LMS-740 ExternalData and dependent classes moved from 'lims_base' to 'openbis'

SVN: 9738

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java

+/*
+ * Copyright 2007 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.generic.shared;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * <b>LIMS</b> <i>Web Service</i> interface for the <b>ETL</b> (<i>Extract, Transform, Load</i>)
+ * server.
+ * 
+ * @author Christian Ribeaud
+ */
+public interface IETLLIMSService extends IWebService, IDataStoreInfoProvider
+{
+    /**
+     * Returns the home database instance.
+     */
+    public DatabaseInstancePE getHomeDatabaseInstance();
+
+    /**
+     * Gets an {@link ExperimentPE} object specified by experiment ID and sample code.
+     * 
+     * @param sessionToken the user authentication token. Must not be <code>null</code>.
+     * @param sampleIdentifier an identifier which uniquely identifies the sample.
+     * @return <code>null</code> if no experiment could be found for given <var>dataSetInfo</var>.
+     */
+    public ExperimentPE getBaseExperiment(final String sessionToken,
+            final SampleIdentifier sampleIdentifier) throws UserFailureException;
+
+    /**
+     * Tries to return the properties of the top sample (e.g. master plate) registered for the
+     * specified sample code.
+     * 
+     * @param sessionToken the user authentication token. Must not be <code>null</code>.
+     * @param sampleIdentifier an identifier which uniquely identifies the sample.
+     * @return <code>null</code> if no appropriated sample found. Returns an empty array if a a
+     *         sample found with no properties.
+     */
+    public SamplePropertyPE[] getPropertiesOfTopSampleRegisteredFor(final String sessionToken,
+            final SampleIdentifier sampleIdentifier) throws UserFailureException;
+
+    /**
+     * Registers the specified data.
+     * 
+     * @param sessionToken The user authentication token. Must not be <code>null</code>.
+     * @param sampleIdentifier an identifier which uniquely identifies the sample.
+     * @param procedureTypeCode Type of the procedure for which this data set will be registered.
+     * @param externalData Data set to be registered. It is assumed that the attributes
+     *            <code>location</code>, <code>fileFormatType</code>, <code>dataSetType</code>,
+     *            and <code>locatorType</code> are not-<code>null</code>.
+     * @throws UserFailureException if given data set code could not be found in the persistence
+     *             layer.
+     */
+    public void registerDataSet(final String sessionToken, final SampleIdentifier sampleIdentifier,
+            final String procedureTypeCode, final ExternalData externalData)
+            throws UserFailureException;
+
+    /**
+     * Creates and returns a unique code for a new data set.
+     */
+    public String createDataSetCode(final String sessionToken) throws UserFailureException;
+
+}
\ No newline at end of file

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetType.java

+/*
+ * Copyright 2007 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.generic.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about an data set type.
+ * 
+ * @author Christian Ribeaud
+ */
+public final class DataSetType extends EntityType
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    public DataSetType()
+    {
+    }
+
+    public DataSetType(final String code)
+    {
+        setCode(code);
+    }
+}

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityType.java

+/*
+ * Copyright 2008 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.generic.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * An <i>abstract</i> <code>Code</code> extension for types.
+ * 
+ * @author Christian Ribeaud
+ */
+public class EntityType extends Code<EntityType> implements IEntityType
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    private String description;
+
+    public EntityType()
+    {
+    }
+
+    public EntityType(final String code, final String description)
+    {
+        setCode(code);
+        setDescription(description);
+    }
+
+    //
+    // IEntityType
+    //
+
+    public final String getDescription()
+    {
+        return description;
+    }
+
+    public final void setDescription(final String description)
+    {
+        this.description = description;
+    }
+}

