R/x_print_concept_hierarchy.R
print_concept_hierarchy.RdIf a level of the hierarchy has more than 10 concepts, the first 10 are printed with an ellipses is included to indicate only the first 10 rows are shown.
print_concept_hierarchy( concept_obj, level_of_separation_type = c("max", "min"), write_schema = "patelm9", vocab_schema = "omop_vocabulary", conn, conn_fun = "connectAthena()", cache_only = FALSE, skip_cache = FALSE, override_cache = FALSE, verbose = TRUE, render_sql = TRUE, render_only = FALSE )
| concept_obj | Concept class object or a concept id. |
|---|
#> [2021-05-26 16:07:16] Connected to 'athena'#>#>#> ✓ Concept Id is a valid integer#>#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────#> ✓ Concept Id `1308216` found in Concept Table#>#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────#>#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────concept_obj#> An object of class "concept" #> Slot "concept_id": #> [1] 1308216 #> #> Slot "concept_name": #> [1] "lisinopril" #> #> Slot "concept_synonym_names": #> [1] "" #> #> Slot "maps_to_concept_names": #> [1] "lisinopril" #> #> Slot "domain_id": #> [1] "Drug" #> #> Slot "vocabulary_id": #> [1] "RxNorm" #> #> Slot "concept_class_id": #> [1] "Ingredient" #> #> Slot "standard_concept": #> [1] "S" #> #> Slot "concept_code": #> [1] "29046" #> #> Slot "valid_start_date": #> [1] "1970-01-01" #> #> Slot "valid_end_date": #> [1] "2099-12-31" #> #> Slot "invalid_reason": #> [1] NA #>print_concept_hierarchy(conn = conn, concept_obj = concept_obj)#> [2021-05-26 16:07:16] Loading Cache... #> [2021-05-26 16:07:16] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (1308216) #> [2021-05-26 16:07:16] Cached resultset found... #> [2021-05-26 16:07:16] Target column: concept_hierarchy_id #> [2021-05-26 16:07:16] Dropping patelm9.V20210526160716... #> [2021-05-26 16:07:16] ✓ Open connection #> [2021-05-26 16:07:16] ✓ JDBC connection #> [2021-05-26 16:07:16] SQL: DROP TABLE IF EXISTS patelm9.V20210526160716; #> [2021-05-26 16:07:16] Sending... #> [2021-05-26 16:07:16] Sending...complete #> [2021-05-26 16:07:16] Dropping patelm9.V20210526160716...complete #> [2021-05-26 16:07:16] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:16] Writing patelm9.V20210526160716... #> [2021-05-26 16:07:16] Writing patelm9.V20210526160716...complete #> [2021-05-26 16:07:16] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160716 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:17] Querying... #> [2021-05-26 16:07:17] Querying...complete #> [2021-05-26 16:07:17] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160716... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160716; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160716...complete #> [2021-05-26 16:07:17] Target column: ancestor_concept_id #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717... #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: SELECT a.*, b.* FROM patelm9.V20210526160717 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:17] Querying... #> [2021-05-26 16:07:17] Querying...complete #> [2021-05-26 16:07:17] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] Target column: concept_hierarchy_id #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717... #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160717 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:17] Querying... #> [2021-05-26 16:07:17] Querying...complete #> [2021-05-26 16:07:17] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] Target column: descendant_concept_id #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717... #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: SELECT a.*, b.* FROM patelm9.V20210526160717 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:17] Querying... #> [2021-05-26 16:07:17] Querying...complete #> [2021-05-26 16:07:17] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [V] [C] 21601237 CARDIOVASCULAR SYSTEM [ATC C] [Drug] [ATC 1st] #> [V] [C] 21601782 AGENTS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM [ATC C09] [Drug] [ATC 2nd] #> [V] [C] 21601487 Thiazides, combinations with other drugs [ATC C03AX] [Drug] [ATC 4th] #> [V] [C] 21601783 ACE INHIBITORS, PLAIN [ATC C09A] [Drug] [ATC 3rd] #> [V] [C] 21601801 ACE INHIBITORS, COMBINATIONS [ATC C09B] [Drug] [ATC 3rd] #> [V] [C] 21601898 LIPID MODIFYING AGENTS, COMBINATIONS [ATC C10B] [Drug] [ATC 3rd] #> [V] [C] 21601488 hydrochlorothiazide, combinations [ATC C03AX01] [Drug] [ATC 5th] #> [V] [C] 21601784 ACE inhibitors, plain [ATC C09AA] [Drug] [ATC 4th] #> [V] [C] 21601802 ACE inhibitors and diuretics [ATC C09BA] [Drug] [ATC 4th] #> [V] [C] 21601815 ACE inhibitors and calcium channel blockers [ATC C09BB] [Drug] [ATC 4th] #> [V] [C] 21601903 HMG CoA reductase inhibitors, other combinations [ATC C10BX] [Drug] [ATC 4th] #> *[V] [S] 1308216 lisinopril [RxNorm 29046] [Drug] [Ingredient] #> [V] [S] 40828597 Lisinopril 2.5 MG [LISINOPRIL TEVA] [RxNorm Extension OMOP2026559] [Drug] [Branded Drug Comp] #> [V] [S] 43852073 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG [Lisodura] [RxNorm Extension OMOP788577] [Drug] [Branded Drug Comp] #> [V] [S] 21151219 Hydrochlorothiazide 12.5 MG / Lisinopril 10 MG [Lisicostad] [RxNorm Extension OMOP373878] [Drug] [Branded Drug Comp] #> [V] [S] 19047477 lisinopril 40 MG [Prinivil] [RxNorm 567581] [Drug] [Branded Drug Comp] #> [V] [S] 40859888 Lisinopril 20 MG [Lisi Abz] [RxNorm Extension OMOP2057850] [Drug] [Branded Drug Comp] #> [V] [S] 43210520 Lisinopril 5 MG [LISINOPRIL RPG] [RxNorm Extension OMOP499198] [Drug] [Branded Drug Comp] #> [V] [S] 41078259 