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Merge pull request #533 from OHDSI/Release-1.12.2
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Release 1.12.2
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@agackovka
agackovka authored Jul 4, 2018
2 parents 6467ff8 + 892a579 commit 7d93dce
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Showing 39 changed files with 598 additions and 254 deletions.
12 changes: 9 additions & 3 deletions pom.xml
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Expand Up @@ -6,7 +6,7 @@

<artifactId>portal</artifactId>
<groupId>com.odysseusinc.arachne</groupId>
<version>1.12.1</version>
<version>1.12.2</version>
<packaging>jar</packaging>

<parent>
Expand All @@ -24,7 +24,7 @@
<java.version>1.8</java.version>
<jjwt.version>0.6.0</jjwt.version>
<ehcache.version>1.3.0</ehcache.version>
<postgresql.version>9.1-901-1.jdbc4</postgresql.version>
<postgresql.version>42.2.1</postgresql.version>
<flyway.version>4.2.0</flyway.version>
<gson.version>2.7</gson.version>
<commons.lang3.version>3.5</commons.lang3.version>
Expand Down Expand Up @@ -117,6 +117,12 @@
<version>${project.version}</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.odysseusinc.arachne</groupId>
<artifactId>arachne-no-handler-found-exception-util</artifactId>
<version>${project.version}</version>
<type>jar</type>
</dependency>
<dependency>
<artifactId>arachne-sys-settings</artifactId>
<groupId>com.odysseusinc.arachne</groupId>
Expand Down Expand Up @@ -185,7 +191,7 @@
<!--<version>${ehcache.version}</version>-->
<!--</dependency>-->
<dependency>
<groupId>postgresql</groupId>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgresql.version}</version>
</dependency>
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1 change: 1 addition & 0 deletions solr_config/conf/managed-schema
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Expand Up @@ -147,6 +147,7 @@
<dynamicField name="*_fs" type="pfloats" indexed="true" stored="true"/>
<dynamicField name="*_d" type="pdouble" indexed="true" stored="true"/>
<dynamicField name="*_ds" type="pdoubles" indexed="true" stored="true"/>
<dynamicField name="*_sortable" type="text_not_split" indexed="true" stored="true"/>

<!-- Type used for data-driven schema, to add a string copy for each text field -->
<dynamicField name="*_str" type="strings" stored="false" docValues="true" indexed="false" />
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2 changes: 1 addition & 1 deletion src/main/docker/Dockerfile
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@@ -1,4 +1,4 @@
FROM hub.arachnenetwork.com/portal_env:1.0.9
FROM hub.arachnenetwork.com/portal_env:1.0.12
MAINTAINER [email protected]
USER root
VOLUME /tmp
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62 changes: 24 additions & 38 deletions src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseAnalysisController.java
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Expand Up @@ -31,6 +31,7 @@
import static org.springframework.web.bind.annotation.RequestMethod.POST;
import static org.springframework.web.bind.annotation.RequestMethod.PUT;

import com.google.common.collect.ImmutableMap;
import com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType;
import com.odysseusinc.arachne.commons.api.v1.dto.CommonEntityRequestDTO;
import com.odysseusinc.arachne.commons.api.v1.dto.OptionDTO;
Expand All @@ -53,6 +54,7 @@
import com.odysseusinc.arachne.portal.api.v1.dto.SubmissionInsightUpdateDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.UpdateNotificationDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.UploadFileDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.UploadFilesDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.converters.FileDtoContentHandler;
import com.odysseusinc.arachne.portal.exception.AlreadyExistException;
import com.odysseusinc.arachne.portal.exception.NotEmptyException;
Expand Down Expand Up @@ -100,6 +102,7 @@
import java.util.Set;
import java.util.UUID;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import java.util.zip.ZipOutputStream;
import javax.jms.JMSException;
Expand Down Expand Up @@ -345,24 +348,15 @@ public JsonResult addCommonEntityToAnalysis(@PathVariable("analysisId") Long ana
final T analysis = analysisService.getById(analysisId);
final DataReference dataReference = dataReferenceService.addOrUpdate(entityReference.getEntityGuid(), dataNode);
final List<MultipartFile> entityFiles = getEntityFiles(entityReference, dataNode, analysisType);
doAddCommonEntityToAnalysis(analysis, dataReference, user, analysisType, entityFiles);
return new JsonResult(NO_ERROR);
return doAddCommonEntityToAnalysis(analysis, dataReference, user, analysisType, entityFiles);
}

