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Add submissionId to input fields qsd getting there yasss yup big moment Short and working? First draft of input fields Add submissionId to input fields qsd getting there yasss yup big moment Short and working? getting rid of stuff undo change for quick image build speed up ingest by not sleeping fix More flexible rename sioll mistake no tag need to keep genbank accession in any case f add length to metadata fix prepro dataset servers f fix taxon ids correct syntax for no input fix defaults add back dummy organism towards parity with current main Default header to "Other" Document metadata schema fields Use default "string" for "type" field wip wip Sort input fields in order of appearance in metadata Make sure the config processor output directory exists The dir can be removed, we just recreate it Output ingest config files with deploy.py Allow generation of local file with "environment=local" in values.yaml don't require sample collectio ndate try this don't require anything f update u f Display more in table avoid dupe country Hide admin from search fields update values Suppress warnings on missing fields as it would overwhelm submitters Allow date not to be required Add more headers Allow adding extra metadata per organism Add lineage to west-nile Add header for site Linkify dataUseTermsUrl Organism display improvements Replace escape syntax with something safer in helm Replace attempt 2 Support pangolineage_alias.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| {{- define "loculus.ingestRename" -}} | ||
| {{- $metadata := . }} | ||
| {{- $ingestRename := dict }} | ||
| {{- range $field := $metadata }} | ||
| {{- if hasKey $field "ingest" }} | ||
| {{- $_ := set $ingestRename (index $field "ingest") (index $field "name") }} | ||
| {{- end }} | ||
| {{- end }} | ||
| {{- $output := dict "rename" $ingestRename }} | ||
| {{- toYaml $output }} | ||
| {{- end -}} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| {{- define "loculus.inputFields" -}} | ||
| {{- $data := . }} | ||
| {{- $metadata := $data.metadata }} | ||
| {{- $extraFields := $data.extraInputFields }} | ||
| {{- $TO_KEEP := list "name" "displayName" "definition" "guidance" "example" "required" }} | ||
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| {{- $fieldsDict := dict }} | ||
| {{- $index := 0 }} | ||
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| {{- /* Add fields with position "first" to the dict */}} | ||
| {{- range $field := $extraFields }} | ||
| {{- if eq $field.position "first" }} | ||
| {{- $_ := set $fieldsDict (printf "%03d" $index) $field }} | ||
| {{- $index = add $index 1 }} | ||
| {{- end }} | ||
| {{- end }} | ||
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| {{- /* Add filtered metadata fields to the dict */}} | ||
| {{- range $field := $metadata }} | ||
| {{- if not (hasKey $field "noInput") }} | ||
| {{- $_ := set $fieldsDict (printf "%03d" $index) $field }} | ||
| {{- $index = add $index 1 }} | ||
| {{- end }} | ||
| {{- end }} | ||
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| {{- /* Add fields with position "last" to the dict */}} | ||
| {{- range $field := $extraFields }} | ||
| {{- if eq $field.position "last" }} | ||
| {{- $_ := set $fieldsDict (printf "%03d" $index) $field }} | ||
| {{- $index = add $index 1 }} | ||
| {{- end }} | ||
| {{- end }} | ||
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| {{- /* Iterate over sorted index to get list of values (sorted by key) */}} | ||
| {{- $inputFields := list }} | ||
| {{- range $k:= keys $fieldsDict | sortAlpha }} | ||
| {{- $toAdd := dict }} | ||
| {{- range $k, $v := (index $fieldsDict $k) }} | ||
| {{- if has $k $TO_KEEP }} | ||
| {{- $_ := set $toAdd $k $v }} | ||
| {{- end }} | ||
| {{- end }} | ||
| {{- $inputFields = append $inputFields $toAdd }} | ||
| {{- end }} | ||
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| {{- toYaml $inputFields }} | ||
| {{- end -}} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| {{- define "loculus.preprocessingSpecs" -}} | ||
| {{- $metadata := . }} | ||
| {{- $specs := dict }} | ||
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| {{- range $field := $metadata }} | ||
| {{- $name := index $field "name" }} | ||
| {{- $spec := dict "function" "identity" "inputs" (dict "input" $name) }} | ||
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| {{- if hasKey $field "type" }} | ||
| {{- $type := index $field "type" }} | ||
| {{- if eq $type "int" }} | ||
| {{- $_ := set $spec "args" (dict "type" "int") }} | ||
| {{- else if eq $type "float" }} | ||
| {{- $_ := set $spec "args" (dict "type" "float") }} | ||
| {{- end }} | ||
| {{- end }} | ||
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| {{- if hasKey $field "preprocessing" }} | ||
| {{- $preprocessing := index $field "preprocessing" }} | ||
| {{- if eq (typeOf $preprocessing) "string" }} | ||
| {{- $_ := set $spec "inputs" (dict "input" $preprocessing) }} | ||
| {{- else }} | ||
| {{- if hasKey $preprocessing "function" }} | ||
| {{- $_ := set $spec "function" (index $preprocessing "function") }} | ||
| {{- end }} | ||
| {{- if hasKey $preprocessing "args" }} | ||
| {{- $_ := set $spec "args" (index $preprocessing "args") }} | ||
| {{- end }} | ||
| {{- if hasKey $preprocessing "inputs" }} | ||
| {{- $_ := set $spec "inputs" (index $preprocessing "inputs") }} | ||
| {{- end }} | ||
| {{- end }} | ||
| {{- end }} | ||
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| {{- $_ := set $specs $name $spec }} | ||
| {{- end }} | ||
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| {{- toYaml $specs }} | ||
| {{- end -}} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| {{- $testconfig := .Values.testconfig | default false }} | ||
| {{- $backendHost := .Values.environment | eq "server" | ternary (printf "https://backend-%s" $.Values.host) ($testconfig | ternary "http://localhost:8079" "http://loculus-backend-service:8079") }} | ||
| {{- $keycloakHost := .Values.environment | eq "server" | ternary (printf "https://authentication-%s" $.Values.host) ($testconfig | ternary "http://localhost:8083" "http://loculus-keycloak-service:8083") }} | ||
| {{- range $key, $values := (.Values.organisms | default .Values.defaultOrganisms) }} | ||
| {{- if $values.ingest }} | ||
| {{- $metadata := (include "loculus.patchMetadataSchema" $values.schema | fromYaml).metadata -}} | ||
| --- | ||
| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
| name: loculus-ingest-config-{{ $key }} | ||
| data: | ||
| config.yaml: | | ||
| {{- $values.ingest.configFile | toYaml | nindent 4 }} | ||
| organism: {{ $key }} | ||
| backend_url: {{ $backendHost }} | ||
| keycloak_token_url: {{ $keycloakHost -}}/realms/loculus/protocol/openid-connect/token | ||
| {{- include "loculus.ingestRename" $metadata | nindent 4 }} | ||
| {{- end }} | ||
| {{- end }} |
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