directory
+        config["job_config_file"] = cls.job_config_file
+        disable_dependency_resolution(config)
+        container_resolvers_config = [{
+            'type': 'mapping',
+            'mappings': [{
+                'container_type': 'docker',
+                'tool_id': 'mulled_example_broken_no_requirements',
+                'identifier': 'quay.io/biocontainers/bwa:0.7.15--0',
+            }],
+        }]
+        config["container_resolvers"] = container_resolvers_config
+
+
 # Singularity 2.4 in the official Vagrant issue has some problems running this test
 # case by default because subdirectories of /tmp don't bind correctly. Overridding
 # TMPDIR can fix this.