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Update swagger methods for clickhouse #11862

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Update swagger methods for clickhouse #11862

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41 changes: 16 additions & 25 deletions ...n/java/org/cbioportal/application/rest/vcolumnstore/ColumnarStoreStudyViewController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,6 @@ public ResponseEntity<List<SampleDTO>> fetchFilteredSamples(
SampleMapper.INSTANCE.toDtos(studyViewService.getFilteredSamples(studyViewFilter)));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/mutated-genes/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -129,7 +128,6 @@ public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
return ResponseEntity.ok(studyViewService.getMutatedGenes(studyViewFilter));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/molecular-profile-sample-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -151,7 +149,6 @@ public ResponseEntity<List<GenomicDataCount>> fetchMolecularProfileSampleCounts(
return ResponseEntity.ok(studyViewService.getMolecularProfileSampleCounts(studyViewFilter));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/cna-genes/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -164,7 +161,6 @@ public ResponseEntity<List<CopyNumberCountByGene>> fetchCnaGenes(
return ResponseEntity.ok(studyViewService.getCnaGenes(studyViewFilter));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/structuralvariant-genes/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -187,7 +183,6 @@ public ResponseEntity<List<AlterationCountByGene>> fetchStructuralVariantGenes(
return ResponseEntity.ok(studyViewService.getStructuralVariantGenes(studyViewFilter));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/clinical-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -210,7 +205,6 @@ public ResponseEntity<List<ClinicalDataCountItem>> fetchClinicalDataCounts(
return ResponseEntity.ok(result);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/sample-lists-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -227,7 +221,6 @@ public List<CaseListDataCount> fetchCaseListCounts(
return studyViewService.getCaseListDataCounts(studyViewFilter);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/clinical-data-bin-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -243,7 +236,6 @@ public ResponseEntity<List<ClinicalDataBin>> fetchClinicalDataBinCounts(
return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/clinical-data-density-plot/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand Down Expand Up @@ -312,7 +304,6 @@ public ResponseEntity<DensityPlotData> fetchClinicalDataDensityPlot(
return new ResponseEntity<>(result, HttpStatus.OK);
}

@Hidden // should unhide when we remove legacy controller
@PreAuthorize(
"hasPermission(#studyViewFilter, 'StudyViewFilter', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
@PostMapping(
Expand Down Expand Up @@ -365,7 +356,8 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
// this new modified filter is used to fetch sample and patient clinical data.
// this is required to get the complete violin plot data.
// filteredSamples reflects only the original unmodified study view filter.
// we will need to fetch samples again to get the samples corresponding to this modified filter,
// we will need to fetch samples again to get the samples corresponding to this
// modified filter,
// otherwise patient to sample mapping may be incomplete.
if (studyViewFilter.getClinicalDataFilters() != null) {
studyViewFilter.getClinicalDataFilters().stream()
Expand Down Expand Up @@ -402,7 +394,6 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
return new ResponseEntity<>(result, HttpStatus.OK);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/genomic-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -424,9 +415,11 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
throws StudyNotFoundException {
List<GenomicDataFilter> genomicDataFilters = genomicDataCountFilter.getGenomicDataFilters();
StudyViewFilter studyViewFilter = genomicDataCountFilter.getStudyViewFilter();
// when there is only one filter, it means study view is doing a single chart filter operation
// when there is only one filter, it means study view is doing a single chart
// filter operation
// remove filter from studyViewFilter to return all data counts
// the reason we do this is to make sure after chart get filtered, user can still see unselected
// the reason we do this is to make sure after chart get filtered, user can
// still see unselected
// portion of the chart
if (genomicDataFilters.size() == 1) {
NewStudyViewFilterUtil.removeSelfFromGenomicDataFilter(
Expand All @@ -435,15 +428,15 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
studyViewFilter);
}

// This endpoint is CNA specific. The name choice of "genomic data" does not imply it support
// This endpoint is CNA specific. The name choice of "genomic data" does not
// imply it support
// other genomic data types
List<GenomicDataCountItem> result =
studyViewService.getCNACountsByGeneSpecific(studyViewFilter, genomicDataFilters);

return new ResponseEntity<>(result, HttpStatus.OK);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/generic-assay-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -467,9 +460,11 @@ public ResponseEntity<List<GenericAssayDataCountItem>> fetchGenericAssayDataCoun
List<GenericAssayDataFilter> gaFilters =
genericAssayDataCountFilter.getGenericAssayDataFilters();
StudyViewFilter studyViewFilter = genericAssayDataCountFilter.getStudyViewFilter();
// when there is only one filter, it means study view is doing a single chart filter operation
// when there is only one filter, it means study view is doing a single chart
// filter operation
// remove filter from studyViewFilter to return all data counts
// the reason we do this is to make sure after chart get filtered, user can still see unselected
// the reason we do this is to make sure after chart get filtered, user can
// still see unselected
// portion of the chart

if (gaFilters.size() == 1) {
Expand All @@ -481,7 +476,6 @@ public ResponseEntity<List<GenericAssayDataCountItem>> fetchGenericAssayDataCoun
studyViewService.getGenericAssayDataCounts(studyViewFilter, gaFilters));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/mutation-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -499,9 +493,11 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchMutationDataCounts(
GenomicDataCountFilter genomicDataCountFilter) {
List<GenomicDataFilter> genomicDataFilters = genomicDataCountFilter.getGenomicDataFilters();
StudyViewFilter studyViewFilter = genomicDataCountFilter.getStudyViewFilter();
// when there is only one filter, it means study view is doing a single chart filter operation
// when there is only one filter, it means study view is doing a single chart
// filter operation
// remove filter from studyViewFilter to return all data counts
// the reason we do this is to make sure after chart get filtered, user can still see unselected
// the reason we do this is to make sure after chart get filtered, user can
// still see unselected
// portion of the chart
if (genomicDataFilters.size() == 1 && projection == Projection.SUMMARY) {
NewStudyViewFilterUtil.removeSelfFromMutationDataFilter(
Expand All @@ -520,7 +516,6 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchMutationDataCounts(
return ResponseEntity.ok(result);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/clinical-event-type-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand Down Expand Up @@ -588,7 +583,6 @@ public ResponseEntity<SampleTreatmentReport> fetchSampleTreatmentCounts(
studyViewService.getSampleTreatmentReport(studyViewFilter, projection));
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/custom-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand Down Expand Up @@ -638,7 +632,6 @@ public ResponseEntity<List<ClinicalDataCountItem>> fetchCustomDataCounts(
return new ResponseEntity<>(result, HttpStatus.OK);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/custom-data-bin-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -663,7 +656,6 @@ public ResponseEntity<List<ClinicalDataBin>> fetchCustomDataBinCounts(
return ResponseEntity.ok(customDataBins);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/genomic-data-bin-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand All @@ -683,7 +675,6 @@ public ResponseEntity<List<GenomicDataBin>> fetchGenomicDataBinCounts(
return ResponseEntity.ok(genomicDataBins);
}

@Hidden // should unhide when we remove legacy controller
@PostMapping(
value = "/generic-assay-data-bin-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE,
Expand Down
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