@Override
protected void addColumns(CohortReportDescriptor report, PatientDataSetDefinition dsd) {
PatientIdentifierType upn =
MetadataUtils.existing(
PatientIdentifierType.class, HivMetadata._PatientIdentifierType.UNIQUE_PATIENT_NUMBER);
DataDefinition identifierDefUpn =
new ConvertedPatientDataDefinition(
"identifier",
new PatientIdentifierDataDefinition(upn.getName(), upn),
new IdentifierConverter());
PatientIdentifierType districtNo =
MetadataUtils.existing(
PatientIdentifierType.class, TbMetadata._PatientIdentifierType.DISTRICT_REG_NUMBER);
DataDefinition identifierDefDn =
new ConvertedPatientDataDefinition(
"identifier",
new PatientIdentifierDataDefinition(upn.getName(), districtNo),
new IdentifierConverter());
addStandardColumns(report, dsd);
dsd.addColumn("Unique Patient Number", identifierDefUpn, "");
dsd.addColumn("District Registration Number", identifierDefDn, "");
dsd.addColumn(
"Due date",
new CalculationDataDefinition("Date Eligible", new NeedsTbSputumTestDateCalculation()),
"",
new CalculationResultConverter());
}
@Override
protected void addColumns(CohortReportDescriptor report, PatientDataSetDefinition dsd) {
PatientIdentifierType upn =
MetadataUtils.existing(
PatientIdentifierType.class, HivMetadata._PatientIdentifierType.UNIQUE_PATIENT_NUMBER);
DataDefinition identifierDef =
new ConvertedPatientDataDefinition(
"identifier",
new PatientIdentifierDataDefinition(upn.getName(), upn),
new IdentifierConverter());
addStandardColumns(report, dsd);
dsd.addColumn("UPN", identifierDef, "");
dsd.addColumn(
"Death date",
new CalculationDataDefinition("Death date", new DateOfDeathCalculation()),
"",
new CalculationResultConverter());
}
@RequestMapping(method = RequestMethod.POST)
public void process(
final @RequestParam(required = false, value = "cohort") Integer cohortId,
final @RequestParam(required = true, value = "template") MultipartFile template,
final HttpServletResponse response)
throws IOException, EvaluationException {
EvaluationContext context = new EvaluationContext();
context.addParameterValue("currentDate", new Date());
if (cohortId != null) {
context.setBaseCohort(Context.getCohortService().getCohort(cohortId));
}
PatientDataSetDefinition definition = new PatientDataSetDefinition();
definition.addColumn(
"id", new PatientIdDataDefinition(), StringUtils.EMPTY, new ObjectFormatter());
ListConverter listConverter = new ListConverter();
listConverter.setMaxNumberOfItems(1);
PatientIdentifierDataDefinition preferredIdentifier = new PatientIdentifierDataDefinition();
preferredIdentifier.addType(Context.getPatientService().getPatientIdentifierType(1));
definition.addColumn("identifier", preferredIdentifier, StringUtils.EMPTY, listConverter);
definition.addColumn(
"name",
new PreferredNameDataDefinition(),
StringUtils.EMPTY,
new ObjectFormatter("{familyName}, {givenName}"));
AgeDataDefinition ageOnDate = new AgeDataDefinition();
ageOnDate.addParameter(new Parameter("effectiveDate", "effective date", Date.class));
definition.addColumn("age", ageOnDate, "effectiveDate=${currentDate}", new AgeConverter());
definition.addColumn(
"birthdate",
new BirthdateDataDefinition(),
StringUtils.EMPTY,
new BirthdateConverter("dd-MMM-yyyy"));
definition.addColumn(
"gender", new GenderDataDefinition(), StringUtils.EMPTY, new ObjectFormatter());
ReportDefinition reportDefinition = new ReportDefinition();
reportDefinition.setName("Test Report");
reportDefinition.addDataSetDefinition("PatientDataSetDefinition", definition, null);
final ReportDesign design = new ReportDesign();
design.setName("Test Report Design With Excel Template Renderer");
design.setReportDefinition(reportDefinition);
design.setRendererType(ExcelTemplateRenderer.class);
Properties properties = new Properties();
properties.put("repeatingSections", "sheet:1,dataset:PatientDataSetDefinition");
