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Import handled by one endpoint 190 #66

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c243d83
[kbss/record-manager-ui#190] Add one import handler for all types of …
palagdan Jul 23, 2024
4f2f6e4
[kbss/record-manager-ui#190] Correct return type in getRecordsFromTsv
palagdan Jul 23, 2024
7514dc4
[kbss/record-manager-ui#190] Correct request's endpoints in tests for…
palagdan Jul 23, 2024
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139 changes: 75 additions & 64 deletions src/main/java/cz/cvut/kbss/study/rest/PatientRecordController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import cz.cvut.kbss.study.dto.PatientRecordDto;
import cz.cvut.kbss.study.dto.RecordImportResult;
import cz.cvut.kbss.study.exception.NotFoundException;
import cz.cvut.kbss.study.exception.ValidationException;
import cz.cvut.kbss.study.model.PatientRecord;
import cz.cvut.kbss.study.model.RecordPhase;
import cz.cvut.kbss.study.model.User;
Expand Down Expand Up @@ -41,6 +42,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.sql.Array;
import java.util.*;
import java.util.stream.Stream;

Expand All @@ -61,7 +63,7 @@ public class PatientRecordController extends BaseController {
public PatientRecordController(PatientRecordService recordService, ApplicationEventPublisher eventPublisher,
ExcelRecordConverter excelRecordConverter, RestTemplate restTemplate,
ConfigReader configReader, ObjectMapper objectMapper,
UserService userService) {
UserService userService) {
this.recordService = recordService;
this.eventPublisher = eventPublisher;
this.excelRecordConverter = excelRecordConverter;
Expand All @@ -78,7 +80,7 @@ public List<PatientRecordDto> getRecords(
@RequestParam MultiValueMap<String, String> params,
UriComponentsBuilder uriBuilder, HttpServletResponse response) {
final Page<PatientRecordDto> result = recordService.findAll(RecordFilterMapper.constructRecordFilter(params),
RestUtils.resolvePaging(params));
RestUtils.resolvePaging(params));
eventPublisher.publishEvent(new PaginatedResultRetrievedEvent(this, uriBuilder, response, result));
return result.getContent();
}
Expand All @@ -98,25 +100,25 @@ public ResponseEntity<?> exportRecords(
.map(o -> o.filter(l -> !l.isEmpty()))
.filter(Optional::isPresent)
.map(o -> o.map(l -> l.stream().flatMap(s ->
MediaType.parseMediaTypes(s).stream()
.filter(RestUtils::isSupportedExportType)
).max(Comparator.comparing(MediaType::getQualityValue)).orElse(null)))
MediaType.parseMediaTypes(s).stream()
.filter(RestUtils::isSupportedExportType)
).max(Comparator.comparing(MediaType::getQualityValue)).orElse(null)))
.filter(Optional::isPresent)
.map(o -> o.orElse(null))
.findFirst()
.orElse(MediaType.APPLICATION_JSON)
.removeQualityValue();

return switch (exportType.toString()){
case Constants.MEDIA_TYPE_EXCEL -> exportRecordsExcel(params, uriBuilder, response);
return switch (exportType.toString()) {
case Constants.MEDIA_TYPE_EXCEL -> exportRecordsExcel(params, uriBuilder, response);
case MediaType.APPLICATION_JSON_VALUE -> exportRecordsAsJson(params, uriBuilder, response);
default -> throw new IllegalArgumentException("Unsupported export type: " + exportType);
};
}

protected ResponseEntity<List<PatientRecord>> exportRecordsAsJson(
MultiValueMap<String, String> params,
UriComponentsBuilder uriBuilder, HttpServletResponse response){
UriComponentsBuilder uriBuilder, HttpServletResponse response) {
final Page<PatientRecord> result = recordService.findAllFull(RecordFilterMapper.constructRecordFilter(params),
RestUtils.resolvePaging(params));
eventPublisher.publishEvent(new PaginatedResultRetrievedEvent(this, uriBuilder, response, result));
Expand All @@ -126,7 +128,7 @@ protected ResponseEntity<List<PatientRecord>> exportRecordsAsJson(
}

public ResponseEntity<InputStreamResource> exportRecordsExcel(MultiValueMap<String, String> params,
UriComponentsBuilder uriBuilder, HttpServletResponse response){
UriComponentsBuilder uriBuilder, HttpServletResponse response) {
RecordFilterParams filterParams = new RecordFilterParams();
filterParams.setMinModifiedDate(null);
filterParams.setMaxModifiedDate(null);
Expand Down Expand Up @@ -157,13 +159,11 @@ private PatientRecord findInternal(String key) {
return record;
}



@PostMapping(consumes = MediaType.APPLICATION_JSON_VALUE)
@ResponseStatus(HttpStatus.CREATED)
public ResponseEntity<String> createRecord(@RequestBody PatientRecord record) {

if(userService.getCurrentUser().getInstitution() == null)
if (userService.getCurrentUser().getInstitution() == null)
return ResponseEntity.status(HttpStatus.CONFLICT).body("User is not assigned to any institution");

recordService.persist(record);
Expand All @@ -176,22 +176,22 @@ public ResponseEntity<String> createRecord(@RequestBody PatientRecord record) {
}

