Merge branch 'mi-rna-cache-problem' into 'master'

Mi rna cache problem

See merge request piotr.gawron/minerva!263

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

@@ -32,7 +32,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.cache.BigFileEntry;
 import lcsb.mapviewer.model.user.ConfigurationElementType;
@@ -227,8 +226,9 @@ public class BigFileCache {
    * @return new {@link BigFileEntry} for given url
    * @throws URISyntaxException
    *           thrown when url is invalid
+   * @throws IOException
    */
-  private BigFileEntry createEntryForBigFile(String url) throws URISyntaxException {
+  private BigFileEntry createEntryForBigFile(String url) throws URISyntaxException, IOException {
     String localPath = configurationDao.getValueByType(ConfigurationElementType.BIG_FILE_STORAGE_DIR);
     BigFileEntry entry = new BigFileEntry();
     entry.setDownloadDate(Calendar.getInstance());
@@ -237,7 +237,12 @@ public class BigFileCache {
     bigFileEntryDao.add(entry);
 
     localPath = entry.getLocalPath() + "/" + entry.getId() + "/";
-    new File(Configuration.getWebAppDir() + localPath).mkdirs();
+    File dirFile = new File(Configuration.getWebAppDir() + localPath);
+
+    if (!dirFile.mkdirs()) {
+      throw new IOException("Cannot create directory: " + dirFile.getAbsolutePath());
+    }
+
     localPath += getFileName(url);
 
     entry.setLocalPath(localPath);
@@ -461,6 +466,9 @@ public class BigFileCache {
         output.close();
 
         return null;
+      } catch (Exception e) {
+        logger.error(e, e);
+        throw e;
       } finally {
         bigFileEntryDao.commit();
         // close the transaction for this thread
@@ -838,7 +846,6 @@ public class BigFileCache {
       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);
         return false;
       }
     }

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

@@ -133,7 +133,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
    */
   @Autowired
   private BigFileCache bigFileCache;
-  
+
   @Autowired
   private ProjectDao projectDao;
 
@@ -187,7 +187,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
           }
           List<String> list = getSuggestedQueryListWithoutCache(project);
           result = StringUtils.join(list, "\n");
-        } else  {
+        } else {
           result = super.refreshCacheQuery(query);
         }
       } else {
@@ -229,6 +229,9 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
     if (!idsToFind.isEmpty()) {
       // logger.debug("MiRNAParser.getMiRNA Start:"+new Date());
       List<MiRNA> fromDBList = this.getMiRnasByNameFromDb(idsToFind);
+      for (MiRNA mirna : fromDBList) {
+        super.setCacheValue(MI_RNA_PREFIX + mirna.getName().toLowerCase(), miRnaSerializer.objectToString(mirna));
+      }
       // logger.debug("MiRNAParser.getMiRNA End:"+new Date());
       // Add them to result
       miRNAs.addAll(fromDBList);

annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java

@@ -32,6 +32,7 @@ import org.mockito.stubbing.Answer;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -140,6 +141,23 @@ public class BigFileCacheTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testSavingToInvalidDirectory() throws Exception {
+    try {
+      String url = httpUrl + "?invalid";
+      Configuration.setWebAppDir("/");
+      bigFileCache.downloadFile(url, false, null);
+      fail("Exception expected");
+    } catch (IOException e) {
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    } finally {
+      Configuration.setWebAppDir("./");
+    }
+  }
+
   private void waitForDownload() throws InterruptedException {
     while (bigFileCache.getDownloadThreadCount() > 0) {
       logger.debug("Waiting for download to finish");
@@ -457,9 +475,6 @@ public class BigFileCacheTest extends AnnotationTestFunctions {
   public void testRemoveFileThatDoesntExist() throws Exception {
     try {
       bigFileCache.removeFile("unexisting file");
-      fail("Exception expected");
-    } catch (InvalidArgumentException e) {
-      assertTrue(e.getMessage().contains("Cannot remove file. File wasn't downloaded"));
     } catch (Exception e) {
       e.printStackTrace();
       throw e;

web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java

@@ -6,6 +6,8 @@ import javax.annotation.PostConstruct;
 import javax.faces.bean.ApplicationScoped;
 import javax.faces.bean.ManagedBean;
 import javax.faces.bean.ManagedProperty;
+import javax.faces.context.FacesContext;
+import javax.servlet.ServletContext;
 
 import org.apache.log4j.Logger;
 
@@ -64,6 +66,10 @@ public class StartupBean {
   @PostConstruct
   public void init() {
     logger.debug("Application startup script starts");
+    ServletContext servletContext = (ServletContext) FacesContext.getCurrentInstance().getExternalContext()
+        .getContext();
+    Configuration.setWebAppDir(servletContext.getRealPath(".") + "/../");
+
     setInterruptedProjectsStatuses();
     modifyXFrameDomain();
     removeInterruptedReferenceGenomeDownloads();