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Unverified Commit 60315be2 authored by Martin Weise's avatar Martin Weise
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Fixed the tests

parent 548410c4
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3 merge requests!129New module for citation as they occur multiple,!123Resolve "Concepts for columns, Units for values of columns",!121Modified logging, modified logging level, modified flasgger endpoint
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with 52 additions and 32 deletions
fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageEnvironmentItem.java
+ 2
− 2
View file @ 60315be2
......@@ -32,10 +32,10 @@ public class ContainerImageEnvironmentItem {
@EqualsAndHashCode.Include
public Long iid;
@Column(nullable = false)
@Column(nullable = false, columnDefinition = "VARCHAR(255)")
private String key;
@Column(nullable = false)
@Column(nullable = false, columnDefinition = "VARCHAR(255)")
private String value;
@Column(nullable = false, name = "etype", columnDefinition = "enum('USERNAME', 'PASSWORD', 'PRIVILEGED_USERNAME', 'PRIVILEGED_PASSWORD')")
......
fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
+ 2
− 4
View file @ 60315be2
......@@ -2,8 +2,6 @@ package at.tuwien.entities.database.table.columns;
import at.tuwien.entities.container.image.ContainerImageDate;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
import at.tuwien.entities.database.table.columns.units.ColumnUnit;
import at.tuwien.entities.user.User;
import lombok.*;
import net.sf.jsqlparser.statement.select.SelectItem;
......@@ -123,7 +121,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
},
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
private ColumnConcept concept;
private TableColumnConcept concept;
@ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.MERGE)
@JoinTable(name = "mdb_columns_units",
......@@ -133,7 +131,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
},
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
private ColumnUnit unit;
private TableColumnUnit unit;
@Column
@LastModifiedDate
......
fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java → fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnConcept.java
+ 2
− 3
View file @ 60315be2
package at.tuwien.entities.database.table.columns.concepts;
package at.tuwien.entities.database.table.columns;
import at.tuwien.entities.database.table.columns.TableColumn;
import lombok.*;
import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener;
......@@ -18,7 +17,7 @@ import java.util.List;
@EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
@javax.persistence.Table(name = "mdb_concepts")
public class ColumnConcept {
public class TableColumnConcept {
@Id
@EqualsAndHashCode.Include
......
fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/units/ColumnUnit.java → fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnUnit.java
+ 2
− 3
View file @ 60315be2
package at.tuwien.entities.database.table.columns.units;
package at.tuwien.entities.database.table.columns;
import at.tuwien.entities.database.table.columns.TableColumn;
import lombok.*;
import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener;
......@@ -18,7 +17,7 @@ import java.util.List;
@EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
@javax.persistence.Table(name = "mdb_units")
public class ColumnUnit {
public class TableColumnUnit {
@Id
@EqualsAndHashCode.Include
......
fda-table-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
+ 2
− 2
View file @ 60315be2
......@@ -7,7 +7,7 @@ import at.tuwien.api.database.table.columns.ColumnCreateDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.user.UserDto;
import at.tuwien.entities.container.image.*;
import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
import at.tuwien.entities.database.table.columns.TableColumnConcept;
import at.tuwien.entities.user.RoleType;
import at.tuwien.entities.user.User;
import at.tuwien.querystore.Query;
......@@ -744,7 +744,7 @@ public abstract class BaseUnitTest {
public final static String CONCEPT_1_NAME = "Temperature";
public final static Instant CONCEPT_1_CREATED = Instant.now().minus(1, HOURS);
public final static ColumnConcept CONCEPT_1 = ColumnConcept.builder()
public final static TableColumnConcept CONCEPT_1 = TableColumnConcept.builder()
.name(CONCEPT_1_NAME)
.created(CONCEPT_1_CREATED)
.uri("http://www.ontology-of-units-of-measure.org/resource/om-2/")
......
fda-table-service/rest-service/src/test/java/at/tuwien/hibernate/DbrepoSchemaFilter.java
+ 7
− 1
View file @ 60315be2
......@@ -5,6 +5,8 @@ import org.hibernate.boot.model.relational.Sequence;
import org.hibernate.mapping.Table;
import org.hibernate.tool.schema.spi.SchemaFilter;
import java.util.List;
/**
* Do not create table for class {@link at.tuwien.entities.database.table.columns.concepts.ColumnConcept} when using JUnit test
*/
......@@ -19,7 +21,11 @@ public class DbrepoSchemaFilter implements SchemaFilter {
@Override
public boolean includeTable(Table table) {
return !table.getName().matches("mdb_concepts");
final List<String> exclude = List.of("mdb_units", "mdb_concepts");
if (table.getSchema().matches("fda") && exclude.contains(table.getName())) {
return false;
}
return true;
}
@Override
......
