diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index 889496388a1ba60b3a46d043fa10d26d87dcbf71..ba4b9765f89ba7a99ae78e30ab029ce49e4eaa7a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
@@ -44,7 +44,6 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
* <pre>
* column1 column2 column2
* </pre>
- *
* <li>Comment section:
*
* <pre>
@@ -53,7 +52,6 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
* # ...
* column1 column2 column2
* </pre>
- *
* <li>Column headers at the end of the comment section:
*
* <pre>
@@ -71,7 +69,7 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
public class TabFileLoader<T>
{
- private static final String PREFIX = "#";
+ public static final String COMMENT_PREFIX = "#";
private final IParserObjectFactoryFactory<T> factory;
@@ -129,10 +127,10 @@ public class TabFileLoader<T>
while (lineIterator.hasNext())
{
previousLineHasColumnHeaders =
- (previousLine != null) && PREFIX.equals(previousLine.getText());
+ (previousLine != null) && COMMENT_PREFIX.equals(previousLine.getText());
previousLine = line;
line = lineIterator.next();
- if (line.getText().startsWith(PREFIX) == false)
+ if (line.getText().startsWith(COMMENT_PREFIX) == false)
{
break;
}
@@ -180,7 +178,8 @@ public class TabFileLoader<T>
* Note that the search is case-insensitive.
* </p>
*
- * @throws IllegalArgumentException if there is at least one duplicate in the given <var>tokens</var>.
+ * @throws IllegalArgumentException if there is at least one duplicate in the given
+ * <var>tokens</var>.
*/
private final static void notUnique(final String[] tokens)
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
index eac9ffef91860c50fad4954649d3f79b5bb9a859..597ab729006d190fb9e435595b35b0e7e4ef6e0e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
@@ -58,25 +58,26 @@ public class BatchDataSetHandler implements IDataSetHandler
{
return processedDatasetFiles;
}
+ LogUtils log = new LogUtils(datasetsParentDir);
TableMap<String, DataSetMappingInformation> datasetsMapping =
DatasetMappingUtil.tryGetDatasetsMapping(datasetsParentDir);
if (datasetsMapping == null)
{
- touchErrorMarkerFile(datasetsParentDir);
+ touchErrorMarkerFile(datasetsParentDir, log);
return processedDatasetFiles;
}
Set<String> processedFiles = new HashSet<String>();
List<File> files = listAll(datasetsParentDir);
for (File file : files)
{
- if (canDatasetBeProcessed(file, datasetsMapping))
+ if (canDatasetBeProcessed(file, datasetsMapping, log))
{
processedDatasetFiles.addAll(delegator.handleDataSet(file));
processedFiles.add(file.getName().toLowerCase());
}
}
- cleanMappingFile(datasetsParentDir, processedFiles);
- finish(datasetsParentDir, datasetsMapping.values().size() - processedFiles.size());
+ clean(datasetsParentDir, processedFiles, log, datasetsMapping.values().size());
+ log.sendNotificationsIfNecessary();
return processedDatasetFiles;
}
@@ -108,30 +109,33 @@ public class BatchDataSetHandler implements IDataSetHandler
return new File(datasetsParentDir, ERROR_MARKER_FILE).isFile();
}
- private void cleanMappingFile(File datasetsParentDir, Set<String> processedFiles)
+ private void cleanMappingFile(File datasetsParentDir, Set<String> processedFiles, LogUtils log)
{
try
{
DatasetMappingUtil.cleanMappingFile(datasetsParentDir, processedFiles);
} catch (IOException ex)
{
- LogUtils.error(datasetsParentDir, "Cannot clean dataset mappings file: "
- + ex.getMessage());
+ log.userError("Cannot clean dataset mappings file: " + ex.getMessage());
}
}
- private void finish(File datasetsParentDir, int unprocessedDatasetsCounter)
+ private void clean(File datasetsParentDir, Set<String> processedFiles, LogUtils log,
+ int datasetMappingsNumber)
{
+ cleanMappingFile(datasetsParentDir, processedFiles, log);
+
+ int unprocessedDatasetsCounter = datasetMappingsNumber - processedFiles.size();
if (unprocessedDatasetsCounter == 0 && hasNoPotentialDatasetFiles(datasetsParentDir))
{
- clean(datasetsParentDir);
+ cleanDatasetsDir(datasetsParentDir);
} else
{
- touchErrorMarkerFile(datasetsParentDir);
+ touchErrorMarkerFile(datasetsParentDir, log);
}
}
- private static void touchErrorMarkerFile(File parentDir)
+ private static void touchErrorMarkerFile(File parentDir, LogUtils log)
{
File errorMarkerFile = new File(parentDir, ERROR_MARKER_FILE);
if (errorMarkerFile.isFile())
@@ -151,13 +155,13 @@ public class BatchDataSetHandler implements IDataSetHandler
.getPath());
} else
{
- LogUtils.warn(parentDir,
+ log.userWarning(
"Correct the errors and delete the '%s' file to start processing again.",
ERROR_MARKER_FILE);
}
}
- private void clean(File datasetsParentDir)
+ private void cleanDatasetsDir(File datasetsParentDir)
{
LogUtils.deleteUserLog(datasetsParentDir);
DatasetMappingUtil.deleteMappingFile(datasetsParentDir);
@@ -167,7 +171,7 @@ public class BatchDataSetHandler implements IDataSetHandler
// Checks that the sample from the mapping exists and is assigned to the experiment - we do not
// want to move datasets to unidentified directory in this case.
private boolean canDatasetBeProcessed(File file,
- TableMap<String, DataSetMappingInformation> datasetsMapping)
+ TableMap<String, DataSetMappingInformation> datasetsMapping, LogUtils log)
{
if (DatasetMappingUtil.isMappingFile(file))
{
@@ -179,7 +183,7 @@ public class BatchDataSetHandler implements IDataSetHandler
{
return false;
}
- return datasetMappingResolver.isMappingCorrect(mapping, file.getParentFile());
+ return datasetMappingResolver.isMappingCorrect(mapping, log);
}
private void deleteEmptyDir(File dir)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
index 3462b82a9768c899598b341c35e05fc249cf24e1..8a1a974929dc3599e2625dbd9d03d1a7765d9948 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
@@ -33,12 +33,9 @@ public class BatchDataSetInfoExtractor implements IDataSetInfoExtractor
{
private final Properties properties;
- private final String groupCode;
-
public BatchDataSetInfoExtractor(final Properties globalProperties)
{
this.properties = ExtendedProperties.getSubset(globalProperties, EXTRACTOR_KEY + '.', true);
- this.groupCode = DatasetMappingResolver.getGroupCode(properties);
}
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
@@ -55,7 +52,7 @@ public class BatchDataSetInfoExtractor implements IDataSetInfoExtractor
String sampleCode =
getSampleCode(plainInfo, openbisService, incomingDataSetPath.getParentFile());
info.setSampleCode(sampleCode);
- info.setGroupCode(groupCode);
+ info.setGroupCode(plainInfo.getGroupCode());
MLConversionType conversion = getConversion(plainInfo.getConversion());
info.setConversion(conversion);
return info;
@@ -83,7 +80,7 @@ public class BatchDataSetInfoExtractor implements IDataSetInfoExtractor
{
String sampleCode =
new DatasetMappingResolver(properties, openbisService).tryFigureSampleCode(mapping,
- logDir);
+ new LogUtils(logDir));
if (sampleCode == null)
{
// should not happen, the dataset handler should skip datasets with incorrect mapping
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
index 8274cb3e21f07886b4f335fca8e18e237347732f..9af7d942ed061b96b9ed56874de03d1658c34a96 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
@@ -39,6 +39,8 @@ public class DataSetMappingInformation
private String projectCode;
+ private String groupCode;
+
private String conversion;
private List<NewProperty> properties;
@@ -87,6 +89,17 @@ public class DataSetMappingInformation
this.projectCode = StringUtils.trimToNull(projectCode);
}
+ public String getGroupCode()
+ {
+ return groupCode;
+ }
+
+ @BeanProperty(label = "group")
+ public void setGroupCode(String groupCode)
+ {
+ this.groupCode = groupCode;
+ }
+
public String getConversion()
{
return conversion;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformationParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformationParser.java
index 4e4d2b04abeed46ea94aa63880369eed6b51c696..f87a74cb737aae6b8a7f993c69b3044cc3a553de 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformationParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformationParser.java
@@ -71,7 +71,7 @@ class DataSetMappingInformationParser
{
causeMsg = "\nThe exception was caused by: " + cause.getMessage();
}
- LogUtils.error(mappingFile.getParentFile(),
+ LogUtils.basicError(mappingFile.getParentFile(),
"The datasets cannot be processed because the mapping file '%s' has incorrect format."
+ " The following exception occured:\n%s%s", mappingFile.getPath(), e
.getMessage(), causeMsg);
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
index 869d79cab62f7fbb12140f42aea32fb54d40364c..be8d4350427a7edf0fcd98227472f7de74724e48 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
@@ -16,14 +16,12 @@
package ch.systemsx.cisd.yeastx.etl;
-import java.io.File;
import java.util.List;
import java.util.Properties;
import org.apache.commons.io.FilenameUtils;
import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -48,23 +46,8 @@ class DatasetMappingResolver
*/
private final static String PROPERTY_TYPE_CODE_PROPERTY_NAME = "unique-property-type-code";
- private static final String GROUP_CODE_PROPERTY_NAME = "group-code";
-
private static final String PROPERTIES_PREFIX = "USER.";
- public static String getGroupCode(Properties properties)
- {
- String groupCode = properties.getProperty(GROUP_CODE_PROPERTY_NAME);
- if (groupCode == null)
- {
- throw ConfigurationFailureException
- .fromTemplate(
- "No group code defined in server configuration. Use '%s' property to specify it.",
- GROUP_CODE_PROPERTY_NAME);
- }
- return groupCode;
- }
-
public static String tryGetUniquePropertyTypeCode(Properties properties)
{
return tryGetPropertyTypeCode(properties);
@@ -72,15 +55,12 @@ class DatasetMappingResolver
private final IEncapsulatedOpenBISService openbisService;
- private final String groupCode;
-
private final String propertyCodeOrNull;
public DatasetMappingResolver(Properties properties, IEncapsulatedOpenBISService openbisService)
{
this.openbisService = openbisService;
this.propertyCodeOrNull = tryGetPropertyTypeCode(properties);
- this.groupCode = properties.getProperty(GROUP_CODE_PROPERTY_NAME);
}
private static String tryGetPropertyTypeCode(Properties properties)
@@ -95,7 +75,7 @@ class DatasetMappingResolver
}
}
- public String tryFigureSampleCode(DataSetMappingInformation mapping, File logDir)
+ public String tryFigureSampleCode(DataSetMappingInformation mapping, LogUtils log)
{
String sampleCodeOrLabel = mapping.getSampleCodeOrLabel();
if (propertyCodeOrNull == null)
@@ -107,21 +87,21 @@ class DatasetMappingResolver
// The main purpose of this checks is to ensure that sample with the given code exists.
// If it is not a case, we will try to check if the specified sample label is unique (in
// all experiments).
- if (tryFigureExperiment(sampleCodeOrLabel) != null)
+ if (tryFigureExperiment(sampleCodeOrLabel, mapping, log) != null)
{
return sampleCodeOrLabel;
}
}
ListSamplesByPropertyCriteria criteria =
- new ListSamplesByPropertyCriteria(propertyCodeOrNull, sampleCodeOrLabel, groupCode,
- tryGetExperimentIdentifier(mapping));
+ new ListSamplesByPropertyCriteria(propertyCodeOrNull, sampleCodeOrLabel, mapping
+ .getGroupCode(), tryGetExperimentIdentifier(mapping));
List<String> samples;
try
{
samples = openbisService.listSamplesByCriteria(criteria);
} catch (UserFailureException e)
{
- logMappingError(mapping, logDir, e.getMessage());
+ logMappingError(mapping, log, e.getMessage());
return null;
}
if (samples.size() == 1)
@@ -129,7 +109,7 @@ class DatasetMappingResolver
return samples.get(0);
} else if (samples.size() == 0)
{
- logMappingError(mapping, logDir, "there is no sample which matches the criteria <"
+ logMappingError(mapping, log, "there is no sample which matches the criteria <"
+ criteria + ">");
return null;
} else
@@ -139,7 +119,7 @@ class DatasetMappingResolver
"there should be exacty one sample which matches the criteria '%s', but %d of them were found."
+ " Consider using the unique sample code.", criteria, samples
.size());
- logMappingError(mapping, logDir, errMsg);
+ logMappingError(mapping, log, errMsg);
return null;
}
}
@@ -158,29 +138,29 @@ class DatasetMappingResolver
}
}
- public boolean isMappingCorrect(DataSetMappingInformation mapping, File logDir)
+ public boolean isMappingCorrect(DataSetMappingInformation mapping, LogUtils log)
{
- if (isExperimentColumnCorrect(mapping, logDir) == false)
+ if (isExperimentColumnCorrect(mapping, log) == false)
{
return false;
}
- String sampleCode = tryFigureSampleCode(mapping, logDir);
+ String sampleCode = tryFigureSampleCode(mapping, log);
if (sampleCode == null)
{
return false;
}
- return isConversionColumnValid(mapping, logDir)
- && existsAndBelongsToExperiment(mapping, logDir, sampleCode);
+ return isConversionColumnValid(mapping, log)
+ && existsAndBelongsToExperiment(mapping, log, sampleCode);
}
private static boolean isConversionColumnValid(final DataSetMappingInformation mapping,
- File logDir)
+ LogUtils log)
{
String conversionText = mapping.getConversion();
MLConversionType conversion = MLConversionType.tryCreate(conversionText);
if (conversion == null)
{
- LogUtils.error(logDir, String.format(
+ log.userError(String.format(
"Error for file '%s'. Unexpected value '%s' in 'conversion' column. "
+ "Leave the column empty or use one of the allowed values: %s.",
mapping.getFileName(), conversionText, CollectionUtils.abbreviate(
@@ -191,18 +171,14 @@ class DatasetMappingResolver
boolean conversionRequired = isConversionRequired(mapping);
if (conversion == MLConversionType.NONE && conversionRequired)
{
- LogUtils
- .error(
- logDir,
- "Error for file '%s'. Conversion column cannot be empty for this type of file.",
- mapping.getFileName());
+ log.userError("Error for file '%s'. Conversion column cannot be empty "
+ + "for this type of file.", mapping.getFileName());
return false;
}
if (conversion != MLConversionType.NONE && conversionRequired == false)
{
- LogUtils.error(logDir,
- "Error for file '%s'. Conversion column must be empty for this type of file.",
- mapping.getFileName());
+ log.userError("Error for file '%s'. Conversion column must be empty "
+ + "for this type of file.", mapping.getFileName());
return false;
}
return true;
@@ -215,36 +191,46 @@ class DatasetMappingResolver
return conversionRequired;
}
- private boolean existsAndBelongsToExperiment(DataSetMappingInformation mapping, File logDir,
+ private boolean existsAndBelongsToExperiment(DataSetMappingInformation mapping, LogUtils log,
String sampleCode)
{
- ExperimentPE experiment = tryFigureExperiment(sampleCode);
+ ExperimentPE experiment = tryFigureExperiment(sampleCode, mapping, log);
if (experiment == null)
{
- logMappingError(mapping, logDir, String.format(
- "sample with the code '%s' does not exist"
- + " or is not connected to any experiment", sampleCode));
+ logMappingError(mapping, log, String.format("sample with the code '%s' does not exist"
+ + " or is not connected to any experiment", sampleCode));
return false;
}
return true;
}
- private ExperimentPE tryFigureExperiment(String sampleCode)
+ private ExperimentPE tryFigureExperiment(String sampleCode, DataSetMappingInformation mapping,
+ LogUtils log)
{
- SampleIdentifier sampleIdentifier = createSampleIdentifier(sampleCode);
- return openbisService.getBaseExperiment(sampleIdentifier);
+ SampleIdentifier sampleIdentifier = createSampleIdentifier(sampleCode, mapping);
+ try
+ {
+ return openbisService.getBaseExperiment(sampleIdentifier);
+ } catch (UserFailureException e)
+ {
+ log.userError("Error when checking if sample '%s' belongs to an experiment: %s",
+ sampleIdentifier, e.getMessage());
+ return null;
+ }
}
- private SampleIdentifier createSampleIdentifier(String sampleCode)
+ private SampleIdentifier createSampleIdentifier(String sampleCode,
+ DataSetMappingInformation mapping)
{
- return new SampleIdentifier(new GroupIdentifier((String) null, groupCode), sampleCode);
+ return new SampleIdentifier(new GroupIdentifier((String) null, mapping.getGroupCode()),
+ sampleCode);
}
- private boolean isExperimentColumnCorrect(DataSetMappingInformation mapping, File logDir)
+ private boolean isExperimentColumnCorrect(DataSetMappingInformation mapping, LogUtils log)
{
if ((mapping.getExperimentCode() == null) != (mapping.getProjectCode() == null))
{
- logMappingError(mapping, logDir,
+ logMappingError(mapping, log,
"experiment and project columns should be both empty or should be both filled.");
return false;
}
@@ -252,7 +238,7 @@ class DatasetMappingResolver
{
logMappingError(
mapping,
- logDir,
+ log,
"openBis is not configured to use the sample label to identify the sample."
