diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
index 7ba035b93199fbedbc027c740c34f13c2885ee4a..85d66a9a00b3775302103503e2f6400fecec9ba4 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataSet.java
@@ -46,7 +46,7 @@ public final class DataSet implements IStorable
public static final String PRODUCER_CODE = "producer_code";
- public static final String OBSERVABLE_TYPE = "observable_type";
+ public static final String DATA_SET_TYPE = "data_set_type";
public static final String IS_MEASURED = "is_measured";
@@ -61,7 +61,7 @@ public final class DataSet implements IStorable
private final String producerCode;
/** Is a code that describes the type of data that is stored in this standard. */
- private final String observableTypeCode;
+ private final String dataSetTypeCode;
/**
* Specifies whether the data set has been measured from a sample or whether it has been derived
@@ -81,32 +81,32 @@ public final class DataSet implements IStorable
* Creates an instance of data set.
*
* @param code A non-empty string of the data set code. Can not be empty.
- * @param observableType type of this data set. Can not be <code>null</code>.
+ * @param dataSetType type of this data set. Can not be <code>null</code>.
*/
- public DataSet(final String code, final String observableType)
+ public DataSet(final String code, final String dataSetType)
{
- this(code, observableType, Boolean.TRUE, null, null, null);
+ this(code, dataSetType, Boolean.TRUE, null, null, null);
}
/**
* Creates an instance of data set.
*
* @param code A non-empty string of the data set code. Can not be empty.
- * @param observableType type of this data set. Can not be <code>null</code>.
+ * @param dataSetType type of this data set. Can not be <code>null</code>.
* @param isMeasured measured or derived.
* @param productionTimestampOrNull production timestamp or <code>null</code> if unknown.
* @param producerCodeOrNull producer code (aka "device id") or <code>null</code> if unknown.
* @param parentCodesOrNull list of parent data sets. Must be <code>null</code> or empty for
* measured data (or not empty for derived data).
*/
- public DataSet(final String code, final String observableType, final Boolean isMeasured,
+ public DataSet(final String code, final String dataSetType, final Boolean isMeasured,
final Date productionTimestampOrNull, final String producerCodeOrNull,
final List<String> parentCodesOrNull)
{
this.code = code == null ? "" : code;
this.isMeasured = isMeasured;
- assert StringUtils.isEmpty(observableType) == false : "Unspecified observable type.";
- this.observableTypeCode = observableType;
+ assert StringUtils.isEmpty(dataSetType) == false : "Unspecified data set type.";
+ this.dataSetTypeCode = dataSetType;
if (isMeasured.toBoolean() == true && parentCodesOrNull != null
&& parentCodesOrNull.size() > 0)
{
@@ -138,9 +138,9 @@ public final class DataSet implements IStorable
return producerCode;
}
- public final String getObservableTypeCode()
+ public final String getDataSetTypeCode()
{
- return observableTypeCode;
+ return dataSetTypeCode;
}
public final Boolean isMeasured()
@@ -168,7 +168,7 @@ public final class DataSet implements IStorable
assert directory != null : "Given directory can not be null.";
final IDirectory idFolder = Utilities.getSubDirectory(directory, FOLDER);
final String code = Utilities.getTrimmedString(idFolder, CODE);
- final String observableTypeCode = Utilities.getTrimmedString(idFolder, OBSERVABLE_TYPE);
+ final String dataSetTypeCode = Utilities.getTrimmedString(idFolder, DATA_SET_TYPE);
final Boolean isMeasured = Utilities.getBoolean(idFolder, IS_MEASURED);
final Date productionTimestampOrNull = Utilities.tryGetDate(idFolder, PRODUCTION_TIMESTAMP);
final String producerCode = Utilities.getTrimmedString(idFolder, PRODUCER_CODE);
@@ -184,7 +184,7 @@ public final class DataSet implements IStorable
}
assert completeFlag != null : "Complete flag not specified.";
final DataSet dataSet =
- new DataSet(code, observableTypeCode, isMeasured, productionTimestampOrNull,
+ new DataSet(code, dataSetTypeCode, isMeasured, productionTimestampOrNull,
(producerCode.length() == 0 ? null : producerCode), parentCodes);
dataSet.isComplete = completeFlag;
return dataSet;
@@ -203,7 +203,7 @@ public final class DataSet implements IStorable
.get().format(productionTimestamp));
folder.addKeyValuePair(PRODUCER_CODE, StringUtils.emptyIfNull(producerCode));
folder.addKeyValuePair(IS_MEASURED, isMeasured.toString());
- folder.addKeyValuePair(OBSERVABLE_TYPE, observableTypeCode);
+ folder.addKeyValuePair(DATA_SET_TYPE, dataSetTypeCode);
folder.addKeyValuePair(IS_COMPLETE, isComplete.getNiceRepresentation());
final String value;
if (parentCodes.size() > 0)
@@ -252,7 +252,7 @@ public final class DataSet implements IStorable
builder.append(CODE, code);
builder.append(IS_COMPLETE, isComplete);
builder.append(IS_MEASURED, isMeasured);
- builder.append(OBSERVABLE_TYPE, observableTypeCode);
+ builder.append(DATA_SET_TYPE, dataSetTypeCode);
builder.append(PARENT_CODES, parentCodes);
builder.append(PRODUCER_CODE, producerCode);
builder.append(PRODUCTION_TIMESTAMP, productionTimestamp);
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
index d50db73393a764266a671b2699bb2c3c9c30dcc2..8b9c23b5d875281adddf730ffdcb12baf3bdb950 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataSetFileSystemTestCase.java
@@ -45,11 +45,11 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
{
final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
final String dataSetCode = "code";
- final String observableType = "HCS_IMAGE";
- final DataSet dataSet = new DataSet(dataSetCode, observableType);
+ final String dataSetType = "HCS_IMAGE";
+ final DataSet dataSet = new DataSet(dataSetCode, dataSetType);
dataSet.saveTo(directory);
final IDirectory folder = Utilities.getSubDirectory(directory, DataSet.FOLDER);
- checkBasicDataSet(folder, dataSetCode, observableType, Boolean.TRUE);
+ checkBasicDataSet(folder, dataSetCode, dataSetType, Boolean.TRUE);
assertEquals(0, Utilities.getStringList(folder, DataSet.PARENT_CODES).size());
assertEquals(StringUtils.EMPTY_STRING, Utilities.getTrimmedString(folder,
DataSet.PRODUCER_CODE));
@@ -59,10 +59,10 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
}
private final static void checkBasicDataSet(final IDirectory directory,
- final String dataSetCode, final String observableType, final Boolean isMeasured)
+ final String dataSetCode, final String dataSetType, final Boolean isMeasured)
{
assertEquals(dataSetCode, Utilities.getTrimmedString(directory, DataSet.CODE));
- assertEquals("HCS_IMAGE", Utilities.getTrimmedString(directory, DataSet.OBSERVABLE_TYPE));
+ assertEquals("HCS_IMAGE", Utilities.getTrimmedString(directory, DataSet.DATA_SET_TYPE));
assertEquals(isMeasured, Utilities.getBoolean(directory, DataSet.IS_MEASURED));
}
@@ -71,15 +71,15 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
{
final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
final String dataSetCode = "code";
- final String observableType = "HCS_IMAGE";
+ final String dataSetType = "HCS_IMAGE";
final String producerCode = "producerCode";
final Date productionTimestamp = new Date(0L);
final DataSet dataSet =
- new DataSet(dataSetCode, observableType, Boolean.TRUE, productionTimestamp,
+ new DataSet(dataSetCode, dataSetType, Boolean.TRUE, productionTimestamp,
producerCode, null);
dataSet.saveTo(directory);
final IDirectory folder = Utilities.getSubDirectory(directory, DataSet.FOLDER);
- checkBasicDataSet(folder, dataSetCode, observableType, Boolean.TRUE);
+ checkBasicDataSet(folder, dataSetCode, dataSetType, Boolean.TRUE);
assertEquals(0, Utilities.getStringList(folder, DataSet.PARENT_CODES).size());
assertEquals(producerCode, Utilities.getTrimmedString(folder, DataSet.PRODUCER_CODE));
assertEquals(productionTimestamp, Utilities.tryGetDate(folder,
@@ -91,24 +91,24 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
{
final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
final String dataSetCode = "code";
- final String observableType = "HCS_IMAGE";
+ final String dataSetType = "HCS_IMAGE";
final List<String> parentCodes = new ArrayList<String>();
final String parentCode = "parent1";
parentCodes.add(parentCode);
parentCodes.add("parent2");
try
{
- new DataSet(dataSetCode, observableType, Boolean.TRUE, null, null, parentCodes);
+ new DataSet(dataSetCode, dataSetType, Boolean.TRUE, null, null, parentCodes);
fail(DataSet.NO_PARENT_FOR_MEASURED_DATA);
} catch (final IllegalArgumentException ex)
{
assertEquals(DataSet.NO_PARENT_FOR_MEASURED_DATA, ex.getMessage());
}
final DataSet dataSet =
- new DataSet(dataSetCode, observableType, Boolean.FALSE, null, null, parentCodes);
+ new DataSet(dataSetCode, dataSetType, Boolean.FALSE, null, null, parentCodes);
dataSet.saveTo(directory);
final IDirectory folder = Utilities.getSubDirectory(directory, DataSet.FOLDER);
- checkBasicDataSet(folder, dataSetCode, observableType, Boolean.FALSE);
+ checkBasicDataSet(folder, dataSetCode, dataSetType, Boolean.FALSE);
final List<String> parentList = Utilities.getStringList(folder, DataSet.PARENT_CODES);
assertEquals(2, parentList.size());
assertEquals(parentCode, parentList.get(0));
@@ -134,17 +134,17 @@ public final class DataSetFileSystemTestCase extends AbstractFileSystemTestCase
{
final IDirectory directory = NodeFactory.createDirectoryNode(workingDirectory);
final String dataSetCode = "code";
- final String observableType = "HCS_IMAGE";
+ final String dataSetType = "HCS_IMAGE";
final List<String> parentCodes = new ArrayList<String>();
final String parentCode = "parent1";
parentCodes.add(parentCode);
parentCodes.add("parent2");
final DataSet dataSet =
- new DataSet(dataSetCode, observableType, Boolean.FALSE, productionTimestamp,
+ new DataSet(dataSetCode, dataSetType, Boolean.FALSE, productionTimestamp,
producerCode, parentCodes);
dataSet.saveTo(directory);
final DataSet newDataSet = DataSet.loadFrom(directory);
- assertEquals(observableType, newDataSet.getObservableTypeCode());
+ assertEquals(dataSetType, newDataSet.getDataSetTypeCode());
assertEquals(dataSetCode, newDataSet.getCode());
assertEquals(parentCodes, newDataSet.getParentCodes());
assertEquals(productionTimestamp, newDataSet.getProductionTimestamp());
diff --git a/integration-tests/run.sh b/integration-tests/run.sh
index e08150395717b16fd3d5c180dd0d1b272737dded..5cb13bd7dc9b9818fa0c27f3892454e3af07f52a 100755
--- a/integration-tests/run.sh
+++ b/integration-tests/run.sh
@@ -598,7 +598,7 @@ function assert_correct_content_of_processing_dir {
assert_same_content $TEMPLATE/openBIS-client/testdata/register-experiments/processing-parameters.txt \
$DATA/processing-dir/processing-parameters-from-openbis
local instance_dir=$DATA/main-store/`ls -1 $DATA/main-store/ | grep -i 'Instance_[0-9a-f]\{8\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{12\}'`
- local bds_container=$instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_3VCP1/
+ local bds_container=$instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/DataSetType_HCS_IMAGE/Sample_3VCP1/
bds_container=$bds_container`ls -1 $bds_container | head -1`
assert_dir_exists $bds_container
local data_set2=$bds_container/data/original/microX_200801011213_3VCP1
@@ -612,7 +612,7 @@ function assert_correct_content_of_plate_3VCP1_in_store {
local instance_dir=$DATA/main-store/`ls -1 $DATA/main-store/ | grep -i 'Instance_[0-9a-f]\{8\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{12\}'`
local main_dir=$instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1
- local raw_data_dir=$main_dir/ObservableType_HCS_IMAGE/Sample_3VCP1/
+ local raw_data_dir=$main_dir/DataSetType_HCS_IMAGE/Sample_3VCP1/
assert_dir_exists $raw_data_dir
# Picks up the first directory found
raw_data_dir=$raw_data_dir`ls -1 $raw_data_dir | head -1`
@@ -650,7 +650,7 @@ function assert_correct_content_of_plate_3VCP1_in_store {
assert_equals_as_in_file microX-3VCP1 $metadata_dir/data_set/code
assert_equals_as_in_file TRUE $metadata_dir/data_set/is_measured
assert_equals_as_in_file FALSE $metadata_dir/data_set/is_complete
