diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java
index cf0574cf0d52c9112668f8f0776dec5999adb4db..aeb2f70497b751525bcb65cd33ca8989c25daeba 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java
@@ -31,35 +31,11 @@ import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+
public class ConfigReader
{
- private static final String DATA_SOURCE_URL_PROPERTY_NAME = "resource-list-url";
-
- private static final String DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME = "data-source-openbis-url";
-
- private static final String DATA_SOURCE_DSS_URL_PROPERTY_NAME = "data-source-dss-url";
-
- private static final String DATA_SOURCE_SPACES_PROPERTY_NAME = "data-source-spaces";
-
- private static final String DATA_SOURCE_PREFIX_PROPERTY_NAME = "data-souce-prefix";
-
- private static final String DATA_SOURCE_AUTH_REALM_PROPERTY_NAME = "data-source-auth-realm";
-
- private static final String DATA_SOURCE_AUTH_USER_PROPERTY_NAME = "data-source-auth-user";
-
- private static final String DATA_SOURCE_AUTH_PASS_PROPERTY_NAME = "data-source-auth-pass";
-
- private static final String HARVESTER_SPACES_PROPERTY_NAME = "harvester-spaces";
-
- private static final String HARVESTER_TEMP_DIR_PROPERTY_NAME = "harvester-tmp-dir";
-
- private static final String DEFAULT_LAST_SYNC_TIMESTAMP_FILE = "last-sync-timestamp-file.txt";
-
- private static final String HARVESTER_LAST_SYNC_TIMESTAMP_FILE = "last-sync-timestamp-file";
-
-
-
private Pattern sectionRegex = Pattern.compile("\\s*\\[([^]]*)\\]\\s*");
private Pattern keyValueRegex = Pattern.compile("\\s*([^=]*)=(.*)");
@@ -87,21 +63,6 @@ public class ConfigReader
System.out.println(reader.getSection(i));
}
- SyncConfig config = new SyncConfig();
- String section1 = reader.getSection(0);
-
- config.setDataSourceURI(reader.getString(section1, DATA_SOURCE_URL_PROPERTY_NAME, null));
- config.setDataSourceOpenbisURL(reader.getString(section1, DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME, null));
- config.setDataSourceDSSURL(reader.getString(section1, DATA_SOURCE_DSS_URL_PROPERTY_NAME, null));
- config.setRealm(reader.getString(section1, DATA_SOURCE_AUTH_REALM_PROPERTY_NAME, null));
- config.setUser(reader.getString(section1,DATA_SOURCE_AUTH_USER_PROPERTY_NAME, null));
- config.setPass(reader.getString(section1, DATA_SOURCE_AUTH_PASS_PROPERTY_NAME, null));
- config.setDataSourceSpaces(reader.getString(section1, DATA_SOURCE_SPACES_PROPERTY_NAME, null));
- config.setHarvesterSpaces(reader.getString(section1, DATA_SOURCE_PREFIX_PROPERTY_NAME, null));
- config.setHarvesterTempDir(reader.getString(section1, HARVESTER_TEMP_DIR_PROPERTY_NAME, "targets/store"));
- config.setLastSyncTimestampFileName(reader.getString(section1, HARVESTER_LAST_SYNC_TIMESTAMP_FILE, DEFAULT_LAST_SYNC_TIMESTAMP_FILE));
-
- config.printConfig();
} catch (IOException e)
{
// TODO Auto-generated catch block
@@ -170,33 +131,60 @@ public class ConfigReader
loadFile(new File(path));
}
- public String getString(String section, String key, String defaultvalue)
+ public String getString(String section, String key, String defaultvalue, boolean mandatory)
{
- Map<String, String> map = entries.get(section);
- if (map == null)
+ String val = getValue(section, key);
+ if (val == null)
{
+ if (mandatory)
+ {
+ throw new ConfigurationFailureException("Property '" + key + "' in section '" + section + "' is mandatory.");
+ }
return defaultvalue;
}
- return map.get(key);
+ return val;
}
- public int getInt(String section, String key, int defaultvalue)
+ private String getValue(String section, String key) throws ConfigurationFailureException
{
Map<String, String> map = entries.get(section);
if (map == null)
{
+ throw new ConfigurationFailureException("Section '" + section + " does not exist.");
+ }
+ String val = map.get(key).trim();
+ if (val.equals("") == true)
+ {
+ return null;
+ }
+ return val;
+ }
+
+ public int getInt(String section, String key, int defaultvalue, boolean mandatory)
+ {
+ String val = getValue(section, key);
+ if (val == null)
+ {
+ if (mandatory)
+ {
