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package eu.dnetlib.data.mapreduce.util;
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import com.google.protobuf.GeneratedMessage;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.proto.DNGFProtos.DNGF;
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import eu.dnetlib.data.proto.DNGFProtos.DNGFEntity;
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import eu.dnetlib.data.proto.DNGFProtos.DNGFRel;
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import eu.dnetlib.data.proto.DatasourceProtos.Datasource;
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import eu.dnetlib.data.proto.FieldTypeProtos.*;
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import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty.Builder;
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import eu.dnetlib.data.proto.KindProtos.Kind;
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import eu.dnetlib.data.proto.OrganizationProtos.Organization;
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import eu.dnetlib.data.proto.PersonProtos.Person;
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import eu.dnetlib.data.proto.ProjectProtos.Project;
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import eu.dnetlib.data.proto.PublicationProtos.Publication;
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import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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public class DNGFTest {
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public static final String CITATION_JSON =
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"<citations>\n <citation>\n <rawText>[10] M. Foret et al., Phys. Rev. B 66, 024204 (2002).</rawText>\n </citation>\n <citation>\n <rawText>[11] B. Ru\175404\264e et al., Phys. Rev. Lett. 90, 095502 (2003).</rawText>\n </citation>\n <citation>\n <rawText>[12] U. Buchenau et al., Phys. Rev. B 34, 5665 (1986).</rawText>\n </citation>\n <citation>\n <rawText>[13] S.N. Taraskin and S.R. Elliott, J. Phys.: Condens. Mat- ter 11, A219 (1999).</rawText>\n </citation>\n <citation>\n <rawText>[14] B. Hehlen et al., Phys. Rev. Lett. 84, 5355 (2000).</rawText>\n </citation>\n <citation>\n <rawText>[15] N.V. Surotsev et al., J. Phys.: Condens. Matter 10, L113 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[16] D.A. Parshin and C. Laermans, Phys. Rev. B 63, 132203 (2001).</rawText>\n </citation>\n <citation>\n <rawText>[17] V.L. Gurevich et al., Phys. Rev. B 67, 094203 (2003).</rawText>\n </citation>\n <citation>\n <rawText>[18] A. Matic et al., Phys. Rev. Lett. 86, 3803 (2001).</rawText>\n </citation>\n <citation>\n <rawText>[19] E. Rat et al., arXiv:cond-mat/0505558, 23 May 2005.</rawText>\n </citation>\n <citation>\n <rawText>[1] R.C. Zeller and R.O. Pohl, Phys. Rev. B 4, 2029 (1971).</rawText>\n </citation>\n <citation>\n <rawText>[20] C.A. Angell, J. Non-Cryst. Solids 131\20023133, 13 (1991).</rawText>\n </citation>\n <citation>\n <rawText>[21] A.P. Sokolov et al., Phys. Rev. Lett. 71, 2062 (1993).</rawText>\n </citation>\n <citation>\n <rawText>[22] T. Matsuo et al., Solid State Ionics 154-155, 759 (2002).</rawText>\n </citation>\n <citation>\n <rawText>[23] V.K. Malinovsky et al., Europhys. Lett. 11, 43 (1990).</rawText>\n </citation>\n <citation>\n <rawText>[24] J. Lor\250osch et al., J. Non-Cryst. Solids 69, 1 (1984).</rawText>\n </citation>\n <citation>\n <rawText>[25] U. Buchenau, Z. Phys. B 58, 181 (1985).</rawText>\n </citation>\n <citation>\n <rawText>[26] A.F. Io\175400e and A.R. Regel, Prog. Semicond. 4, 237 (1960).</rawText>\n </citation>\n <citation>\n <rawText>[27] R. Dell\20031Anna et al., Phys. Rev. Lett. 80, 1236 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[28] D. Fioretto et al., Phys. Rev. E 59, 4470 (1999).</rawText>\n </citation>\n <citation>\n <rawText>[29] U. Buchenau et al., Phys. Rev. Lett. 77, 4035 (1996).</rawText>\n </citation>\n <citation>\n <rawText>[2] M. Rothenfusser et al., Phys. Rev. B 27, 5196 (1983).</rawText>\n </citation>\n <citation>\n <rawText>[30] J. Mattsson et al., J. Phys.: Condens. Matter 15, S1259 (2003).</rawText>\n </citation>\n <citation>\n <rawText>[31] T. Scopigno et al., Phys. Rev. Lett. 92, 025503 (2004).</rawText>\n </citation>\n <citation>\n <rawText>[32] M. Foret et al., Phys. Rev. Lett. 81, 2100 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[33] F. Sette et al., Science 280, 1550 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[34] J. Wuttke et al., Phys. Rev. E 52, 4026 (1995).