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This commit is contained in:
Michele Artini 2020-04-29 12:56:58 +02:00
parent a5d7007005
commit c43b4c8962
2 changed files with 473 additions and 508 deletions
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977
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString;
@ -10,6 +11,23 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import java.io.Closeable;
import java.io.IOException;
import java.sql.Array;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
@ -31,512 +49,459 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.io.Closeable;
import java.io.IOException;
import java.sql.Array;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
implements Closeable {
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
private final DbClient dbClient;
private final long lastUpdateTimestamp;
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateDbEntitiesApplication.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
parser.parseArgument(args);
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath");
final boolean processClaims =
parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
try (final MigrateDbEntitiesApplication smdbe =
new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) {
if (processClaims) {
log.info("Processing claims...");
smdbe.execute("queryClaims.sql", smdbe::processClaims);
} else {
log.info("Processing datasources...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
log.info("Processing projects...");
smdbe.execute("queryProjects.sql", smdbe::processProject);
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing relations ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
}
log.info("All done.");
}
}
protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST
super();
this.dbClient = null;
this.lastUpdateTimestamp = new Date().getTime();
}
public MigrateDbEntitiesApplication(
final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword)
throws Exception {
super(hdfsPath);
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.lastUpdateTimestamp = new Date().getTime();
}
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
throws Exception {
final String sql =
IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
dbClient.processResults(sql, consumer);
}
public List<Oaf> processDatasource(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Datasource ds = new Datasource();
ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true));
ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
ds.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
ds.setPid(new ArrayList<>());
ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
ds.setDateoftransformation(null); // Value not returned by the SQL query
ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
ds.setOaiprovenance(null); // Values not present in the DB
ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
ds.setOfficialname(field(rs.getString("officialname"), info));
ds.setEnglishname(field(rs.getString("englishname"), info));
ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
ds.setLogourl(field(rs.getString("logourl"), info));
ds.setContactemail(field(rs.getString("contactemail"), info));
ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info));
ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info));
ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info));
ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info));
ds.setDescription(field(rs.getString("description"), info));
ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info));
ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info));
ds.setOdpolicies(field(rs.getString("odpolicies"), info));
ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info));
ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info));
ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info));
ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info));
ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info));
ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info));
ds.setDataprovider(field(rs.getBoolean("dataprovider"), info));
ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info));
ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info));
ds.setDatauploadtype(field(rs.getString("datauploadtype"), info));
ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info));
ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info));
ds.setVersioning(field(rs.getBoolean("versioning"), info));
ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info));
ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info));
ds.setPidsystems(field(rs.getString("pidsystems"), info));
ds.setCertificates(field(rs.getString("certificates"), info));
ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
ds.setJournal(
prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
ds.setDataInfo(info);
ds.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(ds);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processProject(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Project p = new Project();
p.setId(createOpenaireId(40, rs.getString("projectid"), true));
p.setOriginalId(Arrays.asList(rs.getString("projectid")));
p.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
p.setPid(new ArrayList<>());
p.setDateofcollection(asString(rs.getDate("dateofcollection")));
p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
p.setExtraInfo(new ArrayList<>()); // Values not present in the DB
p.setOaiprovenance(null); // Values not present in the DB
p.setWebsiteurl(field(rs.getString("websiteurl"), info));
p.setCode(field(rs.getString("code"), info));
p.setAcronym(field(rs.getString("acronym"), info));
p.setTitle(field(rs.getString("title"), info));
p.setStartdate(field(asString(rs.getDate("startdate")), info));
p.setEnddate(field(asString(rs.getDate("enddate")), info));
p.setCallidentifier(field(rs.getString("callidentifier"), info));
p.setKeywords(field(rs.getString("keywords"), info));
p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
p.setOamandatepublications(
field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info));
p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype")));
p.setOptional1(field(rs.getString("optional1"), info));
p.setOptional2(field(rs.getString("optional2"), info));
p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info));
p.setContactfullname(field(rs.getString("contactfullname"), info));
p.setContactfax(field(rs.getString("contactfax"), info));
p.setContactphone(field(rs.getString("contactphone"), info));
p.setContactemail(field(rs.getString("contactemail"), info));
p.setSummary(field(rs.getString("summary"), info));
