error handling/reporting improved

annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java

@@ -811,6 +811,14 @@ public class BigFileCache {
 	 */
 	public boolean isCached(String sourceUrl) {
 		BigFileEntry entry = bigFileEntryDao.getByUrl(sourceUrl);
+		if (entry != null) {
+			File f = new File(Configuration.getWebAppDir() + entry.getLocalPath());
+			if (!f.exists()) {
+				logger.warn("File is supposed to be cached but it's not there... " + sourceUrl);
+				bigFileEntryDao.delete(entry);
+				entry = null;
+			}
+		}
 		return entry != null;
 	}
 

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

@@ -572,7 +572,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
 
 			int id = page.indexOf("<th>DrugBank ID</th>");
 			if (id < 0) {
-				throw new InvalidArgumentException("Problematic web page");
+				throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
 			}
 
 			int i = page.indexOf("/polypeptides/");

service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java

@@ -320,7 +320,7 @@ public class ChemicalService implements IChemicalService {
 						chemicalViewFactory.create(chemical);
 					}
 				} catch (ChemicalSearchException e) {
-					logger.error("Problem with accessing info about chemical for target", e);
+					logger.error("Problem with accessing info about chemical for target: " + md, e);
 				}
 				counter += 1;
 				progress = counter / (double) targetMiriams.size();

service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java

@@ -399,7 +399,7 @@ public class DrugService implements IDrugService {
 						drugViewFactory.create(chemical);
 					}
 				} catch (DrugSearchException e) {
-					logger.error("Problem with accessing info about drugbank for target", e);
+					logger.error("Problem with accessing info about drugbank for target: " + md, e);
 				}
 				try {
 					List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md);
@@ -407,7 +407,7 @@ public class DrugService implements IDrugService {
 						drugViewFactory.create(chemical);
 					}
 				} catch (DrugSearchException e) {
-					logger.error("Problem with accessing info about chembl for target", e);
+					logger.error("Problem with accessing info about chembl for target: " + md, e);
 				}
 				counter += 1;
 				progress = counter / (double) targetMiriams.size();

service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java

@@ -240,7 +240,7 @@ public class MiRNAService implements IMiRNAService {
 						miRNAViewFactory.create(chemical);
 					}
 				} catch (MiRNASearchException e) {
-					logger.error("Problem with accessing info about mirna for target", e);
+					logger.error("Problem with accessing info about mirna for target: " + md, e);
 				}
 				progress = counter / (double) targetMiriams.size();
 				iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);