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Adapter for Scala Grounders (rvacareanu/grounder) (#887)
## Summary of Changes Added an Adapter for the Scala Grounders package. --------- Co-authored-by: Gus Hahn-Powell <[email protected]>
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...scala/src/main/scala/org/ml4ai/skema/text_reading/grounding/scala_grounders/Adapter.scala
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| package org.ml4ai.skema.grounding.scala_grounders | ||
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| import org.clulab.scala_grounders.grounding.GroundingConfig | ||
| import org.ml4ai.skema.text_reading.grounding.Grounder | ||
| import org.ml4ai.skema.text_reading.grounding.GroundingCandidate | ||
| import org.ml4ai.skema.text_reading.grounding.GroundingConcept | ||
| import com.typesafe.config.Config | ||
| import org.clulab.scala_grounders.grounding.SequentialGrounder | ||
| import org.clulab.scala_grounders.model.DKG | ||
| import org.clulab.scala_grounders.model.DKGSynonym | ||
| import com.typesafe.config.ConfigFactory | ||
| import org.clulab.scala_grounders.using | ||
| import org.clulab.scala_grounders.model.DKG | ||
| import scala.io.Source | ||
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| /** | ||
| * This class adapts the data definitions from this project to work with scala-grounder's definition | ||
| * Concretely, the changes needed are: | ||
| * - SKEMA's GroundingConcept to scala-grounder's DKG (avalaible in `fromConceptToDKG`) | ||
| * - scala-grounder's DKG to SKEMA's GroundingConcept (avalaible in `fromDKGToConcept`) | ||
| * - Create the scala-grounder Grounder (`grounder = SequentialGrounder()`) | ||
| * - Changing `groundingCandidates` to call the right method from the scala-grounder side | ||
| * | ||
| * @param groundingConcepts -> The concepts which we will use to do the grounding | ||
| * Every candidate text for grounding (i.e. any text that we | ||
| * want to ground) will be grounded on these concepts | ||
| * (Note: depending on the implementation, it is possible that | ||
| * none of these groundingConcepts candidates are suitable, so | ||
| * we might not return anything; however, we will never return | ||
| * a concept that is outside this) | ||
| */ | ||
| class ScalaGroundersAdapter(groundingConcepts: Seq[GroundingConcept]) extends Grounder { | ||
| lazy val concepts = groundingConcepts.map(fromConceptToDKG) | ||
| lazy val grounder = SequentialGrounder().mkFast(concepts) | ||
| def groundingCandidates(texts: Seq[String], k: Int): Seq[Seq[GroundingCandidate]] = { | ||
| texts.map { text => | ||
| // TODO Maybe provide additional context (useful for NeuralGrounder) | ||
| grounder.ground(text, None, concepts, k) | ||
| .map { result => | ||
| GroundingCandidate(fromDKGToConcept(result.dkg), result.score, details = Some(result.groundingDetails.grounderName)) | ||
| } | ||
| .force.toSeq | ||
| } | ||
| } | ||
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| /** | ||
| * Transform a SKEMA's `GroundingConcept` to a scala-grounders' `DKG` | ||
| * They have similar meanings, so the map is 1:1 | ||
| * | ||
| * @param concept | ||
| * @return | ||
| */ | ||
| def fromConceptToDKG(concept: GroundingConcept): DKG = { | ||
| DKG(concept.id, concept.name, concept.description, concept.synonyms.map { synonyms => synonyms.map { s => DKGSynonym(s, None) } }.getOrElse(Seq.empty)) | ||
| } | ||
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| /** | ||
| * Transform a scala-grounder' `DKG` to SKEMA's `GroundingConcept` | ||
| * They have similar meanings, so the map is 1:1 | ||
| * | ||
| * @param dkg | ||
| * @return | ||
| */ | ||
| def fromDKGToConcept(dkg: DKG): GroundingConcept = { | ||
| GroundingConcept(dkg.id, dkg.name, dkg.description, Option(dkg.synonyms.map(_.value)), None) | ||
| } | ||
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| } | ||
| /** | ||
| * Provide altenatives way of creating a `ScalaGroundersAdapter` | ||
| */ | ||
| object ScalaGroundersAdapter { | ||
| def apply(groundingConcepts: Seq[GroundingConcept]): ScalaGroundersAdapter = new ScalaGroundersAdapter(groundingConcepts) | ||
| def fromDkgs(dkgs: Seq[DKG]): ScalaGroundersAdapter = new ScalaGroundersAdapter(dkgs.map(dkg => GroundingConcept(dkg.id, dkg.name, dkg.description, Option(dkg.synonyms.map(_.value)), None))) | ||
| def fromFile(groundingConceptsPath: String): ScalaGroundersAdapter = { | ||
| val concepts = using(Source.fromFile(groundingConceptsPath)) { it => | ||
| ujson.read(it.mkString).arr.map(it => DKG.fromJson(it)) | ||
| } | ||
| ScalaGroundersAdapter.fromDkgs(concepts) | ||
| } | ||
| } |
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..._reading/scala/src/test/scala/org/ml4ai/skema/grounding/scala_grounders/TestAdapter.scala
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| package org.ml4ai.skema.grounding.scala_grounders | ||
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| import org.ml4ai.skema.test.Test | ||
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| import java.nio.{Buffer, ByteBuffer, ByteOrder} | ||
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| import org.ml4ai.skema.text_reading.grounding.Grounder | ||
| import org.ml4ai.skema.text_reading.grounding.GroundingCandidate | ||
| import org.ml4ai.skema.text_reading.grounding.GroundingConcept | ||
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| /** | ||
| * | ||
| * Running command: | ||
| * sbt "testOnly org.ml4ai.skema.grounding.scala_grounders.TestAdapter" | ||
| */ | ||
| class TestAdapter extends Test { | ||
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| behavior of "ScalaGroundersAdapter" | ||
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| val gcs = Seq( | ||
| GroundingConcept( | ||
| id = "id1", | ||
| name = "dog", | ||
| description = Some("this is a cute dog"), | ||
| synonyms = None, | ||
| embedding = None | ||
| ), | ||
| GroundingConcept( | ||
| id = "id2", | ||
| name = "cat", | ||
| description = Some("this is a cute cat"), | ||
| synonyms = None, | ||
| embedding = None | ||
| ), | ||
| GroundingConcept( | ||
| id = "id3", | ||
| name = "dog cat", | ||
| description = Some("here we have a dog and a cat"), | ||
| synonyms = None, | ||
| embedding = None | ||
| ), | ||
| GroundingConcept( | ||
| id = "id4", | ||
| name = "cat", | ||
| description = Some("this is a cute cat"), | ||
| synonyms = None, | ||
| embedding = None | ||
| ), | ||
| ) | ||
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| val sga = new ScalaGroundersAdapter(gcs) | ||
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| val result = sga.groundingCandidates(Seq("dog"), 10).head | ||
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| // Check that the first one is a GroundingCandidate with id1 | ||
| it should "ground" in { | ||
| result.foreach(println) | ||
| result.head.concept.id should be ("id1") | ||
| } | ||
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| } |