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[GLT-4068] added case TAT report (#194)
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| Case TAT report generated from the Cases list and uses the same filters that are applied to the list |
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src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/reports/CaseTatReport.java
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| package ca.on.oicr.gsi.dimsum.util.reporting.reports; | ||
|
|
||
| import java.time.LocalDate; | ||
| import java.time.format.DateTimeFormatter; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
| import com.fasterxml.jackson.databind.JsonNode; | ||
| import ca.on.oicr.gsi.cardea.data.Case; | ||
| import ca.on.oicr.gsi.cardea.data.CaseDeliverable; | ||
| import ca.on.oicr.gsi.cardea.data.CaseRelease; | ||
| import ca.on.oicr.gsi.cardea.data.Project; | ||
| import ca.on.oicr.gsi.cardea.data.Requisition; | ||
| import ca.on.oicr.gsi.cardea.data.Sample; | ||
| import ca.on.oicr.gsi.cardea.data.Test; | ||
| import ca.on.oicr.gsi.dimsum.controller.mvc.MvcUtils; | ||
| import ca.on.oicr.gsi.dimsum.controller.rest.request.DataQuery; | ||
| import ca.on.oicr.gsi.dimsum.controller.rest.request.KeyValuePair; | ||
| import ca.on.oicr.gsi.dimsum.service.CaseService; | ||
| import ca.on.oicr.gsi.dimsum.service.filtering.CaseFilter; | ||
| import ca.on.oicr.gsi.dimsum.util.SampleUtils; | ||
| import ca.on.oicr.gsi.dimsum.util.reporting.Column; | ||
| import ca.on.oicr.gsi.dimsum.util.reporting.Report; | ||
| import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection; | ||
| import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection.TableReportSection; | ||
|
|
||
| public class CaseTatReport extends Report { | ||
|
|
||
| private static class RowData { | ||
|
|
||
| private final Case kase; | ||
| private final Test test; | ||
|
|
||
| public RowData(Case kase, Test test) { | ||
| this.kase = kase; | ||
| this.test = test; | ||
| } | ||
|
|
||
| public Case getCase() { | ||
| return kase; | ||
| } | ||
|
|
||
| public Test getTest() { | ||
| return test; | ||
| } | ||
| } | ||
|
|
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| private static final ReportSection<RowData> caseSection = | ||
| new TableReportSection<>("Case Report", | ||
| Arrays.asList( | ||
| Column.forString("Case ID", x -> x.getCase().getId()), | ||
| Column.forString("Projects", | ||
| x -> getSortedProjectNameOrPipeline(x.getCase(), Project::getName)), | ||
| Column.forString("Pipeline", | ||
| x -> getSortedProjectNameOrPipeline(x.getCase(), Project::getPipeline)), | ||
| Column.forString("Requisition", x -> x.getCase().getRequisition().getName()), | ||
| Column.forString("Assay", x -> x.getCase().getAssayName()), | ||
| Column.forString("Start Date", | ||
| x -> x.getCase().getStartDate().format(DateTimeFormatter.ISO_LOCAL_DATE)), | ||
| Column.forString("Receipt Completed", | ||
| x -> findLatestCompletionDate(x.getCase().getReceipts())), | ||
| Column.forInteger("Receipt Days", x -> x.getCase().getReceiptDaysSpent()), | ||
| Column.forString("Test", x -> x.getTest().getName()), | ||
| Column.forString("Supplemental Only", | ||
| x -> isSupplementalOnly(x.getTest(), x.getCase().getRequisition()) ? "Yes" | ||
| : "No"), | ||
| Column.forString("Extraction Completed", | ||
| x -> findLatestCompletionDate(x.getTest().getExtractions())), | ||
