[SE-260] use PlasMapperUploader in PlasmidStorageProcessor (instead of creating dummy files)

SVN: 17521

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java

@@ -17,15 +17,18 @@
 package ch.ethz.bsse.cisd.plasmid.dss;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.Properties;
 
 import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
 
+import ch.ethz.bsse.cisd.plasmid.plasmapper.PlasMapperUploader;
+import ch.ethz.bsse.cisd.plasmid.plasmapper.PlasMapperUploader.PlasMapperService;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.common.mail.IMailClient;
 import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
-import ch.systemsx.cisd.etlserver.IStorageProcessor;
 import ch.systemsx.cisd.etlserver.ITypeExtractor;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 
@@ -44,6 +47,12 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
  */
 public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
 {
+    private static final Logger operationLog =
+            LogFactory.getLogger(LogCategory.OPERATION, PlasmidStorageProcessor.class);
+
+    // TODO 2010-08-28, Piotr Buczek: get from properties
+    private final static String PLASMAPPER_PATH = "/Users/buczekp/CISD/cifex/jetty/webapps";
+
     private static final String ORIGINAL_DIR = "original";
 
     private static final String GENERATED_DIR = "generated";
@@ -52,16 +61,13 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
 
     private static final String PNG_FILE_EXTENSION = ".png";
 
+    private PlasMapperUploader uploader = new PlasMapperUploader();
+
     public PlasmidStorageProcessor(Properties properties)
     {
         super(properties);
     }
 
-    public PlasmidStorageProcessor(IStorageProcessor delegatedProcessor)
-    {
-        super(delegatedProcessor);
-    }
-
     @Override
     public File storeData(final DataSetInformation dataSetInformation,
             final ITypeExtractor typeExtractor, final IMailClient mailClient,
@@ -74,7 +80,6 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
                 DataSetTypeOracle.DataSetTypeInfo.SEQ_FILE.name()))
         {
             File originalDir = new File(answer, ORIGINAL_DIR);
-            assert originalDir.isDirectory();
             File[] files = originalDir.listFiles();
             assert files.length == 1;
             File seqFile = files[0];
@@ -86,10 +91,12 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
             File generatedDir = new File(answer, GENERATED_DIR);
             if (generatedDir.mkdir())
             {
-                File pngFile = new File(generatedDir, pngFileName);
-                File gbFile = new File(generatedDir, gbFileName);
-                createEmptyFileHandled(pngFile);
-                createEmptyFileHandled(gbFile);
+                final File pngFileDest = new File(generatedDir, pngFileName);
+                final File gbFileDest = new File(generatedDir, gbFileName);
+
+                operationLog.info("Uploading '" + seqFile.getName() + "' to PlasMapper.");
+                uploadAndMoveGeneratedFile(seqFile, PlasMapperService.GRAPHIC_MAP, pngFileDest);
+                uploadAndMoveGeneratedFile(seqFile, PlasMapperService.GENEBANK_OUTPUT, gbFileDest);
             } else
             {
                 throw new EnvironmentFailureException("Couldn't create directory '" + generatedDir
@@ -99,14 +106,24 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
         return answer;
     }
 
-    private static final void createEmptyFileHandled(File file)
+    private void uploadAndMoveGeneratedFile(final File seqFile, final PlasMapperService service,
+            final File destinationFile)
     {
-        try
+        String outputFilePath = uploader.upload(seqFile, service);
+        File outputFile = new File(PLASMAPPER_PATH + outputFilePath);
+        if (outputFile.isFile())
         {
-            file.createNewFile();
-        } catch (IOException ex)
+            operationLog.info("Moving file '" + outputFile.getName() + "' from '" + outputFile
+                    + "' to " + destinationFile);
+            if (outputFile.renameTo(destinationFile) == false)
+            {
+                throw new EnvironmentFailureException("Couldn't move file '" + outputFile
+                        + "' to '" + destinationFile + "'.");
+            }
+        } else
         {
-            throw new EnvironmentFailureException("Couldn't create file '" + file + "'.", ex);
+            throw new EnvironmentFailureException("'" + outputFile
+                    + "' doesn't exist or is not a file.");
         }
     }
 

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/plasmapper/PlasMapperUploader.java

@@ -39,7 +39,7 @@ import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
 
 /**
- * Uploads provided file to PlasMapper.
+ * Uploads provided sequence file to PlasMapper.
  * 
  * @author Piotr Buczek
  */
@@ -47,7 +47,59 @@ public class PlasMapperUploader
 {
     // http://www.java-tips.org/other-api-tips/httpclient/how-to-use-multipart-post-method-for-uploading.html
 