</rawText>\n </citation>\n <citation>\n <rawText>[35] M.A. Ramos et al., Phys. Rev. Lett. 78, 82 (1997).</rawText>\n </citation>\n <citation>\n <rawText>[36] G. Monaco et al., Phys. Rev. Lett. 80, 2161 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[37] A. T\250olle, Rep. Prog. Phys. 64, 1473 (2001).</rawText>\n </citation>\n <citation>\n <rawText>[38] As the straight lines do not cross the origin, this does not 2 imply \1623 \21035 \1651 .</rawText>\n </citation>\n <citation>\n <rawText>[39] A. Matic et al., Europhys. Lett. 54, 77 (2001).</rawText>\n </citation>\n <citation>\n <rawText>[3] S. Hunklinger and W. Arnold, in Physical Acoustics, Vol. XII, W.P. Mason and R.N. Thurston Eds. (Academic Press, N.Y. 1976), p. 155.</rawText>\n </citation>\n <citation>\n <rawText>[40] IXS data are usually not available below \1651co, mostly for experimental reasons. E.g., that the rapid onset was not evidenced in vitreous silica [27], is not indicative of its absence but rather of a low qco \21074 1 nm\210221.</rawText>\n </citation>\n <citation>\n <rawText>[41] G. Ruocco et al., Phys. Rev. Lett. 83, 5583 (1999).</rawText>\n </citation>\n <citation>\n <rawText>[42] D. C\1307 iplys et al., J. Physique (Paris) 42, C6-184 (1981).</rawText>\n </citation>\n <citation>\n <rawText>[43] R. Vacher et al., Rev. Sci. Instrum. 51, 288 (1980).</rawText>\n </citation>\n <citation>\n <rawText>[44] R. Vacher et al., arXiv:cond-mat/0505560, 23 May 2005.</rawText>\n </citation>\n <citation>\n <rawText>[45] T.N. Claytor et al., Phys. Rev. B 18, 5842 (1978).</rawText>\n </citation>\n <citation>\n <rawText>[46] M. Arai et al., Physica B 263-264, 268 (1999).</rawText>\n </citation>\n <citation>\n <rawText>[4] R. Vacher et al., J. Non-Cryst. Solids 45, 397 (1981); T.C. Zhu et al., Phys. Rev. B 44, 4281 (1991).</rawText>\n </citation>\n <citation>\n <rawText>[5] J.E. Graebner et al., Phys. Rev. B 34, 5696 (1986).</rawText>\n </citation>\n <citation>\n <rawText>[6] E. Duval and A. Mermet, Phys. Rev. B 58, 8159 (1998).</rawText>\n </citation>\n <citation>\n <rawText>[7] A. Matic et al., Phys. Rev. Lett. 93, 145502 (2004).</rawText>\n </citation>\n <citation>\n <rawText>[8] Often alluded to, e.g. in the Encyclopedia of Materials: Science and Technology, K.H.J. Buschow et al., Eds., Vol. 1 (Elsevier, Oxford, 2001), articles by S.R. Elliott on pp. 171-174 and U. Buchenau on pp. 212-215.</rawText>\n </citation>\n <citation>\n <rawText>[9] E. Rat et al., Phys. Rev. Lett. 83, 1355 (1999).</rawText>\n </citation>\n</citations>";
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public static final String STATISTICS_JSON =
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"[{ \"citationsPerYear\": \"many\", \"anotherCoolStatistic\": \"WoW\", \"nestedStat\": { \"firstNestedStat\" : \"value 1\", \"secondNestedStat\" : \"value 2\"}, \"listingStat\" : [ \"one\", \"two\" ] }]";
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private static final Log log = LogFactory.getLog(DNGFTest.class);
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private static String basePathProfiles = "/eu/dnetlib/test/profiles/OntologyDSResources/OntologyDSResourceType";
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public static StructuredProperty.Builder getStructuredproperty(final String value, final String classname, final String schemename) {
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return getStructuredproperty(value, classname, schemename, null);
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}
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public static StructuredProperty.Builder getStructuredproperty(final String value, final String classname, final String schemename, final DataInfo dataInfo) {
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final Builder sp = StructuredProperty.newBuilder().setValue(value).setQualifier(getQualifier(classname, schemename));
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if (dataInfo != null) {
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sp.setDataInfo(dataInfo);
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}
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return sp;
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}
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public static Qualifier.Builder getQualifier(final String classname, final String schemename) {
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return Qualifier.newBuilder().setClassid(classname).setClassname(classname).setSchemeid(schemename).setSchemename(schemename);
