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Feature/mutated genes AlterationFilter and Fix unit test (#10803)
* Create new wide table sql file and rename package * Remove genomic_event view * Add AlterationFilter to mutated_genes endpoint * Add AlterationFilter to mutated-genes endpoint * Fix unit test * Fix sonar issues * Add test for mutation types and status * remove unused imports
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138 changes: 138 additions & 0 deletions
138
src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| package org.cbioportal.persistence.helper; | ||
|
|
||
| import org.cbioportal.model.AlterationFilter; | ||
| import org.cbioportal.model.CNA; | ||
| import org.cbioportal.model.MutationEventType; | ||
| import org.cbioportal.model.util.Select; | ||
| import org.springframework.lang.NonNull; | ||
| import org.springframework.lang.Nullable; | ||
|
|
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| import java.util.Objects; | ||
|
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| public final class AlterationFilterHelper { | ||
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| public static AlterationFilterHelper build(@Nullable AlterationFilter alterationFilter) { | ||
| if (Objects.isNull(alterationFilter)) { | ||
| alterationFilter = new AlterationFilter(); | ||
| } | ||
| return new AlterationFilterHelper(alterationFilter); | ||
| } | ||
|
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| private final AlterationFilter alterationFilter; | ||
| private final Select<String> mappedMutationTypes; | ||
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| private AlterationFilterHelper(@NonNull AlterationFilter alterationFilter){ | ||
| this.alterationFilter = alterationFilter; | ||
| this.mappedMutationTypes = buildMutationTypeList(); | ||
| } | ||
|
|
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| private Select<String> buildMutationTypeList() { | ||
| if (alterationFilter.getMutationTypeSelect().hasNone()) { | ||
| return Select.none(); | ||
| } | ||
| if (alterationFilter.getMutationTypeSelect().hasAll()) { | ||
| return Select.all(); | ||
| } | ||
| Select<String> typeSelects = alterationFilter.getMutationTypeSelect().map(MutationEventType::getMutationType); | ||
| typeSelects.inverse(alterationFilter.getMutationTypeSelect().inverse()); | ||
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| return typeSelects; | ||
| } | ||
|
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| public Select<String> getMutationTypeList() { | ||
| return mappedMutationTypes; | ||
| } | ||
|
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| public Select<Short> getCnaTypeList() { | ||
| if (alterationFilter.getCNAEventTypeSelect().hasNone()) { | ||
| return Select.none(); | ||
| } | ||
| if (alterationFilter.getCNAEventTypeSelect().hasAll()) { | ||
| return Select.all(); | ||
| } | ||
| return alterationFilter.getCNAEventTypeSelect().map(CNA::getCode); | ||
| } | ||
|
|
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| public boolean hasDriver() { | ||
| return alterationFilter.getIncludeDriver(); | ||
| } | ||
|
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| public boolean hasVUSDriver() { | ||
| return alterationFilter.getIncludeVUS(); | ||
| } | ||
|
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| public boolean hasUnknownOncogenicity() { | ||
| return alterationFilter.getIncludeUnknownOncogenicity(); | ||
| } | ||
|
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| public boolean hasGermline() { | ||
| return alterationFilter.getIncludeGermline(); | ||
| } | ||
|
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| public boolean hasSomatic() { | ||
| return alterationFilter.getIncludeSomatic(); | ||
| } | ||
|
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| public boolean hasUnknownMutationStatus() { | ||
| return alterationFilter.getIncludeUnknownStatus(); | ||
| } | ||
|
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| public Select<String> getSelectedTiers() { | ||
| return alterationFilter.getSelectedTiers(); | ||
| } | ||
|
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| public boolean hasUnknownTier() { | ||
| return alterationFilter.getIncludeUnknownTier(); | ||
| } | ||
|
