From 4eff4a061d69176569a96bcd02ba2c9cf6770494 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 16 Jun 2010 11:28:15 +0000
Subject: [PATCH] LMS-1569 Package renaming.
SVN: 16552
---
.../fvec/CSVToCanonicalFeatureVectorTest.java | 92 ---------
.../fvec/FeatureVectorUploaderTest.java | 193 ------------------
2 files changed, 285 deletions(-)
delete mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java
delete mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/FeatureVectorUploaderTest.java
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java
deleted file mode 100644
index f49f6d06b79..00000000000
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * Copyright 2010 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.
- */
-
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess.fvec;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import com.csvreader.CsvReader;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CSVToCanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CSVToCanonicalFeatureVector.CSVToCanonicalFeatureVectorConfiguration;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class CSVToCanonicalFeatureVectorTest extends AssertJUnit
-{
- @Test
- public void testConversion() throws IOException
- {
- CSVToCanonicalFeatureVectorConfiguration config =
- new CSVToCanonicalFeatureVectorConfiguration("WellName", "WellName", true);
- CSVToCanonicalFeatureVector convertor =
- new CSVToCanonicalFeatureVector(getDatasetFileLines(), config);
- ArrayList<CanonicalFeatureVector> fvs = convertor.convert();
- // Not all the the columns contain numerical data
- assertEquals(16, fvs.size());
- }
-
- /**
- * Return the tabular data as a DatasetFileLines.
- */
- protected DatasetFileLines getDatasetFileLines() throws IOException
- {
- File file =
- new File(
- "sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/CP037-1df.csv");
- CsvReader reader = getCsvReader(file);
- List<String[]> lines = new ArrayList<String[]>();
- while (reader.readRecord())
- {
- lines.add(reader.getValues());
- }
-
- return new DatasetFileLines(file, "test", lines);
-
- }
-
- /**
- * Get a CsvReader for parsing a tabular data file.
- */
- protected CsvReader getCsvReader(File file) throws IOException
- {
- if (file.isFile() == false)
- {
- throw new UserFailureException(file + " does not exist or is not a file.");
- }
- FileInputStream fileInputStream = new FileInputStream(file);
-
- CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
- csvReader.setDelimiter(';');
- csvReader.setSkipEmptyRecords(true);
- csvReader.setUseComments(true);
- csvReader.setComment('#');
-
- return csvReader;
- }
-}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/FeatureVectorUploaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/FeatureVectorUploaderTest.java
deleted file mode 100644
index 6ef0fe8a841..00000000000
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/FeatureVectorUploaderTest.java
+++ /dev/null
@@ -1,193 +0,0 @@
-/*
- * Copyright 2010 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.
- */
-
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess.fvec;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.convert.NativeTaggedArray;
-import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
-import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.AbstractDBTest;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.DBUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorUploader;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class FeatureVectorUploaderTest extends AbstractDBTest
-{
- private static final String EXP_PERM_ID = "expFvuId";
-
- private static final String CONTAINER_PERM_ID = "cFvuId";
-
- private static final String DS_PERM_ID = "dsFvuId";
-
- private static final String TEST_FEATURE_NAME = "test";
-
- private IImagingUploadDAO dao;
-
- @BeforeClass(alwaysRun = true)
- public void init() throws SQLException
- {
- dao = DBUtils.getQuery(datasource, IImagingUploadDAO.class);
- }
-
- @Test
- public void testInit()
- {
- // tests that parameter bindings in all queries are correct
- }
-
- @Test
- public void testCreateFeatureValues()
- {
- ScreeningContainerDatasetInfo info = new ScreeningContainerDatasetInfo();
- info.setExperimentPermId(EXP_PERM_ID);
- info.setContainerPermId(CONTAINER_PERM_ID);
- info.setDatasetPermId(DS_PERM_ID);
- FeatureVectorUploader uploader = new FeatureVectorUploader(dao, info);
- ArrayList<CanonicalFeatureVector> fvecs = new ArrayList<CanonicalFeatureVector>();
- new FeatureVectorProducer(fvecs).produce();
-
- uploader.uploadFeatureVectors(fvecs);
-
- new FeatureVectorVerifier(fvecs.get(0).getFeatureDef().getDataSetId()).verify();
- }
-
- // Class should be non-static to call the assert methods
- private class FeatureVectorVerifier
- {
- private final long datasetId;
-
- // Execution state
- private ImgFeatureDefDTO featureDef;
-
- private ImgFeatureValuesDTO featureValues;
-
- private int count;
-
- private FeatureVectorVerifier(long datasetId)
- {
- this.datasetId = datasetId;
- }
-
- private void verify()
- {
- List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetId(datasetId);
- assertEquals(2, featureDefs.size());
-
- count = 0;
- featureDef = featureDefs.get(count);
- verifyFeatureDef();
-
- featureDef = featureDefs.get(++count);
- verifyFeatureDef();
- }
-
- private void verifyFeatureDef()
- {
- assertEquals(TEST_FEATURE_NAME + count, featureDef.getName());
- List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
- assertEquals(1, featureValuesList.size());
- featureValues = featureValuesList.get(0);
- verifyFeatureValues();
- }
-
- private void verifyFeatureValues()
- {
- assertEquals(0.0, featureValues.getT());
- assertEquals(0.0, featureValues.getZ());
-
- MDDoubleArray spreadsheet =
- NativeTaggedArray.tryToDoubleArray(featureValues.getValues());
- int[] dims =
- { 3, 5 };
- int[] spreadsheetDims = spreadsheet.dimensions();
- assertEquals(spreadsheetDims.length, dims.length);
- assertEquals(spreadsheetDims[0], dims[0]);
- assertEquals(spreadsheetDims[1], dims[1]);
-
- for (int i = 0; i < dims[0]; ++i)
- {
- for (int j = 0; j < dims[1]; ++j)
- {
- assertEquals((double) (i + j), spreadsheet.get(i, j));
- }
- }
- }
- }
-
- private static class FeatureVectorProducer
- {
- private final ArrayList<CanonicalFeatureVector> fvecs;
-
- private FeatureVectorProducer(ArrayList<CanonicalFeatureVector> fvecs)
- {
- this.fvecs = fvecs;
- }
-
- private void produce()
- {
-
- fvecs.add(createFeatureVector(0, 3, 5));
- fvecs.add(createFeatureVector(1, 3, 5));
- }
-
- private CanonicalFeatureVector createFeatureVector(int i, int rowCount, int columnCount)
- {
- CanonicalFeatureVector fvec = new CanonicalFeatureVector();
-
- String featureName = TEST_FEATURE_NAME + i;
- String featureDesc = featureName + " desc";
- ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO(featureName, featureDesc, 0);
- fvec.setFeatureDef(featureDef);
- byte[] values = createValues(rowCount, columnCount);
- ImgFeatureValuesDTO featureValues = new ImgFeatureValuesDTO(0.0, 0.0, values, 0);
-
- fvec.setValues(Collections.singletonList(featureValues));
-
- return fvec;
- }
-
- private byte[] createValues(int rowCount, int columnCount)
- {
- int[] dims =
- { rowCount, columnCount };
- MDDoubleArray array = new MDDoubleArray(dims);
- for (int i = 0; i < dims[0]; ++i)
- {
- for (int j = 0; j < dims[1]; ++j)
- {
- array.set(i + j, i, j);
- }
- }
- return NativeTaggedArray.toByteArray(array);
- }
- }
-}
--
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