Lisinopril 20 MG [Lisinopril 1a Pharma] [RxNorm Extension OMOP2276221] [Drug] [Branded Drug Comp] #> [V] [S] 43605575 Lisinopril 10 MG [Lisinopril Stada] [RxNorm Extension OMOP682868] [Drug] [Branded Drug Comp] #> [V] [S] 35157486 Lisinopril 20 MG [Longes] [RxNorm Extension OMOP4814492] [Drug] [Branded Drug Comp] #> [V] [S] 41015894 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG [Lisihexal] [RxNorm Extension OMOP2213856] [Drug] [Branded Drug Comp] #> ... #> [V] [S] 41144467 Lisinopril Oral Tablet [Lisi Lichtenstein] [RxNorm Extension OMOP2342429] [Drug] [Branded Drug Form] #> [V] [S] 43166720 Lisinopril Oral Tablet [LISINOPRIL SANDOZ] [RxNorm Extension OMOP499088] [Drug] [Branded Drug Form] #> [V] [S] 41081631 Lisinopril Oral Tablet [Lisibeta] [RxNorm Extension OMOP2279593] [Drug] [Branded Drug Form] #> [V] [S] 43177787 Hydrochlorothiazide / Lisinopril Oral Tablet [LISINOPRIL HYDROCHLOROTHIAZIDE ARROW LAB] [RxNorm Extension OMOP500554] [Drug] [Branded Drug Form] #> [V] [S] 43690171 Hydrochlorothiazide / Lisinopril Oral Tablet [Lisinopril Hct Aaa] [RxNorm Extension OMOP788237] [Drug] [Branded Drug Form] #> [V] [S] 43695624 Lisinopril Oral Tablet [Lino] [RxNorm Extension OMOP682620] [Drug] [Branded Drug Form] #> [V] [S] 43294275 Lisinopril Oral Tablet [Lisinotrust] [RxNorm Extension OMOP536736] [Drug] [Branded Drug Form] #> [V] [S] 43821506 Lisinopril Oral Tablet [Lisinopril Abz] [RxNorm Extension OMOP682628] [Drug] [Branded Drug Form] #> [V] [S] 37593439 Lisinopril Oral Tablet [Lisinopril Puren] [RxNorm Extension OMOP4782876] [Drug] [Branded Drug Form] #> [V] [S] 41112854 Lisinopril Oral Tablet [Lisi Hennig] [RxNorm Extension OMOP2310816] [Drug] [Branded Drug Form] #> ... #> [V] [S] 43188717 Lisinopril 20 MG Oral Tablet [LISINOPRIL CRISTERS] [RxNorm Extension OMOP500061] [Drug] [Branded Drug] #> [V] [S] 44099063 Lisinopril 20 MG Oral Tablet [Mint-Lisinopril] [RxNorm Extension OMOP1093694] [Drug] [Branded Drug] #> [V] [S] 40999884 Lisinopril 30 MG Oral Tablet [Lisinopril 1a Pharma] [RxNorm Extension OMOP2197846] [Drug] [Branded Drug] #> [V] [S] 43210545 Lisinopril 20 MG Oral Tablet [LISINOPRIL ZYDUS] [RxNorm Extension OMOP500426] [Drug] [Branded Drug] #> [V] [S] 44111838 Lisinopril 20 MG Oral Tablet [Act Lisinopril] [RxNorm Extension OMOP1106469] [Drug] [Branded Drug] #> [V] [S] 41280508 Lisinopril 10 MG Oral Tablet [Lisinopril 1a Pharma] [RxNorm Extension OMOP2478470] [Drug] [Branded Drug] #> [V] [S] 43785460 Lisinopril 5 MG Oral Tablet [Lisodura] [RxNorm Extension OMOP682753] [Drug] [Branded Drug] #> [V] [S] 40906111 Lisinopril 5 MG Oral Tablet [Aceday] [RxNorm Extension OMOP2104073] [Drug] [Branded Drug] #> [V] [S] 43133675 Lisinopril 20 MG Oral Tablet [LISINOPRIL QUALIMED] [RxNorm Extension OMOP500244] [Drug] [Branded Drug] #> [V] [S] 43283405 Lisinopril 10 MG Oral Tablet [Lisoril] [RxNorm Extension OMOP536957] [Drug] [Branded Drug] #> ... #> [V] [S] 41218712 Lisinopril 20 MG Oral Tablet [Lisinopril Heumann] Box of 50 [RxNorm Extension OMOP2416674] [Drug] [Branded Drug Box] #> [V] [S] 43605572 Lisinopril 20 MG Oral Tablet [Lisi Lichtenstein] by Winthrop [RxNorm Extension OMOP682828] [Drug] [Marketed Product] #> [V] [S] 41187492 Lisinopril 20 MG Oral Tablet [Lisinopril Q] Box of 100 [RxNorm Extension OMOP2385454] [Drug] [Branded Drug Box] #> [V] [S] 40938805 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet [Zestoretic] Box of 98 [RxNorm Extension OMOP2136767] [Drug] [Branded Drug Box] #> [V] [S] 40844022 Lisinopril 20 MG Oral Tablet [Lisibeta] Box of 30 [RxNorm Extension OMOP2041984] [Drug] [Branded Drug Box] #> [V] [S] 41063402 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet [Lisinopril Basics Plus] Box of 25 [RxNorm Extension OMOP2261364] [Drug] [Branded Drug Box] #> [V] [S] 21033379 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet by A A H [RxNorm Extension OMOP373820] [Drug] [Marketed Product] #> [V] [S] 35159665 Lisinopril 5 MG Oral Tablet by Pfizer [RxNorm Extension OMOP4816648] [Drug] [Marketed Product] #> [V] [S] 21033354 Lisinopril 20 MG Oral Tablet by Relonchem [RxNorm Extension OMOP373441] [Drug] [Marketed Product] #> [V] [S] 43713462 Lisinopril 10 MG Oral Tablet [Lisinopril Abz] by AbZ-Pharma [RxNorm Extension OMOP682887] [Drug] [Marketed Product] #> ... #> [V] [S] 21151214 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet Box of 28 by Alliance [RxNorm Extension OMOP373833] [Drug] [Marketed Product] #> [V] [S] 43294291 Lisinopril 10 MG Oral Tablet Box of 84 by Ipca [RxNorm Extension OMOP536937] [Drug] [Marketed Product] #> [V] [S] 43288882 Lisinopril 2.5 MG Oral Tablet Box of 56 by Dr Reddy's [RxNorm Extension OMOP536981] [Drug] [Marketed Product] #> [V] [S] 21072814 Lisinopril 2.5 MG Oral Tablet [Carace] Box of 28 by Bristol Myers Squibb [RxNorm Extension OMOP373741] [Drug] [Marketed Product] #> [V] [S] 41228801 Lisinopril 5 MG Oral Tablet [Lisibeta] Box of 30 by Betapharm [RxNorm Extension OMOP2426763] [Drug] [Marketed Product] #> [V] [S] 41197743 Lisinopril 20 MG Oral Tablet [Lisinopril 1a Pharma] Box of 100 by 1 A [RxNorm Extension OMOP2395705] [Drug] [Marketed Product] #> [V] [S] 40885296 Lisinopril 20 MG Oral Tablet [Lisinopril Heumann] Box of 100 by Heunet [RxNorm Extension OMOP2083258] [Drug] [Marketed Product] #> [V] [S] 40885967 Hydrochlorothiazide 12.5 MG / Lisinopril 10 MG Oral Tablet Box of 100 by AbZ-Pharma [RxNorm Extension OMOP2083929] [Drug] [Marketed Product] #> [V] [S] 21112000 Lisinopril 2.5 MG Oral Tablet Box of 28 by TEVA [RxNorm Extension OMOP373733] [Drug] [Marketed Product] #> [V] [S] 41260299 Hydrochlorothiazide 12.5 MG / Lisinopril 