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| public boolean isAllDriverAnnotationSelected() { | ||
| return alterationFilter.getIncludeDriver() && alterationFilter.getIncludeVUS() && alterationFilter.getIncludeUnknownOncogenicity(); | ||
| } | ||
|
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| public boolean isNoDriverAnnotationSelected() { | ||
| return !alterationFilter.getIncludeDriver() && !alterationFilter.getIncludeVUS() && !alterationFilter.getIncludeUnknownOncogenicity(); | ||
| } | ||
|
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| public boolean isSomeDriverAnnotationsSelected() { | ||
| return !isAllDriverAnnotationSelected() && !isNoDriverAnnotationSelected(); | ||
| } | ||
|
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| public boolean isAllMutationStatusSelected() { | ||
| return alterationFilter.getIncludeGermline() | ||
| && alterationFilter.getIncludeSomatic() | ||
| && alterationFilter.getIncludeUnknownStatus(); | ||
| } | ||
|
|
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| public boolean isNoMutationStatusSelected() { | ||
| return !alterationFilter.getIncludeGermline() | ||
| && !alterationFilter.getIncludeSomatic() | ||
| && !alterationFilter.getIncludeUnknownStatus(); | ||
| } | ||
|
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| public boolean isSomeMutationStatusSelected() { | ||
| return !isAllMutationStatusSelected() && !isNoMutationStatusSelected(); | ||
| } | ||
|
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| public boolean isAllTierOptionsSelected() { | ||
| return !Objects.isNull(alterationFilter.getSelectedTiers()) | ||
| && alterationFilter.getSelectedTiers().hasAll() | ||
| && alterationFilter.getIncludeUnknownTier(); | ||
| } | ||
|
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| public boolean isNoTierOptionsSelected() { | ||
| return (Objects.isNull(alterationFilter.getSelectedTiers()) || alterationFilter.getSelectedTiers().hasNone()) | ||
| && !alterationFilter.getIncludeUnknownTier(); | ||
| } | ||
|
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| public boolean isSomeTierOptionsSelected() { | ||
| return !isAllTierOptionsSelected() && !isNoTierOptionsSelected(); | ||
| } | ||
|
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| public boolean shouldApply() { | ||
| return isSomeDriverAnnotationsSelected() | ||
| || isSomeMutationStatusSelected() | ||
| || isSomeTierOptionsSelected() | ||
| || mappedMutationTypes.hasNone() | ||
| || (!mappedMutationTypes.hasNone() && !mappedMutationTypes.hasAll()); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| DROP TABLE IF EXISTS genomic_event_mutation; | ||
| DROP TABLE IF EXISTS genomic_event; | ||
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| CREATE TABLE IF NOT EXISTS genomic_event | ||
| ( | ||
| sample_unique_id String, | ||
| variant String, | ||
| variant_type String, | ||
| hugo_gene_symbol String, | ||
| gene_panel_stable_id String, | ||
| cancer_study_identifier String, | ||
| genetic_profile_stable_id String | ||
| ) ENGINE = MergeTree | ||
| ORDER BY ( variant_type, sample_unique_id, hugo_gene_symbol); | ||
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| CREATE TABLE IF NOT EXISTS genomic_event_mutation | ||
| ( | ||
| sample_unique_id String, | ||
| variant String, | ||
| hugo_gene_symbol String, | ||
| gene_panel_stable_id String, | ||
| cancer_study_identifier String, | ||
| genetic_profile_stable_id String, | ||
| mutation_type String, | ||
| mutation_status String, | ||
| driver_filter String, | ||
| driver_tiers_filter String | ||
| ) ENGINE = MergeTree | ||
| ORDER BY ( hugo_gene_symbol, genetic_profile_stable_id); |
91 changes: 91 additions & 0 deletions
91
src/main/resources/db-scripts/clickhouse/clickhouse_migration.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
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| -- Genomic Event Mutation Data | ||
| Insert into genomic_event_mutation | ||
| SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, | ||
| me.protein_change as variant, | ||
| gene.hugo_gene_symbol as hugo_gene_symbol, | ||
| gp.stable_id as gene_panel_stable_id, | ||
| cs.cancer_study_identifier as cancer_study_identifier, | ||
| g.stable_id as genetic_profile_stable_id, | ||
| me.mutation_type as mutation_type, | ||
