Support setting per-job-environment container resolvers using the container_resolvers key in the environment config.

lib/galaxy/config/__init__.py

@@ -1208,8 +1208,8 @@ class ConfiguresGalaxyMixin:
                 for enabled_container_type in self.container_finder._enabled_container_types(destination.params):
                     container_types_to_destinations[enabled_container_type].append(destination)
         self.toolbox.dependency_manager.set_enabled_container_types(container_types_to_destinations)
-        self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.container_registry.resolver_classes)
-        self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.container_registry.container_resolvers)
+        self.toolbox.dependency_manager.resolver_classes.update(self.container_finder.default_container_registry.resolver_classes)
+        self.toolbox.dependency_manager.dependency_resolvers.extend(self.container_finder.default_container_registry.container_resolvers)
 
     def _configure_tool_data_tables(self, from_shed_config):
         from galaxy.tools.data import ToolDataTableManager

lib/galaxy/tool_util/deps/containers.py

@@ -42,7 +42,9 @@ class ContainerFinder:
 
     def __init__(self, app_info, mulled_resolution_cache=None):
         self.app_info = app_info
-        self.container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
+        self.mulled_resolution_cache = mulled_resolution_cache
+        self.default_container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
+        self.destination_container_registeries = {}
 
     def _enabled_container_types(self, destination_info):
         return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)]
@@ -51,11 +53,26 @@ class ContainerFinder:
         """Regardless of destination properties - find best container for tool.
 
         Given container types and container.ToolInfo description of the tool."""
-        return self.container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
+        return self.default_container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
         """Regardless of destination properties - find ResolvedContainerDescription for tool."""
-        return self.container_registry.resolve(enabled_container_types, tool_info, **kwds)
+        return self.default_container_registry.resolve(enabled_container_types, tool_info, **kwds)
+
+    def _container_registry_for_destination(self, destination_info):
+        destination_id = destination_info.get("id")  # Probably not the way to get the ID?
+        destination_container_registry = None
+        if destination_id and destination_id not in self.destination_container_registeries:
+            if 'container_resolvers' in destination_info:
+                destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+                self.destination_container_registeries[destination_id] = destination_container_registry
+        elif not destination_id and 'container_resolvers' in destination_info:
+            destination_container_registry = ContainerRegistry(self.app_info, destination_info=destination_info, mulled_resolution_cache=self.mulled_resolution_cache)
+
+        if destination_container_registry is None and destination_id and destination_id in self.destination_container_registeries:
+            destination_container_registry = self.destination_container_registeries[destination_id]
+
+        return destination_container_registry or self.default_container_registry
 
     def find_container(self, tool_info, destination_info, job_info):
         enabled_container_types = self._enabled_container_types(destination_info)
@@ -102,7 +119,8 @@ class ContainerFinder:
                     return container
 
         # Otherwise lets see if we can find container for the tool.
-        container_description = self.find_best_container_description(enabled_container_types, tool_info)
+        container_registry = self._container_registry_for_destination(destination_info)
+        container_description = container_registry.find_best_container_description(enabled_container_types, tool_info)
         container = __destination_container(container_description)
         if container:
             return container
@@ -124,7 +142,7 @@ class ContainerFinder:
         return NULL_CONTAINER
 
     def resolution_cache(self):
-        return self.container_registry.get_resolution_cache()
+        return self.default_container_registry.get_resolution_cache()
 
     def __overridden_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
@@ -186,25 +204,33 @@ class NullContainerFinder:
 class ContainerRegistry:
     """Loop through enabled ContainerResolver plugins and find first match."""
 
-    def __init__(self, app_info, mulled_resolution_cache=None):
+    def __init__(self, app_info, destination_info=None, mulled_resolution_cache=None):
         self.resolver_classes = self.__resolvers_dict()
         self.enable_mulled_containers = app_info.enable_mulled_containers
         self.app_info = app_info
-        self.container_resolvers = self.__build_container_resolvers(app_info)
+        self.container_resolvers = self.__build_container_resolvers(app_info, destination_info)
         self.mulled_resolution_cache = mulled_resolution_cache
 