10 MG Oral Tablet [Lisinopril Basics Plus] Box of 100 by Basics [RxNorm Extension OMOP2458261] [Drug] [Marketed Product] #> ...print_concept_hierarchy(conn = conn, concept_obj = concept_obj, level_of_separation_type = "min")#> [2021-05-26 16:07:17] Loading Cache... #> [2021-05-26 16:07:17] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (1308216) #> [2021-05-26 16:07:17] Cached resultset found... #> [2021-05-26 16:07:17] Target column: concept_hierarchy_id #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717... #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160717 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:17] Querying... #> [2021-05-26 16:07:17] Querying...complete #> [2021-05-26 16:07:17] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] Target column: ancestor_concept_id #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:17] ✓ Open connection #> [2021-05-26 16:07:17] ✓ JDBC connection #> [2021-05-26 16:07:17] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:17] Sending... #> [2021-05-26 16:07:17] Sending...complete #> [2021-05-26 16:07:17] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:17] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:17] Writing patelm9.V20210526160717... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160717...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.* FROM patelm9.V20210526160717 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160717... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160717; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160717...complete #> [2021-05-26 16:07:18] Target column: concept_hierarchy_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] Target column: descendant_concept_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.* FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [V] [C] 21601237 CARDIOVASCULAR SYSTEM [ATC C] [Drug] [ATC 1st] #> [V] [C] 21601782 AGENTS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM [ATC C09] [Drug] [ATC 2nd] #> [V] [C] 21601487 Thiazides, combinations with other drugs [ATC C03AX] [Drug] [ATC 4th] #> [V] [C] 21601783 ACE INHIBITORS, PLAIN [ATC C09A] [Drug] [ATC 3rd] #> [V] [C] 21601801 ACE INHIBITORS, COMBINATIONS [ATC C09B] [Drug] [ATC 3rd] #> [V] [C] 21601898 LIPID MODIFYING AGENTS, COMBINATIONS [ATC C10B] [Drug] [ATC 3rd] #> [V] [C] 21601488 hydrochlorothiazide, combinations [ATC C03AX01] [Drug] [ATC 5th] #> [V] [C] 21601784 ACE inhibitors, plain [ATC C09AA] [Drug] [ATC 4th] #> [V] [C] 21601802 ACE inhibitors and diuretics [ATC C09BA] [Drug] [ATC 4th] #> [V] [C] 21601815 ACE inhibitors and calcium channel blockers [ATC C09BB] [Drug] [ATC 4th] #> [V] [C] 21601903 HMG CoA reductase inhibitors, other combinations [ATC C10BX] [Drug] [ATC 4th] #> *[V] [S] 1308216 lisinopril [RxNorm 29046] [Drug] [Ingredient] #> [V] [S] 40828597 Lisinopril 2.5 MG [LISINOPRIL TEVA] [RxNorm Extension OMOP2026559] [Drug] [Branded Drug Comp] #> [V] [S] 43852073 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG [Lisodura] [RxNorm Extension OMOP788577] [Drug] [Branded Drug Comp] #> [V] [S] 21151219 Hydrochlorothiazide 12.5 MG / Lisinopril 10 MG [Lisicostad] [RxNorm Extension OMOP373878] [Drug] [Branded Drug Comp] #> [V] [S] 19047477 lisinopril 40 MG [Prinivil] [RxNorm 567581] [Drug] [Branded Drug Comp] #> [V] [S] 40859888 Lisinopril 20 MG [Lisi Abz] [RxNorm Extension OMOP2057850] [Drug] [Branded Drug Comp] #> [V] [S] 43210520 Lisinopril 5 MG [LISINOPRIL RPG] [RxNorm Extension OMOP499198] [Drug] [Branded Drug Comp] #> [V] [S] 41078259 Lisinopril 20 MG [Lisinopril 1a Pharma] [RxNorm Extension OMOP2276221] [Drug] [Branded Drug Comp] #> [V] [S] 43605575 Lisinopril 10 MG [Lisinopril Stada] [RxNorm Extension OMOP682868] [Drug] [Branded Drug Comp] #> [V] [S] 35157486 Lisinopril 20 MG [Longes] [RxNorm Extension OMOP4814492] [Drug] [Branded Drug Comp] #> [V] [S] 41015894 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG [Lisihexal] [RxNorm Extension OMOP2213856] [Drug] [Branded Drug Comp] #> ... #> [V] [S] 43188717 Lisinopril 20 MG Oral Tablet [LISINOPRIL CRISTERS] [RxNorm Extension OMOP500061] [Drug] [Branded Drug] #> [V] [S] 44099063 Lisinopril 20 MG Oral Tablet [Mint-Lisinopril] [RxNorm Extension OMOP1093694] [Drug] [Branded Drug] #> [V] [S] 40999884 Lisinopril 30 MG Oral Tablet [Lisinopril 1a Pharma] [RxNorm Extension OMOP2197846] [Drug] [Branded Drug] #> [V] [S] 43210545 Lisinopril 20 MG Oral Tablet [LISINOPRIL ZYDUS] [RxNorm Extension OMOP500426] [Drug] [Branded Drug] #> [V] [S] 35869279 lisinopril 10 MG Oral Capsule [Yijikang] [RxNorm Extension OMOP5025606] [Drug] [Branded Drug] #> [V] [S] 44111838 Lisinopril 20 MG Oral Tablet [Act Lisinopril] [RxNorm Extension OMOP1106469] [Drug] [Branded Drug] #> [V] [S] 41280508 Lisinopril 10 MG Oral Tablet [Lisinopril 1a Pharma] [RxNorm Extension OMOP2478470] [Drug] [Branded Drug] #> [V] [S] 43785460 Lisinopril 5 MG Oral Tablet [Lisodura] [RxNorm Extension OMOP682753] [Drug] [Branded Drug] #> [V] [S] 40906111 Lisinopril 5 MG Oral Tablet [Aceday] [RxNorm Extension OMOP2104073] [Drug] [Branded Drug] #> [V] [S] 43133675 Lisinopril 20 MG Oral Tablet [LISINOPRIL QUALIMED] [RxNorm Extension OMOP500244] [Drug] [Branded Drug] #> ... #> [V] [S] 41218712 Lisinopril 20 MG Oral Tablet [Lisinopril Heumann] Box of 50 [RxNorm Extension OMOP2416674] [Drug] [Branded Drug Box] #> [V] [S] 21151214 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet Box of 28 by Alliance [RxNorm Extension OMOP373833] [Drug] [Marketed Product] #> [V] [S] 43294291 Lisinopril 10 MG Oral Tablet Box of 84 by Ipca [RxNorm Extension OMOP536937] [Drug] [Marketed