From 548410c43a8ef94ae573f9d4e88c13a021244064 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Thu, 5 Jan 2023 08:38:26 +0100
Subject: [PATCH] WIP
---
.../database/table/TableCreateRawQuery.java | 4 +-
.../database/table/TableInsertRawQuery.java | 4 +-
.../database/table/columns/TableColumn.java | 8 ++--
.../table/columns/concepts/ColumnConcept.java | 45 +++++++++---------
.../columns/concepts/ColumnConceptKey.java | 16 -------
.../table/columns/concepts/Concept.java | 46 -------------------
.../Unit.java => units/ColumnUnit.java} | 4 +-
fda-table-service/.dockerignore | 1 -
fda-table-service/.gitignore | 4 --
fda-table-service/Dockerfile | 12 ++---
fda-table-service/README.md | 7 +++
fda-table-service/api/pom.xml | 21 ---------
fda-table-service/pom.xml | 1 -
fda-table-service/report/pom.xml | 7 ++-
fda-table-service/rest-service/pom.xml | 8 +++-
.../at/tuwien/FdaTableServiceApplication.java | 2 +-
.../src/test/java/at/tuwien/BaseUnitTest.java | 4 +-
.../tuwien/hibernate/DbrepoSchemaFilter.java | 2 +-
.../src/test/resources/application.properties | 2 +-
.../rest-service/src/test/resources/init.sql | 10 ----
.../src/test/resources/schema.sql | 2 +
fda-table-service/services/pom.xml | 11 +----
.../java/at/tuwien/mapper/TableMapper.java | 8 ++--
.../repository/jpa/ConceptRepository.java | 4 +-
.../tuwien/repository/jpa/UnitRepository.java | 4 +-
.../tuwien/service/impl/TableServiceImpl.java | 30 ++++++------
26 files changed, 89 insertions(+), 178 deletions(-)
rename fda-table-service/api/src/main/java/at/tuwien/CreateTableRawQuery.java => fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableCreateRawQuery.java (81%)
rename fda-table-service/api/src/main/java/at/tuwien/InsertTableRawQuery.java => fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableInsertRawQuery.java (75%)
delete mode 100644 fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConceptKey.java
delete mode 100644 fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
rename fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/{concepts/Unit.java => units/ColumnUnit.java} (94%)
delete mode 100644 fda-table-service/.dockerignore
create mode 100644 fda-table-service/README.md
delete mode 100644 fda-table-service/api/pom.xml
delete mode 100644 fda-table-service/rest-service/src/test/resources/init.sql
create mode 100644 fda-table-service/rest-service/src/test/resources/schema.sql
diff --git a/fda-table-service/api/src/main/java/at/tuwien/CreateTableRawQuery.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableCreateRawQuery.java
similarity index 81%
rename from fda-table-service/api/src/main/java/at/tuwien/CreateTableRawQuery.java
rename to fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableCreateRawQuery.java
index 2b9c7a1276..a587587d2f 100644
--- a/fda-table-service/api/src/main/java/at/tuwien/CreateTableRawQuery.java
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableCreateRawQuery.java
@@ -1,4 +1,4 @@
-package at.tuwien;
+package at.tuwien.api.database.table;
import lombok.*;
@@ -10,7 +10,7 @@ import java.sql.PreparedStatement;
@Builder
@AllArgsConstructor
@NoArgsConstructor
-public class CreateTableRawQuery {
+public class TableCreateRawQuery {
private PreparedStatement preparedStatement;
diff --git a/fda-table-service/api/src/main/java/at/tuwien/InsertTableRawQuery.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableInsertRawQuery.java
similarity index 75%
rename from fda-table-service/api/src/main/java/at/tuwien/InsertTableRawQuery.java
rename to fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableInsertRawQuery.java
index 4541a7786d..66d09bb136 100644
--- a/fda-table-service/api/src/main/java/at/tuwien/InsertTableRawQuery.java
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/TableInsertRawQuery.java
@@ -1,4 +1,4 @@
-package at.tuwien;
+package at.tuwien.api.database.table;
