[LMS-1879] minor: renaming; introduced incoming-dir-create to simplify...

[LMS-1879] minor: renaming; introduced incoming-dir-create to simplify development/testing of datastore

SVN: 18947

datastore_server/dist/etc/service.properties

@@ -169,7 +169,7 @@ main-thread.incoming-data-completeness-condition = marker-file
 
 # Path to the script that will be executed after successful data set registration. 
 # The script will be called with two parameters: <data-set-code> and <absolute-data-set-path> (in the data store).
-# main-thread.postregistration-script = /example/scripts/my-script.sh
+# main-thread.post-registration-script = /example/scripts/my-script.sh
 
 # ---------------------------------------------------------------------------
 # maintenance plugins configuration

datastore_server/etc/service.properties

@@ -110,7 +110,7 @@ demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.D
 # The property file. Its content will be passed as a parameter to the plugin.
 demo-reporter.properties-file = 
 
-tsv-viewer.label = TSV View 	
+tsv-viewer.label = TSV View 
 tsv-viewer.dataset-types = TSV
 tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
 tsv-viewer.properties-file =
@@ -177,6 +177,10 @@ validator.site.value-range = [0,Infinity)
 # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
 inputs=main-thread, tsv-thread, csv-thread, simple-thread, hdf5-thread, dss-system-test-thread
 
+# True if incoming directories should be created on server startup if they don't exist. 
+# Default - false (server will fail at startup if one of incoming directories doesn't exist). 
+incoming-dir-create = true
+
 # ---------------------------------------------------------------------------
 # Dataset uploader 'main-thread' configuration
 # ---------------------------------------------------------------------------
@@ -228,7 +232,7 @@ main-thread.storage-processor.file-extractor = ch.systemsx.cisd.etlserver.imsb.H
 
 # Path to the script that will be executed after successful data set registration. 
 # The script will be called with two parameters: <data-set-code> and <absolute-data-set-path> (in the data store).
-# main-thread.postregistration-script = /example/scripts/my-script.sh
+# main-thread.post-registration-script = /example/scripts/my-script.sh
 
 # The directory to watch for incoming data.
 tsv-thread.incoming-dir = ${root-dir}/incoming-tsv

datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java

@@ -45,7 +45,7 @@ public final class ThreadParameters
      * in the data store.
      */
     @Private
-    static final String POSTREFGISTRATION_SCRIPT_KEY = "postregistration-script";
+    static final String POST_REGISTRATION_SCRIPT_KEY = "post-registration-script";
 
     @Private
     static final String GROUP_CODE_KEY = "group-code";
@@ -65,6 +65,8 @@ public final class ThreadParameters
 
     private static final String INCOMING_DIR = "incoming-dir";
 
+    private static final String INCOMING_DIR_CREATE = "incoming-dir-create";
+
     private static final String DELETE_UNIDENTIFIED_KEY = "delete-unidentified";
 
     private static final String REPROCESS_FAULTY_DATASETS_NAME = "reprocess-faulty-datasets";
@@ -75,6 +77,8 @@ public final class ThreadParameters
      */
     private final File incomingDataDirectory;
 
+    private final boolean createIncomingDirectories;
+
     private final IETLServerPlugin plugin;
 
     private final String threadName;
@@ -96,6 +100,8 @@ public final class ThreadParameters
     public ThreadParameters(final Properties threadProperties, final String threadName)
     {
         this.incomingDataDirectory = extractIncomingDataDir(threadProperties);
+        this.createIncomingDirectories =
+                PropertyUtils.getBoolean(threadProperties, INCOMING_DIR_CREATE, false);
         this.plugin = new PropertiesBasedETLServerPlugin(threadProperties);
         this.groupCode = tryGetGroupCode(threadProperties);
         this.postRegistrationScript = tryGetPostRegistartionScript(threadProperties);
@@ -136,6 +142,11 @@ public final class ThreadParameters
 
