Renames for consistency

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

@@ -20,15 +20,15 @@ import com.mongodb.casbah.BulkWriteResult
 import com.novus.salat._
 import com.novus.salat.global._
 
-import nl.lumc.sasc.sentinel.models.{ BaseLibDocument, BaseSampleDocument }
+import nl.lumc.sasc.sentinel.models.{ BaseLibRecord, BaseSampleRecord }
 
 /**
  * Trait for storing samples and libraries from run summaries.
  *
- * @tparam S Subclass of [[nl.lumc.sasc.sentinel.models.BaseSampleDocument]] representing a sample run by a pipeline.
- * @tparam L Subclass of [[nl.lumc.sasc.sentinel.models.BaseLibDocument]] representing a library run by a pipeline.
+ * @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 <: BaseSampleDocument, L <: BaseLibDocument] extends MongodbConnector { this: RunsAdapter =>
+trait UnitsAdapter[S <: BaseSampleRecord, L <: BaseLibRecord] extends MongodbConnector { this: RunsAdapter =>
 
   /** Name of the pipeline that produces the run summary file. */
   def pipelineName: String

src/main/scala/nl/lumc/sasc/sentinel/models/BaseFileDocument.scala → src/main/scala/nl/lumc/sasc/sentinel/models/BaseFileRecord.scala

@@ -19,7 +19,7 @@ package nl.lumc.sasc.sentinel.models
 import com.novus.salat.annotations.Salat
 
 /** Base class for file entries in [[nl.lumc.sasc.sentinel.models.RunRecord]]. */
-@Salat abstract class BaseFileDocument {
+@Salat abstract class BaseFileRecord {
 
   /** File system path of the file. */
   def path: String
@@ -29,4 +29,4 @@ import com.novus.salat.annotations.Salat
 }
 
 /** Minimal implementation of a file entry. */
-case class FileDocument(path: String, md5: String) extends BaseFileDocument
+case class FileRecord(path: String, md5: String) extends BaseFileRecord

src/main/scala/nl/lumc/sasc/sentinel/models/BaseUnitDocument.scala → src/main/scala/nl/lumc/sasc/sentinel/models/BaseUnitRecord.scala

@@ -22,7 +22,7 @@ import com.novus.salat.annotations.{ Persist, Salat }
 import org.bson.types.ObjectId
 
 /** Representation of a sequencing accumulation level unit. */
-@Salat abstract class BaseUnitDocument {
+@Salat abstract class BaseUnitRecord {
 
   /** Internal database ID for the library document. */
   def id: ObjectId
@@ -41,14 +41,14 @@ import org.bson.types.ObjectId
 }
 
 /** Representation of a sample within a run. */
-@Salat abstract class BaseSampleDocument extends BaseUnitDocument {
+@Salat abstract class BaseSampleRecord extends BaseUnitRecord {
 
   /** Sample name. */
   def sampleName: Option[String]
 }
 
 /** Representation of a library within a sample. */
-@Salat abstract class BaseLibDocument extends BaseUnitDocument {
+@Salat abstract class BaseLibRecord extends BaseUnitRecord {
 
   /** Name of the sample which this library belongs to. */
   def sampleName: Option[String]

src/main/scala/nl/lumc/sasc/sentinel/models/SeqFiles.scala

@@ -22,4 +22,4 @@ package nl.lumc.sasc.sentinel.models
  * @param read1 The first read (if paired-end) or the only read (if single end).
  * @param read2 The second read. Only defined for paired-end inputs.
  */
-case class SeqFiles(read1: FileDocument, read2: Option[FileDocument] = None)
+case class SeqFiles(read1: FileRecord, read2: Option[FileRecord] = None)

src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapLibDocument.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapLibRecord.scala

@@ -42,7 +42,7 @@ import nl.lumc.sasc.sentinel.utils.getUtcTimeNow
  * @param creationTimeUtc UTC time when this sample entry was created.
  * @param id Internal database ID.
  */
-case class GentrapLibDocument(
+case class GentrapLibRecord(
   alnStats: GentrapAlignmentStats,
   seqStatsRaw: SeqStats,
   seqStatsProcessed: Option[SeqStats],
@@ -57,4 +57,4 @@ case class GentrapLibDocument(
   sampleName: Option[String] = None,
   runName: Option[String] = None,
   creationTimeUtc: Date = getUtcTimeNow,
-  @Key("_id") id: ObjectId = new ObjectId) extends BaseLibDocument
+  @Key("_id") id: ObjectId = new ObjectId) extends BaseLibRecord

src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapSampleDocument.scala → src/main/scala/nl/lumc/sasc/sentinel/processors/gentrap/GentrapSampleRecord.scala

