feat(lapis2): support url encoded form POST requests

This adds support for using LAPIS via plain HTML forms with `method="POST"` and content type `application/x-www-form-urlencoded` resolves #754
GenSpectrum · Apr 30, 2024 · f2f62b1 · f2f62b1
1 parent ac1d719
commit f2f62b1
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Showing 24 changed files with 1,286 additions and 705 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/auth/DataOpennessAuthorizationFilter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/auth/DataOpennessAuthorizationFilter.kt
@@ -74,7 +74,7 @@ abstract class DataOpennessAuthorizationFilter(protected val objectMapper: Objec
     }
 
     private fun makeRequestBodyReadableMoreThanOnce(request: HttpServletRequest) =
-        CachedBodyHttpServletRequest(request, objectMapper)
+        CachedBodyHttpServletRequest.from(request, objectMapper)
 
     abstract fun isAuthorizedForEndpoint(request: CachedBodyHttpServletRequest): AuthorizationResult
 }

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/CompressionFilter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/CompressionFilter.kt
@@ -123,7 +123,7 @@ class CompressionFilter(val objectMapper: ObjectMapper, val requestCompression:
         response: HttpServletResponse,
         filterChain: FilterChain,
     ) {
-        val reReadableRequest = CachedBodyHttpServletRequest(request, objectMapper)
+        val reReadableRequest = CachedBodyHttpServletRequest.from(request, objectMapper)
 
         val compressionPropertyInRequest = try {
             getValidatedCompressionProperty(reReadableRequest)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DataFormatParameterFilter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DataFormatParameterFilter.kt
@@ -32,7 +32,7 @@ class DataFormatParameterFilter(val objectMapper: ObjectMapper) : OncePerRequest
         response: HttpServletResponse,
         filterChain: FilterChain,
     ) {
-        val reReadableRequest = CachedBodyHttpServletRequest(request, objectMapper)
+        val reReadableRequest = CachedBodyHttpServletRequest.from(request, objectMapper)
 
         val requestWithModifiedAcceptHeader = HeaderModifyingRequestWrapper(
             reReadableRequest,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DownloadAsFileFilter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/DownloadAsFileFilter.kt
@@ -24,7 +24,7 @@ class DownloadAsFileFilter(
         response: HttpServletResponse,
         filterChain: FilterChain,
     ) {
-        val reReadableRequest = CachedBodyHttpServletRequest(request, objectMapper)
+        val reReadableRequest = CachedBodyHttpServletRequest.from(request, objectMapper)
 
         val downloadAsFile = reReadableRequest.getBooleanField(DOWNLOAD_AS_FILE_PROPERTY) ?: false
         if (downloadAsFile) {

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/JacksonFormHttpMessageConverter.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/JacksonFormHttpMessageConverter.kt
@@ -0,0 +1,48 @@
+package org.genspectrum.lapis.controller
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import org.genspectrum.lapis.util.tryToGuessTheType
+import org.springframework.http.HttpInputMessage
+import org.springframework.http.HttpOutputMessage
+import org.springframework.http.MediaType
+import org.springframework.http.converter.AbstractHttpMessageConverter
+import org.springframework.http.converter.FormHttpMessageConverter
+import org.springframework.stereotype.Component
+
+@Component
+class JacksonFormHttpMessageConverter(
+    private val objectMapper: ObjectMapper,
+) : AbstractHttpMessageConverter<Any>(MediaType.APPLICATION_FORM_URLENCODED) {
+    private val formHttpMessageConverter = FormHttpMessageConverter()
+
+    override fun canWrite(
+        clazz: Class<*>,
+        mediaType: MediaType?,
+    ): Boolean {
+        return false
+    }
+
+    override fun supports(clazz: Class<*>): Boolean {
+        return true
+    }
+
+    override fun writeInternal(
+        t: Any,
+        outputMessage: HttpOutputMessage,
+    ) {
+        throw NotImplementedError("This class should never need to write.")
+    }
+
+    override fun readInternal(
+        clazz: Class<out Any>,
+        inputMessage: HttpInputMessage,
+    ): Any {
+        val multiValueMap = formHttpMessageConverter.read(null, inputMessage)
+
+        val mapValues = multiValueMap.mapValues(::tryToGuessTheType)
+
+        val json = objectMapper.writeValueAsString(mapValues)
+
+        return objectMapper.readValue(json, clazz)
+    }
+}
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -244,7 +244,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, TAB, siloQueryModel::getAggregated)
     }
 
-    @PostMapping(AGGREGATED_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        AGGREGATED_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAggregatedResponse
     @Operation(
         operationId = "postAggregated",
@@ -259,7 +263,11 @@ class LapisController(
         return LapisResponse(siloQueryModel.getAggregated(request).toList())
     }
 
-    @PostMapping(AGGREGATED_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        AGGREGATED_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AGGREGATED_ENDPOINT_DESCRIPTION,
         operationId = "postAggregatedAsCsv",
@@ -274,7 +282,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, COMMA, siloQueryModel::getAggregated)
     }
 
-    @PostMapping(AGGREGATED_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        AGGREGATED_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AGGREGATED_ENDPOINT_DESCRIPTION,
         operationId = "postAggregatedAsTsv",
@@ -452,7 +464,11 @@ class LapisController(
         )
     }
 
-    @PostMapping(NUCLEOTIDE_MUTATIONS_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_MUTATIONS_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisNucleotideMutationsResponse
     @Operation(
         operationId = "postNucleotideMutations",
@@ -468,7 +484,11 @@ class LapisController(
         return LapisResponse(result.toList())
     }
 
-    @PostMapping(NUCLEOTIDE_MUTATIONS_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_MUTATIONS_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = NUCLEOTIDE_MUTATION_ENDPOINT_DESCRIPTION,
         operationId = "postNucleotideMutationsAsCsv",
@@ -489,7 +509,11 @@ class LapisController(
         )
     }
 
-    @PostMapping(NUCLEOTIDE_MUTATIONS_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_MUTATIONS_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = NUCLEOTIDE_MUTATION_ENDPOINT_DESCRIPTION,
         operationId = "postNucleotideMutationsAsTsv",
@@ -669,7 +693,11 @@ class LapisController(
         )
     }
 
-    @PostMapping(AMINO_ACID_MUTATIONS_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        AMINO_ACID_MUTATIONS_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAminoAcidMutationsResponse
     @Operation(
         operationId = "postAminoAcidMutations",
@@ -685,7 +713,11 @@ class LapisController(
         return LapisResponse(result.toList())
     }
 
-    @PostMapping(AMINO_ACID_MUTATIONS_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        AMINO_ACID_MUTATIONS_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AMINO_ACID_MUTATIONS_ENDPOINT_DESCRIPTION,
         operationId = "postAminoAcidMutationsAsCsv",
@@ -708,7 +740,11 @@ class LapisController(
         )
     }
 
-    @PostMapping(AMINO_ACID_MUTATIONS_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        AMINO_ACID_MUTATIONS_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AMINO_ACID_MUTATIONS_ENDPOINT_DESCRIPTION,
         operationId = "postAminoAcidMutationsAsCsv",
@@ -882,7 +918,11 @@ class LapisController(
         return writeCsvToResponse(response, request, httpHeaders.accept, TAB, siloQueryModel::getDetails)
     }
 
-    @PostMapping(DETAILS_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        DETAILS_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisDetailsResponse
     @Operation(
         operationId = "postDetails",
@@ -897,7 +937,11 @@ class LapisController(
         return LapisResponse(siloQueryModel.getDetails(request).toList())
     }
 
-    @PostMapping(DETAILS_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        DETAILS_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = DETAILS_ENDPOINT_DESCRIPTION,
         operationId = "postDetailsAsCsv",
@@ -912,7 +956,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, COMMA, siloQueryModel::getDetails)
     }
 
-    @PostMapping(DETAILS_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        DETAILS_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = DETAILS_ENDPOINT_DESCRIPTION,
         operationId = "postDetailsAsTsv",
@@ -1079,7 +1127,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, TAB, siloQueryModel::getNucleotideInsertions)
     }
 
-    @PostMapping(NUCLEOTIDE_INSERTIONS_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_INSERTIONS_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisNucleotideInsertionsResponse
     @Operation(
         operationId = "postNucleotideInsertions",
@@ -1095,7 +1147,11 @@ class LapisController(
         return LapisResponse(result.toList())
     }
 
-    @PostMapping(NUCLEOTIDE_INSERTIONS_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_INSERTIONS_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = NUCLEOTIDE_INSERTIONS_ENDPOINT_DESCRIPTION,
         operationId = "postNucleotideInsertionsAsCsv",
@@ -1112,7 +1168,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, COMMA, siloQueryModel::getNucleotideInsertions)
     }
 
-    @PostMapping(NUCLEOTIDE_INSERTIONS_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        NUCLEOTIDE_INSERTIONS_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = NUCLEOTIDE_INSERTIONS_ENDPOINT_DESCRIPTION,
         operationId = "postNucleotideInsertionsAsTsv",
@@ -1279,7 +1339,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, TAB, siloQueryModel::getAminoAcidInsertions)
     }
 