+ throw new ConfigurationFailureException("Property '" + key + "' in section '" + section + "' is mandatory.");
+ }
return defaultvalue;
}
- return Integer.parseInt(map.get(key));
+ return Integer.parseInt(val);
}
- public double getDouble(String section, String key, double defaultvalue)
+ public double getDouble(String section, String key, double defaultvalue, boolean mandatory)
{
- Map<String, String> map = entries.get(section);
- if (map == null)
+ String val = getValue(section, key);
+ if (val == null)
{
+ if (mandatory)
+ {
+ throw new ConfigurationFailureException("Property '" + key + "' in section '" + section + "' is mandatory.");
+ }
return defaultvalue;
}
- return Double.parseDouble(map.get(key));
+ return Double.parseDouble(val);
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
index 7578bddea3ead96dff4c5f847da0c646eb9622eb..1ad30eda3d650865a0e0c72a8e044f629dd50a12 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
@@ -176,6 +176,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
{
protected static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, DataSetRegistrationTask.class);
+
// private static final String DATA_SOURCE_URI = "https://bs-mbpr121.d.ethz.ch:8444/datastore_server/re-sync"; //
// "http://localhost:8889/datastore_server/re-sync";
@@ -205,10 +206,12 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
private static final String DEFAULT_LAST_SYNC_TIMESTAMP_FILE = "last-sync-timestamp-file.txt";
+ private static final String DEFAULT_LOG_FILE_NAME = "../../syncronization.log";
+
private static final String HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME = "last-sync-timestamp-file";
private static final String EMAIL_ADDRESSES_PROPERTY_NAME = "email-addresses";
-
+
private static final String DEFAULT_DATA_SOURCE_SECTION = "DataSource1";
private static final String HARVESTER_CONFIG_FILE_NAME = "harvester-config-file";
@@ -239,8 +242,6 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
private IMailClient mailClient;
- private Set<EMailAddress> emailAddresses;
-
private void initializePluginProperties()
{
config = new SyncConfig();
@@ -264,7 +265,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// file.mkdirs();
//
// System.exit(0);
-
+
Properties properties = new Properties();
properties.put(PluginTaskInfoProvider.STOREROOT_DIR_KEY, "targets/store");
@@ -312,9 +313,10 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
private List<String> extractSpaces(String spaces)
{
StringTokenizer st = new StringTokenizer(spaces, SEPARATOR);
-
- List<String> harvesterSpaceList = new ArrayList<String>();
- while(st.hasMoreElements()) {
+
+ List<String> harvesterSpaceList = new ArrayList<String>();
+ while (st.hasMoreElements())
+ {
harvesterSpaceList.add(st.nextToken().trim());
}
return harvesterSpaceList;
@@ -348,7 +350,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
if (statusCode != HttpStatus.Code.OK.getCode())
{
- throw new IOException ("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
+ throw new IOException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
}
byte[] content = contentResponse.getContent();
@@ -379,7 +381,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
Properties props = setProperties();
- DataSetRegistrationIngestionService ingestionService = new DataSetRegistrationIngestionService(props, storeRoot, dataSetCodes, dataSet.getDataSet());
+ DataSetRegistrationIngestionService ingestionService =
+ new DataSetRegistrationIngestionService(props, storeRoot, dataSetCodes, dataSet.getDataSet());
ingestionService.createAggregationReport(new HashMap<String, Object>(), context);
System.out.println("finished " + dataSet.getDataSet().getCode());
dataSetCodes.add(dataSet.getDataSet().getCode());
@@ -456,7 +459,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
List<NewProperty> dataSetProperties = dataSet.getDataSetProperties();
- if (dataSetForUpdate == null) {
+ if (dataSetForUpdate == null)
+ {
// REGISTER NEW DATA SET
IDataSet ds = transaction.createNewDataSet(dataSet.getDataSetType().getCode(), dataSet.getCode());
