From 9a75effced8e3db0354483498187d502059576ff Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Thu, 19 Aug 2010 16:08:06 +0000
Subject: [PATCH] [SE-260] new configuration properties for PlasMapper
SVN: 17539
---
plasmid/etc/service.properties | 5 ++-
.../plasmid/dss/PlasmidStorageProcessor.java | 33 +++++++++++++++----
.../plasmapper/PlasMapperUploader.java | 22 +++++++------
3 files changed, 42 insertions(+), 18 deletions(-)
diff --git a/plasmid/etc/service.properties b/plasmid/etc/service.properties
index d7a42287c5c..7abaf91824e 100644
--- a/plasmid/etc/service.properties
+++ b/plasmid/etc/service.properties
@@ -112,9 +112,12 @@ main-thread.type-extractor.default-file-type = PROPRIETARY
main-thread.type-extractor.directory-file-type = DIRECTORY
# The storage processor (IStorageProcessor implementation)
-#main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
main-thread.storage-processor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidStorageProcessor
main-thread.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+# path to the root directory of the server where PlasMapper is deployed (webapps in jetty)
+main-thread.storage-processor.plasmapper-root-dir = /Users/buczekp/CISD/cifex/jetty/webapps
+# the base URL of PlasMapper web application
+main-thread.storage-processor.plasmapper-base-url = http://localhost:8082/PlasMapper
# The dataset handler (IDataSetHandler implementation)
main-thread.dataset-handler = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetHandler
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 e7a54a4bf61..1fa593d0346 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
@@ -28,6 +28,7 @@ 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.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -50,8 +51,9 @@ 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 final static String PLASMAPPER_BASE_URL_KEY = "plasmapper-base-url";
+
+ private final static String PLASMAPPER_ROOT_DIR_KEY = "plasmapper-root-dir";
private static final String ORIGINAL_DIR = "original";
@@ -61,11 +63,28 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
private static final String PNG_FILE_EXTENSION = ".png";
- private PlasMapperUploader uploader = new PlasMapperUploader();
+ private final PlasMapperUploader uploader;
+
+ private final String serverRootDir;
public PlasmidStorageProcessor(Properties properties)
{
super(properties);
+ final String baseUrl =
+ PropertyUtils.getMandatoryProperty(properties, PLASMAPPER_BASE_URL_KEY);
+ this.uploader = new PlasMapperUploader(baseUrl);
+ this.serverRootDir =
+ PropertyUtils.getMandatoryProperty(properties, PLASMAPPER_ROOT_DIR_KEY);
+
+ final File serverRootFile = new File(serverRootDir);
+ if ((serverRootFile.isDirectory() && serverRootFile.canRead()) == false)
+ {
+ final String msg =
+ String.format("'%s' (value of '%s' property) is supposed to be a path "
+ + "to an existing readable directory but isn't.", serverRootDir,
+ PLASMAPPER_ROOT_DIR_KEY);
+ throw new EnvironmentFailureException(msg);
+ }
}
@Override
@@ -110,14 +129,14 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
final File destinationFile)
{
String outputFilePath = uploader.upload(seqFile, service);
- File outputFile = new File(PLASMAPPER_PATH + outputFilePath);
+ File outputFile = new File(serverRootDir + outputFilePath);
if (outputFile.isFile())
{
- operationLog.info("Moving file '" + outputFile.getName() + "' from '" + outputFile
- + "' to " + destinationFile);
+ operationLog.info("Renaming and moving file '" + outputFile.getName() + "' from '"
+ + outputFile + "' to " + destinationFile);
if (outputFile.renameTo(destinationFile) == false)
{
- throw new EnvironmentFailureException("Couldn't move file '" + outputFile
+ throw new EnvironmentFailureException("Couldn't rename file '" + outputFile
+ "' to '" + destinationFile + "'.");
}
} else
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 c56d9327548..40cc2b471a2 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
@@ -45,9 +45,8 @@ import ch.systemsx.cisd.common.logging.LogFactory;
*/
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:8082/PlasMapper";
+ private final static String DEFAULT_PLASMAPPER_URL = "http://localhost:8082/PlasMapper";
private static Properties createDefaultProperties()
{
@@ -113,9 +112,9 @@ public class PlasMapperUploader
this.servletPath = servletPath;
}
- String getServiceURL()
+ String getServletPath()
{
- return PLASMAPPER_URL + servletPath;
+ return servletPath;
}
}
@@ -133,20 +132,23 @@ public class PlasMapperUploader
public static void main(String[] args)
{
Properties p = createDefaultProperties();
- PlasMapperUploader uploader = new PlasMapperUploader(p);
+ PlasMapperUploader uploader = new PlasMapperUploader(DEFAULT_PLASMAPPER_URL, p);
uploader.upload(new File("PRS316.gb"), PlasMapperService.GRAPHIC_MAP);
}
- private Properties properties;
+ private final String baseUrl;
- public PlasMapperUploader(Properties properties)
+ private final Properties properties;
+
+ public PlasMapperUploader(String baseUrl, Properties properties)
{
+ this.baseUrl = baseUrl;
this.properties = properties;
}
- public PlasMapperUploader()
+ public PlasMapperUploader(String baseUrl)
{
- this(createDefaultProperties());
+ this(baseUrl, createDefaultProperties());
}
/**
@@ -159,7 +161,7 @@ public class PlasMapperUploader
*/
public String upload(File seqFile, PlasMapperService service)
{
- final PostMethod post = new PostMethod(service.getServiceURL());
+ final PostMethod post = new PostMethod(baseUrl + service.getServletPath());
try
{
Part filePart = new FilePart(FILE_PART_NAME, seqFile);
--
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