-    @PostMapping(AMINO_ACID_INSERTIONS_ROUTE, produces = [MediaType.APPLICATION_JSON_VALUE])
+    @PostMapping(
+        AMINO_ACID_INSERTIONS_ROUTE,
+        produces = [MediaType.APPLICATION_JSON_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAminoAcidInsertionsResponse
     @Operation(
         operationId = "postAminoAcidInsertions",
@@ -1295,7 +1359,11 @@ class LapisController(
         return LapisResponse(result.toList())
     }
 
-    @PostMapping(AMINO_ACID_INSERTIONS_ROUTE, produces = [TEXT_CSV_VALUE])
+    @PostMapping(
+        AMINO_ACID_INSERTIONS_ROUTE,
+        produces = [TEXT_CSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AMINO_ACID_INSERTIONS_ENDPOINT_DESCRIPTION,
         operationId = "postAminoAcidInsertionsAsCsv",
@@ -1310,7 +1378,11 @@ class LapisController(
         writeCsvToResponse(response, request, httpHeaders.accept, COMMA, siloQueryModel::getAminoAcidInsertions)
     }
 
-    @PostMapping(AMINO_ACID_INSERTIONS_ROUTE, produces = [TEXT_TSV_VALUE])
+    @PostMapping(
+        AMINO_ACID_INSERTIONS_ROUTE,
+        produces = [TEXT_TSV_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @StringResponseOperation(
         description = AMINO_ACID_INSERTIONS_ENDPOINT_DESCRIPTION,
         operationId = "postAminoAcidInsertionsAsTsv",
@@ -1374,7 +1446,11 @@ class LapisController(
             .writeFastaTo(response, dataVersion)
     }
 
-    @PostMapping("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = [TEXT_X_FASTA_VALUE])
+    @PostMapping(
+        "$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}",
+        produces = [TEXT_X_FASTA_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAlignedAminoAcidSequenceResponse
     fun postAlignedAminoAcidSequence(
         @PathVariable(name = "gene", required = true)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt
@@ -30,6 +30,7 @@ import org.genspectrum.lapis.response.writeFastaTo
 import org.genspectrum.lapis.silo.DataVersion
 import org.genspectrum.lapis.silo.SequenceType
 import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression
+import org.springframework.http.MediaType
 import org.springframework.web.bind.annotation.GetMapping
 import org.springframework.web.bind.annotation.PathVariable
 import org.springframework.web.bind.annotation.PostMapping
@@ -102,7 +103,11 @@ class MultiSegmentedSequenceController(
             .writeFastaTo(response, dataVersion)
     }
 
-    @PostMapping("$ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}", produces = [TEXT_X_FASTA_VALUE])
+    @PostMapping(
+        "$ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}",
+        produces = [TEXT_X_FASTA_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAlignedMultiSegmentedNucleotideSequenceResponse
     fun postAlignedNucleotideSequence(
         @PathVariable(name = "segment", required = true)
@@ -176,7 +181,11 @@ class MultiSegmentedSequenceController(
             .writeFastaTo(response, dataVersion)
     }
 
-    @PostMapping("$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}", produces = [TEXT_X_FASTA_VALUE])
+    @PostMapping(
+        "$UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE/{segment}",
+        produces = [TEXT_X_FASTA_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisUnalignedMultiSegmentedNucleotideSequenceResponse
     fun postUnalignedNucleotideSequence(
         @PathVariable(name = "segment", required = true)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt
@@ -30,6 +30,7 @@ import org.genspectrum.lapis.response.writeFastaTo
 import org.genspectrum.lapis.silo.DataVersion
 import org.genspectrum.lapis.silo.SequenceType
 import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression
+import org.springframework.http.MediaType
 import org.springframework.web.bind.annotation.GetMapping
 import org.springframework.web.bind.annotation.PostMapping
 import org.springframework.web.bind.annotation.RequestBody
@@ -99,7 +100,11 @@ class SingleSegmentedSequenceController(
             .writeFastaTo(response, dataVersion)
     }
 
-    @PostMapping(ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE, produces = [TEXT_X_FASTA_VALUE])
+    @PostMapping(
+        ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE,
+        produces = [TEXT_X_FASTA_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisAlignedSingleSegmentedNucleotideSequenceResponse
     fun postAlignedNucleotideSequence(
         @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA"))
@@ -167,7 +172,11 @@ class SingleSegmentedSequenceController(
             .writeFastaTo(response, dataVersion)
     }
 
-    @PostMapping(UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE, produces = [TEXT_X_FASTA_VALUE])
+    @PostMapping(
+        UNALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE,
+        produces = [TEXT_X_FASTA_VALUE],
+        consumes = [MediaType.APPLICATION_JSON_VALUE, MediaType.APPLICATION_FORM_URLENCODED_VALUE],
+    )
     @LapisUnalignedSingleSegmentedNucleotideSequenceResponse
     fun postUnalignedNucleotideSequence(
         @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_SEQUENCE_REQUEST_SCHEMA"))