p.setCurrency(field(rs.getString("currency"), info));
p.setTotalcost(new Float(rs.getDouble("totalcost")));
p.setFundedamount(new Float(rs.getDouble("fundedamount")));
p.setDataInfo(info);
p.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(p);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Organization o = new Organization();
o.setId(createOpenaireId(20, rs.getString("organizationid"), true));
o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
o.setCollectedfrom(
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
o.setPid(new ArrayList<>());
o.setDateofcollection(asString(rs.getDate("dateofcollection")));
o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
o.setExtraInfo(new ArrayList<>()); // Values not present in the DB
o.setOaiprovenance(null); // Values not present in the DB
o.setLegalshortname(field(rs.getString("legalshortname"), info));
o.setLegalname(field(rs.getString("legalname"), info));
o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query
o.setWebsiteurl(field(rs.getString("websiteurl"), info));
o.setLogourl(field(rs.getString("logourl"), info));
o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
o.setEcresearchorganization(
field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info));
o.setEcinternationalorganizationeurinterests(
field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
o.setEcinternationalorganization(
field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
o.setCountry(prepareQualifierSplitting(rs.getString("country")));
o.setDataInfo(info);
o.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(o);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processDatasourceOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final String orgId = createOpenaireId(20, rs.getString("organization"), true);
final String dsId = createOpenaireId(10, rs.getString("datasource"), true);
final List<KeyValue> collectedFrom =
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType("datasourceOrganization");
r1.setSubRelType("provision");
r1.setRelClass("isProvidedBy");
r1.setSource(dsId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType("datasourceOrganization");
r2.setSubRelType("provision");
r2.setRelClass("provides");
r2.setSource(orgId);
r2.setTarget(dsId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processProjectOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final String orgId = createOpenaireId(20, rs.getString("resporganization"), true);
final String projectId = createOpenaireId(40, rs.getString("project"), true);
final List<KeyValue> collectedFrom =
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType("projectOrganization");
r1.setSubRelType("participation");
r1.setRelClass("hasParticipant");
r1.setSource(projectId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType("projectOrganization");
r2.setSubRelType("participation");
r2.setRelClass("isParticipant");
r2.setSource(orgId);
r2.setTarget(projectId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processClaims(final ResultSet rs) {
final DataInfo info =
dataInfo(
false,
null,
false,
false,
qualifier(
"user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"),
"0.9");
final List<KeyValue> collectedFrom =
listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
try {
if (rs.getString("source_type").equals("context")) {
final Result r;
if (rs.getString("target_type").equals("dataset")) {
r = new Dataset();
r.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("software")) {
r = new Software();
r.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("other")) {
r = new OtherResearchProduct();
r.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
} else {
r = new Publication();
r.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
}
r.setId(createOpenaireId(50, rs.getString("target_id"), false));
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setContext(prepareContext(rs.getString("source_id"), info));
r.setDataInfo(info);
r.setCollectedfrom(collectedFrom);
return Arrays.asList(r);
} else {
final String sourceId =
createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false);
final String targetId =
createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false);
final Relation r1 = new Relation();
final Relation r2 = new Relation();
if (rs.getString("source_type").equals("project")) {
r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultProject");
r1.setSubRelType("outcome");
r1.setRelClass("produces");
r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultProject");
r2.setSubRelType("outcome");
r2.setRelClass("isProducedBy");
} else {
r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultResult");
r1.setSubRelType("relationship");
r1.setRelClass("isRelatedTo");
r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultResult");
r2.setSubRelType("relationship");
r2.setRelClass("isRelatedTo");
}
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
}
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
private List<Context> prepareContext(final String id, final DataInfo dataInfo) {
final Context context = new Context();
context.setId(id);
context.setDataInfo(Arrays.asList(dataInfo));
return Arrays.asList(context);
}
private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
final String inferenceprovenance = rs.getString("inferenceprovenance");
final Boolean inferred = rs.getBoolean("inferred");
final String trust = rs.getString("trust");
return dataInfo(
deletedbyinference,
inferenceprovenance,
inferred,
false,
MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION,
trust);
}
private Qualifier prepareQualifierSplitting(final String s) {
if (StringUtils.isBlank(s)) {
return null;
}
final String[] arr = s.split("@@@");
return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
}
private List<Field<String>> prepareListFields(final Array array, final DataInfo info) {
try {
return array != null ? listFields(info, (String[]) array.getArray()) : new ArrayList<>();
} catch (final SQLException e) {
throw new RuntimeException("Invalid SQL array", e);
}
}
private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
if (StringUtils.isBlank(s)) {
return null;
}
final String[] parts = s.split("###");
if (parts.length == 2) {
final String value = parts[0];
final String[] arr = parts[1].split("@@@");
if (arr.length == 4) {
return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo);
}
}
return null;
}
private List<StructuredProperty> prepareListOfStructProps(
final Array array, final DataInfo dataInfo) throws SQLException {
final List<StructuredProperty> res = new ArrayList<>();
if (array != null) {
for (final String s : (String[]) array.getArray()) {
final StructuredProperty sp = prepareStructProp(s, dataInfo);
