D-Net

{"type_source": "SVN", "goal": "package -U -T 4C source:jar", "url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet40/modules/dnet-objectstore-rmi/trunk/", "deploy_repository": "dnet4-snapshots", "version": "4", "mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it, claudio.atzori@isti.cnr.it, alessia.bardi@isti.cnr.it", "deploy_repository_url": "http://maven.research-infrastructures.eu/nexus/content/repositories/dnet4-snapshots", "name": "dnet-objectstore-rmi"}

package eu.dnetlib.data.objectstore.rmi;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

import org.junit.Test;

public class ObjectStoreFileTest {

	private final String inputJson = "{\"objectID\":\"1\",\"mimeType\":\"PDF\",\"accessProtocol\":\"FTP\",\"URI\":\"prova=p\",\"usernameAuth\":\"user\",\"passwordAuth\":\"pass\",\"fileSizeKB\":0}";

	@Test

	public void testSerializeObjectStoreFile() {

		ObjectStoreFile f = new ObjectStoreFile();

		f.setAccessProtocol(Protocols.FTP);

		f.setMimeType("PDF");

		f.setObjectID("1");

		f.setPasswordAuth("pass");

		f.setUsernameAuth("user");

		f.setURI("prova=p");

		System.out.println(f.toJSON());

		assertNotNull(f.toJSON());

	}

	@Test

	public void testDeserializeObjectStoreFile() {

		ObjectStoreFile f = ObjectStoreFile.createObject(inputJson);

		assertNotNull(f);

		assertEquals(inputJson, f.toJSON());

	}

}

package eu.dnetlib.data.objectstore.rmi;

import java.io.FileInputStream;

import java.io.IOException;

import java.net.URL;

import org.apache.commons.io.IOUtils;

import org.junit.Assert;

import org.junit.Test;

import eu.dnetlib.data.objectstore.rmi.MetadataObjectRecord;

public class MetadataObjectRecordTest {

	@Test

	public void test() throws IOException {

		URL resource = MetadataObjectRecordTest.class.getResource("input.xml");

		FileInputStream inputStream = new FileInputStream(resource.getPath());

		String everything = IOUtils.toString(inputStream);

		MetadataObjectRecord record = new MetadataObjectRecord();

		record.setId("1");

		record.setRecord(everything);

		MetadataObjectRecord newrecord = MetadataObjectRecord.initFromJson(record.toJSON());

		Assert.assertEquals(everything, newrecord.getRecord());

		inputStream.close();

	}

}

<?xml version="1.0" encoding="UTF-8"?>

<oai:record xmlns:oai="http://www.openarchives.org/OAI/2.0/"

	xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:oaf="http://namespace.openaire.eu/oaf"

	xmlns:dnet="eu.dnetlib.data.transform.xml.DataciteToHbaseXsltFunctions">

	<header>

		<dri:objIdentifier>issn18663516::00024ad2ad3c0d32eee67c9a6bc4a54a

		</dri:objIdentifier>

		<dri:recordIdentifier>WOS:000308558000053</dri:recordIdentifier>

		<dri:dateOfCollection>2013-10-29T12:45:29+01:00</dri:dateOfCollection>

		<dri:repositoryId>ac41dbfc-9f0e-479d-8489-fd6596c3858a_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU=

		</dri:repositoryId>

		<oaf:datasourceprefix>issn18663516</oaf:datasourceprefix>

	</header>

	<metadata>

		<csvRecord>

			<row name="OA">false</row>

			<row name="PT">J</row>

			<row name="AU">Ribeiro, RM; Li, H; Wang, SY; Stoddard, MB; Learn, GH;

				Korber, BT; Bhattacharya, T; Guedj, J; Parrish, EH; Hahn, BH; Shaw,

				GM; Perelson, AS</row>

			<row name="BA" />

			<row name="BE" />

			<row name="GP" />

			<row name="AF">Ribeiro, Ruy M.; Li, Hui; Wang, Shuyi; Stoddard, Mark

				B.; Learn, Gerald H.; Korber, Bette T.; Bhattacharya, Tanmoy; Guedj,

				Jeremie; Parrish, Erica H.; Hahn, Beatrice H.; Shaw, George M.;

				Perelson, Alan S.</row>

			<row name="BF" />

			<row name="CA" />

			<row name="TI">Quantifying the Diversification of Hepatitis C Virus

				(HCV) during Primary Infection: Estimates of the In Vivo Mutation

				Rate</row>

			<row name="SO">PLOS PATHOGENS</row>

			<row name="SE" />

			<row name="LA">English</row>

			<row name="DT">Article</row>

			<row name="CT" />

			<row name="CY" />

			<row name="CL" />

			<row name="SP" />

			<row name="HO" />

			<row name="DE" />

			<row name="ID">VIRAL DYNAMICS; SUPERINFECTION EXCLUSION; PHYLOGENETIC

				ANALYSIS; REPLICATION MODE; DRUG-RESISTANCE; RNA VIRUSES; CELLS;

