run xsd linter in all linter unit tests

contrary to the previous linters the xsd linter covers more than one
section of the tool xml (i.e. all of them) and therefor may cover
other linters.

consequently all linters that are redundant with the xsd linter
are removed.

lib/galaxy/tool_util/linters/citations.py

@@ -26,17 +26,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             lint_ctx.warn("No citations found, consider adding citations to your tool.", node=root)
 
 
-class CitationsMultiple(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        citations = tool_xml.findall("citations")
-        if len(citations) > 1:
-            lint_ctx.error("More than one citation section found, behavior undefined.", node=citations[1])
-
-
 class CitationsNoText(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

lib/galaxy/tool_util/linters/command.py

@@ -12,17 +12,6 @@
     from galaxy.tool_util.parser.interface import ToolSource
 
 
-class CommandMultiple(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        commands = tool_xml.findall("./command")
-        if len(commands) > 1:
-            lint_ctx.error("More than one command tag found, behavior undefined.", node=commands[1])
-
-
 class CommandMissing(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

lib/galaxy/tool_util/linters/help.py

@@ -15,17 +15,6 @@
     from galaxy.tool_util.parser.interface import ToolSource
 
 
-class HelpMultiple(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        helps = tool_xml.findall("./help")
-        if len(helps) > 1:
-            lint_ctx.error("More than one help section found, behavior undefined.", node=helps[1])
-
-
 class HelpMissing(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

lib/galaxy/tool_util/linters/inputs.py

@@ -121,7 +121,7 @@
 PARAM_TYPE_CHILD_COMBINATIONS = [
     ("./options", ["data", "select", "drill_down"]),
     ("./options/option", ["drill_down"]),
-    ("./column", ["data_column"]),
+    ("./options/column", ["select"]),
 ]
 
 # TODO lint for valid param type - attribute combinations
@@ -1167,38 +1167,6 @@ def _iter_conditional(tool_xml: "ElementTree") -> Iterator[Tuple["Element", Opti
         yield conditional, conditional_name, first_param, first_param_type
 
 
-class ConditionalName(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        conditionals = tool_xml.findall("./inputs//conditional")
-        for conditional in conditionals:
-            conditional_name = conditional.get("name")
-            if not conditional_name:
-                lint_ctx.error("Conditional without a name", node=conditional)
-
-
-class ConditionalParamNumber(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        conditionals = tool_xml.findall("./inputs//conditional")
-        for conditional in conditionals:
-            conditional_name = conditional.get("name")
-            if conditional.get("value_from"):  # Probably only the upload tool use this, no children elements
-                continue
-            first_param = conditional.findall("param")
-            if len(first_param) != 1:
-                lint_ctx.error(
-                    f"Conditional [{conditional_name}] needs exactly one child <param> found {len(first_param)}",
-                    node=conditional,
-                )
-
-
 class ConditionalParamTypeBool(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
@@ -1242,20 +1210,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                     )
 
 
-class ConditionalWhenValue(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        for conditional, conditional_name, _, first_param_type in _iter_conditional(tool_xml):
-            if first_param_type not in ["boolean", "select"]:
-                continue
-            whens = conditional.findall("./when")
-            if any("value" not in when.attrib for when in whens):
-                lint_ctx.error(f"Conditional [{conditional_name}] when without value", node=conditional)
-
-
 class ConditionalWhenMissing(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

lib/galaxy/tool_util/linters/outputs.py

@@ -4,14 +4,13 @@
 from packaging.version import Version
 
 from galaxy.tool_util.lint import Linter
-from galaxy.util import string_as_bool
 from ._util import is_valid_cheetah_placeholder
 from ..parser.output_collection_def import NAMED_PATTERNS
 
 if TYPE_CHECKING:
     from galaxy.tool_util.lint import LintContext
     from galaxy.tool_util.parser import ToolSource
-    from galaxy.util.etree import Element
+    from galaxy.util.etree import Element, ElementTree
 
 
 class OutputsMissing(Linter):
@@ -27,17 +26,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.", node=tool_node)
 
 
-class OutputsMultiple(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        outputs = tool_xml.findall("./outputs")
-        if len(outputs) > 1:
-            lint_ctx.warn("Tool contains multiple output sections, behavior undefined.", node=outputs[1])
-
-
 class OutputsOutput(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
@@ -49,18 +37,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             lint_ctx.warn("Avoid the use of 'output' and replace by 'data' or 'collection'", node=output)
 