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}
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public static KeyValue getKV(final String id, final String name) {
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return KeyValue.newBuilder().setKey(id).setValue(name).build();
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}
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public static DNGFEntity getDatasource(final String datasourceId) {
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return DNGFEntity
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.newBuilder()
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.setType(Type.datasource)
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.setId(datasourceId)
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.setDatasource(
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Datasource.newBuilder().setMetadata(
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Datasource.Metadata.newBuilder().setOfficialname(sf("officialname")).setEnglishname(sf("englishname"))
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.setWebsiteurl(sf("websiteurl")).setContactemail(sf("contactemail")).addAccessinfopackage(sf("accessinforpackage"))
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.setNamespaceprefix(sf("namespaceprofix")).setDescription(sf("description")).setOdnumberofitems(sf("numberofitems"))
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.setOdnumberofitemsdate(sf("numberofitems date"))
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// .addOdsubjects("subjects")
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.setOdpolicies(sf("policies")).addOdlanguages(sf("languages")).addOdcontenttypes(sf("contenttypes"))
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.setDatasourcetype(getQualifier("type class", "type scheme")))).build();
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}
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public static DNGFEntity getResult(final String id) {
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return getResultBuilder(id).build();
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}
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public static DNGFEntity.Builder getResultBuilder(final String id) {
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return DNGFEntity
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.newBuilder()
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.setType(Type.publication)
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.setId(id)
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.setPublication(
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Publication.newBuilder()
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.setMetadata(
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Publication.Metadata
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.newBuilder()
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.addTitle(
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getStructuredproperty(
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"Analysis of cell viability in intervertebral disc: Effect of endplate permeability on cell population",
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"main title", "dnet:result_titles", getDataInfo()))
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.addTitle(getStructuredproperty("Another title", "alternative title", "dnet:result_titles", getDataInfo()))
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.addSubject(getStructuredproperty("Biophysics", "subject", "dnet:result_sujects"))
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.setDateofacceptance(sf("2010-01-01")).addSource(sf("sourceA")).addSource(sf("sourceB"))
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.addContext(Context.newBuilder().setId("egi::virtual::970"))
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.addContext(Context.newBuilder().setId("egi::classification::natsc::math::applied"))
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.addContext(Context.newBuilder().setId("egi::classification::natsc::math"))
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.addContext(Context.newBuilder().setId("egi::classification::natsc"))
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.addContext(Context.newBuilder().setId("egi::classification")).addContext(Context.newBuilder().setId("egi"))
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.addDescription(sf("Responsible for making and maintaining the extracellular matrix ..."))
