updated aries dependencies, added leistungen reader

pom.xml

@@ -53,16 +53,21 @@
             <artifactId>khttp</artifactId>
             <version>1.0.0</version>
         </dependency>
+        <dependency>
+            <groupId>com.github.doyaaaaaken</groupId>
+            <artifactId>kotlin-csv-jvm</artifactId>
+            <version>0.15.2</version>
+        </dependency>
 
         <dependency>
             <groupId>de.uniwue.aries</groupId>
             <artifactId>aries-ontology-model-io</artifactId>
-            <version>1.0.0</version>
+            <version>1.1.0</version>
         </dependency>
         <dependency>
             <groupId>de.uniwue.aries</groupId>
             <artifactId>aries-algorithm</artifactId>
-            <version>1.1.15</version>
+            <version>1.3.0</version>
         </dependency>
     </dependencies>
     <build>

src/main/kotlin/ExtractorTest.kt

 import de.uniwue.aries.algorithm.ARIESAlgorithm
-import de.uniwue.aries.ontology.io.ExcelFileReader
+import de.uniwue.aries.ontology.io.excel.ExcelFileReader
 import de.uniwue.aries.uima.types.Types
+import org.apache.uima.cas.text.AnnotationFS
 import org.apache.uima.util.CasCreationUtils
 
 fun main() {
@@ -10,9 +11,9 @@ fun main() {
     val system = pairs.map { it.first["CONTENT"] }.map {
         val cas = CasCreationUtils.createCas(Types.getTypeSystem(), null, null)
         cas.documentText = it
-        algo.extract(cas, ontology)
+        algo.extract(cas, ontology, "")
         val tEntity = Types.getType(cas, Types.IEENTITY)
-        val owlid = cas.getAnnotationIndex(tEntity)
+        val owlid = cas.getAnnotationIndex<AnnotationFS>(tEntity)
                 .sortedBy { it.begin }
                 .map { it.getFeatureValueAsString(tEntity.getFeatureByBaseName("owlid")) }
                 .firstOrNull()

src/main/kotlin/LeistungReader.kt

+import com.github.doyaaaaaken.kotlincsv.dsl.csvReader
+import java.io.File
+import java.lang.IllegalArgumentException
+
+class LeistungReader {
+    fun read(csvFileName: String): List<Map<String, String>> {
+        return csvReader().readAllWithHeader(File(csvFileName))
+    }
+}
+
+fun filterByModality(leistungen: List<Map<String, String>>, modality: String): List<Map<String, String>> {
+    val modalityCode = when(modality) {
+        "konv. Röntgen" -> "RKR"
+        "Computer-Tomographie" -> "RCT"
+        "MR - Tomographie Rö" -> "RMR"
+        "Ultraschall" -> "RUS"
+        "Durchleuchtung" -> "RDL"
+        else -> {
+            throw IllegalArgumentException("unknown modality")
+        }
+    }
+    return leistungen.filter { it["id"]!!.startsWith(modalityCode) }
+}
+
+fun filterByLocalizationOrModifier(leistungen: List<Map<String, String>>, localizationOrModifier: String): List<Map<String, String>> {
+    return leistungen.filter{ it["description"]!!.contains(localizationOrModifier)}
+}
+
+fun main() {
+    val leistungen = LeistungReader().read("C:\\users\\jok3r\\domains\\anordnungen\\radio_hierarchy.csv")
+    val requestable = leistungen.filter { it["requestable"] == "True" }
+    var filtered = filterByModality(requestable, "konv. Röntgen")
+    listOf<String>("Handgelenk", "2 Ebenen").forEach {
+        filtered = filterByLocalizationOrModifier(filtered, it)
+    }
+    var res = filtered.minBy { it["description"]!!.length }
+    println()
+}
\ No newline at end of file

src/main/kotlin/de/dzptm/server/Extractor.kt

@@ -2,15 +2,15 @@ package de.dzptm.server
 
 import com.google.gson.Gson
 import de.uniwue.aries.algorithm.ARIESAlgorithm
-import de.uniwue.aries.ontology.io.ExcelFileReader
+import de.uniwue.aries.ontology.io.excel.ExcelFileReader
 import de.uniwue.aries.uima.types.Types
 import org.apache.uima.cas.CAS
+import org.apache.uima.cas.text.AnnotationFS
 import org.apache.uima.util.CasCreationUtils
 import org.json.JSONArray
 import org.json.JSONObject
 import spark.Request
 import spark.Response
-import java.lang.NumberFormatException
 import java.time.LocalDate
 import java.time.LocalDateTime
 import java.time.LocalTime
@@ -93,7 +93,7 @@ object Extractor {
         }
 
         val type = Types.getType(cas, Types.IEENTITY)
-        val annotation = cas.getAnnotationIndex(type)
+        val annotation = cas.getAnnotationIndex<AnnotationFS>(type)
             .filter { it.getFeatureValueAsString(type.getFeatureByBaseName("owlid")).contains("Date|||") }
             .sortedBy { it.begin }.last()
         val format = annotation.getFeatureValueAsString(type.getFeatureByBaseName("owlid")).substringAfterLast("|")
@@ -135,7 +135,7 @@ object Extractor {
     private fun applyARIES(cas: CAS) {
         val ontology = ExcelFileReader.read(ClassLoader.getSystemResourceAsStream("KlinischerAuftrag20210608.xlsx"))
         val algo = ARIESAlgorithm()
-        algo.extract(cas, ontology)
+        algo.extract(cas, ontology, "")
     }
 
     private fun convertProbs(json: JSONArray): List<List<Double>> {
@@ -165,7 +165,7 @@ object Extractor {
 
     private fun getModality(cas: CAS): String {
         val tEntity = Types.getType(cas, Types.IEENTITY)
-        val owlid = cas.getAnnotationIndex(tEntity)
+        val owlid = cas.getAnnotationIndex<AnnotationFS>(tEntity)
             .sortedBy { it.begin }
             .map { it.getFeatureValueAsString(tEntity.getFeatureByBaseName("owlid")) }
             .firstOrNull {
@@ -188,7 +188,7 @@ object Extractor {
 
     private fun getSAPEnumValueForAttributeID(cas: CAS, attributeID: String): String {
         val tEntity = Types.getType(cas, Types.IEENTITY)
-        val owlids = cas.getAnnotationIndex(tEntity)
+        val owlids = cas.getAnnotationIndex<AnnotationFS>(tEntity)
             .sortedBy { it.begin }
             .map { it.getFeatureValueAsString(tEntity.getFeatureByBaseName("owlid")) }
             .filter { it.contains(attributeID) }