From c3493a86e85836bc658c198e3e335bde0fd6acb5 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Fri, 30 Jul 2010 09:43:06 +0000
Subject: [PATCH] LMS-1671: screening api tests
SVN: 17297
---
.../client/api/v1/ScreeningClientApiTest.java | 55 ++++++++++++++-----
1 file changed, 42 insertions(+), 13 deletions(-)
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 329f413b086..3ad8b691546 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
@@ -34,13 +34,18 @@ import org.apache.log4j.PropertyConfigurator;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
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.FeatureVectorWithDescription;
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.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
@@ -73,6 +78,31 @@ public class ScreeningClientApiTest
System.err.println("Authentication failed: check the user name and password.");
return;
}
+ List<ExperimentIdentifier> experiments = facade.listExperiments();
+ System.out.println("Experiments: " + experiments);
+
+ MaterialIdentifier gene = new MaterialIdentifier(MaterialTypeIdentifier.GENE, "OPRS1");
+ ExperimentIdentifier experimentIdentifer = experiments.get(0);
+ List<PlateWellReferenceWithDatasets> plateWells =
+ facade.listPlateWells(experimentIdentifer, gene, true);
+ System.out.println(String.format("Wells with gene '%s' in experiment '%s': %s", gene,
+ experimentIdentifer, plateWells));
+
+ List<FeatureVectorWithDescription> featuresForPlateWells =
+ facade.loadFeaturesForPlateWells(experimentIdentifer, gene, null);
+ System.out.println("Features for wells: " + featuresForPlateWells);
+
+ List<FeatureVectorWithDescription> featuresForPlateWellsCheck =
+ facade.loadFeaturesForDatasetWellReferences(facade
+ .convertToFeatureVectorDatasetWellIdentifier(plateWells), null);
+
+ if (featuresForPlateWellsCheck.equals(featuresForPlateWells) == false)
+ {
+ throw new IllegalStateException(String.format(
+ "Inconsistent results to fetch feature vectors, expected:\n%s\nbut got:\n%s",
+ featuresForPlateWells, featuresForPlateWellsCheck));
+ }
+
List<Plate> plates = facade.listPlates();
System.out.println("Plates: " + plates);
List<ImageDatasetReference> imageDatasets = facade.listImageDatasets(plates);
@@ -110,9 +140,8 @@ public class ScreeningClientApiTest
facade.logout();
}
-
- private static List<IDatasetIdentifier> getFirstFive(
- IScreeningOpenbisServiceFacade facade,
+
+ private static List<IDatasetIdentifier> getFirstFive(IScreeningOpenbisServiceFacade facade,
List<? extends DatasetIdentifier> identfiers)
{
List<IDatasetIdentifier> result = new ArrayList<IDatasetIdentifier>();
@@ -141,7 +170,7 @@ public class ScreeningClientApiTest
{
File dir = new File(datasetIdentifier.getDatasetCode());
dir.mkdir();
-
+
for (int wellRow = 1; wellRow <= 5; wellRow++)
{
for (int wellCol = 1; wellCol <= 5; wellCol++)
@@ -150,10 +179,10 @@ public class ScreeningClientApiTest
{
for (int tile = 0; tile < 1; tile++)
{
-
+
PlateImageReference imageRef =
- new PlateImageReference(wellRow, wellCol, tile, "dapi",
- datasetIdentifier);
+ new PlateImageReference(wellRow, wellCol, tile, "dapi",
+ datasetIdentifier);
imageRefs.add(imageRef);
imageFiles.add(new File(dir, createImageFileName(imageRef)));
}
@@ -180,13 +209,13 @@ public class ScreeningClientApiTest
try
{
facade.loadImages(imageReferences, new IImageOutputStreamProvider()
- {
- public OutputStream getOutputStream(PlateImageReference imageReference)
- throws IOException
{
- return imageRefToFileMap.get(imageReference);
- }
- });
+ public OutputStream getOutputStream(PlateImageReference imageReference)
+ throws IOException
+ {
+ return imageRefToFileMap.get(imageReference);
+ }
+ });
} finally
{
closeOutputStreams(imageRefToFileMap.values());
--
GitLab