import lombok.*;
@@ -11,7 +11,7 @@ import java.util.List;
@Builder
@AllArgsConstructor
@NoArgsConstructor
-public class InsertTableRawQuery {
+public class TableInsertRawQuery {
private String query;
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
index 4c0faa0029..9cf3d52728 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
@@ -2,8 +2,8 @@ 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.Concept;
-import at.tuwien.entities.database.table.columns.concepts.Unit;
+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 +123,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
},
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
- private Concept concept;
+ private ColumnConcept concept;
@ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.MERGE)
@JoinTable(name = "mdb_columns_units",
@@ -133,7 +133,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
},
inverseJoinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri"))
- private Unit unit;
+ private ColumnUnit unit;
@Column
@LastModifiedDate
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java
index 711a86286e..4d0e5f6048 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java
@@ -1,43 +1,46 @@
package at.tuwien.entities.database.table.columns.concepts;
+import at.tuwien.entities.database.table.columns.TableColumn;
import lombok.*;
-import org.hibernate.annotations.GenericGenerator;
+import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener;
import javax.persistence.*;
-import java.io.Serializable;
+import java.time.Instant;
+import java.util.List;
-/**
- * Join Table
- */
@Data
@Entity
@Builder
@AllArgsConstructor
@NoArgsConstructor
@ToString
-@IdClass(ColumnConceptKey.class)
@EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
-@javax.persistence.Table(name = "mdb_columns_concepts")
-public class ColumnConcept implements Serializable {
+@javax.persistence.Table(name = "mdb_concepts")
+public class ColumnConcept {
@Id
@EqualsAndHashCode.Include
- @GeneratedValue(generator = "columns-concepts-sequence")
- @GenericGenerator(name = "columns-concepts-sequence", strategy = "increment")
- @Column(updatable = false, nullable = false)
- private Long cid;
+ @Column(nullable = false, columnDefinition = "TEXT")
+ private String uri;
- @Id
- @EqualsAndHashCode.Include
- private Long tid;
+ @Column(name = "name", nullable = false)
+ private String name;
- @Id
- @EqualsAndHashCode.Include
- private Long cdbid;
+ @org.springframework.data.annotation.Transient
+ @ToString.Exclude
+ @OneToMany(fetch = FetchType.LAZY)
+ @JoinTable(name = "mdb_columns_concepts",
+ joinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri", insertable = false, updatable = false),
+ inverseJoinColumns = {
+ @JoinColumn(name = "cid", referencedColumnName = "id", insertable = false, updatable = false),
+ @JoinColumn(name = "tid", referencedColumnName = "tid", insertable = false, updatable = false),
+ @JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
+ })
+ private List<TableColumn> columns;
- @EqualsAndHashCode.Include
- @Column(columnDefinition = "TEXT")
- private String uri;
+ @Column(nullable = false, updatable = false)
+ @CreatedDate
+ private Instant created;
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConceptKey.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConceptKey.java
deleted file mode 100644
index 7b0b79ee86..0000000000
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConceptKey.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package at.tuwien.entities.database.table.columns.concepts;
-
-import lombok.EqualsAndHashCode;
-
-import java.io.Serializable;
-
-@EqualsAndHashCode
-public class ColumnConceptKey implements Serializable {
-
- private Long cid;
-
- private Long cdbid;
-
- private Long tid;
-
-}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
deleted file mode 100644