| Column.forInteger("Extraction Days", x -> x.getTest().getExtractionDaysSpent()), | ||
| Column.forString("Library Prep Completed", | ||
| x -> findLatestCompletionDate(x.getTest().getLibraryPreparations())), | ||
| Column.forInteger("Library Prep. Days", | ||
| x -> x.getTest().getLibraryPreparationDaysSpent()), | ||
| Column.forString("Library Qual Completed", | ||
| x -> findLatestCompletionDate(x.getTest().getLibraryQualifications())), | ||
| Column.forInteger("Library Qual. Days", | ||
| x -> x.getTest().getLibraryQualificationDaysSpent()), | ||
| Column.forString("Full-Depth Completed", | ||
| x -> findLatestCompletionDate(x.getTest().getFullDepthSequencings())), | ||
| Column.forInteger("Full-Depth Days", | ||
| x -> x.getTest().getFullDepthSequencingDaysSpent()), | ||
| Column.forString("Analysis Review Completed", | ||
| x -> getMaxDateFromDeliverables(x.getCase(), | ||
| CaseDeliverable::getAnalysisReviewQcDate)), | ||
| Column.forInteger("Analysis Review Days", | ||
| x -> x.getCase().getAnalysisReviewDaysSpent()), | ||
| Column.forString("Release Approval Completed", | ||
| x -> getMaxDateFromDeliverables(x.getCase(), | ||
| CaseDeliverable::getReleaseApprovalQcDate)), | ||
| Column.forInteger("Release Approval Days", | ||
| x -> x.getCase().getReleaseApprovalDaysSpent()), | ||
| Column.forString("Release Completed", x -> { | ||
| if (!x.getCase().isStopped()) { | ||
| return getCompletionDate(x.getCase()); | ||
| } | ||
| List<LocalDate> dates = x.getCase().getDeliverables().stream() | ||
| .flatMap(deliverable -> deliverable.getReleases().stream()) | ||
| .map(CaseRelease::getQcDate) | ||
| .collect(Collectors.toList()); | ||
| if (dates.contains(null)) { | ||
| return null; | ||
| } | ||
| return dates.stream().max(LocalDate::compareTo) | ||
| .map(date -> date.format(DateTimeFormatter.ISO_LOCAL_DATE)).orElse(null); | ||
| }), | ||
| Column.forInteger("Release Days", x -> x.getCase().getReleaseDaysSpent()), | ||
| Column.forString("Completion Date", x -> getCompletionDate(x.getCase())), | ||
| Column.forInteger("Total Days", x -> x.getCase().getCaseDaysSpent()))) { | ||
|
|
||
| @Override | ||
| public List<RowData> getData(CaseService caseService, JsonNode parameters) { | ||
| List<CaseFilter> filters = convertParametersToFilters(parameters); | ||
| return caseService.getCaseStream(filters) | ||
| .flatMap(kase -> kase.getTests().stream().map(test -> new RowData(kase, test))) | ||
| .collect(Collectors.toList()); | ||
| } | ||
| }; | ||
|
|
||
| public static final CaseTatReport INSTANCE = new CaseTatReport(); | ||
|
|
||
| private CaseTatReport() { | ||
| super("Case TAT Report", caseSection); | ||
| } | ||
|
|
||
| private static String getSortedProjectNameOrPipeline(Case kase, | ||
| Function<Project, String> function) { | ||
| return kase.getProjects().stream() | ||
| .map(function) | ||
| .sorted() | ||
| .collect(Collectors.joining(", ")); | ||
| } | ||
|
|
||
| private static List<CaseFilter> convertParametersToFilters(JsonNode parameters) { | ||
| DataQuery dataQuery = new DataQuery(); | ||
| List<KeyValuePair> kvpFilters = new ArrayList<>(); | ||
|
|
||
| if (parameters.isArray()) { | ||
| for (JsonNode parameter : parameters) { | ||
| String key = parameter.get("key").asText(); | ||
| String value = parameter.get("value").asText(); | ||
| kvpFilters.add(new KeyValuePair(key, value)); | ||
