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bug fixing

This commit is contained in:
Michele Artini 2020-02-11 12:48:03 +01:00
parent 95740767e0
commit 5fc09b179c
4 changed files with 20 additions and 4 deletions
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6
dhp-workflows/dhp-aggregation/pom.xml
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@ -56,6 +56,12 @@
<artifactId>mongo-java-driver</artifactId> <artifactId>mongo-java-driver</artifactId>
</dependency> </dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.2.10</version>
</dependency>
<dependency> <dependency>
<groupId>org.mockito</groupId> <groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId> <artifactId>mockito-core</artifactId>

7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java
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@ -10,6 +10,8 @@ import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors; import java.util.stream.Collectors;
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.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
@ -42,7 +44,12 @@ public class AbstractMigrationExecutor implements Closeable {
private final SequenceFile.Writer writer; private final SequenceFile.Writer writer;
private static final Log log = LogFactory.getLog(AbstractMigrationExecutor.class);
public AbstractMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception { public AbstractMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception {
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser));
this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
.keyClass(IntWritable.class), SequenceFile.Writer.valueClass(Text.class)); .keyClass(IntWritable.class), SequenceFile.Writer.valueClass(Text.class));
} }

7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/DbClient.java
View File

@ -9,6 +9,7 @@ import java.sql.SQLException;
import java.sql.Statement; import java.sql.Statement;
import java.util.function.Consumer; import java.util.function.Consumer;
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;
@ -22,7 +23,9 @@ public class DbClient implements Closeable {
try { try {
Class.forName("org.postgresql.Driver"); Class.forName("org.postgresql.Driver");
this.connection = DriverManager.getConnection(address, login, password);
this.connection =
StringUtils.isNoneBlank(login, password) ? DriverManager.getConnection(address, login, password) : DriverManager.getConnection(address);
this.connection.setAutoCommit(false); this.connection.setAutoCommit(false);
} catch (final Exception e) { } catch (final Exception e) {
log.error(e.getClass().getName() + ": " + e.getMessage()); log.error(e.getClass().getName() + ": " + e.getMessage());
@ -34,7 +37,7 @@ public class DbClient implements Closeable {
public void processResults(final String sql, final Consumer<ResultSet> consumer) { public void processResults(final String sql, final Consumer<ResultSet> consumer) {
try (final Statement stmt = connection.createStatement()) { try (final Statement stmt = connection.createStatement()) {
try (final ResultSet rs = stmt.executeQuery("SELECT * FROM COMPANY;")) { try (final ResultSet rs = stmt.executeQuery(sql)) {
while (rs.next()) { while (rs.next()) {
consumer.accept(rs); consumer.accept(rs);
} }

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json
View File

@ -27,12 +27,12 @@
"paramName": "dbuser", "paramName": "dbuser",
"paramLongName": "postgresUser", "paramLongName": "postgresUser",
"paramDescription": "postgres user", "paramDescription": "postgres user",
"paramRequired": true "paramRequired": false
}, },
{ {
"paramName": "dbpasswd", "paramName": "dbpasswd",
"paramLongName": "postgresPassword", "paramLongName": "postgresPassword",
"paramDescription": "postgres password", "paramDescription": "postgres password",
"paramRequired": true "paramRequired": false
} }
] ]