Add simple logging to endpoints

src/main/scala/nl/lumc/sasc/sentinel/api/AnnotationsController.scala

@@ -41,11 +41,13 @@ class AnnotationsController(implicit val swagger: Swagger, mongo: MongodbAccessO
   protected val annots = new AnnotationsAdapter { val mongo = self.mongo }
 
   options("/?") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
 
   options("/:annotId") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
@@ -58,6 +60,7 @@ class AnnotationsController(implicit val swagger: Swagger, mongo: MongodbAccessO
   // format: ON
 
   get("/:annotId", operation(annotationsRefIdGetOperation)) {
+    logger.info(requestLog)
     val errMsg = ApiMessage("Annotation ID can not be found.")
     val annotId = params("annotId")
       .getObjectId
@@ -74,6 +77,7 @@ class AnnotationsController(implicit val swagger: Swagger, mongo: MongodbAccessO
   // format: ON
 
   get("/", operation(annotationsGetOperation)) {
+    logger.info(requestLog)
     annots.getAnnotations()
   }
 }

src/main/scala/nl/lumc/sasc/sentinel/api/ReferencesController.scala

@@ -41,11 +41,13 @@ class ReferencesController(implicit val swagger: Swagger, mongo: MongodbAccessOb
   protected val refs = new ReferencesAdapter { val mongo = self.mongo }
 
   options("/?") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
 
   options("/:refId") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
@@ -58,6 +60,7 @@ class ReferencesController(implicit val swagger: Swagger, mongo: MongodbAccessOb
   // format: ON
 
   get("/:refId", operation(referencesRefIdGetOperation)) {
+    logger.info(requestLog)
     val errMsg = ApiMessage("Reference ID can not be found.")
     val refId = params("refId")
       .getObjectId
@@ -74,6 +77,7 @@ class ReferencesController(implicit val swagger: Swagger, mongo: MongodbAccessOb
   // format: ON
 
   get("/", operation(referencesGetOperation)) {
+    logger.info(requestLog)
     refs.getReferences()
   }
 }

src/main/scala/nl/lumc/sasc/sentinel/api/RunsController.scala

@@ -75,11 +75,13 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   }
 
   options("/?") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD,POST")
   }
 
   options("/:runId") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "DELETE,GET,HEAD")
   }
@@ -106,6 +108,7 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   delete("/:runId", operation(runsRunIdDeleteOperation)) {
+    logger.info(requestLog)
     val runId = params("runId")
       .getObjectId
       .getOrElse(halt(404, CommonMessages.MissingRunId))
@@ -147,6 +150,7 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   get("/:runId", operation(runsRunIdGetOperation)) {
+    logger.info(requestLog)
     val doDownload = params.getAs[Boolean]("download").getOrElse(false)
     val runId = params("runId")
       .getObjectId
@@ -192,6 +196,7 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   post("/", operation(runsPostOperation)) {
+    logger.info(requestLog)
     val pipeline = params.getOrElse("pipeline", halt(400, CommonMessages.UnspecifiedPipeline))
     val uploadedRun = fileParams.getOrElse("run", halt(400, ApiMessage("Run summary file not specified.")))
 
@@ -245,6 +250,7 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   get("/", operation(runsGetOperation)) {
+    logger.info(requestLog)
     val pipelines = splitParam(params.getAs[String]("pipelines"))
     val (validPipelines, invalidPipelines) = pipelines.partition { AllowedPipelineParams.contains }
 

src/main/scala/nl/lumc/sasc/sentinel/api/SentinelServlet.scala

@@ -16,11 +16,14 @@
  */
 package nl.lumc.sasc.sentinel.api
 
+import javax.servlet.http.HttpServletRequest
+
 import org.bson.types.ObjectId
 import org.json4s._
 import org.scalatra.{ CorsSupport, NotFound, ScalatraServlet }
 import org.scalatra.json.JacksonJsonSupport
 import org.scalatra.swagger.{ DataType, Model, SwaggerSupport }
+import org.slf4j.LoggerFactory
 
 import nl.lumc.sasc.sentinel.models.ApiMessage
 import nl.lumc.sasc.sentinel.utils.{ SentinelJsonFormats, separateObjectIds, splitParam }
@@ -31,6 +34,15 @@ abstract class SentinelServlet extends ScalatraServlet
     with JacksonJsonSupport
     with SwaggerSupport {
 
