feat: add unaligned nucleotide sequence route

GenSpectrum · Jan 25, 2024 · adda1dc · adda1dc
1 parent 7c0f597
commit adda1dc
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diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ControllerDescriptions.kt
@@ -26,9 +26,15 @@ const val ALIGNED_AMINO_ACID_SEQUENCE_ENDPOINT_DESCRIPTION =
 const val ALIGNED_SINGLE_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION =
     """Returns a string of fasta formatted aligned nucleotide sequences. Only sequences matching the 
     specified sequence filters are considered."""
+const val UNALIGNED_SINGLE_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION =
+    """Returns a string of fasta formatted unaligned nucleotide sequences. Only sequences matching the 
+    specified sequence filters are considered."""
 const val ALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION =
     """Returns a string of fasta formatted aligned nucleotide sequences of the requested segment.
     Only sequences matching the specified sequence filters are considered."""
+const val UNALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION =
+    """Returns a string of fasta formatted unaligned nucleotide sequences of the requested segment.
+    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
@@ -73,6 +73,7 @@ const val NUCLEOTIDE_INSERTIONS_ROUTE = "/nucleotideInsertions"
 const val AMINO_ACID_INSERTIONS_ROUTE = "/aminoAcidInsertions"
 const val ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE = "/alignedNucleotideSequences"
 const val ALIGNED_AMINO_ACID_SEQUENCES_ROUTE = "/alignedAminoAcidSequences"
+const val UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE = "/unalignedNucleotideSequences"
 
 @RestController
 @RequestMapping("/sample")