protected void doAddCommonEntityToAnalysis(T analysis, DataReference dataReference, IUser user,
CommonAnalysisType analysisType,
List<MultipartFile> files) throws IOException {

files.stream()
.filter(f -> !CommonAnalysisType.COHORT.equals(analysisType) || !f.getName().endsWith(CommonFileUtils.OHDSI_JSON_EXT))
.forEach(f -> {
try {
analysisService.saveFile(f, user, analysis, f.getName(), detectExecutable(analysisType, f), dataReference);
} catch (IOException e) {
LOGGER.error("Failed to save file", e);
}
}
);
protected JsonResult doAddCommonEntityToAnalysis(T analysis, DataReference dataReference, IUser user,
CommonAnalysisType analysisType,
List<MultipartFile> files) throws IOException {

JsonResult result = new JsonResult(NO_ERROR);
analysisService.saveFiles(files, user, analysis, analysisType, dataReference);
if (analysisType.equals(CommonAnalysisType.COHORT)) {
final ByteArrayOutputStream out = new ByteArrayOutputStream();
class StringContainer {
Expand Down Expand Up @@ -404,13 +398,13 @@ class StringContainer {
String fileName = generatedFileName.value + ".zip";
final MultipartFile sqlArchive = new MockMultipartFile(fileName, fileName, "application/zip",
out.toByteArray());
analysisService.saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
try {
analysisService.saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
} catch (AlreadyExistException e) {
LOGGER.error("Failed to save file", e);
}
}
}

protected boolean detectExecutable(CommonAnalysisType type, MultipartFile file) {

return false;
return result;
}

@ApiOperation("update common entity in analysis")
Expand Down Expand Up @@ -444,30 +438,22 @@ public JsonResult updateCommonEntityInAnalysis(@PathVariable("analysisId") Long
@ApiOperation("Upload file to attach to analysis.")
@RequestMapping(value = "/api/v1/analysis-management/analyses/{analysisId}/upload", method = POST)
public JsonResult<List<AnalysisFileDTO>> uploadFile(Principal principal,
@Valid UploadFileDTO uploadFileDTO,
@Valid UploadFilesDTO uploadFilesLinks,
@PathVariable("analysisId") Long id)
throws PermissionDeniedException, NotExistException, IOException {

IUser user = getUser(principal);
T analysis = analysisService.getById(id);
List<UploadFileDTO> files = Stream.concat(uploadFilesLinks.getFiles().stream(), uploadFilesLinks.getLinks().stream()).collect(Collectors.toList());
return saveFiles(files, user, analysis);
}

JsonResult<List<AnalysisFileDTO>> result = new JsonResult<>(NO_ERROR);
private JsonResult<List<AnalysisFileDTO>> saveFiles(List<UploadFileDTO> files, IUser user, T analysis) throws IOException {

List<AnalysisFileDTO> createdFiles = new ArrayList<>();

if (uploadFileDTO.getFile() != null) {
AnalysisFile createdFile = analysisService.saveFile(uploadFileDTO.getFile(), user, analysis, uploadFileDTO.getLabel(), uploadFileDTO.getExecutable(), null);
createdFiles.add(conversionService.convert(createdFile, AnalysisFileDTO.class));
} else {
if (StringUtils.hasText(uploadFileDTO.getLink())) {
AnalysisFile createdFile = analysisService.saveFile(uploadFileDTO.getLink(), user, analysis, uploadFileDTO.getLabel(), uploadFileDTO.getExecutable());
createdFiles.add(conversionService.convert(createdFile, AnalysisFileDTO.class));
} else {
result.setErrorCode(VALIDATION_ERROR.getCode());
}

}

JsonResult<List<AnalysisFileDTO>> result = new JsonResult<>(NO_ERROR);
analysisService.saveFiles(files, user, analysis)
.forEach(createdFile -> createdFiles.add(conversionService.convert(createdFile, AnalysisFileDTO.class)));
result.setResult(createdFiles);
return result;
}
Expand Down
29 changes: 19 additions & 10 deletions ...n/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseAuthenticationController.java
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Expand Up @@ -31,6 +31,7 @@
import com.odysseusinc.arachne.portal.api.v1.dto.RemindPasswordDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.ResetPasswordDTO;
import com.odysseusinc.arachne.portal.api.v1.dto.UserInfoDTO;
import com.odysseusinc.arachne.portal.exception.NoDefaultTenantException;
import com.odysseusinc.arachne.portal.exception.NotExistException;
import com.odysseusinc.arachne.portal.exception.PasswordValidationException;
import com.odysseusinc.arachne.portal.exception.PermissionDeniedException;
Expand Down Expand Up @@ -59,8 +60,8 @@
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.mail.MailSendException;
import org.springframework.security.authentication.AuthenticationManager;
import org.springframework.security.authentication.BadCredentialsException;
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.AuthenticationException;
Expand Down Expand Up @@ -127,8 +128,8 @@ public JsonResult<CommonAuthenticationResponse> login(@RequestBody CommonAuthent

