feat(lapis2): delete insertions metadata types #804

In SILO the insertions are now handled separately from metadata.

lapis2/README.md

@@ -77,3 +77,12 @@ Creating a release means:
 The changelog and the version number are determined by the commit messages.
 Therefore, commit messages should follow the [Conventional Commits](https://www.conventionalcommits.org/) specification.
 Also refer to the Release Please documentation for more information on how to write commit messages.
+
+## SILO Compatibility
+
+This table shows which LAPIS version is required for which SILO version:
+
+| LAPIS | SILO  |
+|-------|-------|
+| 0.1.2 | 0.2.0 |
+| 0.1   | 0.1.0 |

lapis2/src/main/kotlin/org/genspectrum/lapis/config/DatabaseConfig.kt

@@ -35,12 +35,6 @@ enum class MetadataType {
 
     @JsonProperty("boolean")
     BOOLEAN,
-
-    @JsonProperty("insertion")
-    NUCLEOTIDE_INSERTION,
-
-    @JsonProperty("aaInsertion")
-    AMINO_ACID_INSERTION,
 }
 
 data class DatabaseFeature(val name: String)

lapis2/src/main/kotlin/org/genspectrum/lapis/config/SequenceFilterFields.kt

@@ -94,9 +94,6 @@ private fun mapToSequenceFilterField(databaseMetadata: DatabaseMetadata) =
                 type = SequenceFilterFieldType.Boolean,
             ),
         )
-
-        MetadataType.NUCLEOTIDE_INSERTION -> emptyList()
-        MetadataType.AMINO_ACID_INSERTION -> emptyList()
     }
 
 private const val VARIANT_QUERY_FIELD = "variantQuery"

lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt

@@ -316,9 +316,8 @@ private fun aggregatedMetadataFieldSchemas(databaseConfig: DatabaseConfig) =
     databaseConfig.schema.metadata.associate { it.name to Schema<String>().type(mapToOpenApiType(it.type)) }
 
 private fun detailsMetadataFieldSchemas(databaseConfig: DatabaseConfig) =
-    databaseConfig.schema.metadata.filter {
-        it.type != MetadataType.AMINO_ACID_INSERTION && it.type != MetadataType.NUCLEOTIDE_INSERTION
-    }
+    databaseConfig.schema
+        .metadata
         .associate { it.name to Schema<String>().type(mapToOpenApiType(it.type)) }
 
 private fun mapToOpenApiType(type: MetadataType): String =
@@ -328,8 +327,6 @@ private fun mapToOpenApiType(type: MetadataType): String =
         MetadataType.DATE -> "string"
         MetadataType.INT -> "integer"
         MetadataType.FLOAT -> "number"
-        MetadataType.NUCLEOTIDE_INSERTION -> "string"
-        MetadataType.AMINO_ACID_INSERTION -> "string"
         MetadataType.BOOLEAN -> "boolean"
     }
 
@@ -538,10 +535,10 @@ private fun aminoAcidInsertions() =
         .items(
             Schema<String>()
                 .type("string")
-                .example("ins_ORF1:123:ATT")
+                .example("ins_ORF1a:123:ATT")
                 .description(
                     """
-                    |A amino acid insertion in the format "ins_\<gene\>:\<position\>:\<insertion\>".  
+                    |An amino acid insertion in the format "ins_\<gene\>:\<position\>:\<insertion\>".  
                     """.trimMargin(),
                 ),
         )

lapis2/src/test/kotlin/org/genspectrum/lapis/config/DatabaseConfigTest.kt

@@ -27,8 +27,6 @@ class DatabaseConfigTest {
                 DatabaseMetadata(name = "country", type = MetadataType.STRING),
                 DatabaseMetadata(name = "pangoLineage", type = MetadataType.PANGO_LINEAGE),
                 DatabaseMetadata(name = "test_boolean_column", type = MetadataType.BOOLEAN),
-                DatabaseMetadata(name = "nucInsertion", type = MetadataType.NUCLEOTIDE_INSERTION),
-                DatabaseMetadata(name = "aaInsertion", type = MetadataType.AMINO_ACID_INSERTION),
             ),
         )
         assertThat(
@@ -59,8 +57,6 @@ class DatabaseConfigWithoutFeaturesTest {
                 DatabaseMetadata(name = "region", type = MetadataType.STRING),
                 DatabaseMetadata(name = "country", type = MetadataType.STRING),
                 DatabaseMetadata(name = "pangoLineage", type = MetadataType.PANGO_LINEAGE),
-                DatabaseMetadata(name = "nucInsertion", type = MetadataType.NUCLEOTIDE_INSERTION),
-                DatabaseMetadata(name = "aaInsertion", type = MetadataType.AMINO_ACID_INSERTION),
             ),
         )
         assertThat(underTest.schema.features, `is`(emptyList()))

lapis2/src/test/resources/config/testDatabaseConfig.yaml

@@ -14,10 +14,6 @@ schema:
       type: pango_lineage
     - name: test_boolean_column
       type: boolean
-    - name: nucInsertion
-      type: insertion
-    - name: aaInsertion
-      type: aaInsertion
   features:
     - name: sarsCoV2VariantQuery
   primaryKey: primaryKey

lapis2/src/test/resources/config/testDatabaseConfigWithoutFeatures.yaml

@@ -12,8 +12,4 @@ schema:
       type: string
     - name: pangoLineage
       type: pango_lineage
-    - name: nucInsertion
-      type: insertion
-    - name: aaInsertion
-      type: aaInsertion
   primaryKey: primaryKey

siloLapisTests/test/aminoAcidInsertions.spec.ts

@@ -21,7 +21,7 @@ describe('The /aminoAcidInsertions endpoint', () => {
   it('should order by specified fields', async () => {
     const ascendingOrderedResult = await lapisClient.postAminoAcidInsertions1({
       insertionsRequest: {
-        orderBy: [{ field: 'count', type: 'ascending' }],
+        orderBy: [{ field: 'count', type: 'ascending' }, { field: 'insertion' }],
       },
     });
 
@@ -39,7 +39,7 @@ describe('The /aminoAcidInsertions endpoint', () => {
   it('should apply limit and offset', async () => {
     const resultWithLimit = await lapisClient.postAminoAcidInsertions1({
       insertionsRequest: {
-        orderBy: [{ field: 'count', type: 'ascending' }],
+        orderBy: [{ field: 'count', type: 'ascending' }, { field: 'insertion' }],
         limit: 2,
       },
     });
@@ -49,7 +49,7 @@ describe('The /aminoAcidInsertions endpoint', () => {
 
     const resultWithLimitAndOffset = await lapisClient.postAminoAcidInsertions1({
       insertionsRequest: {
-        orderBy: [{ field: 'count', type: 'ascending' }],
+        orderBy: [{ field: 'count', type: 'ascending' }, { field: 'insertion' }],
         limit: 2,
         offset: 1,
       },
@@ -81,6 +81,7 @@ describe('The /aminoAcidInsertions endpoint', () => {
     const result = await lapisClient.postAminoAcidInsertions1({
       insertionsRequest: {
         aminoAcidInsertions: ['ins_S:143:T', 'ins_ORF1a:3602:F?P'],
+        orderBy: [{ field: 'insertion' }],
       },
     });
 

siloLapisTests/testData/aa_insertions.tsv

@@ -0,0 +1,101 @@
+primaryKey	S	ORF1a	E	M	N	ORF1b	ORF3a	ORF6	ORF7a	ORF7b	ORF8	ORF9b
+key_1408408	[214:EPE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1749899	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2016901	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1749892	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1597932	[214:EPE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1407962	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1750503	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1360935	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2019235	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1749960	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1361468	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1408062	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1597890	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1682849	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1408805	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1750868	[214:EPE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2019350	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2017036	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1599113	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2214128	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2408472	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_830864	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_581968	[214:EPE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2213804	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2405276	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2213934	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2213984	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2574088	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2544226	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2360326	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2379651	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1036103	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_931279	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_931031	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1273458	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1273715	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_737604	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1129663	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003629	[214:EPE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_737715	[247:SGE]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003036	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_899762	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_899725	[210:IV]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1195052	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003519	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003010	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1119584	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1002052	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_466942	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003849	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_768148	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1080536	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1002156	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1119315	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1004495	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1001920	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1131102	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003373	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_721941	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1130868	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1003425	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_737860	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1001493	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1260480	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1747885	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1747752	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1005148	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1748243	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1748215	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1748395	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1760534	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2086867	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_1840634	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2180995	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2181005	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2180023	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2270139	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2544452	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2544332	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2307766	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2375490	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2374969	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2307888	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2375247	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2308054	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2375165	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2375097	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3128737	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3128811	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3086369	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3259931	[143:T]	[3602:FEP]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3267832	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3128796	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3016465	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3247294	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3578231	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3465732	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2367431	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_3465556	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]
+key_2359636	[]	[3602:F]	[]	[]	[]	[]	[]	[]	[]	[]	[]	[]

siloLapisTests/testData/nuc_insertions.tsv

@@ -0,0 +1,101 @@
+primaryKey	main
+key_1408408	[]
+key_1749899	[]
+key_2016901	[]
+key_1749892	[]
+key_1597932	[]
+key_1407962	[]
+key_1750503	[]
+key_1360935	[]
+key_2019235	[]
+key_1749960	[]
+key_1361468	[]
+key_1408062	[22204:CAGAA]
+key_1597890	[22339:GCTGGT]
+key_1682849	[]
+key_1408805	[]
+key_1750868	[]
+key_2019350	[]
+key_2017036	[]
+key_1599113	[]
+key_2214128	[]
+key_2408472	[]
+key_830864	[]
+key_581968	[]
+key_2213804	[25701:CCC]
+key_2405276	[]
+key_2213934	[]
+key_2213984	[25701:CCC]
+key_2574088	[25701:CCC]
+key_2544226	[]
+key_2360326	[]
+key_2379651	[]
+key_1036103	[]
+key_931279	[]
+key_931031	[]
+key_1273458	[25701:CCC]
+key_1273715	[]
+key_737604	[]
+key_1129663	[]
+key_1003629	[]
+key_737715	[]
+key_1003036	[5959:TAT]
+key_899762	[]
+key_899725	[]
+key_1195052	[]
+key_1003519	[]
+key_1003010	[]
+key_1119584	[]
+key_1002052	[]
+key_466942	[]
+key_1003849	[]
+key_768148	[25701:CCC]
+key_1080536	[]
+key_1002156	[]
+key_1119315	[]
+key_1004495	[25701:CCC]
+key_1001920	[]
+key_1131102	[]
+key_1003373	[]
+key_721941	[]
+key_1130868	[25701:CCC]
+key_1003425	[]
+key_737860	[]
+key_1001493	[]
+key_1260480	[]
+key_1747885	[]
+key_1747752	[]
+key_1005148	[25701:CCC]
+key_1748243	[]
+key_1748215	[]
+key_1748395	[]
+key_1760534	[]
+key_2086867	[25701:CCC]
+key_1840634	[]
+key_2180995	[]
+key_2181005	[]
+key_2180023	[25701:CCC]
+key_2270139	[]
+key_2544452	[]
+key_2544332	[25701:CCC]
+key_2307766	[]
+key_2375490	[]
+key_2374969	[25701:CCC]
+key_2307888	[]
+key_2375247	[25701:CCC]
+key_2308054	[]
+key_2375165	[]
+key_2375097	[]
+key_3128737	[]
+key_3128811	[]
+key_3086369	[25701:CCC]
+key_3259931	[]
+key_3267832	[]
+key_3128796	[25701:CCC]
+key_3016465	[]
+key_3247294	[]
+key_3578231	[25701:CCC,5959:TAT]
+key_3465732	[]
+key_2367431	[]
+key_3465556	[]
+key_2359636	[25701:CCC]

siloLapisTests/testData/protectedTestDatabaseConfig.yaml

@@ -23,10 +23,6 @@ schema:
       type: float
     - name: test_boolean_column
       type: boolean
-    - name: insertions
-      type: insertion
-    - name: aaInsertions
-      type: aaInsertion
   features:
     - name: sarsCoV2VariantQuery
   primaryKey: primaryKey