Export NER in NAF

Author: PrinsINT

server/src/main/kotlin/org/ivdnt/galahad/annotations/AnnotationReader.kt

@@ -1,7 +1,5 @@
 package org.ivdnt.galahad.annotations
 
-import kotlin.collections.plus
-
 abstract class AnnotationReader {
     val layer: Layer by lazy { read() }
 
@@ -47,23 +45,29 @@ abstract class AnnotationReader {
     }
 
     protected open fun newSentence() {
+        newWordform()
         if (terms.isNotEmpty()) {
-            // loop through all the terms and turn the NER into a span
-            val indices = mutableListOf<Int>()
-            terms.forEachIndexed { i, t ->
-                t.ner?.let {
-                   indices += i
-                }
-            }
-            if (indices.isNotEmpty()) {
-                val ners = mutableListOf<TermSpan>()
-                ners += TermSpan(indices, terms[indices.first()].annotationHead(Annotation.NER)!!)
-                spans[Annotation.NER] = ners.toTypedArray()
-            }
-
+            extractSpans()
             sentences.add(SentenceLayer(sentID(), terms.toTypedArray(), spans.toMap()))
             terms.clear()
             spans.clear()
         }
     }
+
+    protected open fun newWordform() {}
+
+    private fun extractSpans() {
+        // loop through all the terms and turn the NER into a span
+        val indices = mutableListOf<Int>()
+        terms.forEachIndexed { i, t ->
+            t.ner?.let {
+                indices += i
+            }
+        }
+        if (indices.isNotEmpty()) {
+            val ners = mutableListOf<TermSpan>()
+            ners += TermSpan(indices, terms[indices.first()].annotationHead(Annotation.NER)!!)
+            spans[Annotation.NER] = ners.toTypedArray()
+        }
+    }
 }

server/src/main/kotlin/org/ivdnt/galahad/app/Galahad.kt

@@ -6,7 +6,7 @@ import io.swagger.v3.oas.models.info.Contact
 import io.swagger.v3.oas.models.info.Info
 import io.swagger.v3.oas.models.info.License
 import io.swagger.v3.oas.models.servers.Server
-import org.ivdnt.galahad.corpora.documents.DocumentFormat
+import org.ivdnt.galahad.documents.DocumentFormat
 import org.springframework.boot.autoconfigure.SpringBootApplication
 import org.springframework.boot.context.properties.ConfigurationProperties
 import org.springframework.boot.runApplication

server/src/main/kotlin/org/ivdnt/galahad/corpora/Corpus.kt

@@ -1,21 +1,12 @@
 package org.ivdnt.galahad.corpora
 
-import org.ivdnt.galahad.corpora.documents.Document
-import org.ivdnt.galahad.corpora.documents.DocumentFormat
-import org.ivdnt.galahad.corpora.documents.Documents
-import org.ivdnt.galahad.corpora.jobs.Jobs
-import org.ivdnt.galahad.export.CmdiMetadata
-import org.ivdnt.galahad.export.CorpusExport
-import org.ivdnt.galahad.export.DocumentExport
+import org.ivdnt.galahad.documents.Documents
+import org.ivdnt.galahad.jobs.Jobs
 import org.ivdnt.galahad.files.DiskValue
 import org.ivdnt.galahad.files.GalahadFolder
 import org.ivdnt.galahad.files.ValidatedDiskValue
-import org.ivdnt.galahad.util.createZipFile
 import java.io.File
-import java.io.OutputStream
-import java.nio.file.Files
 import java.util.*
-import kotlin.io.path.createTempDirectory
 
 /**
  * A corpus is a collection of documents, metadata and jobs, saved to a folder. The folder contents are:

…nt/galahad/corpora/documents/Document.kt …/org/ivdnt/galahad/documents/Document.ktserver/src/main/kotlin/org/ivdnt/galahad/corpora/documents/Document.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/Document.kt server/src/main/kotlin/org/ivdnt/galahad/corpora/documents/Document.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/Document.kt

@@ -1,4 +1,4 @@
-package org.ivdnt.galahad.corpora.documents
+package org.ivdnt.galahad.documents
 
 import org.apache.logging.log4j.kotlin.Logging
 import org.ivdnt.galahad.annotations.SOURCE_LAYER_NAME

