post merge cleanup

galaxyproject · Sep 13, 2022 · 2d2f1f1 · 2d2f1f1
1 parent e2e66b4
commit 2d2f1f1
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Showing 4 changed files with 69 additions and 31 deletions.
diff --git a/lib/galaxy/tool_util/linters/_util.py b/lib/galaxy/tool_util/linters/_util.py
@@ -40,7 +40,7 @@ def get_code(tool_xml):
         labelcode += cn.attrib["label"] + "\n"
 
     actioncode = ""
-    for cn in tool_xml.findall('./outputs//conditional[@name]'):
+    for cn in tool_xml.findall("./outputs//conditional[@name]"):
         actioncode += cn.attrib["name"] + "\n"
     for cn in tool_xml.findall('./outputs//action/option[@type="from_param"]'):
         actioncode += cn.attrib.get("name", "") + "\n"

diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
@@ -2,11 +2,7 @@
 import re
 
 from galaxy.util import string_as_bool
-from ._util import (
-    get_code,
-    is_datasource,
-    is_valid_cheetah_placeholder
-)
+from ._util import get_code, is_datasource, is_valid_cheetah_placeholder
 from ..parser.util import _parse_name, _prepare_argument
 
 FILTER_TYPES = [
@@ -163,15 +159,15 @@ def _param_in_compiled_cheetah(param, param_name, code):
     # gets
     # set $rg_id = str($rg_param('read_group_id_conditional').ID)
     # rg_id = str(VFN(VFFSL(SL,"rg_param",False)('read_group_id_conditional'),"ID",True))
-    if re.search(r'(VFN|VFFSL)\(.*[\"\']([\w.]+\.)?' + param_name + r'(\.[\w.]+)?[\"\']', code):
+    if re.search(r"(VFN|VFFSL)\(.*[\"\']([\w.]+\.)?" + param_name + r"(\.[\w.]+)?[\"\']", code):
         return True
 
     # #for i, r in enumerate($repeat_name)
     #     #set x = $str(r[ 'param_name' ])
     # #end for
     # the loop content gets
     # x = VFFSL(SL,"str",False)(r[ 'var_in_repeat' ])
-    if re.search(r'(VFFSL|VFN)\(.*\[\s*[\"\']' + param_name + r'[\"\']\s*\]', code):
+    if re.search(r"(VFFSL|VFN)\(.*\[\s*[\"\']" + param_name + r"[\"\']\s*\]", code):
         # print(f"    G")
         return True
 
@@ -571,7 +567,10 @@ def lint_inputs_used(tool_xml, lint_ctx):
             continue
         if param_name in filter_code:
             continue
-        if tool_xml.find("./inputs//param/options[@from_dataset]") is not None or tool_xml.find("./inputs//param/options/filter[@ref]") is not None:
+        if (
+            tool_xml.find("./inputs//param/options[@from_dataset]") is not None
+            or tool_xml.find("./inputs//param/options/filter[@ref]") is not None
+        ):
             continue
         if param.getparent().tag == "conditional":
             continue
@@ -581,11 +580,17 @@ def lint_inputs_used(tool_xml, lint_ctx):
             param_type = param.attrib.get("type")
             if param_type in ["data", "collection"]:
                 if not conf_inputs.attrib.get("data_style"):
-                    lint_ctx.error(f"Param input [{param_name}] not found in command or configfiles. Does the present inputs config miss the 'data_style' attribute?", line=param.sourceline, xpath=tool_xml.getpath(param))
-            inputs_conf_name = conf_inputs.attrib.get('name', conf_inputs.attrib.get('filename', None))
+                    lint_ctx.error(
+                        f"Param input [{param_name}] not found in command or configfiles. Does the present inputs config miss the 'data_style' attribute?",
+                        node=param,
+                    )
+            inputs_conf_name = conf_inputs.attrib.get("name", conf_inputs.attrib.get("filename", None))
             if inputs_conf_name:
                 if not re.search(r"(^|[^\w])" + inputs_conf_name + r"([^\w]|$)", code):
-                    lint_ctx.error(f"Param input [{param_name}] only used inputs configfile {inputs_conf_name}, but this is not used in the command", line=param.sourceline, xpath=tool_xml.getpath(param))
+                    lint_ctx.error(
+                        f"Param input [{param_name}] only used inputs configfile {inputs_conf_name}, but this is not used in the command",
+                        node=param,
+                    )
             continue
 
         change_format = tool_xml.find(f"./outputs//change_format/when[@input='{param_name}']") is not None
@@ -599,17 +604,24 @@ def lint_inputs_used(tool_xml, lint_ctx):
                 only = ""
             # TODO check that template is used??
             if template:
-                lint_ctx.warn(f"Param input [{param_name}] {only}used in a template macro, use a macro token instead.", line=param.sourceline, xpath=tool_xml.getpath(param))
+                lint_ctx.warn(
+                    f"Param input [{param_name}] {only}used in a template macro, use a macro token instead.", node=param
+                )
             if action:
-                lint_ctx.warn(f"Param input [{param_name}] {only}found in output actions, better use extended metadata.", line=param.sourceline, xpath=tool_xml.getpath(param))
+                lint_ctx.warn(
+                    f"Param input [{param_name}] {only}found in output actions, better use extended metadata.",
+                    node=param,
+                )
             if label:
-                lint_ctx.warn(f"Param input [{param_name}] {only}found in a label attribute, this is discouraged.", line=param.sourceline, xpath=tool_xml.getpath(param))
+                lint_ctx.warn(
+                    f"Param input [{param_name}] {only}found in a label attribute, this is discouraged.", node=param
+                )
             continue
 