design.setProperties(properties);
ReportDesignResource resource = new ReportDesignResource();
resource.setName("excel-template.xls");
InputStream inputStream = template.getInputStream();
resource.setContents(IOUtils.toByteArray(inputStream));
IOUtils.closeQuietly(inputStream);
design.addResource(resource);
ExcelTemplateRenderer renderer =
new ExcelTemplateRenderer() {
public ReportDesign getDesign(String argument) {
return design;
}
};
ReportDefinitionService rs = Context.getService(ReportDefinitionService.class);
ReportData data = rs.evaluate(reportDefinition, context);
CsvReportRenderer csvReportRenderer = new CsvReportRenderer();
csvReportRenderer.render(data, "output:csv", System.out);
File file = File.createTempFile("excel", "summary");
BufferedOutputStream bufferedOutputStream =
new BufferedOutputStream(new FileOutputStream(file));
renderer.render(data, "output:xls", bufferedOutputStream);
bufferedOutputStream.close();
response.setHeader("Content-Disposition", "attachment; filename=patient-summary.xls");
response.setContentType("application/vnd.ms-excel");
response.setContentLength((int) file.length());
FileCopyUtils.copy(new FileInputStream(file), response.getOutputStream());
if (file.delete()) log.info("Temporary file deleted!");
}
/** @see DataSetEvaluator#evaluate(DataSetDefinition, EvaluationContext) */
@SuppressWarnings("unchecked")
public DataSet evaluate(DataSetDefinition dataSetDefinition, EvaluationContext context)
throws EvaluationException {
PatientDataSetDefinition dsd = (PatientDataSetDefinition) dataSetDefinition;
context = ObjectUtil.nvl(context, new EvaluationContext());
SimpleDataSet dataSet = new SimpleDataSet(dsd, context);
dataSet.setSortCriteria(dsd.getSortCriteria());
// Construct a new EvaluationContext based on the passed filters
Cohort c = context.getBaseCohort();
if (dsd.getRowFilters() != null) {
for (Mapped<? extends CohortDefinition> q : dsd.getRowFilters()) {
Cohort s = Context.getService(CohortDefinitionService.class).evaluate(q, context);
c = CohortUtil.intersectNonNull(c, s);
}
}
if (c == null) {
c =
Context.getService(CohortDefinitionService.class)
.evaluate(new AllPatientsCohortDefinition(), context);
}
EvaluationContext ec = context.shallowCopy();
if (!CohortUtil.areEqual(ec.getBaseCohort(), c)) {
ec.setBaseCohort(c);
}
// Evaluate each specified ColumnDefinition for all of the included rows and add these to the
// dataset
for (RowPerObjectColumnDefinition cd : dsd.getColumnDefinitions()) {
if (log.isDebugEnabled()) {
log.debug("Evaluating column: " + cd.getName());
log.debug(
"With Data Definition: "
+ DefinitionUtil.format(cd.getDataDefinition().getParameterizable()));
log.debug("With Mappings: " + cd.getDataDefinition().getParameterMappings());
log.debug("With Parameters: " + ec.getParameterValues());
}
StopWatch sw = new StopWatch();
sw.start();
MappedData<? extends PatientDataDefinition> dataDef =
(MappedData<? extends PatientDataDefinition>) cd.getDataDefinition();
EvaluatedPatientData data =
Context.getService(PatientDataService.class).evaluate(dataDef, ec);
for (Integer id : c.getMemberIds()) {
for (DataSetColumn column : cd.getDataSetColumns()) {
Object val = data.getData().get(id);
val = DataUtil.convertData(val, dataDef.getConverters());
dataSet.addColumnValue(id, column, val);
}
}
sw.stop();
if (log.isDebugEnabled()) {
log.debug("Evaluated column. Duration: " + sw.toString());
}
}
return dataSet;
}
/**
* @see
* org.openmrs.module.kenyacore.report.builder.AbstractCohortReportBuilder#addColumns(CohortReportDescriptor,
* PatientDataSetDefinition)
*/
@Override
protected void addColumns(HybridReportDescriptor report, PatientDataSetDefinition dsd) {
PatientIdentifierType upn =
MetadataUtils.existing(
PatientIdentifierType.class, HivMetadata._PatientIdentifierType.UNIQUE_PATIENT_NUMBER);
