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chore(helm): move earliestReleaseDate to _common-metadata.tpl #3428

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Original file line number Diff line number Diff line change
Expand Up @@ -78,4 +78,4 @@ data class ExternalMetadata(
override val required: Boolean = false,
) : BaseMetadata()

data class EarliestReleaseDate(val enabled: Boolean = false, val externalFields: List<String>)
data class EarliestReleaseDate(val externalFields: List<String>)
Original file line number Diff line number Diff line change
Expand Up @@ -60,19 +60,15 @@ open class ReleasedDataModel(
val latestRevocationVersions = submissionDatabaseService.getLatestRevocationVersions(organism)

val earliestReleaseDateConfig = backendConfig.getInstanceConfig(organism).schema.earliestReleaseDate
val finder = if (earliestReleaseDateConfig.enabled) {
EarliestReleaseDateFinder(earliestReleaseDateConfig.externalFields)
} else {
null
}
val earliestReleaseDateFinder = EarliestReleaseDateFinder(earliestReleaseDateConfig.externalFields)

return submissionDatabaseService.streamReleasedSubmissions(organism)
.map {
computeAdditionalMetadataFields(
it,
latestVersions,
latestRevocationVersions,
finder,
earliestReleaseDateFinder,
)
}
}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -591,6 +591,7 @@ class SubmissionDatabaseService(
organism,
)
}
// The order by on versions MUST NOT be removed as earliestReleaseDateFinder relies on ordered versions
.orderBy(
SequenceEntriesView.accessionColumn to SortOrder.ASC,
SequenceEntriesView.versionColumn to SortOrder.ASC,
Expand Down
6 changes: 0 additions & 6 deletions docs/src/content/docs/reference/helm-chart-config.mdx
Original file line number Diff line number Diff line change
Expand Up @@ -549,12 +549,6 @@ Each organism object has the following fields:
of where the sequence was first released.
</td>
</tr>
<tr>
<td>`earliestReleaseDate.enabled`</td>
<td>boolean</td>
<td></td>
<td>Whether to enable the `earliestReleaseDate` metadata field.</td>
</tr>
<tr>
<td>`earliestReleaseDate.externalFields`</td>
<td>Array of strings</td>
Expand Down
16 changes: 9 additions & 7 deletions kubernetes/loculus/templates/_common-metadata.tpl
Original file line number Diff line number Diff line change
Expand Up @@ -58,23 +58,26 @@ fields:
displayName: Date submitted
header: Submission details
- name: submittedDate
type: string
type: date
hideOnSequenceDetailsPage: true
generateIndex: true
autocomplete: true
displayName: Date submitted (exact)
- name: releasedAtTimestamp
type: timestamp
displayName: Date released
header: Submission details
columnWidth: 100
- name: releasedDate
type: string
type: date
hideOnSequenceDetailsPage: true
generateIndex: true
autocomplete: true
displayName: Date released (exact)
columnWidth: 100
- name: earliestReleaseDate
type: date
displayName: Earliest release date
header: Sample details
noInput: true
columnWidth: 100
order: 15
- name: dataUseTerms
type: string
generateIndex: true
Expand Down Expand Up @@ -289,7 +292,6 @@ organisms:
{{- if .earliestReleaseDate }}
{{ .earliestReleaseDate | toYaml | nindent 8 }}
{{- else }}
enabled: false
externalFields: []
{{- end }}
{{- end }}
Expand Down
13 changes: 3 additions & 10 deletions kubernetes/loculus/values.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ defaultOrganismConfig: &defaultOrganismConfig
organismName: "Ebola Sudan"
image: "/images/organisms/ebolasudan_small.jpg"
earliestReleaseDate:
enabled: true
externalFields:
- ncbiReleaseDate
### Field list
Expand Down Expand Up @@ -135,12 +134,6 @@ defaultOrganismConfig: &defaultOrganismConfig
timestamp: ncbiReleaseDate
noInput: true
columnWidth: 100
- name: earliestReleaseDate
displayName: Earliest release date
header: Sample details
type: date
rangeSearch: true
noInput: true
- name: ncbiUpdateDate
type: date
displayName: NCBI update date
Expand Down Expand Up @@ -1133,7 +1126,7 @@ defaultOrganismConfig: &defaultOrganismConfig
website: &website
tableColumns:
- sampleCollectionDate
- ncbiReleaseDate
- earliestReleaseDate
- authors
- authorAffiliations
- geoLocCountry
Expand Down Expand Up @@ -1228,7 +1221,7 @@ defaultOrganisms:
<<: *website
tableColumns:
- sampleCollectionDate
- ncbiReleaseDate
- earliestReleaseDate
- authors
- authorAffiliations
- geoLocCountry
Expand Down Expand Up @@ -1458,7 +1451,7 @@ defaultOrganisms:
- geoLocAdmin1
- authors
- authorAffiliations
- ncbiReleaseDate
- earliestReleaseDate
- hostNameScientific
- length_M
- length_S
Expand Down
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