Revert changes

Author: aherbst-broad

transformation/src/main/scala/org/broadinstitute/monster/encode/transformation/BiosampleTransformations.scala

@@ -55,20 +55,6 @@ object BiosampleTransformations {
       treatments = biosampleInput.read[List[String]]("treatments"),
       wasPerturbed = biosampleInput.read[Boolean]("perturbed"),
       submittedBy = biosampleInput.read[String]("submitted_by"),
-      flyLifeStage = biosampleInput.tryRead[String]("fly_life_stage"),
-      flySynchronizationStage = biosampleInput.tryRead[String]("fly_synchronization_stage"),
-      modelOrganismAge = biosampleInput.tryRead[Long]("model_organism_age"),
-      modelOrganismAgeUnit = biosampleInput.tryRead[String]("model_organism_age_units"),
-      mouseLifeStage = biosampleInput.tryRead[String]("mouse_life_stage"),
-      originBatch = Some("test"),
-      passageNumber = biosampleInput.tryRead[Long]("passage_number"),
-      postNucleicAcidDeliveryTime = biosampleInput.tryRead[Long]("post_nucleic_acid_delivery_time"),
-      postNucleicAcidDeliveryTimeUnit =
-        biosampleInput.tryRead[String]("post_nucleic_acid_delivery_time_units"),
-      pulseChaseTime = biosampleInput.tryRead[Long]("pulse_chase_time"),
-      pulseChaseTimeUnit = biosampleInput.tryRead[String]("pulse_chase_time_units"),
-      wormLifeStage = biosampleInput.tryRead[String]("worm_life_stage"),
-      wormSynchronizationStage = biosampleInput.tryRead[String]("worm_synchronization_stage"),
       productId = if (productIds.size > 1) {
         logger.warn(
           s"Biosample '$biosampleId' has multiple product ids: [${productIds.mkString(",")}]."

transformation/src/main/scala/org/broadinstitute/monster/encode/transformation/DonorTransformations.scala

@@ -26,6 +26,7 @@ object DonorTransformations {
         }
       }
     }
+
     Donor(
       id = CommonTransformations.readId(donorInput),
       crossReferences = donorInput.read[List[String]]("dbxrefs"),

transformation/src/main/scala/org/broadinstitute/monster/encode/transformation/LibraryTransformations.scala

@@ -35,8 +35,7 @@ object LibraryTransformations {
       spikeIns = libraryInput.read[List[String]]("spikeins_used"),
       biosampleId = CommonTransformations.transformId(libraryInput.read[String]("biosample")),
       prepMaterial = libraryInput.tryRead[String]("nucleic_acid_term_id"),
-      prepMaterialName = libraryInput.tryRead[String]("nucleic_acid_term_name"),
-      constructionMethod = Some("test")
+      prepMaterialName = libraryInput.tryRead[String]("nucleic_acid_term_name")
     )
   }
 

transformation/src/test/scala/org/broadinstitute/monster/encode/transformation/DonorTransformationsSpec.scala

@@ -18,8 +18,7 @@ class DonorTransformationsSpec extends AnyFlatSpec with Matchers {
         |"lab": "/labs/example-lab",
         |"parents": [],
         |"submitted_by": "/users/123-abc",
-        |"age": "30-33",
-        |"uuid": "C12A1ED2-454C-47AB-B7D4-A47570F464A0"
+        |"age": "30-33"
         |}
         |""".stripMargin
     val inputMsg: Msg = JsonParser.parseEncodedJson(inputJson)
@@ -48,8 +47,7 @@ class DonorTransformationsSpec extends AnyFlatSpec with Matchers {
         |"lab": "/labs/example-lab",
         |"parents": [],
         |"submitted_by": "/users/123-abc",
-        |"age": "90 or above",
-        |"uuid": "C12A1ED2-454C-47AB-B7D4-A47570F464A0"
+        |"age": "90 or above"
         |}
         |""".stripMargin
     val inputMsg: Msg = JsonParser.parseEncodedJson(inputJson)