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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
...@@ -32,10 +32,10 @@ public class ContainerImageEnvironmentItem { ...@@ -32,10 +32,10 @@ public class ContainerImageEnvironmentItem {
@EqualsAndHashCode.Include @EqualsAndHashCode.Include
public Long iid; public Long iid;
@Column(nullable = false) @Column(nullable = false, columnDefinition = "VARCHAR(255)")
private String key; private String key;
@Column(nullable = false) @Column(nullable = false, columnDefinition = "VARCHAR(255)")
private String value; private String value;
@Column(nullable = false, name = "etype", columnDefinition = "enum('USERNAME', 'PASSWORD', 'PRIVILEGED_USERNAME', 'PRIVILEGED_PASSWORD')") @Column(nullable = false, name = "etype", columnDefinition = "enum('USERNAME', 'PASSWORD', 'PRIVILEGED_USERNAME', 'PRIVILEGED_PASSWORD')")
......
...@@ -2,8 +2,6 @@ package at.tuwien.entities.database.table.columns; ...@@ -2,8 +2,6 @@ package at.tuwien.entities.database.table.columns;
import at.tuwien.entities.container.image.ContainerImageDate; import at.tuwien.entities.container.image.ContainerImageDate;
import at.tuwien.entities.database.table.Table; 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 at.tuwien.entities.user.User;
import lombok.*; import lombok.*;
import net.sf.jsqlparser.statement.select.SelectItem; import net.sf.jsqlparser.statement.select.SelectItem;
...@@ -123,7 +121,7 @@ public class TableColumn implements Comparable<TableColumn> { ...@@ -123,7 +121,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false) @JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
}, },
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri")) inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
private ColumnConcept concept; private TableColumnConcept concept;
@ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.MERGE) @ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.MERGE)
@JoinTable(name = "mdb_columns_units", @JoinTable(name = "mdb_columns_units",
...@@ -133,7 +131,7 @@ public class TableColumn implements Comparable<TableColumn> { ...@@ -133,7 +131,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false) @JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
}, },
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri")) inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
private ColumnUnit unit; private TableColumnUnit unit;
@Column @Column
@LastModifiedDate @LastModifiedDate
......
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 lombok.*;
import org.springframework.data.annotation.CreatedDate; import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener; import org.springframework.data.jpa.domain.support.AuditingEntityListener;
...@@ -18,7 +17,7 @@ import java.util.List; ...@@ -18,7 +17,7 @@ import java.util.List;
@EntityListeners(AuditingEntityListener.class) @EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true) @EqualsAndHashCode(onlyExplicitlyIncluded = true)
@javax.persistence.Table(name = "mdb_concepts") @javax.persistence.Table(name = "mdb_concepts")
public class ColumnConcept { public class TableColumnConcept {
@Id @Id
@EqualsAndHashCode.Include @EqualsAndHashCode.Include
......
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 lombok.*;
import org.springframework.data.annotation.CreatedDate; import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener; import org.springframework.data.jpa.domain.support.AuditingEntityListener;
...@@ -18,7 +17,7 @@ import java.util.List; ...@@ -18,7 +17,7 @@ import java.util.List;
@EntityListeners(AuditingEntityListener.class) @EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true) @EqualsAndHashCode(onlyExplicitlyIncluded = true)
@javax.persistence.Table(name = "mdb_units") @javax.persistence.Table(name = "mdb_units")
public class ColumnUnit { public class TableColumnUnit {
@Id @Id
@EqualsAndHashCode.Include @EqualsAndHashCode.Include
......
...@@ -7,7 +7,7 @@ import at.tuwien.api.database.table.columns.ColumnCreateDto; ...@@ -7,7 +7,7 @@ import at.tuwien.api.database.table.columns.ColumnCreateDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto; import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.user.UserDto; import at.tuwien.api.user.UserDto;
import at.tuwien.entities.container.image.*; 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.RoleType;
import at.tuwien.entities.user.User; import at.tuwien.entities.user.User;
import at.tuwien.querystore.Query; import at.tuwien.querystore.Query;
...@@ -744,7 +744,7 @@ public abstract class BaseUnitTest { ...@@ -744,7 +744,7 @@ public abstract class BaseUnitTest {
public final static String CONCEPT_1_NAME = "Temperature"; public final static String CONCEPT_1_NAME = "Temperature";
public final static Instant CONCEPT_1_CREATED = Instant.now().minus(1, HOURS); 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) .name(CONCEPT_1_NAME)
.created(CONCEPT_1_CREATED) .created(CONCEPT_1_CREATED)
.uri("http://www.ontology-of-units-of-measure.org/resource/om-2/") .uri("http://www.ontology-of-units-of-measure.org/resource/om-2/")
......
...@@ -5,6 +5,8 @@ import org.hibernate.boot.model.relational.Sequence; ...@@ -5,6 +5,8 @@ import org.hibernate.boot.model.relational.Sequence;
import org.hibernate.mapping.Table; import org.hibernate.mapping.Table;
import org.hibernate.tool.schema.spi.SchemaFilter; 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 * 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 { ...@@ -19,7 +21,11 @@ public class DbrepoSchemaFilter implements SchemaFilter {
@Override @Override
public boolean includeTable(Table table) { 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 @Override
......
