Add another taxon corpus for annotated-taxa. Rename taxa corpus to ta…

…xon-variation. (#579)
phenoscape · Jul 10, 2022 · d628970 · d628970
1 parent f861de1
commit d628970
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Showing 3 changed files with 27 additions and 15 deletions.
diff --git a/src/main/resources/swaggerDocs/swagger.yaml b/src/main/resources/swaggerDocs/swagger.yaml
@@ -744,7 +744,7 @@ paths:
           format: IRI
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: true
           type: string
       responses:
@@ -770,7 +770,7 @@ paths:
           format: IRI
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: true
           type: string
       responses:
@@ -790,7 +790,7 @@ paths:
       parameters:
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: true
           type: string
       responses:
@@ -849,7 +849,7 @@ paths:
           format: JSON
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: false
           type: string
       responses:
@@ -888,7 +888,7 @@ paths:
           format: JSON
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: false
           type: string
       responses:
@@ -925,7 +925,7 @@ paths:
           type: string
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: false
           type: string
       responses:
@@ -958,7 +958,7 @@ paths:
           type: string
         - name: corpus
           in: formData
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: false
           type: string
       responses:
@@ -990,7 +990,7 @@ paths:
           type: string
         - name: corpus
           in: query
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: true
           type: string
         - name: type
@@ -1021,7 +1021,7 @@ paths:
           type: string
         - name: corpus
           in: formData
-          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'taxa' and 'states'.
+          description: Name of corpus of items to count. A corpus is a particular type of item that can be associated with phenotypes. Allowed values are 'annotated-taxa', 'taxon-variation', and 'states'.
           required: true
           type: string
         - name: type

diff --git a/src/main/scala/org/phenoscape/kb/Main.scala b/src/main/scala/org/phenoscape/kb/Main.scala
@@ -37,7 +37,7 @@ import akka.util.ByteString
 import ch.megard.akka.http.cors.scaladsl.CorsDirectives._
 import ch.megard.akka.http.cors.scaladsl.settings.CorsSettings
 import org.apache.commons.io.IOUtils
-import org.phenoscape.kb.Similarity.{AnatomyTerm, GenesCorpus, PhenotypeCorpus, PhenotypeTerm, SimilarityTermType, StatesCorpus, TaxaCorpus}
+import org.phenoscape.kb.Similarity.{AnatomyTerm, AnnotatedTaxaCorpus, GenesCorpus, PhenotypeCorpus, PhenotypeTerm, SimilarityTermType, StatesCorpus, TaxonVariationCorpus}
 import org.phenoscape.kb.queries.QueryUtil.{InferredAbsence, InferredPresence, PhenotypicQuality, QualitySpec}
 import scalaz._
 import spray.json._
@@ -77,10 +77,12 @@ object Main extends HttpApp with App {
   }
 
   implicit val PhenotypeCorpusUnmarshaller: Unmarshaller[String, PhenotypeCorpus] = Unmarshaller.strict {
-    case "taxa"   => TaxaCorpus
-    case "states" => StatesCorpus
-    case "genes"  => GenesCorpus
-    case _        => throw new Exception(s"Invalid phenotype corpus name")
+    case "taxa"            => AnnotatedTaxaCorpus
+    case "annotated-taxa"  => AnnotatedTaxaCorpus
+    case "taxon-variation" => TaxonVariationCorpus
+    case "states"          => StatesCorpus
+    case "genes"           => GenesCorpus
+    case _                 => throw new Exception(s"Invalid phenotype corpus name")
   }
 
   implicit val OWLClassUnmarshaller: Unmarshaller[String, OWLClass] =

diff --git a/src/main/scala/org/phenoscape/kb/Similarity.scala b/src/main/scala/org/phenoscape/kb/Similarity.scala
@@ -323,7 +323,7 @@ object Similarity {
 
   }
 
-  object TaxaCorpus extends PhenotypeCorpus {
+  object TaxonVariationCorpus extends PhenotypeCorpus {
 
     val path: Path = PropertyPathParser
       .parsePropertyPath(sparql"$has_phenotypic_profile/$rdfType".text)
@@ -333,6 +333,16 @@ object Similarity {
 
   }
 
+  object AnnotatedTaxaCorpus extends PhenotypeCorpus {
+
+    val path: Path = PropertyPathParser
+      .parsePropertyPath(sparql"$exhibits_state/$describes_phenotype".text)
+      .getOrElse(throw new Exception("Invalid property path"))
+
+    def constraint(node: QueryText): QueryText = sparql"$node $rdfsIsDefinedBy $VTO ."
+
+  }
+
   object GenesCorpus extends PhenotypeCorpus {
 
     val path: Path = PropertyPathParser