feat: add /sample to query paths #501

GenSpectrum · Dec 14, 2023 · 7ad9746 · 7ad9746
1 parent 556552f
commit 7ad9746
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Showing 21 changed files with 119 additions and 136 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
@@ -103,7 +103,7 @@ private class ProtectedDataAuthorizationFilter(
             AMINO_ACID_MUTATIONS_ROUTE,
             NUCLEOTIDE_INSERTIONS_ROUTE,
             AMINO_ACID_INSERTIONS_ROUTE,
-        )
+        ).map { "/sample$it" }
     }
 
     override fun isAuthorizedForEndpoint(request: CachedBodyHttpServletRequest): AuthorizationResult {

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -57,6 +57,7 @@ import org.springframework.web.bind.annotation.GetMapping
 import org.springframework.web.bind.annotation.PathVariable
 import org.springframework.web.bind.annotation.PostMapping
 import org.springframework.web.bind.annotation.RequestBody
+import org.springframework.web.bind.annotation.RequestMapping
 import org.springframework.web.bind.annotation.RequestParam
 import org.springframework.web.bind.annotation.RestController
 
@@ -70,6 +71,7 @@ const val ALIGNED_NUCLEOTIDE_SEQUENCES_ROUTE = "/alignedNucleotideSequences"
 const val ALIGNED_AMINO_ACID_SEQUENCES_ROUTE = "/alignedAminoAcidSequences"
 
 @RestController
+@RequestMapping("/sample")
 class LapisController(
     private val siloQueryModel: SiloQueryModel,
     private val requestContext: RequestContext,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt
@@ -27,6 +27,7 @@ import org.springframework.web.bind.annotation.GetMapping
 import org.springframework.web.bind.annotation.PathVariable
 import org.springframework.web.bind.annotation.PostMapping
 import org.springframework.web.bind.annotation.RequestBody
+import org.springframework.web.bind.annotation.RequestMapping
 import org.springframework.web.bind.annotation.RequestParam
 import org.springframework.web.bind.annotation.RestController
 
@@ -35,6 +36,7 @@ const val IS_MULTI_SEGMENT_SEQUENCE_EXPRESSION =
 
 @RestController
 @ConditionalOnExpression(IS_MULTI_SEGMENT_SEQUENCE_EXPRESSION)
+@RequestMapping("/sample")
 class MultiSegmentedSequenceController(
     private val siloQueryModel: SiloQueryModel,
     private val requestContext: RequestContext,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt
@@ -27,6 +27,7 @@ import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression
 import org.springframework.web.bind.annotation.GetMapping
 import org.springframework.web.bind.annotation.PostMapping
 import org.springframework.web.bind.annotation.RequestBody
+import org.springframework.web.bind.annotation.RequestMapping
 import org.springframework.web.bind.annotation.RequestParam
 import org.springframework.web.bind.annotation.RestController
 
@@ -35,6 +36,7 @@ const val IS_SINGLE_SEGMENT_SEQUENCE_EXPRESSION =
 
 @RestController
 @ConditionalOnExpression(IS_SINGLE_SEGMENT_SEQUENCE_EXPRESSION)
+@RequestMapping("/sample")
 class SingleSegmentedSequenceController(
     private val siloQueryModel: SiloQueryModel,
     private val requestContext: RequestContext,

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/SwaggerUiTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/SwaggerUiTest.kt
@@ -34,7 +34,7 @@ class SwaggerUiTest(
             .andExpect(status().isOk)
             .andExpect(content().contentType("application/json"))
             .andExpect(jsonPath("\$.openapi").exists())
-            .andExpect(jsonPath("\$.paths./aggregated").exists())
+            .andExpect(jsonPath("\$.paths./sample/aggregated").exists())
     }
 
     @Test
@@ -47,6 +47,6 @@ class SwaggerUiTest(
         val objectMapper = ObjectMapper(YAMLFactory()).registerKotlinModule()
         val yaml = objectMapper.readTree(result.response.contentAsString)
         assertTrue(yaml.has("openapi"))
-        assertTrue(yaml.get("paths").has("/aggregated"))
+        assertTrue(yaml.get("paths").has("/sample/aggregated"))
     }
 }
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/auth/ProtectedDataAuthorizationTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/auth/ProtectedDataAuthorizationTest.kt
@@ -5,6 +5,8 @@ import io.mockk.MockKAnnotations
 import io.mockk.every
 import io.mockk.verify
 import org.genspectrum.lapis.controller.AGGREGATED_ROUTE
+import org.genspectrum.lapis.controller.getSample
+import org.genspectrum.lapis.controller.postSample
 import org.genspectrum.lapis.model.SiloQueryModel
 import org.genspectrum.lapis.request.LapisInfo
 import org.genspectrum.lapis.request.SequenceFiltersRequestWithFields
@@ -15,7 +17,6 @@ import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMock
 import org.springframework.boot.test.context.SpringBootTest
 import org.springframework.http.MediaType
 import org.springframework.test.web.servlet.MockMvc
-import org.springframework.test.web.servlet.request.MockMvcRequestBuilders
 import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get
 import org.springframework.test.web.servlet.result.MockMvcResultMatchers.content
 import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
@@ -24,7 +25,16 @@ private const val NOT_AUTHORIZED_TO_ACCESS_ENDPOINT_ERROR = """
 {
     "error" : {
         "title": "Forbidden",
-        "detail": "You are not authorized to access /aggregated."
+        "detail": "You are not authorized to access /sample/aggregated."
+    }
+}
+"""
+
+private const val FORBIDDEN_TO_ACCESS_ENDPOINT_ERROR = """
+{
+    "error" : {
+        "title": "Forbidden",
+        "detail": "An access key is required to access /sample/aggregated."
     }
 }
 """
@@ -55,70 +65,40 @@ class ProtectedDataAuthorizationTest(
 
