Refactor Processors base classes

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

@@ -17,17 +17,19 @@
 package nl.lumc.sasc.sentinel.api
 
 import java.io.File
-import scala.util.{ Failure, Success, Try }
+
+import scala.util.{ Failure, Success }
 
 import org.scalatra._
 import org.scalatra.swagger._
-import org.scalatra.servlet.{ FileItem, FileUploadSupport, MultipartConfig, SizeConstraintExceededException }
+import org.scalatra.servlet.{ FileUploadSupport, MultipartConfig, SizeConstraintExceededException }
 
 import nl.lumc.sasc.sentinel.{ AllowedPipelineParams, HeaderApiKey, Pipeline }
 import nl.lumc.sasc.sentinel.api.auth.AuthenticationSupport
 import nl.lumc.sasc.sentinel.db._
-import nl.lumc.sasc.sentinel.processors.gentrap.GentrapV04InputProcessor
-import nl.lumc.sasc.sentinel.processors.plain.PlainInputProcessor
+import nl.lumc.sasc.sentinel.processors.gentrap.GentrapV04RunsProcessor
+import nl.lumc.sasc.sentinel.processors.plain.PlainRunsProcessor
+import nl.lumc.sasc.sentinel.processors.GenericRunsProcessor
 import nl.lumc.sasc.sentinel.settings._
 import nl.lumc.sasc.sentinel.models._
 import nl.lumc.sasc.sentinel.utils._
@@ -50,19 +52,16 @@ class RunsController(implicit val swagger: Swagger, mongo: MongodbAccessObject)
   protected val applicationDescription: String = "Submission and retrieval of run summaries"
 
   /** Adapter for connecting to run collections. */
-  val runs = new RunsAdapter {
-    val mongo = self.mongo
-    def processRun(fi: FileItem, user: User, pipeline: Pipeline.Value) = Try(throw new NotImplementedError)
-  }
+  val runs = new GenericRunsProcessor(mongo)
 
   /** Adapter for connecting to users collection. */
   val users = new UsersAdapter { val mongo = self.mongo }
 
   /** Adapter for connecting to the plain summary collections. */
-  val plain = new PlainInputProcessor(mongo)
+  val plain = new PlainRunsProcessor(mongo)
 
   /** Adapter for connecting to the gentrap summary collections. */
-  val gentrap = new GentrapV04InputProcessor(mongo)
+  val gentrap = new GentrapV04RunsProcessor(mongo)
 
   /** Set maximum allowed file upload size. */
   configureMultipartHandling(MultipartConfig(maxFileSize = Some(MaxRunSummarySize)))

src/main/scala/nl/lumc/sasc/sentinel/db/UnitsAdapter.scala

@@ -21,6 +21,7 @@ import com.novus.salat._
 import com.novus.salat.global._
 
 import nl.lumc.sasc.sentinel.models.{ BaseLibRecord, BaseSampleRecord }
+import nl.lumc.sasc.sentinel.processors.RunsProcessor
 
 /**
  * Trait for storing samples and libraries from run summaries.
@@ -28,10 +29,7 @@ import nl.lumc.sasc.sentinel.models.{ BaseLibRecord, BaseSampleRecord }
  * @tparam S Subclass of [[nl.lumc.sasc.sentinel.models.BaseSampleRecord]] representing a sample run by a pipeline.
  * @tparam L Subclass of [[nl.lumc.sasc.sentinel.models.BaseLibRecord]] representing a library run by a pipeline.
  */
-trait UnitsAdapter[S <: BaseSampleRecord, L <: BaseLibRecord] extends MongodbConnector { this: RunsAdapter =>
-
-  /** Name of the pipeline that produces the run summary file. */
-  def pipelineName: String
+trait UnitsAdapter[S <: BaseSampleRecord, L <: BaseLibRecord] extends MongodbConnector { this: RunsProcessor =>
 
   /** Collection for the samples. */
   private lazy val samplesColl = mongo.db(collectionNames.pipelineSamples(pipelineName))

src/main/scala/nl/lumc/sasc/sentinel/processors/GenericRunsProcessor.scala

+/*
+ * Copyright (c) 2015 Leiden University Medical Center and contributors
+ *                    (see AUTHORS.md file for details).
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nl.lumc.sasc.sentinel.processors
+
+import scala.util.Try
+
+import org.scalatra.servlet.FileItem
+
+import nl.lumc.sasc.sentinel.Pipeline
+import nl.lumc.sasc.sentinel.db.MongodbAccessObject
+import nl.lumc.sasc.sentinel.models._
+
+/**
+ * Input processor that does not process incoming runs. Rather, it is used for querying run data of any pipelines.
+ */
+class GenericRunsProcessor(mongo: MongodbAccessObject) extends RunsProcessor(mongo) {
+  def pipelineName = "generic"
+  def processRun(fi: FileItem, user: User, pipeline: Pipeline.Value) = Try(throw new NotImplementedError)
+}

src/main/scala/nl/lumc/sasc/sentinel/processors/Processor.scala

+/*
+ * Copyright (c) 2015 Leiden University Medical Center and contributors
+ *                    (see AUTHORS.md file for details).
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nl.lumc.sasc.sentinel.processors
+
+import nl.lumc.sasc.sentinel.db.{ MongodbAccessObject, MongodbConnector }
+
+/** Base trait for defining processors. */
+trait Processor extends MongodbConnector {
+
+  /** Run summary pipeline name. */
+  def pipelineName: String
+}

src/main/scala/nl/lumc/sasc/sentinel/db/RunsAdapter.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/RunsProcessor.scala

