From beb4842b8d8ddaa25995425c3dbeb50acfde41de Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 2 Oct 2024 00:10:44 -0400
Subject: [PATCH] Allow multiple xrefs in biotools_mappings.tsv.

---
 .../ontologies/biotools_mappings.tsv          |  2 +-
 .../tool_util/ontologies/ontology_data.py     | 23 +++++++-------
 test/unit/tool_util/test_ontologies.py        | 30 +++++++++++++++++++
 3 files changed, 42 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv b/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
index e3a8abedf495..9cbb1f041360 100644
--- a/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
+++ b/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
@@ -44,6 +44,7 @@ gffcompare	gffcompare
 sample_seqs	biopython
 seq_filter_by_id	biopython
 rxlr_motifs	signalp
+rxlr_motifs	hmmer2
 crossmap_bam	crossmap
 samtools_bam_to_cram	samtools
 crossmap_region	crossmap
@@ -260,7 +261,6 @@ fraggenescan	fraggenescan
 repeatmodeler	repeatmodeler
 promoter2	promoter
 Psortb	psortb
-rxlr_motifs	signalp hmmer2
 signalp3	signalp
 tmhmm2	tmhmm
 wolf_psort	wolf_psort
diff --git a/lib/galaxy/tool_util/ontologies/ontology_data.py b/lib/galaxy/tool_util/ontologies/ontology_data.py
index 67822130e428..63a4d573b4d7 100644
--- a/lib/galaxy/tool_util/ontologies/ontology_data.py
+++ b/lib/galaxy/tool_util/ontologies/ontology_data.py
@@ -1,3 +1,4 @@
+from collections import defaultdict
 from typing import (
     cast,
     Dict,
@@ -34,13 +35,11 @@ def _read_ontology_data_text(filename: str) -> str:
 EDAM_TOPIC_MAPPING_FILENAME = "edam_topic_mappings.tsv"
 
 BIOTOOLS_MAPPING_CONTENT = _read_ontology_data_text(BIOTOOLS_MAPPING_FILENAME)
-BIOTOOLS_MAPPING: Dict[str, str] = dict(
-    [
-        cast(Tuple[str, str], tuple(x.split("\t")))
-        for x in BIOTOOLS_MAPPING_CONTENT.splitlines()
-        if not x.startswith("#")
-    ]
-)
+BIOTOOLS_MAPPING: Dict[str, List[str]] = defaultdict(list)
+for line in BIOTOOLS_MAPPING_CONTENT.splitlines():
+    if not line.startswith("#"):
+        tool_id, xref = line.split("\t")
+        BIOTOOLS_MAPPING[tool_id].append(xref)
 EDAM_OPERATION_MAPPING_CONTENT = _read_ontology_data_text(EDAM_OPERATION_MAPPING_FILENAME)
 EDAM_OPERATION_MAPPING: Dict[str, List[str]] = _multi_dict_mapping(EDAM_OPERATION_MAPPING_CONTENT)
 
@@ -61,11 +60,11 @@ def biotools_reference(xrefs):
     return None
 
 
-def legacy_biotools_external_reference(all_ids: List[str]) -> Optional[str]:
+def legacy_biotools_external_reference(all_ids: List[str]) -> List[str]:
     for tool_id in all_ids:
         if tool_id in BIOTOOLS_MAPPING:
             return BIOTOOLS_MAPPING[tool_id]
-    return None
+    return []
 
 
 def expand_ontology_data(
@@ -74,9 +73,9 @@ def expand_ontology_data(
     xrefs = tool_source.parse_xrefs()
     has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
     if not has_biotools_reference:
-        legacy_biotools_ref = legacy_biotools_external_reference(all_ids)
-        if legacy_biotools_ref is not None:
-            xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
+        for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
+            if legacy_biotools_ref is not None:
+                xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
 
     edam_operations = tool_source.parse_edam_operations()
     edam_topics = tool_source.parse_edam_topics()
diff --git a/test/unit/tool_util/test_ontologies.py b/test/unit/tool_util/test_ontologies.py
index 3991d358c3db..5c1faca4771f 100644
--- a/test/unit/tool_util/test_ontologies.py
+++ b/test/unit/tool_util/test_ontologies.py
@@ -46,6 +46,22 @@
     type: integer
 """
 
+TOOL_YAML_NO_EXPLICIT_XREFS = """
+name: "Bowtie Mapper"
+class: GalaxyTool
+id: sort1
+version: 1.0.2
+description: "The Bowtie Mapper"
+command: "bowtie --map-the-stuff"
+outputs:
+  out1:
+    format: bam
+    from_work_dir: out1.bam
+inputs:
+  - name: input1
+    type: integer
+"""
+
 
 def test_parse_edam_empty():
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_1)
@@ -66,3 +82,17 @@ def test_parse_edam_mapping_operations_legacy():
     ontology_data = expand_ontology_data(test_source, ["sort1"], None)
     assert ontology_data.edam_operations == ["operation_3802"]
     assert ontology_data.edam_topics == []
+
+
+def test_parse_biotools_default_mapping():
+    test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
+    ontology_data = expand_ontology_data(test_source, ["cheetah_problem_unbound_var_input"], None)
+    assert ontology_data.xrefs[0]["reftype"] == "bio.tools"
+    assert ontology_data.xrefs[0]["value"] == "bwa"
+
+    test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
+    ontology_data = expand_ontology_data(test_source, ["rxlr_motifs"], None)
+    assert len(ontology_data.xrefs) == 2
+    values = [x["value"] for x in ontology_data.xrefs]
+    assert "signalp" in values
+    assert "hmmer2" in values