index 1771719c74..0000000000
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package at.tuwien.entities.database.table.columns.concepts;
-
-import at.tuwien.entities.database.table.columns.TableColumn;
-import lombok.*;
-import org.springframework.data.annotation.CreatedDate;
-import org.springframework.data.jpa.domain.support.AuditingEntityListener;
-
-import javax.persistence.*;
-import java.time.Instant;
-import java.util.List;
-
-@Data
-@Entity
-@Builder
-@AllArgsConstructor
-@NoArgsConstructor
-@ToString
-@EntityListeners(AuditingEntityListener.class)
-@EqualsAndHashCode(onlyExplicitlyIncluded = true)
-@javax.persistence.Table(name = "mdb_concepts")
-public class Concept {
-
- @Id
- @EqualsAndHashCode.Include
- @Column(nullable = false, columnDefinition = "TEXT")
- private String uri;
-
- @Column(name = "name", nullable = false)
- private String name;
-
- @org.springframework.data.annotation.Transient
- @ToString.Exclude
- @OneToMany(fetch = FetchType.LAZY)
- @JoinTable(name = "mdb_columns_concepts",
- joinColumns = @JoinColumn(name = "uri", referencedColumnName = "uri", insertable = false, updatable = false),
- inverseJoinColumns = {
- @JoinColumn(name = "cid", referencedColumnName = "id", insertable = false, updatable = false),
- @JoinColumn(name = "tid", referencedColumnName = "tid", insertable = false, updatable = false),
- @JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
- })
- private List<TableColumn> columns;
-
- @Column(nullable = false, updatable = false)
- @CreatedDate
- private Instant created;
-}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Unit.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/units/ColumnUnit.java
similarity index 94%
rename from fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Unit.java
rename to fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/units/ColumnUnit.java
index 699cdf7d89..6969bc7a87 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Unit.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/units/ColumnUnit.java
@@ -1,4 +1,4 @@
-package at.tuwien.entities.database.table.columns.concepts;
+package at.tuwien.entities.database.table.columns.units;
import at.tuwien.entities.database.table.columns.TableColumn;
import lombok.*;
@@ -18,7 +18,7 @@ import java.util.List;
@EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
@javax.persistence.Table(name = "mdb_units")
-public class Unit {
+public class ColumnUnit {
@Id
@EqualsAndHashCode.Include
diff --git a/fda-table-service/.dockerignore b/fda-table-service/.dockerignore
deleted file mode 100644
index fcdfe8de55..0000000000
--- a/fda-table-service/.dockerignore
+++ /dev/null
@@ -1 +0,0 @@
-rest-service/src/main/resources/*.csv
\ No newline at end of file
diff --git a/fda-table-service/.gitignore b/fda-table-service/.gitignore
index 8e5c311b11..7731f1adf2 100644
--- a/fda-table-service/.gitignore
+++ b/fda-table-service/.gitignore
@@ -4,12 +4,8 @@ target/
!**/src/main/**/target/
!**/src/test/**/target/
-### Environment ###
-.env
-
### Generated ###
ready
-mapping.xml
### STS ###
.apt_generated
diff --git a/fda-table-service/Dockerfile b/fda-table-service/Dockerfile
index ec1ab5c64e..4752a4a140 100644
--- a/fda-table-service/Dockerfile
+++ b/fda-table-service/Dockerfile
@@ -14,7 +14,6 @@ COPY --from=dependency /root/.m2/repository/at/tuwien /root/.m2/repository/at/tu
COPY ./rest-service ./rest-service
COPY ./services ./services
COPY ./report ./report
-COPY ./api ./api
# Make sure it compiles
RUN mvn -q clean package -DskipTests > /dev/null
@@ -27,9 +26,8 @@ ENV METADATA_USERNAME=root
ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
-ENV SEARCH_ENDPOINT=search-service
-ENV GATEWAY_ENDPOINT=http://gateway-service:9095
-ENV multipart.location=/tmp
+ENV SHARED_FILESYSTEM=/tmp
+ENV USER_NETWORK=userdb
ENV LOG_LEVEL=debug
COPY ./service_ready /usr/bin