| } | ||
| } | ||
|
|
||
| dataQuery.setFilters(kvpFilters); | ||
| List<CaseFilter> caseFilters = MvcUtils.parseCaseFilters(dataQuery); | ||
| return caseFilters; | ||
| } | ||
|
|
||
| private static boolean isSupplementalOnly(Test test, Requisition requisition) { | ||
| if (test.getExtractions().isEmpty() | ||
| && test.getLibraryPreparations().isEmpty() | ||
| && test.getLibraryQualifications().isEmpty() | ||
| && test.getFullDepthSequencings().isEmpty()) { | ||
| return false; | ||
| } | ||
| return test.getExtractions().stream() | ||
| .allMatch(sample -> !Objects.equals(sample.getRequisitionId(), requisition.getId())) | ||
| && test.getLibraryPreparations().stream() | ||
| .allMatch(sample -> !Objects.equals(sample.getRequisitionId(), requisition.getId())) | ||
| && test.getLibraryQualifications().stream() | ||
| .allMatch(sample -> !Objects.equals(sample.getRequisitionId(), requisition.getId())) | ||
| && test.getFullDepthSequencings().stream() | ||
| .allMatch(sample -> !Objects.equals(sample.getRequisitionId(), requisition.getId())); | ||
| } | ||
|
|
||
| private static String findLatestCompletionDate(List<Sample> samples) { | ||
| LocalDate latestDate = null; | ||
| for (Sample sample : samples) { | ||
| if (SampleUtils.isPassed(sample)) { | ||
| LocalDate dateToCompare = null; | ||
| if (sample.getRun() != null) { | ||
| LocalDate sampleReviewDate = sample.getDataReviewDate(); | ||
| LocalDate runReviewDate = sample.getRun().getDataReviewDate(); | ||
| if (sampleReviewDate != null && runReviewDate != null) { | ||
| dateToCompare = | ||
| runReviewDate.isAfter(sampleReviewDate) ? runReviewDate : sampleReviewDate; | ||
| } | ||
| } else { | ||
| dateToCompare = sample.getQcDate(); | ||
| } | ||
| if (dateToCompare != null && (latestDate == null || dateToCompare.isAfter(latestDate))) { | ||
| latestDate = dateToCompare; | ||
| } | ||
| } | ||
| } | ||
| return latestDate != null ? latestDate.format(DateTimeFormatter.ISO_LOCAL_DATE) : null; | ||
| } | ||
|
|
||
| private static String getMaxDateFromDeliverables(Case x, | ||
| Function<CaseDeliverable, LocalDate> dateExtractor) { | ||
| List<LocalDate> dates = x.getDeliverables().stream() | ||
| .map(dateExtractor) | ||
| .collect(Collectors.toList()); | ||
| if (dates.contains(null)) { | ||
| return null; | ||
| } | ||
| return dates.stream().max(LocalDate::compareTo) | ||
| .map(date -> date.format(DateTimeFormatter.ISO_LOCAL_DATE)).orElse(null); | ||
| } | ||
|
|
||
| private static String getCompletionDate(Case x) { | ||
| if (x.isStopped()) { | ||
| return "STOPPED"; | ||
| } | ||
| List<CaseDeliverable> deliverables = x.getDeliverables(); | ||
| if (deliverables.isEmpty()) { | ||
| return null; | ||
| } | ||
| List<CaseRelease> releases = deliverables.stream() | ||
| .flatMap(deliverable -> deliverable.getReleases().stream()) | ||
| .collect(Collectors.toList()); | ||
| if (releases.isEmpty()) { | ||
| return null; | ||
| } | ||
| if (releases.stream() | ||
| .anyMatch(release -> release.getQcPassed() == null || !release.getQcPassed())) { | ||
| return null; | ||
| } | ||
| LocalDate latestQcDate = releases.stream() | ||
| .map(CaseRelease::getQcDate) | ||
| .max(LocalDate::compareTo) | ||
| .orElse(null); | ||
| return latestQcDate != null ? latestQcDate.toString() : null; | ||
| } | ||
| } |
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