Unverified Commit 84213b58 authored by mvdbeek's avatar mvdbeek
Browse files

Evaulate format_source (again) just before job submission 

At this point the inputs are ready, so expession.json has been replaced
with the true extension.
parent 1e188028

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/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]],