- assert_equals_as_in_file HCS_IMAGE $metadata_dir/data_set/observable_type
+ assert_equals_as_in_file HCS_IMAGE $metadata_dir/data_set/data_set_type
assert_equals_as_in_file microX $metadata_dir/data_set/producer_code
# Sample
assert_equals_as_in_file 3VCP1 $metadata_dir/sample/code
@@ -695,13 +695,13 @@ function assert_correct_content_of_invalid_plate_in_store {
local cell_plate=$1
echo ==== assert correct content of invalid plate $cell_plate in store ====
- local error_dir=$DATA/main-store/error/ObservableType_HCS_IMAGE
+ local error_dir=$DATA/main-store/error/DataSetType_HCS_IMAGE
assert_dir_exists $error_dir
local data_set=$error_dir/microX_200801011213_$cell_plate
assert_same_content $TEST_DATA/$cell_plate $data_set
assert_file_exists $data_set.exception
local instance_dir=$DATA/main-store/`ls -1 $DATA/main-store/ | grep -i 'Instance_[0-9a-f]\{8\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{12\}'`
- assert_dir_empty $instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_$cell_plate
+ assert_dir_empty $instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/DataSetType_HCS_IMAGE/Sample_$cell_plate
}
function assert_correct_content_of_image_analysis_data {
@@ -709,7 +709,7 @@ function assert_correct_content_of_image_analysis_data {
echo ==== check image analysis data for cell plate $cell_plate ====
local instance_dir=$DATA/main-store/`ls -1 $DATA/main-store/ | grep -i 'Instance_[0-9a-f]\{8\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{4\}-[0-9a-f]\{12\}'`
- local img_analysis=$instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE_ANALYSIS_DATA/Sample_$cell_plate/
+ local img_analysis=$instance_dir/Group_CISD/Project_NEMO/Experiment_EXP1/DataSetType_HCS_IMAGE_ANALYSIS_DATA/Sample_$cell_plate/
assert_dir_exists $img_analysis
# Picks up the first directory found
img_analysis=$img_analysis`ls -1 $img_analysis | head -1`
@@ -723,8 +723,8 @@ function assert_correct_content_of_unidentified_plate_in_store {
local unidentified_dir=$DATA/main-store/unidentified
assert_dir_exists $unidentified_dir
- assert_same_content $TEST_DATA/$cell_plate $unidentified_dir/ObservableType_HCS_IMAGE/microX_200801011213_$cell_plate
- assert_same_content $TEST_DATA/$cell_plate $unidentified_dir/ObservableType_HCS_IMAGE_ANALYSIS_DATA/microX_200801011213_$cell_plate
+ assert_same_content $TEST_DATA/$cell_plate $unidentified_dir/DataSetType_HCS_IMAGE/microX_200801011213_$cell_plate
+ assert_same_content $TEST_DATA/$cell_plate $unidentified_dir/DataSetType_HCS_IMAGE_ANALYSIS_DATA/microX_200801011213_$cell_plate
}
function assert_correct_dataset_content_in_database {
diff --git a/integration-tests/templates/etlserver-all/etc/service.properties b/integration-tests/templates/etlserver-all/etc/service.properties
index 6338d2bdc22169b111466cdbf6fb43621795658b..c2a42b8c02443064a8660e0a5d5aeb746e4a62b3 100644
--- a/integration-tests/templates/etlserver-all/etc/service.properties
+++ b/integration-tests/templates/etlserver-all/etc/service.properties
@@ -75,7 +75,7 @@ raw-data.data-set-info-extractor.data-set-code-entities-glue = -
raw-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
raw-data.type-extractor.file-format-type = TIFF
raw-data.type-extractor.locator-type = RELATIVE_LOCATION
-raw-data.type-extractor.observable-type = HCS_IMAGE
+raw-data.type-extractor.data-set-type = HCS_IMAGE
raw-data.type-extractor.procedure-type = DATA_ACQUISITION
# The storage processor plugin (IStorageProcessor implementation)
@@ -109,7 +109,7 @@ image-analysis.data-set-info-extractor.data-set-code-entities-glue = -
image-analysis.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
image-analysis.type-extractor.file-format-type = 3VPROPRIETARY
image-analysis.type-extractor.locator-type = RELATIVE_LOCATION
-image-analysis.type-extractor.observable-type = HCS_IMAGE_ANALYSIS_DATA
+image-analysis.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
image-analysis.type-extractor.procedure-type = IMAGE_ANALYSIS
# The storage processor (IStorageProcessor implementation)