feat: also enable returning TSV #284

GenSpectrum · Aug 4, 2023 · 9597e28 · 9597e28
1 parent 151e18f
commit 9597e28
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Showing 5 changed files with 217 additions and 29 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/CsvWriter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/CsvWriter.kt
@@ -13,11 +13,15 @@ interface CsvRecord {
 
 @Component
 class CsvWriter {
-    fun write(headers: Array<String>, data: List<CsvRecord>): String {
+    fun write(headers: Array<String>, data: List<CsvRecord>, delimiter: Delimiter): String {
         val stringWriter = StringWriter()
         CSVPrinter(
             stringWriter,
-            CSVFormat.DEFAULT.builder().setRecordSeparator("\n").setHeader(*headers).build(),
+            CSVFormat.DEFAULT.builder()
+                .setRecordSeparator("\n")
+                .setDelimiter(delimiter.value)
+                .setHeader(*headers)
+                .build(),
         ).use {
             for (datum in data) {
                 it.printRecord(*datum.asArray())
@@ -32,3 +36,8 @@ fun DetailsData.asCsvRecord() = JsonValuesCsvRecord(this.values)
 data class JsonValuesCsvRecord(val values: Collection<JsonNode>) : CsvRecord {
     override fun asArray() = values.map { it.asText() }.toTypedArray()
 }
+
+enum class Delimiter(val value: Char) {
+    COMMA(','),
+    TAB('\t'),
+}
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DataFormatParameterFilter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DataFormatParameterFilter.kt
@@ -7,13 +7,17 @@ import jakarta.servlet.http.HttpServletRequestWrapper
 import jakarta.servlet.http.HttpServletResponse
 import mu.KotlinLogging
 import org.genspectrum.lapis.util.CachedBodyHttpServletRequest
+import org.springframework.http.MediaType
 import org.springframework.stereotype.Component
 import org.springframework.web.filter.OncePerRequestFilter
 import java.util.Collections
 import java.util.Enumeration
 
 private val log = KotlinLogging.logger {}
 
+const val TEXT_CSV_HEADER = "text/csv"
+const val TEXT_TSV_HEADER = "text/tab-separated-values"
+
 @Component
 class DataFormatParameterFilter(val objectMapper: ObjectMapper) : OncePerRequestFilter() {
 
@@ -36,8 +40,20 @@ class AcceptHeaderModifyingRequestWrapper(
         if (name.equals("Accept", ignoreCase = true)) {
             when (reReadableRequest.getRequestFields()[FORMAT_PROPERTY]?.textValue()?.uppercase()) {
                 "CSV" -> {
-                    log.debug { "Overwriting Accept header to text/csv due to format property" }
-                    return "text/csv"
+                    log.debug { "Overwriting Accept header to $TEXT_CSV_HEADER due to format property" }
+                    return TEXT_CSV_HEADER
+                }
+
+                "TSV" -> {
+                    log.debug { "Overwriting Accept header to $TEXT_TSV_HEADER due to format property" }
+                    return TEXT_TSV_HEADER
+                }
+
+                "JSON" -> {
+                    log.debug {
+                        "Overwriting Accept header to ${MediaType.APPLICATION_JSON_VALUE} due to format property"
+                    }
+                    return MediaType.APPLICATION_JSON_VALUE
                 }
 
                 else -> {}
@@ -51,8 +67,20 @@ class AcceptHeaderModifyingRequestWrapper(
         if (name.equals("Accept", ignoreCase = true)) {
             when (reReadableRequest.getRequestFields()[FORMAT_PROPERTY]?.textValue()?.uppercase()) {
                 "CSV" -> {
-                    log.debug { "Overwriting Accept header to text/csv due to format property" }
-                    return Collections.enumeration(listOf("text/csv"))
+                    log.debug { "Overwriting Accept header to $TEXT_CSV_HEADER due to format property" }
+                    return Collections.enumeration(listOf(TEXT_CSV_HEADER))
+                }
+
+                "TSV" -> {
+                    log.debug { "Overwriting Accept header to $TEXT_TSV_HEADER due to format property" }
+                    return Collections.enumeration(listOf(TEXT_TSV_HEADER))
+                }
+
+                "JSON" -> {
+                    log.debug {
+                        "Overwriting Accept header to ${MediaType.APPLICATION_JSON_VALUE} due to format property"
+                    }
+                    return Collections.enumeration(listOf(MediaType.APPLICATION_JSON_VALUE))
                 }
 