         if change_format:
-            lint_ctx.error(f"Param input [{param_name}] is only used in a change_format tag", line=param.sourceline, xpath=tool_xml.getpath(param))
+            lint_ctx.error(f"Param input [{param_name}] is only used in a change_format tag", node=param)
         else:
-            lint_ctx.error(f"Param input [{param_name}] not found in command or configfiles.", line=param.sourceline, xpath=tool_xml.getpath(param))
+            lint_ctx.error(f"Param input [{param_name}] not found in command or configfiles.", node=param)
 
 
 def lint_repeats(tool_xml, lint_ctx):

diff --git a/lib/galaxy/tool_util/parser/util.py b/lib/galaxy/tool_util/parser/util.py
@@ -11,7 +11,7 @@ def is_dict(item):
 def _prepare_argument(argument):
     if argument is None:
         return ""
-    return argument.lstrip('-').replace("-", "_")
+    return argument.lstrip("-").replace("-", "_")
 
 
 def _parse_name(name, argument):

diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
@@ -428,6 +428,10 @@
         </section>
         <conditional name="cond">
             <param name="dup_in_cond" type="select">
+                <option value="a">a</option>
+                <option value="b">b</option>
+            </param>
+            <when value="a">
                 <param name="dup_in_cond" type="text"/>
             </when>
             <when value="b">
@@ -613,6 +617,7 @@
         <param name="param_that_is_not_in_inputs_configfile" type="text"/>
     </inputs>
 </tool>
+"""
 
 # test tool xml for outputs linter
 OUTPUTS_MISSING = """
@@ -1267,7 +1272,7 @@ def test_inputs_duplicated_options(lint_ctx):
 
 
 def test_inputs_duplicated_options_with_different_select(lint_ctx):
-    tool_source = get_xml_tool_source(SELECT_DUPLICATED_OPTIONS_WITH_DIFF_SELECTED)
+    tool_source = get_xml_tool_source(INPUTS_SELECT_DUPLICATED_OPTIONS_WITH_DIFF_SELECTED)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
     assert not lint_ctx.warn_messages
     assert not lint_ctx.error_messages
@@ -1421,46 +1426,67 @@ def test_inputs_duplicate_names(lint_ctx):
 
 def test_inputs_used_parameter_in_command(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_USED_PARAMETER_IN_COMMAND)
-    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
+    run_lint(lint_ctx, inputs.lint_inputs_used, tool_source)
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
     assert "Param input [hey_a_missing_parameter] not found in command or configfiles." in lint_ctx.error_messages
     assert "Param input [change_format_parameter] is only used in a change_format tag" in lint_ctx.error_messages
     assert len(lint_ctx.error_messages) == 2
-    
+
 
 def test_inputs_used_other(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_USED_OTHER)
-    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
+    run_lint(lint_ctx, inputs.lint_inputs_used, tool_source)
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
-    assert "Param input [variable_in_template_token] only used in a template macro, use a macro token instead." in lint_ctx.warn_messages
-    assert "Param input [action_option_reference] only found in output actions." in lint_ctx.warn_messages
-    assert "Param input [action_filter_reference] only found in output actions." in lint_ctx.warn_messages
-    assert "Param input [action_conditional_reference] only found in output actions." in lint_ctx.warn_messages
-    assert "Param input [param_that_is_used_only_in_output_label] only found in a label attribute." in lint_ctx.warn_messages
+    assert (
+        "Param input [variable_in_template_token] only used in a template macro, use a macro token instead."
+        in lint_ctx.warn_messages
+    )
+    assert (
+        "Param input [action_option_reference] only found in output actions, better use extended metadata."
+        in lint_ctx.warn_messages
+    )
+    assert (
+        "Param input [action_filter_reference] only found in output actions, better use extended metadata."
+        in lint_ctx.warn_messages
+    )
+    assert (
+        "Param input [action_conditional_reference] only found in output actions, better use extended metadata."
+        in lint_ctx.warn_messages
+    )
+    assert (
+        "Param input [param_that_is_used_only_in_output_label] only found in a label attribute, this is discouraged."
+        in lint_ctx.warn_messages
+    )
     assert len(lint_ctx.warn_messages) == 5
     assert len(lint_ctx.error_messages) == 0
 
 
 def test_inputs_used_parameter_in_command_with_inputs(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_USED_PARAMETER_IN_COMMAND_WITH_INPUTS)
-    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
+    run_lint(lint_ctx, inputs.lint_inputs_used, tool_source)
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
-    assert "Param input [param_that_is_not_in_inputs_configfile] not found in command or configfiles. Does the present inputs config miss the 'data_style' attribute?" in lint_ctx.error_messages
+    assert (
+        "Param input [param_that_is_not_in_inputs_configfile] not found in command or configfiles. Does the present inputs config miss the 'data_style' attribute?"
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.error_messages) == 1
 
 
 def test_inputs_used_parameter_in_command_with_inputs2(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_USED_PARAMETER_IN_COMMAND_WITH_INPUTS2)
-    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
+    run_lint(lint_ctx, inputs.lint_inputs_used, tool_source)
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
     assert not lint_ctx.warn_messages
-    assert "Param input [param_that_is_not_in_inputs_configfile] only used inputs configfile inputs, but this is not used in the command" in lint_ctx.error_messages
+    assert (
+        "Param input [param_that_is_not_in_inputs_configfile] only used inputs configfile inputs, but this is not used in the command"
+        in lint_ctx.error_messages
+    )
     assert len(lint_ctx.error_messages) == 1