feat!: rename and surface sraRunAccession

ena-submission/test/approved_ena_submission_list_test.json

@@ -57,7 +57,7 @@
             "hostHealthState": "Hospital care required",
             "ncbiReleaseDate": null,
             "ncbiVirusTaxId": null,
-            "sraRunAccession": null,
+            "insdcRawReadsAccession": null,
             "environmentalSite": null,
             "signsAndSymptoms": null,
             "anatomicalMaterial": null,

ena-submission/test/external_metadata_test.ndjson

@@ -1 +1 @@
-{"accession": "LOC1", "version": 1, "externalMetadata": {"ncbiReleaseDate": null,"ncbiUpdateDate": null,"ncbiSubmitterCountry": null,"insdcAccessionBase": null,"insdcVersion": null,"insdcAccessionFull": null,"bioprojectAccession": null,"biosampleAccession": null,"ncbiSourceDb": null,"ncbiVirusName": null,"ncbiVirusTaxId": null,"sraRunAccession": null}}
+{"accession": "LOC1", "version": 1, "externalMetadata": {"ncbiReleaseDate": null,"ncbiUpdateDate": null,"ncbiSubmitterCountry": null,"insdcAccessionBase": null,"insdcVersion": null,"insdcAccessionFull": null,"bioprojectAccession": null,"biosampleAccession": null,"ncbiSourceDb": null,"ncbiVirusName": null,"ncbiVirusTaxId": null,"insdcRawReadsAccession": null}}

ingest/tests/config_cchf/config.yaml

@@ -4,7 +4,7 @@ insdc_segment_specific_fields:
   - insdcAccessionBase
   - insdcVersion
   - insdcAccessionFull
-  - sraRunAccession
+  - insdcRawReadsAccession
 keycloak_token_url: http://localhost:8083/realms/loculus/protocol/openid-connect/token
 nextclade_dataset_name: nextstrain/cchfv/linked
 nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
@@ -23,7 +23,7 @@ rename:
   ncbiHostTaxId: hostTaxonId
   ncbiIsLabHost: isLabHost
   ncbiIsolateName: specimenCollectorSampleId
-  ncbiSraAccessions: sraRunAccession
+  ncbiSraAccessions: insdcRawReadsAccession
   ncbiSubmitterAffiliation: authorAffiliations
   ncbiSubmitterNames: authors
 taxon_id: 3052518

ingest/tests/expected_output_cchf/metadata_post_prepare.json

@@ -21,7 +21,7 @@
         "sampleCollectionDate": "1989",
         "segment": "L",
         "specimenCollectorSampleId": "K229_194",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX013462.1"
     },
     "KX013463.1": {
@@ -46,7 +46,7 @@
         "sampleCollectionDate": "1989",
         "segment": "M",
         "specimenCollectorSampleId": "K229_194",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX013463.1"
     },
     "KX013464.1": {
@@ -71,7 +71,7 @@
         "sampleCollectionDate": "1989",
         "segment": "S",
         "specimenCollectorSampleId": "K229_194",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX013464.1"
     },
     "KX013483.1": {
@@ -96,7 +96,7 @@
         "sampleCollectionDate": "1958",
         "segment": "L",
         "specimenCollectorSampleId": "Nakiwogo",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX013483.1"
     },
     "KX013485.1": {
@@ -121,7 +121,7 @@
         "sampleCollectionDate": "1958",
         "segment": "S",
         "specimenCollectorSampleId": "Nakiwogo",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX013485.1"
     },
     "KX096703.1": {
@@ -146,7 +146,7 @@
         "sampleCollectionDate": "2015",
         "segment": "S",
         "specimenCollectorSampleId": "tick pool #134",
-        "sraRunAccession": "",
+        "insdcRawReadsAccession": "",
         "submissionId": "KX096703.1"
     }
 }

kubernetes/loculus/values.yaml

@@ -1053,8 +1053,8 @@ defaultOrganismConfig: &defaultOrganismConfig
         hideOnSequenceDetailsPage: true
         noInput: true
         header: "INSDC"
-      - name: sraRunAccession
-        displayName: SRA run accession
+      - name: insdcRawReadsAccession
+        displayName: Raw reads accession
         customDisplay:
           type: link
           url: "https://www.ncbi.nlm.nih.gov/sra/?term=__value__"