                 else -> {}

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -237,10 +237,11 @@ class LapisController(
         return siloQueryModel.getDetails(request)
     }
 
-    @GetMapping("/details", produces = ["text/csv"])
+    @GetMapping("/details", produces = [TEXT_CSV_HEADER])
     @Operation(
         description = DETAILS_ENDPOINT_DESCRIPTION,
         operationId = "getDetailsAsCsv",
+        responses = [ApiResponse(responseCode = "200")],
     )
     fun getDetailsAsCsv(
         @SequenceFilters
@@ -285,7 +286,59 @@ class LapisController(
             offset,
         )
 
-        return getDetailsAsCsv(request)
+        return getDetailsAsCsv(request, Delimiter.COMMA)
+    }
+
+    @GetMapping("/details", produces = [TEXT_TSV_HEADER])
+    @Operation(
+        description = DETAILS_ENDPOINT_DESCRIPTION,
+        operationId = "getDetailsAsTsv",
+        responses = [ApiResponse(responseCode = "200")],
+    )
+    fun getDetailsAsTsv(
+        @SequenceFilters
+        @RequestParam
+        sequenceFilters: Map<String, String>?,
+        @Parameter(description = DETAILS_FIELDS_DESCRIPTION)
+        @RequestParam
+        fields: List<String>?,
+        @Parameter(
+            schema = Schema(ref = "#/components/schemas/$ORDER_BY_FIELDS_SCHEMA"),
+            description = "The fields of the response to order by." +
+                " Fields specified here must also be present in \"fields\".",
+        )
+        @RequestParam
+        orderBy: List<OrderByField>?,
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_MUTATIONS_SCHEMA"))
+        @RequestParam
+        nucleotideMutations: List<NucleotideMutation>?,
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_MUTATIONS_SCHEMA"))
+        @RequestParam
+        aminoAcidMutations: List<AminoAcidMutation>?,
+        @Parameter(
+            schema = Schema(ref = "#/components/schemas/$LIMIT_SCHEMA"),
+            description = LIMIT_DESCRIPTION,
+        )
+        @RequestParam
+        limit: Int? = null,
+        @Parameter(
+            schema = Schema(ref = "#/components/schemas/$OFFSET_SCHEMA"),
+            description = OFFSET_DESCRIPTION,
+        )
+        @RequestParam
+        offset: Int? = null,
+    ): String {
+        val request = SequenceFiltersRequestWithFields(
+            sequenceFilters?.filter { !SPECIAL_REQUEST_PROPERTIES.contains(it.key) } ?: emptyMap(),
+            nucleotideMutations ?: emptyList(),
+            aminoAcidMutations ?: emptyList(),
+            fields ?: emptyList(),
+            orderBy ?: emptyList(),
+            limit,
+            offset,
+        )
+
+        return getDetailsAsCsv(request, Delimiter.TAB)
     }
 
     @PostMapping("/details", produces = [MediaType.APPLICATION_JSON_VALUE])
@@ -304,20 +357,35 @@ class LapisController(
         return siloQueryModel.getDetails(request)
     }
 