if (sp != null) {
res.add(sp);
}
}
}
return res;
}
private Journal prepareJournal(final String name, final String sj, final DataInfo info) {
if (StringUtils.isNotBlank(sj)) {
final String[] arr = sj.split("@@@");
if (arr.length == 3) {
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;
;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;
;
if (issn != null || eissn != null || lissn != null) {
return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
}
}
}
return null;
}
@Override
public void close() throws IOException {
super.close();
dbClient.close();
}
implements Closeable {
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
private final DbClient dbClient;
private final long lastUpdateTimestamp;
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(MigrateDbEntitiesApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
parser.parseArgument(args);
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath");
final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser,
dbPassword)) {
if (processClaims) {
log.info("Processing claims...");
smdbe.execute("queryClaims.sql", smdbe::processClaims);
} else {
log.info("Processing datasources...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
log.info("Processing projects...");
smdbe.execute("queryProjects.sql", smdbe::processProject);
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing relations ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
}
log.info("All done.");
}
}
protected MigrateDbEntitiesApplication() { // ONLY FOR UNIT TEST
super();
this.dbClient = null;
this.lastUpdateTimestamp = new Date().getTime();
}
public MigrateDbEntitiesApplication(
final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword)
throws Exception {
super(hdfsPath);
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.lastUpdateTimestamp = new Date().getTime();
}
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
throws Exception {
final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
dbClient.processResults(sql, consumer);
}
public List<Oaf> processDatasource(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Datasource ds = new Datasource();
ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true));
ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
ds
.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
ds.setPid(new ArrayList<>());
ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
ds.setDateoftransformation(null); // Value not returned by the SQL query
ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
ds.setOaiprovenance(null); // Values not present in the DB
ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
ds.setOfficialname(field(rs.getString("officialname"), info));
ds.setEnglishname(field(rs.getString("englishname"), info));
ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
ds.setLogourl(field(rs.getString("logourl"), info));
ds.setContactemail(field(rs.getString("contactemail"), info));
ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info));
ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info));
ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info));
ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info));
ds.setDescription(field(rs.getString("description"), info));
ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info));
ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info));
ds.setOdpolicies(field(rs.getString("odpolicies"), info));
ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info));
ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info));
ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info));
ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info));
ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info));
ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info));
ds.setDataprovider(field(rs.getBoolean("dataprovider"), info));
ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info));
ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info));
ds.setDatauploadtype(field(rs.getString("datauploadtype"), info));
ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info));
ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info));
ds.setVersioning(field(rs.getBoolean("versioning"), info));
ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info));
ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info));
ds.setPidsystems(field(rs.getString("pidsystems"), info));
ds.setCertificates(field(rs.getString("certificates"), info));
ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
ds
.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
ds.setDataInfo(info);
ds.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(ds);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processProject(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Project p = new Project();
p.setId(createOpenaireId(40, rs.getString("projectid"), true));
p.setOriginalId(Arrays.asList(rs.getString("projectid")));
p
.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
p.setPid(new ArrayList<>());
p.setDateofcollection(asString(rs.getDate("dateofcollection")));
p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
p.setExtraInfo(new ArrayList<>()); // Values not present in the DB
p.setOaiprovenance(null); // Values not present in the DB
p.setWebsiteurl(field(rs.getString("websiteurl"), info));
p.setCode(field(rs.getString("code"), info));
p.setAcronym(field(rs.getString("acronym"), info));
p.setTitle(field(rs.getString("title"), info));
p.setStartdate(field(asString(rs.getDate("startdate")), info));
p.setEnddate(field(asString(rs.getDate("enddate")), info));
p.setCallidentifier(field(rs.getString("callidentifier"), info));
p.setKeywords(field(rs.getString("keywords"), info));
p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
p
.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info));
p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype")));
p.setOptional1(field(rs.getString("optional1"), info));
p.setOptional2(field(rs.getString("optional2"), info));
p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info));
p.setContactfullname(field(rs.getString("contactfullname"), info));
p.setContactfax(field(rs.getString("contactfax"), info));
p.setContactphone(field(rs.getString("contactphone"), info));
p.setContactemail(field(rs.getString("contactemail"), info));
p.setSummary(field(rs.getString("summary"), info));
p.setCurrency(field(rs.getString("currency"), info));
p.setTotalcost(new Float(rs.getDouble("totalcost")));
p.setFundedamount(new Float(rs.getDouble("fundedamount")));
p.setDataInfo(info);
p.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(p);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final Organization o = new Organization();
