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general linter: full test coverage

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- more specific error message for whitespace in pre/suffix in tool
version and name
- do not pront valid tool id message if whitespaces are found
This commit is contained in:
Matthias Bernt
2022-01-17 11:06:10 +01:00
parent d2903f2ba7
commit 93b417643e
2 changed files with 59 additions and 23 deletions
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lib/galaxy/tool_util/linters/general.py
+6 -5
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@@ -19,6 +19,7 @@ PROFILE_INFO_SPECIFIED_MSG = "Tool specifies profile version [%s]."
PROFILE_INVALID_MSG = "Tool specifies an invalid profile version [%s]."
WARN_WHITESPACE_MSG = "%s contains whitespace, this may cause errors: [%s]."
WARN_WHITESPACE_PRESUFFIX = "%s is pre/suffixed by whitespace, this may cause errors: [%s]."
WARN_ID_WHITESPACE_MSG = (
"Tool ID contains whitespace - this is discouraged: [%s].")
@@ -40,7 +41,7 @@ def lint_general(tool_source, lint_ctx):
elif isinstance(parsed_version, packaging.version.LegacyVersion):
lint_ctx.warn(WARN_VERSION_MSG % version, line=tool_line)
elif version != version.strip():
lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool version', version), line=tool_line)
lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ('Tool version', version), line=tool_line)
else:
lint_ctx.valid(VALID_VERSION_MSG % version, line=tool_line)
@@ -48,22 +49,22 @@ def lint_general(tool_source, lint_ctx):
if not name:
lint_ctx.error(ERROR_NAME_MSG, line=tool_line)
elif name != name.strip():
lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool name', name), line=tool_line)
lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ('Tool name', name), line=tool_line)
else:
lint_ctx.valid(VALID_NAME_MSG % name, line=tool_line)
tool_id = tool_source.parse_id()
if not tool_id:
lint_ctx.error(ERROR_ID_MSG, line=tool_line)
elif re.search(r"\s", tool_id):
lint_ctx.warn(WARN_ID_WHITESPACE_MSG % tool_id, line=tool_line)
else:
lint_ctx.valid(VALID_ID_MSG % tool_id, line=tool_line)
if re.search(r"\s", tool_id):
lint_ctx.warn(WARN_ID_WHITESPACE_MSG % tool_id, line=tool_line)
profile = tool_source.parse_profile()
profile_valid = PROFILE_PATTERN.match(profile) is not None
if not profile_valid:
lint_ctx.error(PROFILE_INVALID_MSG, line=tool_line)
lint_ctx.error(PROFILE_INVALID_MSG % profile, line=tool_line)
elif profile == "16.01":
lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG, line=tool_line)
else: