refactor: rename 'amino acid sequence' to 'aligned amino acid sequence'

GenSpectrum · Dec 12, 2023 · 22e5f49 · 22e5f49
1 parent 803808f
commit 22e5f49
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Showing 6 changed files with 27 additions and 27 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt
@@ -16,8 +16,8 @@ const val AMINO_ACID_INSERTIONS_ENDPOINT_DESCRIPTION =
         "than or equal to the specified minProportion. Only sequences matching the specified " +
         "sequence filters are considered."
 
-const val AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION =
-    "Returns a string of fasta formated amino acid sequences. Only sequences matching the specified " +
+const val ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION =
+    "Returns a string of fasta formated aligned amino acid sequences. Only sequences matching the specified " +
         "sequence filters are considered."
 const val AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION =
     "The fields to stratify by. If empty, only the overall count is returned"

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -10,7 +10,7 @@ import org.genspectrum.lapis.controller.Delimiter.TAB
 import org.genspectrum.lapis.logging.RequestContext
 import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.openApi.AGGREGATED_REQUEST_SCHEMA
-import org.genspectrum.lapis.openApi.AMINO_ACID_SEQUENCE_REQUEST_SCHEMA
+import org.genspectrum.lapis.openApi.ALIGNED_AMINO_ACID_SEQUENCE_REQUEST_SCHEMA
 import org.genspectrum.lapis.openApi.AggregatedOrderByFields
 import org.genspectrum.lapis.openApi.AminoAcidInsertions
 import org.genspectrum.lapis.openApi.AminoAcidMutations
@@ -23,9 +23,9 @@ import org.genspectrum.lapis.openApi.FieldsToAggregateBy
 import org.genspectrum.lapis.openApi.INSERTIONS_REQUEST_SCHEMA
 import org.genspectrum.lapis.openApi.InsertionsOrderByFields
 import org.genspectrum.lapis.openApi.LapisAggregatedResponse
+import org.genspectrum.lapis.openApi.LapisAlignedAminoAcidSequenceResponse
 import org.genspectrum.lapis.openApi.LapisAminoAcidInsertionsResponse
 import org.genspectrum.lapis.openApi.LapisAminoAcidMutationsResponse
-import org.genspectrum.lapis.openApi.LapisAminoAcidSequenceResponse
 import org.genspectrum.lapis.openApi.LapisDetailsResponse
 import org.genspectrum.lapis.openApi.LapisNucleotideInsertionsResponse
 import org.genspectrum.lapis.openApi.LapisNucleotideMutationsResponse
@@ -67,7 +67,7 @@ const val AMINO_ACID_MUTATIONS_ROUTE = "/aminoAcidMutations"
 const val NUCLEOTIDE_INSERTIONS_ROUTE = "/nucleotideInsertions"
 const val AMINO_ACID_INSERTIONS_ROUTE = "/aminoAcidInsertions"
 const val ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE = "/alignedNucleotideSequences"
-const val AMINO_ACID_SEQUENCES_ROUTE = "/aminoAcidSequences"
+const val ALIGNED_AMINO_ACID_SEQUENCES_ROUTE = "/alignedAminoAcidSequences"
 
 @RestController
 class LapisController(
@@ -1261,9 +1261,9 @@ class LapisController(
         return getResponseAsCsv(request, TAB, siloQueryModel::getAminoAcidInsertions)
     }
 
-    @GetMapping("$AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
-    @LapisAminoAcidSequenceResponse
-    fun getAminoAcidSequence(
+    @GetMapping("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
+    @LapisAlignedAminoAcidSequenceResponse
+    fun getAlignedAminoAcidSequence(
         @PathVariable(name = "gene", required = true) gene: String,
         @PrimitiveFieldFilters
         @RequestParam
@@ -1306,11 +1306,11 @@ class LapisController(
         return siloQueryModel.getGenomicSequence(request, SequenceType.ALIGNED, gene)
     }
 
-    @PostMapping("$AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
-    @LapisAminoAcidSequenceResponse
-    fun postAminoAcidSequence(
+    @PostMapping("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
+    @LapisAlignedAminoAcidSequenceResponse
+    fun postAlignedAminoAcidSequence(
         @PathVariable(name = "gene", required = true) gene: String,
-        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_SEQUENCE_REQUEST_SCHEMA"))
+        @Parameter(schema = Schema(ref = "#/components/schemas/$ALIGNED_AMINO_ACID_SEQUENCE_REQUEST_SCHEMA"))
         @RequestBody
         request: SequenceFiltersRequest,
     ): String {

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
@@ -96,7 +96,7 @@ fun buildOpenApiSchema(
                     ),
                 )
                 .addSchemas(
-                    AMINO_ACID_SEQUENCE_REQUEST_SCHEMA,
+                    ALIGNED_AMINO_ACID_SEQUENCE_REQUEST_SCHEMA,
                     requestSchemaForCommonSequenceFilters(
                         getSequenceFilters(
                             databaseConfig,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt
@@ -11,11 +11,11 @@ import io.swagger.v3.oas.annotations.responses.ApiResponse
 import org.genspectrum.lapis.controller.AGGREGATED_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION
 import org.genspectrum.lapis.controller.AGGREGATED_ORDER_BY_FIELDS_DESCRIPTION
+import org.genspectrum.lapis.controller.ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.ALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.ALIGNED_SINGLE_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.AMINO_ACID_INSERTIONS_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.AMINO_ACID_MUTATIONS_ENDPOINT_DESCRIPTION
-import org.genspectrum.lapis.controller.AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.DETAILS_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.DETAILS_FIELDS_DESCRIPTION
 import org.genspectrum.lapis.controller.DETAILS_ORDER_BY_FIELDS_DESCRIPTION
@@ -32,7 +32,7 @@ const val REQUEST_SCHEMA_WITH_MIN_PROPORTION = "SequenceFiltersWithMinProportion
 const val AGGREGATED_REQUEST_SCHEMA = "AggregatedPostRequest"
 const val DETAILS_REQUEST_SCHEMA = "DetailsPostRequest"
 const val INSERTIONS_REQUEST_SCHEMA = "InsertionsRequest"
-const val AMINO_ACID_SEQUENCE_REQUEST_SCHEMA = "AminoAcidSequenceRequest"
+const val ALIGNED_AMINO_ACID_SEQUENCE_REQUEST_SCHEMA = "AminoAcidSequenceRequest"
 const val NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA = "NucleotideSequenceRequest"
 
 const val AGGREGATED_RESPONSE_SCHEMA = "AggregatedResponse"
@@ -132,9 +132,9 @@ annotation class LapisAminoAcidInsertionsResponse
 @Target(AnnotationTarget.FUNCTION)
 @Retention(AnnotationRetention.RUNTIME)
 @LapisResponseAnnotation(
-    description = AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION,
+    description = ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION,
 )
-annotation class LapisAminoAcidSequenceResponse
+annotation class LapisAlignedAminoAcidSequenceResponse
 
 @Target(AnnotationTarget.FUNCTION)
 @Retention(AnnotationRetention.RUNTIME)

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCommonFieldsTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCommonFieldsTest.kt
@@ -367,7 +367,7 @@ class LapisControllerCommonFieldsTest(
                 Arguments.of(DETAILS_ROUTE),
                 Arguments.of(NUCLEOTIDE_INSERTIONS_ROUTE),
                 Arguments.of(AMINO_ACID_INSERTIONS_ROUTE),
-                Arguments.of("$AMINO_ACID_SEQUENCES_ROUTE/S"),
+                Arguments.of("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/S"),
             )
 
         @JvmStatic

diff --git a/siloLapisTests/test/aminoAcidSequence.spec.ts b/siloLapisTests/test/aminoAcidSequence.spec.ts
@@ -1,9 +1,9 @@
 import { expect } from 'chai';
 import { basePath, lapisClient, sequenceData } from './common';
 
-describe('The /aminoAcidSequence endpoint', () => {
+describe('The /alignedAminoAcidSequence endpoint', () => {
   it('should return amino acid sequences for Switzerland', async () => {
-    const result = await lapisClient.postAminoAcidSequence({
+    const result = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: { country: 'Switzerland' },
     });
@@ -17,7 +17,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should order ascending by specified fields', async () => {
-    const result = await lapisClient.postAminoAcidSequence({
+    const result = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: { orderBy: [{ field: 'gisaid_epi_isl', type: 'ascending' }] },
     });
@@ -31,7 +31,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should order descending by specified fields', async () => {
-    const result = await lapisClient.postAminoAcidSequence({
+    const result = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: { orderBy: [{ field: 'gisaid_epi_isl', type: 'descending' }] },
     });
@@ -45,7 +45,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should apply limit and offset', async () => {
-    const resultWithLimit = await lapisClient.postAminoAcidSequence({
+    const resultWithLimit = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: {
         orderBy: [{ field: 'gisaid_epi_isl', type: 'ascending' }],
@@ -61,7 +61,7 @@ describe('The /aminoAcidSequence endpoint', () => {
     expect(primaryKeysWithLimit[0]).to.equal('>EPI_ISL_1001493');
     expect(sequencesWithLimit[0]).to.have.length(1274);
 
-    const resultWithLimitAndOffset = await lapisClient.postAminoAcidSequence({
+    const resultWithLimitAndOffset = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: {
         orderBy: [{ field: 'gisaid_epi_isl', type: 'ascending' }],
@@ -80,7 +80,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should correctly handle nucleotide insertion requests', async () => {
-    const result = await lapisClient.postAminoAcidSequence({
+    const result = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: {
         nucleotideInsertions: ['ins_25701:CC?', 'ins_5959:?AT'],
@@ -96,7 +96,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should correctly handle amino acid insertion requests', async () => {
-    const result = await lapisClient.postAminoAcidSequence({
+    const result = await lapisClient.postAlignedAminoAcidSequence({
       gene: 'S',
       aminoAcidSequenceRequest: {
         aminoAcidInsertions: ['ins_S:143:T', 'ins_ORF1a:3602:F?P'],
@@ -111,7 +111,7 @@ describe('The /aminoAcidSequence endpoint', () => {
   });
 
   it('should return the lapis data version in the response', async () => {
-    const result = await fetch(basePath + '/aminoAcidSequences/S');
+    const result = await fetch(basePath + '/alignedAminoAcidSequences/S');
 
     expect(result.status).equals(200);
     expect(result.headers.get('lapis-data-version')).to.match(/\d{10}/);