some debug for CI

annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java

@@ -249,7 +249,6 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
    *           thrown when there is a problem with accessing mirna data file
    */
   private InputStream getSourceInputStream() throws IOException {
-    new Exception().printStackTrace();
     if (this.sourceInputStream == null) {
       this.sourceInputStream = new ByteArrayOutputStream();
 
@@ -298,48 +297,50 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
     NPOIFSFileSystem fileInputStream = null;
     try {
       fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
-      logger.debug("debug 1");
       Workbook workbook = WorkbookFactory.create(fileInputStream);
-      logger.debug("debug 2");
       Sheet sheet = workbook.getSheetAt(0);
-      logger.debug("debug 3");
       Iterator<Row> rows = sheet.rowIterator();
       // Skip header
       if (rows.hasNext()) {
         rows.next();
       }
-      logger.debug("debug 4");
       int counter = 0;
       while (rows.hasNext()) {
         logger.debug("next row"+ (counter++));
         Row row = rows.next();
         Cell targetSpeciesCell = row.getCell(SPECIES_COL, Row.RETURN_BLANK_AS_NULL);
         MiriamData organism = null;
+        logger.debug("debug 1");
         if (targetSpeciesCell != null) {
           targetSpeciesCell.setCellType(Cell.CELL_TYPE_STRING);
           String value = targetSpeciesCell.getStringCellValue();
           organism = taxonomyBackend.getByName(value);
         }
 
+        logger.debug("debug 2");
         Cell mirBaseNamecell = row.getCell(MIR_BASE_NAME_COL, Row.RETURN_BLANK_AS_NULL);
         if (mirBaseNamecell == null) {
           continue;
         }
 
+        logger.debug("debug 3");
         mirBaseNamecell.setCellType(Cell.CELL_TYPE_STRING);
         String name = mirBaseNamecell.getStringCellValue();
         if (name == null || name.trim().isEmpty()) {
           continue;
         }
+        logger.debug("debug 4");
         if (miRNAs.get(name) == null) {
           miRNAs.put(name, new MiRNA(name));
         }
 
+        logger.debug("debug 5");
         MiriamData mirTaRBaseId = null;
         Cell mirTaRBaseIdCell = row.getCell(MIR_TAR_BASE_ID_COL, Row.RETURN_BLANK_AS_NULL);
         if (mirTaRBaseIdCell == null) {
           continue;
         } else {
+          logger.debug("debug 6");
           mirTaRBaseIdCell.setCellType(Cell.CELL_TYPE_STRING);
           String value = mirTaRBaseIdCell.getStringCellValue();
           if (value == null || value.trim().isEmpty()) {
@@ -347,17 +348,22 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
           } else {
             mirTaRBaseId = new MiriamData(MiriamType.MIR_TAR_BASE_MATURE_SEQUENCE, value.trim());
           }
+          logger.debug("debug 7");
         }
 
         Cell hgncCell = row.getCell(GENE_HGNC_ID_COL, Row.RETURN_BLANK_AS_NULL);
+        logger.debug("debug 8");
         if (hgncCell != null) {
           hgncCell.setCellType(Cell.CELL_TYPE_STRING);
           String geneName = hgncCell.getStringCellValue();
+          logger.debug("debug 9");
           if (geneName != null && !geneName.trim().isEmpty()) {
             MiriamData gene = null;
             if (TaxonomyBackend.HUMAN_TAXONOMY.equals(organism)) {
+              logger.debug("debug 10");
               gene = new MiriamData(MiriamType.HGNC_SYMBOL, geneName.trim());
             } else {
+              logger.debug("debug 11");
               Cell entrezCell = row.getCell(GENE_ENTREZ_ID_COL, Row.RETURN_BLANK_AS_NULL);
               if (entrezCell != null) {
                 entrezCell.setCellType(Cell.CELL_TYPE_STRING);
@@ -365,9 +371,11 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
                 // in case of non human target set the entrez
                 gene = new MiriamData(MiriamType.ENTREZ, entrezVal.trim());
               }
+              logger.debug("debug 12");
             }
             MiRNA rna = miRNAs.get(name);
             Target target = null;
+            logger.debug("debug 13");
             for (Target t : rna.getTargets()) {
               if (t.getGenes().contains(gene)) {
                 if (organism == null && t.getOrganism() == null) {
@@ -377,6 +385,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
                 }
               }
             }
+            logger.debug("debug 14");
             if (target == null) {
               target = new Target(mirTaRBaseId, gene, new ArrayList<>());
               target.setType(TargetType.SINGLE_PROTEIN);
@@ -384,6 +393,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
               target.setName(geneName);
               rna.addTarget(target);
             }
+            logger.debug("debug 15");
             Cell pubmedCell = row.getCell(INTERACTION_PEDMED_ID_COL, Row.RETURN_BLANK_AS_NULL);
             if (pubmedCell != null) {
               pubmedCell.setCellType(Cell.CELL_TYPE_STRING);
@@ -392,6 +402,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
                 target.addReference(new MiriamData(MiriamType.PUBMED, value));
               }
             }
+            logger.debug("debug 16");
           }
 
         }