diff --git a/pom.xml b/pom.xml
index c1b59250ad93973b94e9d4fe95fdad97e06d72f2..61e3cf17d776320b60ace816baf0fa79f21e25a2 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/kotlin/AnordnungReader.kt b/src/main/kotlin/AnordnungReader.kt
index d41f5ab6670247d7b32285bf56fadecdf2c5c11c..3f7fc84a27b225a135ac0ebae89dd1ff23e1fd1a 100644
--- a/src/main/kotlin/AnordnungReader.kt
+++ b/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)
}
diff --git a/src/main/kotlin/ExtractorTest.kt b/src/main/kotlin/ExtractorTest.kt
new file mode 100644
index 0000000000000000000000000000000000000000..dbca726aa9d018ab53ae4cbef97d353ba69f3df3
--- /dev/null
+++ b/src/main/kotlin/ExtractorTest.kt
@@ -0,0 +1,44 @@
+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
diff --git a/src/main/kotlin/de/dzptm/server/Extractor.kt b/src/main/kotlin/de/dzptm/server/Extractor.kt
new file mode 100644
index 0000000000000000000000000000000000000000..a35f9ce08dd11f499b3c71e2a3c90212ec62d8af
--- /dev/null
+++ b/src/main/kotlin/de/dzptm/server/Extractor.kt
@@ -0,0 +1,70 @@
+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
+ }
+}
+
diff --git a/src/main/kotlin/de/dzptm/server/IO.kt b/src/main/kotlin/de/dzptm/server/IO.kt
new file mode 100644
index 0000000000000000000000000000000000000000..e6f6b37363fbe38b5ac86474fffc9720ccd03c00
--- /dev/null
+++ b/src/main/kotlin/de/dzptm/server/IO.kt
@@ -0,0 +1,27 @@
+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>
+)
+
diff --git a/src/main/kotlin/de/dzptm/server/Routes.kt b/src/main/kotlin/de/dzptm/server/Routes.kt
new file mode 100644
index 0000000000000000000000000000000000000000..41fb60a9cafe8492731ac354097ff61dc873eb87
--- /dev/null
+++ b/src/main/kotlin/de/dzptm/server/Routes.kt
@@ -0,0 +1,10 @@
+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
diff --git a/src/main/kotlin/de/dzptm/server/Server.kt b/src/main/kotlin/de/dzptm/server/Server.kt
new file mode 100644
index 0000000000000000000000000000000000000000..ab822c820c2cfb28c5a101d10a423e6ac5418390
--- /dev/null
+++ b/src/main/kotlin/de/dzptm/server/Server.kt
@@ -0,0 +1,17 @@
+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
diff --git a/src/main/resources/KlinischerAuftrag20201105.xlsx b/src/main/resources/KlinischerAuftrag20201105.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..738026567d78d41ad75de1ab415030e790dede9d
Binary files /dev/null and b/src/main/resources/KlinischerAuftrag20201105.xlsx differ