Added some file management improvements

skfit-uni-luebeck · May 8, 2022 · 3d85e5f · 3d85e5f
1 parent 35ed8f2
commit 3d85e5f
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Showing 10 changed files with 5 additions and 613 deletions.
diff --git a/.gradle/7.3.3/executionHistory/executionHistory.bin b/.gradle/7.3.3/executionHistory/executionHistory.bin
diff --git a/.gradle/7.3.3/executionHistory/executionHistory.lock b/.gradle/7.3.3/executionHistory/executionHistory.lock
diff --git a/.gradle/7.3.3/fileHashes/fileHashes.bin b/.gradle/7.3.3/fileHashes/fileHashes.bin
diff --git a/.gradle/7.3.3/fileHashes/fileHashes.lock b/.gradle/7.3.3/fileHashes/fileHashes.lock
diff --git a/.gradle/buildOutputCleanup/buildOutputCleanup.lock b/.gradle/buildOutputCleanup/buildOutputCleanup.lock
diff --git a/.gradle/file-system.probe b/.gradle/file-system.probe
diff --git a/build/classes/groovy/main/map/rxnorm/mapping_atc.json b/build/classes/groovy/main/map/rxnorm/mapping_atc.json
diff --git a/src/main/groovy/org/example/syntheakds/Main.groovy b/src/main/groovy/org/example/syntheakds/Main.groovy
@@ -1,5 +1,6 @@
 package org.example.syntheakds
 
+import org.apache.commons.io.FileUtils
 import org.apache.logging.log4j.LogManager
 import org.apache.logging.log4j.Logger
 import org.apache.logging.log4j.core.LoggerContext
@@ -44,6 +45,8 @@ class Main {
         def timeSpan = end - start
         logger.info("[#]Finished conversion in ${Math.floor(timeSpan/60) as int}m ${timeSpan%60}s.")
 
+        //Delete all files generated by Synthea
+        FileUtils.cleanDirectory(SyntheaKDSConfig.patDirPath.toFile())
     }
 
     private static GeneratorOptions configureGeneratorOptions(){

diff --git a/src/main/groovy/org/example/syntheakds/config/SyntheaKDSConfig.groovy b/src/main/groovy/org/example/syntheakds/config/SyntheaKDSConfig.groovy
@@ -9,8 +9,8 @@ import java.nio.file.Paths
 class SyntheaKDSConfig {
 
     //Preset values
-    static final Path mapDirPath = Utils.getJarDir().resolve("map")
     static final Path basePath = Paths.get("").toAbsolutePath()
+    static final Path mapDirPath = basePath.resolve(Paths.get("output", "mappings"))
     static final Path outputDirPath = basePath.resolve(Paths.get("output", System.currentTimeMillis().toString()))
     static final Path tmpDirPath = outputDirPath.resolve('tmp_output')
     static final Path patDirPath = tmpDirPath.resolve('fhir')

diff --git a/src/main/groovy/org/example/syntheakds/processing/ProcessingTask.groovy b/src/main/groovy/org/example/syntheakds/processing/ProcessingTask.groovy
@@ -2,6 +2,7 @@ package org.example.syntheakds.processing
 
 import ca.uhn.fhir.parser.IParser
 import com.fasterxml.jackson.databind.ObjectMapper
+import org.apache.commons.io.FileUtils
 import org.example.syntheakds.config.SyntheaKDSConfig
 import org.example.syntheakds.utils.Utils