     final void check()
     {
+        if (createIncomingDirectories && incomingDataDirectory.exists() == false)
+        {
+            incomingDataDirectory.mkdir();
+            operationLog.info("Created incoming directory '" + incomingDataDirectory + "'.");
+        }
         if (incomingDataDirectory.isDirectory() == false)
         {
             throw new ConfigurationFailureException("Incoming directory '" + incomingDataDirectory
@@ -165,7 +176,7 @@ public final class ThreadParameters
     @Private
     static final String tryGetPostRegistartionScript(final Properties properties)
     {
-        return nullIfEmpty(PropertyUtils.getProperty(properties, POSTREFGISTRATION_SCRIPT_KEY));
+        return nullIfEmpty(PropertyUtils.getProperty(properties, POST_REGISTRATION_SCRIPT_KEY));
     }
 
     private static String nullIfEmpty(String value)
@@ -223,6 +234,10 @@ public final class ThreadParameters
                             : "no write access for some period";
             logLine("Condition of incoming data completeness: %s.", completenessCond);
             logLine("Delete unidentified: '%s'.", deleteUnidentified);
+            if (postRegistrationScript != null)
+            {
+                logLine("Post registration script: '%s'.", postRegistrationScript);
+            }
         }
     }
 

datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java

@@ -40,7 +40,7 @@ import ch.systemsx.cisd.common.mail.IMailClient;
 import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
 import ch.systemsx.cisd.common.utilities.ISelfTestable;
 import ch.systemsx.cisd.etlserver.IStorageProcessor.UnstoreDataAction;
-import ch.systemsx.cisd.etlserver.utils.PostregistrationExecutor;
+import ch.systemsx.cisd.etlserver.utils.PostRegistrationExecutor;
 import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -150,7 +150,7 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
         this.fileOperations = FileOperations.getMonitoredInstanceForCurrentThread();
         this.useIsFinishedMarkerFile = useIsFinishedMarkerFile;
         this.deleteUnidentified = deleteUnidentified;
-        this.postRegistrationAction = PostregistrationExecutor.create(postRegistrationScriptOrNull);
+        this.postRegistrationAction = PostRegistrationExecutor.create(postRegistrationScriptOrNull);
     }
 
     /**

datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostregistrationExecutor.java → datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java

@@ -39,14 +39,14 @@ import ch.systemsx.cisd.etlserver.IPostRegistrationAction;
  * 
  * @author Izabela Adamczyk
  */
-public class PostregistrationExecutor implements IPostRegistrationAction
+public class PostRegistrationExecutor implements IPostRegistrationAction
 {
 
     private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
-            PostregistrationExecutor.class);
+            PostRegistrationExecutor.class);
 
     private final static Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE,
-            PostregistrationExecutor.class);
+            PostRegistrationExecutor.class);
 
     static class EmptyScriptExecutor implements IPostRegistrationAction
     {
@@ -61,7 +61,7 @@ public class PostregistrationExecutor implements IPostRegistrationAction
     {
         if (scriptPath != null)
         {
-            return new PostregistrationExecutor(scriptPath);
+            return new PostRegistrationExecutor(scriptPath);
         } else
         {
             operationLog.debug("No postregistration script found, skipping execution.");
@@ -71,7 +71,7 @@ public class PostregistrationExecutor implements IPostRegistrationAction
 
     private final String scriptPath;
 
-    private PostregistrationExecutor(String script)
+    private PostRegistrationExecutor(String script)
     {
         this.scriptPath = script;
         File file = new File(script);

screening/etc/service.properties

@@ -161,6 +161,10 @@ data-set-clean-up.data-source = imaging-db
 
 incoming-root-dir = ${root-dir}
 
+# True if incoming directories should be created on server startup if they don't exist. 
+# Default - false (server will fail at startup if one of incoming directories doesn't exist). 
+incoming-dir-create = true
+
 # Globally used separator character which separates entities in a data set file name 
 data-set-file-name-entity-separator = _
 
@@ -224,7 +228,6 @@ merged-channels-images.storage-processor.data-source = imaging-db
 merged-channels-images.storage-processor.extract-single-image-channels = GREEN, BLUE
 
 # ---------------------------------------------------------------------------
-
 # The directory to watch for incoming data.
 split-channels-images.incoming-dir = ${incoming-root-dir}/incoming-images-split-channels
 split-channels-images.incoming-data-completeness-condition = auto-detection