Commit 77c0e915 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

fix regex for profile version 

- did not allow for new style profile versions (that may have only a
  single digit after the dot)
- fix: do not allow `,` in profile version
parent 3269758b

lib/galaxy/tool_util/linters/general.py

+1 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ VALID_NAME_MSG = "Tool defines a name [%s]." 
ERROR_ID_MSG = "Tool does not define an id attribute."

VALID_ID_MSG = "Tool defines an id [%s]."



PROFILE_PATTERN = re.compile(r"^[1,2]\d\.[0,1]\d$")

PROFILE_PATTERN = re.compile(r"^[12]\d\.(01|05|09|\d)$")

PROFILE_INFO_DEFAULT_MSG = "Tool targets 16.01 Galaxy profile."

PROFILE_INFO_SPECIFIED_MSG = "Tool specifies profile version [%s]."

PROFILE_INVALID_MSG = "Tool specifies an invalid profile version [%s]."

test/unit/tool_util/test_tool_linters.py

+18 −0
Original line number Diff line number Diff line
@@ -109,6 +109,11 @@ GENERAL_VALID = """ 
</tool>

"""



GENERAL_VALID_NEW_PROFILE_FMT = """

<tool name="valid name" id="valid_id" version="1.0+galaxy1" profile="23.0">

</tool>

"""



# test tool xml for help linter

HELP_MULTIPLE = """

<tool>
@@ -1016,6 +1021,19 @@ def test_general_valid(lint_ctx): 
    assert not lint_ctx.error_messages





def test_general_valid_new_profile_fmt(lint_ctx):

    tool_source = get_xml_tool_source(GENERAL_VALID_NEW_PROFILE_FMT)

    run_lint(lint_ctx, general.lint_general, XmlToolSource(tool_source))

    assert "Tool defines a version [1.0+galaxy1]." in lint_ctx.valid_messages

    assert "Tool specifies profile version [23.0]." in lint_ctx.valid_messages

    assert "Tool defines an id [valid_id]." in lint_ctx.valid_messages

    assert "Tool defines a name [valid name]." in lint_ctx.valid_messages

    assert not lint_ctx.info_messages

    assert len(lint_ctx.valid_messages) == 4

    assert not lint_ctx.warn_messages

    assert not lint_ctx.error_messages





def test_help_multiple(lint_ctx):

    tool_source = get_xml_tool_source(HELP_MULTIPLE)

    run_lint(lint_ctx, help.lint_help, tool_source)