-    def __build_container_resolvers(self, app_info):
-        conf_file = getattr(app_info, 'container_resolvers_config_file', None)
-        conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+    def __build_container_resolvers(self, app_info, destination_info):
+        app_conf_file = getattr(app_info, 'container_resolvers_config_file', None)
+        app_conf_dict = getattr(app_info, 'container_resolvers_config_dict', None)
+
+        if destination_info is not None:
+            conf_file = destination_info.get('container_resolvers_config_file', app_conf_file)
+            conf_dict = destination_info.get('container_resolvers', app_conf_dict)
+        else:
+            conf_file = app_conf_file
+            conf_dict = app_conf_dict
+
         plugin_source = None
-        if conf_file and not os.path.exists(conf_file):
+        if conf_dict:
+            log.debug("Loading container resolution config inline from Galaxy or job configuration file")
+            plugin_source = plugin_config.plugin_source_from_dict(conf_dict)
+        elif 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()

test/functional/tools/mulled_example_broken_no_requirements_fallback.xml

@@ -0,0 +1,25 @@
+<tool id="mulled_example_broken_no_requirements_fallback" name="mulled_example_broken_no_requirements_fallback" version="0.1.0">
+    <!-- mulled_example_explicit without requirements... to test mapping with job conf inline container resolvers config -->
+    <!--
+    <requirements>
+        <requirement type="package" version="0.7.15">bwa</requirement>
+        <container type="docker">quay.io/biocontainers/bwa:0.7.15-\-0</container>
+    </requirements>
+    -->
+    <stdio>
+        <exit_code range="2:" />
+    </stdio>
+    <command><![CDATA[
+bwa > $output_1 2>&1
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="output_1" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+TODO: Fill in help.
+    ]]></help>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -243,6 +243,7 @@
   <tool file="mulled_example_explicit.xml" />
   <tool file="mulled_example_invalid_case.xml" />
   <tool file="mulled_example_broken_no_requirements.xml" />
+  <tool file="mulled_example_broken_no_requirements_fallback.xml" />
 
   <tool file="simple_constructs.yml" />
 

test/integration/dockerized_job_conf.xml

@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-    </plugins>
-
-    <destinations default="local_docker">
-        <destination id="local_docker" runner="local">
-            <param id="docker_enabled">true</param>
-            <param id="docker_sudo">false</param>
-        </destination>
-
-        <destination id="local_upload" runner="local">
-        </destination>
-
-    </destinations>
-
-    <tools>
-        <tool id="upload1" destination="local_upload" />
-    </tools>
-
-</job_conf>

test/integration/dockerized_job_conf.yml

@@ -0,0 +1,26 @@
+---
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+
+execution:
+  default: local_docker
+  environments:
+    local_docker:
+      runner: local
+      docker_enabled: true
+    local_docker_inline_container_resolvers:
+      runner: local
+      docker_enabled: true
+      container_resolvers:
+        - type: fallback
+          identifier: 'quay.io/biocontainers/bwa:0.7.15--0'
+    local_upload:
+      runner: local
+
+tools:
+  - id: upload1
+    environment: local_upload
+  - id: mulled_example_broken_no_requirements_fallback
+    environment: local_docker_inline_container_resolvers

test/integration/singularity_job_conf.xml

@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-    </plugins>
-
-    <destinations default="local_singularity">
-        <destination id="local_singularity" runner="local">
-            <param id="singularity_enabled">true</param>
-        </destination>
-
-        <destination id="local_upload" runner="local">
-        </destination>
-
-    </destinations>
-
-    <tools>
-        <tool class="local" destination="local_upload" />
-    </tools>
-
-</job_conf>

test/integration/singularity_job_conf.yml

@@ -0,0 +1,18 @@
+---
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 1
+
+execution:
+  default: local_singularity
+  environments:
+    local_singularity:
+      runner: local
+      singularity_enabled: true
+    local_upload:
+      runner: local
+
+tools:
+  - id: upload1
+    environment: local_upload

test/integration/test_containerized_jobs.py

@@ -12,8 +12,8 @@ from galaxy_test.driver import integration_util
 from .test_job_environments import RunsEnvironmentJobs
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.xml")
-SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.xml")
+DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.yml")
+SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.yml")
 EXTENDED_TIMEOUT = 120
 
 
@@ -202,6 +202,36 @@ class InlineContainerConfigurationTestCase(MappingContainerResolverTestCase):
         config["container_resolvers"] = container_resolvers_config
 
 
+class InlineJobEnvironmentContainerResolverTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+    container_type = 'docker'
+    job_config_file = DOCKERIZED_JOB_CONFIG_FILE
+
+    @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)
+
+    @classmethod
+    def setUpClass(cls):
+        skip_if_container_type_unavailable(cls)
+        super().setUpClass()
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+    def test_inline_environment_container_resolver_configuration(self):
+        self.dataset_populator.run_tool("mulled_example_broken_no_requirements_fallback", {}, self.history_id)
+        self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
+        output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
+        assert "0.7.15-r1140" in output
+
+
 # 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.