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[GLT-4274] show omissions on the Run Details page
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Omissions table on the Run Details page, showing libraries that are included in the run but not a | ||
| part of any case |
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77 changes: 77 additions & 0 deletions
77
src/main/java/ca/on/oicr/gsi/dimsum/data/RunAndLibraries.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| package ca.on.oicr.gsi.dimsum.data; | ||
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| import static java.util.Objects.requireNonNull; | ||
| import java.util.Collections; | ||
| import java.util.HashSet; | ||
| import java.util.Set; | ||
| import ca.on.oicr.gsi.cardea.data.OmittedRunSample; | ||
| import ca.on.oicr.gsi.cardea.data.Run; | ||
| import ca.on.oicr.gsi.cardea.data.Sample; | ||
|
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| /** | ||
| * Immutable RunAndLibraries | ||
| */ | ||
| public class RunAndLibraries { | ||
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| private final Set<Sample> fullDepthSequencings; | ||
| private final Set<Sample> libraryQualifications; | ||
| private final Set<OmittedRunSample> omittedSamples; | ||
| private final Run run; | ||
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| private RunAndLibraries(Builder builder) { | ||
| this.run = requireNonNull(builder.run); | ||
| this.libraryQualifications = Collections.unmodifiableSet(builder.libraryQualifications); | ||
| this.fullDepthSequencings = Collections.unmodifiableSet(builder.fullDepthSequencings); | ||
| this.omittedSamples = Collections.unmodifiableSet(builder.omittedSamples); | ||
| } | ||
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| public Set<Sample> getFullDepthSequencings() { | ||
| return fullDepthSequencings; | ||
| } | ||
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| public Set<Sample> getLibraryQualifications() { | ||
| return libraryQualifications; | ||
| } | ||
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| public Set<OmittedRunSample> getOmittedSamples() { | ||
| return omittedSamples; | ||
| } | ||
|
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| public Run getRun() { | ||
| return run; | ||
| } | ||
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| public static class Builder { | ||
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| private Set<Sample> fullDepthSequencings = new HashSet<>(); | ||
| private Set<Sample> libraryQualifications = new HashSet<>(); | ||
| private Set<OmittedRunSample> omittedSamples = new HashSet<>(); | ||
| private Run run; | ||
|
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| public Builder addFullDepthSequencing(Sample sample) { | ||
| fullDepthSequencings.add(sample); | ||
| return this; | ||
| } | ||
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| public Builder addLibraryQualification(Sample sample) { | ||
| libraryQualifications.add(sample); | ||
| return this; | ||
| } | ||
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| public Builder addOmittedSample(OmittedRunSample sample) { | ||
| omittedSamples.add(sample); | ||
| return this; | ||
| } | ||
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| public RunAndLibraries build() { | ||
| return new RunAndLibraries(this); | ||
| } | ||
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| public Builder run(Run run) { | ||
| this.run = run; | ||
| return this; | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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55 changes: 55 additions & 0 deletions
55
src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/OmittedRunSampleSort.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| package ca.on.oicr.gsi.dimsum.service.filtering; | ||
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| import java.util.Comparator; | ||
| import java.util.Map; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
| import java.util.stream.Stream; | ||
| import ca.on.oicr.gsi.cardea.data.OmittedRunSample; | ||
| import ca.on.oicr.gsi.dimsum.util.DataUtils; | ||
|
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| public enum OmittedRunSampleSort { | ||
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| // @formatter:off | ||
| NAME("Name", Comparator.comparing(OmittedRunSample::getName)), | ||
| QC_STATUS("QC Status", Comparator.comparing(OmittedRunSampleSort::getQcStatusSortPriority)); | ||
| // @formatter:on | ||
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| private static final Map<String, OmittedRunSampleSort> map = | ||
| Stream.of(OmittedRunSampleSort.values()) | ||
| .collect(Collectors.toMap(OmittedRunSampleSort::getLabel, Function.identity())); | ||
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| public static OmittedRunSampleSort getByLabel(String label) { | ||
| return map.get(label); | ||
| } | ||
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| private final String label; | ||
| private final Comparator<OmittedRunSample> comparator; | ||
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| private OmittedRunSampleSort(String label, Comparator<OmittedRunSample> comparator) { | ||
| this.label = label; | ||
| this.comparator = comparator; | ||
| } | ||
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| public String getLabel() { | ||
| return label; | ||
| } | ||
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| public Comparator<OmittedRunSample> comparator() { | ||
| return comparator; | ||
| } | ||
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| protected static int getQcStatusSortPriority(OmittedRunSample sample) { | ||
| if (sample.getQcDate() == null) { | ||
| return 1; | ||
| } else if (sample.getDataReviewDate() == null) { | ||
| return 2; | ||
| } else if (DataUtils.isTopUpRequired(sample)) { | ||
| return 3; | ||
| } else if (Boolean.TRUE.equals(sample.getQcPassed())) { | ||
| return 4; | ||
| } else { | ||
| return 5; | ||
| } | ||
| } | ||
| } |
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