Commit bd5e8f32 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

fix profile logic for configfile generation 

some follow up fixes to

https://github.com/galaxyproject/galaxy/pull/9279/files
https://github.com/galaxyproject/galaxy/pull/9776/files

- wrong profile for the profile test tool (it used 20.01, but should
have used 20.05)
- the non-profile test tool used wrong assumptions. now fixed
  and also tested against 19.09
- in the profile version `value_wrapper.value` needs to be casted
  for `multiple==False` otherwise we gat `"None"` (which I do not
  understand 100%)
parent e2076fbb

lib/galaxy/tools/parameters/wrapped_json.py

+6 −3
Original line number Diff line number Diff line
@@ -94,8 +94,11 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"): 
    elif input_type == "boolean":

        json_value = _cast_if_not_none(value_wrapper, bool)

    elif input_type == "select":

        if input.multiple and packaging.version.parse(str(profile)) >= packaging.version.parse('20.05'):

            json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]

        if packaging.version.parse(str(profile)) < packaging.version.parse('20.05'):

            json_value = _cast_if_not_none(value_wrapper, str)

        else:

            if input.multiple:

                json_value = [str(_) for _ in _cast_if_not_none(value_wrapper.value, list)]

            else:

                json_value = _cast_if_not_none(value_wrapper.value, str)

    elif input_type == "data_column":

test/functional/tools/inputs_as_json.xml

+3 −3
Original line number Diff line number Diff line
@@ -27,8 +27,8 @@ if test_case == "1": 
    assert_equals(as_dict["inttest"], 12456)

    assert_equals(as_dict["floattest"], 6.789)

    assert_equals(as_dict["radio_select"], "a_radio")

    assert_equals(as_dict["optional_select"], None)

    assert_equals(as_dict["optional_multiple_select"], [])

    assert_equals(as_dict["optional_select"], "None")

    assert_equals(as_dict["optional_multiple_select"], "None")

    assert_equals(as_dict["repeat"][0]["r"], "000000")

    assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")

    assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -43,7 +43,7 @@ elif test_case == "2": 
    assert_equals(as_dict["floattest"], 1.0)

    assert_equals(as_dict["radio_select"], "a_radio")

    assert_equals(as_dict["optional_select"], "a")

    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])

    assert_equals(as_dict["optional_multiple_select"], 'a,b')

    assert_equals(as_dict["repeat"][0]["r"], "000000")

    assert_equals(as_dict["cond"]["cond_test"], "second")

    assert_equals(as_dict["cond"]["more_text"], "sdefault")

test/functional/tools/inputs_as_json_profile.xml

+4 −4
Original line number Diff line number Diff line 
<!-- test if profile version of inputs json generation works, i.e.

     - multiple selects get comma separated string (lists >= 20.05)

     - empty optional selects get "None" ([] >= 20.05) -->

<tool id="inputs_as_json" name="inputs_as_json" profile="20.01" version="1.0.0">

<tool id="inputs_as_json_profile" name="inputs_as_json_profile" profile="20.05" version="1.0.0">

    <command detect_errors="exit_code"><![CDATA[

        cat inputs.json &&

        python $check_inputs inputs.json $test_case
@@ -30,8 +30,8 @@ if test_case == "1": 
    assert_equals(as_dict["inttest"], 12456)

    assert_equals(as_dict["floattest"], 6.789)

    assert_equals(as_dict["radio_select"], "a_radio")

    assert_equals(as_dict["optional_select"], "None")

    assert_equals(as_dict["optional_multiple_select"], "None")

    assert_equals(as_dict["optional_select"], None)

    assert_equals(as_dict["optional_multiple_select"], [])

    assert_equals(as_dict["repeat"][0]["r"], "000000")

    assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")

    assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -46,7 +46,7 @@ elif test_case == "2": 
    assert_equals(as_dict["floattest"], 1.0)

    assert_equals(as_dict["radio_select"], "a_radio")

    assert_equals(as_dict["optional_select"], "a")

    assert_equals(as_dict["optional_multiple_select"], 'a,b')

    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])

    assert_equals(as_dict["repeat"][0]["r"], "000000")

    assert_equals(as_dict["cond"]["cond_test"], "second")

    assert_equals(as_dict["cond"]["more_text"], "sdefault")