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt
@@ -8,6 +8,7 @@ import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.openApi.AminoAcidInsertions
 import org.genspectrum.lapis.openApi.AminoAcidMutations
 import org.genspectrum.lapis.openApi.LapisAlignedMultiSegmentedNucleotideSequenceResponse
+import org.genspectrum.lapis.openApi.LapisUnalignedMultiSegmentedNucleotideSequenceResponse
 import org.genspectrum.lapis.openApi.Limit
 import org.genspectrum.lapis.openApi.NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA
 import org.genspectrum.lapis.openApi.NucleotideInsertions
@@ -112,4 +113,74 @@ class MultiSegmentedSequenceController(
             segment,
         )
     }
+
+    @GetMapping("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}", produces = ["text/x-fasta"])
+    @LapisUnalignedMultiSegmentedNucleotideSequenceResponse
+    fun getUnalignedNucleotideSequence(
+        @PathVariable(name = "segment", required = true)
+        @Segment
+        segment: String,
+        @PrimitiveFieldFilters
+        @RequestParam
+        sequenceFilters: GetRequestSequenceFilters?,
+        @NucleotideSequencesOrderByFields
+        @RequestParam
+        orderBy: List<OrderByField>?,
+        @NucleotideMutations
+        @RequestParam
+        nucleotideMutations: List<NucleotideMutation>?,
+        @AminoAcidMutations
+        @RequestParam
+        aminoAcidMutations: List<AminoAcidMutation>?,
+        @NucleotideInsertions
+        @RequestParam
+        nucleotideInsertions: List<NucleotideInsertion>?,
+        @AminoAcidInsertions
+        @RequestParam
+        aminoAcidInsertions: List<AminoAcidInsertion>?,
+        @Limit
+        @RequestParam
+        limit: Int? = null,
+        @Offset
+        @RequestParam
+        offset: Int? = null,
+    ): String {
+        val request = SequenceFiltersRequest(
+            sequenceFilters?.filter { !SPECIAL_REQUEST_PROPERTIES.contains(it.key) } ?: emptyMap(),
+            nucleotideMutations ?: emptyList(),
+            aminoAcidMutations ?: emptyList(),
+            nucleotideInsertions ?: emptyList(),
+            aminoAcidInsertions ?: emptyList(),
+            orderBy ?: emptyList(),
+            limit,
+            offset,
+        )
+
+        requestContext.filter = request
+
+        return siloQueryModel.getGenomicSequence(
+            request,
+            SequenceType.UNALIGNED,
+            segment,
+        )
+    }
+
+    @PostMapping("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}", produces = ["text/x-fasta"])
+    @LapisUnalignedMultiSegmentedNucleotideSequenceResponse
+    fun postUnalignedNucleotideSequence(
+        @PathVariable(name = "segment", required = true)
+        @Segment
+        segment: String,
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA"))
+        @RequestBody
+        request: SequenceFiltersRequest,
+    ): String {
+        requestContext.filter = request
+
+        return siloQueryModel.getGenomicSequence(
+            request,
+            SequenceType.UNALIGNED,
+            segment,
+        )
+    }
 }
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt
@@ -9,6 +9,7 @@ import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.openApi.AminoAcidInsertions
 import org.genspectrum.lapis.openApi.AminoAcidMutations
 import org.genspectrum.lapis.openApi.LapisAlignedSingleSegmentedNucleotideSequenceResponse
+import org.genspectrum.lapis.openApi.LapisUnalignedSingleSegmentedNucleotideSequenceResponse
 import org.genspectrum.lapis.openApi.Limit
 import org.genspectrum.lapis.openApi.NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA
 import org.genspectrum.lapis.openApi.NucleotideInsertions
@@ -106,4 +107,68 @@ class SingleSegmentedSequenceController(
             referenceGenomeSchema.nucleotideSequences[0].name,
         )
     }
+
+    @GetMapping(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE, produces = ["text/x-fasta"])
+    @LapisUnalignedSingleSegmentedNucleotideSequenceResponse
+    fun getUnalignedNucleotideSequences(
+        @PrimitiveFieldFilters
+        @RequestParam
+        sequenceFilters: GetRequestSequenceFilters?,
+        @NucleotideSequencesOrderByFields
+        @RequestParam
+        orderBy: List<OrderByField>?,
+        @NucleotideMutations
+        @RequestParam
+        nucleotideMutations: List<NucleotideMutation>?,
+        @AminoAcidMutations
+        @RequestParam
+        aminoAcidMutations: List<AminoAcidMutation>?,
+        @NucleotideInsertions
+        @RequestParam
+        nucleotideInsertions: List<NucleotideInsertion>?,
+        @AminoAcidInsertions
+        @RequestParam
+        aminoAcidInsertions: List<AminoAcidInsertion>?,
+        @Limit
+        @RequestParam
+        limit: Int? = null,
+        @Offset
+        @RequestParam
+        offset: Int? = null,
+    ): String {
+        val request = SequenceFiltersRequest(
+            sequenceFilters?.filter { !SPECIAL_REQUEST_PROPERTIES.contains(it.key) } ?: emptyMap(),
+            nucleotideMutations ?: emptyList(),
+            aminoAcidMutations ?: emptyList(),
+            nucleotideInsertions ?: emptyList(),
+            aminoAcidInsertions ?: emptyList(),
+            orderBy ?: emptyList(),
+            limit,
+            offset,
+        )
+
+        requestContext.filter = request
+
+        return siloQueryModel.getGenomicSequence(
+            request,
+            SequenceType.UNALIGNED,
+            referenceGenomeSchema.nucleotideSequences[0].name,
+        )
+    }
+
+    @PostMapping(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE, produces = ["text/x-fasta"])
+    @LapisUnalignedSingleSegmentedNucleotideSequenceResponse
+    fun postUnalignedNucleotideSequence(
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA"))
+        @RequestBody
+        request: SequenceFiltersRequest,
+    ): String {
+        requestContext.filter = request
+
+        return siloQueryModel.getGenomicSequence(
+            request,
+            SequenceType.UNALIGNED,
+            referenceGenomeSchema.nucleotideSequences[0].name,
+        )
+    }
 }
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/Schemas.kt
@@ -24,6 +24,8 @@ import org.genspectrum.lapis.controller.LIMIT_DESCRIPTION
 import org.genspectrum.lapis.controller.NUCLEOTIDE_INSERTIONS_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.NUCLEOTIDE_MUTATION_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.controller.OFFSET_DESCRIPTION
+import org.genspectrum.lapis.controller.UNALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION
+import org.genspectrum.lapis.controller.UNALIGNED_SINGLE_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION
 import org.genspectrum.lapis.request.LAPIS_DATA_VERSION_HEADER
 import org.springframework.core.annotation.AliasFor
 
@@ -161,13 +163,27 @@ annotation class LapisAlignedAminoAcidSequenceResponse
 )
 annotation class LapisAlignedSingleSegmentedNucleotideSequenceResponse
 