@@ -37,7 +37,7 @@ import nl.lumc.sasc.sentinel.utils.getUtcTimeNow
  * @param creationTimeUtc UTC time when this sample entry was created.
  * @param id Internal database ID.
  */
-case class GentrapSampleDocument(
+case class GentrapSampleRecord(
   uploaderId: String,
   runId: ObjectId,
   referenceId: ObjectId,
@@ -46,4 +46,4 @@ case class GentrapSampleDocument(
   sampleName: Option[String] = None,
   runName: Option[String] = None,
   creationTimeUtc: Date = getUtcTimeNow,
-  @Key("_id") id: ObjectId = new ObjectId) extends BaseSampleDocument
+  @Key("_id") id: ObjectId = new ObjectId) extends BaseSampleRecord

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

@@ -38,9 +38,9 @@ import nl.lumc.sasc.sentinel.validation.ValidationAdapter
  * @param mongo MongoDB database access object.
  */
 class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
-    extends UnitsAdapter[GentrapSampleDocument, GentrapLibDocument]
-    with ValidationAdapter
+    extends UnitsAdapter[GentrapSampleRecord, GentrapLibRecord]
     with RunsAdapter
+    with ValidationAdapter
     with ReferencesAdapter
     with AnnotationsAdapter {
 
@@ -123,8 +123,8 @@ class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
   }
 
   /** Extracts an input sequencing file from a library entry in a Gentrap summary. */
-  private[processors] def extractReadFile(libJson: JValue, fileKey: String): FileDocument =
-    (libJson \ "flexiprep" \ "files" \ "pipeline" \ fileKey).extract[FileDocument]
+  private[processors] def extractReadFile(libJson: JValue, fileKey: String): FileRecord =
+    (libJson \ "flexiprep" \ "files" \ "pipeline" \ fileKey).extract[FileRecord]
 
   /** Case class for containing per-base position statistics. */
   private[processors] case class PerBaseStat[T](index: Int, value: T)
@@ -171,7 +171,7 @@ class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
   /** Extracts a library document from a library entry in a Gentrap summary. */
   private[processors] def extractLibDocument(libJson: JValue, uploaderId: String, runId: ObjectId, refId: ObjectId,
                                              annotIds: Seq[ObjectId], libName: String, sampleName: String,
-                                             runName: Option[String] = None): GentrapLibDocument = {
+                                             runName: Option[String] = None): GentrapLibRecord = {
 
     val seqStatsRaw = SeqStats(
       read1 = extractReadStats(libJson, "seqstat_R1", "fastqc_R1"),
@@ -194,7 +194,7 @@ class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
           SeqFiles(read1 = r1f, read2 = Try(extractReadFile(libJson, "output_R2")).toOption)
       }
 
-    GentrapLibDocument(
+    GentrapLibRecord(
       alnStats = extractAlnStats(libJson),
       seqStatsRaw = seqStatsRaw,
       seqStatsProcessed = seqStatsProcessed,
@@ -219,7 +219,7 @@ class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
       .map {
         case (sampleName, sampleJson) =>
           val libJsons = (sampleJson \ "libraries").extract[Map[String, JValue]]
-          val gSample = GentrapSampleDocument(
+          val gSample = GentrapSampleRecord(
             uploaderId = uploaderId,
             sampleName = Option(sampleName),
             runId = runId,
@@ -243,7 +243,7 @@ class GentrapV04InputProcessor(protected val mongo: MongodbAccessObject)
 
   /** Helper function for creating run records. */
   private[processors] def createRun(fileId: ObjectId, refId: ObjectId, annotIds: Seq[ObjectId],
-                                    samples: Seq[GentrapSampleDocument], libs: Seq[GentrapLibDocument],
+                                    samples: Seq[GentrapSampleRecord], libs: Seq[GentrapLibRecord],
                                     user: User, pipeline: Pipeline.Value, runName: Option[String] = None) =
     RunRecord(
       runId = fileId, // NOTE: runId kept intentionally the same as fileId