dataSetCodes.add(ds.getDataSetCode());
@@ -467,22 +471,23 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
{
ds.setPropertyValue(newProperty.getPropertyCode(), newProperty.getValue());
}
-
+
File storeRoot = transaction.getGlobalState().getStoreRootDir();
File temp = new File(storeRoot, this.harvesterTempDir);
temp.mkdirs();
File file = new File(temp, ds.getDataSetCode());
file.mkdirs();
-
+
downloadDataSetFiles(file, ds.getDataSetCode());
-
+
File dsPath = new File(file, "original");
for (File f : dsPath.listFiles())
{
transaction.moveFile(f.getAbsolutePath(), ds);
}
}
- else {
+ else
+ {
// UPDATE data set meta data excluding the container/contained relationships
dataSetForUpdate.setSample(sample);
dataSetForUpdate.setExperiment(experiment);
@@ -600,11 +605,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
{
operationLog.info(this.getClass() + " started.");
- readConfiguration();
-
- if(config.getLogFilePath() != null) {
- configureFileAppender();
- }
+ initConfiguration();
createDataSourceToHarvesterSpaceMappings();
@@ -632,10 +633,10 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// save the current time into a temp file as last sync time
FileUtilities.writeToFile(newLastSyncTimeStampFile, formater.format(new Date()));
- //retrieve the document from the data source
+ // retrieve the document from the data source
operationLog.info("Retrieving the resource list..");
Document doc = getResourceListAsXMLDoc();
-
+
// Parse the resource list: This sends back all projects,
// experiments, samples and data sets contained in the XML together with their last modification date to be used for filtering
operationLog.info("parsing the resource list xml document");
@@ -650,9 +651,9 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
Map<String, MaterialWithLastModificationDate> materialsToProcess = data.materialsToProcess;
AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
-
+
processProjects(projectsToProcess, experimentsToProcess, builder);
-
+
processExperiments(experimentsToProcess, samplesToProcess, dataSetsToProcess, builder);
processSamples(samplesToProcess, builder);
@@ -681,7 +682,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
builder.user(DataSetRegistrationTask.this.config.getUser());
Map<String, NewExternalData> datasetsToUpdate = new HashMap<String, NewExternalData>();
-
+
// set parent and container data set codes before everything else
// container and physical data sets can both be parents/children of each other
Map<String, Set<String>> dsToParents = new HashMap<String, Set<String>>();
@@ -717,14 +718,15 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
if (dsWithConn.getLastModificationDate().after(lastSyncTimestamp))
{
if (physicalDSMap.containsKey(dataSet.getCode()) == false && service.tryGetDataSet(dataSet.getCode()) == null)
- {
+ {
builder.dataSet(dataSet);
}
- else {
-
+ else
+ {
+
datasetsToUpdate.put(dataSet.getCode(), dataSet);
- }
}
+ }
}
// go thru to-be-updated DS list and establish/break relations
@@ -734,7 +736,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
if (dataSet instanceof NewContainerDataSet)
{
NewContainerDataSet containerDS = (NewContainerDataSet) dataSet;
- if(dsToContained.containsKey(containerDS.getCode())) {
+ if (dsToContained.containsKey(containerDS.getCode()))
+ {
dsBatchUpdatesDTO.setModifiedContainedDatasetCodesOrNull(dsToContained.get(dataSet.getCode()).toArray(new
String[containerDS.getContainedDataSetCodes().size()]));
}
@@ -799,17 +802,18 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
} catch (Exception e)
{
operationLog.error("Sync failed: " + e.getMessage());
-
+
sendInfoEmail();
}
}
private void sendInfoEmail()
{
- if(config.getLogFilePath() != null) {
- //send the operation log as attachment
- DataSource dataSource = createDataSource("/Users/gakin/Documents/sync.log");
- for (EMailAddress recipient : emailAddresses)
+ if (config.getLogFilePath() != null)
+ {
+ // send the operation log as attachment
+ DataSource dataSource = createDataSource(config.getLogFilePath()); // /Users/gakin/Documents/sync.log