| mutation.mutation_status as mutation_status, | ||
| 'NA' as driver_filter, | ||
| 'NA' as drivet_tiers_filter | ||
| FROM mutation | ||
| INNER JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id | ||
| INNER JOIN sample_profile sp | ||
| on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id | ||
| LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id | ||
| LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id | ||
| INNER JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id | ||
| INNER JOIN sample on mutation.sample_id = sample.internal_id | ||
| LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id; | ||
|
|
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| -- Genomic Event Data | ||
| Insert into genomic_event | ||
| SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, | ||
| me.protein_change as variant, | ||
| 'mutation' as variant_type, | ||
| gene.hugo_gene_symbol as hugo_gene_symbol, | ||
| gp.stable_id as gene_panel_stable_id, | ||
| cs.cancer_study_identifier as cancer_study_identifier, | ||
| g.stable_id as genetic_profile_stable_id | ||
| FROM mutation | ||
| INNER JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id | ||
| INNER JOIN sample_profile sp | ||
| on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id | ||
| LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id | ||
| LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id | ||
| INNER JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id | ||
| INNER JOIN sample on mutation.sample_id = sample.internal_id | ||
| LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id | ||
| UNION ALL | ||
| SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, | ||
| toString(ce.alteration) as variant, | ||
| 'cna' as variant_type, | ||
| gene.hugo_gene_symbol as hugo_gene_symbol, | ||
| gp.stable_id as gene_panel_stable_id, | ||
| cs.cancer_study_identifier as cancer_study_identifier, | ||
| g.stable_id as genetic_profile_stable_id | ||
| FROM cna_event ce | ||
| INNER JOIN sample_cna_event sce ON ce.cna_event_id = sce.cna_event_id | ||
| INNER JOIN sample_profile sp ON sce.sample_id = sp.sample_id AND sce.genetic_profile_id = sp.genetic_profile_id | ||
| INNER JOIN gene_panel gp ON sp.panel_id = gp.internal_id | ||
| INNER JOIN genetic_profile g ON sp.genetic_profile_id = g.genetic_profile_id | ||
| INNER JOIN cancer_study cs ON g.cancer_study_id = cs.cancer_study_id | ||
| INNER JOIN sample ON sce.sample_id = sample.internal_id | ||
| INNER JOIN gene ON ce.entrez_gene_id = gene.entrez_gene_id | ||
| UNION ALL | ||
| SELECT | ||
| concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, | ||
| event_info as variant, | ||
| 'structural_variant' as variant_type, | ||
| gene2.hugo_gene_symbol as hugo_gene_symbol, | ||
| gene_panel.stable_id as gene_panel_stable_id, | ||
| cs.cancer_study_identifier as cancer_study_identifier, | ||
| gp.stable_id as genetic_profile_stable_id | ||
| FROM | ||
| structural_variant sv | ||
| INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id | ||
| INNER JOIN sample s ON sv.sample_id = s.internal_id | ||
| INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id | ||
| INNER JOIN gene gene2 ON sv.site2_entrez_gene_id = gene2.entrez_gene_id | ||
| INNER JOIN sample_profile on s.internal_id = sample_profile.sample_id | ||
| INNER JOIN gene_panel on sample_profile.panel_id = gene_panel.internal_id | ||
| UNION ALL | ||
| SELECT | ||
| concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, | ||
| event_info as variant, | ||
| 'structural_variant' as variant_type, | ||
| gene1.hugo_gene_symbol as hugo_gene_symbol, | ||
| gene_panel.stable_id as gene_panel_stable_id, | ||
| cs.cancer_study_identifier as cancer_study_identifier, | ||
| gp.stable_id as genetic_profile_stable_id | ||
| FROM | ||
| structural_variant sv | ||
| INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id | ||
| INNER JOIN sample s ON sv.sample_id = s.internal_id | ||
| INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id | ||
| INNER JOIN gene gene1 ON sv.site1_entrez_gene_id = gene1.entrez_gene_id | ||
| INNER JOIN sample_profile on s.internal_id = sample_profile.sample_id | ||
| INNER JOIN gene_panel on sample_profile.panel_id = gene_panel.internal_id; |
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