				POPULATION; INTERFERON; DIVERSITY</row>

			<row name="AB">Hepatitis C virus (HCV) is present in the host with

				multiple variants generated by its error prone RNA-dependent RNA

				polymerase. Little is known about the initial viral diversification

				and the viral life cycle processes that influence diversity. We

				studied the diversification of HCV during acute infection in 17

				plasma donors, with frequent sampling early in infection. To analyze

				these data, we developed a new stochastic model of the HCV life

				cycle. We found that the accumulation of mutations is surprisingly

				slow: at 30 days, the viral population on average is still 46%

				identical to its transmitted viral genome. Fitting the model to the

				sequence data, we estimate the median in vivo viral mutation rate is

				2.5 x 10(-5) mutations per nucleotide per genome replication (range

				1.6-6.2 x 10(-5)), about 5-fold lower than previous estimates. To

				confirm these results we analyzed the frequency of stop codons (N =

				10) among all possible non-sense mutation targets (M = 898,335), and

				found a mutation rate of 2.8-3.2 x 10(-5), consistent with the

				estimate from the dynamical model. The slow accumulation of

				mutations is consistent with slow turnover of infected cells and

				replication complexes within infected cells. This slow turnover is

				also inferred from the viral load kinetics. Our estimated mutation

				rate, which is similar to that of other RNA viruses (e.g., HIV and

				influenza), is also compatible with the accumulation of

				substitutions seen in HCV at the population level. Our model

				identifies the relevant processes (long-lived cells and slow

				turnover of replication complexes) and parameters involved in

				determining the rate of HCV diversification.</row>

			<row name="C1">[Ribeiro, Ruy M.; Korber, Bette T.; Bhattacharya,

				Tanmoy; Guedj, Jeremie; Perelson, Alan S.] Los Alamos Natl Lab, Div

				Theoret, Los Alamos, NM USA; [Li, Hui; Wang, Shuyi; Stoddard, Mark

				B.; Learn, Gerald H.; Parrish, Erica H.; Hahn, Beatrice H.; Shaw,

				George M.] Univ Penn, Perelman Sch Med, Philadelphia, PA 19104 USA

			</row>

			<row name="RP">Ribeiro, RM (reprint author), Univ Lisbon, Fac Med,

				Inst Med Mol, Lisbon, Portugal.</row>

			<row name="EM">asp@lanl.gov</row>

			<row name="RI" />

			<row name="FU">U. S. Department of Energy [DE-AC52-06NA25396];

				National Center for Research Resources; Office of Research

				Infrastructure Programs (ORIP) of the National Institutes of Health

				(NIH) [8R01-OD011095-21]; NIH Center for HIV/AIDS Vaccine Immunology

				[AI67854]; NIH [AI028433, P20-RR018754, AI45008, AI27767];

				University of Pennsylvania Center for AIDS Research; European Union

				[PCOFUND-GA-2009-246542]; Foundation for Science and Technology of

				Portugal</row>

			<row name="FX">Portions of this work were done under the auspices of

				the U. S. Department of Energy under contract DE-AC52-06NA25396 and

				supported by the National Center for Research Resources and the

				Office of Research Infrastructure Programs (ORIP) of the National

				Institutes of Health (NIH) through Grant Number 8R01-OD011095-21,

				the NIH Center for HIV/AIDS Vaccine Immunology (AI67854) and through

				NIH grants AI028433, P20-RR018754, AI45008 and AI27767 and by a

				developmental grant from the University of Pennsylvania Center for

				AIDS Research. RMR has received partial funding from the European

				Union 7th Framework Programme under grant no PCOFUND-GA-2009-246542

				and from the Foundation for Science and Technology of Portugal. The

				funders had no role in study design, data collection and analysis,

				decision to publish, or preparation of the manuscript.</row>

			<row name="CR" />

			<row name="NR">64</row>

			<row name="TC">1</row>

			<row name="Z9">1</row>

			<row name="PU">PUBLIC LIBRARY SCIENCE</row>

			<row name="PI">SAN FRANCISCO</row>

			<row name="PA">1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111

				USA</row>

			<row name="SN">1553-7374</row>

			<row name="BN" />

			<row name="J9">PLOS PATHOG</row>

			<row name="JI">PLoS Pathog.</row>

			<row name="PD">AUG</row>

			<row name="PY">2012</row>

			<row name="VL">8</row>

			<row name="IS">8</row>

			<row name="PN" />

			<row name="SU" />

			<row name="SI" />

			<row name="MA" />

			<row name="BP" />

			<row name="EP" />

			<row name="AR">e1002881</row>

			<row name="DI">10.1371/journal.ppat.1002881</row>

			<row name="D2" />

			<row name="PG">13</row>

			<row name="WC">Microbiology; Parasitology; Virology</row>

			<row name="SC">Microbiology; Parasitology; Virology</row>

			<row name="GA">002TI</row>

			<row isID="true" name="UT">WOS:000308558000053</row>

		</csvRecord>

	</metadata>

</oai:record>

package eu.dnetlib.data.objectstore.rmi;

/**

 * The Class ObjectStoreFileNotFoundException.