@PreAuthorize(
"hasRole('" + SecurityConstants.ROLE_ADMIN + "') or @securityUtils.isMemberOfInstitution(#institutionKey)")
"hasRole('" + SecurityConstants.ROLE_ADMIN + "') or @securityUtils.isMemberOfInstitution(#institutionKey)")
@PostMapping(value = "/publish", produces = {MediaType.APPLICATION_JSON_VALUE})
public RecordImportResult publishRecords(
@RequestParam(name = "institution", required = false) String institutionKey,
@RequestParam(required = false) MultiValueMap<String, String> params,
HttpServletRequest request) {
@RequestParam(name = "institution", required = false) String institutionKey,
@RequestParam(required = false) MultiValueMap<String, String> params,
HttpServletRequest request) {

String onPublishRecordsServiceUrl = configReader.getConfig(ConfigParam.ON_PUBLISH_RECORDS_SERVICE_URL);
if(onPublishRecordsServiceUrl == null || onPublishRecordsServiceUrl.isBlank()) {
if (onPublishRecordsServiceUrl == null || onPublishRecordsServiceUrl.isBlank()) {
LOG.info("No publish service url provided, noop.");
RecordImportResult result = new RecordImportResult(0);
result.addError("Cannot publish completed records. Publish server not configured.");
return result;
}

// export
// export
final Page<PatientRecord> result = recordService.findAllFull(RecordFilterMapper.constructRecordFilter(params),
RestUtils.resolvePaging(params));
List<PatientRecord> records = result.getContent();
Expand Down Expand Up @@ -227,40 +227,66 @@ public String getFilename() {
// Call the import endpoint
LOG.debug("Publishing records.");
ResponseEntity<RecordImportResult> responseEntity = restTemplate.postForEntity(
onPublishRecordsServiceUrl, requestEntity, RecordImportResult.class);
onPublishRecordsServiceUrl, requestEntity, RecordImportResult.class);

// TODO make records published

LOG.debug("Publish server response: ", responseEntity.getBody());
return responseEntity.getBody();
}

@PostMapping(value = "/import/json", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public RecordImportResult importRecordsJson(@RequestPart("file") MultipartFile file,
@RequestParam(name = "phase", required = false) String phase) {
@PostMapping(value = "/import", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public RecordImportResult importRecords(
@RequestPart("file") MultipartFile file,
@RequestParam(name = "phase", required = false) String phase) {

if (file.isEmpty()) {
throw new ValidationException("Cannot import records, missing input file");
}

String filename = file.getOriginalFilename();

if (filename == null) {
throw new ValidationException("Cannot import records, missing filename");
}

List<PatientRecord> records;

if(file.isEmpty())
throw new IllegalArgumentException("Cannot import records, missing input file");
if (filename.endsWith(".json")) {
records = getRecordsFromJson(file, phase);
} else if (filename.endsWith(".xls") || filename.endsWith(".xlsx")) {
records = getRecordsFromExcel(file, phase);
} else if (filename.endsWith(".tsv")) {
records = getRecordsFromTsv(file, phase);
} else {
throw new IllegalArgumentException("Unsupported file type: " + filename);
}

final RecordImportResult importResult;
if (phase != null) {
final RecordPhase targetPhase = RecordPhase.fromIriOrName(phase);
importResult = recordService.importRecords(records, targetPhase);
} else {
importResult = recordService.importRecords(records);
}
LOG.trace("Records imported with result: {}.", importResult);
return importResult;
}

private List<PatientRecord> getRecordsFromJson(MultipartFile file, String phase) {
List<PatientRecord> records;
try {
records = objectMapper.readValue(file.getBytes(), new TypeReference<List<PatientRecord>>(){});
return objectMapper.readValue(file.getBytes(), new TypeReference<List<PatientRecord>>() {
});
} catch (IOException e) {
throw new RuntimeException("Failed to parse JSON content", e);
}
return importRecords(records, phase);
}

@PostMapping(value = "/import/excel", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public RecordImportResult importRecordsExcel(
@RequestPart("file") MultipartFile file,
@RequestParam(name = "phase", required = false) String phase) {
private List<PatientRecord> getRecordsFromExcel(MultipartFile file, String phase) {

List<PatientRecord> records;

if(file.isEmpty())
throw new IllegalArgumentException("Cannot import records, missing input file");

String excelImportServiceUrl = configReader.getConfig(ConfigParam.EXCEL_IMPORT_SERVICE_URL);

if (excelImportServiceUrl == null)
Expand All @@ -273,29 +299,26 @@ public RecordImportResult importRecordsExcel(
body.add("files", file.getResource());

String request = UriComponentsBuilder.fromHttpUrl(excelImportServiceUrl)
.queryParam("datasetResource", "@%s".formatted(file.getOriginalFilename()))
.toUriString();
.queryParam("datasetResource", "@%s".formatted(file.getOriginalFilename()))
.toUriString();

HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(body, headers);

ResponseEntity<List<PatientRecord>> responseEntity = restTemplate.exchange(
URI.create(request),
HttpMethod.POST,
requestEntity,
new ParameterizedTypeReference<List<PatientRecord>>() {}
new ParameterizedTypeReference<List<PatientRecord>>() {
}
);
records = responseEntity.getBody();
return importRecords(records, phase);
return responseEntity.getBody();
}

@PostMapping(value = "/import/tsv", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
public RecordImportResult importRecordsTsv(
@RequestPart("file") MultipartFile file,
@RequestParam(name = "phase", required = false) String phase) {
private List<PatientRecord> getRecordsFromTsv(MultipartFile file, String phase) {

List<PatientRecord> records;

if(file.isEmpty())
if (file.isEmpty())
throw new IllegalArgumentException("Cannot import records, missing input file");

String excelImportServiceUrl = configReader.getConfig(ConfigParam.EXCEL_IMPORT_SERVICE_URL);
Expand All @@ -310,15 +333,15 @@ public RecordImportResult importRecordsTsv(
body.add("files", file.getResource());

String request = UriComponentsBuilder.fromHttpUrl(excelImportServiceUrl)
.queryParam("datasetResource", "@%s".formatted(file.getOriginalFilename()))
.toUriString();
.queryParam("datasetResource", "@%s".formatted(file.getOriginalFilename()))
.toUriString();

HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(body, headers);

ResponseEntity<byte[]> responseEntity = restTemplate.postForEntity(
URI.create(request),
requestEntity,
byte[].class
URI.create(request),
requestEntity,
byte[].class
);

LOG.info("Import finished with status {}", responseEntity.getStatusCode());
Expand All @@ -327,19 +350,7 @@ public RecordImportResult importRecordsTsv(
LOG.debug("Response body length is {}", responseBody.length);
}

return new RecordImportResult();
}

public RecordImportResult importRecords(List<PatientRecord> records, String phase) {
final RecordImportResult importResult;
if (phase != null) {
final RecordPhase targetPhase = RecordPhase.fromIriOrName(phase);
importResult = recordService.importRecords(records, targetPhase);
} else {
importResult = recordService.importRecords(records);
}
LOG.trace("Records imported with result: {}.", importResult);
return importResult;
return new ArrayList<PatientRecord>();
}


Expand All @@ -359,13 +370,13 @@ public void updateRecord(@PathVariable("key") String key, @RequestBody PatientRe
onUpdateRecord(record.getUri());
}

private void onUpdateRecord(URI uri){
private void onUpdateRecord(URI uri) {
Objects.nonNull(uri);
String onRecordUpdateServiceUrl = Optional.ofNullable(configReader)
.map(r -> r.getConfig(ConfigParam.ON_UPDATE_RECORD_SERVICE_URL))
.orElse(null);

if(onRecordUpdateServiceUrl == null || onRecordUpdateServiceUrl.isBlank()) {
if (onRecordUpdateServiceUrl == null || onRecordUpdateServiceUrl.isBlank()) {
LOG.debug("No onRecordUpdateServiceUrl service url provided, noop.");
return;
}
Expand All @@ -374,7 +385,7 @@ private void onUpdateRecord(URI uri){
String requestUrl = UriComponentsBuilder.fromHttpUrl(onRecordUpdateServiceUrl)
.queryParam("record", uri)
.toUriString();
restTemplate.getForObject(requestUrl,String.class);
restTemplate.getForObject(requestUrl, String.class);
}

@DeleteMapping(value = "/{key}")
Expand Down
6 changes: 3 additions & 3 deletions src/test/java/cz/cvut/kbss/study/rest/PatientRecordControllerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -340,7 +340,7 @@ void importRecordsJsonImportsSpecifiedRecordsAndReturnsImportResult() throws Exc
MediaType.MULTIPART_FORM_DATA_VALUE, toJson(records).getBytes());

final MvcResult mvcResult = mockMvc.perform(
multipart("/records/import/json")
multipart("/records/import")
.file(file)
.contentType(MediaType.MULTIPART_FORM_DATA_VALUE)
).andReturn();
Expand Down Expand Up @@ -370,7 +370,7 @@ void importRecordsJsonImportsSpecifiedRecordsWithSpecifiedPhaseAndReturnsImportR
MediaType.MULTIPART_FORM_DATA_VALUE, toJson(records).getBytes());

mockMvc.perform(
multipart("/records/import/json")
multipart("/records/import")
.file(file)
.contentType(MediaType.MULTIPART_FORM_DATA_VALUE)
.param("phase", targetPhase.getIri())
Expand All @@ -389,7 +389,7 @@ void importRecordsJsonReturnsConflictWhenServiceThrowsRecordAuthorNotFound() thr
MediaType.MULTIPART_FORM_DATA_VALUE, toJson(records).getBytes());

mockMvc.perform(
multipart("/records/import/json")
multipart("/records/import")
.file(file)
.contentType(MediaType.MULTIPART_FORM_DATA_VALUE)
).andExpect(status().isConflict());
Expand Down