From b346c8234401e51cc601ccb610de7b9fcb8a4eac Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 22 May 2023 17:32:06 +0200
Subject: [PATCH] Inject None in optional parameters when buidling implicit
 converter params

Fixes:
```
KeyError: 'chrom'
  File "galaxy/tools/__init__.py", line 1909, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2005, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 392, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 327, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 268, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1748, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 159, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 191, in visitor
    input_datasets[prefix + input.name] = process_dataset(value)
  File "galaxy/tools/actions/__init__.py", line 126, in process_dataset
    data = data.get_converted_dataset(trans, target_ext, target_context=parent, history=history)
  File "galaxy/model/__init__.py", line 4211, in get_converted_dataset
    self.datatype.convert_dataset(
  File "galaxy/datatypes/data.py", line 795, in convert_dataset
    job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
  File "galaxy/tools/__init__.py", line 2005, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 453, in execute
    params=wrapped_params.params,
  File "galaxy/tools/parameters/wrapped.py", line 43, in params
    self.wrap_values(self.tool.inputs, params, skip_missing_values=not self.tool.check_values)
  File "galaxy/tools/parameters/wrapped.py", line 58, in wrap_values
    value = input_values[input.name]
```

in https://sentry.galaxyproject.org/share/issue/4f2171798f214f7ba8b947eaaebe2776/
---
 lib/galaxy/datatypes/data.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index f0ae6338602..0e93f8d76f7 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -133,6 +133,8 @@ def get_params_and_input_name(
             params[value.name] = deps[value.name]
         elif value.type == "data":
             input_name = key
+        elif value.optional:
+            params[value.name] = None
 
     # add potentially required/common internal tool parameters e.g. '__job_resource'
     if target_context: