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Lnk 2116 logging improvements #744

Merged
merged 8 commits into from
May 4, 2024
Merged

Lnk 2116 logging improvements #744

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a47542b
Work related to LNK-2116
edward-miller-lcg Mar 22, 2024
c5fa3d7
Merge branch 'development' into LNK-2116-logging-improvements
edward-miller-lcg Apr 10, 2024
d933576
adding report id to db logs
edward-miller-lcg Apr 10, 2024
d48d972
Add report id to arg array
edward-miller-lcg Apr 11, 2024
adf826c
fixes
edward-miller-lcg Apr 11, 2024
f9233ef
Merge branch 'development' into LNK-2116-logging-improvements
smailliwcs May 4, 2024
c8ac29d
Remove custom appender
smailliwcs May 4, 2024
35129a1
Add tenant and version information to MDC
smailliwcs May 4, 2024
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8 changes: 7 additions & 1 deletion api/src/main/java/com/lantanagroup/link/api/ReportGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,11 @@
import org.hl7.fhir.r4.model.MeasureReport;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.slf4j.MDC;

import java.text.ParseException;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ForkJoinPool;
import java.util.concurrent.atomic.AtomicInteger;
Expand Down Expand Up @@ -66,8 +68,12 @@ public void generate(QueryPhase queryPhase) throws ExecutionException, Interrupt
AtomicInteger progress = new AtomicInteger(0);
List<PatientOfInterestModel> pois = measureContext.getPatientsOfInterest(queryPhase);

var contextMapCopy = MDC.getCopyOfContextMap();

forkJoinPool.submit(() -> pois.parallelStream().forEach(patient -> {

MDC.setContextMap(contextMapCopy);
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forkJoinPool.submit(() -> pois.parallelStream().forEach(patient -> {
if (StringUtils.isEmpty(patient.getId())) {
logger.error("Patient {} has no ID; cannot generate measure report", patient);
return;
Expand Down
5 changes: 5 additions & 0 deletions api/src/main/java/com/lantanagroup/link/api/controller/ReportController.java
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Expand Up @@ -35,6 +35,7 @@
import org.hl7.fhir.r4.model.MeasureReport;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.slf4j.MDC;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.http.HttpStatus;
Expand Down Expand Up @@ -402,6 +403,9 @@ private Report generateResponse(TenantService tenantService, LinkCredentials use
report.setVersion(existingReport.getVersion());
}

MDC.put("report", String.format("%s-%s-%s",
tenantService.getConfig().getId(), report.getId(), report.getVersion()));

tenantService.saveReport(report, reportContext.getPatientLists());

this.eventService.triggerEvent(tenantService, EventTypes.BeforePatientDataQuery, criteria, reportContext);
Expand Down Expand Up @@ -454,6 +458,7 @@ private Report generateResponse(TenantService tenantService, LinkCredentials use
}
} finally {
tenantLock.unlock();
MDC.clear();
}

this.stopwatchManager.storeMetrics(tenantService.getConfig().getId(), report.getId(), report.getVersion());
Expand Down
2 changes: 2 additions & 0 deletions api/src/main/resources/logback.xml
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Expand Up @@ -3,6 +3,8 @@
<property name="LOG_FILE" value="logs/link-api.log"/>
<property name="LOGBACK_ROLLINGPOLICY_MAX_FILE_SIZE" value="100MB"/>
<property name="LOGBACK_ROLLINGPOLICY_MAX_HISTORY" value="0"/>
<property name="CONSOLE_LOG_PATTERN" value="${CONSOLE_LOG_PATTERN:-%clr(%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd'T'HH:mm:ss.SSSXXX}}){faint} %clr(${LOG_LEVEL_PATTERN:-%5p}) %clr(${PID:- }){magenta} %clr(---){faint} %clr(${LOGGED_APPLICATION_NAME:-}[%15.15t] [%X{report}]){faint} %clr(${LOG_CORRELATION_PATTERN:-}){faint}%clr(%-40.40logger{39}){cyan} %clr(:){faint} %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}"/>
<property name="FILE_LOG_PATTERN" value="${FILE_LOG_PATTERN:-%d{${LOG_DATEFORMAT_PATTERN:-yyyy-MM-dd'T'HH:mm:ss.SSSXXX}} ${LOG_LEVEL_PATTERN:-%5p} ${PID:- } --- ${LOGGED_APPLICATION_NAME:-}[%t] [%X{report}] ${LOG_CORRELATION_PATTERN:-}%-40.40logger{39} : %m%n${LOG_EXCEPTION_CONVERSION_WORD:-%wEx}}"/>
<include resource="org/springframework/boot/logging/logback/base.xml"/>

<logger name="com.lantanagroup.link" level="DEBUG"/>
Expand Down
8 changes: 8 additions & 0 deletions query/src/main/java/com/lantanagroup/link/query/uscore/PatientScoop.java
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Expand Up @@ -17,6 +17,7 @@
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.slf4j.MDC;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.stereotype.Component;
Expand Down Expand Up @@ -110,7 +111,10 @@ public void loadInitialPatientData(ReportCriteria criteria, ReportContext contex
AtomicInteger progress = new AtomicInteger(0);

try {
var contextMapCopy = MDC.getCopyOfContextMap();
patientFork.submit(() -> patientsOfInterest.parallelStream().map(poi -> {
MDC.setContextMap(contextMapCopy);

int poiIndex = patientsOfInterest.indexOf(poi);

//noinspection unused
Expand Down Expand Up @@ -177,10 +181,12 @@ public void loadInitialPatientData(ReportCriteria criteria, ReportContext contex
progress.set(0);

try {
var contextMapCopy = MDC.getCopyOfContextMap();
// loop through the patient ids to retrieve the patientData using each patient.
List<Patient> patients = new ArrayList<>(patientMap.values());

patientDataFork.submit(() -> patients.parallelStream().map(patient -> {
MDC.setContextMap(contextMapCopy);
logger.debug(String.format("Beginning to load data for patient with logical ID %s", patient.getIdElement().getIdPart()));

PatientData patientData = null;
Expand Down Expand Up @@ -210,7 +216,9 @@ public void loadSupplementalPatientData(ReportCriteria criteria, ReportContext c
AtomicInteger progress = new AtomicInteger(0);

try {
var contextMapCopy = MDC.getCopyOfContextMap();
patientDataFork.submit(() -> patientsOfInterest.parallelStream().map(poi -> {
MDC.setContextMap(contextMapCopy);
logger.debug(String.format("Continuing to load data for patient with logical ID %s", poi.getId()));

Bundle patientBundle = com.lantanagroup.link.db.model.PatientData.asBundle(this.tenantService.findPatientData(context.getMasterIdentifierValue(), poi.getId()));
Expand Down