+  /** Logger instance. */
+  protected val logger = LoggerFactory.getLogger(getClass)
+
+  /** Default log string and helper methods for log string. */
+  protected def reqUri(implicit req: HttpServletRequest): String = req.getRequestURI
+  protected def reqMethod(implicit req: HttpServletRequest): String = req.getMethod
+  protected def reqAddress(implicit req: HttpServletRequest): String = req.getRemoteAddr
+  protected def requestLog: String = s"$reqAddress $reqMethod $reqUri"
+
   override def render(value: JValue)(implicit formats: Formats = DefaultFormats): JValue =
     formats.emptyValueStrategy.replaceEmpty(value)
 

src/main/scala/nl/lumc/sasc/sentinel/api/StatsController.scala

@@ -57,21 +57,25 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   protected val users = new UsersAdapter { val mongo = self.mongo }
 
   options("/runs") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
 
   options("/gentrap/alignments") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
 
   options("/gentrap/alignments/aggregate") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
 
   options("/gentrap/sequences") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD")
   }
@@ -87,6 +91,7 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   get("/runs", operation(statsRunsGetOperation)) {
+    logger.info(requestLog)
     Ok(runs.getGlobalRunStats())
   }
 
@@ -141,6 +146,7 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
 
   get("/gentrap/alignments", operation(statsGentrapAlignmentsGetOperation)) {
 
+    logger.info(requestLog)
     val runIds = getRunObjectIds(params.getAs[String]("runIds"))
     val refIds = getRefObjectIds(params.getAs[String]("refIds"))
     val annotIds = getAnnotObjectIds(params.getAs[String]("annotIds"))
@@ -214,6 +220,7 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
 
   get("/gentrap/alignments/aggregate", operation(statsGentrapAlignmentsAggregateGetOperation)) {
 
+    logger.info(requestLog)
     val runIds = getRunObjectIds(params.getAs[String]("runIds"))
     val refIds = getRefObjectIds(params.getAs[String]("refIds"))
     val annotIds = getAnnotObjectIds(params.getAs[String]("annotIds"))
@@ -293,6 +300,7 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
 
   get("/gentrap/sequences", operation(statsGentrapSequencesGetOperation)) {
 
+    logger.info(requestLog)
     val runIds = getRunObjectIds(params.getAs[String]("runIds"))
     val refIds = getRefObjectIds(params.getAs[String]("refIds"))
     val annotIds = getAnnotObjectIds(params.getAs[String]("annotIds"))
@@ -357,6 +365,7 @@ class StatsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
 
   get("/gentrap/sequences/aggregate", operation(statsGentrapSequencesAggregateGetOperation)) {
 
+    logger.info(requestLog)
     val runIds = getRunObjectIds(params.getAs[String]("runIds"))
     val refIds = getRefObjectIds(params.getAs[String]("refIds"))
     val annotIds = getAnnotObjectIds(params.getAs[String]("annotIds"))

src/main/scala/nl/lumc/sasc/sentinel/api/UsersController.scala

@@ -51,11 +51,13 @@ class UsersController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   val patchValidator = new ValidationAdapter { override val validator = createValidator("/schemas/json_patch.json") }
 
   options("/?") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "HEAD,POST")
   }
 
   options("/:userRecordId") {
+    logger.info(requestLog)
     response.setHeader("Access-Control-Allow-Headers", request.getHeader("Access-Control-Request-Headers"))
     response.setHeader("Access-Control-Allow-Methods", "GET,HEAD,PATCH")
     response.setHeader("Accept-Patch", formats("json"))
@@ -88,6 +90,7 @@ class UsersController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
 
     // TODO: refactor this endpoint ~ use less explicit halts
 
+    logger.info(requestLog)
     // validate and load patch operations ~ based on the JSON patch spec *not* our own requirements (yet)
     val patchOps = Try(patchValidator.parseAndValidate(request.body.getBytes)) match {
 
@@ -154,6 +157,7 @@ class UsersController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: ON
 
   get("/:userRecordId", operation(usersUserIdGetOperation)) {
+    logger.info(requestLog)
     val userRecordId = params("userRecordId")
     val user = simpleKeyAuth(params => params.get("userId"))
     if (user.isAdmin || user.id == userRecordId) {
@@ -185,6 +189,7 @@ class UsersController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   // format: OFF
 
   post("/", operation(usersUserIdPostOperation)) {
+    logger.info(requestLog)
     val userRequest = parsedBody.extractOrElse[UserRequest](halt(400, ApiMessage("Malformed user request.")))
 
     if (userRequest.validationMessages.size > 0)

src/test/resources/logback-test.xml

+<configuration>
+    <appender name="CONSOLE" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
+            <pattern>%msg%n</pattern>
+        </encoder>
+    </appender>
+    <root level="OFF">
+        <appender-ref ref="CONSOLE"/>
+    </root>
+</configuration>
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