Merge pull request #204 from galaxyproject/integrate_linting

Integrate Galaxy linting

server/galaxyls/services/language.py

@@ -32,6 +32,7 @@
 from galaxyls.services.tools.generators.command import GalaxyToolCommandSnippetGenerator
 from galaxyls.services.tools.generators.tests import GalaxyToolTestSnippetGenerator
 from galaxyls.services.tools.iuc import IUCToolParamAttributeSorter
+from galaxyls.services.tools.linting import GalaxyToolLinter
 from galaxyls.services.tools.macros import MacroDefinitionsProvider
 from galaxyls.services.tools.refactor import (
     RefactoringService,
@@ -69,6 +70,7 @@ def __init__(self, server_name: str) -> None:
         self.test_discovery_service: TestsDiscoveryService = ToolTestsDiscoveryService()
         self.macro_expander = MacroExpanderService()
         self.refactoring_service: Optional[RefactoringService] = None
+        self.linter = GalaxyToolLinter()
 
     def set_workspace(self, workspace: Workspace) -> None:
         macro_definitions_provider = MacroDefinitionsProvider(workspace)
@@ -82,7 +84,7 @@ def get_diagnostics(self, xml_document: XmlDocument) -> List[Diagnostic]:
         """Validates the Galaxy tool XML document and returns a list
         of diagnostics if there are any problems.
         """
-        return self.xsd_service.validate_document(xml_document)
+        return self.xsd_service.validate_document(xml_document) + self.linter.lint_document(xml_document)
 
     def get_documentation(self, xml_document: XmlDocument, position: Position) -> Optional[Hover]:
         """Gets the documentation about the element at the given position."""

server/galaxyls/services/tools/common.py

@@ -4,6 +4,7 @@
     Optional,
 )
 
+from pygls.lsp.types import Diagnostic
 from pygls.workspace import Workspace
 
 from galaxyls.services.xml.document import XmlDocument
@@ -41,3 +42,12 @@ def discover_tests_in_workspace(self, workspace: Workspace) -> List[TestSuiteInf
     @abc.abstractmethod
     def discover_tests_in_document(self, xml_document: XmlDocument) -> Optional[TestSuiteInfoResult]:
         raise NotImplementedError
+
+
+class ToolLinter(metaclass=abc.ABCMeta):
+    """Interface class for linting tool documents."""
+
+    @abc.abstractmethod
+    def lint_document(self, xml_document: XmlDocument) -> List[Diagnostic]:
+        """Returns a list of diagnostics with all the issues found in the given document."""
+        raise NotImplementedError

server/galaxyls/services/tools/linting.py

@@ -0,0 +1,64 @@
+from typing import List, cast
+from lxml import etree
+
+from galaxy.tool_util.lint import (
+    lint_tool_source_with,
+    LintContext,
+    LintLevel,
+    XMLLintMessageXPath,
+)
+from galaxy.tool_util.parser import get_tool_source
+from galaxy.util import xml_macros
+from galaxyls.services.tools.common import ToolLinter
+from galaxyls.services.xml.document import XmlDocument
+from pygls.lsp.types import Diagnostic, Range, DiagnosticSeverity
+
+
+class GalaxyToolLinter(ToolLinter):
+    diagnostics_source = "Galaxy Tool Linter"
+
+    def lint_document(self, xml_document: XmlDocument) -> List[Diagnostic]:
+        """ """
+        result: List[Diagnostic] = []
+        if xml_document.is_macros_file:
+            return result
+        xml_tree, _ = xml_macros.load_with_references(xml_document.document.path)
+        tool_source = get_tool_source(xml_tree=xml_tree)
+        lint_context = LintContext(level=LintLevel.SILENT, lint_message_class=XMLLintMessageXPath)
+        context = lint_tool_source_with(lint_context, tool_source)
+        result.extend(
+            [
+                self._to_diagnostic(lint_message, xml_tree, xml_document, DiagnosticSeverity.Error)
+                for lint_message in context.error_messages
+            ]
+        )
+        result.extend(
+            [
+                self._to_diagnostic(lint_message, xml_tree, xml_document, DiagnosticSeverity.Warning)
+                for lint_message in context.warn_messages
+            ]
+        )
+        return result
+
+    def _to_diagnostic(
+        self,
+        lint_message: XMLLintMessageXPath,
+        xml_tree: etree._ElementTree,
+        xml_document: XmlDocument,
+        level: DiagnosticSeverity,
+    ) -> Diagnostic:
+        range = self._get_range_from_xpath(lint_message.xpath, xml_tree, xml_document)
+        result = Diagnostic(
+            range=range,
+            message=lint_message.message,
+            source=self.diagnostics_source,
+            severity=level,
+        )
+        return result
+
+    def _get_range_from_xpath(self, xpath: str, xml_tree: etree._ElementTree, xml_document: XmlDocument) -> Range:
+        result = None
+        found = cast(list, xml_tree.xpath(xpath))[0]
+        if found is not None:
+            result = xml_document.get_element_name_range_at_line(found.tag, found.sourceline - 1)
+        return result or xml_document.get_default_range()

server/galaxyls/services/xml/document.py

@@ -25,6 +25,11 @@
     convert_document_offsets_to_range,
 )
 
+DEFAULT_RANGE = Range(
+    start=Position(line=0, character=0),
+    end=Position(line=0, character=0),
+)
+
 
 class XmlDocument(XmlSyntaxNode):
     """Represents a parsed XML document.
@@ -219,3 +224,19 @@ def get_line_indentation(self, line_number: int) -> str:
         line_text = self.document.lines[line_number]
         indentation = line_text[: len(line_text) - len(line_text.lstrip())]
         return indentation
+
+    def get_default_range(self) -> Range:
+        """Gets the range of the root tag or the first character of the document if there is no root."""
+        if self.root:
+            return self.get_element_name_range(self.root) or DEFAULT_RANGE
+        return DEFAULT_RANGE
+
+    def get_element_name_range_at_line(self, name: str, line_number: int) -> Range:
+        """Gets the range of the element with the given tag name located at the given line number."""
+        line_text = self.document.lines[line_number]
+        start = line_text.index(f"<{name}") + 1
+        end = start + len(name)
+        return Range(
+            start=Position(line=line_number, character=start),
+            end=Position(line=line_number, character=end),
+        )

server/requirements.txt

@@ -1,5 +1,5 @@
 pygls==0.11.3
 lxml==4.9.1
 anytree==2.8.0
-galaxy-tool-util==21.9.2
+galaxy-tool-util==22.1.2
 pydantic==1.8.2