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Commit 3a043e20 authored by Martin Weise's avatar Martin Weise
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fixed latest metadata database issue

parent 0a128b3a
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6 merge requests!81New stable release,!43Merge dev to master,!23Sprint results,!20Pull Request,!19Pull Request,!18Merge Conflicts
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with 139 additions and 34 deletions
.gitignore
+ 3
− 0
View file @ 3a043e20
......@@ -4,6 +4,9 @@ target/
!**/src/main/**/target/
!**/src/test/**/target/
# IDE
fda-analyse-service/venv
### STS ###
.apt_generated
.classpath
......
fda-container-service/rest-service/src/test/java/at/tuwien/service/ContainerServiceIntegrationTest.java
+ 1
− 0
View file @ 3a043e20
......@@ -55,6 +55,7 @@ public class ContainerServiceIntegrationTest extends BaseUnitTest {
@Transactional
@BeforeEach
public void beforeEach() {
afterEach();
/* create network */
dockerClient.createNetworkCmd()
.withName("fda-userdb")
......
fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
+ 1
− 1
View file @ 3a043e20
......@@ -58,7 +58,7 @@ public class ContainerImage {
private Integer defaultPort;
@ToString.Include
@OneToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
@OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
private List<ContainerImageEnvironmentItem> environment;
@Column(nullable = false, updatable = false)
......
fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java
+ 2
− 2
View file @ 3a043e20
......@@ -35,7 +35,7 @@ public class Database {
private Long id;
@ToString.Include
@ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
@ManyToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
private Container container;
@ToString.Include
......@@ -47,7 +47,7 @@ public class Database {
private String internalName;
@ToString.Exclude
@OneToMany(mappedBy = "id", fetch = FetchType.LAZY)
@OneToMany(mappedBy = "id", fetch = FetchType.EAGER, cascade = CascadeType.ALL)
private List<Table> tables;
@ToString.Include
......
fda-table-service/pom.xml
+ 4
− 0
View file @ 3a043e20
......@@ -42,6 +42,10 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.cloud</groupId>
<artifactId>spring-cloud-starter-bootstrap</artifactId>
......
fda-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+ 3
− 2
View file @ 3a043e20
......@@ -20,6 +20,7 @@ import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.multipart.MultipartFile;
import javax.validation.Valid;
import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;
......@@ -68,7 +69,7 @@ public class TableEndpoint {
@ApiResponse(code = 422, message = "The ."),
})
public ResponseEntity<TableBriefDto> create(@PathVariable("id") Long databaseId,
@RequestBody TableCreateDto createDto)
@Valid @RequestBody TableCreateDto createDto)
throws ImageNotSupportedException, DatabaseConnectionException, TableMalformedException,
DatabaseNotFoundException, DataProcessingException {
final Table table = tableService.create(databaseId, createDto);
......@@ -102,7 +103,7 @@ public class TableEndpoint {
@ApiResponse(code = 405, message = "The container is not running."),
@ApiResponse(code = 409, message = "The container image is not supported."),
})
public ResponseEntity<TableDto> createViaCsv(@PathVariable("id") Long databaseId, @RequestBody TableCsvInformationDto tableCSVInformation) throws IOException {
public ResponseEntity<TableDto> createViaCsv(@PathVariable("id") Long databaseId, @Valid @RequestBody TableCsvInformationDto tableCSVInformation) throws IOException {
final Table table = tableService.create(databaseId, tableCSVInformation);
return ResponseEntity.status(HttpStatus.CREATED)
.body(tableMapper.tableToTableDto(table));
......
fda-table-service/rest-service/src/test/java/at/tuwien/service/TableServiceUnitTest.java
+ 0
− 11
View file @ 3a043e20
......@@ -73,17 +73,6 @@ public class TableServiceUnitTest extends BaseUnitTest {
});
}
@Test
public void findAll_noTable_fails() {
when(databaseRepository.findById(DATABASE_2_ID))
.thenReturn(Optional.of(DATABASE_2));
/* test */
assertThrows(TableNotFoundException.class, () -> {
tableService.findAll(DATABASE_2_ID);
});
}
@Disabled("invalid mock")
@Test
public void delete_succeeds() throws TableNotFoundException, DatabaseConnectionException, TableMalformedException,
......
fda-table-service/rest-service/src/test/resources/application.properties
+ 2
− 1
View file @ 3a043e20
......@@ -11,3 +11,4 @@ spring.datasource.driverClassName=org.h2.Driver
spring.datasource.username=sa
spring.datasource.password=password
spring.jpa.database-platform=org.hibernate.dialect.H2Dialect
spring.jpa.hibernate.ddl-auto=update
\ No newline at end of file
fda-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
+ 2
− 1
View file @ 3a043e20
......@@ -21,8 +21,9 @@ public interface TableMapper {
TableDto tableToTableDto(Table data);
@Mappings({
@Mapping(source = "columns", target = "columns", qualifiedByName = "columnMapping"),
@Mapping(target = "columns"),
@Mapping(source = "name", target = "name"),
@Mapping(source = "name", target = "internalName", qualifiedByName = "columnSlug"),
})
Table tableCreateDtoToTable(TableCreateDto data);
......