@@ -14,23 +14,26 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package nl.lumc.sasc.sentinel.db
+package nl.lumc.sasc.sentinel.processors
 
 import java.io.ByteArrayInputStream
-import scala.util.Try
 
-import com.mongodb.casbah.gridfs.GridFSDBFile
 import com.mongodb.casbah.Imports._
+import com.mongodb.casbah.gridfs.GridFSDBFile
 import com.novus.salat._
 import com.novus.salat.global._
-import org.scalatra.servlet.FileItem
-
 import nl.lumc.sasc.sentinel.Pipeline
+import nl.lumc.sasc.sentinel.db.MongodbAccessObject
 import nl.lumc.sasc.sentinel.models.{ PipelineStats, RunRecord, User }
 import nl.lumc.sasc.sentinel.utils.{ DuplicateFileException, calcMd5, getUtcTimeNow }
+import org.scalatra.servlet.FileItem
+
+import scala.util.Try
 
-/** Trait for processing and storing run summary files to a run records collection */
-trait RunsAdapter extends MongodbConnector {
+/**
+ * Base class for processing run summary files.
+ */
+abstract class RunsProcessor(protected val mongo: MongodbAccessObject) extends Processor {
 
   /**
    * Processes and stores the given uploaded file to the run records collection.

src/main/scala/nl/lumc/sasc/sentinel/processors/OutputProcessor.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/StatsProcessor.scala

@@ -23,20 +23,17 @@ import com.novus.salat._
 import com.novus.salat.global._
 import com.mongodb.casbah.Imports._
 
-import nl.lumc.sasc.sentinel.{ AccLevel, LibType, SeqQcPhase }
-import nl.lumc.sasc.sentinel.db.MongodbConnector
+import nl.lumc.sasc.sentinel.{ AccLevel, LibType }
+import nl.lumc.sasc.sentinel.db.MongodbAccessObject
 import nl.lumc.sasc.sentinel.models.{ SeqStatsAggr, User }
 
 /**
- * Base trait that provides support for querying and aggregating metrics for a pipeline.
+ * Base class that provides support for querying and aggregating statistics for a pipeline.
  */
-trait OutputProcessor extends MongodbConnector {
+abstract class StatsProcessor(protected val mongo: MongodbAccessObject) extends Processor {
 
   // TODO: refactor functions in here ~ we can do with less duplication
 
-  /** Name of the pipeline that produces the metrics to query. */
-  def pipelineName: String
-
   /** Name of the unit attribute that denotes whether it comes from a paired-end library or not. */
   protected implicit val pairAttrib = "isPaired"
 

src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapOutputProcessor.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapStatsProcessor.scala

@@ -18,14 +18,14 @@ package nl.lumc.sasc.sentinel.processors.gentrap
 
 import nl.lumc.sasc.sentinel.db.MongodbAccessObject
 import nl.lumc.sasc.sentinel.models._
-import nl.lumc.sasc.sentinel.processors.OutputProcessor
+import nl.lumc.sasc.sentinel.processors.StatsProcessor
 
 /**
  * Output processor for Gentrap endpoints.
  *
  * @param mongo MongoDB database access object.
  */
-class GentrapOutputProcessor(protected val mongo: MongodbAccessObject) extends OutputProcessor {
+class GentrapStatsProcessor(mongo: MongodbAccessObject) extends StatsProcessor(mongo) {
 
   def pipelineName = "gentrap"
 

src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapV04InputProcessor.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapV04RunsProcessor.scala

@@ -16,6 +16,8 @@
  */
 package nl.lumc.sasc.sentinel.processors.gentrap
 
+import nl.lumc.sasc.sentinel.processors.RunsProcessor
+
 import scala.util.Try
 
 import org.apache.commons.io.FilenameUtils.{ getExtension, getName }
@@ -37,9 +39,9 @@ import nl.lumc.sasc.sentinel.validation.ValidationAdapter
  *
  * @param mongo MongoDB database access object.
  */
-class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
-    extends UnitsAdapter[GentrapSampleRecord, GentrapLibRecord]
-    with RunsAdapter
+class GentrapV04RunsProcessor(mongo: MongodbAccessObject)
+    extends RunsProcessor(mongo)
+    with UnitsAdapter[GentrapSampleRecord, GentrapLibRecord]
     with ValidationAdapter
     with ReferencesAdapter
     with AnnotationsAdapter {

src/main/scala/nl/lumc/sasc/sentinel/processors/plain/PlainInputProcessor.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/plain/PlainRunsProcessor.scala

@@ -19,6 +19,7 @@ package nl.lumc.sasc.sentinel.processors.plain
 import java.time.Clock
 import java.util.Date
 import nl.lumc.sasc.sentinel.models.{ RunRecord, User }
+import nl.lumc.sasc.sentinel.processors.RunsProcessor
 import scala.util.Try
 
 import org.scalatra.servlet.FileItem
@@ -37,10 +38,11 @@ import nl.lumc.sasc.sentinel.validation.ValidationAdapter
  *
  * @param mongo MongoDB database access object.
  */
-class PlainInputProcessor(protected val mongo: MongodbAccessObject)
-    extends RunsAdapter
+class PlainRunsProcessor(mongo: MongodbAccessObject) extends RunsProcessor(mongo)
     with ValidationAdapter {
 
+  def pipelineName = "plain"
+
   val validator = createValidator("/schemas/plain.json")
 
   def processRun(fi: FileItem, user: User, pipeline: Pipeline.Value) =

src/test/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapValidationSpec.scala

@@ -28,7 +28,7 @@ class GentrapValidationSpec extends Specification with JsonLoader with Mockito {
   "Support for the 'gentrap' pipeline" should {
     br
 
-    val ipv04 = new GentrapV04InputProcessor(mongo)
+    val ipv04 = new GentrapV04RunsProcessor(mongo)
 
     "exclude non-gentrap summary files" in {
       val summary = loadJson("/schema_examples/plain.json")