ensure biome hierarchical_field is not empty for root-tagged studies

EBI-Metagenomics · Jan 3, 2024 · 6b40098 · 6b40098
1 parent 5852201
commit 6b40098
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/emgapi/management/commands/ebi_search_analysis_dump.py b/emgapi/management/commands/ebi_search_analysis_dump.py
@@ -73,7 +73,8 @@ def get_analysis_context(self, analysis: AnalysisJob):
             logger.debug(f"Could not find IPS terms for {analysis.job_id}")
             ips_annotation = None
 
-        biome_list = analysis.study.biome.lineage.split(":")[1:]
+        biome_list = analysis.study.biome.lineage.split(":")[1:] or ['root']
+        # to ensure there are no empty hierarchical fields
 
         taxonomy_lists = []
         if analysis_taxonomy:

diff --git a/emgapi/management/commands/ebi_search_study_dump.py b/emgapi/management/commands/ebi_search_study_dump.py
@@ -54,7 +54,7 @@ def write_without_blank_lines(fp, string):
 
     @staticmethod
     def get_study_context(study: Study):
-        biome_list = study.biome.lineage.split(":")[1:]
+        biome_list = study.biome.lineage.split(":")[1:] or ['root']
 
         return {
             "study": study,