 */

public class ObjectStoreFileNotFoundException extends ObjectStoreServiceException {

	/** The Constant serialVersionUID. */

	private static final long serialVersionUID = -5418923557898374219L;

	/**

	 * Instantiates a new object store file not found exception.

	 *

	 * @param string

	 *            the string

	 * @param exception

	 *            the exception

	 */

	public ObjectStoreFileNotFoundException(final String string) {

		super(string);

	}

}

package eu.dnetlib.data.objectstore.rmi;

import java.io.Serializable;

import java.util.Set;

import com.google.gson.Gson;

/**

 * The Class ObjectStoreFile.

 */

public class ObjectStoreFile implements Serializable {

	/** The Constant serialVersionUID. */

	private static final long serialVersionUID = -6501291693572693712L;

	/** The metadata related id. */

	private String metadataRelatedID;

	/** The object id. */

	private String objectID;

	/** The mime type. */

	private String mimeType;

	/** The access protocol. */

	private Protocols accessProtocol;

	/** The object uri . */

	private String URI;

	/** The username auth. */

	private String usernameAuth;

	/** The password auth. */

	private String passwordAuth;

	/** The downloaded url. */

	private String downloadedURL;

	/** The md5 sum of the file. */

	private String md5Sum;

	/** The file size. */

	private long fileSizeKB;

	/** The tags. */

	private Set<String> tags;

	/**

	 * Gets the downloaded url.

	 *

	 * @return the downloaded url

	 */

	public String getDownloadedURL() {

		return downloadedURL;

	}

	/**

	 * Sets the downloaded url.

	 *

	 * @param downloadedURL

	 *            the new downloaded url

	 */

	public void setDownloadedURL(final String downloadedURL) {

		this.downloadedURL = downloadedURL.replace("\\u003d", "=").replace("\\u0026", "&");;

	}

	/**

	 * Instantiates a new object store file.

	 */

	public ObjectStoreFile() {

		this.accessProtocol = Protocols.None;

	}

	/**

	 * Return a new instance of the object from a json String.

	 *

	 * @param jsonObject

	 *            the json object

	 * @return the object store file

	 */

	public static ObjectStoreFile createObject(final String jsonObject) {

		Gson g = new Gson();

		return g.fromJson(jsonObject, ObjectStoreFile.class);

	}

	/**

	 * Gets the object id.

	 *

	 * @return the object id

	 */

	public String getObjectID() {

		return objectID;

	}

	/**

	 * Sets the object id.

	 *

	 * @param objectID

	 *            the new object id

	 */

	public void setObjectID(final String objectID) {

		this.objectID = objectID;

	}

	/**

	 * Gets the mime type.

	 *

	 * @return the mime type

	 */

	public String getMimeType() {

		return mimeType;

	}

	/**

	 * Sets the mime type.

	 *

	 * @param mimeType

	 *            the new mime type

	 */

	public void setMimeType(final String mimeType) {

		this.mimeType = mimeType;

	}

	/**

	 * Gets the access protocol.

	 *

	 * @return the access protocol

	 */

	public Protocols getAccessProtocol() {

		return accessProtocol;

	}

	/**

	 * Sets the access protocol.

	 *

	 * @param accessProtocol

	 *            the new access protocol

	 */

	public void setAccessProtocol(final Protocols accessProtocol) {

		this.accessProtocol = accessProtocol;

	}

	/**

	 * Gets the username auth.

	 *

	 * @return the username auth

	 */

	public String getUsernameAuth() {

		return usernameAuth;

	}

	/**

	 * Sets the username auth.

	 *

	 * @param usernameAuth

	 *            the new username auth

	 */

	public void setUsernameAuth(final String usernameAuth) {

		this.usernameAuth = usernameAuth;

	}

	/**

	 * Gets the password auth.

	 *

	 * @return the password auth

	 */

	public String getPasswordAuth() {

		return passwordAuth;

	}

	/**

	 * Sets the password auth.

	 *

	 * @param passwordAuth

	 *            the new password auth

	 */

	public void setPasswordAuth(final String passwordAuth) {

		this.passwordAuth = passwordAuth;

	}

	/**

	 * Gets the uri.

	 *

	 * @return the uri

	 */

	public String getURI() {

		return URI.replace("\\u003d", "=").replace("\\u0026", "&");

	}

	/**

	 * Sets the uri.

	 *

	 * @param uRI

	 *            the new uri

	 */

	public void setURI(final String uRI) {

		URI = uRI.replace("\\u003d", "=").replace("\\u0026", "&");

	}

	/**

	 * Convert the object into a json String.

