added title and version to reference file objs

smaht-dac · Dec 6, 2024 · f96e35f · f96e35f
1 parent 7199e39
commit f96e35f
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Showing 3 changed files with 13 additions and 2 deletions.
diff --git a/pipeline_utils/lib/yaml_parser.py b/pipeline_utils/lib/yaml_parser.py
@@ -645,6 +645,12 @@ def to_json(
         if getattr(self, self.CODE_SCHEMA, None):
             ref_json[self.CODE_SCHEMA] = self.code
 
+        # title
+        ref_json[self.TITLE_SCHEMA] = self._link_title(self.name)
+
+        # version
+        ref_json[self.VERSION_SCHEMA] = self.version
+
         return ref_json
 
 

diff --git a/tests/repo_correct/portal_objects/file_reference.yaml b/tests/repo_correct/portal_objects/file_reference.yaml
@@ -30,3 +30,4 @@ type:
 description: hg38 full reference genome plus decoy for CGAP, fasta format
 format: fa
 version: hg38
+title: "GENOME"
diff --git a/tests/test_yaml_file_reference.py b/tests/test_yaml_file_reference.py
@@ -24,7 +24,9 @@ def test_file_reference():
                 "uuid": "1936f246-22e1-45dc-bb5c-9cfd55537fe7",
                 "data_category": ["Sequencing Reads"],
                 "data_type": ["Unaligned Reads"],
-                "variant_type": ["SNV"]
+                "variant_type": ["SNV"],
+                "version": "hg38",
+                "title": "reference genome"
             },
             {
                 "aliases": ["cgap-core:ReferenceFile-reference_genome_hg38"],
@@ -34,7 +36,9 @@ def test_file_reference():
                 "consortia": ["cgap-core"],
                 "status": None,
                 "data_category": ["Sequencing Reads"],
-                "data_type": ["Aligned Reads"]
+                "data_type": ["Aligned Reads"],
+                "version": "hg38",
+                "title": "GENOME"
             }
         ]