1. Scala
Domain
Modeling
and
Architecture
Experience
Report
Hossam
Karim

7. for {!
!
locus Chromosome ⤞ Gene ⤞ Locus!
if Locus range!
!
path locus ⤞ Sequence ⤞ nucleotide!
if nucleotide alignment (_ > 89)!
!
} yield path!

11.
inputMessage >>= fasta >>= {
case n: Nucleotide ⇒ !
("media" → "nucleotide") ~> n.giNumber
case _: AminoAcid ⇒ !
fail[String](!
"Expected a ‘nucleotide’ Sequence")
case _ ⇒ !
fail[String](!
"Expected a ‘single’ Sequence representation”)
} >>= {
for {
query ← meta.Sequence ⤞ meta.nucleotide
if meta.nucleotide.giNumber === _
} yield query
} >>= xml
!

12.
inputMessage >>= fasta >>= {
case n: Nucleotide ⇒ !
("media" → "nucleotide") ~> n.giNumber
case _: AminoAcid ⇒ !
fail[String](!
"Expected a ‘nucleotide’ Sequence")
case _ ⇒ !
fail[String](!
"Expected a ‘single’ Sequence representation”)
} >>= {
for {
query ← meta.Sequence ⤞ meta.nucleotide
if meta.nucleotide.giNumber === _
} yield query
} >>= xml
!

13.
inputMessage >>= fasta >>= {
case n: Nucleotide ⇒ !
("media" → "nucleotide") ~> n.giNumber
case _: AminoAcid ⇒ !
fail[String](!
"Expected a ‘nucleotide’ Sequence")
case _ ⇒ !
fail[String](!
"Expected a ‘single’ Sequence representation”)
} >>= {
for {
query ← meta.Sequence ⤞ meta.nucleotide
if meta.nucleotide.giNumber === _
} yield query
} >>= xml
!

14.
inputMessage >>= fasta >>= {
case n: Nucleotide ⇒ !
("media" → "nucleotide") ~> n.giNumber
case _: AminoAcid ⇒ !
fail[String](!
"Expected a ‘nucleotide’ Sequence")
case _ ⇒ !
fail[String](!
"Expected a ‘single’ Sequence representation”)
} >>= {
for {
query ← meta.Sequence ⤞ meta.nucleotide
if meta.nucleotide.giNumber === _
} yield query
} >>= xml
!

15.
inputMessage >>= fasta >>= {
case n: Nucleotide ⇒ !
("media" → "nucleotide") ~> n.giNumber
case _: AminoAcid ⇒ !
fail[String](!
"Expected a ‘nucleotide’ Sequence")
case _ ⇒ !
fail[String](!
"Expected a ‘single’ Sequence representation”)
} >>= {
for {
query ← meta.Sequence ⤞ meta.nucleotide
if meta.nucleotide.giNumber === _
} yield query
} >>= xml
!

16. trait Message[A, H] {
val body: Validation[H, Option[A]]
val headers: H
}
trait MessageBuilder {
def build[A, H: Monoid](
body: Validation[H, Option[A]],
headers: H): Message[A, H]
}

17. trait Message[A, H] {
val body: Validation[H, Option[A]]
val headers: H
}
trait MessageBuilder {
def build[A, H: Monoid](
body: Validation[H, Option[A]],
headers: H): Message[A, H]
}

18. implicit def m2m[H]!
(implicit builder: MessageBuilder, !
monoid: Monoid[H]) =!
new Monad[({type λ[α] = Message[α, H]})#λ] {
def pure[A](a: => A): Message[A, H] = . . .!
def bind[A, B]!
(a: Message[A, H], !
f: (A) => Message[B, H]): Message[B, H] = . . .
}

19. def pure[A](a: => A) = !
builder.build[A, H](Success(Option(a)), ∅[H])

20. def bind[A, B](!
m: Message[A, H], !
f: (A) => Message[B, H]): Message[B, H] = {!
val mb: Message[B, H] = m.body match {
case Success(Some(value)) ⇒ f(value)
case Success(None) ⇒!
builder.build[B, H](!
Success(Option.empty[B]), ∅[H])
case Failure(a) ⇒!
builder.build[B, H](!
Failure(a), ∅[H] |+| a)
}!
builder.build[B, H](mb.body, m.headers |+| mb.headers)
}

21. implicit object BasicMessageBuilder extends MessageBuilder {
def build[A, H: Monoid](!
body: Validation[H, Option[A]], headers: H) =
BasicMessage(body, headers)
}
!
implicit object DiagnosisMessageBuilder extends!
MessageBuilder {
def build[A, H: Monoid](!
body: Validation[H, Option[A]], headers: H) =
DiagnosisMessage(body, headers)
}
def body[A](value: A)(implicit builder: MessageBuilder) :!
Message[A, HL] =
builder.build(Success(Some(value)), List.empty[Header])

22. import Basic._!
//import Diagnosis._!
//import Transactional._!
!
gene map {
for (!
e ← meta.Chromosome ⤞ meta.Gene !
if meta.Gene.uuid === _.uuid!
) yield e
} >>= search

23. (genex <**> geney) (_ ++ _) >>=
header("media-type", "application/vnd.x.gene+json") >>=
json
for {
m ← body(<gene xmlns="urn:model:gene:1.0">...</gene>)
gene ← xml(m)
} yield gene
gene map {
for {
e ← meta.Gene ⤞ meta.Gene.uuid
if meta.Gene.uuid === _.uuid
} yield e
} >>= search

24. import scalaz._!
import Scalaz._!
// profit!!

