diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 4e32807c6a289c56621131a970ef4159e90b09da..c921e8733a7a429a886ca6d812b3c7cb2d5663b9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -24,11 +24,7 @@ import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import com.csvreader.CsvReader;
@@ -82,6 +78,29 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
// ------------------ impl -----------------
+ private File getDatasetFile(String sessionToken, IDatasetIdentifier dataset) throws IOException
+ {
+ File originalDir =
+ checkAccessAndGetFile(sessionToken, dataset.getDatasetCode(), "original");
+ if (originalDir.isDirectory() == false)
+ {
+ throw new IllegalArgumentException(String.format(
+ "Dataset %s directory '%s' does not exist.", dataset.getDatasetCode(),
+ originalDir.getPath()));
+ }
+ File[] datasetFiles = originalDir.listFiles();
+ if (datasetFiles.length == 1)
+ {
+ return datasetFiles[0];
+ } else
+ {
+ throw new IllegalArgumentException(String.format(
+ "Exactly one item was expected in the '%s' directory,"
+ + " but %d have been found.", originalDir.getPath(),
+ datasetFiles.length));
+ }
+ }
+
public List<String> listAvailableFeatureNames(String sessionToken,
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
{
@@ -103,9 +122,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return result;
} catch (IOException ex)
{
- wrapIOException(ex);
+ throw wrapIOException(ex);
}
- return null;
}
private String[] extractFeatureNames(String sessionToken,
@@ -114,19 +132,27 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return extractFeatureNames(getDatasetFile(sessionToken, dataset));
}
- private File getDatasetFile(String sessionToken, IDatasetIdentifier dataset)
+ public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
+ List<? extends IImageDatasetIdentifier> imageDatasets)
{
- // FIXME return file in subdirectory
- return checkAccessAndGetRootDirectory(sessionToken, dataset.getDatasetCode());
+ try
+ {
+ List<ImageDatasetMetadata> result = new ArrayList<ImageDatasetMetadata>();
+ for (IImageDatasetIdentifier dataset : imageDatasets)
+ {
+ result.add(extractImageMetadata(sessionToken, dataset));
+ }
+ return result;
+ } catch (IOException ex)
+ {
+ throw wrapIOException(ex);
+ }
}
- //
-
- public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
- List<? extends IImageDatasetIdentifier> imageDatasets)
+ private ImageDatasetMetadata extractImageMetadata(String sessionToken,
+ IImageDatasetIdentifier dataset) throws IOException
{
- // TODO Auto-generated method stub
- return null;
+ return null; // TODO
}
public List<FeatureVectorDataset> loadFeatures(String sessionToken,
@@ -144,9 +170,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return result;
} catch (IOException ex)
{
- wrapIOException(ex);
+ throw wrapIOException(ex);
}
- return null;
}
private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
@@ -266,6 +291,12 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
// helper methods and classes
//
+ private static final String WELL_POSITION_HEADER_NAME = "WellName";
+
+ private static final String WELL_ROW_HEADER_NAME = "Row";
+
+ private static final String WELL_COLUMN_HEADER_NAME = "Col";
+
// exposed for testing
static String[] extractFeatureNames(File datasetFile) throws IOException
{
@@ -295,20 +326,26 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
String[] headerTokens = fileLines.getHeaderTokens();
List<String> existingFeatureNames = new ArrayList<String>();
- Set<String> columnNames = new HashSet<String>(Arrays.asList(headerTokens));
+ int[] headerTokenFeatureIndexes = new int[headerTokens.length];
+ Arrays.fill(headerTokenFeatureIndexes, -1);
for (String featureName : featureNames)
{
- if (columnNames.contains(featureName))
+ if (isWellColumnName(featureName) == false) // well position columns have wrong format
{
- existingFeatureNames.add(featureName);
+ int index = getColumnIndexForHeader(featureName, headerTokens);
+ if (index > -1)
+ {
+ existingFeatureNames.add(featureName);
+ headerTokenFeatureIndexes[index] = existingFeatureNames.size() - 1;
+ }
}
}
- Map<String, Integer> indexByName = new HashMap<String, Integer>();
- for (int i = 0; i < headerTokens.length; i++)
- {
- indexByName.put(headerTokens[i].toLowerCase(), i);
- }
+ int[] wellIndexes = new int[3];
+ Arrays.fill(wellIndexes, -1);
+ wellIndexes[0] = getColumnIndexForHeader(WELL_POSITION_HEADER_NAME, headerTokens);
+ wellIndexes[1] = getColumnIndexForHeader(WELL_ROW_HEADER_NAME, headerTokens);
+ wellIndexes[2] = getColumnIndexForHeader(WELL_COLUMN_HEADER_NAME, headerTokens);
FeatureVectorDatasetBuilder builder =
new FeatureVectorDatasetBuilder(dataset, existingFeatureNames);
@@ -316,38 +353,63 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
for (String[] dataLine : fileLines.getDataLines())
{
FeatureVector vector =