...@@ -9,7 +9,7 @@ spring.cloud.config.discovery.enabled = false ...@@ -9,7 +9,7 @@ spring.cloud.config.discovery.enabled = false
spring.cloud.config.enabled=false spring.cloud.config.enabled=false
# internal datasource # 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.driverClassName=org.h2.Driver
spring.datasource.username=sa spring.datasource.username=sa
spring.datasource.password=password spring.datasource.password=password
......
CREATE SCHEMA IF NOT EXISTS `fda`; CREATE SCHEMA IF NOT EXISTS `fda`;
SET SCHEMA `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
package at.tuwien.repository.jpa; 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.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository; import org.springframework.stereotype.Repository;
@Repository @Repository
public interface ConceptRepository extends JpaRepository<ColumnConcept, String> { public interface ConceptRepository extends JpaRepository<TableColumnConcept, String> {
} }
package at.tuwien.repository.jpa; 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.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository; import org.springframework.stereotype.Repository;
@Repository @Repository
public interface UnitRepository extends JpaRepository<ColumnUnit, String> { public interface UnitRepository extends JpaRepository<TableColumnUnit, String> {
} }
...@@ -7,8 +7,8 @@ import at.tuwien.entities.container.Container; ...@@ -7,8 +7,8 @@ import at.tuwien.entities.container.Container;
import at.tuwien.entities.database.Database; import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.table.Table; import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn; import at.tuwien.entities.database.table.columns.TableColumn;
import at.tuwien.entities.database.table.columns.concepts.ColumnConcept; import at.tuwien.entities.database.table.columns.TableColumnConcept;
import at.tuwien.entities.database.table.columns.units.ColumnUnit; import at.tuwien.entities.database.table.columns.TableColumnUnit;
import at.tuwien.entities.user.User; import at.tuwien.entities.user.User;
import at.tuwien.exception.*; import at.tuwien.exception.*;
import at.tuwien.mapper.TableMapper; import at.tuwien.mapper.TableMapper;
...@@ -217,7 +217,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService ...@@ -217,7 +217,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
final TableColumn column = findColumn(table, columnId); final TableColumn column = findColumn(table, columnId);
/* assign */ /* assign */
if (updateDto.getUnitUri() != null) { if (updateDto.getUnitUri() != null) {
final ColumnUnit unit = findUnit(updateDto.getUnitUri()); final TableColumnUnit unit = findUnit(updateDto.getUnitUri());
column.setUnit(unit); column.setUnit(unit);
log.debug("update unit of column, unit={}, column={}", unit, column); log.debug("update unit of column, unit={}, column={}", unit, column);
} else { } else {
...@@ -225,7 +225,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService ...@@ -225,7 +225,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
log.debug("remove unit of column, column={}", column); log.debug("remove unit of column, column={}", column);
} }
if (updateDto.getConceptUri() != null) { if (updateDto.getConceptUri() != null) {
final ColumnConcept concept = findConcept(updateDto.getConceptUri()); final TableColumnConcept concept = findConcept(updateDto.getConceptUri());
column.setConcept(concept); column.setConcept(concept);
log.debug("update ColumnConcept of column, concept={}, column={}", concept, column); log.debug("update ColumnConcept of column, concept={}, column={}", concept, column);
} else { } else {
...@@ -265,8 +265,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService ...@@ -265,8 +265,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService
* @return The concept, if successful. * @return The concept, if successful.
* @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database. * @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database.
*/ */
protected ColumnConcept findConcept(String uri) throws ConceptNotFoundException { protected TableColumnConcept findConcept(String uri) throws ConceptNotFoundException {
final Optional<ColumnConcept> optional = conceptRepository.findById(uri); final Optional<TableColumnConcept> optional = conceptRepository.findById(uri);
if (optional.isEmpty()) { if (optional.isEmpty()) {
log.error("Failed to find ColumnConcept with uri {}", uri); log.error("Failed to find ColumnConcept with uri {}", uri);
throw new ConceptNotFoundException("Failed to find concept"); throw new ConceptNotFoundException("Failed to find concept");
...@@ -281,8 +281,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService ...@@ -281,8 +281,8 @@ public class TableServiceImpl extends HibernateConnector implements TableService
* @return The unit, if successful. * @return The unit, if successful.
* @throws UnitNotFoundException The unit was not found in the metadata database. * @throws UnitNotFoundException The unit was not found in the metadata database.
*/ */
protected ColumnUnit findUnit(String uri) throws UnitNotFoundException { protected TableColumnUnit findUnit(String uri) throws UnitNotFoundException {
final Optional<ColumnUnit> optional = unitRepository.findById(uri); final Optional<TableColumnUnit> optional = unitRepository.findById(uri);
if (optional.isEmpty()) { if (optional.isEmpty()) {
log.error("Failed to find unit with uri {}", uri); log.error("Failed to find unit with uri {}", uri);
throw new UnitNotFoundException("Failed to find unit"); throw new UnitNotFoundException("Failed to find unit");
......
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