Skip to content

Commit

Permalink
Merge branch 'main' into openTelemetry
Browse files Browse the repository at this point in the history
  • Loading branch information
@sabith-nadakkavil
sabith-nadakkavil authored Dec 11, 2024
2 parents 4b0d61c + c3b812e commit 4b73b10
Show file tree
Hide file tree
Showing 4 changed files with 46 additions and 46 deletions.
Binary file modified hub-prime/lib/techbd-udi-jooq-ingress.auto.jar
View file
Binary file not shown.
88 changes: 43 additions & 45 deletions hub-prime/src/main/java/org/techbd/orchestrate/csv/CsvOrchestrationEngine.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -118,10 +118,12 @@ public OrchestrationSessionBuilder withSessionId(final String sessionId) {
this.sessionId = sessionId;
return this;
}

public OrchestrationSessionBuilder withTenantId(final String tenantId) {
this.tenantId = tenantId;
return this;
}

public OrchestrationSessionBuilder withDevice(final Device device) {
this.device = device;
return this;
Expand Down Expand Up @@ -152,7 +154,7 @@ public OrchestrationSession build() {
if (file == null) {
throw new IllegalArgumentException("File must not be null");
}
return new OrchestrationSession(sessionId, tenantId,device, file, masterInteractionId, request);
return new OrchestrationSession(sessionId, tenantId, device, file, masterInteractionId, request);
}
}

Expand Down Expand Up @@ -182,7 +184,8 @@ public class OrchestrationSession {

HttpServletRequest request;

public OrchestrationSession(final String sessionId,final String tenantId,final Device device, final MultipartFile file,
public OrchestrationSession(final String sessionId, final String tenantId, final Device device,
final MultipartFile file,
final String masterInteractionId,
final HttpServletRequest request) {
this.sessionId = sessionId;
Expand Down Expand Up @@ -235,7 +238,7 @@ public void validate() {

// Trigger CSV processing and validation
this.validationResults = processScreenings(masterInteractionId, intiatedAt, originalFilename, tenantId);
saveValidationResults(this.validationResults,tenantId);
saveValidationResults(this.validationResults, tenantId);
} catch (final IllegalArgumentException e) {
log.error("Validation Error", e);
this.validationResults = Map.of(
Expand Down Expand Up @@ -271,22 +274,17 @@ private void saveScreeningGroup(final HttpServletRequest request,
initRIHR.setCsvDemographicDataPayloadText(fileMap.get(FileType.DEMOGRAPHIC_DATA).content);
initRIHR.setCsvQeAdminDataFileName(fileMap.get(FileType.QE_ADMIN_DATA).filename);
initRIHR.setCsvQeAdminDataPayloadText(fileMap.get(FileType.QE_ADMIN_DATA).content);
initRIHR.setCsvScreeningConsentDataFileName(fileMap.get(FileType.SCREENING_CONSENT_DATA).filename);
initRIHR.setCsvScreeningConsentDataPayloadText(fileMap.get(FileType.SCREENING_CONSENT_DATA).content);
initRIHR.setCsvScreeningEncounterDataFileName(fileMap.get(FileType.SCREENING_ENCOUNTER_DATA).filename);
initRIHR.setCsvScreeningEncounterDataPayloadText(
fileMap.get(FileType.SCREENING_ENCOUNTER_DATA).content);
initRIHR.setCsvScreeningLocationDataFileName(fileMap.get(FileType.SCREENING_LOCATION_DATA).filename);
initRIHR.setCsvScreeningLocationDataPayloadText(fileMap.get(FileType.SCREENING_LOCATION_DATA).content);

initRIHR.setCsvScreeningObservationDataFileName(
fileMap.get(FileType.SCREENING_OBSERVATION_DATA).filename);
initRIHR.setCsvScreeningObservationDataPayloadText(
fileMap.get(FileType.SCREENING_OBSERVATION_DATA).content);
initRIHR.setCsvScreeningResourcesDataFileName(fileMap.get(FileType.SCREENING_RESOURCES_DATA).filename);
// To-Do : setCsvScreeningResourcesDataFileName adeded with new file
// SCREENING_PROFILE_DATA
initRIHR.setCsvScreeningResourcesDataFileName(fileMap.get(FileType.SCREENING_PROFILE_DATA).filename);
initRIHR.setCsvScreeningResourcesDataPayloadText(
fileMap.get(FileType.SCREENING_RESOURCES_DATA).content);
fileMap.get(FileType.SCREENING_PROFILE_DATA).content);
initRIHR.setCreatedAt(forwardedAt);
//initRIHR.setPa
initRIHR.setCreatedBy(CsvService.class.getName());
initRIHR.setToState("CSV_ACCEPT");
final var provenance = "%s.saveScreeningGroup"
Expand Down Expand Up @@ -326,17 +324,15 @@ public static boolean isValid(final Map<String, Object> csvValidationResult) {
}