Product] #> [V] [S] 43605572 Lisinopril 20 MG Oral Tablet [Lisi Lichtenstein] by Winthrop [RxNorm Extension OMOP682828] [Drug] [Marketed Product] #> [V] [S] 41187492 Lisinopril 20 MG Oral Tablet [Lisinopril Q] Box of 100 [RxNorm Extension OMOP2385454] [Drug] [Branded Drug Box] #> [V] [S] 43288882 Lisinopril 2.5 MG Oral Tablet Box of 56 by Dr Reddy's [RxNorm Extension OMOP536981] [Drug] [Marketed Product] #> [V] [S] 40938805 Hydrochlorothiazide 12.5 MG / Lisinopril 20 MG Oral Tablet [Zestoretic] Box of 98 [RxNorm Extension OMOP2136767] [Drug] [Branded Drug Box] #> [V] [S] 40844022 Lisinopril 20 MG Oral Tablet [Lisibeta] Box of 30 [RxNorm Extension OMOP2041984] [Drug] [Branded Drug Box] #> [V] [S] 21072814 Lisinopril 2.5 MG Oral Tablet [Carace] Box of 28 by Bristol Myers Squibb [RxNorm Extension OMOP373741] [Drug] [Marketed Product] #> [V] [S] 41228801 Lisinopril 5 MG Oral Tablet [Lisibeta] Box of 30 by Betapharm [RxNorm Extension OMOP2426763] [Drug] [Marketed Product] #> ...#>#> ── Is Concept Id Valid Integer? ────────────────────────────────────────────────#> ✓ Concept Id is a valid integer#>#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────#> ✓ Concept Id `4187868` found in Concept Table#>#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────#>#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────concept_obj#> An object of class "concept" #> Slot "concept_id": #> [1] 4187868 #> #> Slot "concept_name": #> [1] "pTis: Ductal carcinoma in situ (breast)" #> #> Slot "concept_synonym_names": #> [1] "Ductal carcinoma in situ (breast)|pTis: Ductal carcinoma in situ (breast) (finding)" #> #> Slot "maps_to_concept_names": #> [1] "pTis: Ductal carcinoma in situ (breast)" #> #> Slot "domain_id": #> [1] "Condition" #> #> Slot "vocabulary_id": #> [1] "SNOMED" #> #> Slot "concept_class_id": #> [1] "Clinical Finding" #> #> Slot "standard_concept": #> [1] "S" #> #> Slot "concept_code": #> [1] "373176000" #> #> Slot "valid_start_date": #> [1] "2002-07-31" #> #> Slot "valid_end_date": #> [1] "2099-12-31" #> #> Slot "invalid_reason": #> [1] NA #>print_concept_hierarchy(conn = conn, concept_obj = concept_obj)#> [2021-05-26 16:07:18] Loading Cache... #> [2021-05-26 16:07:18] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (4187868) #> [2021-05-26 16:07:18] Cached resultset found... #> [2021-05-26 16:07:18] Target column: concept_hierarchy_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] Target column: ancestor_concept_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.* FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] Target column: concept_hierarchy_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:18] Querying...complete #> [2021-05-26 16:07:18] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] Target column: descendant_concept_id #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:18] Sending... #> [2021-05-26 16:07:18] Sending...complete #> [2021-05-26 16:07:18] Dropping patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718... #> [2021-05-26 16:07:18] Writing patelm9.V20210526160718...complete #> [2021-05-26 16:07:18] ✓ Open connection #> [2021-05-26 16:07:18] ✓ JDBC connection #> [2021-05-26 16:07:18] SQL: SELECT a.*, b.* FROM patelm9.V20210526160718 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:18] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160718... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160718; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160718...complete #> [V] [S] 441840 Clinical finding [SNOMED 404684003] [Condition] [Clinical Finding] #> [V] [S] 4094294 Clinical history and observation findings [SNOMED 250171008] [Condition] [Clinical Finding] #> [V] [S] 4104314 Finding of lesion [SNOMED 300577008] [Condition] [Clinical Finding] #> [V] [S] 4216788 Tumor finding [SNOMED 395557000] [Condition] [Clinical Finding] #> [V] [S] 4300140 Tumor stage finding [SNOMED 385356007] [Condition] [Clinical Finding] #> [V] [S] 4295649 TNM tumor staging finding [SNOMED 385379008] [Condition] [Clinical Finding] #> [V] [S] 4300144 pT category finding [SNOMED 385385001] [Condition] [Clinical Finding] #> [V] [S] 4225738 pTis category [SNOMED 84921008] [Condition] [Clinical Finding] #> [V] [S] 4300154 Breast TNM finding [SNOMED 385417002] [Condition] [Clinical Finding] #> *[V] [S] 4187868 pTis: Ductal carcinoma in situ (breast) [SNOMED 373176000] [Condition] [Clinical Finding]print_concept_hierarchy(conn = conn, concept_obj = concept_obj, level_of_separation_type = "min")#> [2021-05-26 16:07:19] Loading Cache... #> [2021-05-26 16:07:19] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (4187868) #> [2021-05-26 16:07:19] Cached resultset found... #> [2021-05-26 16:07:19] Target column: concept_hierarchy_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: ancestor_concept_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.* FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: concept_hierarchy_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: descendant_concept_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.* FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [V] [S] 441840 Clinical finding [SNOMED 404684003] [Condition] [Clinical Finding] #> [V] [S] 4094294 Clinical history and observation findings [SNOMED 250171008] [Condition] [Clinical Finding] #> [V] [S] 4104314 Finding of lesion [SNOMED 300577008] [Condition] [Clinical Finding] #> [V] [S] 4216788 Tumor finding [SNOMED 395557000] [Condition] [Clinical Finding] #> [V] [S] 4300140 Tumor stage finding [SNOMED 385356007] [Condition] [Clinical Finding] #> [V] [S] 4295649 TNM tumor staging finding [SNOMED 385379008] [Condition] [Clinical Finding] #> [V] [S] 4300144 pT category finding [SNOMED 385385001] [Condition] [Clinical Finding] #> [V] [S] 4225738 pTis category [SNOMED 84921008] [Condition] [Clinical Finding] #> [V] [S] 4300154 Breast TNM finding [SNOMED 385417002] [Condition] [Clinical Finding] #> *[V] [S] 4187868 pTis: Ductal carcinoma in situ (breast) [SNOMED 373176000] [Condition] [Clinical Finding]#>#> ── Is Concept Id Valid Integer? ────────────────────────────────────────────────#> ✓ Concept Id is a valid integer#>#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────#> ✓ Concept Id `319835` found in Concept Table#>#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────#>#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────concept_obj#> An object of class "concept" #> Slot "concept_id": #> [1] 319835 #> #> Slot "concept_name": #> [1] "Congestive heart failure" #> #> Slot "concept_synonym_names": #> [1] "CCF - Congestive cardiac failure|CHF - Congestive heart failure|Congestive cardiac failure|Congestive heart disease|Congestive heart failure (disorder)" #> #> Slot "maps_to_concept_names": #> [1] "Congestive heart failure" #> #> Slot "domain_id": #> [1] "Condition" #> #> Slot "vocabulary_id": #> [1] "SNOMED" #> #> Slot "concept_class_id": #> [1] "Clinical Finding" #> #> Slot "standard_concept": #> [1] "S" #> #> Slot "concept_code": #> [1] "42343007" #> #> Slot "valid_start_date": #> [1] "2002-01-31" #> #> Slot "valid_end_date": #> [1] "2099-12-31" #> #> Slot "invalid_reason": #> [1] NA #>print_concept_hierarchy(conn = conn, concept_obj = concept_obj)#> [2021-05-26 16:07:19] Loading Cache... #> [2021-05-26 16:07:19] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (319835) #> [2021-05-26 16:07:19] Cached resultset found... #> [2021-05-26 16:07:19] Target column: concept_hierarchy_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: ancestor_concept_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.* FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: concept_hierarchy_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] Target column: descendant_concept_id #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719... #> [2021-05-26 16:07:19] Writing patelm9.V20210526160719...complete #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: SELECT a.*, b.* FROM patelm9.V20210526160719 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:19] Querying... #> [2021-05-26 16:07:19] Querying...complete #> [2021-05-26 16:07:19] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719... #> [2021-05-26 16:07:19] ✓ Open connection #> [2021-05-26 16:07:19] ✓ JDBC connection #> [2021-05-26 16:07:19] SQL: DROP TABLE IF EXISTS patelm9.V20210526160719; #> [2021-05-26 16:07:19] Sending... #> [2021-05-26 16:07:19] Sending...complete #> [2021-05-26 16:07:19] Dropping patelm9.V20210526160719...complete #> [V] [S] 441840 Clinical finding [SNOMED 404684003] [Condition] [Clinical Finding] #> [V] [S] 4042140 Finding by site [SNOMED 118234003] [Condition] [Clinical Finding] #> [V] [S] 4199402 Finding of body region [SNOMED 301857004] [Condition] [Clinical Finding] #> [V] [S] 4274025 Disease [SNOMED 64572001] [Condition] [Clinical Finding] #> [V] [S] 4047779 Disorder by body site [SNOMED 123946008] [Condition] [Clinical Finding] #> [V] [S] 4117930 Finding of trunk structure [SNOMED 302292003] [Condition] [Clinical Finding] #> [V] [S] 4028071 Disorder of trunk [SNOMED 128121009] [Condition] [Clinical Finding] #> [V] [S] 43531057 Finding of upper trunk [SNOMED 609623002] [Condition] [Clinical Finding] #> [V] [S] 4185503 Finding of region of thorax [SNOMED 298705000] [Condition] [Clinical Finding] #> [V] [S] 43531056 Disorder of thoracic segment of trunk [SNOMED 609622007] [Condition] [Clinical Finding] #> [V] [S] 4023995 Cardiovascular finding [SNOMED 106063007] [Condition] [Clinical Finding] #> [V] [S] 4043346 Disorder of thorax [SNOMED 118946009] [Condition] [Clinical Finding] #> [V] [S] 4115390 Mediastinal finding [SNOMED 301296002] [Condition] [Clinical Finding] #> [V] [S] 4180628 Disorder of body system [SNOMED 362965005] [Condition] [Clinical Finding] #> [V] [S] 4227253 Viscus structure finding [SNOMED 406123005] [Condition] [Clinical Finding] #> [V] [S] 134057 Disorder of cardiovascular system [SNOMED 49601007] [Condition] [Clinical Finding] #> [V] [S] 440142 Disorder of mediastinum [SNOMED 49483002] [Condition] [Clinical Finding] #> [V] [S] 4103183 Cardiac finding [SNOMED 301095005] [Condition] [Clinical Finding] #> [V] [S] 321588 Heart disease [SNOMED 56265001] [Condition] [Clinical Finding] #> [V] [S] 4024552 Disorder of cardiac function [SNOMED 105981003] [Condition] [Clinical Finding] #> [V] [C] 500002601 OMOP Congestive Heart Failure 1 [Cohort 500002601] [Condition] [Cohort] #> [V] [S] 316139 Heart failure [SNOMED 84114007] [Condition] [Clinical Finding] #> [V] [S] 4166245 Disorder of cardiac ventricle [SNOMED 415991003] [Condition] [Clinical Finding] #> *[V] [S] 319835 Congestive heart failure [SNOMED 42343007] [Condition] [Clinical Finding] #> [V] [S] 762003 Congestive heart failure as post-operative complication of non-cardiac surgery [SNOMED 285221000119109] [Condition] [Clinical Finding] #> [V] [S] 43021826 Congestive heart failure stage C [SNOMED 67441000119101] [Condition] [Clinical Finding] #> [V] [S] 439696 Hypertensive heart and renal disease with (congestive) heart failure [SNOMED 194779001] [Condition] [Clinical Finding] #> [V] [S] 44784442 Symptomatic congestive heart failure [SNOMED 698594003] [Condition] [Clinical Finding] #> [V] [S] 