Merge pull request #9 from clingen-data-model/dataset-preparation-pro…

…c-refactor

refactor clinvar-ingest dataset prep procs with versioning

scripts/ds-staging-table-procs/00-setup-translation-tables.sql

@@ -0,0 +1,174 @@
+-- CREATE OR REPLACE TABLE `clinvar_ingest.cvc_context_types` (code STRING, label STRING, display_order INT64);  
+
+-- INSERT INTO `clinvar_ingest.cvc_context_types` (code, label, display_order) 
+-- VALUES 
+--     ('gd','Germline Disease', 10),
+--     ('sc','Somatic Cancer',   20),
+--     ('pg','Pharmacogenomic',  30),
+--     ('ot','Other',            40);
+
+CREATE OR REPLACE TABLE `clinvar_ingest.clinvar_clinsig_types` (
+    code STRING, label STRING, significance INT64, 
+    clinvar_prop_type STRING, clinvar_code_order INT64, 
+    clinvar_desc_order INT64, cvc_prop_type STRING, 
+    cvc_code_order INT64, cvc_desc_order INT64, 
+    direction STRING, strength_code STRING, strength_label STRING, 
+    classification_code STRING, penetrance_level STRING
+);  
+INSERT INTO `clinvar_ingest.clinvar_clinsig_types` (
+    code, 
+    label, 
+    significance, 
+    clinvar_prop_type, 
+    clinvar_code_order, 
+    clinvar_desc_order, 
+    cvc_prop_type, 
+    cvc_code_order, 
+    cvc_desc_order, 
+    direction, 
+    strength_code, 
+    strength_label, 
+    classification_code, 
+    penetrance_level
+) 
+VALUES 
+    -- Pathogenic statements
+    ('b',       'Benign',                            0, '?',    30,  30, '?',  30,  30,  'refutes',   'cg000101', 'definitive',    'cg000001', null),
+    ('lb',      'Likely benign',                     0, '?',    31,  31, '?',  31,  31,  'refutes',   'cg000102', 'likely',        'cg000002', null),
+    ('b/lb',    'Benign/Likely benign',              0, '?',    32,  32, '?',  32,  32,  'refutes',   'cg000102', 'likely',        'cg000003', null),
+    ('vus',     'Uncertain significance',            1, '?',    20,  20, '?',  20,  20,  'none',      'cg000103', 'inconclusive',  'cg000004', null),
+    ('ura',     'Uncertain risk allele',             1, '?',    21,  21, '?',  21,  21,  'none',      'cg000103', 'inconclusive',  'cg000005', 'risk allele'),
+    ('p',       'Pathogenic',                        2, '?',    10,  10, '?',  10,  10,  'supports',  'cg000101', 'definitive',    'cg000006', null),
+    ('lp',      'Likely pathogenic',                 2, '?',    11,  11, '?',  11,  11,  'supports',  'cg000102', 'likely',        'cg000007', null),
+    ('p/lp',    'Pathogenic/Likely pathogenic',      2, '?',    12,  12, '?',  12,  12,  'supports',  'cg000102', 'likely',        'cg000008', null),
+    ('p-lp',    'Pathogenic, low penetrance',        2, '?',    13,  13, '?',  13,  13,  'supports',  'cg000101', 'definitive',    'cg000009', 'low'),
+    ('lp-lp',   'Likely pathogenic, low penetrance', 2, '?',    14,  14, '?',  14,  14,  'supports',  'cg000102', 'likely',        'cg000010', 'low'),
+    ('era',     'Established risk allele',           2, '?',    15,  15, '?',  15,  15,  'supports',  'cg000101', 'definitive',    'cg000011', 'risk allele'),
+    ('lra',     'Likely risk allele',                2, '?',    16,  16, '?',  16,  16,  'supports',  'cg000102', 'likely',        'cg000012', 'risk allele'),
+    ('cdfs',    'conflicting data from submitters',  1, '?',    40,  40, '?',  40,  40,  'none',      'cg000103', 'inconclusive',  'cg000013', null),
+    -- ClinVarDrugResponse statements
+    ('dr',      'drug response',                     2, 'dr',      130, 130, 'dr',   130, 130, 'supports',  'cg000100', 'not specified', 'cg000014', null),
+    -- ClinVarNonAssertion statements
+    ('np',      'not provided',                      0, '?',      140, 140, 'oth',  140, 140, 'none',      'cg000100', 'not specified', 'cg000015', null),
+    -- ClinVarOther statements
+    ('rf',      'risk factor',                       2, 'rf',      170, 170, 'oth',  170, 170, 'none',      'cg000100', 'not specified', 'cg000016', null),
+    ('aff',     'Affects',                           2, 'aff',     100, 100, 'oth',  100, 100, 'none',      'cg000100', 'not specified', 'cg000017', null),
+    ('assoc',   'association',                       2, 'assoc',   110, 110, 'oth',  110, 110, 'none',      'cg000100', 'not specified', 'cg000018', null),
+    ('assocnf', 'association not found',             0, 'assoc',   111, 111, 'oth',  111, 111, 'none',      'cg000100', 'not specified', 'cg000019', null),
+    ('cs',      'confers sensitivity',               2, 'cs',      120, 120, 'oth',  120, 120, 'none',      'cg000100', 'not specified', 'cg000020', null),
+    ('oth',     'other',                             0, 'oth',     150, 150, 'oth',  150, 150, 'none',      'cg000100', 'not specified', 'cg000021', null),
+    ('protect', 'protective',                        0, 'protect', 160, 160, 'oth',  160, 160, 'none',      'cg000100', 'not specified', 'cg000022', null),
+    -- SomaticImpact