@@ -37,8 +35,8 @@ RUN chmod +x /usr/bin/service_ready
HEALTHCHECK --interval=10s --timeout=5s --retries=12 CMD service_ready
-COPY --from=build ./rest-service/target/rest-service-*.jar ./table-service.jar
+COPY --from=build ./rest-service/target/rest-service-*.jar ./container-service.jar
-EXPOSE 9094
+EXPOSE 9091
-ENTRYPOINT ["java", "-Dlog4j2.formatMsgNoLookups=true", "-jar", "./table-service.jar"]
+ENTRYPOINT ["java", "-Dlog4j2.formatMsgNoLookups=true", "-jar", "./container-service.jar"]
diff --git a/fda-table-service/README.md b/fda-table-service/README.md
new file mode 100644
index 0000000000..986b2885e1
--- /dev/null
+++ b/fda-table-service/README.md
@@ -0,0 +1,7 @@
+# FDA Container Service
+
+## Documentation
+
+- OpenAPI v3: http://localhost:9091/swagger-ui/index.html
+- OpenAPI v3 endpoint: http://localhost:9091/v3/api-docs/
+- OpenAPI v3 YAML: http://localhost:9091/v3/api-docs.yaml
\ No newline at end of file
diff --git a/fda-table-service/api/pom.xml b/fda-table-service/api/pom.xml
deleted file mode 100644
index 658d47e006..0000000000
--- a/fda-table-service/api/pom.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <artifactId>fda-table-service</artifactId>
- <groupId>at.tuwien</groupId>
- <version>1.1.0-alpha</version>
- </parent>
-
- <artifactId>api</artifactId>
- <name>fda-table-service-api</name>
-
- <properties>
- <jacoco.version>0.8.7</jacoco.version>
- </properties>
-
- <dependencies />
-
-</project>
\ No newline at end of file
diff --git a/fda-table-service/pom.xml b/fda-table-service/pom.xml
index 01d11e6846..e9faf0cbb3 100644
--- a/fda-table-service/pom.xml
+++ b/fda-table-service/pom.xml
@@ -19,7 +19,6 @@
<module>rest-service</module>
<module>services</module>
<module>report</module>
- <module>api</module>
</modules>
<properties>
diff --git a/fda-table-service/report/pom.xml b/fda-table-service/report/pom.xml
index 8b0c154b0f..1992c97aa9 100644
--- a/fda-table-service/report/pom.xml
+++ b/fda-table-service/report/pom.xml
@@ -4,13 +4,18 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <artifactId>fda-table-service</artifactId>
<groupId>at.tuwien</groupId>
+ <artifactId>fda-table-service</artifactId>
<version>1.1.0-alpha</version>
</parent>
<artifactId>report</artifactId>
+ <version>1.1.0-alpha</version>
<name>fda-table-service-report</name>
+ <description>
+ This module is only intended for the pipeline coverage report. See the detailed report in the
+ respective modules
+ </description>
<properties>
<jacoco.version>0.8.7</jacoco.version>
diff --git a/fda-table-service/rest-service/pom.xml b/fda-table-service/rest-service/pom.xml
index b73a6ef216..0fd761d629 100644
--- a/fda-table-service/rest-service/pom.xml
+++ b/fda-table-service/rest-service/pom.xml
@@ -4,14 +4,18 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <artifactId>fda-table-service</artifactId>
<groupId>at.tuwien</groupId>
+ <artifactId>fda-table-service</artifactId>
<version>1.1.0-alpha</version>
</parent>
<artifactId>rest-service</artifactId>
<version>1.1.0-alpha</version>
- <name>fda-table-service-rest</name>
+ <name>fda-table-service-rest-service</name>
+
+ <properties>
+ <jacoco.version>0.8.7</jacoco.version>
+ </properties>
<dependencies>
<dependency>
diff --git a/fda-table-service/rest-service/src/main/java/at/tuwien/FdaTableServiceApplication.java b/fda-table-service/rest-service/src/main/java/at/tuwien/FdaTableServiceApplication.java
index 627cfa68a4..ebc2e89271 100644
--- a/fda-table-service/rest-service/src/main/java/at/tuwien/FdaTableServiceApplication.java
+++ b/fda-table-service/rest-service/src/main/java/at/tuwien/FdaTableServiceApplication.java
@@ -12,9 +12,9 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@EnableJpaAuditing
@SpringBootApplication
@EnableTransactionManagement
+@EntityScan(basePackages = {"at.tuwien.entities"})
@EnableElasticsearchRepositories(basePackages = {"at.tuwien.repository.elastic"})
