diff --git a/screening/build/build.xml b/screening/build/build.xml
index d99f44c6b45abd98c1de4a11c2cb5209f79313bc..d61b7ccc0a05cf7991484577458608861ab3246f 100644
--- a/screening/build/build.xml
+++ b/screening/build/build.xml
@@ -8,12 +8,13 @@
<property name="variant" value="-screening" />
<property name="dist.screening-api" value="${dist}/screening_api" />
- <property name="dist.screening-api.lib" value="${dist.screening-api}/lib" />
+ <property name="dist.screening-api.lib" value="${dist.screening-api}" />
<property name="dist.screening-api.jar" value="${dist.screening-api.lib}/openbis_screening_api.jar" />
<property name="dist.screening-api.javadoc" value="${dist.screening-api}/doc" />
<property name="classes.screening" value="../screening/targets/www/WEB-INF/classes" />
<property name="classes.common-server" value="../server-common/targets/ant/classes" />
+ <property name="classes.common" value="../common/targets/ant/classes" />
<target name="compile" depends="build-common.compile, clean" />
@@ -122,6 +123,7 @@
</fileset>
<manifest>
<attribute name="Main-Class" value="ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTest" />
+ <attribute name="Class-Path" value="spring-ext.jar" />
<attribute name="Version" value="${version.number}" />
<attribute name="Build-Number"
value="${version.number} (r${revision.number},${clean.flag})" />
@@ -129,15 +131,20 @@
</recursive-jar>
<jar update="true" destfile="${dist.screening-api.jar}">
<fileset dir="${classes.common-server}">
- <include name="ch/systemsx/cisd/common/spring/*.class" />
+ <include name="ch/systemsx/cisd/common/spring/HttpInvokerUtils.class" />
</fileset>
+ <fileset dir="${classes.common}">
+ <include name="ch/systemsx/cisd/common/exceptions/**/*.class" />
+ </fileset>
+ </jar>
+ <recursive-jar destfile="${dist.screening-api.lib}/spring-ext.jar">
<zipfileset src="${lib}/spring/spring.jar" />
<zipfileset src="${lib}/spring/third-party/stream-supporting-httpinvoker.jar" />
<zipfileset src="${lib}/commons-logging/commons-logging.jar" />
<zipfileset src="${lib}/commons-httpclient/commons-httpclient.jar" />
<zipfileset src="${lib}/commons-codec/commons-codec.jar" />
<zipfileset src="${lib}/log4j/log4j.jar" />
- </jar>
+ </recursive-jar>
</target>
<target name="screening-api" depends="screening-api-doc, screening-api-libs" />
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
index 281a9da24fa91d604ca36a553035156f6a2476b5..86d16dbaae4b98e62ff74d1c62efdf826d35be8e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
@@ -27,8 +27,10 @@ import java.util.List;
import org.apache.log4j.lf5.util.StreamUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
@@ -68,11 +70,20 @@ public class ScreeningClientApiTest
System.out.println("Feature vector datasets: " + featureVectorDatasets);
// test for feature vector dataset
- // String datasetCode = "20091214153212961-474922"; // feature vector
- String datasetCode = "20091216162628729-475111"; // image
- IDatasetIdentifier datasetIdentifier = getDatasetIdentifier(facade, datasetCode);
+ // String featureVectorDatasetCode = "20100423170945059-29"; // feature vector
+ String imageDatasetCode = "20100423163638457-16"; // image
+ IDatasetIdentifier datasetIdentifier = getDatasetIdentifier(facade, imageDatasetCode);
loadImages(facade, datasetIdentifier);
+ List<String> featureNames = facade.listAvailableFeatureNames(featureVectorDatasets);
+ System.out.println("Feature names: " + featureNames);
+ List<FeatureVectorDataset> features =
+ facade.loadFeatures(featureVectorDatasets, featureNames);
+ System.out.println("Features: " + features);
+
+ List<ImageDatasetMetadata> imageMetadata = facade.listImageMetadata(imageDatasets);
+ System.out.println("Image metadata: " + imageMetadata);
+
facade.logout();
}
@@ -87,17 +98,20 @@ public class ScreeningClientApiTest
private static void loadImages(ScreeningOpenbisServiceFacade facade,
IDatasetIdentifier datasetIdentifier) throws FileNotFoundException, IOException
{
- for (int channel = 1; channel <= 2; channel++)
+ for (int well = 1; well <= 5; well++)
{
- for (int tile = 4; tile <= 6; tile++)
+ for (int channel = 1; channel <= 2; channel++)