- tryExtractFeatureVector(dataLine, indexByName, existingFeatureNames);
+ tryExtractFeatureVector(dataLine, wellIndexes, headerTokenFeatureIndexes,
+ existingFeatureNames.size());
if (vector != null)
{
builder.addFeatureVector(vector);
} else
{
- operationLog.warn(String.format(
- "wrong data format or well not found for data set %s (file: %s, line: %s)",
- dataset.getDatasetCode(), datasetFile, lineNumber));
+ String logMsg =
+ "wrong data format or well position not found for data set %s (file: %s, line: %s)";
+ operationLog.warn(String.format(logMsg, dataset.getDatasetCode(), datasetFile,
+ lineNumber));
}
lineNumber++;
}
return builder.create();
}
- private static FeatureVector tryExtractFeatureVector(String[] dataLine,
- Map<String, Integer> indexByName, List<String> featureNames)
+ private static boolean isWellColumnName(String string)
{
- WellPosition wellPositionOrNull = tryExtractWellPosition(dataLine, indexByName);
+ return string.equalsIgnoreCase(WELL_POSITION_HEADER_NAME)
+ || string.equalsIgnoreCase(WELL_ROW_HEADER_NAME)
+ || string.equalsIgnoreCase(WELL_COLUMN_HEADER_NAME);
+ }
+
+ /** @return the column index for the column header or -1 if none was found */
+ private static int getColumnIndexForHeader(String columnHeader, String[] headers)
+ {
+ for (int i = 0; i < headers.length; i++)
+ {
+ if (columnHeader.equalsIgnoreCase(headers[i]))
+ {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ private static FeatureVector tryExtractFeatureVector(String[] dataLine, int[] wellIndexes,
+ int[] headerTokenFeatureIndexes, int existingFeaturesSize)
+ {
+ WellPosition wellPositionOrNull = tryExtractWellPosition(dataLine, wellIndexes);
if (wellPositionOrNull != null)
{
- double[] values = new double[featureNames.size()];
- for (int i = 0; i < featureNames.size(); i++)
+ double[] values = new double[existingFeaturesSize];
+ for (int i = 0; i < headerTokenFeatureIndexes.length; i++)
{
try
{
- int index = indexByName.get(featureNames.get(i));
- values[i] = Double.parseDouble(dataLine[index]);
+ if (headerTokenFeatureIndexes[i] > -1)
+ {
+ values[headerTokenFeatureIndexes[i]] = Double.parseDouble(dataLine[i]);
+ }
} catch (NumberFormatException ex)
{
- // skip this feature
+ operationLog.warn("feature " + i
+ + " has wrong format - expected double, found: " + dataLine[i]);
return null;
}
}
@@ -356,24 +418,24 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return null;
}
- private static WellPosition tryExtractWellPosition(String[] fileLine,
- Map<String, Integer> indexByName)
+ private static WellPosition tryExtractWellPosition(String[] fileLine, int[] wellIndexes)
{
+ int wellIndex = wellIndexes[0];
+ int rowIndex = wellIndexes[1];
+ int colIndex = wellIndexes[2];
+
String coordinate;
- Integer wellIndexOrNull = indexByName.get("WellName".toLowerCase());
- if (wellIndexOrNull != null)
+ if (wellIndex > -1)
{
- coordinate = fileLine[wellIndexOrNull];
+ coordinate = fileLine[wellIndex];
} else
{
- Integer rowIndexOrNull = indexByName.get("row".toLowerCase());
- Integer colIndexOrNull = indexByName.get("col".toLowerCase());
- if (rowIndexOrNull == null || colIndexOrNull == null)
+ if (rowIndex == -1 || colIndex == -1)
{
- operationLog.warn("well position missing");
+ operationLog.warn("well not found");
return null;
}
- coordinate = fileLine[rowIndexOrNull] + fileLine[colIndexOrNull];
+ coordinate = fileLine[rowIndex] + fileLine[colIndex];
}
Location location = Location.tryCreateLocationFromMatrixCoordinate(coordinate);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
index bb13e2ec41fc9753785497d145c7a204ba198ad9..03cdbe080893ee81eb654961a748500e77d4e865 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDataset.java
@@ -50,11 +50,7 @@ public class FeatureVectorDataset implements Serializable
StringBuilder sb = new StringBuilder();
sb.append("datasetCode: " + dataset.getDatasetCode());
sb.append(", storeUrl: " + dataset.getDatastoreServerUrl());
- sb.append("\n\tfeatures: ");
- for (int i = 0; i < featureNames.size(); i++)
- {
- sb.append(featureNames.get(i) + ", ");
- }
+ sb.append("\n\tfeatures: " + featureNames);
for (int i = 0; i < featureVectors.size(); i++)
{
sb.append("\n\t" + featureVectors.get(i));
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 7ba1e20c2a20238f47f198a558b5c465dfef95ca..99e09cba409fe2567b6c3976529a9ada16570ce7 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -79,11 +79,7 @@ public class DssServiceRpcScreeningTest extends AbstractFileSystemTestCase
{ "f0", "f2", "f3" }));
assertEquals(dataset, result.getDataset());
-
- assertEquals(2, result.getFeatureNames().size());
- assertEquals("f0", result.getFeatureNames().get(0));
- assertEquals("f2", result.getFeatureNames().get(1));
-
+ assertEquals("[f0, f2]", result.getFeatureNames().toString());
assertEquals(3, result.getFeatureVectors().size());
assertEquals("[1, 1]", result.getFeatureVectors().get(0).getWellPosition()