	 *

	 * @return the string

	 */

	public String toJSON() {

		Gson g = new Gson();

		return g.toJson(this).replace("\\u003d", "=").replace("\\u0026", "&");

	}

	/**

	 * Gets the related metadata id.

	 *

	 * @return the related metadata id.

	 */

	public String getMetadataRelatedID() {

		return metadataRelatedID;

	}

	/**

	 * Sets the related metadata id.

	 *

	 * @param metadataRelatedID

	 *            the related metadata id.

	 */

	public void setMetadataRelatedID(final String metadataRelatedID) {

		this.metadataRelatedID = metadataRelatedID;

	}

	/**

	 * @return the md5Sum

	 */

	public String getMd5Sum() {

		return md5Sum;

	}

	/**

	 * @param md5Sum

	 *            the md5Sum to set

	 */

	public void setMd5Sum(final String md5Sum) {

		this.md5Sum = md5Sum;

	}

	/**

	 * @return the fileSizeKB

	 */

	public long getFileSizeKB() {

		return fileSizeKB;

	}

	/**

	 * @param fileSizeKB

	 *            the fileSizeKB to set

	 */

	public void setFileSizeKB(final long fileSizeKB) {

		this.fileSizeKB = fileSizeKB;

	}

	/**

	 * @return the tags

	 */

	public Set<String> getTags() {

		return tags;

	}

	/**

	 * @param tags the tags to set

	 */

	public void setTags(Set<String> tags) {

		this.tags = tags;

	}

}

package eu.dnetlib.data.objectstore.rmi;

import eu.dnetlib.common.rmi.RMIException;

/**

 * The Class ObjectStoreServiceException.

 */

public class ObjectStoreServiceException extends RMIException {

	/** The Constant serialVersionUID. */

	private static final long serialVersionUID = -7073846285219543315L;

	/**

	 * Instantiates a new object store service exception.

	 *

	 * @param string

	 *            the string

	 */

	public ObjectStoreServiceException(final String string) {

		super(string);

	}

	/**

	 * Instantiates a new object store service exception.

	 *

	 * @param string

	 *            the string

	 * @param exception

	 *            the exception

	 */

	public ObjectStoreServiceException(final String string, final Throwable exception) {

		super(string, exception);

	}

	/**

	 * Instantiates a new object store service exception.

	 *

	 * @param exception

	 *            the exception

	 */

	public ObjectStoreServiceException(final Throwable exception) {

		super(exception);

	}

}

package eu.dnetlib.data.objectstore.rmi;

import java.util.List;

import javax.jws.WebMethod;

import javax.jws.WebParam;

import javax.jws.WebService;

import javax.xml.ws.wsaddressing.W3CEndpointReference;

import eu.dnetlib.common.rmi.BaseService;

// TODO: Auto-generated Javadoc

/**

 * Main ObjectStore Service interface.

 *

 * @author <a href="mailto:sandro.labruzzo at isti.cnr.it">Sandro La Bruzzo</a>

 * @version 0.0.1

 */

@WebService(targetNamespace = "http://services.dnetlib.eu/")

public interface ObjectStoreService extends BaseService {

	/**

	 * Returns ResultSet EPR for delivered ObjectStore records in a particular range date.

	 * <p>

	 * Please check service implementations for details on the expected format of the records in the result set epr.

	 * </p>

	 * <p>

	 * This method could be used for a bulk deliver of all objects in the store

	 * </p>

	 *

	 * @param obsId

	 *            identifier of the ObjectStore

	 * @param from

	 *            the minimum date of the object

	 * @param until

	 *            the maximum date of the object

	 * @return a ResultSet EPR. Each element of the result set contains the objIdentifier of a record and its URL for retrieve the

	 *         inputstream of the file.

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "deliverObjects", action = "deliverObjects")

	public W3CEndpointReference deliverObjects(@WebParam(name = "obsId") String obsId, @WebParam(name = "from") Long from, @WebParam(name = "until") Long until)

			throws ObjectStoreServiceException;

	/**

	 * Returns ResultSet EPR for delivered ObjectStore records.

	 * <p>

	 * Please check service implementations for details on the expected format of the records in the result set epr.

	 * </p>

	 *

	 * @param obsId

	 *            identifier of the ObjectStore

	 * @param eprId

	 *            id of a ResultSet EPR with the identifiers of the interesting objects. Each element of the result set contains the

	 *            objIdentifier of a record

	 * @return a ResultSet EPR. Each element of the result set contains the objIdentifier of a record and its URL for retrieve the

	 *         inputstream of the file.

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "deliverObjectsByIds", action = "deliverObjectsByIds")

	public W3CEndpointReference deliverObjectsByIds(@WebParam(name = "obsId") String obsId, @WebParam(name = "eprId") W3CEndpointReference eprId)

			throws ObjectStoreServiceException;

	/**

	 * deliver records with a specified tag.

