Minor updates > Version 3.2

pom.xml

@@ -247,5 +247,5 @@
 	</dependencies>
 
 
-	<version>3.1</version>
+	<version>3.2</version>
 </project>

rtdoc/LocalExecution.md

@@ -6,9 +6,9 @@
 Comorbidity4j has to be executed by Java 1.8 or newer. As a consequence, as a prerequisite for the execution of Comorbidity4j you need to have <a href="https://www.java.com/en/download/" target="_blank">Java</a> installed.  
 
 ## Download the JAR package 
-The compressed archive (comorbidity4j-3.1-bin.zip) that contains the latest version (LATEST_VERS = 3.1) of comorbidity4j can be downloaded at the following URL:  
+The compressed archive (comorbidity4j-3.2-bin.zip) that contains the latest version (LATEST_VERS = 3.2) of comorbidity4j can be downloaded at the following URL:  
 
-<a href="https://github.com/fra82/comorbidity4j/releases/tag/3.1" target="_blank">https://github.com/fra82/comorbidity4j/releases/tag/3.1</a>    
+<a href="https://github.com/fra82/comorbidity4j/releases/tag/3.2" target="_blank">https://github.com/fra82/comorbidity4j/releases/tag/3.2</a>    
 
 
 ## Comorbidity4j Execution  

rtdoc/index.md

@@ -1,7 +1,7 @@
 ![Comorbidity4j](/img/logo.png)
 <h3>Open-source Java tool to analyze comorbidities over large datasets of patients</h3>
 
-**Latest version: 3.1**
+**Latest version: 3.2**
 
 Comorbidity4j is an Open-source java tool tailored to easily perform <a href="https://en.wikipedia.org/wiki/Comorbidity" target="_blank">comorbidity analyses</a>, thus **supporting the analysis of significant cooccurrences of diseases over large datasets of patient data**.  
 

src/main/java/es/imim/ibi/comorbidity4j/loader/DescriptionDataLoader.java

@@ -90,15 +90,15 @@ public DataLoadContainer<Map<String, String>> loadDataFromReader(Reader inputRea
 
 		if(!is_first_column_header) {
 			try {
-				description_index = Integer.valueOf(code.toLowerCase().replace("col_", ""));
+				description_index = Integer.valueOf(description.toLowerCase().replace("col_", ""));
 			} catch (Exception e) {
 				e.printStackTrace();
 				errorString.append(GenericUtils.newLine + "ERROR: while identifying the index of the Patient ID column - EXCEPTION: " + e.getMessage());
 				logger.error(" > EXCEPTION: " + e.getMessage());
 			}
 
 			try {
-				code_index = Integer.valueOf(description.toLowerCase().replace("col_", ""));
+				code_index = Integer.valueOf(code.toLowerCase().replace("col_", ""));
 			} catch (Exception e) {
 				e.printStackTrace();
 				errorString.append(GenericUtils.newLine + "ERROR: while identifying the index of the Visit ID column - EXCEPTION: " + e.getMessage());

src/main/java/es/imim/ibi/comorbidity4j/loader/DiagnosisDataLoader.java

@@ -165,9 +165,13 @@ else if(nextLine[i].trim().toLowerCase().equals(diagnosis_code.toLowerCase())) {
 						String diagnosis_code_value = nextLine[diagnosis_code_index].trim();
 
 						if(!Strings.isNullOrEmpty(patient_id_value) && !Strings.isNullOrEmpty(admission_id_value) && !Strings.isNullOrEmpty(diagnosis_code_value)) {
-
+
+							System.out.println("Checking patient_id_value: '" + patient_id_value + "' and admission_id_value: '" + admission_id_value + "'");
+
 							if(strPatVisitToVisitMap.containsKey(patient_id_value + "_" + admission_id_value)) {
 
+								// System.out.println("       > FOUND patient_id_value: '" + patient_id_value + "' and admission_id_value: '" + admission_id_value + "'");
+
 								// If the diagnosis code belongs to a diagnosis group, substitute the diagnosis code string to the diagnosis group string
 								/*
 								, Map<String, String> diagnosisCodeStringGroupsMap
@@ -185,7 +189,7 @@ else if(nextLine[i].trim().toLowerCase().equals(diagnosis_code.toLowerCase())) {
 										diagnosisCodeCount++;
 										diagnosisCodeIdStringMap.put(diagnosis_code_value, diagnosisCodeCount);
 									}
-
+									
 									visitToEnrichWithDiagnosis.getDiagnosisCodeSet().add(diagnosisCodeIdStringMap.get(diagnosis_code_value));
 
 									addedDiagnosisSet.add(patient_id_value + "_" + admission_id_value + "_" + diagnosis_code_value);
@@ -200,6 +204,9 @@ else if(nextLine[i].trim().toLowerCase().equals(diagnosis_code.toLowerCase())) {
 								}
 							}
 							else {
+
+								System.out.println("       > !!! NOT FOUND patient_id_value: '" + patient_id_value + "' and admission_id_value: '" + admission_id_value + "'");
+
 								skippedLineCount++;
 								unexistingPatientOrVisitID++;
 								if(skippedLineCount <= 500) {

src/main/java/es/imim/ibi/comorbidity4j/server/reservlet/ComputeComorbidityServlet.java

@@ -48,6 +48,7 @@
 import org.slf4j.LoggerFactory;
 
 import com.google.common.base.Strings;
+import com.google.common.io.Files;
 
 import es.imim.ibi.comorbidity4j.analysis.ComorbidityMiner;
 import es.imim.ibi.comorbidity4j.analysis.ComorbidityMinerCache;
@@ -77,7 +78,7 @@ public class ComputeComorbidityServlet extends HttpServlet {
 
 	private static Random rnd = new Random();
 
-	public static String basePathResultStorage = "/home/ronzano/comorbidity4web/results/"; // Files.createTempDir().getAbsolutePath(); 
+	public static String basePathResultStorage = Files.createTempDir().getAbsolutePath();  // "/home/ronzano/comorbidity4web/results/"
 
 	private static DecimalFormat decimFormatThreeDec = new DecimalFormat("#######0.000");