Unverified Commit 9a61e3ce authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19466 from mvdbeek/expression_tool_format_source_backport 

[24.1] Expression tool format source backport
parents f06b0d7f 57b8311b

lib/galaxy/tools/__init__.py

+6 −0
Original line number Diff line number Diff line
@@ -81,6 +81,10 @@ from galaxy.tool_util.parser.interface import ( 
    PageSource,

    ToolSource,

)

from galaxy.tool_util.parser.output_objects import (

    ToolOutput,

    ToolOutputCollection,

)

from galaxy.tool_util.parser.xml import (

    XmlPageSource,

    XmlToolSource,
@@ -811,6 +815,8 @@ class Tool(Dictifiable): 
        self.tool_errors = None

        # Parse XML element containing configuration

        self.tool_source = tool_source

        self.outputs: Dict[str, ToolOutput] = {}

        self.output_collections: Dict[str, ToolOutputCollection] = {}

        self._is_workflow_compatible = None

        self.__help = None

        self.__tests: Optional[str] = None

lib/galaxy/tools/actions/__init__.py

+2 −2
Original line number Diff line number Diff line
@@ -507,7 +507,7 @@ class DefaultToolAction(ToolAction): 
                    output,

                    wrapped_params.params,

                    inp_data,

                    inp_dataset_collections,

                    input_collections,

                    input_ext,

                    python_template_version=tool.python_template_version,

                    execution_cache=execution_cache,
@@ -1206,7 +1206,7 @@ def determine_output_format( 


        if collection_name in input_dataset_collections:

            try:

                input_collection = input_dataset_collections[collection_name][0][0]

                input_collection = input_dataset_collections[collection_name]

                input_collection_collection = input_collection.collection

                if element_index is None:

                    # just pick the first HDA

lib/galaxy/tools/evaluation.py

+21 −0
Original line number Diff line number Diff line
@@ -32,6 +32,7 @@ from galaxy.structured_app import ( 
    MinimalToolApp,

)

from galaxy.tool_util.data import TabularToolDataTable

from galaxy.tools.actions import determine_output_format

from galaxy.tools.parameters import (

    visit_input_values,

    wrapped_json,
@@ -168,6 +169,9 @@ class ToolEvaluator: 
            out_data,

            output_collections=out_collections,

        )

        # late update of format_source outputs

        self._eval_format_source(job, inp_data, out_data)



        self.execute_tool_hooks(inp_data=inp_data, out_data=out_data, incoming=incoming)



    def execute_tool_hooks(self, inp_data, out_data, incoming):
@@ -257,6 +261,23 @@ class ToolEvaluator: 


        return undeferred_objects



    def _eval_format_source(

        self,

        job: model.Job,

        inp_data: Dict[str, Optional[model.DatasetInstance]],

        out_data: Dict[str, model.DatasetInstance],

    ):

        for output_name, output in out_data.items():

            if (

                (tool_output := self.tool.outputs.get(output_name))

                and (tool_output.format_source or tool_output.change_format)

                and output.extension == "expression.json"

            ):

                input_collections = {jtidca.name: jtidca.dataset_collection for jtidca in job.input_dataset_collections}

                ext = determine_output_format(tool_output, self.param_dict, inp_data, input_collections, None)

                if ext:

                    output.extension = ext



    def _replaced_deferred_objects(

        self,

        inp_data: Dict[str, Optional[model.DatasetInstance]],

lib/galaxy_test/api/test_workflows.py

+32 −0
Original line number Diff line number Diff line
@@ -2157,6 +2157,38 @@ some_file: 
        assert dataset_details["metadata_bam_index"]

        assert dataset_details["file_ext"] == "bam"



    def test_expression_tool_output_in_format_source(self):

        with self.dataset_populator.test_history() as history_id:

            self._run_workflow(

                """class: GalaxyWorkflow

inputs:

  input:

    type: data

steps:

  skip:

    tool_id: cat_data_and_sleep

    in:

      input1: input

    when: $(false)

  pick_larger:

    tool_id: expression_pick_larger_file

    in:

      input1: skip/out_file1

      input2: input

  format_source:

    tool_id: cat_data_and_sleep

    in:

      input1: pick_larger/larger_file

test_data:

  input:

    value: 1.fastqsanger.gz

    type: File

    file_type: fastqsanger.gz

""",

                history_id=history_id,

            )

            self.dataset_populator.wait_for_history(history_id=history_id, assert_ok=True)



    def test_run_workflow_simple_conditional_step(self):

        with self.dataset_populator.test_history() as history_id:

            summary = self._run_workflow(

test/functional/tools/expression_pick_larger_file.xml

+1 −1
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ 
        <param name="input2" type="data" optional="true" label="Second file" />

    </inputs>

    <outputs>

        <output name="larger_file" type="data" from="output" />

        <output name="larger_file" type="data" from="output" format_source="input1" />

    </outputs>

    <tests>

        <test>