     @Test
     fun `given no access key in GET request to protected instance, then access is denied`() {
-        mockMvc.perform(get(validRoute))
+        mockMvc.perform(getSample(validRoute))
             .andExpect(status().isForbidden)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
-            .andExpect(
-                content().json(
-                    """
-                    {
-                        "error" : {
-                            "title": "Forbidden",
-                            "detail": "An access key is required to access /aggregated."
-                        }
-                    }
-                    """,
-                ),
-            )
+            .andExpect(content().json(FORBIDDEN_TO_ACCESS_ENDPOINT_ERROR))
     }
 
     @Test
     fun `given no access key in POST request to protected instance, then access is denied`() {
         mockMvc.perform(postRequestWithBody(""))
             .andExpect(status().isForbidden)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
-            .andExpect(
-                content().json(
-                    """
-                    {
-                        "error" : {
-                            "title": "Forbidden",
-                            "detail": "An access key is required to access /aggregated."
-                        }
-                    }
-                    """,
-                ),
-            )
+            .andExpect(content().json(FORBIDDEN_TO_ACCESS_ENDPOINT_ERROR))
     }
 
     @Test
     fun `given wrong access key in GET request to protected instance, then access is denied`() {
-        mockMvc.perform(get("$validRoute?accessKey=invalidKey"))
+        mockMvc.perform(getSample("$validRoute?accessKey=invalidKey"))
             .andExpect(status().isForbidden)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
-            .andExpect(
-                content().json(
-                    NOT_AUTHORIZED_TO_ACCESS_ENDPOINT_ERROR,
-                ),
-            )
+            .andExpect(content().json(NOT_AUTHORIZED_TO_ACCESS_ENDPOINT_ERROR))
     }
 
     @Test
     fun `given wrong access key in POST request to protected instance, then access is denied`() {
         mockMvc.perform(postRequestWithBody("""{"accessKey": "invalidKey"}"""))
             .andExpect(status().isForbidden)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
-            .andExpect(
-                content().json(
-                    NOT_AUTHORIZED_TO_ACCESS_ENDPOINT_ERROR,
-                ),
-            )
+            .andExpect(content().json(NOT_AUTHORIZED_TO_ACCESS_ENDPOINT_ERROR))
     }
 
     @Test
     fun `given valid access key for aggregated data in GET request to protected instance, then access is granted`() {
         mockMvc.perform(
-            get("$validRoute?accessKey=testAggregatedDataAccessKey&field1=value1"),
+            getSample("$validRoute?accessKey=testAggregatedDataAccessKey&field1=value1"),
         )
             .andExpect(status().isOk)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
@@ -145,7 +125,7 @@ class ProtectedDataAuthorizationTest(
     @Test
     fun `given aggregated access key in GET request but filters are too fine-grained, then access is denied`() {
         mockMvc.perform(
-            get("$validRoute?accessKey=testAggregatedDataAccessKey&gisaid_epi_isl=value"),
+            getSample("$validRoute?accessKey=testAggregatedDataAccessKey&gisaid_epi_isl=value"),
         )
             .andExpect(status().isForbidden)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
@@ -170,7 +150,7 @@ class ProtectedDataAuthorizationTest(
     @Test
     fun `given valid access key for full access in GET request to protected instance, then access is granted`() {
         mockMvc.perform(
-            get("$validRoute?accessKey=testFullAccessKey&field1=value1"),
+            getSample("$validRoute?accessKey=testFullAccessKey&field1=value1"),
         )
             .andExpect(status().isOk)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
@@ -217,7 +197,7 @@ class ProtectedDataAuthorizationTest(
     }
 
     private fun postRequestWithBody(body: String) =
-        MockMvcRequestBuilders.post(validRoute)
+        postSample(validRoute)
             .contentType(MediaType.APPLICATION_JSON)
             .content(body)
 }
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/ExceptionHandlerTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/ExceptionHandlerTest.kt
@@ -59,7 +59,7 @@ class ExceptionHandlerTest(
     fun `throw INTERNAL_SERVER_ERROR(500) with additional info for any non specific error`() {
         every { validControllerCall() } throws Exception("SomeMessage")
 
-        mockMvc.perform(get(validRoute))
+        mockMvc.perform(getSample(validRoute))
             .andExpect(status().isInternalServerError)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
             .andExpect(
@@ -83,7 +83,7 @@ class ExceptionHandlerTest(
     fun `Passes through exception with status code from SILO`() {
         every { validControllerCall() } throws SiloException(123, "SomeTitle", "SomeMessage")
 
-        mockMvc.perform(get(validRoute))
+        mockMvc.perform(getSample(validRoute))
             .andExpect(status().`is`(123))
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
             .andExpect(
@@ -107,7 +107,7 @@ class ExceptionHandlerTest(
     fun `throw BAD_REQUEST(400) with additional info for bad requests`() {
         every { validControllerCall() } throws BadRequestException("SomeMessage")
 
-        mockMvc.perform(get(validRoute))
+        mockMvc.perform(getSample(validRoute))
             .andExpect(status().isBadRequest)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
             .andExpect(
@@ -131,7 +131,7 @@ class ExceptionHandlerTest(
     fun `throw NOT_IMPLEMENTED(501) with additional info for request of a not implemented resource in SILO`() {
         every { validControllerCall() } throws SiloNotImplementedError("SomeMessage", Exception("SomeCause"))
 
-        mockMvc.perform(get(validRoute))
+        mockMvc.perform(getSample(validRoute))
             .andExpect(status().isNotImplemented)
             .andExpect(content().contentType(MediaType.APPLICATION_JSON))
             .andExpect(