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dnet-hadoop
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bug fixing

This commit is contained in:
Michele Artini 2020-02-12 16:34:00 +01:00
parent 69336195d3
commit cdea0dae75
2 changed files with 22 additions and 7 deletions
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19
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java
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@ -11,6 +11,8 @@ import java.util.Map;
import java.util.Map.Entry; import java.util.Map.Entry;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.dom4j.DocumentFactory; import org.dom4j.DocumentFactory;
@ -49,6 +51,8 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
private static final Log log = LogFactory.getLog(AbstractMongoExecutor.class);
public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
final String mongoDb, final String dbUrl, final String dbUser, final String mongoDb, final String dbUrl, final String dbUser,
final String dbPassword) throws Exception { final String dbPassword) throws Exception {
@ -66,6 +70,9 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
} }
private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException { private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
log.info("Loading vocabulary terms from db...");
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
code2name.clear(); code2name.clear();
dbClient.processResults("select code, name from class", rs -> { dbClient.processResults("select code, name from class", rs -> {
@ -77,12 +84,19 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
}); });
} }
log.info("Found " + code2name.size() + " terms.");
} }
public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException { public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException {
for (final Entry<String, String> entry : mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation).entrySet()) { log.info(String.format("Searching mdstores (format: %s, layout: %s, interpretation: %s)", mdFormat, mdLayout, mdInterpretation));
// final String mdId = entry.getKey();
final Map<String, String> colls = mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation);
log.info("Found " + colls.size() + " mdstores");
for (final Entry<String, String> entry : colls.entrySet()) {
log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
final String currentColl = entry.getValue(); final String currentColl = entry.getValue();
for (final String xml : mdstoreClient.listRecords(currentColl)) { for (final String xml : mdstoreClient.listRecords(currentColl)) {
@ -101,6 +115,7 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
} }
} }
} }
log.info("All Done.");
} }
protected void registerNamespaces(final Map<String, String> nsContext) { protected void registerNamespaces(final Map<String, String> nsContext) {

10
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json
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@ -48,21 +48,21 @@
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName": "postgresUrl", "paramName": "pgurl",
"paramLongName": "postgresUrl", "paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName": "postgresUser", "paramName": "pguser",
"paramLongName": "postgresUser", "paramLongName": "postgresUser",
"paramDescription": "postgres user", "paramDescription": "postgres user",
"paramRequired": true "paramRequired": false
}, },
{ {
"paramName": "postgresPassword", "paramName": "pgpasswd",
"paramLongName": "postgresPassword", "paramLongName": "postgresPassword",
"paramDescription": "postgres password", "paramDescription": "postgres password",
"paramRequired": true "paramRequired": false
} }
] ]