Unverified Commit d2597738 authored by mvdbeek's avatar mvdbeek
Browse files

Make to_cwl compatible with pulsar

parent 259bee36

lib/galaxy/tools/evaluation.py

+1 −1
Original line number Diff line number Diff line
@@ -945,7 +945,7 @@ class UserToolEvaluator(ToolEvaluator): 
        from galaxy.workflow.modules import to_cwl



        hda_references: List[model.HistoryDatasetAssociation] = []

        cwl_style_inputs = to_cwl(incoming, hda_references=hda_references)

        cwl_style_inputs = to_cwl(incoming, hda_references=hda_references, compute_environment=compute_environment)

        return {"inputs": cwl_style_inputs, "outdir": job_working_directory}



    def _build_command_line(self):

lib/galaxy/workflow/modules.py

+20 −6
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ from galaxy.exceptions import ( 
    ToolMissingException,

)

from galaxy.job_execution.actions.post import ActionBox

from galaxy.job_execution.compute_environment import ComputeEnvironment

from galaxy.model import (

    Job,

    PostJobAction,
@@ -149,7 +150,9 @@ class ConditionalStepWhen(BooleanToolParameter): 
    pass





def to_cwl(value, hda_references, step: Optional[WorkflowStep] = None):

def to_cwl(

    value, hda_references, step: Optional[WorkflowStep] = None, compute_environment: Optional[ComputeEnvironment] = None

):

    element_identifier = None

    if isinstance(value, model.HistoryDatasetCollectionAssociation):

        value = value.collection
@@ -179,7 +182,7 @@ def to_cwl(value, hda_references, step: Optional[WorkflowStep] = None): 
                "class": "File",

                "location": f"step_input://{len(hda_references)}",

                "format": value.extension,

                "path": value.get_file_name(),

                "path": compute_environment.input_path_rewrite(value) if compute_environment else value.get_file_name(),

            }

            set_basename_and_derived_properties(

                properties, value.dataset.created_from_basename or element_identifier or value.name
@@ -187,22 +190,33 @@ def to_cwl(value, hda_references, step: Optional[WorkflowStep] = None): 
            return properties

    elif isinstance(value, model.DatasetCollection):

        if value.collection_type == "list":

            return [to_cwl(dce, hda_references=hda_references, step=step) for dce in value.dataset_elements]

            return [

                to_cwl(dce, hda_references=hda_references, step=step, compute_environment=compute_environment)

                for dce in value.dataset_elements

            ]

        else:

            # Could be record or nested lists

            rval = {}

            for element in value.elements:

                rval[element.element_identifier] = to_cwl(

                    element.element_object, hda_references=hda_references, step=step

                    element.element_object,

                    hda_references=hda_references,

                    step=step,

                    compute_environment=compute_environment,

                )

            return rval

    elif isinstance(value, list):

        return [to_cwl(v, hda_references=hda_references, step=step) for v in value]

        return [

            to_cwl(v, hda_references=hda_references, step=step, compute_environment=compute_environment) for v in value

        ]

    elif is_runtime_value(value):

        return None

    elif isinstance(value, dict):

        # Nested tool state, such as conditionals

        return {k: to_cwl(v, hda_references=hda_references, step=step) for k, v in value.items()}

        return {

            k: to_cwl(v, hda_references=hda_references, step=step, compute_environment=compute_environment)

            for k, v in value.items()

        }

    else:

        return value

test/functional/tools/cat_user_defined.yml

0 → 100644
+21 −0
Original line number Diff line number Diff line 
class: GalaxyUserTool

id: cat_user_defined

version: "0.1"

name: cat_user_defined

description: concatenates a file

container: busybox

shell_command: cat '$(inputs.input1.path)' > output.txt

inputs:

  - name: input1

    type: data

    format: txt

outputs:

  - name: output1

    type: data

    format: txt

    from_work_dir: output.txt

tests:

  - inputs:

      input1: simple_line.txt

    outputs:

      output1: simple_line.txt

test/functional/tools/sample_tool_conf.xml

+1 −0
Original line number Diff line number Diff line
@@ -305,6 +305,7 @@ 
  <tool file="explicit_container.xml" />

  <tool file="explicit_singularity_container.xml"/>

  <tool file="simple_constructs.yml" />

  <tool file="cat_user_defined.yml" />

  <tool file="from_work_dir_glob.xml" />



  <!-- Tools without tool test but useful for hand-crafted, artisanal test cases. -->

test/integration/test_pulsar_embedded.py

+3 −0
Original line number Diff line number Diff line
@@ -17,6 +17,8 @@ class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance): 
    def handle_galaxy_config_kwds(cls, config):

        super().handle_galaxy_config_kwds(config)

        config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE

        config["enable_celery_tasks"] = False

        config["metadata_strategy"] = "directory"





instance = integration_util.integration_module_instance(EmbeddedPulsarIntegrationInstance)
@@ -24,6 +26,7 @@ instance = integration_util.integration_module_instance(EmbeddedPulsarIntegratio 
test_tools = integration_util.integration_tool_runner(

    [

        "cat_default",

        "cat_user_defined",

        "collection_nested_default",

        "collection_creates_dynamic_nested_from_json",

        "composite",