+ for (EMailAddress recipient : config.getEmailAddresses())
{
mailClient.sendEmailMessageWithAttachment("Synchronization failed",
"Hi, the syncronization failed. See the attached file for details.",
@@ -817,13 +821,14 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
dataSource), null, null, recipient);
}
}
- else {
- for (EMailAddress recipient : emailAddresses)
+ else
+ {
+ for (EMailAddress recipient : config.getEmailAddresses())
{
mailClient.sendEmailMessage("Synchronization failed",
"Hi, the syncronization failed. See the data store server log for details.", null, null, recipient);
}
- }
+ }
}
private DataSource createDataSource(final String filePath)
@@ -836,53 +841,44 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
- private void readConfiguration() throws IOException
+
+ private void initConfiguration() throws IOException
{
ConfigReader reader = new ConfigReader(harvesterConfigFile);
-
+
config = new SyncConfig();
- if (reader.sectionExists(DEFAULT_DATA_SOURCE_SECTION) == false) {
+ if (reader.sectionExists(DEFAULT_DATA_SOURCE_SECTION) == false)
+ {
throw new ConfigurationFailureException("Please specify at least one data source section.");
}
- // TODO check that all required parameters are set in the config file
- config.setDataSourceURI(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_URL_PROPERTY_NAME, null));
- config.setDataSourceOpenbisURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME, null));
- config.setDataSourceDSSURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_DSS_URL_PROPERTY_NAME, null));
- config.setRealm(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_REALM_PROPERTY_NAME, null));
- config.setUser(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_USER_PROPERTY_NAME, null));
- config.setPass(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_PASS_PROPERTY_NAME, null));
- config.setDataSourceSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_SPACES_PROPERTY_NAME, null));
- config.setHarvesterSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_SPACES_PROPERTY_NAME, null));
- config.setDataSourcePrefix(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_PREFIX_PROPERTY_NAME, null));
- config.setHarvesterTempDir(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_TEMP_DIR_PROPERTY_NAME, "targets/store"));
- config.setEmailAddresses(reader.getString(DEFAULT_DATA_SOURCE_SECTION, EMAIL_ADDRESSES_PROPERTY_NAME, null));
- config.setLastSyncTimestampFileName(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME,
- DEFAULT_LAST_SYNC_TIMESTAMP_FILE));
- config.setLogFilePath(reader.getString(DEFAULT_DATA_SOURCE_SECTION, LOG_FILE_PROPERTY_NAME, null));
+ config.setEmailAddresses(reader.getString(DEFAULT_DATA_SOURCE_SECTION, EMAIL_ADDRESSES_PROPERTY_NAME, null, true));
+ config.setLogFilePath(reader.getString(DEFAULT_DATA_SOURCE_SECTION, LOG_FILE_PROPERTY_NAME, DEFAULT_LOG_FILE_NAME, false));
+ if (config.getLogFilePath() != null)
+ {
+ configureFileAppender();
+ }
+ config.setDataSourceURI(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_URL_PROPERTY_NAME, null, true));
+ config.setDataSourceOpenbisURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME, null, true));
+ config.setDataSourceDSSURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_DSS_URL_PROPERTY_NAME, null, true));
+ config.setRealm(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_REALM_PROPERTY_NAME, null, true));
+ config.setUser(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_USER_PROPERTY_NAME, null, true));
+ config.setPass(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_PASS_PROPERTY_NAME, null, true));
+ config.setDataSourceSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_SPACES_PROPERTY_NAME, null, true));
+ config.setHarvesterSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_SPACES_PROPERTY_NAME, null, true));
+ config.setDataSourcePrefix(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_PREFIX_PROPERTY_NAME, null, false));
+ config.setHarvesterTempDir(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_TEMP_DIR_PROPERTY_NAME, "targets/store", false));
