Merge pull request #17839 from bernt-matthias/topic/lint_edam

Add tool linting for valid EDAM terms

lib/galaxy/tool_util/linters/general.py

@@ -9,6 +9,7 @@
 from packaging.version import Version
 
 from galaxy.tool_util.biotools.source import ApiBiotoolsMetadataSource
+from galaxy.tool_util.edam_util import load_edam_tree
 from galaxy.tool_util.lint import Linter
 from galaxy.tool_util.version import (
     LegacyVersion,
@@ -241,3 +242,14 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             metadata_source = ApiBiotoolsMetadataSource()
             if not metadata_source.get_biotools_metadata(xref["value"]):
                 lint_ctx.warn(f'No entry {xref["value"]} in bio.tools.', linter=cls.name(), node=tool_node)
+
+
+class EDAMTermsValid(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        _, tool_node = _tool_xml_and_root(tool_source)
+        edam = load_edam_tree(None, "operation_", "topic_")
+        terms = tool_source.parse_edam_operations() + tool_source.parse_edam_topics()
+        for term in terms:
+            if term not in edam:
+                lint_ctx.warn(f"No entry '{term}' in EDAM.", linter=cls.name(), node=tool_node)

test/unit/tool_util/test_tool_linters.py

@@ -128,6 +128,19 @@
 </tool>
 """
 
+GENERAL_VALID_EDAM = """
+<tool name="valid name" id="valid_id" version="1.0+galaxy1" profile="23.0">
+    <edam_topics>
+        <edam_topic>topic_2269</edam_topic>
+        <edam_topic>topic_000</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3434</edam_operation>
+        <edam_operation>operation_000</edam_operation>
+    </edam_operations>
+</tool>
+"""
+
 # test tool xml for help linter
 HELP_MULTIPLE = """
 <tool id="id" name="name">
@@ -1102,6 +1115,19 @@ def test_general_valid_biotools(lint_ctx):
     assert not lint_ctx.error_messages
 
 
+def test_general_valid_edam(lint_ctx):
+    tool_source = get_xml_tool_source(GENERAL_VALID_EDAM)
+    run_lint_module(lint_ctx, general, tool_source)
+    assert "No entry 'operation_000' in EDAM." in lint_ctx.warn_messages
+    assert "No entry 'topic_000' in EDAM." in lint_ctx.warn_messages
+    assert not lint_ctx.info_messages
+    assert len(lint_ctx.valid_messages) == 4
+    assert len(lint_ctx.warn_messages) == 2
+    # accept 2 xsd errors due to malformed topic/operation ID
+    # which should make sure that the id never becomes valid
+    assert len(lint_ctx.error_messages) == 2
+
+
 def test_help_multiple(lint_ctx):
     tool_source = get_xml_tool_source(HELP_MULTIPLE)
     run_lint_module(lint_ctx, help, tool_source)
@@ -2099,7 +2125,7 @@ def test_xml_comments_are_ignored(lint_ctx: LintContext):
 def test_list_linters():
     linter_names = Linter.list_listers()
     # make sure to add/remove a test for new/removed linters if this number changes
-    assert len(linter_names) == 131
+    assert len(linter_names) == 132
     assert "Linter" not in linter_names
     # make sure that linters from all modules are available
     for prefix in [