{
- List<PlateImageReference> imageRefs = new ArrayList<PlateImageReference>();
- imageRefs.add(new PlateImageReference(1, 3, tile, channel, datasetIdentifier));
- List<PlateSingleImage> images = facade.loadImages(imageRefs);
- saveImages(images);
+ for (int tile = 1; tile <= 1; tile++)
+ {
+ List<PlateImageReference> imageRefs = new ArrayList<PlateImageReference>();
+ imageRefs.add(new PlateImageReference(well, well, tile, channel,
+ datasetIdentifier));
+ List<PlateSingleImage> images = facade.loadImages(imageRefs);
+ saveImages(images);
+ }
}
}
-
}
private static void saveImages(List<PlateSingleImage> images) throws FileNotFoundException,
@@ -116,7 +130,7 @@ public class ScreeningClientApiTest
private static String createImageFileName(PlateSingleImage image)
{
WellPosition well = image.getWellPosition();
- return "img_r" + well.getWellRow() + "_c" + well.getWellColumn() + "_ch"
- + image.getChannel() + "_t" + image.getTile() + ".png";
+ return "img_row" + well.getWellRow() + "_col" + well.getWellColumn() + "_channel"
+ + image.getChannel() + "_tile" + image.getTile() + ".png";
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 61464bbbc2b194a60a14dda2880ffbdf2b6595d0..3773bbe592a2206f0514c0dd1208937e28dc0bfe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -190,83 +190,40 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
{
- try
- {
- return createScreeningApiImpl(sessionToken).listFeatureVectorDatasets(plates);
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ return createScreeningApiImpl(sessionToken).listFeatureVectorDatasets(plates);
}
public List<ImageDatasetReference> listImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
{
- try
- {
- return createScreeningApiImpl(sessionToken).listImageDatasets(plates);
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ return createScreeningApiImpl(sessionToken).listImageDatasets(plates);
}
public List<Plate> listPlates(String sessionToken)
{
- try
- {
- return createScreeningApiImpl(sessionToken).listPlates();
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ return createScreeningApiImpl(sessionToken).listPlates();
}
public List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken,
List<String> datasetCodes)
{
- try
- {
- return createScreeningApiImpl(sessionToken).getDatasetIdentifiers(datasetCodes);
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ return createScreeningApiImpl(sessionToken).getDatasetIdentifiers(datasetCodes);
}
private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
{
- try
- {
- final Session session = getSession(sessionToken);
- return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory());
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ final Session session = getSession(sessionToken);
+ return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory());
}
public void logoutScreening(String sessionToken)
{
- try
- {
- logout(sessionToken);
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ logout(sessionToken);
}
public String tryLoginScreening(String userId, String userPassword)
{
- SessionContextDTO sessionContext;
- try
- {
- sessionContext = tryToAuthenticate(userId, userPassword);
- } catch (UserFailureException e)
- {
- throw translateException(e);
- }
+ SessionContextDTO sessionContext = tryToAuthenticate(userId, userPassword);
if (sessionContext != null)
{
return sessionContext.getSessionToken();
@@ -275,10 +232,4 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return null;
}
}
-
- private static RuntimeException translateException(UserFailureException e)
- {
- return new IllegalArgumentException(e.getMessage());
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
index 9635f8cbe00ad7e4158d9bdffc18d359f931bc3a..087878928be0d9a222de3d67ff6a729ed4b2473f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
@@ -46,7 +46,8 @@ public interface IScreeningApiServer
*
*@return sessionToken if authentication suceeded, null otherwise
*/
- @Transactional(readOnly = true)
+ @Transactional
+ // this is not a readOnly transaction - it can create new users
String tryLoginScreening(String userId, String userPassword) throws IllegalArgumentException;
/**