LMS-1569 Code for interacting with the feature defs and feature values tables.

SVN: 16465

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IFeatureVectorDAO.java

+/*
+ * 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;
+
+import java.util.List;
+
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TransactionQuery;
+
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.ByteArrayMapper;
+
+/**
+ * DAO for interacting with feature vector tables.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface IFeatureVectorDAO extends TransactionQuery
+{
+    public static final int FETCH_SIZE = 1000;
+
+    @Select("SELECT * from FEATURE_DEFS where PERM_ID = ?{1}")
+    public ImgImageDTO tryGetFeatureDef(long channelId, long datasetId, Location tileLocation,
+            Location wellLocation);
+
+    // Simple Getters
+    @Select("SELECT * from FEATURE_DEFS where DS_ID = ?{1}")
+    public List<ImgFeatureDefDTO> listFeatureDefsByDataSetId(long dataSetId);
+
+    @Select("SELECT * from FEATURE_VALUES where FD_ID = ?{1.id}")
+    public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDev);
+
+    // Inserts
+    @Select("INSERT into FEATURE_DEFS (NAME, DESCRIPTION, DS_ID) values "
+            + "(?{1.name}, ?{1.description}, ?{1.dataSetId}) RETURNING ID")
+    public long addFeatureDef(ImgFeatureDefDTO featureVectorDef);
+
+    @Select(value = "INSERT into FEATURE_VALUES (BYTEA, Z_in_M, T_in_SEC, FD_ID, DS_ID) values "
+            + "(?{1.values}, ?{1.z}, ?{1.t}, ?{1.featureDefId}, ?{1.dataSetId}) RETURNING ID", parameterBindings =
+        { ByteArrayMapper.class })
+    public long addFeatureValues(ImgFeatureValuesDTO featureVectorDef);
+}

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureDefDTO.java

+/*
+ * 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;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
+/**
+ * Corresponds to a row in the FEATURE_DEFS table.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImgFeatureDefDTO extends AbstractHashable
+{
+    @AutoGeneratedKeys
+    private long id;
+
+    @ResultColumn("NAME")
+    private String name;
+
+    @ResultColumn("DESCRIPTION")
+    private String description;
+
+    @ResultColumn("DS_ID")
+    private long dataSetId;
+
+    @SuppressWarnings("unused")
+    private ImgFeatureDefDTO()
+    {
+        // All Data-Object classes must have a default constructor.
+    }
+
+    public ImgFeatureDefDTO(String name, String description, long dataSetId)
+    {
+        this.name = name;
+        this.description = description;
+        this.dataSetId = dataSetId;
+    }
+
+    public long getId()
+    {
+        return id;
+    }
+
+    public void setId(long id)
+    {
+        this.id = id;
+    }
+
+    public String getName()
+    {
+        return name;
+    }
+
+    public void setName(String name)
+    {
+        this.name = name;
+    }
+
+    public long getDataSetId()
+    {
+        return dataSetId;
+    }
+
+    public void setDataSetId(long dataSetId)
+    {
+        this.dataSetId = dataSetId;
+    }
+
+    public String getDescription()
+    {
+        return description;
+    }
+
+    public void setDescription(String description)
+    {
+        this.description = description;
+    }
+
+}

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureValuesDTO.java

+/*
+ * 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;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
+/**
+ * Corresponds to a row in the FEATURE_VALUES table.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImgFeatureValuesDTO extends AbstractHashable
+{
+    @AutoGeneratedKeys
+    private long id;
+
+    @ResultColumn("Z_IN_M")
+    private Double z;
+
+    @ResultColumn("T_IN_SEC")
+    private Double t;
+
+    @ResultColumn("VALUES")
+    private byte[] values;
+
+    @ResultColumn("FD_ID")
+    private long featureDefId;
+
+    @ResultColumn("DS_ID")
+    private long dataSetId;
+
+    @SuppressWarnings("unused")
+    private ImgFeatureValuesDTO()
+    {
+        // All Data-Object classes must have a default constructor.
+    }
+
+    public ImgFeatureValuesDTO(Double zInM, Double tInSec, byte[] values, long featureDefId,
+            long dataSetId)
+    {
+        this.z = zInM;
+        this.t = tInSec;
+        this.values = values;
+        this.featureDefId = featureDefId;
+        this.dataSetId = dataSetId;
+    }
+
+    public long getId()
+    {
+        return id;
+    }
+
+    public void setId(long id)
+    {
+        this.id = id;
+    }
+
+    /**
+     * Z in meters
+     */
+    public Double getZ()
+    {
+        return z;
+    }
+
+    public void setZ(Double zInM)
+    {
+        this.z = zInM;
+    }
+
+    public byte[] getValues()
+    {
+        return values;
+    }
+
+    public void setValues(byte[] values)
+    {
+        this.values = values;
+    }
+
+    public long getFeatureDefId()
+    {
+        return featureDefId;
+    }
+
+    public void setFeatureDefId(Integer featureDefId)
+    {
+        this.featureDefId = featureDefId;
+    }
+
+    public long getDataSetId()
+    {
+        return dataSetId;
+    }
+
+    public void setDataSetId(long dataSetId)
+    {
+        this.dataSetId = dataSetId;
+    }
+
+    /**
+     * Time in seconds
+     */
+    public Double getT()
+    {
+        return t;
+    }
+
+    public void setT(Double tInSec)
+    {
+        this.t = tInSec;
+    }
+
+}