762002 Congestive heart failure as post-operative complication of cardiac surgery [SNOMED 285211000119102] [Condition] [Clinical Finding] #> [V] [S] 43022068 Exacerbation of congestive heart failure [SNOMED 96311000119109] [Condition] [Clinical Finding] #> [V] [S] 4242669 Biventricular congestive heart failure [SNOMED 92506005] [Condition] [Clinical Finding] #> [V] [S] 439698 Benign hypertensive heart disease with congestive cardiac failure [SNOMED 194767001] [Condition] [Clinical Finding] #> [V] [S] 315295 Congestive rheumatic heart failure [SNOMED 82523003] [Condition] [Clinical Finding] #> [V] [S] 44782428 Congestive heart failure due to cardiomyopathy [SNOMED 101281000119107] [Condition] [Clinical Finding] #> ... #> [V] [S] 4215446 Acute right-sided congestive heart failure [SNOMED 80479009] [Condition] [Clinical Finding] #> [V] [S] 44782728 Hypertensive heart AND chronic kidney disease with congestive heart failure [SNOMED 15781000119107] [Condition] [Clinical Finding] #> [V] [S] 4206009 Chronic left-sided congestive heart failure [SNOMED 5375005] [Condition] [Clinical Finding] #> [V] [S] 36712928 Congestive heart failure stage B due to ischemic cardiomyopathy [SNOMED 15629591000119103] [Condition] [Clinical Finding] #> [V] [S] 44782655 Acute exacerbation of chronic congestive heart failure [SNOMED 698296002] [Condition] [Clinical Finding] #> [V] [S] 4184497 Rheumatic left ventricular failure [SNOMED 43736008] [Condition] [Clinical Finding] #> [V] [S] 316994 Malignant hypertensive heart disease with congestive heart failure [SNOMED 83105008] [Condition] [Clinical Finding] #> [V] [S] 4327205 Acute left-sided congestive heart failure [SNOMED 74960003] [Condition] [Clinical Finding] #> [V] [S] 36712927 Congestive heart failure stage C due to ischemic cardiomyopathy [SNOMED 15629541000119106] [Condition] [Clinical Finding] #> [V] [S] 4284562 Chronic right-sided congestive heart failure [SNOMED 66989003] [Condition] [Clinical Finding] #> [V] [S] 764874 Acute on chronic heart failure co-occurrent with normal ejection fraction [SNOMED 7401000175100] [Condition] [Clinical Finding] #> [V] [S] 37309625 Acute on chronic right-sided congestive heart failure [SNOMED 16838951000119100] [Condition] [Clinical Finding]print_concept_hierarchy(conn = conn, concept_obj = concept_obj, level_of_separation_type = "min")#> [2021-05-26 16:07:20] Loading Cache... #> [2021-05-26 16:07:20] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (319835) #> [2021-05-26 16:07:20] Cached resultset found... #> [2021-05-26 16:07:20] Target column: concept_hierarchy_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: ancestor_concept_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.* FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: concept_hierarchy_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: descendant_concept_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.* FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [V] [S] 4199402 Finding of body region [SNOMED 301857004] [Condition] [Clinical Finding] #> [V] [S] 4117930 Finding of trunk structure [SNOMED 302292003] [Condition] [Clinical Finding] #> [V] [S] 441840 Clinical finding [SNOMED 404684003] [Condition] [Clinical Finding] #> [V] [S] 4028071 Disorder of trunk [SNOMED 128121009] [Condition] [Clinical Finding] #> [V] [S] 4274025 Disease [SNOMED 64572001] [Condition] [Clinical Finding] #> [V] [S] 43531057 Finding of upper trunk [SNOMED 609623002] [Condition] [Clinical Finding] #> [V] [S] 4042140 Finding by site [SNOMED 118234003] [Condition] [Clinical Finding] #> [V] [S] 4047779 Disorder by body site [SNOMED 123946008] [Condition] [Clinical Finding] #> [V] [S] 4185503 Finding of region of thorax [SNOMED 298705000] [Condition] [Clinical Finding] #> [V] [S] 43531056 Disorder of thoracic segment of trunk [SNOMED 609622007] [Condition] [Clinical Finding] #> [V] [S] 4023995 Cardiovascular finding [SNOMED 106063007] [Condition] [Clinical Finding] #> [V] [S] 4043346 Disorder of thorax [SNOMED 118946009] [Condition] [Clinical Finding] #> [V] [S] 4115390 Mediastinal finding [SNOMED 301296002] [Condition] [Clinical Finding] #> [V] [S] 4180628 Disorder of body system [SNOMED 362965005] [Condition] [Clinical Finding] #> [V] [S] 4227253 Viscus structure finding [SNOMED 406123005] [Condition] [Clinical Finding] #> [V] [S] 134057 Disorder of cardiovascular system [SNOMED 49601007] [Condition] [Clinical Finding] #> [V] [S] 440142 Disorder of mediastinum [SNOMED 49483002] [Condition] [Clinical Finding] #> [V] [S] 4103183 Cardiac finding [SNOMED 301095005] [Condition] [Clinical Finding] #> [V] [S] 321588 Heart disease [SNOMED 56265001] [Condition] [Clinical Finding] #> [V] [S] 4024552 Disorder of cardiac function [SNOMED 105981003] [Condition] [Clinical Finding] #> [V] [S] 316139 Heart failure [SNOMED 84114007] [Condition] [Clinical Finding] #> [V] [S] 4166245 Disorder of cardiac ventricle [SNOMED 415991003] [Condition] [Clinical Finding] #> [V] [C] 500002601 OMOP Congestive Heart Failure 1 [Cohort 500002601] [Condition] [Cohort] #> *[V] [S] 319835 Congestive heart failure [SNOMED 42343007] [Condition] [Clinical Finding] #> [V] [S] 762003 Congestive heart failure as post-operative complication of non-cardiac surgery [SNOMED 285221000119109] [Condition] [Clinical Finding] #> [V] [S] 43021826 Congestive heart failure stage C [SNOMED 67441000119101] [Condition] [Clinical Finding] #> [V] [S] 439696 Hypertensive heart and renal disease with (congestive) heart failure [SNOMED 194779001] [Condition] [Clinical Finding] #> [V] [S] 44784442 Symptomatic congestive heart failure [SNOMED 698594003] [Condition] [Clinical Finding] #> [V] [S] 762002 Congestive heart failure as post-operative complication of cardiac surgery [SNOMED 285211000119102] [Condition] [Clinical Finding] #> [V] [S] 43022068 Exacerbation of congestive heart failure [SNOMED 96311000119109] [Condition] [Clinical Finding] #> [V] [S] 4242669 Biventricular congestive heart failure [SNOMED 92506005] [Condition] [Clinical Finding] #> [V] [S] 439698 Benign hypertensive heart disease with congestive cardiac failure [SNOMED 194767001] [Condition] [Clinical Finding] #> [V] [S] 315295 Congestive rheumatic heart failure [SNOMED 82523003] [Condition] [Clinical Finding] #> [V] [S] 44782428 Congestive heart failure due to cardiomyopathy [SNOMED 101281000119107] [Condition] [Clinical Finding] #> ... #> [V] [S] 4215446 Acute right-sided congestive heart failure [SNOMED 80479009] [Condition] [Clinical Finding] #> [V] [S] 44782728 Hypertensive heart AND chronic kidney disease with congestive heart failure [SNOMED 15781000119107] [Condition] [Clinical Finding] #> [V] [S] 4206009 Chronic left-sided congestive heart failure [SNOMED 5375005] [Condition] [Clinical Finding] #> [V] [S] 36712928 Congestive heart failure stage B due to ischemic cardiomyopathy [SNOMED 15629591000119103] [Condition] [Clinical Finding] #> [V] [S] 44782655 Acute exacerbation of chronic congestive heart failure [SNOMED 698296002] [Condition] [Clinical Finding] #> [V] [S] 4184497 Rheumatic left ventricular failure [SNOMED 43736008] [Condition] [Clinical Finding] #> [V] [S] 316994 Malignant hypertensive heart disease with congestive heart failure [SNOMED 83105008] [Condition] [Clinical Finding] #> [V] [S] 4327205 Acute left-sided congestive heart failure [SNOMED 74960003] [Condition] [Clinical Finding] #> [V] [S] 36712927 Congestive heart failure stage C due to ischemic cardiomyopathy [SNOMED 15629541000119106] [Condition] [Clinical Finding] #> [V] [S] 4284562 Chronic right-sided congestive heart failure [SNOMED 66989003] [Condition] [Clinical Finding] #> [V] [S] 764874 Acute on chronic heart failure co-occurrent with normal ejection fraction [SNOMED 7401000175100] [Condition] [Clinical Finding] #> [V] [S] 37309625 Acute on chronic right-sided congestive heart failure [SNOMED 16838951000119100] [Condition] [Clinical Finding]#>#> ── Is Concept Id Valid Integer? ────────────────────────────────────────────────#> ✓ Concept Id is a valid integer#>#> ── Lookup Concept Id in Concept Table ──────────────────────────────────────────#> ✓ Concept Id `4298431` found in Concept Table#>#> ── Lookup Synonyms ─────────────────────────────────────────────────────────────#>#> ── Lookup 'Maps to' Concept Names ──────────────────────────────────────────────concept_obj#> An object of class "concept" #> Slot "concept_id": #> [1] 4298431 #> #> Slot "concept_name": #> [1] "White blood cell count" #> #> Slot "concept_synonym_names": #> [1] "WBC - White blood cell count|WBC count|WCC - White blood cell count|White blood cell count (procedure)|White blood cell count - observation" #> #> Slot "maps_to_concept_names": #> [1] "White blood cell count" #> #> Slot "domain_id": #> [1] "Measurement" #> #> Slot "vocabulary_id": #> [1] "SNOMED" #> #> Slot "concept_class_id": #> [1] "Procedure" #> #> Slot "standard_concept": #> [1] "S" #> #> Slot "concept_code": #> [1] "767002" #> #> Slot "valid_start_date": #> [1] "2002-01-31" #> #> Slot "valid_end_date": #> [1] "2099-12-31" #> #> Slot "invalid_reason": #> [1] NA #>print_concept_hierarchy(conn = conn, concept_obj = concept_obj)#> [2021-05-26 16:07:20] Loading Cache... #> [2021-05-26 16:07:20] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (4298431) #> [2021-05-26 16:07:20] Cached resultset found... #> [2021-05-26 16:07:20] Target column: concept_hierarchy_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: ancestor_concept_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.* FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: concept_hierarchy_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] Target column: descendant_concept_id #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720... #> [2021-05-26 16:07:20] Writing patelm9.V20210526160720...complete #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: SELECT a.*, b.* FROM patelm9.V20210526160720 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:20] Querying... #> [2021-05-26 16:07:20] Querying...complete #> [2021-05-26 16:07:20] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720... #> [2021-05-26 16:07:20] ✓ Open connection #> [2021-05-26 16:07:20] ✓ JDBC connection #> [2021-05-26 16:07:20] SQL: DROP TABLE IF EXISTS patelm9.V20210526160720; #> [2021-05-26 16:07:20] Sending... #> [2021-05-26 16:07:20] Sending...complete #> [2021-05-26 16:07:20] Dropping patelm9.V20210526160720...complete #> [V] [S] 4322976 Procedure [SNOMED 71388002] [Procedure] [Procedure] #> [V] [S] 4029205 Procedure by method [SNOMED 128927009] [Procedure] [Procedure] #> [V] [S] 4297090 Evaluation procedure [SNOMED 386053000] [Procedure] [Procedure] #> [V] [S] 4048365 Measurement [SNOMED 122869004] [Measurement] [Procedure] #> [V] [S] 4038498 Cell count [SNOMED 118218001] [Measurement] [Procedure] #> [V] [S] 4339397 Blood cell count [SNOMED 88308000] [Measurement] [Procedure] #> *[V] [S] 4298431 White blood cell count [SNOMED 767002] [Measurement] [Procedure] #> [V] [S] 2213329 Leukocyte assessment, fecal, qualitative or semiquantitative [CPT4 89055] [Measurement] [CPT4] #> [V] [S] 2212656 Blood count; leukocyte (WBC), automated [CPT4 85048] [Measurement] [CPT4] #> [V] [S] 4174071 White blood