+ config.setLastSyncTimestampFileName(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME,
+ DEFAULT_LAST_SYNC_TIMESTAMP_FILE, false));
String fileName = config.getLastSyncTimestampFileName();
lastSyncTimestampFile = new File(fileName);
newLastSyncTimeStampFile = new File(fileName + ".new");
- emailAddresses = getEMailAddresses();
-
config.printConfig();
}
- private Set<EMailAddress> getEMailAddresses()
- {
- String[] tokens =
- config.getEmailAddresses().split(SEPARATOR);
- Set<EMailAddress> addresses = new HashSet<EMailAddress>();
- for (String token : tokens)
- {
- addresses.add(new EMailAddress(token.trim()));
- }
- return addresses;
- }
-
private void processDeletions(ResourceListParserData data)
{
String sessionToken = ServiceProvider.getOpenBISService().getSessionToken();
@@ -941,14 +937,15 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
}
List<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material> materials = entityRetriever.fetchMaterials();
-
- for(ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material material: materials) {
+
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material material : materials)
+ {
if (incomingMaterialCodes.contains(material.getCode()) == false)
{
matPermIds.add(new MaterialPermId(material.getCode(), material.getType().getCode()));
}
}
-
+
IApplicationServerApi v3Api = ServiceProvider.getV3ApplicationService();
// delete data sets
@@ -1013,7 +1010,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
for (MaterialWithLastModificationDate newMaterialWithType : materialsToProcess.values())
{
NewMaterialWithType newIncomingMaterial = newMaterialWithType.getMaterial();
- if (newMaterialWithType.getLastModificationDate().after(lastSyncTimestamp)) {
+ if (newMaterialWithType.getLastModificationDate().after(lastSyncTimestamp))
+ {
Material material = service.tryGetMaterial(new MaterialIdentifier(newIncomingMaterial.getCode(), newIncomingMaterial.getType()));
if (material == null)
{
@@ -1038,7 +1036,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
for (SampleWithConnections sample : samplesToProcess.values())
{
NewSample incomingSample = sample.getSample();
- if (sample.getLastModificationDate().after(lastSyncTimestamp)) {
+ if (sample.getLastModificationDate().after(lastSyncTimestamp))
+ {
SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(incomingSample);
Sample sampleWithExperiment = null;
try
@@ -1061,19 +1060,19 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
List<Sample> childSamples = getChildSamples(sampleWithExperiment);
for (Sample child : childSamples)
{
- String childSampleIdentifier = child.getIdentifier();//edgeNodePair.getNode().getIdentifier();
- SampleWithConnections childSampleWithConns = findChildInSamplesToProcess(childSampleIdentifier, samplesToProcess);
- if (childSampleWithConns == null)
- {
- // TODO Handle sample delete
- }
- else
- {
- // the childSample will appear in the incoming samples list anyway
- // but we want to make sure its parent modification is handled
- NewSample childSample = childSampleWithConns.getSample();
- sampleWithUpdatedParents.add(childSample.getIdentifier());
- }
+ String childSampleIdentifier = child.getIdentifier();// edgeNodePair.getNode().getIdentifier();
+ SampleWithConnections childSampleWithConns = findChildInSamplesToProcess(childSampleIdentifier, samplesToProcess);
+ if (childSampleWithConns == null)
+ {
+ // TODO Handle sample delete
+ }
+ else
+ {
+ // the childSample will appear in the incoming samples list anyway
+ // but we want to make sure its parent modification is handled
+ NewSample childSample = childSampleWithConns.getSample();
+ sampleWithUpdatedParents.add(childSample.getIdentifier());
+ }
}
}
}
@@ -1108,7 +1107,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// }
}
}
-
+
// create sample update dtos for the samples that need to be updated
for (SampleIdentifier sampleIdentifier : samplesToUpdate.keySet())
{
@@ -1151,7 +1150,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
