Wire up and test resource requirement via tpv

lib/galaxy/dependencies/conditional-requirements.txt

@@ -13,7 +13,7 @@ ldap3==2.9.1
 python-pam
 galaxycloudrunner
 pkce
-total-perspective-vortex>=2.3.2,<3
+total-perspective-vortex>=3.1.0,<4
 openai
 # upper version constraint because of https://github.com/galaxyproject/galaxy/issues/20600
 redis>=5.3.0,<6

lib/galaxy/dependencies/dev-requirements.txt

@@ -18,6 +18,7 @@ boto3==1.40.18
 botocore==1.40.18
 build==1.3.0
 cachecontrol==0.14.3
+cachetools==5.5.2
 cattrs==25.2.0
 certifi==2025.8.3
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
@@ -90,6 +91,7 @@ mistune==3.0.2
 more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.1
 multidict==6.6.4
+mypy==1.18.2
 mypy-extensions==1.1.0
 myst-parser==3.0.1 ; python_full_version < '3.10'
 myst-parser==4.0.1 ; python_full_version >= '3.10'
@@ -197,11 +199,16 @@ text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.2.1 ; python_full_version <= '3.11'
+total-perspective-vortex==3.1.0
 trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
 twine==6.2.0
+types-cachetools==6.2.0.20250827
+types-requests==2.31.0.6 ; python_full_version < '3.10'
+types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
+types-urllib3==1.26.25.14 ; python_full_version < '3.10'
 typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1

lib/galaxy/dependencies/pinned-requirements.txt

@@ -124,7 +124,8 @@ mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version == '3.10.*'
 networkx==3.5 ; python_full_version >= '3.11'
-nodejs-wheel==22.13.0
+nodejs-wheel==22.20.0
+nodejs-wheel-binaries==22.20.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
 numpy==2.3.3 ; python_full_version >= '3.11'

lib/galaxy/dependencies/pinned-test-requirements.txt

@@ -12,6 +12,7 @@ backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 boto3==1.40.18
 botocore==1.40.18
 cachecontrol==0.14.3
+cachetools==5.5.2
 cattrs==25.2.0
 certifi==2025.8.3
 cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt'
@@ -66,6 +67,7 @@ mirakuru==2.6.1
 mistune==3.0.2
 msgpack==1.1.1
 multidict==6.6.4
+mypy==1.18.2
 mypy-extensions==1.1.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
@@ -76,6 +78,7 @@ owlrl==6.0.2 ; python_full_version < '3.10'
 owlrl==7.1.4 ; python_full_version >= '3.10'
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
+pathspec==0.12.1
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
@@ -145,10 +148,15 @@ text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.2.1 ; python_full_version <= '3.11'
+total-perspective-vortex==3.1.0
 trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
+types-cachetools==6.2.0.20250827
+types-requests==2.31.0.6 ; python_full_version < '3.10'
+types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
+types-urllib3==1.26.25.14 ; python_full_version < '3.10'
 typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1

lib/galaxy/tool_util/deps/requirements.py

@@ -302,7 +302,9 @@ def resource_requirements_from_list(requirements: Iterable[Dict[str, Any]]) -> L
         for key in valid_key_set.intersection(set(r.keys())):
             value = r[key]
             key = cast(ResourceType, cwl_to_galaxy.get(key, key))
-            rr.append(ResourceRequirement(value_or_expression=value, resource_type=key))
+            if value is not None:
+                # all resoure requirement fields are optional
+                rr.append(ResourceRequirement(value_or_expression=value, resource_type=key))
     return rr
 
