added webservice classes and ontology to project

pom.xml

@@ -12,6 +12,16 @@
         <maven.compiler.target>1.8</maven.compiler.target>
         <maven.compiler.source>1.8</maven.compiler.source>
     </properties>
+
+    <repositories>
+        <repository>
+            <id>ifi-central</id>
+            <name>artifactory-releases</name>
+            <url>http://artifactory-ls6.informatik.uni-wuerzburg.de/artifactory/libs-release
+            </url>
+        </repository>
+    </repositories>
+
     <dependencies>
         <dependency>
             <groupId>org.jetbrains.kotlin</groupId>
@@ -23,6 +33,28 @@
             <artifactId>junit</artifactId>
             <version>4.8.2</version>
         </dependency>
+
+        <dependency>
+            <groupId>com.sparkjava</groupId>
+            <artifactId>spark-kotlin</artifactId>
+            <version>1.0.0-alpha</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.8.6</version>
+        </dependency>
+
+        <dependency>
+            <groupId>de.uniwue.aries</groupId>
+            <artifactId>aries-ontology-model-io</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>de.uniwue.aries</groupId>
+            <artifactId>aries-algorithm</artifactId>
+            <version>1.1.13</version>
+        </dependency>
     </dependencies>
     <build>
         <sourceDirectory>src/main/kotlin</sourceDirectory>
@@ -66,6 +98,11 @@
                     <descriptorRefs>
                         <descriptorRef>jar-with-dependencies</descriptorRef>
                     </descriptorRefs>
+                    <archive>
+                        <manifest>
+                            <mainClass>de.dzptm.server.ServerKt</mainClass>
+                        </manifest>
+                    </archive>
                 </configuration>
                 <executions>
                     <execution>

src/main/kotlin/AnordnungReader.kt

@@ -4,6 +4,7 @@ import java.nio.file.Paths
 val inputPathAnordnung = Paths.get("C:\\users\\jok3r\\domains\\anordnungen\\anordnungen.txt")
 val inputPathAuftraege = Paths.get("C:\\users\\jok3r\\domains\\anordnungen\\N1CORDER.txt")
 val outputHTML = Paths.get("C:\\users\\jok3r\\domains\\anordnungen\\anordnung2auftrag.html")
+val outputFolder = "C:\\users\\jok3r\\domains\\anordnungen\\training00\\"
 
 fun main() {
     val anordnungen = readAnordnungen()
@@ -17,31 +18,31 @@ fun main() {
         }
     }.filterNotNull()
     val counter = mutableMapOf<String, Double>()
-    pairs.forEach {
+    pairs.shuffled().subList(0,100).forEach {
         counter.putIfAbsent(it.second["CORDTITLE"]!!, 0.0)
         counter.computeIfPresent(it.second["CORDTITLE"]!!) { _, v -> v + 1}
+        val content = it.first["CONTENT"]
+        Files.writeString(Paths.get(outputFolder + it.first["Dokumentnummer"]!!.trimStart('0')+".txt"), content)
     }
-    counter.keys.forEach {
-        counter[it] = counter.get(it)!! / pairs.size
+    println(pairs.size)
+    counter.forEach { t, u ->
+        println("$t\t$u")
     }
-    println(counter)
+
 }
 
-//fun main() {
-//    val anordnungen = readAnordnungen()
-//    val auftraege = readAuftraege()
-//    val pairs = anordnungen.map {
-//        try {
-//            it to getAuftrag(it, auftraege)
-//        } catch (e: Exception) {
-//            println(e.message)
-//            null
-//        }
-//    }.filterNotNull()
-//    val html = createHTMLPage(pairs.shuffled().subList(0,20))
-//    Files.deleteIfExists(outputHTML)
-//    Files.writeString(outputHTML, html)
-//}
+fun getPairs(): List<Pair<Map<String, String>, Map<String, String>>> {
+    val anordnungen = readAnordnungen()
+    val auftraege = readAuftraege()
+    return anordnungen.map {
+        try {
+            it to getAuftrag(it, auftraege)
+        } catch (e: Exception) {
+            println(e.message)
+            null
+        }
+    }.filterNotNull()
+}
 
 private fun createHTMLPage(pairs: List<Pair<Map<String, String>, Map<String, String>>>): String {
     var html = "<html>\n<body>\n<table>\n"
@@ -87,7 +88,8 @@ private fun getAuftrag(anordnung: Map<String, String>, auftraege: List<Map<Strin
 private fun readAuftraege(): List<Map<String, String>> {
     val lines = Files.readAllLines(inputPathAuftraege)
     val headers = lines[0].split("\t")
-    val whitelist = listOf<String>("PATNR", "CORDTITLE", "KANAM", "FRAGE", "SCHWKZ", "ERDAT", "ERTIM", "ERUSR", "IFG")
+    //val whitelist = listOf<String>("PATNR", "CORDTITLE", "KANAM", "FRAGE", "SCHWKZ", "ERDAT", "ERTIM", "ERUSR", "IFG")
+    val whitelist = null
     return readCSVData(lines, headers, whitelist)
 }
 