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java

+/*
+ * Copyright 2007 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.generic.shared.dto;
+
+import java.util.Date;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.common.types.BooleanOrUnknown;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about external data.
+ * 
+ * @author Christian Ribeaud
+ */
+public final class ExternalData extends ExtractableData
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    private String location;
+
+    private StorageFormat storageFormat;
+
+    private Date registrationDate;
+
+    private FileFormatType fileFormatType;
+
+    private DataSetType dataSetType;
+
+    private LocatorType locatorType;
+
+
+    private BooleanOrUnknown complete = BooleanOrUnknown.U;
+
+    private String associatedSampleCode;
+
+    /** Returns <code>dataSetType</code>. */
+    public final DataSetType getDataSetType()
+    {
+        return dataSetType;
+    }
+
+    /** Sets <code>dataSetType</code>. */
+    public final void setDataSetType(final DataSetType dataSetType)
+    {
+        this.dataSetType = dataSetType;
+    }
+
+    /** Returns <code>locator</code>. */
+    public final String getLocation()
+    {
+        return location;
+    }
+
+    /** Sets <code>locator</code>. */
+    public final void setLocation(final String locator)
+    {
+        this.location = locator;
+    }
+
+    /**
+     * Returns the storage format (proprietary or BDS) of this external data set.
+     */
+    public StorageFormat getStorageFormat()
+    {
+        return storageFormat;
+    }
+
+    /**
+     * Sets the storage format (proprietary or BDS) of this external data set.
+     */
+    public void setStorageFormat(final StorageFormat storageFormat)
+    {
+        this.storageFormat = storageFormat;
+    }
+
+    /** Returns the date when the data set has been registered to the database. */
+    public Date getRegistrationDate()
+    {
+        return registrationDate;
+    }
+
+    /** Sets the date when the data set has been registered to the database. */
+    public void setRegistrationDate(final Date registrationDate)
+    {
+        this.registrationDate = registrationDate;
+    }
+
+    /** Returns <code>fileFormatType</code>. */
+    public final FileFormatType getFileFormatType()
+    {
+        return fileFormatType;
+    }
+
+    /** Sets <code>fileFormatType</code>. */
+    public final void setFileFormatType(final FileFormatType fileFormatType)
+    {
+        this.fileFormatType = fileFormatType;
+    }
+
+    /** Returns <code>locatorType</code>. */
+    public final LocatorType getLocatorType()
+    {
+        return locatorType;
+    }
+
+    /** Sets <code>locatorType</code>. */
+    public final void setLocatorType(final LocatorType locatorType)
+    {
+        this.locatorType = locatorType;
+    }
+
+
+    /**
+     * Returns {@link BooleanOrUnknown#T}, if the data set is complete in the data store and
+     * {@link BooleanOrUnknown#F}, if some parts of the data are missing. If the completeness is
+     * not known (e.g. because the data set is stored in a format that does not allow to assess the
+     * completeness, {@link BooleanOrUnknown#U} is returned.
+     */
+    public final BooleanOrUnknown getComplete()
+    {
+        return complete;
+    }
+
+    /**
+     * Sets whether this data set is complete in the data store or not. The default is
+     * {@link BooleanOrUnknown#U}, which corresponds to the case where the data are stored in a
+     * format that does not allow to assess completeness.
+     */
+    public final void setComplete(final BooleanOrUnknown complete)
+    {
+        this.complete = complete;
+    }
+
+    public String getAssociatedSampleCode()
+    {
+        return associatedSampleCode;
+    }
+
+    public void setAssociatedSampleCode(final String sampleCode)
+    {
+        this.associatedSampleCode = sampleCode;
+    }
+
+    //
+    // Object
+    //
+
+    @Override
+    public final boolean equals(final Object obj)
+    {
+        if (obj == this)
+        {
+            return true;
+        }
+        if (obj instanceof ExternalData == false)
+        {
+            return false;
+        }
+        final ExternalData that = (ExternalData) obj;
+        final EqualsBuilder builder = new EqualsBuilder();
+        builder.append(that.location, location);
+        return builder.isEquals();
+    }
+
+    @Override
+    public final int hashCode()
+    {
+        final HashCodeBuilder builder = new HashCodeBuilder();
+        builder.append(location);
+        return builder.toHashCode();
+    }
+
+    //
+    // Comparable
+    //
+
+    /**
+     * If <code>null</code> values are present for <code>code</code>, then they come first.
+     */
+    @Override
+    public final int compareTo(final ExtractableData o)
+    {
+        final String thatLocation = ((ExternalData) o).location;
+        if (location == null)
+        {
+            return thatLocation == null ? 0 : -1;
+        }
+        if (thatLocation == null)
+        {
+            return 1;
+        }
+        return location.compareTo(thatLocation);
+    }
+
+}
\ No newline at end of file

