diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
index cceed4f93b3c78bf920eefa67fd5a8e6ba4484fd..a45b7535b0e28e7748e650d1efecc9e7c035bd37 100644
--- a/screening/sourceTest/java/OpenBISScreeningMLTest.java
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -81,6 +81,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
*/
public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
+ private static String DATASETS_FOLDER = "DataSets";
+
private static final PlateIdentifier PLATE_1 = PlateIdentifier
.createFromAugmentedCode("/S/PLATE-1");
@@ -414,7 +416,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
FeatureVectorWithDescription f1 =
new FeatureVectorWithDescription(well1, Arrays.asList("F1", "F3"),
new double[]
- { 1.5, 42 });
+ { 1.5, 42 });
FeatureVectorDatasetReference fds2 =
new FeatureVectorDatasetReference("ds2", "MY-TYPE", "", p2,
ExperimentIdentifier.createFromAugmentedCode("/S/P/E"),
@@ -425,7 +427,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
FeatureVectorWithDescription f2 =
new FeatureVectorWithDescription(well2, Arrays.asList("F1", "F2"),
new double[]
- { -3, 7.125 });
+ { -3, 7.125 });
will(returnValue(Arrays.asList(f1, f2)));
}
});
@@ -495,11 +497,11 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Geometry.createFromCartesianDimensions(3, 2), new Date(4711),
null, null);
FeatureVector v1 = new FeatureVector(new WellPosition(2, 1), new double[]
- { 1.5, 42 });
+ { 1.5, 42 });
FeatureVector v2 = new FeatureVector(new WellPosition(1, 3), new double[]
- { 1.25, 42.5 }, new boolean[]
- { true, false }, new String[]
- { "a", "b" });
+ { 1.25, 42.5 }, new boolean[]
+ { true, false }, new String[]
+ { "a", "b" });
FeatureVectorDataset d1 =
new FeatureVectorDataset(ref, Arrays.asList("F1", "F3"), Arrays.asList(
"f1", "f3"), Arrays.asList(v1, v2));
@@ -509,7 +511,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Object[][][][] matrix =
OpenBISScreeningML.getFeatureMatrixForPlate("/S/PLATE-1", null, new String[]
- { "F1", "F2", "F3" });
+ { "F1", "F2", "F3" });
assertPlateFeatures("[a, 1.5]", matrix[0][0]);
assertPlateFeatures("[42.5, 42.0]", matrix[0][1]);
@@ -590,7 +592,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
});
OpenBISScreeningML.updateWellProperties("/S/PLATE-1", 1, 2, new Object[][]
- {
+ {
{ "A", "42" },
{ "B", "43" } });
@@ -610,14 +612,14 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
one(ds1).listFiles("/", true);
will(returnValue(new FileInfoDssDTO[]
- { new FileInfoDssDTO("a", "a", true, -1),
- new FileInfoDssDTO("a/b", "a/b", false, 42) }));
+ { new FileInfoDssDTO("a", "a", true, -1),
+ new FileInfoDssDTO("a/b", "a/b", false, 42) }));
one(ds1).getCode();
will(returnValue("ds1"));
one(ds2).listFiles("/", true);
will(returnValue(new FileInfoDssDTO[]
- { new FileInfoDssDTO("c", "c", false, 137) }));
+ { new FileInfoDssDTO("c", "c", false, 137) }));
one(ds2).getCode();
will(returnValue("ds2"));
}
@@ -658,9 +660,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testLoadDataSets()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
- File ds2Folder = new File(dataSetFolder, "ds-2");
+ final File ds2Folder = new File(dataSetFolder, "ds-2");
ds2Folder.mkdirs();
final String datasetTypePattern = "blablaCode";
final String mountPoint = "/mount/openbis/store";
@@ -678,9 +680,12 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
with(filterMatcher));
will(returnValue(Arrays.asList(dataSet1, dataSet2)));
- one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
+ one(ds1).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
will(returnValue(ds1Folder));
+ one(ds2).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
+ will(returnValue(ds2Folder));
+
}
});
@@ -702,9 +707,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testLoadDataSetsFilteredOnProperties()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
- File ds2Folder = new File(dataSetFolder, "ds-2");
+ final File ds2Folder = new File(dataSetFolder, "ds-2");
ds2Folder.mkdirs();
final String datasetTypePattern = "blablaCode";
final String mountPoint = "/mount/openbis/store";
@@ -722,13 +727,16 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
with(filterMatcher));
will(returnValue(Arrays.asList(dataSet1, dataSet2)));
