diff --git a/datastore_server/dist/etc/service.properties b/datastore_server/dist/etc/service.properties
index f8291b1fa726f89e255374774ac4176b01adf2ed..1779870c710ea1136719859e9ba2148aebc152c8 100644
--- a/datastore_server/dist/etc/service.properties
+++ b/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
diff --git a/datastore_server/etc/service.properties b/datastore_server/etc/service.properties
index 4bfb06a5b38209ad4b151fc1692d638d574fb933..992c0d91c1683203ac456f45ec7b38a9fe0279d5 100644
--- a/datastore_server/etc/service.properties
+++ b/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
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
index 5d03ab456ea176d31eadd78ff742e7d808613563..3bd642b2567eadc1ed9bec45e3733b30990b3c9f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
+++ b/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);
+ }
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index 2826b9fc3a16d9a708c5ebcd249fe7de1e86ee38..e5cb3faf0fe734f8779d9e74ffc1ef7885652481 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/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);
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostregistrationExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java
similarity index 93%
rename from datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostregistrationExecutor.java
rename to datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java
index 330943d00023d6eb29b5565e92668c3a025eb7b8..3724d44339a6dce686c30b2c5260bb46b7386ffb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostregistrationExecutor.java
+++ b/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);
diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 83e9cc6ed3157cecf0f00b99b0a82fe80fc16d89..8b203d9b54269a85731a624b11c04caadbe4db21 100644
--- a/screening/etc/service.properties
+++ b/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