	 *

	 * @param obsId

	 *            identifier of the ObjectStore

	 * @param tags

	 *            the tags

	 * @return the URL for retrieve the record

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "deliverRecordsByTag", action = "deliverRecordsByTag")

	public W3CEndpointReference deliverRecordsByTag(@WebParam(name = "obsId") String obsId, @WebParam(name = "tags") List<String> tags)

			throws ObjectStoreServiceException;

	/**

	 * Returns an URL to retrieve the ObjectStore record.

	 *

	 * @param obsId

	 *            identifier of the ObjectStore

	 * @param objectId

	 *            the id of the object

	 * @return the URL for retrieve the record

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "deliverRecord", action = "deliverRecord")

	public String deliverRecord(@WebParam(name = "obsId") String obsId, @WebParam(name = "objectId") String objectId) throws ObjectStoreServiceException;

	/**

	 * Feed the object in the objectStore.

	 *

	 * @param obsId

	 *            identifier of the ObjectStore

	 * @param objectMetadata

	 *            the String serialized of the JSON object ObjectStoreFile

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "feedObject", action = "feedObject")

	public void feedObject(@WebParam(name = "obsId") String obsId, @WebParam(name = "objectMetadata") String objectMetadata) throws ObjectStoreServiceException;

	/**

	 * Returns list of all stored indices.

	 *

	 * @return list of all stored indices

	 */

	@WebMethod(operationName = "getListOfObjectStores", action = "getListOfObjectStores")

	public List<String> getListOfObjectStores();

	/**

	 * Gets the size of the objectStore ID.

	 *

	 * @param obsId

	 *            the obs id

	 * @return the size

	 * @throws ObjectStoreServiceException

	 *             the object store service exception

	 */

	@WebMethod(operationName = "getSize", action = "getSize")

	public int getSize(@WebParam(name = "obsId") String obsId) throws ObjectStoreServiceException;

	/**

	 * Tag a set of of object with a particular tag.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param eprId

	 *            the epr id

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "tagIds", action = "tagIds")

	public int tagIds(@WebParam(name = "objectStoreId") String objectStoreId,

			@WebParam(name = "eprId") W3CEndpointReference eprId,

			@WebParam(name = "tag") String tag);

	/**

	 * Tag ids by a list of identifiers.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param ids

	 *            the ids

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "tagIdsByList", action = "tagIds")

	public int tagIdsByList(@WebParam(name = "objectStoreId") String objectStoreId,

			@WebParam(name = "ids") List<String> ids,

			@WebParam(name = "tag") String tag);

	/**

	 * UnTag a set of of object with a particular tag.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param eprId

	 *            the epr id

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "untagIds", action = "untagIds")

	public int untagIds(@WebParam(name = "objectStoreId") String objectStoreId,

			@WebParam(name = "eprId") W3CEndpointReference eprId,

			@WebParam(name = "tag") String tag);

	/**

	 * Untag ids by a list of identifiers.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param ids

	 *            the ids

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "untagIdsByList", action = "tagIds")

	public int untagIdsByList(@WebParam(name = "objectStoreId") String objectStoreId,

			@WebParam(name = "ids") List<String> ids,

			@WebParam(name = "tag") String tag);

	/**

	 * Tag all record of the objectstore with a particular tag.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "tagObjectstore", action = "tagObjectstore")

	public int tagObjectstore(@WebParam(name = "objectStoreId") String objectStoreId, @WebParam(name = "tag") String tag);

	/**

	 * UnTag all record of the objectstore with a particular tag.

	 *

	 * @param objectStoreId

	 *            the object store id

	 * @param tag

	 *            the tag

	 * @return the int

	 */

	@WebMethod(operationName = "untagObjectstore", action = "untagObjectstore")

	public int untagObjectstore(@WebParam(name = "objectStoreId") String objectStoreId, @WebParam(name = "tag") String tag);

}

package eu.dnetlib.data.objectstore.rmi;

/**

  * The Enum Protocols.

  */

 public enum Protocols {

	 None,

	 HTTP, 

	 HTTPS,

	 FTP,

	 File_System,

	 FTPS

}

package eu.dnetlib.data.objectstore.rmi;

import java.io.Serializable;

import com.google.gson.Gson;

public class MetadataObjectRecord implements Serializable {

	/** The Constant serialVersionUID. */

	private static final long serialVersionUID = -5640196854633924754L;

	public static MetadataObjectRecord initFromJson(final String input) {

		return new Gson().fromJson(input, MetadataObjectRecord.class);

	}

	public MetadataObjectRecord() {

	}

	public MetadataObjectRecord(final String id, final String record, final String mime) {

		super();

		this.id = id;

		this.record = record;

		this.mime = mime;

	}

	private String id;

	private String record;

	private String mime;

	public String getId() {

		return id;

	}

	public String getRecord() {

		return record;

	}

	public void setId(final String id) {

		this.id = id;

	}

	public void setRecord(final String record) {

		this.record = record;

	}

	public String toJSON() {

		return new Gson().toJson(this);

	}

	public String getMime() {

		return mime;

