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feat: filter by insertions at all endpoints
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56 changes: 56 additions & 0 deletions
56
lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| package org.genspectrum.lapis.request | ||
|
|
||
| import com.fasterxml.jackson.core.JsonParser | ||
| import com.fasterxml.jackson.databind.DeserializationContext | ||
| import com.fasterxml.jackson.databind.JsonDeserializer | ||
| import org.springframework.boot.jackson.JsonComponent | ||
| import org.springframework.core.convert.converter.Converter | ||
| import org.springframework.stereotype.Component | ||
|
|
||
| data class AminoAcidInsertion(val position: Int, val gene: String, val insertions: String) { | ||
| companion object { | ||
| fun fromString(aminoAcidInsertion: String): AminoAcidInsertion { | ||
| val match = AMINO_ACID_INSERTION_REGEX.find(aminoAcidInsertion) | ||
| ?: throw IllegalArgumentException("Invalid nucleotide mutation: $aminoAcidInsertion") | ||
|
|
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| val matchGroups = match.groups | ||
|
|
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| val position = matchGroups["position"]?.value?.toInt() | ||
| ?: throw IllegalArgumentException( | ||
| "Invalid amino acid insertion: $aminoAcidInsertion: Did not find position", | ||
| ) | ||
|
|
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| val gene = matchGroups["gene"]?.value | ||
| ?: throw IllegalArgumentException( | ||
| "Invalid amino acid insertion: $aminoAcidInsertion: Did not find gene", | ||
| ) | ||
|
|
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| val insertions = matchGroups["insertion"]?.value?.replace("?", ".*") | ||
| ?: throw IllegalArgumentException( | ||
| "Invalid amino acid insertion: $aminoAcidInsertion: Did not find insertions", | ||
| ) | ||
|
|
||
| return AminoAcidInsertion( | ||
| position, | ||
| gene, | ||
| insertions, | ||
| ) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| private val AMINO_ACID_INSERTION_REGEX = | ||
| Regex( | ||
| """^ins_(?<gene>[a-zA-Z0-9_-]+):(?<position>\d+):(?<insertion>[a-zA-Z0-9?_-]+)?$""", | ||
| ) | ||
|
|
||
| @JsonComponent | ||
| class AminoAcidInsertionDeserializer : JsonDeserializer<AminoAcidInsertion>() { | ||
| override fun deserialize(p: JsonParser, ctxt: DeserializationContext) = | ||
| AminoAcidInsertion.fromString(p.valueAsString) | ||
| } | ||
|
|
||
| @Component | ||
| class StringToAminoAcidInsertionConverter : Converter<String, AminoAcidInsertion> { | ||
| override fun convert(source: String) = AminoAcidInsertion.fromString(source) | ||
| } |
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