DataDefinition identifierDef =
new ConvertedPatientDataDefinition(
"identifier",
new PatientIdentifierDataDefinition(upn.getName(), upn),
new IdentifierConverter());
DataConverter nameFormatter = new ObjectFormatter("{familyName}, {givenName}");
DataDefinition nameDef =
new ConvertedPersonDataDefinition("name", new PreferredNameDataDefinition(), nameFormatter);
dsd.setName("artCohortAnalysis");
dsd.addColumn("id", new PatientIdDataDefinition(), "");
dsd.addColumn("Name", nameDef, "");
dsd.addColumn("UPN", identifierDef, "");
dsd.addColumn(
"Enrollment into care date",
hivProgramEnrollment(),
"onDate=${endDate}",
new CalculationResultConverter());
dsd.addColumn("DOB", new BirthdateDataDefinition(), "", new BirthdateConverter());
dsd.addColumn(
"DOB approx",
new CalculationDataDefinition("DOB approx", new IsBirthDateApproximatedCalculation()),
"",
new CalculationResultConverter());
dsd.addColumn(
"Age at ART initiation",
new CalculationDataDefinition("Age at ART initiation", new AgeAtARTInitiationCalculation()),
"",
new CalculationResultConverter());
dsd.addColumn("Sex", new GenderDataDefinition(), "");
dsd.addColumn("TI", ti(), "", new TransferInAndDateConverter("state"));
dsd.addColumn("Date TI", ti(), "", new TransferInAndDateConverter("date"));
dsd.addColumn("TO", to(report), "onDate=${endDate}", new TransferInAndDateConverter("state"));
dsd.addColumn(
"Date TO", to(report), "onDate=${endDate}", new TransferInAndDateConverter("date"));
dsd.addColumn(
"ARV Start Date",
new CalculationDataDefinition("ARV Start Date", new DateARV1Calculation()),
"",
new CalculationResultConverter());
dsd.addColumn(
"Days from enrollment in care to ART Initiation",
new CalculationDataDefinition(
"Days from enrollment in care to ART Initiation",
new DaysFromEnrollmentToArtInitiationCalculation()),
"",
new CalculationResultConverter());
dsd.addColumn(
"Days from ART eligibility to ART Initiation",
fromEligibilityToArtStart(report),
"onDate=${endDate}",
new CalculationResultConverter());
dsd.addColumn(
"Date first medically eligible for ART",
dateAndReasonFirstMedicallyEligibleForArtCalculation(report),
"onDate=${endDate}",
new MedicallyEligibleConverter("date"));
dsd.addColumn(
"Reason first medically eligible For ART",
dateAndReasonFirstMedicallyEligibleForArtCalculation(report),
"onDate=${endDate}",
new MedicallyEligibleConverter("reason"));
dsd.addColumn(
"ART baseline CD4 count",
baselineCd4(report),
"onDate=${endDate}",
new Cd4ValueAndDateConverter("value"));
dsd.addColumn(
"Date of ART baseline CD4 count",
baselineCd4(report),
"onDate=${endDate}",
new Cd4ValueAndDateConverter("date"));
dsd.addColumn(
"Initial ART regimen",
new CalculationDataDefinition("First ART regimen", new InitialArtRegimenCalculation()),
"",
new RegimenConverter());
dsd.addColumn(
"Current ART regimen",
currentARTRegimen(report),
"onDate=${endDate}",
new ArtCohortRegimenConverter());
dsd.addColumn(
"Current ART line",
currentARTRegimen(report),
"onDate=${endDate}",
new RegimenLineConverter());
dsd.addColumn(
"CD4 at end of follow up",
currentCd4Count(report),
"onDate=${endDate}",
new CurrentCd4Converter("value"));
dsd.addColumn(
"CD4 at end of follow up date",
currentCd4Count(report),
"onDate=${endDate}",
new CurrentCd4Converter("date"));
dsd.addColumn(
"Change in cd4 count",
changeInCd4Count(report),
"onDate=${endDate}",
new ChangeInCd4Converter());
dsd.addColumn(
"Viral load at end of follow up",
viralLoad(report),
"onDate=${endDate}",
new CurrentCd4Converter("value"));
dsd.addColumn(
"Date viral load at end of follow up",
viralLoad(report),
"onDate=${endDate}",
new CurrentCd4Converter("date"));
dsd.addColumn(
"Viral suppression",
viralSuppression(report),
"onDate=${endDate}",
new CalculationResultConverter());
dsd.addColumn(
"Date of Last visit",
lastSeen(report),
"onDate=${endDate}",
new CalculationResultConverter());