…ahad/corpora/documents/DocumentFormat.kt …vdnt/galahad/documents/DocumentFormat.ktserver/src/main/kotlin/org/ivdnt/galahad/corpora/documents/DocumentFormat.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/DocumentFormat.kt server/src/main/kotlin/org/ivdnt/galahad/corpora/documents/DocumentFormat.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/DocumentFormat.kt

@@ -1,4 +1,4 @@
-package org.ivdnt.galahad.corpora.documents
+package org.ivdnt.galahad.documents
 
 import com.fasterxml.jackson.annotation.JsonCreator
 import com.fasterxml.jackson.annotation.JsonValue

…ad/corpora/documents/DocumentMetadata.kt …nt/galahad/documents/DocumentMetadata.ktserver/src/main/kotlin/org/ivdnt/galahad/corpora/documents/DocumentMetadata.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/DocumentMetadata.kt server/src/main/kotlin/org/ivdnt/galahad/corpora/documents/DocumentMetadata.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/DocumentMetadata.kt

@@ -1,10 +1,9 @@
-package org.ivdnt.galahad.corpora.documents
+package org.ivdnt.galahad.documents
 
 import org.ivdnt.galahad.annotations.Annotation
 import org.ivdnt.galahad.annotations.LayerPreview
 import org.ivdnt.galahad.annotations.LayerSummary
 import org.ivdnt.galahad.formats.InternalFile
-import java.util.*
 
 data class DocumentMetadata(
     /** Name of the uploaded file including extension. Used as a working directory name. */

…t/galahad/corpora/documents/Documents.kt …org/ivdnt/galahad/documents/Documents.ktserver/src/main/kotlin/org/ivdnt/galahad/corpora/documents/Documents.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/Documents.kt server/src/main/kotlin/org/ivdnt/galahad/corpora/documents/Documents.kt renamed to server/src/main/kotlin/org/ivdnt/galahad/documents/Documents.kt

@@ -1,4 +1,4 @@
-package org.ivdnt.galahad.corpora.documents
+package org.ivdnt.galahad.documents
 
 import org.ivdnt.galahad.corpora.Corpus
 import org.ivdnt.galahad.exceptions.DocumentNotFoundException

server/src/main/kotlin/org/ivdnt/galahad/evaluation/distribution/DocumentDistribution.kt

@@ -2,7 +2,7 @@ package org.ivdnt.galahad.evaluation.distribution
 
 import org.ivdnt.galahad.annotations.Annotation
 import org.ivdnt.galahad.annotations.Layer
-import org.ivdnt.galahad.corpora.documents.DocumentMetadata
+import org.ivdnt.galahad.documents.DocumentMetadata
 
 /**
  * The frequency distribution of terms in a document for a specific tagger layer.

server/src/main/kotlin/org/ivdnt/galahad/evaluation/metrics/CorpusMetrics.kt

@@ -3,7 +3,7 @@ package org.ivdnt.galahad.evaluation.metrics
 import com.fasterxml.jackson.annotation.JsonProperty
 import org.ivdnt.galahad.annotations.SOURCE_LAYER_NAME
 import org.ivdnt.galahad.corpora.Corpus
-import org.ivdnt.galahad.corpora.jobs.Job
+import org.ivdnt.galahad.jobs.Job
 import org.ivdnt.galahad.evaluation.comparison.LayerFilter
 import org.ivdnt.galahad.taggers.Tagger
 

server/src/main/kotlin/org/ivdnt/galahad/evaluation/metrics/DocumentMetrics.kt

@@ -1,8 +1,8 @@
 package org.ivdnt.galahad.evaluation.metrics
 
 import org.ivdnt.galahad.annotations.Term
-import org.ivdnt.galahad.corpora.documents.Document
-import org.ivdnt.galahad.corpora.jobs.Job
+import org.ivdnt.galahad.documents.Document
+import org.ivdnt.galahad.jobs.Job
 import org.ivdnt.galahad.evaluation.comparison.LayerComparison
 import org.ivdnt.galahad.evaluation.comparison.LayerFilter
 import org.ivdnt.galahad.evaluation.comparison.TermComparison