-    private final static String PLASMAPPER_URL = "http://localhost:8080/PlasMapper";
+    private final static String PLASMAPPER_URL = "http://localhost:8082/PlasMapper";
+
+    private static Properties createDefaultProperties()
+    {
+        Properties result = new Properties();
+        result.setProperty("vendor", "Amersham%20Pharmacia");
+        result.setProperty("showOption", "1,2,3,4,5,6,7,8,9");
+        result.setProperty("restriction", "1");
+        result.setProperty("orfLen", "200");
+        result.setProperty("strand", "1,2");
+        result.setProperty("featureName1", "");
+        result.setProperty("featureName2", "");
+        result.setProperty("featureName3", "");
+        result.setProperty("featureName4", "");
+        result.setProperty("featureName5", "");
+        result.setProperty("featureName6", "");
+        result.setProperty("dir1", "1");
+        result.setProperty("dir2", "1");
+        result.setProperty("dir3", "1");
+        result.setProperty("dir4", "1");
+        result.setProperty("dir5", "1");
+        result.setProperty("dir6", "1");
+        result.setProperty("category1", "origin_of_replication");
+        result.setProperty("category2", "origin_of_replication");
+        result.setProperty("category3", "origin_of_replication");
+        result.setProperty("category4", "origin_of_replication");
+        result.setProperty("category5", "origin_of_replication");
+        result.setProperty("category6", "origin_of_replication");
+        result.setProperty("stop1", "");
+        result.setProperty("stop2", "");
+        result.setProperty("stop3", "");
+        result.setProperty("stop4", "");
+        result.setProperty("stop5", "");
+        result.setProperty("stop6", "");
+        result.setProperty("scheme", "0");
+        result.setProperty("shading", "0");
+        result.setProperty("labColor", "0");
+        result.setProperty("labelBox", "1");
+        result.setProperty("labels", "0");
+        result.setProperty("innerLabels", "0");
+        result.setProperty("legend", "0");
+        result.setProperty("arrow", "0");
+        result.setProperty("tickMark", "0");
+        result.setProperty("mapTitle", "");
+        result.setProperty("comment", "Created using PlasMapper");
+        result.setProperty("imageFormat", "PNG");
+        result.setProperty("imageSize", "900 x 900");
+        result.setProperty("backbone", "medium");
+        result.setProperty("arc", "medium");
+        result.setProperty("biomoby", "true"); // special: result of request == relative path to PNG
+        // file
+        return result;
+    }
 
     public enum PlasMapperService
     {
@@ -80,53 +132,7 @@ public class PlasMapperUploader
 
     public static void main(String[] args)
     {
-        Properties p = new Properties();
-        p.setProperty("vendor", "Amersham%20Pharmacia");
-        p.setProperty("showOption", "1,2,3,4,5,6,7,8,9");
-        p.setProperty("restriction", "1");
-        p.setProperty("orfLen", "200");
-        p.setProperty("strand", "1,2");
-        p.setProperty("featureName1", "");
-        p.setProperty("featureName2", "");
-        p.setProperty("featureName3", "");
-        p.setProperty("featureName4", "");
-        p.setProperty("featureName5", "");
-        p.setProperty("featureName6", "");
-        p.setProperty("dir1", "1");
-        p.setProperty("dir2", "1");
-        p.setProperty("dir3", "1");
-        p.setProperty("dir4", "1");
-        p.setProperty("dir5", "1");
-        p.setProperty("dir6", "1");
-        p.setProperty("category1", "origin_of_replication");
-        p.setProperty("category2", "origin_of_replication");
-        p.setProperty("category3", "origin_of_replication");
-        p.setProperty("category4", "origin_of_replication");
-        p.setProperty("category5", "origin_of_replication");
-        p.setProperty("category6", "origin_of_replication");
-        p.setProperty("stop1", "");
-        p.setProperty("stop2", "");
-        p.setProperty("stop3", "");
-        p.setProperty("stop4", "");
-        p.setProperty("stop5", "");
-        p.setProperty("stop6", "");
-        p.setProperty("scheme", "0");
-        p.setProperty("shading", "0");
-        p.setProperty("labColor", "0");
-        p.setProperty("labelBox", "1");
-        p.setProperty("labels", "0");
-        p.setProperty("innerLabels", "0");
-        p.setProperty("legend", "0");
-        p.setProperty("arrow", "0");
-        p.setProperty("tickMark", "0");
-        p.setProperty("mapTitle", "");
-        p.setProperty("comment", "Created using PlasMapper");
-        p.setProperty("imageFormat", "PNG");
-        p.setProperty("imageSize", "900 x 900");
-        p.setProperty("backbone", "medium");
-        p.setProperty("arc", "medium");
-        p.setProperty("biomoby", "true"); // special: result of request == relative path to PNG file
-
+        Properties p = createDefaultProperties();
         PlasMapperUploader uploader = new PlasMapperUploader(p);
         uploader.upload(new File("PRS316.gb"), PlasMapperService.GRAPHIC_MAP);
     }
@@ -138,23 +144,25 @@ public class PlasMapperUploader
         this.properties = properties;
     }
 
+    public PlasMapperUploader()
+    {
+        this(createDefaultProperties());
+    }
+
     /**
      * Makes an HTTP multipart POST request with given file.
      * 
-     * @param gbFile file to be uploaded
+     * @param seqFile file to be uploaded
      * @param service service to be used for upload
      * @return the server's response to the request depending on the service (path to output image
      *         or sequence in genebank format)
      */
-    public String upload(File gbFile, PlasMapperService service)
+    public String upload(File seqFile, PlasMapperService service)
     {
-        assert gbFile.getName().toLowerCase().endsWith(".gb");
-        assert gbFile.exists();
-
         final PostMethod post = new PostMethod(service.getServiceURL());
         try
         {
-            Part filePart = new FilePart(FILE_PART_NAME, gbFile);
+            Part filePart = new FilePart(FILE_PART_NAME, seqFile);
             Part[] parts = createParts(filePart, properties);
             post.setRequestEntity(new MultipartRequestEntity(parts, post.getParams()));
             HttpClient client = new HttpClient();
@@ -167,8 +175,12 @@ public class PlasMapperUploader
                         + post.getStatusLine()));
             }
             String response = post.getResponseBodyAsString();
-            System.err.println(String.format("Response of service: '%s'", response));
-            operationLog.info(String.format("Response of service: '%s'", response));
+            if (response.endsWith("\n"))
+            {
+                response = response.substring(0, response.lastIndexOf("\n"));
+            }
+            System.err.println(String.format("Response of %s service: '%s'", service, response));
+            operationLog.info(String.format("Response of %s service: '%s'", service, response));
             return response;
         } catch (final Exception ex)
         {