Merge pull request #20880 from jmchilton/validate_columns (3b215326) · Commits · NDIP / Galaxy

lib/galaxy/dependencies/pinned-requirements.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -82,7 +82,7 @@ greenlet==3.2.4 ; (python_full_version < '3.14' and platform_machine == 'AMD64')
		grpcio==1.74.0
		grpcio-status==1.74.0
		gunicorn==23.0.0
		gxformat2==0.20.0
		gxformat2==0.21.0
		h11==0.16.0
		h5grove==2.3.0
		h5py==3.14.0

lib/galaxy/workflow/modules.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -41,6 +41,7 @@ from galaxy.model.base import ensure_object_added_to_session
		from galaxy.model.dataset_collections import matching
		from galaxy.model.dataset_collections.query import HistoryQuery
		from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY
		from galaxy.model.dataset_collections.types.sample_sheet_util import validate_column_definitions
		from galaxy.schema.invocation import (
		CancelReason,
		FailureReason,
		@@ -1166,6 +1167,9 @@ class InputDataCollectionModule(InputModule):
		fields=fields,
		)
		collection_type_description.validate()
		column_definitions = state.get("column_definitions")
		if column_definitions:
		validate_column_definitions(column_definitions)
		return None

		def get_runtime_inputs(self, step, connections: Optional[Iterable[WorkflowStepConnection]] = None):

lib/galaxy_test/api/test_workflows.py

+66 −0

Original line number	Diff line number	Diff line
		@@ -7836,6 +7836,72 @@ steps:
		assert r.status_code == 400
		assert "Invalid collection type:" in r.json()["err_msg"]

		@skip_without_tool("multi_data_optional")
		def test_invalid_sample_sheet_definitions_rejected(self):
		valid_collection_type = """
		class: GalaxyWorkflow
		inputs:
		input:
		type: collection
		collection_type: sample_sheet
		column_definitions:
		- type: string
		name: condition
		default_value: treatment
		optional: false
		restrictions: ["treatment", "control"]
		steps:
		multi_data_optional:
		tool_id: multi_data_optional
		in:
		input1: input
		"""
		r = self._post("workflows", files={"archive_file": io.StringIO(valid_collection_type)})
		assert r.status_code == 200

		invalid_collection_type = """
		class: GalaxyWorkflow
		inputs:
		input:
		type: collection
		collection_type: sample_sheet
		column_definitions:
		- type: stringx
		name: condition
		default_value: treatment
		optional: false
		restrictions: ["treatment", "control"]
		steps:
		multi_data_optional:
		tool_id: multi_data_optional
		in:
		input1: input
		"""
		r = self._post("workflows", files={"archive_file": io.StringIO(invalid_collection_type)})
		assert r.status_code == 400

		invalid_collection_type = """
		class: GalaxyWorkflow
		inputs:
		input:
		type: collection
		collection_type: sample_sheet
		column_definitions:
		- type: string
		name: condition
		default_value: treatment
		optional: false
		restrictions: ["treatment", "control"]
		extra_key: not_allowed
		steps:
		multi_data_optional:
		tool_id: multi_data_optional
		in:
		input1: input
		"""
		r = self._post("workflows", files={"archive_file": io.StringIO(invalid_collection_type)})
		assert r.status_code == 400

		@skip_without_tool("random_lines1")
		def test_run_replace_params_over_default_delayed(self):
		with self.dataset_populator.test_history() as history_id:

pyproject.toml

+1 −1

Original line number	Diff line number	Diff line
		@@ -43,7 +43,7 @@ dependencies = [
		"future>=1.0.0", # Python 3.12 support
		"gravity>=1.1.1",
		"gunicorn",
		"gxformat2",
		"gxformat2>=0.21.0",
		"h5grove>=1.2.1",
		"h5py>=3.12", # Python 3.13 support
		"httpx",

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