for (ExperimentWithConnections exp : experimentsToProcess.values())
{
NewExperiment newIncomingExp = exp.getExperiment();
- if (exp.getLastModificationDate().after(lastSyncTimestamp)) {
+ if (exp.getLastModificationDate().after(lastSyncTimestamp))
+ {
Experiment experiment = null;
try
{
@@ -1167,7 +1167,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// ADD EXPERIMENT
builder.experiment(newIncomingExp);
}
- else {
+ else
+ {
// UPDATE EXPERIMENT
ExperimentUpdatesDTO expUpdate = new ExperimentUpdatesDTO();
expUpdate.setProjectIdentifier(ExperimentIdentifierFactory.parse(newIncomingExp.getIdentifier()));
@@ -1231,16 +1232,16 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
ProjectIdentifier projectIdentifier = ProjectIdentifierFactory.parse(incomingProject.getIdentifier());
prjUpdate.setSpaceCode(projectIdentifier.getSpaceCode());
builder.projectUpdate(prjUpdate); // ConversionUtils.convertToProjectUpdateDTO(new
- // ch.systemsx.cisd.etlserver.registrator.api.v2.impl.Project(project))
+ // ch.systemsx.cisd.etlserver.registrator.api.v2.impl.Project(project))
}
}
for (Connection conn : prj.getConnections())
{
String connectedExpPermId = conn.getToPermId();
// TODO we need to do the same check for samples to support project samples
- if (experimentsToProcess.containsKey(connectedExpPermId))
+ if (experimentsToProcess.containsKey(connectedExpPermId))
{
- //the project is connected to an experiment
+ // the project is connected to an experiment
ExperimentWithConnections exp = experimentsToProcess.get(connectedExpPermId);
NewExperiment newExp = exp.getExperiment();
// check if our local graph has the same connection
@@ -1255,19 +1256,19 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// add new experiment node
}// TODO can the following happen. i.e. a project experiment connection is always of type Connection so we should be safe to
// remove the following?
- // else
- // {
- // if (harvesterEntityGraph.edgeExists(incomingProject.getIdentifier(), newExp.getIdentifier(), conn.getType()) == false)
- // {
- // // add new edge
- // // String fullExpIdentifier = newExp.getIdentifier().replace("{1}", incomingProject.getIdentifier());
- // // newExp.setIdentifier(fullExpIdentifier);
- // }
- // else
- // {
- // // do nothing
- // }
- // }
+ // else
+ // {
+ // if (harvesterEntityGraph.edgeExists(incomingProject.getIdentifier(), newExp.getIdentifier(), conn.getType()) == false)
+ // {
+ // // add new edge
+ // // String fullExpIdentifier = newExp.getIdentifier().replace("{1}", incomingProject.getIdentifier());
+ // // newExp.setIdentifier(fullExpIdentifier);
+ // }
+ // else
+ // {
+ // // do nothing
+ // }
+ // }
}
else
{
@@ -1295,7 +1296,8 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
{
for (SampleWithConnections sample : samplesToProcess.values())
{
- if(sample.getSample().getIdentifier().equals(childSampleIdentifier)) {
+ if (sample.getSample().getIdentifier().equals(childSampleIdentifier))
+ {
return sample;
}
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java
index 43e9abc236840d5beb54548b992e489f906323cf..773b221ecffaea119c0eed22ac1f86795cd07119 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java
@@ -17,6 +17,10 @@
package ch.ethz.sis.openbis.generic.server.dss.plugins;
import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.common.mail.EMailAddress;
/**
*
@@ -180,10 +184,12 @@ class SyncConfig
private String harvesterTempDir;
- private String emailAddresses;
+ private List<EMailAddress> emailAddresses = new ArrayList<>();
private String logFilePath;
+ private static final String SEPARATOR = ",";;
+
public String getLogFilePath()
{
return logFilePath;
@@ -194,13 +200,18 @@ class SyncConfig
this.logFilePath = logFilePath;
}
- public String getEmailAddresses()
+ public List<EMailAddress> getEmailAddresses()
{
return emailAddresses;
}
public void setEmailAddresses(String emailAddresses)
{
- this.emailAddresses = emailAddresses;
+ String[] tokens =
+ emailAddresses.split(SEPARATOR);
+ for (String token : tokens)
+ {
+ this.emailAddresses.add(new EMailAddress(token.trim()));
+ }
}
}