full test coverage for stdio

galaxyproject · Nov 30, 2021 · 3f8554d · 3f8554d
1 parent 4d1f557
commit 3f8554d
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diff --git a/lib/galaxy/tool_util/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py
@@ -42,9 +42,13 @@ def _lint_exit_code(tool_xml, child, lint_ctx):
     for key in child.attrib.keys():
         if key not in ["description", "level", "range"]:
             lint_ctx.warn(f"Unknown attribute [{key}] encountered on exit_code tag.", line=child.sourceline, xpath=tool_xml.getpath(child))
+        # TODO lint range, or is regexp in xsd sufficient?
+        # TODO lint required attributes
 
 
 def _lint_regex(tool_xml, child, lint_ctx):
     for key in child.attrib.keys():
         if key not in ["description", "level", "match", "source"]:
             lint_ctx.warn(f"Unknown attribute [{key}] encountered on regex tag.", line=child.sourceline, xpath=tool_xml.getpath(child))
+        # TODO lint match (re.compile)
+        # TODO lint required attributes
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
@@ -8,6 +8,7 @@
     help,
     inputs,
     outputs,
+    stdio,
     tests,
 )
 from galaxy.tool_util.parser.xml import XmlToolSource
@@ -365,6 +366,34 @@
 </tool>
 """
 
+# tool xml for stdio linter
+STDIO_DEFAULT_FOR_DEFAULT_PROFILE = """
+<tool>
+</tool>
+"""
+
+STDIO_DEFAULT_FOR_NONLEGACY_PROFILE = """
+<tool profile="21.09">
+</tool>
+"""
+
+STDIO_MULTIPLE_STDIO = """
+<tool profile="21.09">
+    <stdio/>
+    <stdio/>
+</tool>
+"""
+
+STDIO_INVALID_CHILD_OR_ATTRIB = """
+<tool profile="21.09">
+    <stdio>
+        <reqex/>
+        <regex descriptio="blah" level="fatal" match="error" source="stdio"/>
+        <exit_code descriptio="blah" level="fatal" range="1:"/>
+    </stdio>
+</tool>
+"""
+
 # check that linter does complain about tests wo assumptions
 TESTS_WO_EXPECTATIONS = """
 <tool>
@@ -632,6 +661,36 @@
         lambda x:
             len(x.warn_messages) == 0 and len(x.error_messages) == 0
     ),
+    (
+        STDIO_DEFAULT_FOR_DEFAULT_PROFILE, stdio.lint_stdio,
+        lambda x:
+            "No stdio definition found, tool indicates error conditions with output written to stderr." in x.info_messages
+            and len(x.info_messages) == 1 and len(x.warn_messages) == 0 and len(x.error_messages) == 0
+
+    ),
+    (
+        STDIO_DEFAULT_FOR_NONLEGACY_PROFILE, stdio.lint_stdio,
+        lambda x:
+            "No stdio definition found, tool indicates error conditions with non-zero exit codes."  in x.info_messages
+            and len(x.info_messages) == 1 and len(x.warn_messages) == 0 and len(x.error_messages) == 0
+
+    ),
+    (
+        STDIO_MULTIPLE_STDIO, stdio.lint_stdio,
+        lambda x:
+            "More than one stdio tag found, behavior undefined." in x.error_messages
+            and len(x.info_messages) == 0 and len(x.warn_messages) == 0 and len(x.error_messages) == 1
+
+    ),
+    (
+        STDIO_INVALID_CHILD_OR_ATTRIB, stdio.lint_stdio,
+        lambda x:
+            "Unknown stdio child tag discovered [reqex]. Valid options are exit_code and regex." in x.warn_messages
+            and "Unknown attribute [descriptio] encountered on exit_code tag." in x.warn_messages
+            and "Unknown attribute [descriptio] encountered on regex tag." in x.warn_messages
+            and len(x.info_messages) == 0 and len(x.warn_messages) == 3 and len(x.error_messages) == 0
+
+    ),
     (
         TESTS_WO_EXPECTATIONS, tests.lint_tsts,
         lambda x:
@@ -682,6 +741,10 @@
     'repeats',
     'outputs collection static elements with format_source',
     'outputs discover datatsets with tool provided metadata',
+    'stdio: default for default profile',
+    'stdio: default for non-legacy profile',
+    'stdio: multiple stdio',
+    'stdio: invalid tag or attribute',
     'test without expectations',
     'test param missing from inputs',
     'test expecting failure with outputs',