LMS-1449 Modified CINA Storage processor to send the file marker as an attachment.

SVN: 15161

rtd_cina/.classpath

@@ -15,5 +15,6 @@
 	<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
 	<classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
 	<classpathentry kind="lib" path="/libraries/gwt1.7/gwt-isserializable.jar"/>
+	<classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
 	<classpathentry kind="output" path="targets/classes"/>
 </classpath>

rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java

@@ -21,6 +21,7 @@ import java.util.Properties;
 
 import ch.systemsx.cisd.cina.dss.info.EntityRegistrationSuccessEmail;
 import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.mail.MailClient;
 import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
 import ch.systemsx.cisd.etlserver.IStorageProcessor;
 import ch.systemsx.cisd.etlserver.ITypeExtractor;
@@ -74,8 +75,21 @@ public class StorageProcessor extends AbstractDelegatingStorageProcessor
             emailAddress = defaultEmailAddress;
         }
 
-        mailClient.sendMessage(successEmail.getSubject(), successEmail.getContent(), null, null,
-                emailAddress);
+        // WORKAROUND: The IMailClient interface is used in many places. I added the
+        // sendMessageWithAttachment method to the MailClient class, but I don't want to make a
+        // large, global change to introduce the method into the interface, so I do an instanceof
+        // test here.
+        if (mailClient instanceof MailClient)
+        {
+            ((MailClient) mailClient).sendMessageWithAttachment(successEmail.getSubject(),
+                    successEmail.getContentMimeText(), successEmail
+                            .getContentMimeAttachmentFileName(), successEmail
+                            .getContentMimeAttachmentContent(), null, null, emailAddress);
+        } else
+        {
+            mailClient.sendMessage(successEmail.getSubject(), successEmail.getContentTextOnly(),
+                    null, null, emailAddress);
+        }
 
         return answer;
     }

rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java

@@ -18,6 +18,8 @@ package ch.systemsx.cisd.cina.dss.info;
 
 import java.io.File;
 
+import javax.activation.DataHandler;
+
 import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 
@@ -29,6 +31,8 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
  */
 public class EntityRegistrationSuccessEmail
 {
+    private static final String MARKER_FILE_MIME_TYPE = "application/octet-stream";
+
     private final DataSetInformation dataSetInformation;
 
     private final EntityEmailDetails entityEmailDetails;
@@ -63,11 +67,17 @@ public class EntityRegistrationSuccessEmail
         }
     }
 
+    /**
+     * Return true if the incoming data set requires that an email be sent on registration.
+     */
     public boolean shouldSendEmail()
     {
         return entityEmailDetails.shouldSendEmail();
     }
 
+    /**
+     * Return the subject of the email
+     */
     public String getSubject()
     {
         StringBuffer subject = new StringBuffer();
@@ -79,7 +89,11 @@ public class EntityRegistrationSuccessEmail
         return subject.toString();
     }
 
-    public String getContent()
+    /**
+     * Return the body of the email for a text-only (no attachments) email. Used if the mail client
+     * does no support sending attachments.
+     */
+    public String getContentTextOnly()
     {
         StringBuffer content = new StringBuffer();
         entityEmailDetails.appendEntityName(content);
@@ -95,6 +109,40 @@ public class EntityRegistrationSuccessEmail
         return content.toString();
     }
 
+    /**
+     * Return the body of the email for a MIME email. In a MIME email, the marker file is sent as a
+     * file attachment, not part of the text body of the email.
+     */
+    public String getContentMimeText()
+    {
+        StringBuffer content = new StringBuffer();
+        entityEmailDetails.appendEntityName(content);
+        content.append(" was successfully registered. Use the attached metadata file to register ");
+        entityEmailDetails.appendFollowOnEntityName(content);
+
+        return content.toString();
+    }
+
+    /**
+     * Return the file name of the MIME file attachment.
+     */
+    public String getContentMimeAttachmentFileName()
+    {
+        StringBuffer content = new StringBuffer();
+        entityEmailDetails.appendMetadataFileName(content);
+
+        return content.toString();
+    }
+
+    public DataHandler getContentMimeAttachmentContent()
+    {
+        StringBuffer content = new StringBuffer();
+        entityEmailDetails.appendMetadataFileContent(content);
+        DataHandler attachment = new DataHandler(content.toString(), MARKER_FILE_MIME_TYPE);
+
+        return attachment;
+    }
+
     private abstract class EntityEmailDetails
     {
         boolean shouldSendEmail()

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/MockDefaultStorageProcessor.java

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.cina.dss;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+
+public class MockDefaultStorageProcessor extends AbstractStorageProcessor
+{
+
+    public MockDefaultStorageProcessor(final Properties properties)
+    {
+        super(properties);
+    }
+
+    public StorageFormat getStorageFormat()
+    {
+        System.err.println("getStorageFormat");
+        return StorageFormat.PROPRIETARY;
+    }
+
+    public UnstoreDataAction rollback(File incomingDataSetDirectory, File storedDataDirectory,
+            Throwable exception)
+    {
+        System.err.println("rollback");
+        return null;
+    }
+
+    public File storeData(DataSetInformation dataSetInformation, ITypeExtractor typeExtractor,
+            IMailClient mailClient, File incomingDataSetDirectory, File rootDir)
+    {
+        System.err.println("storeData");
+        return null;
+    }
+
+    public File tryGetProprietaryData(File storedDataDirectory)
+    {
+        System.err.println("tryGetProprietaryData");
+        return null;
+    }
+
+}
\ No newline at end of file

