Unverified Commit e680f627 authored by mvdbeek's avatar mvdbeek
Browse files

Raise exception if collection element has unknown extension 

These might be typo's or the result of bugs as in
https://github.com/galaxyproject/galaxy/issues/17938.

Fixes:
```

Exception caught while attempting to execute tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.1':

AttributeError: 'NoneType' object has no attribute 'matches_any'
  File "galaxy/tools/__init__.py", line 1968, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2065, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 418, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 352, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 292, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1792, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 211, in visit_input_values
    visit_input_values(
  File "galaxy/tools/parameters/__init__.py", line 227, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 162, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 259, in visitor
    if not datatype.matches_any(input.formats):
```

into something more useful for users.
parent 32327ae4

lib/galaxy/tools/actions/__init__.py

+10 −2
Original line number Diff line number Diff line
@@ -17,8 +17,12 @@ from typing import ( 
from packaging.version import Version



from galaxy import model

from galaxy.exceptions import ItemAccessibilityException

from galaxy.exceptions import (

    ItemAccessibilityException,

    RequestParameterInvalidException,

)

from galaxy.job_execution.actions.post import ActionBox

from galaxy.managers.context import ProvidesHistoryContext

from galaxy.model import (

    HistoryDatasetAssociation,

    Job,
@@ -98,7 +102,7 @@ class DefaultToolAction(ToolAction): 
        self,

        tool,

        param_values,

        trans,

        trans: ProvidesHistoryContext,

        history,

        current_user_roles=None,

        dataset_collection_elements=None,
@@ -256,6 +260,10 @@ class DefaultToolAction(ToolAction): 
                for ext in extensions:

                    if ext:

                        datatype = trans.app.datatypes_registry.get_datatype_by_extension(ext)

                        if not datatype:

                            raise RequestParameterInvalidException(

                                f"Extension '{ext}' unknown, cannot use dataset collection as input"

                            )

                        if not datatype.matches_any(input.formats):

                            conversion_required = True

                            break