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use regular views instead of materialized views (#10793)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,144 @@ | ||
| DROP VIEW IF EXISTS sample_clinical_attribute_numeric_view; | ||
| DROP VIEW IF EXISTS sample_clinical_attribute_categorical_view; | ||
| DROP VIEW IF EXISTS patient_clinical_attribute_numeric_view; | ||
| DROP VIEW IF EXISTS patient_clinical_attribute_categorical_view; | ||
| DROP VIEW IF EXISTS sample_view; | ||
| DROP VIEW IF EXISTS sample_list_view; | ||
| DROP VIEW IF EXISTS genomic_event_view; | ||
|
|
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| CREATE VIEW sample_clinical_attribute_numeric_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, | ||
| concat(cs.cancer_study_identifier, '_', p.stable_id) as patient_unique_id, | ||
| clinical_sample.attr_id as attribute_name, | ||
| cast(clinical_sample.attr_value as float) as attribute_value, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM cancer_study cs | ||
| INNER JOIN patient p on cs.cancer_study_id = p.cancer_study_id | ||
| INNER JOIN sample s on p.internal_id = s.patient_id | ||
| INNER JOIN clinical_sample ON s.internal_id = clinical_sample.internal_id | ||
| WHERE match(clinical_sample.attr_value, '^[\d\.]+$'); | ||
|
|
||
| CREATE VIEW sample_clinical_attribute_categorical_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, | ||
| concat(cs.cancer_study_identifier, '_', p.stable_id) as patient_unique_id, | ||
| cl.attr_id as attribute_name, | ||
| cl.attr_value as attribute_value, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM cancer_study cs | ||
| INNER JOIN patient p on cs.cancer_study_id = p.cancer_study_id | ||
| INNER JOIN sample s on p.internal_id = s.patient_id | ||
| INNER JOIN clinical_sample cl on s.internal_id = cl.internal_id | ||
| WHERE NOT match(cl.attr_value, '^[\d\.]+$'); | ||
|
|
||
| CREATE VIEW patient_clinical_attribute_numeric_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', p.stable_id) as patient_unique_id, | ||
| cp.attr_id as attribute_name, | ||
| cast(cp.attr_value as float) as attribute_value, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM cancer_study cs | ||
| INNER JOIN patient p on cs.cancer_study_id = p.cancer_study_id | ||
| INNER JOIN clinical_patient cp on p.internal_id = cp.internal_id | ||
| WHERE match(cp.attr_value, '^[\d\.]+$'); | ||
|
|
||
| CREATE VIEW patient_clinical_attribute_categorical_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', p.stable_id) as patient_unique_id, | ||
| cp.attr_id as attribute_name, | ||
| cp.attr_value as attribute_value, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM cancer_study cs | ||
| INNER JOIN patient p on cs.cancer_study_id = p.cancer_study_id | ||
| INNER JOIN clinical_patient cp on p.internal_id = cp.internal_id | ||
| WHERE NOT match(cp.attr_value, '^[\d\.]+$'); | ||
|
|
||
| CREATE VIEW sample_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, | ||
| base64Encode(sample.stable_id) as sample_unique_id_base64, | ||
| sample.stable_id as sample_stable_id, | ||
| concat(cs.cancer_study_identifier, '_', p.stable_id) as patient_unique_id, | ||
| p.stable_id as patient_stable_id, | ||
| base64Encode(p.stable_id) as patient_unique_id_base64, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM sample | ||
| INNER JOIN patient p on sample.patient_id = p.internal_id | ||
| INNER JOIN cancer_study cs on p.cancer_study_id = cs.cancer_study_id; | ||
|
|
||
| CREATE VIEW sample_list_view | ||
| AS | ||
| SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, | ||
| sl.stable_id as sample_list_stable_id, | ||
| sl.name as name, | ||
| cs.cancer_study_identifier as cancer_study_identifier | ||
| FROM sample_list as sl | ||
| INNER JOIN sample_list_list AS sll on sll.list_id = sl.list_id | ||
| INNER JOIN sample AS s on s.internal_id = sll.sample_id | ||
| INNER JOIN cancer_study cs on sl.cancer_study_id = cs.cancer_study_id; | ||
|
|
||
| CREATE VIEW genomic_event_view | ||
| AS | ||
| 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 | ||
| LEFT JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id | ||
| LEFT 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 | ||
| LEFT JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id | ||
| LEFT 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, | ||
| gp.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, | ||
| 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 | ||
| 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; |
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