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.addDescription(sf("Another description ...")).setPublisher(sf("ELSEVIER SCI LTD"))
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.setResulttype(getQualifier("publication", "dnet:result_types"))
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.setLanguage(getQualifier("eng", "dnet:languages"))).addInstance(getInstance("10|od__10", "Uk pubmed"))
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.addInstance(getInstance("10|od__10", "arxiv")))
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.addCollectedfrom(getKV("opendoar____::1064", "Oxford University Research Archive"))
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.addPid(getStructuredproperty("doi:74293", "doi", "dnet:pids")).addPid(getStructuredproperty("oai:74295", "oai", "dnet:pids"))
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.setDateofcollection("");
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}
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public static DataInfo getDataInfo() {
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return getDataInfo("0.4");
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}
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public static DataInfo getDataInfo(final String trust) {
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return DataInfo.newBuilder().setDeletedbyinference(false).setTrust("0.4").setInferenceprovenance("algo").setProvenanceaction(getQualifier("xx", "yy"))
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.build();
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}
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public static Instance.Builder getInstance(final String hostedbyId, final String hostedbyName) {
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return Instance.newBuilder().setHostedby(getKV(hostedbyId, hostedbyName)).setLicence(getQualifier("OpenAccess", "dnet:access_modes"))
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.setInstancetype(getQualifier("publication", "dnet:result_typologies")).addUrl("webresource url");
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}
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public static DNGFRel getDedupRel(final String source, final String target) {
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return DNGFRel.newBuilder().setSource(source).setTarget(target).setRelType(getQualifier("dedup", "dedupScheme"))
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.setChild(false).setCachedTarget(getResult(target)).build();
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}
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public static DNGFEntity getPerson() {
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return DNGFEntity
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.newBuilder()
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.setType(Type.person)
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.setId("WOS:000277866500014_A._Shirazi-Adl")
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.setPerson(
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Person.newBuilder().setMetadata(
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Person.Metadata.newBuilder().addSecondnames(sf("Shirazi-Adl")).setFullname(sf("A. Shirazi-Adl"))
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.setEmail(sf("name.surname@gmail.com")).setPhone(sf("12345")).setNationality(getQualifier("EN", "dnet:countries"))))
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.build();
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}
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public static RelMetadata.Builder relMetadata(final String classname, final String schemename) {
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return RelMetadata.newBuilder().setSemantics(getQualifier(classname, schemename));
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}
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public static DNGFEntity getOrganization(final String orgId) {
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return DNGFEntity
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.newBuilder()
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.setType(Type.organization)
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.setId(orgId)
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.addCollectedfrom(getKV("opendoar_1234", "UK pubmed"))
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.setOrganization(
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Organization.newBuilder().setMetadata(
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Organization.Metadata.newBuilder().setLegalname(sf("CENTRE D'APPUI A LA RECHERCHE ET A LA FORMATION GIE"))
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.setLegalshortname(sf("CAREF")).setWebsiteurl(sf("www.caref-mali.org"))
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.setCountry(getQualifier("ML", "dnet:countries")))).build();
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}
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public static DNGFEntity getProjectFP7(final String projectId, final String fundingProgram) throws InvalidProtocolBufferException {
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return DNGFEntity
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.newBuilder()
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.setType(Type.project)
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.setId(projectId)
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.addCollectedfrom(getKV("opendoar_1234", "UK pubmed"))
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.setProject(
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Project.newBuilder()
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.setMetadata(
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Project.Metadata
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.newBuilder()
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.setAcronym(sf("5CYRQOL"))
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.setTitle(sf("Cypriot Researchers Contribute to our Quality of Life"))
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.setStartdate(sf("2007-05-01"))
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.setEnddate(sf("2007-10-31"))
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.setEcsc39(sf("false"))
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.setContracttype(getQualifier("CSA", "ec:FP7contractTypes"))
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.addFundingtree(
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sf("<fundingtree><funder><id>ec__________::EC</id><shortname>EC</shortname><name>European Commission</name></funder><funding_level_2><id>ec__________::EC::FP7::"
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+ fundingProgram
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+ "::PEOPLE</id><description>Marie-Curie Actions</description><name>PEOPLE</name><class>ec:program</class><parent><funding_level_1><id>ec__________::EC::FP7::"
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+ fundingProgram
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+ "</id><description>"
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+ fundingProgram
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+ "-People</description><name>"
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+ fundingProgram
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+ "</name><class>ec:specificprogram</class><parent><funding_level_0><id>ec__________::EC::FP7</id><description>SEVENTH FRAMEWORK PROGRAMME</description><name>FP7</name><parent/><class>ec:frameworkprogram</class></funding_level_0></parent></funding_level_1></parent></funding_level_2></fundingtree>"))))
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.build();
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}
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public static DNGFEntity getProjectWT() throws InvalidProtocolBufferException {
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return DNGFEntity
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.newBuilder()
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.setType(Type.project)
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.setId("project|wt::087536")
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.addCollectedfrom(getKV("wellcomeTrust", "wellcome trust"))
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.setProject(
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Project.newBuilder()
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.setMetadata(
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Project.Metadata
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.newBuilder()
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.setAcronym(sf("UNKNOWN"))
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.setTitle(sf("Research Institute for Infectious Diseases of Poverty (IIDP)."))