	}

	public void setMime(final String mime) {

		this.mime = mime;

	}

}

* {

	font-size: inherit;

	font-family: inherit;

}

@font-face {

  font-family: Helvetica Neue;

  src: url("Porcospino.eot");

  src: local("Helvetica Neue Light"), local("HelveticaNeue-Light"), url("Porcospino.woff") format("woff"), url("Porcospino.ttf") format("truetype"), url("Porcospino.svg#HelveticaNeue-Light") format("svg");

}

body {

    height: 100%;

	margin: 40px;

	background-color: #f3f1e5;

  font: 300 100.01%/1.5 "Helvetica Neue", Helvetica, "Arial Unicode MS", Arial, sans-serif; 

 	font-size: 16px;

  color:  	#333;

}

h1 {

	margin-top: 35px;

	font-size: 38px;

  padding:0;

}

h1.title {

	font-size: 52px;

  margin-bottom: 0;

}

h2 {

	margin-top: 35px;

	font-size: 28px;

  border-bottom: 1px solid #666;

}

h3 {

	margin-top: 35px;

	font-size: 20px;

  font-family: "HelveticaNeue-Light","Helvetica Neue Light","Helvetica Neue",Helvetica,Arial,sans-serif;

  font-weight: 200;

}

h4 {

	margin-top: 35px;

	font-size: 18px;

  font-family: "HelveticaNeue-Light","Helvetica Neue Light","Helvetica Neue",Helvetica,Arial,sans-serif;

  font-weight: 200;

}

code, pre, span.command {

	font-family:'andale mono','lucida console', monospace;

	font-size:1em;

}

table {

	border-collapse: collapse;

}

table th {

	background-color: #3E6B99;

	color: white;

	padding: 4px

}

table td {

	padding: 4px;

}

a { 

  color:#3E6B99; 

	font-weight:bold;

	text-decoration:none;

  font-family: 'Helvetica Neue',Helvetica,Arial,sans-serif;

}

a:visited { 

	color:#3E6B99;

}

a:hover { 

	color:#5184B9;

}

span.command {

	white-space:nowrap;

}

pre.programlisting {

	background-color: #FFFFDD;

	border: 1px solid #DDDD00;

	padding: 10px;

}

.authorgroup {

  font-size: 80%;

  margin-top: 24px;

    margin-left: 64px;

}

.authorgroup h3 {

  margin-bottom: 4px;

}

.author {

  margin: 0;

  margin-bottom: 4px;

 }

.affiliation {

  margin-top: 2px;

 }

.code, .screen {

  white-space: pre-line;

  margin: 12px;

  display: block;

  margin-right: 8px;

  margin-left: 8px;

  padding: 8px;

  width: 100%;

 }

.code, .screen, .note, .programlisting {

  border: 1px solid #FFFFFF;

  -moz-border-radius: 8px;

  -webkit-border-radius: 8px;

  -khtml-border-radius: 8px;

  border-radius: 8px;

 -moz-box-shadow: 3px 3px 5px #DFDFDF;

  -webkit-box-shadow: 3px 3px 5px #DFDFDF;

  -khtml-box-shadow: 3px 3px 5px #DFDFDF;

  -o-box-shadow: 3px 3px 5px #DFDFDF;

  box-shadow: 3px 3px 5px #DFDFDF;

  -moz-box-shadow: 2px 2px 4px #666;

  -webkit-box-shadow: 2px 2px 4px #666;

  box-shadow: 2px 2px 4px #666;

 }

.code {  background-color: #777777; }

.screen {  background-color: #fff8e3;  }

.note {  background-color: #fff8e3; margin-top: 24px; padding: 8px; padding-top: 0px; padding-bottom: 0px;}

.note p { margin-left: 16px; margin-top: 4px; }

.note h3 { margin-top: 8px; margin-bottom: 8px;}

.note .screen, .code { 

  width: auto;

}

.note .screen { 

  background-color: #fff7d3; 

 }

.prompt { 

-webkit-user-select:none;

-moz-user-select:-moz-none;

user-select: none;

 }

video 

{

  /*width: 400px; */

  height: 300px;

 -moz-box-shadow: 3px 3px 5px #444;

  -webkit-box-shadow: 3px 3px 5px #444;

  -khtml-box-shadow: 3px 3px 5px #444;

  -o-box-shadow: 3px 3px 5px #444;

  box-shadow: 3px 3px 5px #444;

  }

video.active

{ 

  position: fixed;

  margin-left: auto;

  margin-right: auto;

  top: 40px;

  left: 0;

  right: 0;

  bottom: 0;

    /*width: 90%; */

    height: 90%; 

  z-index: 7;

}

#videonav 

{ 

  position: fixed;

  top: 0;

  left: 0;

  display: none;

  z-index: 10;

}

#overlay 

{

position: fixed;

display: none;

opacity: 0.5;

  top: 0;

  left: 0;

background-color: black;

width: 100%; 

height: 100%; 

  z-index: 5;

 }

.set {

  margin-left: 160px;

  margin-right: 100px;

 }

h1,h2,h3,h4 {

  margin-left: -40px;

}

div.note h3 {

  margin-left: inherit;

}

/*

 * Copyright (c) 2001, 2003, 2010 The FreeBSD Documentation Project

 * All rights reserved.