+    ('t1', 'Tier I - Strong',                        2, 'somatic', 10, 10, 'somatic', 10, 10,  'supports',  'cg000100', 'definitive',    'cg000023', null),
+    ('t2', 'Tier II - Potential',                    2, 'somatic', 11, 11, 'somatic', 11, 11,  'supports',  'cg000102', 'likely',        'cg000024', null),
+    ('t3', 'Tier III - Unknown',                     1, 'somatic', 20, 20, 'somatic', 20, 20,  'none',      'cg000103', 'inconclusive',  'cg000025', null),
+    ('t4', 'Tier IV - Benign/Likely benign',         0, 'somatic', 32, 32, 'somatic', 32, 32,  'refutes',   'cg000102', 'likely',        'cg000026', null),
+    -- Oncogenic
+    ('o',       'Oncogenic',                         2, '?',    10,  10, 'onco',   10, 10,  'supports',  'cg000101', 'definitive',    'cg000027', null),
+    ('lo',      'Likely oncogenic',                  2, '?',    11,  11, 'onco',   11, 11,  'supports',  'cg000102', 'likely',        'cg000028', null);
+
+
+CREATE OR REPLACE TABLE `clinvar_ingest.clinvar_proposition_types` (code STRING, label STRING, display_order INT64);  
+INSERT INTO `clinvar_ingest.clinvar_proposition_types` (code, label, display_order) 
+VALUES 
+    ('path', 'Pathogenicity', 10),
+    ('dr',   'DrugResponse', 11),  
+    ('oth',  'Other', 12),
+    ('somatic', 'SomaticClinicalImpact', 20),
+    ('onco', 'Oncogenicity', 30);
+
+    -- ('rf',   'RiskFactor',30),
+    -- ('np',   'NotProvided',60),
+    -- put affects, associated, confresSensitivity and protect in other category
+    -- ('aff',  'Affects',20),
+    -- ('assoc','Associated',30),
+    -- ('cs',   'ConfersSensitivity',40),
+    -- ('protect','Protective',80),
+
+
+CREATE OR REPLACE TABLE `clinvar_ingest.scv_clinsig_map` (scv_term STRING, cv_clinsig_type STRING);  
+INSERT INTO `clinvar_ingest.scv_clinsig_map` (scv_term, cv_clinsig_type) VALUES 
+    ('affects', 'aff'),
+    ('associated with leiomyomas', 'np'),
+    ('association', 'assoc'),
+    ('association not found', 'assocnf'),
+    ('benign', 'b'),
+    ('benign/likely benign', 'b/lb'),
+    ('cancer', 'oth'),
+    ('confers sensitivity', 'cs'),
+    ('conflicting data from submitters', 'cdfs'),
+    ('drug response', 'dr'),
+    ('drug-response', 'dr'),
+    ('established risk allele', 'era'),
+    ('likely benign', 'lb'),
+    ('likely oncogenic', 'lo'),
+    ('likely pathogenic', 'lp'),
+    ('likely pathogenic - adrenal bilateral pheochromocy', 'lp'),
+    ('likely pathogenic - adrenal pheochromocytoma', 'lp'),
+    ('likely pathogenic, low penetrance', 'lp-lp'),
+    ('likely risk allele', 'lra'),
+    ('moderate', 'p'),
+    ('mut', 'p'),
+    ('mutation', 'p'),
+    ('no known pathogenicity', 'b'),
+    ('non-pathogenic', 'b'),
+    ('not provided', 'np'),
+    ('oncogenic', 'o'),
+    ('other', 'oth'),
+    ('pathogenic', 'p'),
+    ('pathogenic, low penetrance', 'p-lp'),
+    ('pathogenic variant for bardet-biedl syndrome', 'p'),
+    ('pathogenic/likely pathogenic', 'p/lp'),
+    ('pathologic', 'p'),
+    ('poly', 'b'),
+    ('probable-non-pathogenic', 'lb'), 
+    ('probable-pathogenic', 'lp'),
+    ('probably not pathogenic', 'lb'),
+    ('probably pathogenic', 'lp'),
+    ('protective', 'protect'),
+    ('risk factor', 'rf'),
+    ('suspected benign', 'lb'),
+    ('suspected pathogenic', 'lp'),
+    ('tier i - strong', 't1'),
+    ('tier ii - potential', 't2'),
+    ('tier iii - unknown', 't3'),
+    ('tier iv - benign/likely benign', 't4'),
+    ('uncertain', 'vus'),
+    ('uncertain risk allele', 'ura'),
+    ('uncertain significance', 'vus'),
+    ('unknown', 'vus'),
+    ('unknown significance', 'vus'),
+    ('untested', 'np'),
+    ('variant of unknown significance', 'vus'),
+    ('vsb', 'lb'),
+    ('vlb', 'lb'),
+    ('vous', 'vus'),
+    ('vus', 'vus'),
+    ('vlm', 'lp'),
+    ('uncertain significance: likely benign', 'vus'),
+    ('uncertain significance: likely pathogenic','vus'),
+    ('na','oth');
+
+CREATE OR REPLACE TABLE `clinvar_ingest.clinvar_status` (rank INT64, label STRING, scv BOOL);
+INSERT INTO `clinvar_ingest.clinvar_status` (rank, label, scv) 
+VALUES
+    (-3, 'no classifications from unflagged records', FALSE),
+    (-3, 'flagged submission', TRUE),
+    (-2, 'no interpretation for the single variant', FALSE),
+    (-2, 'no classification for the single variant', FALSE),
+    (-1, 'no assertion provided', TRUE),
+    (-1, 'no classification provided', TRUE),
+    (-1, 'not classified by submitter', FALSE),
+    (0,  'no assertion criteria provided', TRUE),
+    (1,  'criteria provided, single submitter', TRUE),
+    (1,  'classified by single submitter', FALSE),
+    (1,  'criteria provided, conflicting interpretations', FALSE),
+    (1,  'criteria provided, conflicting classifications', FALSE),
+    (2,  'criteria provided, multiple submitters, no conflicts', FALSE),
+    (2,  'criteria provided, multiple submitters', FALSE),
+    (2,  'classified by multiple submitters', FALSE),
+    (3,  'reviewed by expert panel', TRUE),
+    (4,  'practice guideline', TRUE),
+    (4,  'reviewed by professional society', FALSE) ;
+
+