-    @PostMapping("/details", produces = ["text/csv"])
+    @PostMapping("/details", produces = [TEXT_CSV_HEADER])
     @Operation(
         description = DETAILS_ENDPOINT_DESCRIPTION,
         operationId = "postDetailsAsCsv",
+        responses = [ApiResponse(responseCode = "200")],
     )
     fun postDetailsAsCsv(
         @Parameter(schema = Schema(ref = "#/components/schemas/$DETAILS_REQUEST_SCHEMA"))
         @RequestBody
         request: SequenceFiltersRequestWithFields,
     ): String {
-        return getDetailsAsCsv(request)
+        return getDetailsAsCsv(request, Delimiter.COMMA)
+    }
+
+    @PostMapping("/details", produces = [TEXT_TSV_HEADER])
+    @Operation(
+        description = DETAILS_ENDPOINT_DESCRIPTION,
+        operationId = "postDetailsAsTsv",
+        responses = [ApiResponse(responseCode = "200")],
+    )
+    fun postDetailsAsTsv(
+        @Parameter(schema = Schema(ref = "#/components/schemas/$DETAILS_REQUEST_SCHEMA"))
+        @RequestBody
+        request: SequenceFiltersRequestWithFields,
+    ): String {
+        return getDetailsAsCsv(request, Delimiter.TAB)
     }
 
-    private fun getDetailsAsCsv(request: SequenceFiltersRequestWithFields): String {
+    private fun getDetailsAsCsv(request: SequenceFiltersRequestWithFields, delimiter: Delimiter): String {
         requestContext.filter = request
 
         val data = siloQueryModel.getDetails(request)
@@ -327,7 +395,7 @@ class LapisController(
         }
 
         val headers = data[0].keys.toTypedArray<String>()
-        return csvWriter.write(headers, data.map { it.asCsvRecord() })
+        return csvWriter.write(headers, data.map { it.asCsvRecord() }, delimiter)
     }
 }
 

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCsvTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerCsvTest.kt
@@ -26,6 +26,23 @@ class LapisControllerCsvTest(@Autowired val mockMvc: MockMvc) {
     @MockkBean
     lateinit var siloQueryModelMock: SiloQueryModel
 
+    val listOfMetadata = listOf(
+        mapOf("country" to TextNode("Switzerland"), "age" to IntNode(42)),
+        mapOf("country" to TextNode("Switzerland"), "age" to IntNode(43)),
+    )
+
+    val metadataCsv = """
+        country,age
+        Switzerland,42
+        Switzerland,43
+    """.trimIndent()
+
+    val metadataTsv = """
+        country	age
+        Switzerland	42
+        Switzerland	43
+    """.trimIndent()
+
     @Test
     fun `GET empty details return empty CSV`() {
         every {
@@ -61,27 +78,40 @@ class LapisControllerCsvTest(@Autowired val mockMvc: MockMvc) {
             )
     }
 
+    @Test
+    fun `GET details as TSV with accept header`() {
+        every {
+            siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
+        } returns listOfMetadata
+
+        mockMvc.perform(get("/details?country=Switzerland").header("Accept", "text/tab-separated-values"))
+            .andExpect(status().isOk)
+            .andExpect(header().string("Content-Type", "text/tab-separated-values;charset=UTF-8"))
+            .andExpect(content().string(metadataTsv))
+    }
+
     @Test
     fun `GET details as CSV with request parameter`() {
         every {
             siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
-        } returns listOf(
-            mapOf("country" to TextNode("Switzerland"), "age" to IntNode(42)),
-            mapOf("country" to TextNode("Switzerland"), "age" to IntNode(43)),
-        )
+        } returns listOfMetadata
 
         mockMvc.perform(get("/details?country=Switzerland&dataFormat=csv"))
             .andExpect(status().isOk)
             .andExpect(header().string("Content-Type", "text/csv;charset=UTF-8"))
-            .andExpect(
-                content().string(
-                    """
-                        country,age
-                        Switzerland,42
-                        Switzerland,43
-                    """.trimIndent(),
-                ),
-            )
+            .andExpect(content().string(metadataCsv))
+    }
+
+    @Test
+    fun `GET details as TSV with request parameter`() {
+        every {
+            siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
+        } returns listOfMetadata
+
+        mockMvc.perform(get("/details?country=Switzerland&dataFormat=tsv"))
+            .andExpect(status().isOk)
+            .andExpect(header().string("Content-Type", "text/tab-separated-values;charset=UTF-8"))
+            .andExpect(content().string(metadataTsv))
     }
 
