diff --git a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java b/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java
index 5920fd8b8e7a823674bf2fcfd6d7d5173691d296..e7a54a4bf615d69fa3482ad5dde2141880931426 100644
--- a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java
+++ b/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.");
}
}
diff --git a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/plasmapper/PlasMapperUploader.java b/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/plasmapper/PlasMapperUploader.java
index d346439819e2ff04eab3edde07f156353a592fe4..c56d93275485bcd8ef3b90827f6fd337fa128bea 100644
--- a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/plasmapper/PlasMapperUploader.java
+++ b/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)
{