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.setStartdate(sf("2007-05-01"))
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.setEnddate(sf("2007-10-31"))
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.setEcsc39(sf("false"))
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.setContracttype(getQualifier("UNKNOWN", "wt:contractTypes"))
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.addFundingtree(
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sf("<fundingtree><funder><id>wt__________::WT</id><shortname>WT</shortname><name>Wellcome Trust</name></funder><funding_level_0><id>wt__________::WT::UNKNOWN</id><description>UNKNOWN</description><name>UNKNOWN</name><class>wt:fundingStream</class><parent/></funding_level_0></fundingtree>"))
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.addFundingtree(
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sf("<fundingtree><funder><id>wt__________::WT</id><shortname>WT</shortname><name>Wellcome Trust</name></funder><funding_level_0><id>wt__________::WT::Technology Transfer</id><description>Technology Transfer</description><name>Technology Transfer</name><class>wt:fundingStream</class><parent/></funding_level_0></fundingtree>"))))
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.build();
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}
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public static ExtraInfo extraInfo(final String name, final String provenance, final String trust, final String typology, final String value) {
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final ExtraInfo.Builder e = ExtraInfo.newBuilder().setName(name).setProvenance(provenance).setTrust(trust).setTypology(typology).setValue(value);
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return e.build();
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}
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public static StringField sf(final String s) {
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return sf(s, null);
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}
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public static StringField sf(final String s, final DataInfo dataInfo) {
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final StringField.Builder sf = StringField.newBuilder().setValue(s);
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if (dataInfo != null) {
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sf.setDataInfo(dataInfo);
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}
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return sf.build();
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}
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public static DNGFDecoder embed(final GeneratedMessage msg,
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final Kind kind,
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226
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final boolean deletedByInference,
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227
|
final boolean inferred,
|
|
228
|
final String provenance,
|
|
229
|
final String action) {
|
|
230
|
|
|
231
|
final DNGF.Builder dngf = DNGF.newBuilder()
|
|
232
|
.setKind(kind)
|
|
233
|
.setLastupdatetimestamp(System.currentTimeMillis())
|
|
234
|
.setDataInfo(
|
|
235
|
DataInfo.newBuilder().setDeletedbyinference(deletedByInference).setInferred(inferred).setTrust("0.5")
|
|
236
|
.setInferenceprovenance(provenance).setProvenanceaction(getQualifier(action, action)));
|
|
237
|
switch (kind) {
|
|
238
|
case entity:
|
|
239
|
dngf.setEntity((DNGFEntity) msg);
|
|
240
|
break;
|
|
241
|
case relation:
|
|
242
|
dngf.setRel((DNGFRel) msg);
|
|
243
|
break;
|
|
244
|
default:
|
|
245
|
break;
|
|
246
|
}
|
|
247
|
|
|
248
|
return DNGFDecoder.decode(dngf.build());
|
|
249
|
}
|
|
250
|
|
|
251
|
public static DNGFDecoder embed(final GeneratedMessage msg, final Kind kind) {
|
|
252
|
return embed(msg, kind, false, false, "inference_provenance", "provenance_action");
|
|
253
|
}
|
|
254
|
|
|
255
|
|
|
256
|
}
|