@EnableJpaRepositories(basePackages = {"at.tuwien.repository.jpa"})
-@EntityScan(basePackages = {"at.tuwien.entities"})
public class FdaTableServiceApplication {
public static void main(String[] args) {
diff --git a/fda-table-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java b/fda-table-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
index ce3c4aa05d..119eaa6688 100644
--- a/fda-table-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
+++ b/fda-table-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
@@ -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.Concept;
+import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
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 Concept CONCEPT_1 = Concept.builder()
+ public final static ColumnConcept CONCEPT_1 = ColumnConcept.builder()
.name(CONCEPT_1_NAME)
.created(CONCEPT_1_CREATED)
.uri("http://www.ontology-of-units-of-measure.org/resource/om-2/")
diff --git a/fda-table-service/rest-service/src/test/java/at/tuwien/hibernate/DbrepoSchemaFilter.java b/fda-table-service/rest-service/src/test/java/at/tuwien/hibernate/DbrepoSchemaFilter.java
index bdbe4aebe2..1f0ad27cc0 100644
--- a/fda-table-service/rest-service/src/test/java/at/tuwien/hibernate/DbrepoSchemaFilter.java
+++ b/fda-table-service/rest-service/src/test/java/at/tuwien/hibernate/DbrepoSchemaFilter.java
@@ -6,7 +6,7 @@ import org.hibernate.mapping.Table;
import org.hibernate.tool.schema.spi.SchemaFilter;
/**
- * Do not create table for class {@link at.tuwien.entities.database.table.columns.concepts.Concept} when using JUnit test
+ * Do not create table for class {@link at.tuwien.entities.database.table.columns.concepts.ColumnConcept} when using JUnit test
*/
public class DbrepoSchemaFilter implements SchemaFilter {
diff --git a/fda-table-service/rest-service/src/test/resources/application.properties b/fda-table-service/rest-service/src/test/resources/application.properties
index ef996777c5..d82af2fbd7 100644
--- a/fda-table-service/rest-service/src/test/resources/application.properties
+++ b/fda-table-service/rest-service/src/test/resources/application.properties
@@ -9,7 +9,7 @@ spring.cloud.config.discovery.enabled = false
spring.cloud.config.enabled = false
# internal datasource
-spring.datasource.url=jdbc:h2:mem:testdb;DATABASE_TO_UPPER=false;DB_CLOSE_ON_EXIT=FALSE;INIT=RUNSCRIPT FROM './src/test/resources/init.sql'
+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.driverClassName=org.h2.Driver
spring.datasource.username=sa
spring.datasource.password=password
diff --git a/fda-table-service/rest-service/src/test/resources/init.sql b/fda-table-service/rest-service/src/test/resources/init.sql
deleted file mode 100644
index e25e2d0d03..0000000000
--- a/fda-table-service/rest-service/src/test/resources/init.sql
+++ /dev/null
@@ -1,10 +0,0 @@
-CREATE SCHEMA IF NOT EXISTS fda;
-DROP TABLE IF EXISTS fda.mdb_concepts CASCADE;
-CREATE TABLE IF NOT EXISTS fda.mdb_concepts
-(
- uri varchar(255) not null,
- name VARCHAR(255),
- created timestamp NOT NULL DEFAULT NOW(),
- created_by bigint,
- PRIMARY KEY (uri)
-);
\ No newline at end of file
diff --git a/fda-table-service/rest-service/src/test/resources/schema.sql b/fda-table-service/rest-service/src/test/resources/schema.sql
new file mode 100644
index 0000000000..095a1096ea
--- /dev/null
+++ b/fda-table-service/rest-service/src/test/resources/schema.sql
@@ -0,0 +1,2 @@
+CREATE SCHEMA IF NOT EXISTS `fda`;
+SET SCHEMA `fda`;
\ No newline at end of file
diff --git a/fda-table-service/services/pom.xml b/fda-table-service/services/pom.xml
index 4a87bfe0d3..8deff1d33e 100644
--- a/fda-table-service/services/pom.xml
+++ b/fda-table-service/services/pom.xml
@@ -13,15 +13,6 @@
<version>1.1.0-alpha</version>
<name>fda-table-service-services</name>
- <dependencies >
- <dependency>