 *

 * Redistribution and use in source and binary forms, with or without

 * modification, are permitted provided that the following conditions

 * are met:

 * 1. Redistributions of source code must retain the above copyright

 *    notice, this list of conditions and the following disclaimer.

 * 2. Redistributions in binary form must reproduce the above copyright

 *    notice, this list of conditions and the following disclaimer in the

 *    documentation and/or other materials provided with the distribution.

 *

 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND

 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

 * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE

 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS

 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)

 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT

 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY

 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF

 * SUCH DAMAGE.

 *

 * $FreeBSD: doc/share/misc/docbook.css,v 1.21 2012/01/25 22:16:36 wblock Exp $

 */

BODY ADDRESS {

	line-height: 1.3;

	margin: .6em 0;

}

BODY BLOCKQUOTE {

	margin-top: .75em;

	line-height: 1.3;

	margin-bottom: .75em;

}

HTML BODY {

	margin: 1em 8% 1em 10%;

	line-height: 1.2;

}

.LEGALNOTICE {

	font-size: small;

	font-variant: small-caps;

}

BODY DIV {

	margin: 0;

}

DL {

	margin: .8em 0;

	line-height: 1.2;

}

DIV.CALLOUTLIST DT {

	float: left;

	width: 1em;

}

DIV.CALLOUTLIST DD {

	clear: right;

	margin-bottom: 1ex;

}

BODY FORM {

	margin: .6em 0;

}

H1, H2, H3, H4, H5, H6,

DIV.EXAMPLE P B,

.QUESTION,

DIV.TABLE P B,

DIV.PROCEDURE P B {

	color: #990000;

}

BODY H1, BODY H2, BODY H3, BODY H4, BODY H5, BODY H6 {

	line-height: 1.3;

	margin-left: 0;

}

BODY H1, BODY H2 {

	margin: .8em 0 0 -4%;

}

BODY H3, BODY H4 {

	margin: .8em 0 0 -3%;

}

BODY H5 {

	margin: .8em 0 0 -2%;

}

BODY H6 {

	margin: .8em 0 0 -1%;

}

BODY HR {

	margin: .6em;

	border-width: 0 0 1px 0;

	border-style: solid;

	border-color: #cecece;

}

BODY IMG.NAVHEADER {

	margin: 0 0 0 -4%;

}

OL {

	margin: 0 0 0 5%;

	line-height: 1.2;

}

BODY PRE {

	margin: .75em 0;

	line-height: 1.0;

	font-family: monospace;

}

BODY TD, BODY TH {

	line-height: 1.2;

}

UL, BODY DIR, BODY MENU {

	margin: 0 0 0 5%;

	line-height: 1.2;

}

HTML {

	margin: 0;

	padding: 0;

}

BODY P B.APPLICATION {

	color: #000000;

}

.FILENAME {

	color: #007a00;

}

SVNREF {

	color: #007a00;

}

.GUIMENU, .GUIMENUITEM, .GUISUBMENU,

.GUILABEL, .INTERFACE,

.SHORTCUT, .SHORTCUT .KEYCAP {

	font-weight: bold;

}

.GUIBUTTON {

	background-color: #CFCFCF;

	padding: 2px;

}

.ACCEL {

	background-color: #F0F0F0;

	text-decoration: underline;

}

.SCREEN {

	padding: 1ex;

}

.PROGRAMLISTING {

	padding: 1ex;

	background-color: #eee;

	border: 1px solid #ccc;

	line-height: 1.1;

}

@media screen {  /* hide from IE3 */

	a[href]:hover { background: #ffa }

}

.INFORMALTABLE, .TABLE TH {

	padding-left: 02.em;

	text-align: left;

}

BLOCKQUOTE, .EXAMPLE, .PROGRAMLISTING {

	-moz-border-radius: 6px;

	-webkit-border-radius: 6px;

	-khtml-border-radius: 6px;

	border-radius: 6px;

}

BLOCKQUOTE {

	padding: 0 2ex;

}

BLOCKQUOTE.NOTE {

	color: #222;

	background: #eee;

	border: 1px solid #ccc;

	width: 85%;

}

BLOCKQUOTE.TIP {

	color: #004F00;

	background: #d8ecd6;

	border: 1px solid green;

	width: 85%;

}

BLOCKQUOTE.IMPORTANT {

	font-style:italic;

	border: 1px solid #a00;

	border-left: 12px solid #c00;

}

BLOCKQUOTE.WARNING {

	color: #9F1313;

	background: #f8e8e8;

	border: 1px solid #e59595;

	width: 85%;