+ " You can still identify the sample by the code (clear the experiment column in this case)."
+ " You can also contact your administrator to change the server configuration and set the property type code which should be used.");
@@ -261,10 +247,10 @@ class DatasetMappingResolver
return true;
}
- private void logMappingError(DataSetMappingInformation mapping, File logDir, String errorMessage)
+ private void logMappingError(DataSetMappingInformation mapping, LogUtils log,
+ String errorMessage)
{
- LogUtils.error(logDir, "Mapping for file " + mapping.getFileName() + " is incorrect: "
- + errorMessage);
+ log.userError("Mapping for file " + mapping.getFileName() + " is incorrect: " + errorMessage);
}
public static void adaptPropertyCodes(List<DataSetMappingInformation> list)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingUtil.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingUtil.java
index e5135eaf1a968d8c74d3dc6adc259a4bd60538fd..895b1eeda37e56de7b8e04c84bd934c43f135d7b 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingUtil.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingUtil.java
@@ -27,6 +27,7 @@ import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
@@ -34,6 +35,7 @@ import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.collections.TableMap.UniqueKeyViolationException;
import ch.systemsx.cisd.common.collections.TableMap.UniqueKeyViolationStrategy;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.parser.TabFileLoader;
/**
* @author Tomasz Pylak
@@ -62,7 +64,8 @@ class DatasetMappingUtil
UniqueKeyViolationStrategy.ERROR);
} catch (UniqueKeyViolationException e)
{
- LogUtils.error(logDir,
+ // TODO 2009-06-16, Tomasz Pylak: use email to send notifications
+ LogUtils.basicError(logDir,
"The file '%s' appears more than once. No datasets will be processed.", e
.getInvalidKey());
return null;
@@ -87,18 +90,82 @@ class DatasetMappingUtil
return datasetsMapping.tryGet(datasetFileName.toLowerCase());
}
+ // returns the content of the first line comment or null if there is no comment or it is empty
+ private static String tryGetFirstLineCommentContent(File mappingFile)
+ {
+ List<String> lines;
+ try
+ {
+ lines = readLines(mappingFile);
+ } catch (IOException e)
+ {
+ errorInFile(mappingFile, e.getMessage());
+ return null;
+ }
+ if (lines.size() == 0)
+ {
+ return null;
+ }
+ String firstLine = lines.get(0);
+ if (StringUtils.isBlank(firstLine))
+ {
+ return null;
+ }
+ firstLine = firstLine.trim();
+ if (firstLine.startsWith(TabFileLoader.COMMENT_PREFIX) == false)
+ {
+ return null;
+ }
+ firstLine = firstLine.substring(1).trim();
+ return firstLine;
+ }
+
+ private static void errorInFile(File file, String message)
+ {
+ LogUtils.basicError(file.getParentFile(), "Error while reading the file '%s': %s", file
+ .getPath(), message);
+ }
+
+ // returns email address from the first line of the mapping file or null if there is no emai or
+ // it is invalid
+ private static String tryGetEmail(File mappingFile)
+ {
+ String email = tryGetFirstLineCommentContent(mappingFile);
+ if (email == null)
+ {
+ errorInFile(mappingFile, String.format(
+ "There should be a '%s' character followed by an email address "
+ + "in the first line of the file. "
+ + "The email is needed to send messages about errors.",
+ TabFileLoader.COMMENT_PREFIX));
+ return null;
+ }
+ if (email.contains("@") == false || email.contains(".") == false)
+ {
+ errorInFile(mappingFile, String.format(
+ "The text '%s' does not seem to be an email address.", email));
+ return null;
+ }
+ return email;
+ }
+
public static TableMap<String/* file name in lowercase */, DataSetMappingInformation> tryGetDatasetsMapping(
File parentDir)
{
File mappingFile = tryGetMappingFile(parentDir);
if (mappingFile == null)
{
- LogUtils.warn(parentDir, "Cannot process the directory '%s' "