+@Target(AnnotationTarget.FUNCTION)
+@Retention(AnnotationRetention.RUNTIME)
+@LapisResponseAnnotation(
+    description = UNALIGNED_SINGLE_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION,
+)
+annotation class LapisUnalignedSingleSegmentedNucleotideSequenceResponse
+
 @Target(AnnotationTarget.FUNCTION)
 @Retention(AnnotationRetention.RUNTIME)
 @LapisResponseAnnotation(
     description = ALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION,
 )
 annotation class LapisAlignedMultiSegmentedNucleotideSequenceResponse
 
+@Target(AnnotationTarget.FUNCTION)
+@Retention(AnnotationRetention.RUNTIME)
+@LapisResponseAnnotation(
+    description = UNALIGNED_MULTI_SEGMENTED_NUCLEOTIDE_SEQUENCE_ENDPOINT_DESCRIPTION,
+)
+annotation class LapisUnalignedMultiSegmentedNucleotideSequenceResponse
+
 @Target(AnnotationTarget.VALUE_PARAMETER)
 @Retention(AnnotationRetention.RUNTIME)
 @Parameter(

diff --git a/.../src/test/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceControllerTest.kt b/.../src/test/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceControllerTest.kt
@@ -150,4 +150,80 @@ class MultiSegmentedSequenceControllerTest(
         mockMvc.perform(request)
             .andExpect(status().isNotFound)
     }
+
+    @Test
+    fun `should GET unalignedNucleotideSequences with empty filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(emptyMap()),
+                SequenceType.UNALIGNED,
+                "otherSegment",
+            )
+        } returns returnedValue
+
+        mockMvc.perform(getSample("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/otherSegment"))
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should GET unalignedNucleotideSequences with filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(mapOf("country" to "Switzerland")),
+                SequenceType.UNALIGNED,
+                "otherSegment",
+            )
+        } returns returnedValue
+
+        mockMvc.perform(getSample("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/otherSegment?country=Switzerland"))
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should POST unalignedNucleotideSequences with empty filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(emptyMap()),
+                SequenceType.UNALIGNED,
+                "otherSegment",
+            )
+        } returns returnedValue
+
+        val request = postSample("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/otherSegment")
+            .content("""{}""")
+            .contentType(MediaType.APPLICATION_JSON)
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should POST unalignedNucleotideSequences with filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(mapOf("country" to "Switzerland")),
+                SequenceType.UNALIGNED,
+                "otherSegment",
+            )
+        } returns returnedValue
+
+        val request = postSample("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/otherSegment")
+            .content("""{"country":"Switzerland"}""")
+            .contentType(MediaType.APPLICATION_JSON)
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
 }
diff --git a/...src/test/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceControllerTest.kt b/...src/test/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceControllerTest.kt
@@ -150,4 +150,80 @@ class SingleSegmentedSequenceControllerTest(
         mockMvc.perform(request)
             .andExpect(status().isNotFound)
     }
+
+    @Test
+    fun `should GET unalignedNucleotideSequence with empty filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(emptyMap()),
+                SequenceType.UNALIGNED,
+                "someSegment",
+            )
+        } returns returnedValue
+
+        mockMvc.perform(getSample(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE))
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should GET unalignedNucleotideSequence with filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(mapOf("country" to "Switzerland")),
+                SequenceType.UNALIGNED,
+                "someSegment",
+            )
+        } returns returnedValue
+
+        mockMvc.perform(getSample("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE?country=Switzerland"))
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should POST unalignedNucleotideSequence with empty filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(emptyMap()),
+                SequenceType.UNALIGNED,
+                "someSegment",
+            )
+        } returns returnedValue
+
+        val request = postSample(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE)
+            .content("""{}""")
+            .contentType(MediaType.APPLICATION_JSON)
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
+
+    @Test
+    fun `should POST unalignedNucleotideSequence with filter`() {
+        val returnedValue = "TestSequenceContent"
+        every {
+            siloQueryModelMock.getGenomicSequence(
+                sequenceFiltersRequest(mapOf("country" to "Switzerland")),
+                SequenceType.UNALIGNED,
+                "someSegment",
+            )
+        } returns returnedValue
+
+        val request = postSample(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE)
+            .content("""{"country": "Switzerland"}""")
+            .contentType(MediaType.APPLICATION_JSON)
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(content().string(returnedValue))
+            .andExpect(header().stringValues("Lapis-Data-Version", "1234"))
+    }
 }