Merge pull request #17655 from bernt-matthias/topic/lint-bio.tools

tool linter: check for valid bio.tools entries

lib/galaxy/tool_util/linters/general.py

@@ -8,6 +8,7 @@
 
 from packaging.version import Version
 
+from galaxy.tool_util.biotools.source import ApiBiotoolsMetadataSource
 from galaxy.tool_util.lint import Linter
 from galaxy.tool_util.version import (
     LegacyVersion,
@@ -227,3 +228,16 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
                 lint_ctx.warn(
                     "Expressions in resource requirement not supported yet", linter=cls.name(), node=tool_node
                 )
+
+
+class BioToolsValid(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        _, tool_node = _tool_xml_and_root(tool_source)
+        xrefs = tool_source.parse_xrefs()
+        for xref in xrefs:
+            if xref["reftype"] != "bio.tools":
+                continue
+            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)

test/unit/tool_util/test_tool_linters.py

@@ -30,6 +30,7 @@
     ElementTree,
     parse_xml,
 )
+from galaxy.util.unittest_utils import skip_if_site_down
 from galaxy.util.xml_macros import load_with_references
 
 # TODO tests tool xml for general linter
@@ -118,6 +119,15 @@
 </tool>
 """
 
+GENERAL_VALID_BIOTOOLS = """
+<tool name="valid name" id="valid_id" version="1.0+galaxy1" profile="23.0">
+    <xrefs>
+        <xref type="bio.tools">bwa</xref>
+        <xref type="bio.tools">johnscoolbowtie</xref>
+    </xrefs>
+</tool>
+"""
+
 # test tool xml for help linter
 HELP_MULTIPLE = """
 <tool id="id" name="name">
@@ -1081,6 +1091,17 @@ def test_general_valid_new_profile_fmt(lint_ctx):
     assert not lint_ctx.error_messages
 
 
+@skip_if_site_down("https://bio.tools/")
+def test_general_valid_biotools(lint_ctx):
+    tool_source = get_xml_tool_source(GENERAL_VALID_BIOTOOLS)
+    run_lint_module(lint_ctx, general, tool_source)
+    assert "No entry johnscoolbowtie in bio.tools." in lint_ctx.warn_messages
+    assert not lint_ctx.info_messages
+    assert len(lint_ctx.valid_messages) == 4
+    assert len(lint_ctx.warn_messages) == 1
+    assert not lint_ctx.error_messages
+
+
 def test_help_multiple(lint_ctx):
     tool_source = get_xml_tool_source(HELP_MULTIPLE)
     run_lint_module(lint_ctx, help, tool_source)
@@ -2078,7 +2099,7 @@ 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) == 130
+    assert len(linter_names) == 131
     assert "Linter" not in linter_names
     # make sure that linters from all modules are available
     for prefix in [