scripts/ds-staging-table-procs/01-validate-ds-terms-v1-proc.sql

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+CREATE OR REPLACE PROCEDURE `clinvar_ingest.validate_dataset_terms_v1`(
+  schema_name STRING
+)
+BEGIN
+  -- Declare variables to hold results and error messages
+  DECLARE scv_classification_terms ARRAY<STRING>;
+  DECLARE scv_review_status_terms ARRAY<STRING>;
+  DECLARE combined_issues STRING;
+
+  -- Check for new interpretation_descriptions in clinical_assertion
+  EXECUTE IMMEDIATE FORMAT("""
+      SELECT ARRAY_AGG(DISTINCT ca.interpretation_description)
+      FROM `%s.clinical_assertion` ca
+      LEFT JOIN `clinvar_ingest.scv_clinsig_map` map
+      ON map.scv_term = LOWER(IFNULL(ca.interpretation_description,'not provided'))
+      WHERE map.scv_term IS NULL
+  """, schema_name) INTO scv_classification_terms;
+
+  -- Check for new review_status terms in clinical_assertion
+  EXECUTE IMMEDIATE FORMAT("""
+      SELECT ARRAY_AGG(DISTINCT ca.review_status)
+      FROM `%s.clinical_assertion` ca
+      LEFT JOIN `clinvar_ingest.clinvar_status` cs
+      ON cs.label = LOWER(ca.review_status)
+      WHERE cs.label IS NULL
+  """, schema_name) INTO scv_review_status_terms;
+
+  -- Construct a combined error message if there are issues
+  SET combined_issues = '';
+
+  IF scv_classification_terms IS NOT NULL AND ARRAY_LENGTH(scv_classification_terms) > 0 THEN
+    SET combined_issues = FORMAT("""
+      New SCV classification terms found: [%s].
+      NOTE: Add scv_clinsig_map records to the '00-setup-translation-tables.sql' script and update, then rerun this script.
+    """, ARRAY_TO_STRING(scv_classification_terms, ', '));
+  END IF;
+
+  IF scv_review_status_terms IS NOT NULL AND ARRAY_LENGTH(scv_review_status_terms) > 0 THEN
+    SET combined_issues = FORMAT("""
+      %s
+      New SCV review status terms found: [%s].
+      NOTE: Add clinvar_status records to the '00-setup-translation-tables.sql' script and update, then rerun this script.
+    """, combined_issues, ARRAY_TO_STRING(scv_review_status_terms, ', '));
+  END IF;
+
+  -- Raise a single exception if there are any issues
+  IF combined_issues != '' THEN
+    RAISE USING message = combined_issues;
+  END IF;
+
+END;