Commit a8df2c8e authored by John Chilton's avatar John Chilton
Browse files

Validate column definitions.

parent 8a8112e6

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",