sra_run_accession is for per sequence not per segment

loculus-project · Aug 13, 2024 · 003340f · 003340f
1 parent 36b6995
commit 003340f
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Showing 4 changed files with 4 additions and 13 deletions.
diff --git a/ena-submission/config/config.yaml b/ena-submission/config/config.yaml
@@ -73,13 +73,7 @@ organisms:
         name: ncbi_virus_tax_id
         type: int
       - externalMetadataUpdater: ena
-        name: sra_run_accession_L
-        type: string
-      - externalMetadataUpdater: ena
-        name: sra_run_accession_M
-        type: string
-      - externalMetadataUpdater: ena
-        name: sra_run_accession_S
+        name: sra_run_accession
         type: string
   ebola-sudan:
     ingest:

diff --git a/ena-submission/test/ena_submission_list.json b/ena-submission/test/ena_submission_list.json
@@ -100,9 +100,7 @@
             "total_ambiguous_nucs_L": 0,
             "total_ambiguous_nucs_M": 0,
             "total_ambiguous_nucs_S": 0,
-            "bioproject_accessions_L": null,
-            "bioproject_accessions_M": null,
-            "bioproject_accessions_S": null,
+            "bioproject_accession": null,
             "food_product_properties": null,
             "host_vaccination_status": null,
             "quality_control_details": null,

diff --git a/ingest/config/defaults.yaml b/ingest/config/defaults.yaml
@@ -29,7 +29,7 @@ keep:
 # Used to deduplicate samples
 # Used for segmented viruses only
 shared_fields:
-  - bioproject_accessions
+  - bioproject_accession
   - biosample_accession
   - geo_loc_country
   - geo_loc_admin_1

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -456,7 +456,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         noInput: true
         perSegment: true
         oneHeader: true
-      - name: bioproject_accessions
+      - name: bioproject_accession
         customDisplay:
           type: link
           url: "https://www.ncbi.nlm.nih.gov/bioproject/__value__"
@@ -941,7 +941,6 @@ defaultOrganismConfig: &defaultOrganismConfig
         header: "INSDC"
         ingest: ncbi_sra_accessions
         noInput: true
-        perSegment: true
       - name: total_snps
         type: int
         header: "Alignment states and QC metrics"