+ LogUtils.basicWarn(parentDir, "Cannot process the directory '%s' "
+ "because a file with extension '%s' which contains dataset descriptions "
+ "does not exist or there is more than one.", parentDir.getPath(),
CollectionUtils.abbreviate(MAPPING_FILE_EXTENSIONS, -1));
return null;
}
+ String notificationEmail = tryGetEmail(mappingFile);
+ if (notificationEmail == null)
+ {
+ return null;
+ }
List<DataSetMappingInformation> list =
DataSetMappingInformationParser.tryParse(mappingFile);
if (list == null)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
index 936f638062ded6d8066e334ed91d64227d790f13..c7664344e461f08433366ebf9079b4583e69fa8e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
@@ -40,34 +40,75 @@ class LogUtils
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, LogUtils.class);
- public static void error(File loggingDir, String messageFormat, Object... arguments)
+ private final File loggingDir;
+
+ private final StringBuffer messageToSend;
+
+ public LogUtils(File loggingDir)
{
- notifyUser(loggingDir, "ERROR", messageFormat, arguments);
- adminError(messageFormat, arguments);
+ this.loggingDir = loggingDir;
+ this.messageToSend = new StringBuffer();
}
- public static void warn(File loggingDir, String messageFormat, Object... arguments)
+ public void userError(String messageFormat, Object... arguments)
{
- notifyUser(loggingDir, "WARNING", messageFormat, arguments);
- adminWarn(messageFormat, arguments);
+ String message = basicError(loggingDir, messageFormat, arguments);
+ messageToSend.append(message);
}
- private static void notifyUser(File loggingDir, String messageKind, String messageFormat,
- Object... arguments)
+ public void userWarning(String messageFormat, Object... arguments)
+ {
+ String message = basicWarn(loggingDir, messageFormat, arguments);
+ messageToSend.append(message);
+ }
+
+ public void sendNotificationsIfNecessary()
+ {
+ // TODO 2009-06-16, Tomasz Pylak: add email notification
+ if (messageToSend.length() > 0)
+ {
+ System.out.println("Email content: ");
+ System.out.println(messageToSend);
+ }
+ }
+
+ /** Adds an entry about an error to the user log file. Does not send an email. */
+ public static String basicError(File loggingDir, String messageFormat, Object... arguments)
+ {
+ String message = createUserMessage("ERROR", messageFormat, arguments);
+ notifyUserByLogFile(loggingDir, message);
+ return message;
+ }
+
+ /** Adds an entry about a warning to the user log file. Does not send an email. */
+ public static String basicWarn(File loggingDir, String messageFormat, Object... arguments)
+ {
+ String message = createUserMessage("WARNING", messageFormat, arguments);
+ notifyUserByLogFile(loggingDir, message);
+ return message;
+ }
+
+ private static void notifyUserByLogFile(File loggingDir, String message)
{
- String now = new Date().toString();
- String message = now + " " + messageKind + ": " + format(messageFormat, arguments);
OutputStream output;
try
{
output = new FileOutputStream(getUserLogFile(loggingDir), true);
- IOUtils.writeLines(Arrays.asList(message), "\n", output);
+ IOUtils.writeLines(Arrays.asList(message), "", output);
} catch (IOException ex)
{
adminError("Cannot notify a user: " + ex.getMessage());
}
}
+ private static String createUserMessage(String messageKind, String messageFormat,
+ Object... arguments)
+ {
+ String now = new Date().toString();
+ String message = now + " " + messageKind + ": " + format(messageFormat, arguments) + "\n";
+ return message;
+ }
+
private static File getUserLogFile(File loggingDir)
{
return new File(loggingDir, ConstantsYeastX.USER_LOG_FILE);
@@ -83,7 +124,7 @@ class LogUtils
operationLog.warn(format(messageFormat, arguments));
}
- public static void info(String messageFormat, Object... arguments)
+ public static void adminInfo(String messageFormat, Object... arguments)
{
operationLog.info(format(messageFormat, arguments));
}