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/StorageProcessorTest.java

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.cina.dss;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Properties;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.cina.dss.info.CinaDataSetInfoExtractor;
+import ch.systemsx.cisd.cina.dss.info.CinaTypeExtractor;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.mail.MailClient;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class StorageProcessorTest extends AbstractFileSystemTestCase
+{
+    Mockery context;
+
+    IEncapsulatedOpenBISService openbisService;
+
+    CinaDataSetInfoExtractor extractor;
+
+    CinaTypeExtractor typeExtractor;
+
+    StorageProcessor storageProcessor;
+
+    IMailClient mailClient;
+
+    File rootDir;
+
+    File emailDir;
+
+    private void initializeDSSInfrastructure()
+    {
+        context = new Mockery();
+        openbisService = context.mock(IEncapsulatedOpenBISService.class);
+        extractor = new CinaDataSetInfoExtractor(new Properties());
+        typeExtractor = new CinaTypeExtractor(new Properties());
+        rootDir = new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/");
+    }
+
+    private void initializeMailClient()
+    {
+        String emailFolderPath = workingDirectory.getPath() + "/emails";
+        mailClient = new MailClient("sender", "file://" + emailFolderPath);
+        emailDir = new File(emailFolderPath);
+    }
+
+    private void initializeStorageProcessor()
+    {
+        final Properties props = new Properties();
+        props.setProperty("data-store-server-code", "DSS1");
+        // Don't use this
+        // props.setProperty("data-folder", "targets/playground/data") ;
+        props.setProperty("storeroot-dir", "store");
+        // workingDirectory
+        props.setProperty("mail.smtp.host", emailDir.getPath());
+        props.setProperty("mail.from", "datastore_server@localhost");
+        props.setProperty("processor", "ch.systemsx.cisd.cina.dss.MockDefaultStorageProcessor");
+        storageProcessor = new StorageProcessor(props);
+    }
+
+    @Override
+    @BeforeMethod
+    public void setUp() throws IOException
+    {
+        // Override setUp and call super first to make sure the working directory has been created
+        super.setUp();
+
+        // create openbis, extractor, other necessary infrastructure
+        initializeDSSInfrastructure();
+
+        initializeMailClient();
+
+        initializeStorageProcessor();
+    }
+
+    @AfterMethod
+    public void afterMethod()
+    {
+        // To following line of code should also be called at the end of each test method.
+        // Otherwise one do not known which test failed.
+        context.assertIsSatisfied();
+    }
+
+    @Test
+    public void testRegisterExperiment()
+    {
+        // set up the expectations
+        context.checking(new Expectations()
+            {
+                {
+                    one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
+                    will(returnValue(null));
+                    one(openbisService).registerExperiment(with(any(NewExperiment.class)));
+                }
+            });
+
+        // "store" the data set
+        doStoreData(new File(
+                "sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder"));
+
+        // Check the email
+        assert emailDir.exists();
+        assert emailDir.isDirectory();
+        File[] files = emailDir.listFiles();
+        assertEquals(1, files.length);
+        assertEquals("email", files[0].getName());
+        String fileContent = FileUtilities.loadToString(files[0]);
+
+        // Split the file into lines and check one line at a time
+        String[] lines = fileContent.split("\n+");
+        assertEquals(lines.length, 13);
+        assertTrue(lines[0] + " should start with "
+                + "Subj: [CINA] Registered Experiment /CINA/CINA1/EXP-", lines[0]
+                .startsWith("Subj: [CINA] Registered Experiment /CINA/CINA1/EXP-"));
+        assertEquals(lines[1], "From: sender");
+        assertEquals(lines[2], "To:   no-one@nowhere.ch");
+        assertEquals(lines[3], "Reply-To: sender");
+        assertEquals(lines[4], "Content:");
+        assertTrue(lines[5].startsWith("------=_Part_0"));
+        assertEquals(lines[6],
+                "Experiment was successfully registered. Use the attached metadata file to register Samples");
+
+        assertTrue(lines[7].startsWith("------=_Part_0"));
+        assertEquals(lines[8], "Content-Disposition: attachment; filename=sample.properties");
+        assertTrue(lines[9].startsWith("experiment.identifier=/CINA/CINA1/EXP-"));
+        assertEquals(lines[10], "experiment.owner-email=no-one@nowhere.ch");
+        assertEquals(lines[11], "sample.code-prefix=S");
+        assertTrue(lines[12].startsWith("------=_Part_0"));
+    }
+
+    private void doStoreData(File datasetFolder)
+    {
+        DataSetInformation dataSetInformation =
+                extractor.getDataSetInformation(datasetFolder, openbisService);
+
+        storageProcessor.storeData(dataSetInformation, typeExtractor, mailClient, datasetFolder,
+                rootDir);
+    }
+}