fda-table-service/services/src/main/java/at/tuwien/service/PostgresService.java
+ 2
− 1
View file @ 3a043e20
......@@ -117,7 +117,7 @@ public class PostgresService extends JdbcConnector {
@Override
public final PreparedStatement getCreateTableStatement(Connection connection, TableCreateDto createDto) throws DataProcessingException {
log.debug("create table columns {}", Arrays.toString(createDto.getColumns()));
log.debug("create table columns {}", Arrays.asList(createDto.getColumns()));
final StringBuilder queryBuilder = new StringBuilder()
.append("CREATE TABLE ")
.append(tableMapper.columnNameToString(createDto.getName()))
......@@ -231,6 +231,7 @@ public class PostgresService extends JdbcConnector {
*/
private List<String> mockAnalyzeService(ColumnCreateDto[] columnDto) {
final List<String> columns = new LinkedList<>();
log.debug("will map column: {}", Arrays.asList(columnDto));
for (ColumnCreateDto column : columnDto) {
final StringBuilder columnBuilder = new StringBuilder()
.append(tableMapper.columnNameToString(column.getName()))
......
fda-table-service/services/src/main/java/at/tuwien/service/TableService.java
+ 30
− 15
View file @ 3a043e20
......@@ -53,6 +53,7 @@ public class TableService {
this.tableMapper = tableMapper;
}
@Transactional
public List<Table> findAll(Long databaseId) throws DatabaseNotFoundException, TableNotFoundException {
final Optional<Database> database;
try {
......@@ -65,19 +66,17 @@ public class TableService {
log.error("Unable to find database {}", databaseId);
throw new DatabaseNotFoundException("Unable to find database.");
}
if (database.get().getTables().size() == 0) {
log.error("Unable to find tables for database {}.", database);
throw new TableNotFoundException("Unable to find tables.");
}
return database.get().getTables();
}
@Transactional
public void delete(Long databaseId, Long tableId) throws TableNotFoundException, DatabaseConnectionException, TableMalformedException, DataProcessingException {
final Table table = findById(databaseId, tableId);
postgresService.deleteTable(table);
tableRepository.deleteById(tableId);
}
@Transactional
public Table findById(Long databaseId, Long tableId) throws TableNotFoundException {
final Database database = Database.builder()
.id(databaseId)
......@@ -96,7 +95,6 @@ public class TableService {
log.error("no database with this id found in metadata database");
throw new DatabaseNotFoundException("database not found in metadata database");
}
log.debug("retrieved db {}", database);
if (!database.get().getContainer().getImage().getRepository().equals("postgres")) {
log.error("Right now only PostgreSQL is supported!");
throw new ImageNotSupportedException("Currently only PostgreSQL is supported");
......@@ -112,15 +110,32 @@ public class TableService {
/* save in metadata db */
postgresService.createTable(database, createDto);
final Table table = tableMapper.tableCreateDtoToTable(createDto);
table.setDatabase(database);
table.setInternalName(tableMapper.columnNameToString(table.getName()));
final Table out = tableRepository.save(table);
log.debug("saved table {}", out);
final Table mappedTable = tableMapper.tableCreateDtoToTable(createDto);
mappedTable.setDatabase(database);
mappedTable.setTdbid(databaseId);
mappedTable.setColumns(List.of());
final Table table;
try {
table = tableRepository.save(mappedTable);
} catch (EntityNotFoundException e) {
throw new DataProcessingException("failed to create table compound key", e);
}
table.getColumns().forEach(column -> {
column.setCdbid(databaseId);
column.setTid(table.getId());
});
final Table out;
try {
out = tableRepository.save(table);
} catch (EntityNotFoundException e) {
throw new DataProcessingException("failed to create column compound key", e);
}
log.debug("saved table: {}", out);
log.info("Created table {} in database {}", out.getName(), out.getDatabase().getId());
return out;
}
@Transactional
public QueryResultDto insert(Long databaseId, Long tableId, MultipartFile file) throws TableNotFoundException,
ImageNotSupportedException, DatabaseNotFoundException, DatabaseConnectionException, DataProcessingException {
Table t = findById(databaseId, tableId);
......