try {
checkIfUserBlocked(username);
Authentication authentication = authenticate(authenticationRequest);
SecurityContextHolder.getContext().setAuthentication(authentication);
checkIfUserHasTenant(username);
authenticate(authenticationRequest);
String token = this.tokenUtils.generateToken(username);
CommonAuthenticationResponse authenticationResponse = new CommonAuthenticationResponse(token);
jsonResult = new JsonResult<>(JsonResult.ErrorCode.NO_ERROR, authenticationResponse);
Expand Down Expand Up @@ -163,19 +164,27 @@ private void checkIfUserBlocked(String username) throws PermissionDeniedExceptio
}
}

private Authentication authenticate(CommonAuthenticationRequest authenticationRequest) {
protected void checkIfUserHasTenant(String email) throws AuthenticationException {

return this.authenticationManager.authenticate(
IUser user = userService.getByEmailInAnyTenant(email);
if (user == null) {
throw new BadCredentialsException("Bad credentials");
}
if (user.getTenants() == null || user.getTenants().isEmpty()) {
throw new NoDefaultTenantException("Request admin to add you into a tenant.");
}
}

protected Authentication authenticate(CommonAuthenticationRequest authenticationRequest) {

Authentication authentication = this.authenticationManager.authenticate(
new UsernamePasswordAuthenticationToken(
authenticationRequest.getUsername(),
authenticationRequest.getPassword()
)
);
}

protected IUser getUser(String userName) {

return userService.getByUsername(userName);
SecurityContextHolder.getContext().setAuthentication(authentication);
return authentication;
}

@ApiOperation("Logout.")
Expand Down
27 changes: 11 additions & 16 deletions src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseDataSourceController.java
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Expand Up @@ -38,6 +38,7 @@
import com.odysseusinc.arachne.portal.exception.NotExistException;
import com.odysseusinc.arachne.portal.exception.PermissionDeniedException;
import com.odysseusinc.arachne.portal.exception.ValidationException;
import com.odysseusinc.arachne.portal.model.DataSourceFields;
import com.odysseusinc.arachne.portal.model.IDataSource;
import com.odysseusinc.arachne.portal.model.IUser;
import com.odysseusinc.arachne.portal.service.BaseDataSourceService;
Expand All @@ -55,7 +56,6 @@
import org.springframework.core.convert.support.GenericConversionService;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Sort;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.PathVariable;
Expand All @@ -75,6 +75,7 @@ public abstract class BaseDataSourceController<
protected final ArachneConverterUtils converterUtils;
protected final StudyDataSourceService studyDataSourceService;


public BaseDataSourceController(GenericConversionService conversionService,
BaseDataSourceService<DS> dataSourceService,
ArachneConverterUtils converterUtils,
Expand Down Expand Up @@ -114,7 +115,7 @@ private JsonResult<DTO> updateDataSource(Principal principal, Long dataSourceId,
result = setValidationErrors(bindingResult);
} else {
IUser user = getUser(principal);
final DS exist = dataSourceService.getNotDeletedByIdInAnyTenant(dataSourceId);
final DS exist = dataSourceService.getByIdInAnyTenant(dataSourceId);
DS dataSource = convertDTOToDataSource(commonDataSourceDTO);
dataSource.setId(dataSourceId);
dataSource.setDataNode(exist.getDataNode());
Expand Down Expand Up @@ -153,8 +154,7 @@ public JsonResult<Page<DS_DTO>> suggestDataSource(Principal principal,
throw new javax.validation.ValidationException();
}
final IUser user = getUser(principal);
PageRequest pageRequest = getPageRequest(pageDTO);