dsd.addColumn(
"Date of expected next visit",
nextAppointmentDate(report),
"onDate=${endDate}",
new CalculationResultConverter());
dsd.addColumn(
"Date of death", death(report), "onDate=${endDate}", new CalculationResultConverter());
dsd.addColumn(
"ART Outcomes",
patientOutComes(report),
"onDate=${endDate}",
new CalculationResultConverter());
}
@Override
public ReportDefinition getReportDefinition() {
String nullString = null;
ObjectFormatter nullStringConverter = new ObjectFormatter();
MohCoreService service = Context.getService(MohCoreService.class);
ReportDefinition report = new PeriodIndicatorReportDefinition();
report.setName("MOH 361A Report");
// set up the DSD
PatientDataSetDefinition dsd = new PatientDataSetDefinition();
dsd.setName("allPatients");
// set up parameters
Parameter facility = new Parameter();
facility.setName("facility");
facility.setType(MOHFacility.class);
// add to report and data set definition
report.addParameter(facility);
dsd.addParameter(facility);
// sort by serial number, then by date
dsd.addSortCriteria("Transfer Status", SortCriteria.SortDirection.ASC);
dsd.addSortCriteria("Date Chronic HIV Care Started", SortCriteria.SortDirection.ASC);
dsd.addSortCriteria("Serial Number", SortCriteria.SortDirection.ASC);
// set up the columns ...
// patient id ... until we get this thing working proper
dsd.addColumn("Person ID", new PersonIdDataDefinition(), nullString);
// a. serial number
dsd.addColumn("Serial Number", new SerialNumberDataDefinition(), "facility=${facility}");
// b. date chronic HIV+ care started
EnrollmentDateDataDefinition enrollmentDate = new EnrollmentDateDataDefinition();
dsd.addColumn("Date Chronic HIV Care Started", enrollmentDate, nullString);
// extra column to help understand reason for including in this cohort
dsd.addColumn(
"First Encounter Date At Facility",
new FirstEncounterAtFacilityDataDefinition(),
"facility=${facility}",
new EncounterDatetimeConverter());
// c. Unique Patient Number
PatientIdentifierType pit = service.getCCCNumberIdentifierType();
CohortRestrictedPatientIdentifierDataDefinition cccColumn =
new CohortRestrictedPatientIdentifierDataDefinition("CCC", pit);
cccColumn.setIncludeFirstNonNullOnly(true);
dsd.addColumn("Unique Patient Number", cccColumn, nullString);
// AMRS Universal ID
CohortRestrictedPatientIdentifierDataDefinition uidColumn =
new CohortRestrictedPatientIdentifierDataDefinition(
"AMRS Universal ID", Context.getPatientService().getPatientIdentifierType(8));
uidColumn.setIncludeFirstNonNullOnly(true);
dsd.addColumn("AMRS Universal ID", uidColumn, nullString);
// AMRS Medical Record Number
CohortRestrictedPatientIdentifierDataDefinition mrnColumn =
new CohortRestrictedPatientIdentifierDataDefinition(
"AMRS Medical Record Number", Context.getPatientService().getPatientIdentifierType(3));
mrnColumn.setIncludeFirstNonNullOnly(true);
dsd.addColumn("AMRS Medical Record Number", mrnColumn, nullString);
// d. Patient's Name
dsd.addColumn("Name", new CohortRestrictedPreferredNameDataDefinition(), nullString);
// e1. Date of Birth
dsd.addColumn(
"Date of Birth",
new CohortRestrictedBirthdateDataDefinition(),
nullString,
new BirthdateConverter(MOHReportUtil.DATE_FORMAT));
// e2. Age at Enrollment
MappedData<EnrollmentDateDataDefinition> mappedDef =
new MappedData<EnrollmentDateDataDefinition>();
mappedDef.setParameterizable(enrollmentDate);
mappedDef.addConverter(new DateConverter());
CohortRestrictedAgeAtDateOfOtherDataDefinition ageAtEnrollment =
new CohortRestrictedAgeAtDateOfOtherDataDefinition();
ageAtEnrollment.setEffectiveDateDefinition(mappedDef);
dsd.addColumn("Age at Enrollment", ageAtEnrollment, nullString, new DecimalAgeConverter(2));
// f. Sex
dsd.addColumn("Sex", new CohortRestrictedGenderDataDefinition(), nullString);
// g. Entry point: From where?