     @Test
@@ -105,7 +135,7 @@ class LapisControllerCsvTest(@Autowired val mockMvc: MockMvc) {
     fun `POST details as CSV with accept header`() {
         every {
             siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
-        } returns emptyList()
+        } returns listOfMetadata
 
         val request = post("/details")
             .content("""{"country": "Switzerland"}""")
@@ -115,14 +145,31 @@ class LapisControllerCsvTest(@Autowired val mockMvc: MockMvc) {
         mockMvc.perform(request)
             .andExpect(status().isOk)
             .andExpect(header().string("Content-Type", "text/csv;charset=UTF-8"))
-            .andExpect(content().string(""))
+            .andExpect(content().string(metadataCsv))
+    }
+
+    @Test
+    fun `POST details as TSV with accept header`() {
+        every {
+            siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
+        } returns listOfMetadata
+
+        val request = post("/details")
+            .content("""{"country": "Switzerland"}""")
+            .contentType(MediaType.APPLICATION_JSON)
+            .accept("text/tab-separated-values")
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(header().string("Content-Type", "text/tab-separated-values;charset=UTF-8"))
+            .andExpect(content().string(metadataTsv))
     }
 
     @Test
     fun `POST details as CSV with request parameter`() {
         every {
             siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
-        } returns emptyList()
+        } returns listOfMetadata
 
         val request = post("/details")
             .content("""{"country": "Switzerland", "dataFormat": "csv"}""")
@@ -131,7 +178,23 @@ class LapisControllerCsvTest(@Autowired val mockMvc: MockMvc) {
         mockMvc.perform(request)
             .andExpect(status().isOk)
             .andExpect(header().string("Content-Type", "text/csv;charset=UTF-8"))
-            .andExpect(content().string(""))
+            .andExpect(content().string(metadataCsv))
+    }
+
+    @Test
+    fun `POST details as TSV with request parameter`() {
+        every {
+            siloQueryModelMock.getDetails(sequenceFiltersRequestWithFields(mapOf("country" to "Switzerland")))
+        } returns listOfMetadata
+
+        val request = post("/details")
+            .content("""{"country": "Switzerland", "dataFormat": "tsv"}""")
+            .contentType(MediaType.APPLICATION_JSON)
+
+        mockMvc.perform(request)
+            .andExpect(status().isOk)
+            .andExpect(header().string("Content-Type", "text/tab-separated-values;charset=UTF-8"))
+            .andExpect(content().string(metadataTsv))
     }
 
     private fun sequenceFiltersRequestWithFields(

diff --git a/siloLapisTests/test/details.spec.ts b/siloLapisTests/test/details.spec.ts
@@ -109,4 +109,24 @@ Solothurn,EPI_ISL_1002052,B.1
     `.trim()
     );
   });
+
+  it('should return the data as TSV', async () => {
+    const urlParams = new URLSearchParams({
+      fields: 'gisaid_epi_isl,pango_lineage,division',
+      orderBy: 'gisaid_epi_isl',
+      limit: '3',
+      dataFormat: 'tsv',
+    });
+
+    const result = await fetch(basePath + '/details?' + urlParams.toString());
+
+    expect(await result.text()).to.be.equal(
+      String.raw`
+division	gisaid_epi_isl	pango_lineage
+Vaud	EPI_ISL_1001493	B.1.177.44
+Bern	EPI_ISL_1001920	B.1.177
+Solothurn	EPI_ISL_1002052	B.1
+    `.trim()
+    );
+  });
 });