fda-ui/package-lock.json
+ 89
− 0
View file @ 3a043e20
......@@ -2239,6 +2239,11 @@
"picomatch": "^2.0.4"
}
},
"append-field": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/append-field/-/append-field-1.0.0.tgz",
"integrity": "sha1-HjRA6RXwsSA9I3SOeO3XubW0PlY="
},
"aproba": {
"version": "1.2.0",
"resolved": "https://registry.yarnpkg.com/aproba/-/aproba-1.2.0.tgz",
......@@ -2780,6 +2785,38 @@
"resolved": "https://registry.yarnpkg.com/builtin-status-codes/-/builtin-status-codes-3.0.0.tgz",
"integrity": "sha1-hZgoeOIbmOHGZCXgPQF0eI9Wnug="
},
"busboy": {
"version": "0.2.14",
"resolved": "https://registry.npmjs.org/busboy/-/busboy-0.2.14.tgz",
"integrity": "sha1-bCpiLvz0fFe7vh4qnDetNseSVFM=",
"requires": {
"dicer": "0.2.5",
"readable-stream": "1.1.x"
},
"dependencies": {
"isarray": {
"version": "0.0.1",
"resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz",
"integrity": "sha1-ihis/Kmo9Bd+Cav8YDiTmwXR7t8="
},
"readable-stream": {
"version": "1.1.14",
"resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.1.14.tgz",
"integrity": "sha1-fPTFTvZI44EwhMY23SB54WbAgdk=",
"requires": {
"core-util-is": "~1.0.0",
"inherits": "~2.0.1",
"isarray": "0.0.1",
"string_decoder": "~0.10.x"
}
},
"string_decoder": {
"version": "0.10.31",
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
"integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
}
}
},
"bytes": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/bytes/-/bytes-3.0.0.tgz",
......@@ -3732,6 +3769,38 @@
"integrity": "sha1-+hN8S9aY7fVc1c0CrFWfkaTEups=",
"dev": true
},
"dicer": {
"version": "0.2.5",
"resolved": "https://registry.npmjs.org/dicer/-/dicer-0.2.5.tgz",
"integrity": "sha1-WZbAhrszIYyBLAkL3cCc0S+stw8=",
"requires": {
"readable-stream": "1.1.x",
"streamsearch": "0.1.2"
},
"dependencies": {
"isarray": {
"version": "0.0.1",
"resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz",
"integrity": "sha1-ihis/Kmo9Bd+Cav8YDiTmwXR7t8="
},
"readable-stream": {
"version": "1.1.14",
"resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.1.14.tgz",
"integrity": "sha1-fPTFTvZI44EwhMY23SB54WbAgdk=",
"requires": {
"core-util-is": "~1.0.0",
"inherits": "~2.0.1",
"isarray": "0.0.1",
"string_decoder": "~0.10.x"
}
},
"string_decoder": {
"version": "0.10.31",
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
"integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
}
}
},
"diffie-hellman": {
"version": "5.0.3",
"resolved": "https://registry.yarnpkg.com/diffie-hellman/-/diffie-hellman-5.0.3.tgz",
......@@ -6425,6 +6494,21 @@
"resolved": "https://registry.yarnpkg.com/ms/-/ms-2.0.0.tgz",
"integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g="
},
"multer": {
"version": "1.4.2",
"resolved": "https://registry.npmjs.org/multer/-/multer-1.4.2.tgz",
"integrity": "sha512-xY8pX7V+ybyUpbYMxtjM9KAiD9ixtg5/JkeKUTD6xilfDv0vzzOFcCp4Ljb1UU3tSOM3VTZtKo63OmzOrGi3Cg==",
"requires": {
"append-field": "^1.0.0",
"busboy": "^0.2.11",
"concat-stream": "^1.5.2",
"mkdirp": "^0.5.1",
"object-assign": "^4.1.1",
"on-finished": "^2.3.0",
"type-is": "^1.6.4",
"xtend": "^4.0.0"
}
},
"multimap": {
"version": "1.1.0",
"resolved": "https://registry.yarnpkg.com/multimap/-/multimap-1.1.0.tgz",
......@@ -8977,6 +9061,11 @@
"resolved": "https://registry.yarnpkg.com/stream-shift/-/stream-shift-1.0.1.tgz",
"integrity": "sha512-AiisoFqQ0vbGcZgQPY1cdP2I76glaVA/RauYR4G4thNFgkTqr90yXTo4LYX60Jl+sIlPNHHdGSwo01AvbKUSVQ=="
},
"streamsearch": {
"version": "0.1.2",
"resolved": "https://registry.npmjs.org/streamsearch/-/streamsearch-0.1.2.tgz",
"integrity": "sha1-gIudDlb8Jz2Am6VzOOkpkZoanxo="
},
"strict-uri-encode": {
"version": "1.1.0",
"resolved": "https://registry.npmjs.org/strict-uri-encode/-/strict-uri-encode-1.1.0.tgz",
......
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