@SuppressWarnings("unchecked")
final
Map<String, Object> validationResultsMap = (Map<String, Object>) validationResults;
final Map<String, Object> validationResultsMap = (Map<String, Object>) validationResults;
final Object report = validationResultsMap.get("report");

if (!(report instanceof Map<?, ?>)) {
return false;
}

@SuppressWarnings("unchecked")
final
Map<String, Object> reportMap = (Map<String, Object>) report;
final Map<String, Object> reportMap = (Map<String, Object>) report;
final Object valid = reportMap.get("valid");

return Boolean.TRUE.equals(valid);
Expand All @@ -360,14 +356,14 @@ private void saveValidationResults(final Map<String, Object> validationResults,
initRIHR.setContentType(MimeTypeUtils.APPLICATION_JSON_VALUE);
initRIHR.setCreatedAt(createdAt);
initRIHR.setCreatedBy(CsvService.class.getName());
initRIHR.setPayload((JsonNode)Configuration.objectMapper.valueToTree(validationResults));
initRIHR.setPayload((JsonNode) Configuration.objectMapper.valueToTree(validationResults));
initRIHR.setFromState("CSV_ACCEPT");
if (isValid(validationResults)) {
initRIHR.setToState("VALIDATION_SUCCESS");
} else {
initRIHR.setToState("VALIDATION_FAILED");
}
//initRIHR.setValidation
// initRIHR.setValidation
final var provenance = "%s.saveValidationResults"
.formatted(CsvService.class.getName());
initRIHR.setProvenance(provenance);
Expand Down Expand Up @@ -447,38 +443,43 @@ private static Map<String, Object> populateProvenance(final String interactionId
public Map<String, Object> processScreenings(final String interactionId, final Instant initiatedAt,
final String originalFileName, final String tenantId) {
try {
log.info("Inbound Folder Path: {} for interactionid :{} ", appConfig.getCsv().validation().inboundPath(),interactionId);
log.info("Ingress Home Path: {} for interactionId : {}", appConfig.getCsv().validation().ingessHomePath(),interactionId);
log.info("Inbound Folder Path: {} for interactionid :{} ",
appConfig.getCsv().validation().inboundPath(), interactionId);
log.info("Ingress Home Path: {} for interactionId : {}",
appConfig.getCsv().validation().ingessHomePath(), interactionId);
// Process ZIP files and get the session ID
final UUID processId = processZipFilesFromInbound(interactionId);
log.info("ZIP files processed with session ID: {} for interaction id :{} ", processId,interactionId);
log.info("ZIP files processed with session ID: {} for interaction id :{} ", processId, interactionId);

// Construct processed directory path
final String processedDirPath = appConfig.getCsv().validation().ingessHomePath() + "/" + processId
+ "/ingress";

copyFilesToProcessedDir(processedDirPath);
createOutputFileInProcessedDir(processedDirPath);
log.info("Attempting to resolve processed directory: {} for interactionId : {}", processedDirPath,interactionId);
log.info("Attempting to resolve processed directory: {} for interactionId : {}", processedDirPath,
interactionId);

// Get processed files for validation
final FileObject processedDir = vfsCoreService
.resolveFile(Paths.get(processedDirPath).toAbsolutePath().toString());

if (!vfsCoreService.fileExists(processedDir)) {
log.error("Processed directory does not exist: {} for interactionId : {}", processedDirPath,interactionId);
log.error("Processed directory does not exist: {} for interactionId : {}", processedDirPath,
interactionId);
throw new FileSystemException("Processed directory not found: " + processedDirPath);
}

// Collect CSV files for validation
final List<String> csvFiles = scanForCsvFiles(processedDir,interactionId);
final List<String> csvFiles = scanForCsvFiles(processedDir, interactionId);

final Map<FileType, FileDetail> files = processFiles(csvFiles);
saveScreeningGroup(request, file, files, tenantId);
log.info("Found {} CSV files for validation for interactionId :{}", csvFiles.size(),interactionId);
log.info("Found {} CSV files for validation for interactionId :{}", csvFiles.size(), interactionId);

if (csvFiles.isEmpty()) {
log.warn("No CSV files found for validation. Skipping validation.for interactionId :{} ",interactionId);
log.warn("No CSV files found for validation. Skipping validation.for interactionId :{} ",
interactionId);
return null;
}

Expand All @@ -494,6 +495,7 @@ public Map<String, Object> processScreenings(final String interactionId, final I
throw new RuntimeException("Error processing ZIP files: " + e.getMessage(), e);
}
}

private void createOutputFileInProcessedDir(final String processedDirPathStr) throws IOException {
final Path processedDirPath = Paths.get(processedDirPathStr);
final Path outputJsonPath = processedDirPath.resolve("output.json");
Expand Down Expand Up @@ -524,7 +526,8 @@ private UUID processZipFilesFromInbound(final String interactionId)
.resolveFile(
Paths.get(appConfig.getCsv().validation().ingessHomePath()).toAbsolutePath().toString());
if (!vfsCoreService.fileExists(inboundFO)) {
log.error("Inbound folder does not exist: {} for interactionId :{} ", inboundFO.getName().getPath(),interactionId);
log.error("Inbound folder does not exist: {} for interactionId :{} ", inboundFO.getName().getPath(),
interactionId);
throw new FileSystemException("Inbound folder does not exist: " + inboundFO.getName().getPath());
}
vfsCoreService.validateAndCreateDirectories(ingresshomeFO);
Expand All @@ -539,14 +542,16 @@ private UUID processZipFilesFromInbound(final String interactionId)
return processId;
}