 

pyproject.toml

@@ -60,7 +60,7 @@ dependencies = [
     "mercurial>=6.8.2",  # Python 3.13 support
     "mrcfile",
     "msal",
-    "nodejs-wheel==22",
+    "nodejs-wheel>=22,<23",
     "numpy>=1.26.0",  # Python 3.12 support
     "numpy>=2.1.0 ; python_version>='3.10'",  # Python 3.13 support
     "openpyxl>=3.1.5",  # Minimum version ever tested with
@@ -146,6 +146,7 @@ test = [
     "seletools",
     "statsd",
     "testfixtures",
+    "total-perspective-vortex>=3.1.0,<4",  # https://github.com/galaxyproject/total-perspective-vortex/pull/166
     "tuspy",
     "twill>=3.2.5",  # Python 3.13 support
     "watchdog",

test/integration/embedded_pulsar_tpv_job_conf.yml

@@ -0,0 +1,44 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+  pulsar_embed:
+    load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+    pulsar_app_config:  # this doesn't start without disabling - filelock problem
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
+
+execution:
+  default: tpv
+  environments:
+    tpv:
+      runner: dynamic_tpv
+      tpv_configs:
+        - destinations:
+            local:
+              runner: local
+              env:
+                GALAXY_SLOTS: '{cores}'
+            user_defined:
+              runner: pulsar_embed
+              env:
+                GALAXY_SLOTS: '{cores}'
+              scheduling:
+                accept:
+                  - support_user_defined
+              params:
+                remote_metadata: true
+                docker_enabled: true
+                require_container: true
+                docker_net: "none"
+          global:
+            default_inherits: default
+
+          tools:
+            default:
+              abstract: true
+              cores: 1
+            user_defined-*:
+              scheduling:
+                require:
+                  - support_user_defined

test/integration/test_user_defined_tool_job_conf.py

@@ -2,6 +2,8 @@
 
 import os
 
+import yaml
+
 from galaxy.tool_util_models import UserToolSource
 from galaxy_test.api.test_tools import TestsTools
 from galaxy_test.base.populators import (
@@ -12,18 +14,39 @@
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
+EMBEDDED_PULSAR_TPV_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_tpv_job_conf.yml")
+TOOL_WITH_RESOURCE_SPECIFICATION = yaml.safe_load(
+    """class: GalaxyUserTool
+id: resource_requirement
+version: "0.1"
+name: resource_requirement
+description: test resource requirement
+container: busybox
+requirements:
+  - type: resource
+    cores_min: 2
+shell_command: |
+  echo $GALAXY_SLOTS > galaxy_cores.txt
+outputs:
+  - name: output2
+    type: data
+    format: txt
+    from_work_dir: galaxy_cores.txt
+"""
+)
 
 
 class TestUserDefinedToolRecommendedJobSetup(integration_util.IntegrationTestCase, TestsTools):
     """Exercies how user defined tools could be run in production."""
 
     framework_tool_and_types = True
+    job_config_file = EMBEDDED_PULSAR_JOB_CONFIG_FILE
     dataset_populator: DatasetPopulator
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
+        config["job_config_file"] = cls.job_config_file
         config["enable_celery_tasks"] = False
         config["metadata_strategy"] = "directory"
         config["admin_users"] = "[email protected]"
@@ -57,3 +80,30 @@ def test_user_defined_runs_in_correct_destination(self):
 
         assert destination_params["Runner"] == "pulsar_embed"
         assert destination_params["require_container"]
+
+
+class TestUserDefinedToolRecommendedJobSetupTPV(TestUserDefinedToolRecommendedJobSetup):
+
+    job_config_file = EMBEDDED_PULSAR_TPV_JOB_CONFIG_FILE
+
+    def test_user_defined_applies_resource_requirements(self):
+        with (
+            self.dataset_populator.test_history() as history_id,
+            self.dataset_populator.user_tool_execute_permissions(),
+        ):
+            # Create a new dynamic tool.
+            # This is a shell command tool that will echo the input dataset.
+            dynamic_tool = self.dataset_populator.create_unprivileged_tool(
+                UserToolSource(**TOOL_WITH_RESOURCE_SPECIFICATION)
+            )
+            # Run tool.
+            response = self._run(
+                history_id=history_id,
+                tool_uuid=dynamic_tool["uuid"],
+                inputs={},
+                wait_for_job=True,
+                assert_ok=True,
+            )
+            cores = response["outputs"][0]
+            cores_content = self.dataset_populator.get_history_dataset_content(history_id, content_id=cores["id"])
+            assert cores_content == "2.0\n"