PageRequest pageRequest = dataSourceService.getPageRequest(pageDTO);
Page<DS> dataSources = dataSourceService.suggestDataSource(query, studyId, user.getId(), pageRequest);
List<DS_DTO> dataSourceDTOs = converterUtils.convertList(dataSources.getContent(), getDataSourceDTOClass());
CustomPageImpl<DS_DTO> resultPage =
Expand All @@ -179,23 +179,18 @@ public JsonResult<R> list(Principal principal,
@RequestMapping(value = "/api/v1/data-sources/my", method = RequestMethod.GET)
public Page<DS_DTO> getUserDataSources(Principal principal,
@RequestParam(name = "query", required = false, defaultValue = "") String query,
@RequestParam(name = "sort", required = false, defaultValue = DataSourceFields.UI_NAME) String sortBy,
@RequestParam(name = "order", required = false, defaultValue = "asc") String order,
@ModelAttribute PageDTO pageDTO
) throws PermissionDeniedException {

final IUser user = getUser(principal);
PageRequest pageRequest = getPageRequest(pageDTO);

PageRequest pageRequest = dataSourceService.getPageRequest(pageDTO, sortBy, order);
Page<DS> dataSources = dataSourceService.getUserDataSources(query, user.getId(), pageRequest);
List<DS_DTO> dataSourceDTOs = converterUtils.convertList(dataSources.getContent(), getDataSourceDTOClass());
return new CustomPageImpl<>(dataSourceDTOs, pageRequest, dataSources.getTotalElements());
}

private PageRequest getPageRequest(PageDTO pageDTO) throws PermissionDeniedException {

Sort sort = new Sort(Sort.Direction.ASC, "name");
return new PageRequest(pageDTO.getPage() - 1, pageDTO.getPageSize(), sort);
}

@RequestMapping(value = "/api/v1/data-sources/byuuid/{uuid}", method = RequestMethod.GET)
public JsonResult<DTO> getByUuid(@PathVariable("uuid") String dataSourceUuid) throws NotExistException {

Expand Down Expand Up @@ -245,9 +240,9 @@ public void unpublishDataSource(@PathVariable("id") Long dataSourceId) throws IO
@ApiOperation("Publish data source")
@RequestMapping(value = "/api/v1/data-sources/{id}/registration", method = RequestMethod.POST)
public JsonResult<DTO> publishDataSource(Principal principal,
@PathVariable("id") Long dataSourceId,
@RequestBody @Valid DTO commonDataSourceDTO,
BindingResult bindingResult
@PathVariable("id") Long dataSourceId,
@RequestBody @Valid DTO commonDataSourceDTO,
BindingResult bindingResult
) throws NotExistException,
PermissionDeniedException,
FieldException,
Expand Down Expand Up @@ -279,7 +274,7 @@ public JsonResult<List<CommonCDMVersionDTO>> getCDMVersions() {
@RequestMapping(value = "/api/v1/data-sources/{id}/complete", method = RequestMethod.GET)
public JsonResult<DS_DTO> getWhole(@PathVariable("id") Long dataSourceId) throws NotExistException {

DS dataSource = dataSourceService.getNotDeletedByIdInAnyTenant(dataSourceId);
DS dataSource = dataSourceService.getByIdInAnyTenant(dataSourceId);
return new JsonResult<>(NO_ERROR, conversionService.convert(dataSource, getDataSourceDTOClass()));
}

Expand Down
12 changes: 8 additions & 4 deletions src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseUserController.java
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Expand Up @@ -103,6 +103,7 @@
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.servlet.http.HttpServletRequest;
Expand Down Expand Up @@ -733,17 +734,17 @@ public JsonResult<List<CommonUserDTO>> relinkAllUsersToDataNode(@PathVariable("d
) throws NotExistException {

final DN dataNode = baseDataNodeService.getById(dataNodeId);

final Set<DataNodeUser> users = linkUserToDataNodes.stream()
.map(link -> new DataNodeUser(userService.getByUnverifiedEmailInAnyTenant(link.getUserName()), dataNode))
.collect(Collectors.toSet());

baseDataNodeService.relinkAllUsersToDataNode(dataNode, users);

final List<CommonUserDTO> userDTOs = users.stream()
.map(user -> conversionService.convert(user.getUser(), CommonUserDTO.class))
.collect(Collectors.toList());

return new JsonResult<>(NO_ERROR, userDTOs);
}

Expand Down Expand Up @@ -775,6 +776,9 @@ public CommonUserDTO confirmEmail(@PathVariable("uuid") String userUuid,

U user = userService.getByIdInAnyTenantAndInitializeCollections(UserIdUtils.uuidToId(userUuid));
user.setEmailConfirmed(confirm);
if (!confirm) {
user.setRegistrationCode(UUID.randomUUID().toString());
}
userService.updateInAnyTenant(user);
return conversionService.convert(user, CommonUserDTO.class);
}
Expand Down
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