src/main/kotlin/ExtractorTest.kt

+import de.uniwue.aries.algorithm.ARIESAlgorithm
+import de.uniwue.aries.ontology.io.ExcelFileReader
+import de.uniwue.aries.uima.types.Types
+import org.apache.uima.util.CasCreationUtils
+
+fun main() {
+    val ontology = ExcelFileReader.read("C:\\users\\jok3r\\domains\\anordnungen\\KlinischerAuftrag20201105.xlsx")
+    val algo = ARIESAlgorithm()
+    val pairs = getPairs()
+    val system = pairs.map { it.first["CONTENT"] }.map {
+        val cas = CasCreationUtils.createCas(Types.getTypeSystem(), null, null)
+        cas.documentText = it
+        algo.extract(cas, ontology)
+        val tEntity = Types.getType(cas, Types.IEENTITY)
+        val owlid = cas.getAnnotationIndex(tEntity)
+                .sortedBy { it.begin }
+                .map { it.getFeatureValueAsString(tEntity.getFeatureByBaseName("owlid")) }
+                .firstOrNull()
+        val result = when (owlid) {
+            "ModalitätCT" -> "Computer-Tomographie"
+            "Modalitätkonv. Röntgen" -> "konv. Röntgen"
+            "ModalitätMR-Tomographie" -> "MR - Tomographie Rö"
+            "ModalitätUltraschall" -> "Ultraschall"
+            null -> "nothingFound"
+            else -> owlid
+        }
+        return@map result
+    }
+    val gold = pairs.map { it.second["CORDTITLE"]}
+    val rights = mutableMapOf<String, Double>()
+    val wrongs = mutableMapOf<String, Double>()
+    for (i in system.indices) {
+        if (system[i] == gold[i]) {
+            rights.computeIfPresent(gold[i]!!) {_, v -> v + 1 }
+            rights.putIfAbsent(gold[i]!!, 1.0)
+        } else {
+            wrongs.computeIfPresent(gold[i]!!) {_, v -> v + 1 }
+            wrongs.putIfAbsent(gold[i]!!, 1.0)
+        }
+    }
+    for (key in wrongs.keys) {
+        println("$key: ${rights.getOrDefault(key, 0.0)}/${rights.getOrDefault(key, 0.0) + wrongs[key]!!} = ${rights.getOrDefault(key, 0.0) / (rights.getOrDefault(key, 0.0) + wrongs[key]!!)}")
+    }
+}
\ No newline at end of file

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

+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.uima.types.Types
+import org.apache.uima.cas.CAS
+import org.apache.uima.util.CasCreationUtils
+import spark.Request
+import spark.Response
+
+object Extractor {
+    fun extract(req: Request, res: Response): String {
+        val temp = req.queryParamOrDefault("input", "no input")
+        val input = Gson().fromJson(temp, Input::class.java)
+
+        val cas = CasCreationUtils.createCas(Types.getTypeSystem(), null, null)
+        cas.documentText = input.doctext
+
+        applyARIES(cas)
+        val modality = getModality(cas)
+
+        //TODO do something meaningful
+        val output = Output(
+                input.docid,
+                input.doctime,
+                modality,
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                "",
+                emptyList<Service>().toMutableList()
+        )
+        return Gson().toJson(output)
+    }
+
+    private fun applyARIES(cas: CAS) {
+        val ontology = ExcelFileReader.read(ClassLoader.getSystemResourceAsStream("KlinischerAuftrag20201105.xlsx"))
+        val algo = ARIESAlgorithm()
+        algo.extract(cas, ontology)
+    }
+
+    private fun getModality(cas: CAS): String {
+        val tEntity = Types.getType(cas, Types.IEENTITY)
+        val owlid = cas.getAnnotationIndex(tEntity)
+                .sortedBy { it.begin }
+                .map { it.getFeatureValueAsString(tEntity.getFeatureByBaseName("owlid")) }
+                .firstOrNull()
+        val result = when (owlid) {
+            "ModalitätCT" -> "Computer-Tomographie"
+            "Modalitätkonv. Röntgen" -> "konv. Röntgen"
+            "ModalitätMR-Tomographie" -> "MR - Tomographie Rö"
+            "ModalitätUltraschall" -> "Ultraschall"
+            null -> "nothingFound"
+            else -> owlid
+        }
+        return result
+    }
+}
+

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

+package de.dzptm.server
+
+data class Input(val docid: String, val doctime: String, val doctext: String)
+
+data class Service(val code: String, val description: String, val number: String, val localisation: String)
+
+data class Output (
+        val docid: String,
+        val doctime: String,
+        val modality: String,
+        val anamnesis: String,
+        val diagnosis: String,
+        val question: String,
+        val notice: String,
+        val pregnancy: String,
+        val pregnancy_week: String,
+        val infection: String,
+        val implantate: String,
+        val pacemaker: String,
+        val allergy: String,
+        val allergy_type_iodine: String,
+        val allergy_type_other: String,
+        val preferred_date: String,
+        val preferred_date_cycle: String,
+        val services: MutableList<Service>
+)
+

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

+package de.dzptm.server
+
+import spark.Spark.get
+import spark.Spark.post
+
+object Routes {
+    fun register(): Unit {
+        get("/extract") { req, res -> Extractor.extract(req, res) }
+    }
+}
\ No newline at end of file

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

+package de.dzptm.server
+
+import spark.kotlin.port
+
+fun main(args: Array<String>) {
+    if (args.isNotEmpty()) {
+        val port = args[0].toIntOrNull()
+        if (port != null) {
+            port(port)
+        }
+    } else {
+        port(8080)
+        println("No valid port given... defaulting to 8080.")
+    }
+    Routes.register()
+
+}
\ No newline at end of file