- <groupId>at.tuwien</groupId>
- <artifactId>api</artifactId>
- <version>1.1.0-alpha</version>
- <scope>compile</scope>
- </dependency>
- </dependencies>
-
<build>
<plugins>
<plugin>
@@ -48,4 +39,4 @@
</plugins>
</build>
-</project>
+</project>
\ No newline at end of file
diff --git a/fda-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java b/fda-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
index c4a316dd06..a90f951708 100644
--- a/fda-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
+++ b/fda-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
@@ -1,8 +1,8 @@
package at.tuwien.mapper;
-import at.tuwien.CreateTableRawQuery;
import at.tuwien.api.database.table.TableBriefDto;
import at.tuwien.api.database.table.TableCreateDto;
+import at.tuwien.api.database.table.TableCreateRawQuery;
import at.tuwien.api.database.table.TableDto;
import at.tuwien.api.database.table.columns.ColumnCreateDto;
import at.tuwien.api.database.table.columns.ColumnDto;
@@ -72,7 +72,7 @@ public interface TableMapper {
@Mapping(source = "data.dfid", target = "dfid"),
@Mapping(source = "data.lastModified", target = "lastModified"),
})
- TableColumn tableColumnToTableColumn(Table table, TableColumn data, CreateTableRawQuery query);
+ TableColumn tableColumnToTableColumn(Table table, TableColumn data, TableCreateRawQuery query);
@Named("internalMapping")
default String nameToInternalName(String data) {
@@ -172,7 +172,7 @@ public interface TableMapper {
* @param data The table
* @return The create table query
*/
- default CreateTableRawQuery tableToCreateTableRawQuery(Connection connection, Database database, TableCreateDto data)
+ default TableCreateRawQuery tableToCreateTableRawQuery(Connection connection, Database database, TableCreateDto data)
throws ImageNotSupportedException, TableMalformedException, QueryMalformedException {
if (!database.getContainer().getImage().getRepository().equals("mariadb")) {
log.error("Currently only MariaDB is supported");
@@ -263,7 +263,7 @@ public interface TableMapper {
try {
final PreparedStatement pstmt = connection.prepareStatement(query.toString());
log.trace("prepared create table statement {}", query);
- return CreateTableRawQuery.builder()
+ return TableCreateRawQuery.builder()
.preparedStatement(pstmt)
.generated(!primaryColumnExists)
.build();
diff --git a/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/ConceptRepository.java b/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/ConceptRepository.java
index 2f29e71962..61d4cfe57e 100644
--- a/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/ConceptRepository.java
+++ b/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/ConceptRepository.java
@@ -1,10 +1,10 @@
package at.tuwien.repository.jpa;
-import at.tuwien.entities.database.table.columns.concepts.Concept;
+import at.tuwien.entities.database.table.columns.concepts.ColumnConcept;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
@Repository
-public interface ConceptRepository extends JpaRepository<Concept, String> {
+public interface ConceptRepository extends JpaRepository<ColumnConcept, String> {
}
diff --git a/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/UnitRepository.java b/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/UnitRepository.java
index 01cbeeaa41..5408cc4961 100644
--- a/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/UnitRepository.java
+++ b/fda-table-service/services/src/main/java/at/tuwien/repository/jpa/UnitRepository.java
@@ -1,10 +1,10 @@
package at.tuwien.repository.jpa;
-import at.tuwien.entities.database.table.columns.concepts.Unit;
+import at.tuwien.entities.database.table.columns.units.ColumnUnit;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
@Repository
-public interface UnitRepository extends JpaRepository<Unit, String> {
+public interface UnitRepository extends JpaRepository<ColumnUnit, String> {
