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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/04/08 23:33:32 UTC
svn commit: r1585839 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Author: tmill
Date: Tue Apr 8 21:33:32 2014
New Revision: 1585839
URL: http://svn.apache.org/r1585839
Log:
CTAKES-82: Fixed a recnetly checked in error that broke anafora reading code in temporal.
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1585839&r1=1585838&r2=1585839&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Tue Apr 8 21:33:32 2014
@@ -203,76 +203,74 @@ public abstract class Evaluation_ImplBas
private List<File> getFilesFor(List<Integer> patientSets) {
List<File> files = new ArrayList<File>();
if (this.rawTextDirectory == null
- && this.xmlFormat == XMLFormat.Anafora) {
- for (File dir : this.xmlDirectory.listFiles()) {
- Set<String> ids = new HashSet<String>();
- for (Integer set : patientSets) {
- ids.add(String.format("ID%03d", set));
- }
- if (dir.isDirectory()) {
- if (ids.contains(dir.getName().substring(0, 5))) {
- File file = new File(dir, dir.getName());
- if (file.exists()) {
- files.add(file);
- } else {
- LOGGER.warn("Missing note: " + file);
- }
- } else {
- LOGGER.info("Skipping note: " + dir);
- }
- }
- }
- } else if(this.xmlFormat == XMLFormat.Knowtator) {
- for (Integer set : patientSets) {
- final int setNum = set;
- for (File file : rawTextDirectory.listFiles(new FilenameFilter(){
- @Override
- public boolean accept(File dir, String name) {
- return name.contains(String.format("ID%03d", setNum));
- }})) {
- // skip hidden files like .svn
- if (!file.isHidden()) {
- if(xmlFormat == XMLFormat.Knowtator){
- files.add(file);
- }else{
- // look for equivalent in xml directory:
- File xmlFile = new File(xmlDirectory, file.getName());
- if(xmlFile.exists()){
- files.add(file);
- }else{
- System.err.println("Missing patient file : " + xmlFile);
- }
- }
- }
+ && this.xmlFormat == XMLFormat.Anafora) {
+ for (File dir : this.xmlDirectory.listFiles()) {
+ Set<String> ids = new HashSet<String>();
+ for (Integer set : patientSets) {
+ ids.add(String.format("ID%03d", set));
+ }
+ if (dir.isDirectory()) {
+ if (ids.contains(dir.getName().substring(0, 5))) {
+ File file = new File(dir, dir.getName());
+ if (file.exists()) {
+ files.add(file);
+ } else {
+ LOGGER.warn("Missing note: " + file);
+ }
+ } else {
+ LOGGER.info("Skipping note: " + dir);
+ }
+ }
}
- }
- } else if(this.xmlFormat == XMLFormat.I2B2) {
- File trainDir = new File(this.xmlDirectory, "training");
- File testDir = new File(this.xmlDirectory, "test");
- for (Integer pt : patientSets){
- File xmlTrain = new File(trainDir, pt+".xml");
- File train = new File(trainDir, pt+".xml.txt");
- if(train.exists()){
- if(xmlTrain.exists()){
- files.add(train);
- }else{
- System.err.println("Text file in training has no corresponding xml -- skipping: " + train);
- }
- }
- File xmlText = new File(testDir, pt+".xml");
- File test = new File(testDir, pt+".xml.txt");
- if(test.exists()){
- if(xmlText.exists()){
- files.add(test);
- }else{
- System.err.println("Text file in test has no corresponding xml -- skipping: " + test);
- }
- }
- assert !(train.exists() && test.exists());
- }
- } else{
- throw new UnsupportedOperationException("Did not supply a valid xml format type.");
- }
+ } else if(this.xmlFormat == XMLFormat.I2B2) {
+ File trainDir = new File(this.xmlDirectory, "training");
+ File testDir = new File(this.xmlDirectory, "test");
+ for (Integer pt : patientSets){
+ File xmlTrain = new File(trainDir, pt+".xml");
+ File train = new File(trainDir, pt+".xml.txt");
+ if(train.exists()){
+ if(xmlTrain.exists()){
+ files.add(train);
+ }else{
+ System.err.println("Text file in training has no corresponding xml -- skipping: " + train);
+ }
+ }
+ File xmlText = new File(testDir, pt+".xml");
+ File test = new File(testDir, pt+".xml.txt");
+ if(test.exists()){
+ if(xmlText.exists()){
+ files.add(test);
+ }else{
+ System.err.println("Text file in test has no corresponding xml -- skipping: " + test);
+ }
+ }
+ assert !(train.exists() && test.exists());
+ }
+ } else {
+ for (Integer set : patientSets) {
+ final int setNum = set;
+ for (File file : rawTextDirectory.listFiles(new FilenameFilter(){
+ @Override
+ public boolean accept(File dir, String name) {
+ return name.contains(String.format("ID%03d", setNum));
+ }})) {
+ // skip hidden files like .svn
+ if (!file.isHidden()) {
+ if(xmlFormat == XMLFormat.Knowtator){
+ files.add(file);
+ }else{
+ // look for equivalent in xml directory:
+ File xmlFile = new File(xmlDirectory, file.getName());
+ if(xmlFile.exists()){
+ files.add(file);
+ }else{
+ System.err.println("Missing patient file : " + xmlFile);
+ }
+ }
+ }
+ }
+ }
+ }
return files;
}