allow empyt value for optional numeric inputs

[bernt-matthias]

The CTDConverter fails for value="" for numeric non-mandatory inputs:

  File "CTDConverter/convert.py", line 215, in main
    converter.get_preferred_file_extension())
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDConverter/common/utils.py", line 118, in parse_input_ctds
    parsed_ctds.append(ParsedCTD(CTDModel(from_file=input_ctd), input_ctd, output_file))
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 643, in __init__
    self._load_from_file(from_file)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 688, in _load_from_file
    self.parameters = self._build_param_model(params_container_node, base=None)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 708, in _build_param_model
    self._build_param_model(child, current_group)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 708, in _build_param_model
    self._build_param_model(child, current_group)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 713, in _build_param_model
    base.add(**setup)  # register parameter in model
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 564, in add
    self.parameters[name] = Parameter(name, self, **kwargs)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 376, in __init__
    self._validate_numerical_defaults(default)
  File "/home/berntm/projects/tools-galaxyp/tools/openms/gen-test/CTDopts/CTDopts/CTDopts.py", line 456, in _validate_numerical_defaults
    "default": ', '.join(map(str, errors_so_far))})
ModelParsingError: An error occurred while parsing the CTD file: Invalid default value(s) provided for parameter param_wodefault_mandatory_unrestricted of type <type 'float'>: ''
ERROR: There seems to be a problem with one of your input CTDs.

Not sure if there is a better way to do it (e.g. alternatively "" could be removed from the list)

[bernt-matthias]

@b-schubert @andras86 @bgruening : any chance to get this merged?

[jpfeuffer]

In which cases is this needed?
Shouldn't the parameter then be skipped completely?

[bernt-matthias]

Happens for instance for this parameter:

      <ITEM name="wodefault_mandatory_unrestricted"     value=""    type="double" description="float" required="true"  advanced="false" />

I assumed in my test cases that there might be mandatory arguments for which no default is available.

[jpfeuffer]

Hmm I dont know if this should happen. If I designed a tool, I would avoid such parameters.
With string parameters this wont be distinguishable from an empty string for example. In case of string parameters with restrictions this is even more complicated (you would need to add the empty string as a possible selection).
Do you have any real-world examples of such tools, where a reasonable default cannot be given?

[bernt-matthias]

I had a tool developer in mind who want's to implement a parameter for which no useful default exists, but depends in a non-computable way on the input. Such a parameter could be for instance a taxon name for choosing a reference data base.

Or a case where the developer wants to "force" the user to think about the parameter.

[jpfeuffer]

I mean in general I do not care much. But you need to be careful with dependent programs/code that do a validation on provided CTDs (e.g. GenericKnimeNodes). They will probably start to complain before the user even does anything.
And there is still the problem of how to differentiate between an empty string for string parameters.

[bernt-matthias]

Seems to boil down to the question if the empty string (ie the default given by value="") is acceptable if its a required parameter.

I assumed that tools won't accept that the user leaves this empty and only run when a value has been entered.

[timosachsenberg]

I think we had quite some trouble in the past with optional vs. empty parameters. I would only add this if really required

[bernt-matthias]

Currently I can live with it :)