private List<String> scanForCsvFiles(final FileObject processedDir,String interactionId) throws FileSystemException {
private List<String> scanForCsvFiles(final FileObject processedDir, String interactionId)
throws FileSystemException {
final List<String> csvFiles = new ArrayList<>();

try {
final FileObject[] children = processedDir.getChildren();

if (children == null) {
log.warn("No children found in processed directory: {} for interactionId :{}", processedDir.getName().getPath(),interactionId);
log.warn("No children found in processed directory: {} for interactionId :{}",
processedDir.getName().getPath(), interactionId);
return csvFiles;
}

Expand Down Expand Up @@ -707,22 +712,18 @@ private List<String> buildValidationCommand(final AppConfig.CsvValidation.Valida
command.add("validate-nyher-fhir-ig-equivalent.py");
command.add("datapackage-nyher-fhir-ig-equivalent.json");
Map<FileType, String> fileTypeToFileNameMap = filePaths.stream()
.map(path -> path.substring(path.lastIndexOf("/") + 1))
.collect(Collectors.toMap(
FileType::fromFilename,
filename -> filename
));
.map(path -> path.substring(path.lastIndexOf("/") + 1))
.collect(Collectors.toMap(
FileType::fromFilename,
filename -> filename));
command.add(fileTypeToFileNameMap.get(FileType.QE_ADMIN_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_OBSERVATION_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_LOCATION_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_ENCOUNTER_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_CONSENT_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_RESOURCES_DATA));
command.add(fileTypeToFileNameMap.get(FileType.SCREENING_PROFILE_DATA));
command.add(fileTypeToFileNameMap.get(FileType.DEMOGRAPHIC_DATA));

// Pad with empty strings if fewer than 7 files
while (command.size() < 10) { // 1 (python) + 1 (script) + 1 (package) + 7 (files) //TODO CHECK IF THIS IS
// NEEDED
while (command.size() < 7) { // 1 (python) + 1 (script) + 1 (package) + 4 (files) //TODO CHECK IF THIS IS
// NEEDED ACCORDING TO NUMBER OF FILES.
command.add("");
}

Expand Down Expand Up @@ -792,11 +793,8 @@ public static Map<FileType, FileDetail> processFiles(final List<String> filePath
public enum FileType {
DEMOGRAPHIC_DATA,
QE_ADMIN_DATA,
SCREENING_CONSENT_DATA,
SCREENING_ENCOUNTER_DATA,
SCREENING_LOCATION_DATA,
SCREENING_OBSERVATION_DATA,
SCREENING_RESOURCES_DATA;
SCREENING_PROFILE_DATA;

public static FileType fromFilename(final String filename) {
for (final FileType type : values()) {
Expand Down
3 changes: 2 additions & 1 deletion hub-prime/src/main/resources/templates/page/interactions/httpsfhir.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -110,14 +110,15 @@
},
{ headerName: "Source MRN", field: "source_mrn", filter: "agTextColumnFilter", headerTooltip: "Combination of tenant, organization and patient MRN" },
{ headerName: "Patient MRN", field: "patient_mrn", filter: "agTextColumnFilter", headerTooltip: "Medical Record Number of the patient involved in the interaction" },
{ headerName: "MRN Source", field: "patient_mrn_source_system", filter: "agTextColumnFilter", headerTooltip: "Source of the patient MRN" },
{
headerName: "Interaction ID",
field: "interaction_id",
filter: "agTextColumnFilter", headerTooltip: "Unique identifier for each interaction",
cellRenderer: AGGridAide.modalCellRenderer((params, modalAide) => {
modalAide.viewFetchedJsonValue(window.shell.serverSideUrl(`/api/ux/tabular/jooq/${schemaName}/${viewName}/sat_interaction_http_request_id/${params.data.sat_interaction_http_request_id}.json`));
}, modalAide)
},
},
{ headerName: "Tenant ID", field: "tenant_id", filter: "agTextColumnFilter", headerTooltip: "ID of the tenant involved in the interaction" },
{ headerName: "URI", field: "uri", filter: "agTextColumnFilter", headerTooltip: "The URI associated with the interaction" },
{ headerName: "Bundle ID", field: "bundle_id", filter: "agTextColumnFilter", headerTooltip: "The ID of the Bundle sent through the interaction" },
Expand Down
1 change: 1 addition & 0 deletions udi-prime/src/main/postgres/ingestion-center/001_idempotent_interaction.psql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ AS SELECT hub_interaction_id AS interaction_id,
EXTRACT(epoch FROM interaction_end_time::timestamp without time zone - interaction_start_time::timestamp without time zone) * 1000::numeric AS duration_millisecs,
patient_id,
patient_mrn,
patient_mrn_source_system,
organization_id,
organization_name,
concat_ws('-'::text, tenant_id, organization_id, patient_mrn) AS source_mrn,
Expand Down

0 comments on commit 4b73b10

Please sign in to comment.