diff --git a/ena-submission/config/config.yaml b/ena-submission/config/config.yaml index be0c548a1..4f66d313a 100644 --- 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 index eb37e86c8..e820eee11 100644 --- 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 index d4eb6f255..72d026b81 100644 --- 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 index 820be60f7..723bfcdbf 100644 --- 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"