28. trait Resource {!
val name: String!
} !
trait Ontology extends Resource {!
val nestingOntology: Option[Ontology]!
val nestedOntology: List[Ontology]!
val ownedType: List[Type]!
val ownedRelation: List[Relation]!
}!

29. trait GraphResource {
this: Resource =>
}
trait GraphVertex extends GraphResource {
this: Entity =>
val graphFeatures: List[PrimitiveFeature]
val master: Boolean
val rootToMasterEdge: GraphEdge with Relation
val masterToSelf: Option[GraphEdge with Relation] = None
}
trait GraphEdge extends GraphResource {
this: Relation =>
}

30. trait RelationalResource {
this: Resource =>
}
trait NamedRelationalResource extends RelationalResource {
this: Resource =>
val relationalName: String
}
trait RelationalEntity extends NamedRelationalResource {
this: Entity =>
}
trait RelationalCompositeFeature extends RelationalResource {
this: CompositeFeature =>
val mapping: Map[String, String]
}

31. object Chromosome extends
Entity
with RelationalEntity!
with GraphVertex
with XmlElement {
self =>
sealed trait ChromosomePart {
val ownerType = self
}
// Ontology Trait
val featuringType = self
val ownedFeature = chromatine :: Nil
// XML Trait
val namespace = "urn:domain:chromosome:1.0"
val prefix = "chr"
// Features
val chromatine =
new Chromatine(
name = "chromatine",
ownerType = Chromosome,
mapping = Map.empty[String, String])
}

32. implicit def enrich[A <: DomainModel](model: A) = new {
def metamodel: Option[Type] = Ontology.typeOf(model)
}
def xmlFilter[A <: DomainModel] =
(model: A) ⇒ model.metamodel match {
case Some(_: XmlElement) ⇒ body(XmlModel[A](model))
case _ ⇒ fail[XmlModel[A]]!
("No XmlElement meta-model definition could be found")
}
def ingoingEdges[A <: DomainModel] =
(model: A) ⇒ model.metamodel match {
case Some(vertex: GraphVertex) ⇒ !
Ontology.edges.filter(_.target == vertex)
case _ ⇒ List.empty[GraphEdge]
}

33. implicit def enrich[A <: DomainModel](model: A) = new {
def metamodel: Option[Type] = Ontology.typeOf(model)
}
def xmlFilter[A <: DomainModel] =
(model: A) ⇒ model.metamodel match {
case Some(_: XmlElement) ⇒ body(XmlModel[A](model))
case _ ⇒ fail[XmlModel[A]]!
("No XmlElement meta-model definition could be found")
}
def ingoingEdges[A <: DomainModel] =
(model: A) ⇒ model.metamodel match {
case Some(vertex: GraphVertex) ⇒ !
Ontology.edges.filter(_.target == vertex)
case _ ⇒ List.empty[GraphEdge]
}

34. trait Type extends Resource
trait SimpleType extends Type
trait Entity extends Type!
!
trait Relation extends Type
trait Feature[+T <: Type] extends Resource
trait SimpleFeature[+T <: SimpleType] extends Feature[T]
trait PrimitiveFeature extends SimpleFeature[Primitive]
trait EnumerationFeature extends SimpleFeature[Enumeration]
trait CompositeFeature extends SimpleFeature[Composite]
trait Primitive extends SimpleType
trait Enumeration extends SimpleType
trait Composite extends SimpleType

35. trait PrimitiveLogic {
val resource: Primitive
def ===[A](value: Primitive[A]): Operator = . . .
def in[A](values: PrimitiveList[A]): Operator = . . .
}
def find(operator: Operator): Option[T]
def list(operator: Operator): List[T]!
import PrimitiveLogic._
dao list (Locus.locusUUID in list)
dao find (Locus.locusUUID === uuid)

36. import Logic._
val validation =
Sequence.nucleotide.accession.accessionNumber !== x
import GraphOps._
val path =
Sequence.nucleotide ⤞
Sequence.protein ⤞
Locus.typeOfGene where (_ !== y)

37. for {!
!
locus Chromosome ⤞ Gene ⤞ Locus!
if Locus range!
!
path locus ⤞ Sequence ⤞ nucleotide!
if nucleotide alignment (_ > 89)!
!
} yield path!

39. trait Qvt[PIM, Query, View, PSM] {
def query(pim: PIM): List[Query]
def view(query: Query): View
def transform(view: View): PSM
}

40. class GraphSimpleQvt(
ontologyProfile: OntologyProfile,
graphProfile: GraphProfile)
extends SimpleQvt[Model, Package, GraphOntology] {
def query(pim: Model) = {
walk[Package](pim)(_.getNestedPackages).
filter(graphProfile.graphPredicate)
}
def transform(view: Package) = graph(view)
def graph(element: Package): GraphOntology = {
...
}
.
.
.
}

41. def walk[A]
(element: A)
(f: A => Iterable[A]): List[A] = {
val children = f(element).toList
children ++ !
(children.flatMap(walk(_, f)))
}

42. def packageName(element: Package): String =
Stream!
.iterate(element)(_.getNestingPackage)
.takeWhile(!_.isInstanceOf[Model])
.map(_.getName)
.reverse
.mkString(".") //.scala rocks !!

44. Thank
You