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mdstore collector plugin

This commit is contained in:
Claudio Atzori 2021-02-25 12:30:30 +01:00
parent dc98c39500
commit b830e33392
3 changed files with 16 additions and 13 deletions
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13
dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java
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@ -9,16 +9,16 @@ import java.util.Map;
import java.util.Optional; import java.util.Optional;
import java.util.stream.StreamSupport; import java.util.stream.StreamSupport;
import com.mongodb.BasicDBObject;
import com.mongodb.QueryBuilder;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.bson.Document; import org.bson.Document;
import com.google.common.collect.Iterables; import com.google.common.collect.Iterables;
import com.mongodb.BasicDBObject;
import com.mongodb.MongoClient; import com.mongodb.MongoClient;
import com.mongodb.MongoClientURI; import com.mongodb.MongoClientURI;
import com.mongodb.QueryBuilder;
import com.mongodb.client.MongoCollection; import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase; import com.mongodb.client.MongoDatabase;
@ -40,10 +40,11 @@ public class MdstoreClient implements Closeable {
public MongoCollection<Document> mdStore(final String mdId) { public MongoCollection<Document> mdStore(final String mdId) {
BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get(); BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
final String currentId = Optional.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query)) final String currentId = Optional
.map(r -> r.first()) .ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
.map(d -> d.getString("currentId")) .map(r -> r.first())
.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId)); .map(d -> d.getString("currentId"))
.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
return getColl(db, currentId, true); return getColl(db, currentId, true);
} }

14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MDStoreCollectorPlugin.java
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@ -7,27 +7,29 @@ import java.util.Spliterators;
import java.util.stream.Stream; import java.util.stream.Stream;
import java.util.stream.StreamSupport; import java.util.stream.StreamSupport;
import org.bson.Document;
import com.mongodb.client.MongoCollection; import com.mongodb.client.MongoCollection;
import eu.dnetlib.dhp.common.MdstoreClient;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport; import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor; import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException; import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import org.bson.Document; import eu.dnetlib.dhp.common.MdstoreClient;
public class MDStoreCollectorPlugin implements CollectorPlugin { public class MDStoreCollectorPlugin implements CollectorPlugin {
public static final String MONGODB_BASEURL = "mongodb_baseurl";
public static final String MONGODB_DBNAME = "mongodb_dbname"; public static final String MONGODB_DBNAME = "mongodb_dbname";
public static final String MDSTORE_ID = "mongodb_collection"; public static final String MDSTORE_ID = "mdstore_id";
@Override @Override
public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException {
final String mongoBaseUrl = Optional final String mongoBaseUrl = Optional
.ofNullable(api.getParams().get(MONGODB_BASEURL)) .ofNullable(api.getBaseUrl())
.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MONGODB_BASEURL))); .orElseThrow(
() -> new CollectorException(
"missing mongodb baseUrl, expected in eu.dnetlib.dhp.collection.ApiDescriptor.baseUrl"));
final String dbName = Optional final String dbName = Optional
.ofNullable(api.getParams().get(MONGODB_DBNAME)) .ofNullable(api.getParams().get(MONGODB_DBNAME))

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java
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@ -11,8 +11,8 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.common.MdstoreClient; import eu.dnetlib.dhp.common.MdstoreClient;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication
implements Closeable { implements Closeable {