 
-class OutputsNameMissing(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        for output in tool_xml.findall("./outputs/data") + tool_xml.findall("./outputs/collection"):
-            if "name" not in output.attrib:
-                # TODO make this an error if there is no discover_datasets / from_work_dir (is this then still a problem)
-                lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.", node=output)
-
-
 class OutputsNameInvalidCheetah(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
@@ -187,7 +163,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 if "structured_like" in output.attrib and "inherit_format" in output.attrib:
                     format_set = True
             for sub in output:
-                if _check_pattern(sub):
+                if _check_pattern(sub) or _has_tool_provided_metadata(tool_xml):
                     format_set = True
                 elif _check_format(sub):
                     format_set = True
@@ -241,14 +217,25 @@ def _check_pattern(node):
     """
     if node.tag != "discover_datasets":
         return False
-    if "from_tool_provided_metadata" in node.attrib and string_as_bool(
-        node.attrib.get("from_tool_provided_metadata", "false")
-    ):
-        return True
     if "pattern" not in node.attrib:
         return False
     pattern = node.attrib["pattern"]
     regex_pattern = NAMED_PATTERNS.get(pattern, pattern)
     # TODO error on wrong pattern or non-regexp
     if "(?P<ext>" in regex_pattern:
         return True
+
+
+def _has_tool_provided_metadata(tool_xml: "ElementTree") -> bool:
+    outputs = tool_xml.find("./outputs")
+    if outputs is not None:
+        if "provided_metadata_file" in outputs.attrib or "provided_metadata_style" in outputs.attrib:
+            return True
+    command = tool_xml.find("./command")
+    if command is not None:
+        if "galaxy.json" in command.text:
+            return True
+    config = tool_xml.find("./configfiles/configfile[@filename='galaxy.json']")
+    if config is not None:
+        return True
+    return False

lib/galaxy/tool_util/linters/stdio.py

@@ -53,21 +53,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 )
 
 
-class StdIOMultiple(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            # Can only lint XML tools at this point.
-            # Should probably use tool_source.parse_stdio() to abstract away XML details
-            return
-        stdios = tool_xml.findall("./stdio") if tool_xml else []
-
-        if len(stdios) > 1:
-            lint_ctx.error("More than one stdio tag found, behavior undefined.", node=stdios[1])
-            return
-
-
 class StdIORegex(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):

lib/galaxy/tool_util/linters/tests.py

@@ -1,8 +1,4 @@
 """This module contains a linting functions for tool tests."""
-from inspect import (
-    Parameter,
-    signature,
-)
 from typing import (
     List,
     Optional,
@@ -12,7 +8,6 @@
 from galaxy.tool_util.lint import Linter
 from galaxy.util import asbool
 from ._util import is_datasource
-from ..verify import asserts
 
 if TYPE_CHECKING:
     from galaxy.tool_util.lint import LintContext
@@ -66,66 +61,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                     )
 
 
-class TestsAssertsUnknown(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        tests = tool_xml.findall("./tests/test")
-        for test_idx, test in enumerate(tests, start=1):
-            for a in test.xpath(
-                ".//*[self::assert_contents or self::assert_stdout or self::assert_stderr or self::assert_command]//*"
-            ):
-                assert_function_name = "assert_" + a.tag
-                if assert_function_name not in asserts.assertion_functions:
-                    lint_ctx.error(f"Test {test_idx}: unknown assertion '{a.tag}'", node=a)
-
-
-class TestsAssertsUnknownAttrib(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        tests = tool_xml.findall("./tests/test")
-        for test_idx, test in enumerate(tests, start=1):
-            for a in test.xpath(
-                ".//*[self::assert_contents or self::assert_stdout or self::assert_stderr or self::assert_command]//*"
-            ):
-                assert_function_name = "assert_" + a.tag
-                if assert_function_name not in asserts.assertion_functions:
-                    continue
-                assert_function_sig = signature(asserts.assertion_functions[assert_function_name])
-                # check of the attributes
-                for attrib in a.attrib:
-                    if attrib not in assert_function_sig.parameters:
-                        lint_ctx.error(f"Test {test_idx}: unknown attribute '{attrib}' for '{a.tag}'", node=a)
-
-
-class TestsAssertsMissingAttrib(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        tests = tool_xml.findall("./tests/test")
-        for test_idx, test in enumerate(tests, start=1):
-            for a in test.xpath(
-                ".//*[self::assert_contents or self::assert_stdout or self::assert_stderr or self::assert_command]//*"
-            ):
-                assert_function_name = "assert_" + a.tag
-                if assert_function_name not in asserts.assertion_functions:
-                    continue
-                assert_function_sig = signature(asserts.assertion_functions[assert_function_name])
-                # check missing required attributes
-                for p in assert_function_sig.parameters:
-                    if p in ["output", "output_bytes", "verify_assertions_function", "children"]:
-                        continue
-                    if assert_function_sig.parameters[p].default is Parameter.empty and p not in a.attrib:
-                        lint_ctx.error(f"Test {test_idx}: missing attribute '{p}' for '{a.tag}'", node=a)
-
-
 class TestsAssertsHasNQuant(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
@@ -181,19 +116,6 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 )
 
 
-class TestsParamName(Linter):
-    @classmethod
-    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
-        tool_xml = getattr(tool_source, "xml_tree", None)
-        if not tool_xml:
-            return
-        tests = tool_xml.findall("./tests/test")
-        for test_idx, test in enumerate(tests, start=1):
-            for param in test.findall("param"):
-                if not param.attrib.get("name", None):
-                    lint_ctx.error(f"Test {test_idx}: Found test param tag without a name defined.", node=param)
-
-
 class TestsParamInInputs(Linter):
     """
     really simple linter that test parameters are also present in the inputs
@@ -233,7 +155,8 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             return
         tests = tool_xml.findall("./tests/test")
         for test_idx, test in enumerate(tests, start=1):
-            for output in test.findall("output") + test.findall("output_collection"):
+            # note output_collections are covered by xsd, but output is not required to have one by xsd
+            for output in test.findall("output"):
                 if not output.attrib.get("name", None):
                     lint_ctx.error(f"Test {test_idx}: Found {output.tag} tag without a name defined.", node=output)