}
diff --git a/fda-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java b/fda-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
index 542fd15136..6c8d45d11a 100644
--- a/fda-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
+++ b/fda-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
@@ -1,14 +1,14 @@
package at.tuwien.service.impl;
-import at.tuwien.CreateTableRawQuery;
import at.tuwien.api.database.table.TableCreateDto;
+import at.tuwien.api.database.table.TableCreateRawQuery;
import at.tuwien.api.database.table.columns.concepts.ColumnSemanticsUpdateDto;
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.Concept;
-import at.tuwien.entities.database.table.columns.concepts.Unit;
+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.exception.*;
import at.tuwien.mapper.TableMapper;
@@ -134,7 +134,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
}
/* run query */
final ComboPooledDataSource dataSource = getDataSource(database.getContainer().getImage(), database.getContainer(), database);
- final CreateTableRawQuery query;
+ final TableCreateRawQuery query;
try {
final Connection connection = dataSource.getConnection();
query = tableMapper.tableToCreateTableRawQuery(connection, database, createDto);
@@ -217,7 +217,7 @@ public class TableServiceImpl extends HibernateConnector implements TableService
final TableColumn column = findColumn(table, columnId);
/* assign */
if (updateDto.getUnitUri() != null) {
- final Unit unit = findUnit(updateDto.getUnitUri());
+ final ColumnUnit unit = findUnit(updateDto.getUnitUri());
column.setUnit(unit);
log.debug("update unit of column, unit={}, column={}", unit, column);
} else {
@@ -225,12 +225,12 @@ public class TableServiceImpl extends HibernateConnector implements TableService
log.debug("remove unit of column, column={}", column);
}
if (updateDto.getConceptUri() != null) {
- final Concept concept = findConcept(updateDto.getConceptUri());
+ final ColumnConcept concept = findConcept(updateDto.getConceptUri());
column.setConcept(concept);
- log.debug("update concept of column, concept={}, column={}", concept, column);
+ log.debug("update ColumnConcept of column, concept={}, column={}", concept, column);
} else {
column.setConcept(null);
- log.debug("remove concept of column, column={}", column);
+ log.debug("remove ColumnConcept of column, column={}", column);
}
final TableColumn out = tableColumnRepository.save(column);
log.info("Updated table column with id {} of table with id {}", columnId, tableId);
@@ -259,16 +259,16 @@ public class TableServiceImpl extends HibernateConnector implements TableService
}
/**
- * Finds a concept with given uri
+ * Finds a ColumnConcept with given uri
*
* @param uri The uri.
* @return The concept, if successful.
- * @throws ConceptNotFoundException The concept was not found in the metadata database.
+ * @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database.
*/
- protected Concept findConcept(String uri) throws ConceptNotFoundException {
- final Optional<Concept> optional = conceptRepository.findById(uri);
+ protected ColumnConcept findConcept(String uri) throws ConceptNotFoundException {
+ final Optional<ColumnConcept> optional = conceptRepository.findById(uri);
if (optional.isEmpty()) {
- log.error("Failed to find concept with uri {}", uri);
+ log.error("Failed to find ColumnConcept with uri {}", uri);
throw new ConceptNotFoundException("Failed to find concept");
}
return optional.get();
@@ -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 Unit findUnit(String uri) throws UnitNotFoundException {
- final Optional<Unit> optional = unitRepository.findById(uri);
+ protected ColumnUnit findUnit(String uri) throws UnitNotFoundException {
+ final Optional<ColumnUnit> 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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