From 4170020fe2608bbc12e2ca4fe9e586cfc7607db3 Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Fri, 5 Jul 2024 23:57:22 +0100
Subject: [PATCH] Remove NCBI completeness

---
 ingest/config/defaults.yaml    | 4 ----
 kubernetes/loculus/values.yaml | 6 ------
 2 files changed, 10 deletions(-)

diff --git a/ingest/config/defaults.yaml b/ingest/config/defaults.yaml
index de584e31d..6c3f0016d 100644
--- a/ingest/config/defaults.yaml
+++ b/ingest/config/defaults.yaml
@@ -13,7 +13,6 @@ keep:
   - insdc_version
   - bioprojects
   - biosample_accession
-  - ncbi_completeness
   - ncbi_host_name
   - ncbi_host_tax_id
   - ncbi_is_lab_host
@@ -63,7 +62,6 @@ shared_fields:
 segment_specific_fields:
   - biosample_accession # Should usually be same for each segment
   - bioproject_accessions # Should usually be same for each segment?
-  - ncbi_completeness
   - sra_run_accession # Usually the same for each segment?
   - ncbi_protein_count
   - insdc_accession_base
@@ -123,7 +121,6 @@ column_mapping:
   Accession: genbank_accession
   BioProjects: bioprojects
   BioSample accession: biosample_accession
-  Completeness: ncbi_completeness
   Gene count: ncbi_gene_count
   Geographic Location: ncbi_geo_location
   Geographic Region: ncbi_geo_region
@@ -147,7 +144,6 @@ column_mapping:
   Lab Host: ncbi_lab_host
   Mature peptide count: ncbi_mature_peptide_count
   Molecule type: ncbi_mol_type
-  Nucleotide completeness: ncbi_nucleotide_completeness
   Protein count: ncbi_protein_count
   Purpose of Sampling: ncbi_purpose_of_sampling
   Release date: ncbi_release_date
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index b12e18720..cca2a0384 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -576,12 +576,6 @@ defaultOrganismConfig: &defaultOrganismConfig
       - name: diagnostic_measurement_unit
         displayName: Diagnostic measurement unit
         header: Diagnostics
-      - name: ncbi_completeness
-        generateIndex: true
-        autocomplete: true
-        header: "INSDC"
-        noInput: true
-        perSegment: true
       - name: length
         type: int
         header: "Alignment states and QC metrics"