- one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
+ one(ds1).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
will(returnValue(ds1Folder));
+
+ one(ds2).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
+ will(returnValue(ds2Folder));
}
});
Object[][] properties = new Object[][]
- { new Object[]
+ { new Object[]
{ "a", "alpha" }, new Object[]
{ "b", "beta" } };
Object[][] result =
@@ -751,9 +759,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testLoadDataSetsForExperiment()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
- File ds2Folder = new File(dataSetFolder, "ds-2");
+ final File ds2Folder = new File(dataSetFolder, "ds-2");
ds2Folder.mkdirs();
final String datasetTypePattern = "blablaCode";
final String mountPoint = "/mount/openbis/store";
@@ -770,9 +778,12 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
one(openbis).getFullDataSets(with(eId1), with(filterMatcher));
will(returnValue(Arrays.asList(dataSet1, dataSet2)));
- one(ds1).getLinkOrCopyOfContents(mountPoint, dataSetFolder);
+ one(ds1).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
will(returnValue(ds1Folder));
+ one(ds2).getLinkOrCopyOfContents(with(mountPoint), with(any(File.class)));
+ will(returnValue(ds2Folder));
+
}
});
@@ -795,7 +806,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testUpdateDataSet()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
ds1Folder.mkdirs();
final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher =
@@ -824,7 +835,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Object code =
OpenBISScreeningML.uploadDataSet("/S/PLATE-1", ds1Folder.getPath(), "my-type",
new Object[][]
- {
+ {
{ "A", "42" },
{ "B", "43" } });
@@ -838,7 +849,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testUploadDataSetForPlateAndParents()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
ds1Folder.mkdirs();
final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher =
@@ -865,8 +876,8 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
});
Object code = OpenBISScreeningML.uploadDataSetForPlateAndParents("/S/PLATE-1", new Object[]
- { "DATA-SET-CODE1", "DATA-SET-CODE2" }, ds1Folder.getPath(), "my-type", new Object[][]
- {
+ { "DATA-SET-CODE1", "DATA-SET-CODE2" }, ds1Folder.getPath(), "my-type", new Object[][]
+ {
{ "A", "42" },
{ "B", "43" } });
@@ -882,7 +893,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
public void testUploadDataSetForExperimentAndParents()
{
final File dataSetFolder =
- new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ new File(OpenBISScreeningML.tempDir, DATASETS_FOLDER);
final File ds1Folder = new File(dataSetFolder, "ds-1");
ds1Folder.mkdirs();
final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher =
@@ -911,9 +922,9 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
Object code =
OpenBISScreeningML.uploadDataSetForExperimentAndParents("/S/P/E1", new Object[]
- { "DATA-SET-CODE1", "DATA-SET-CODE2" }, ds1Folder.getPath(), "my-type",
+ { "DATA-SET-CODE1", "DATA-SET-CODE2" }, ds1Folder.getPath(), "my-type",
new Object[][]
- {
+ {
{ "A", "42" },
{ "B", "43" } });
@@ -1036,7 +1047,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
});
Object[][][] result1 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2, 1, new String[]
- { "G" });
+ { "G" });
List<PlateImageReference> imgRefs1 = imgRefsMatcher1.recordedObject();
for (PlateImageReference plateImageReference : imgRefs1)
{
@@ -1110,7 +1121,7 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
{
final String[] analysisProcedures = new String[]
- { "PROC-1", "PROC-2", "PROC-3" };
+ { "PROC-1", "PROC-2", "PROC-3" };
context.checking(new Expectations()
{
@@ -1144,11 +1155,14 @@ public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
createDataSet("ds1", ds1, Arrays.asList("ds3", "ds4"), noCodes),
createDataSet("ds2", ds2, Arrays.asList("ds1"),
Arrays.asList("ds3", "ds5")))));
+
+ one(ds1).tryGetInternalPathInDataStore();
+ one(ds2).tryGetInternalPathInDataStore();
}
});
Object[][][] dataSets = OpenBISScreeningML.getDataSetMetaData(new String[]
- { "ds1", "ds2" });
+ { "ds1", "ds2" });
assertEquals("ds1", dataSets[0][0][0]);
assertEquals("ds-type", dataSets[0][0][1]);