PersonAttributeType pat =
Context.getPersonService()
.getPersonAttributeTypeByName(MohEvaluableNameConstants.POINT_OF_HIV_TESTING);
dsd.addColumn(
"Entry Point",
new CohortRestrictedPersonAttributeDataDefinition("entryPoint", pat),
nullString,
new EntryPointConverter());
// h. Confirmed HIV+ Date
dsd.addColumn("Confirmed HIV Date", enrollmentDate, nullString);
// // i. PEP Start / Stop Date
// LogicDataDefinition columnI = new LogicDataDefinition();
// columnI.setLogicQuery("\"MOH PEP Start Stop Date\"");
// dsd.addColumn("PEP Start / Stop Date", columnI, nullString);
//
// // j. Reasons for PEP use:
// LogicDataDefinition columnJ = new LogicDataDefinition();
// columnJ.setLogicQuery("\"MOH Reasons For PEP\"");
// dsd.addColumn("Reasons for PEP Use", columnJ, nullString);
// k. CTX startdate and stopdate:
dsd.addColumn("CTX Start Stop Date", new CtxStartStopDataDefinition(), nullString);
// l. Fluconazole startdate and stopdate
dsd.addColumn(
"Fluconazole Start Stop Date", new FluconazoleStartStopDataDefinition(), nullString);
// m. TB treatment startdate and stopdate
dsd.addColumn("TB Treatment Start Stop Date", new TbStartStopDataDefinition(), nullString);
// n. Pregnancy Yes?, Due date, PMTCT refer
dsd.addColumn(
"Pregnancy EDD and Referral",
new PmtctPregnancyDataDefinition(),
nullString,
new PMTCTDatesConverter());
// o. LTFU / TO / Dead and date when the event occurred
dsd.addColumn("LTFU TO DEAD", new LTFUTODeadDataDefinition(), nullString, nullStringConverter);
// p. WHO clinical Stage and date
dsd.addColumn(
"WHO Clinical Stage",
new FirstWHOStageDataDefinition(),
nullString,
new WHOStageAndDateConverter());
// q. Date medically eligible for ART
EligibilityForARTDataDefinition eligibility = new EligibilityForARTDataDefinition();
dsd.addColumn(
"Date Medically Eligible for ART",
eligibility,
nullString,
new ARVPatientSnapshotDateConverter());
// r. Reason Medically Eligible for ART
dsd.addColumn(
"Reason Medically Eligible for ART",
eligibility,
nullString,
new ARVPatientSnapshotReasonConverter());
// s. Date ART started (Transfer to ART register)
dsd.addColumn("Date ART Started", new DateARTStartedDataDefinition(), nullString);
// additional columns for troubleshooting
LastHIVEncounterDataDefinition lastHIVEncounter = new LastHIVEncounterDataDefinition();
dsd.addColumn(
"Last HIV Encounter Date", lastHIVEncounter, nullString, new EncounterDatetimeConverter());
dsd.addColumn(
"Last HIV Encounter Location",
lastHIVEncounter,
nullString,
new EncounterLocationConverter());
// informative column for the destination clinics
dsd.addColumn(
"Last Return to Clinic Date",
new LastRTCDateDataDefinition(),
nullString,
new ObsValueDatetimeConverter());
// transfer status column (used for sorting, not needed in output)
dsd.addColumn("Transfer Status", new TransferStatusDataDefinition(), nullString);
Map<String, Object> mappings = new HashMap<String, Object>();
mappings.put("facility", "${facility}");
report.addDataSetDefinition(dsd, mappings);
return report;
}