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java

+/*
+ * Copyright 2008 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.generic.shared.dto;
+
+import java.util.Date;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A basic {@link ExternalData} object.
+ * <p>
+ * {@link ExternalData} extends this class and completes it with additional fields.
+ * </p>
+ * 
+ * @author Christian Ribeaud
+ */
+public class ExtractableData extends Code<ExtractableData>
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    private Date productionDate;
+
+    private String dataProducerCode;
+
+    private String parentDataSetCode;
+
+    /**
+     * Returns the date when the measurement / calculation that produced this external data set has
+     * been performed.
+     * <p>
+     * This may not be known in which case this method will return <code>null</code>.
+     */
+    public Date getProductionDate()
+    {
+        return productionDate;
+    }
+
+    /**
+     * Sets the date when the measurement / calculation that produced this external data set has
+     * been performed.
+     */
+    public void setProductionDate(final Date productionDate)
+    {
+        this.productionDate = productionDate;
+    }
+
+    /**
+     * Returns the code identifying the data source (i.e. measurement device or software pipeline)
+     * that produced this external data set.
+     * <p>
+     * This may not be known in which case this method will return <code>null</code>.
+     */
+    public String getDataProducerCode()
+    {
+        return dataProducerCode;
+    }
+
+    /**
+     * Sets the code identifying the data source (i.e. measurement device or software pipeline) that
+     * produced this external data set.
+     */
+    public void setDataProducerCode(final String dataProducerCode)
+    {
+        this.dataProducerCode = dataProducerCode;
+    }
+
+    public final String getParentDataSetCode()
+    {
+        return parentDataSetCode;
+    }
+
+    public final void setParentDataSetCode(String parentDataSetCode)
+    {
+        this.parentDataSetCode = parentDataSetCode;
+    }
+}

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatType.java

+/*
+ * Copyright 2007 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.generic.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a file format type.
+ * 
+ * @author Christian Ribeaud
+ */
+public final class FileFormatType extends EntityType
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    public static final String DEFAULT_FILE_FORMAT_TYPE_CODE = "TIFF";
+
+    public FileFormatType()
+    {
+    }
+
+    public FileFormatType(final String code)
+    {
+        setCode(code);
+    }
+}

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorType.java

+/*
+ * Copyright 2007 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.generic.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
+ * know about a locator type.
+ * 
+ * @author Christian Ribeaud
+ */
+public final class LocatorType extends EntityType
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    public static final String DEFAULT_LOCATOR_TYPE_CODE = "RELATIVE_LOCATION";
+
+    public LocatorType()
+    {
+    }
+
+    public LocatorType(final String code)
+    {
+        setCode(code);
+    }
+}
\ No newline at end of file

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureType.java

+/*
+ * Copyright 2007 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.generic.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a procedure type.
+ * 
+ * @author Christian Ribeaud
+ */
+public final class ProcedureType extends EntityType
+{
+    private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+    private boolean dataAcquisition;
+
+    public ProcedureType()
+    {
+    }
+
+    public ProcedureType(final String code)
+    {
+        ProcedureTypeCode procedureTypeCode = ProcedureTypeCode.getProcedureTypeCode(code);
+        setCode(procedureTypeCode.getCode());
+        // TODO 2008-04-17, Franz-Josef Elmer: data acquisition flag should come from application
+        // server
+        setDataAcquisition(procedureTypeCode == ProcedureTypeCode.DATA_ACQUISITION);
+    }
+
+    /**
+     * Returns <code>true</code> if and only if this procedure type represents a data acquisition
+     * (or measurement) rather than a data processing (or derivation) step in a workflow.
+     */
+    public final boolean isDataAcquisition()
+    {
+        return dataAcquisition;
+    }
+
+    /**
+     * Sets the attribute which determines whether this procedure type represents a data acquisition
+     * (or measurement) rather than a data processing (or derivation) step in a workflow.
+     */
+    public final void setDataAcquisition(final boolean dataAcquisition)
+    {
+        this.dataAcquisition = dataAcquisition;
+    }
+}