/*
* Copyright 2011 ETH Zuerich, CISD
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* Integration tests of MatLab API on Biozentrum server.
*
* @author Tomasz Pylak
*/
public class BiozentrumMatLabApiTest
{
public static void main(String[] args)
{
if (args.length == 0)
{
System.err
.println("Specify the password and optionally the plate identifier, mount point and dataset type pattern!");
}
String passwd = "xxx";
String chosenPlate = "/GROUP_DEHIO/KB03-2O-130";
String mountPoint = null;
String datasetTypePattern = "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT";
if (args.length > 1)
{
chosenPlate = args[1];
}
if (args.length > 2)
{
mountPoint = args[2];
}
// OpenBISScreeningML.login("tpylak", passwd, "https://infectx.biozentrum.unibas.ch");
// Object[][] metadata = OpenBISScreeningML.getImagesMetadata("/RESEARCH_IT/TEST2");
// System.out.println(Arrays.toString(metadata[0]));
// Object[][][] loadImages =
// OpenBISScreeningML.loadImages("/INFECTX/DZ56-1K", 1, 1, 1, new String[]
// { "CY5", "DAPI" });
// System.out.println(loadImages[0][0][0]);
// OpenBISScreeningML.login("cisd", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
OpenBISScreeningML.login("admin", passwd, "https://sprint-openbis.ethz.ch:8446");
// OpenBISScreeningML.login("admin", passwd, "http://127.0.0.1:8888");
// Object[][] metadata = OpenBISScreeningML.getImagesMetadata("/TEST/PLATE1");
// System.out.println(Arrays.toString(metadata[0]));
// Object[][][] loadImages =
Object[][][] images = OpenBISScreeningML.loadImages("/TEST/PLATE1", 1, 1, 1, new String[]
{ "DAPI" });
// String experiment = "/TEST/TEST-USER/MY-ASSAY";
// testListChannels(experiment);
// testLoadFeatures(chosenPlate, experiment);
// testImagesMetadata(chosenPlate);
// testLoadImage(chosenPlate);
// testWellProperties(chosenPlate);
// testLoadDataset(chosenPlate, mountPoint, datasetTypePattern);
// testUploadDataset(chosenPlate);
// testUploadDataset("/RESEARCH_IT/TEST2");
// testUploadDataset("/DEMO/VL0206A-FV1801");
// testUploadDataset("/TEST/PLATE1");
// integration server test
// OpenBISScreeningML.login("admin", passwd, "https://127.0.0.1:8443");
// String datasetType = "HCS_MODULESETTINGS_OBJECTCLASSIFICATION_MAT";
// String datasetType = "HCS_ANALYSIS_WELL_CLASSIFICATION_SUMMARIES";
// String datasetType = "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT";
// String datasetType = "UNKNOWN";
// testUploadDataset("/GROUP_RESEARCHIT/DZ01-1A", datasetType);
// PlateMetadata[] plateMetadataList = OpenBISScreeningML.getPlateMetadataList(new String[]
// { "/TEST/PLATE1", "/TEST/PLATE2", "/TEST/PLATE1.96WELLS", "/TEST/PLATE1.SUFFIX", });
sleepLong();
OpenBISScreeningML.logout();
}
private static void sleepLong()
{
try
{
Thread.sleep(1000000);
} catch (InterruptedException ex)
{
ex.printStackTrace();
}
}
private static void testListChannels(String experiment)
{
Object[][] channels = OpenBISScreeningML.listChannels(experiment);
print2DArray(channels);
}
private static void testUploadDataset(String chosenPlate, String datasetType)
{
String file = "/Users/tpylak/main/tmp/bioz-test/PlateSummary.csv";
String datasetCode;
Object[][] dataSetProperties = new Object[][]
{ new Object[] {} };
datasetCode =
(String) OpenBISScreeningML.uploadDataSet(chosenPlate, file, datasetType,
dataSetProperties);
System.out.println("Uploaded any dataset " + datasetCode);
}
private static void testLoadFeatures(String chosenPlate, String experiment)
{
Object[][] features = OpenBISScreeningML.listFeatures(experiment, null);
print2DArray(features);
Object[][][] featureMatrix =
OpenBISScreeningML.getFeatureMatrixForPlate(chosenPlate, null, null);
System.out.println("per plate features -------------------------------");
print3DArray(featureMatrix);
String[] featureNames = new String[]
{ "OOF" };
featureMatrix =
OpenBISScreeningML.getFeatureMatrixForPlate(chosenPlate, null, featureNames);
System.out.println("one per plate feature -------------------------------");
print3DArray(featureMatrix);
featureMatrix = OpenBISScreeningML.getFeatureMatrix(experiment, "149420", featureNames);
System.out.println("one per gene feature -------------------------------");
print3DArray(featureMatrix);
}
private static void print3DArray(Object[][][] array)
{
System.out.println("{");
for (int i = 0; i < array.length; i++)
{
print2DArray(array[i]);
}
System.out.println("}");
}
private static void print2DArray(Object[][] array)
{
System.out.println("[");
for (int i = 0; i < array.length; i++)
{
printAsRow(array[i]);
}
System.out.println("]");
}
private static void printAsRow(Object[] objects)
{
StringBuffer sb = new StringBuffer();
sb.append("[");
for (int i = 0; i < objects.length; i++)
{
sb.append(objects[i]);
sb.append(",");
}
sb.append("]");
System.out.println(sb.toString());
}
private static void testImagesMetadata(String chosenPlate)
{
Object[][] meta = OpenBISScreeningML.getImagesMetadata(chosenPlate);
System.out.println(String.format("Number of tiles: %s. Plate geometry %sx%s", meta[0][2],
meta[0][5], meta[0][6]));
}
private static void testLoadDataset(String chosenPlate, String mountPoint,
String datasetTypePattern)
{
// Loads dataset with classification results.
// OpenBIS store diretcory is mounted locally in "/mount/openbis/store", so no data are
// copied and just a path to the appropriate location
// is returned.
Object[][] datasets =
OpenBISScreeningML.loadDataSets(chosenPlate, datasetTypePattern, mountPoint);
System.out.println("Path to the first downloaded dataset: " + datasets[0][1]);
}
private static void testLoadImage(String chosenPlate)
{
// fetch 3ed tile of well (1,1). The second call to fetch this image will return it from the
// local cache.
// The last optional parameter can specify a list of channels to load (otherwise all
// channels are loaded).
long start = System.currentTimeMillis();
Object[][][] images = OpenBISScreeningML.loadImages(chosenPlate, 1, 1, 3, new String[]
{ "CY3" });
System.out.println("Image path: " + images[0][0][0]);
System.out.println("Took: " + (System.currentTimeMillis() - start));
}
private static void testWellProperties(String chosenPlate)
{
// properties of well (2,4)
Object[][] props = OpenBISScreeningML.getWellProperties(chosenPlate, 2, 4);
for (int i = 0; i < props.length; i++)
{
System.out.println(String.format("Property %s = %s ", props[i][0], props[i][1]));
}
// save description of the well (2,4)
props = new Object[][]
{
{ "DESCRIPTION", "hello example" } };
OpenBISScreeningML.updateWellProperties(chosenPlate, 2, 4, props);
}
}