From 4e1a6d3b94b29ce0d2823a94050da0713e2dd69c Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 11 Mar 2024 11:47:55 +0100
Subject: [PATCH] tool tinter: check for valid bio.tools entries

---
 lib/galaxy/tool_util/linters/general.py  | 14 ++++++++++++++
 test/unit/tool_util/test_tool_linters.py | 23 ++++++++++++++++++++++-
 2 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/linters/general.py b/lib/galaxy/tool_util/linters/general.py
index f395e335090..35642210f06 100644
--- a/lib/galaxy/tool_util/linters/general.py
+++ b/lib/galaxy/tool_util/linters/general.py
@@ -8,6 +8,7 @@ from typing import (
 
 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 @@ class ResourceRequirementExpression(Linter):
                 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.error(f'No entry {xref["value"]} in bio.tools.', linter=cls.name(), node=tool_node)
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index e553d2c1688..324825c44e2 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -30,6 +30,7 @@ from galaxy.util import (
     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 @@ GENERAL_VALID_NEW_PROFILE_FMT = """
 </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.error_messages
+    assert not lint_ctx.info_messages
+    assert len(lint_ctx.valid_messages) == 4
+    assert not lint_ctx.warn_messages
+    assert len(lint_ctx.error_messages) == 1
+
+
 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 [