o.setId(createOpenaireId(20, rs.getString("organizationid"), true));
o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
o
.setCollectedfrom(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
o.setPid(new ArrayList<>());
o.setDateofcollection(asString(rs.getDate("dateofcollection")));
o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
o.setExtraInfo(new ArrayList<>()); // Values not present in the DB
o.setOaiprovenance(null); // Values not present in the DB
o.setLegalshortname(field(rs.getString("legalshortname"), info));
o.setLegalname(field(rs.getString("legalname"), info));
o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query
o.setWebsiteurl(field(rs.getString("websiteurl"), info));
o.setLogourl(field(rs.getString("logourl"), info));
o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
o
.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info));
o
.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
o
.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
o.setCountry(prepareQualifierSplitting(rs.getString("country")));
o.setDataInfo(info);
o.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(o);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processDatasourceOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final String orgId = createOpenaireId(20, rs.getString("organization"), true);
final String dsId = createOpenaireId(10, rs.getString("datasource"), true);
final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType("datasourceOrganization");
r1.setSubRelType("provision");
r1.setRelClass("isProvidedBy");
r1.setSource(dsId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType("datasourceOrganization");
r2.setSubRelType("provision");
r2.setRelClass("provides");
r2.setSource(orgId);
r2.setTarget(dsId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processProjectOrganization(final ResultSet rs) {
try {
final DataInfo info = prepareDataInfo(rs);
final String orgId = createOpenaireId(20, rs.getString("resporganization"), true);
final String projectId = createOpenaireId(40, rs.getString("project"), true);
final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType("projectOrganization");
r1.setSubRelType("participation");
r1.setRelClass("hasParticipant");
r1.setSource(projectId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType("projectOrganization");
r2.setSubRelType("participation");
r2.setRelClass("isParticipant");
r2.setSource(orgId);
r2.setTarget(projectId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public List<Oaf> processClaims(final ResultSet rs) {
final DataInfo info =
dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
try {
if (rs.getString("source_type").equals("context")) {
final Result r;
if (rs.getString("target_type").equals("dataset")) {
r = new Dataset();
r.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("software")) {
r = new Software();
r.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("other")) {
r = new OtherResearchProduct();
r.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
} else {
r = new Publication();
r.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
}
r.setId(createOpenaireId(50, rs.getString("target_id"), false));
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setContext(prepareContext(rs.getString("source_id"), info));
r.setDataInfo(info);
r.setCollectedfrom(collectedFrom);
return Arrays.asList(r);
} else {
final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false);
final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false);
final Relation r1 = new Relation();
final Relation r2 = new Relation();
if (rs.getString("source_type").equals("project")) {
r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultProject");
r1.setSubRelType("outcome");
r1.setRelClass("produces");
r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultProject");
r2.setSubRelType("outcome");
r2.setRelClass("isProducedBy");
} else {
r1.setCollectedfrom(collectedFrom);
r1.setRelType("resultResult");
r1.setSubRelType("relationship");
r1.setRelClass("isRelatedTo");
r2.setCollectedfrom(collectedFrom);
r2.setRelType("resultResult");
r2.setSubRelType("relationship");
r2.setRelClass("isRelatedTo");
}
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r1, r2);
}
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
private List<Context> prepareContext(final String id, final DataInfo dataInfo) {
final Context context = new Context();
context.setId(id);
context.setDataInfo(Arrays.asList(dataInfo));
return Arrays.asList(context);
}
private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
final String inferenceprovenance = rs.getString("inferenceprovenance");
final Boolean inferred = rs.getBoolean("inferred");
final String trust = rs.getString("trust");
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION, trust);
}
private Qualifier prepareQualifierSplitting(final String s) {
if (StringUtils.isBlank(s)) { return null; }
final String[] arr = s.split("@@@");
return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
}
private List<Field<String>> prepareListFields(final Array array, final DataInfo info) {
try {
return array != null ? listFields(info, (String[]) array.getArray()) : new ArrayList<>();
} catch (final SQLException e) {
throw new RuntimeException("Invalid SQL array", e);
}
}
private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
if (StringUtils.isBlank(s)) { return null; }
final String[] parts = s.split("###");
if (parts.length == 2) {
final String value = parts[0];
final String[] arr = parts[1].split("@@@");
if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); }
}
return null;
}
private List<StructuredProperty> prepareListOfStructProps(
final Array array,
final DataInfo dataInfo) throws SQLException {
final List<StructuredProperty> res = new ArrayList<>();
if (array != null) {
for (final String s : (String[]) array.getArray()) {
final StructuredProperty sp = prepareStructProp(s, dataInfo);
if (sp != null) {
res.add(sp);
}
}
}
return res;
}
private Journal prepareJournal(final String name, final String sj, final DataInfo info) {
if (StringUtils.isNotBlank(sj)) {
final String[] arr = sj.split("@@@");
if (arr.length == 3) {
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;;
if (issn != null || eissn != null || lissn != null) {
return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
}
}
}
return null;
}
@Override
public void close() throws IOException {
super.close();
dbClient.close();
}
}

4
dhp-workflows/dhp-stats-update/pom.xml
View File

@ -3,10 +3,10 @@
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-statistics-workflow</artifactId>
<artifactId>dhp-stats-update</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>