fda-table-service/rest-service/src/test/resources/application.properties
+ 4
− 4
View file @ 60315be2
......@@ -9,7 +9,7 @@ spring.cloud.config.discovery.enabled = false
spring.cloud.config.enabled=false
# internal datasource
spring.datasource.url=jdbc:h2:mem:fda;DATABASE_TO_UPPER=false;DB_CLOSE_ON_EXIT=FALSE;MODE=MYSQL;INIT=RUNSCRIPT FROM 'classpath:schema.sql'
spring.datasource.url=jdbc:h2:mem:testdb;DATABASE_TO_UPPER=false;DB_CLOSE_ON_EXIT=FALSE;MODE=MYSQL;INIT=RUNSCRIPT FROM 'classpath:schema.sql'
spring.datasource.driverClassName=org.h2.Driver
spring.datasource.username=sa
spring.datasource.password=password
......
fda-table-service/rest-service/src/test/resources/schema.sql
+ 19
− 1
View file @ 60315be2
CREATE SCHEMA IF NOT EXISTS `fda`;
SET SCHEMA `fda`;
DROP TABLE IF EXISTS fda.mdb_concepts;
CREATE TABLE fda.mdb_concepts
(
uri VARCHAR(500) not null,
name VARCHAR(255),
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint,
PRIMARY KEY (uri)
);
DROP TABLE IF EXISTS fda.mdb_units;
CREATE TABLE fda.mdb_units
(
uri VARCHAR(500) not null,
name VARCHAR(255),
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint,
PRIMARY KEY (uri)
);
\ No newline at end of file
fda-table-service/services/src/main/java/at/tuwien/repository/jpa/ConceptRepository.java
+ 2
− 2
View file @ 60315be2
package at.tuwien.repository.jpa;
import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
import at.tuwien.entities.database.table.columns.TableColumnConcept;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
@Repository
public interface ConceptRepository extends JpaRepository<ColumnConcept, String> {
public interface ConceptRepository extends JpaRepository<TableColumnConcept, String> {
}
fda-table-service/services/src/main/java/at/tuwien/repository/jpa/UnitRepository.java
+ 2
− 2
View file @ 60315be2
package at.tuwien.repository.jpa;
import at.tuwien.entities.database.table.columns.units.ColumnUnit;
import at.tuwien.entities.database.table.columns.TableColumnUnit;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
@Repository
public interface UnitRepository extends JpaRepository<ColumnUnit, String> {
public interface UnitRepository extends JpaRepository<TableColumnUnit, String> {
}
fda-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
+ 8
− 8
View file @ 60315be2
......@@ -7,8 +7,8 @@ import at.tuwien.entities.container.Container;
import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn;
import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
import at.tuwien.entities.database.table.columns.units.ColumnUnit;
import at.tuwien.entities.database.table.columns.TableColumnConcept;
import at.tuwien.entities.database.table.columns.TableColumnUnit;
import at.tuwien.entities.user.User;
import at.tuwien.exception.*;
import at.tuwien.mapper.TableMapper;
......@@ -217,7 +217,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
final TableColumn column = findColumn(table, columnId);
/* assign */
if (updateDto.getUnitUri() != null) {
final ColumnUnit unit = findUnit(updateDto.getUnitUri());
final TableColumnUnit unit = findUnit(updateDto.getUnitUri());
column.setUnit(unit);
log.debug("update unit of column, unit={}, column={}", unit, column);
} else {
......@@ -225,7 +225,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
log.debug("remove unit of column, column={}", column);
}
if (updateDto.getConceptUri() != null) {
final ColumnConcept concept = findConcept(updateDto.getConceptUri());
final TableColumnConcept concept = findConcept(updateDto.getConceptUri());
column.setConcept(concept);
log.debug("update ColumnConcept of column, concept={}, column={}", concept, column);
} else {
......@@ -265,8 +265,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService
* @return The concept, if successful.
* @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database.
*/
protected ColumnConcept findConcept(String uri) throws ConceptNotFoundException {
final Optional<ColumnConcept> optional = conceptRepository.findById(uri);
protected TableColumnConcept findConcept(String uri) throws ConceptNotFoundException {
final Optional<TableColumnConcept> optional = conceptRepository.findById(uri);
if (optional.isEmpty()) {
log.error("Failed to find ColumnConcept with uri {}", uri);
throw new ConceptNotFoundException("Failed to find concept");
......@@ -281,8 +281,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService
* @return The unit, if successful.
* @throws UnitNotFoundException The unit was not found in the metadata database.
*/
protected ColumnUnit findUnit(String uri) throws UnitNotFoundException {
final Optional<ColumnUnit> optional = unitRepository.findById(uri);
protected TableColumnUnit findUnit(String uri) throws UnitNotFoundException {
final Optional<TableColumnUnit> optional = unitRepository.findById(uri);
if (optional.isEmpty()) {
log.error("Failed to find unit with uri {}", uri);
throw new UnitNotFoundException("Failed to find unit");
......
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