}

BLOCKQUOTE.CAUTION {

	color: #3E3535;

	background: #FFC;

	border: 1px solid #e59595;

	width: 85%;

}

.EXAMPLE {

	background: #fefde6;

	border: 1px solid #f1bb16;

	margin: 1em 0;

	padding: 0.2em 2em;

	width: 90%;

}

.INFORMALTABLE TABLE.CALSTABLE TR TD {

        padding-left: 1em;

        padding-right: 1em;

}

<?xml version="1.0" encoding="UTF-8"?>

<?xml-model href="http://www.oasis-open.org/docbook/xml/5.0/rng/docbook.rng" schematypens="http://relaxng.org/ns/structure/1.0"?>

<?xml-model href="http://www.oasis-open.org/docbook/xml/5.0/rng/docbook.rng" type="application/xml" schematypens="http://purl.oclc.org/dsdl/schematron"?>

<book xmlns="http://docbook.org/ns/docbook"

    xmlns:xlink="http://www.w3.org/1999/xlink" version="5.0">

    <info>

        <title>DNet Object Store Module</title>

        <author>

            <orgname>ISTI CNR</orgname>

            <email>sandro.labruzzo@isti.cnr.it</email>

        </author>

    </info>

    <part>

        <title>ObjectStore API</title>

        <chapter>

            <title>Introduction</title>            

            <sect1>

                <title>What is an Object Store</title>                

                <para>Object Store Service is a DNet service that provides functions for perstistent

                    storage of files, and provides a REST API for fetching them back. </para>

                <para>It is composed by three different sub-modules:</para>

                <para>

                    <itemizedlist>

                        <listitem>

                            <para><link

                                    xlink:href="https://svn.driver.research-infrastructures.eu/driver/dnet11/modules/dnet-objectstore-rmi/trunk/"

                                    >dnet-objectstore -rmi</link>: it contains the interface of the

                                Object Store Service and includes some utility classes defining

                                metadata information for each file (i.e., ObjectStoreFile). These

                                metadata allow the Object Store Service to store and fetch the

                                associated files in a consistent way.</para>

                        </listitem>

                        <listitem>

                            <para><link

                                    xlink:href="https://svn.driver.research-infrastructures.eu/driver/dnet11/modules/dnet-modular-objectstore-service/trunk/"

                                    >dnet-modular-objectstore-service</link>: it contains the high

                                level implementation of the service. It manages blackboard messages,

                                the creation of profiles in dnet, and defines the REST API.</para>

                        </listitem>

                        <listitem>

                            <para><link

                                    xlink:href="https://svn.driver.research-infrastructures.eu/driver/dnet11/modules/dnet-gridfs-objectstore/trunks/"

                                    >dnet-gridfs-objectstore</link>: low level implementation for

                                storing and retreiving files using mongo GRIDFS. </para>

                        </listitem>

                    </itemizedlist>

                </para>

            </sect1>

            <sect1>

                <title>The ObjectStoreFile Metadata</title>

                <para>To enable the object store to store a file, it is necessary give some

                    information about it such as:<itemizedlist>

                        <listitem>

                            <para>ObjectID (Required to identify the file)</para>

                        </listitem>

                        <listitem>

                            <para>Mime type</para>

                        </listitem>

                        <listitem>

                            <para>Access protocol (required). At the moment the only protocols

                                available are: http, ftp, file system.</para>

                        </listitem>

                        <listitem>

                            <para>URI (required)</para>

                        </listitem>

                        <listitem>

                            <para>username, password for connection (optional, if needed).</para>

                        </listitem>

                    </itemizedlist></para>

            </sect1>

        </chapter>

        <chapter>

            <title>Feeding Object Store</title>

            <sect1>

                <title></title>

                <para>Feeding Object Store Service can be done in two different ways:</para>

                <para><itemizedlist>

                        <listitem>

                            <para>Feed of a single file: performed by invoking the following web

                                service method

                                <programlisting>feedObject( String obsId, String objectMetadata)</programlisting>where

                                objectMetadata is a JSON serialization of an ObjectStoreFile

                                instance defined in the objectStore-RMI.</para>

                        </listitem>

                        <listitem>

                            <para>Feed of multiple files in bulk: performed via blackboard message

                                on the profile of the Object Store Service. The blackboard message

                                has to specify an EPR of ObjectStoreFile result set and the targeted

                                the ObjectstoreID.</para>

                        </listitem>

                    </itemizedlist> Please find two example of feeding techniques below.</para>

            </sect1>

            <sect1>

                <title>Feeding of single object</title>

                <para>The code below shows how to upload a single file into an objectStore</para>

                <para>

                    <programlisting>

 private void feedTest(ServiceLocator <ObjectStoreService> ObjectStoreServicelocator,

			String objectStoreID) throws ObjectStoreServiceException {

        //Get a reference of the Service       

        ObjectStoreService obsService = ObjectStoreServicelocator.getService();

        //Create the FILE