cell estimate [SNOMED 42396003] [Measurement] [Procedure] #> [V] [S] 4013251 Differential white blood cell count procedure [SNOMED 165511009] [Measurement] [Procedure] #> [V] [S] 4014488 White blood cell count, automated, cerebrospinal fluid [SNOMED 104112007] [Measurement] [Procedure] #> [V] [S] 4152974 Plasma cell count [SNOMED 270924002] [Measurement] [Procedure] #> [V] [S] 4016931 White blood cell count, automated, pleural fluid [SNOMED 104119003] [Measurement] [Procedure] #> [V] [S] 4015169 Lymphocytes and monocytes, count, blood [SNOMED 104105003] [Measurement] [Procedure] #> [V] [S] 4016930 White blood cell count, automated, peritoneal fluid [SNOMED 104115009] [Measurement] [Procedure] #> [V] [S] 4097616 Reversed neutrophil/lymphocyte ratio measurement [SNOMED 250298004] [Measurement] [Procedure] #> ... #> [V] [S] 2212810 Mononuclear cell antigen, quantitative (eg, flow cytometry), not otherwise specified, each antigen [CPT4 86356] [Measurement] [CPT4] #> [V] [S] 4039856 T lymphocyte count [SNOMED 118136006] [Measurement] [Procedure] #> [V] [S] 44807689 Count of cells negative for CD33 antigen and positive for CD34 antigen [SNOMED 797791000000108] [Measurement] [Procedure] #> [V] [S] 4154342 Granulocyte percent differential count [SNOMED 271042003] [Measurement] [Procedure] #> [V] [S] 4014490 Neutrophil count, automated, urine [SNOMED 104123006] [Measurement] [Procedure] #> [V] [S] 37208690 Lymphocyte percent count in blood [SNOMED 1107971000000104] [Measurement] [Procedure] #> [V] [S] 37208689 Lymphocyte count in blood [SNOMED 1107961000000106] [Measurement] [Procedure] #> [V] [S] 4041971 B lymphocyte count [SNOMED 118135005] [Measurement] [Procedure] #> [V] [S] 40484040 Count of eosinophils in urine specimen [SNOMED 442562007] [Measurement] [Procedure] #> [V] [S] 4236306 Percentage plasma cell count [SNOMED 407663004] [Measurement] [Procedure] #> ... #> [V] [S] 2212811 Natural killer (NK) cells, total count [CPT4 86357] [Measurement] [CPT4] #> [V] [S] 2213341 Nasal smear for eosinophils [CPT4 89190] [Measurement] [CPT4] #> [V] [S] 2213219 Sex chromatin identification; peripheral blood smear, polymorphonuclear drumsticks [CPT4 88140] [Measurement] [CPT4] #> [V] [S] 44809933 Natural killer (dim) cell absolute count [SNOMED 876601000000102] [Measurement] [Procedure] #> [V] [S] 4268302 Total B lymphocyte count [SNOMED 401074004] [Measurement] [Procedure] #> [V] [S] 4014756 T cells, total count [SNOMED 104373001] [Measurement] [Procedure] #> [V] [S] 4100147 Neutrophil band count [SNOMED 25340006] [Measurement] [Procedure] #> [V] [S] 44809936 Natural killer (bright) cell percentage of lymphocytes [SNOMED 876681000000107] [Measurement] [Procedure] #> [V] [S] 4195185 Myelocyte percent differential count [SNOMED 313696009] [Measurement] [Procedure] #> [V] [S] 2212809 B cells, total count [CPT4 86355] [Measurement] [CPT4] #> ... #> [V] [S] 4212900 T cell total % [SNOMED 391560001] [Measurement] [Procedure] #> [V] [S] 44807941 Band neutrophil percent differential count [SNOMED 827591000000105] [Measurement] [Procedure]print_concept_hierarchy(conn = conn, concept_obj = concept_obj, level_of_separation_type = "min")#> [2021-05-26 16:07:21] Loading Cache... #> [2021-05-26 16:07:21] Cached SQL: SELECT * FROM omop_vocabulary.concept c WHERE c.concept_id IN (4298431) #> [2021-05-26 16:07:21] Cached resultset found... #> [2021-05-26 16:07:21] Target column: concept_hierarchy_id #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721... #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: SELECT a.*, b.ancestor_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160721 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.descendant_concept_id #> [2021-05-26 16:07:21] Querying... #> [2021-05-26 16:07:21] Querying...complete #> [2021-05-26 16:07:21] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] Target column: ancestor_concept_id #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721... #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: SELECT a.*, b.* FROM patelm9.V20210526160721 a LEFT JOIN omop_vocabulary.concept b ON a.ancestor_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:21] Querying... #> [2021-05-26 16:07:21] Querying...complete #> [2021-05-26 16:07:21] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] Target column: concept_hierarchy_id #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721... #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: SELECT a.*, b.descendant_concept_id,b.min_levels_of_separation,b.max_levels_of_separation FROM patelm9.V20210526160721 a LEFT JOIN omop_vocabulary.concept_ancestor b ON a.concept_hierarchy_id = b.ancestor_concept_id #> [2021-05-26 16:07:21] Querying... #> [2021-05-26 16:07:21] Querying...complete #> [2021-05-26 16:07:21] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] Target column: descendant_concept_id #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Data 'data' has more than 0 rows #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721... #> [2021-05-26 16:07:21] Writing patelm9.V20210526160721...complete #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: SELECT a.*, b.* FROM patelm9.V20210526160721 a LEFT JOIN omop_vocabulary.concept b ON a.descendant_concept_id = b.concept_id WHERE b.invalid_reason IS NULL #> [2021-05-26 16:07:21] Querying... #> [2021-05-26 16:07:21] Querying...complete #> [2021-05-26 16:07:21] ✓ Returned data has more than 0 rows #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721... #> [2021-05-26 16:07:21] ✓ Open connection #> [2021-05-26 16:07:21] ✓ JDBC connection #> [2021-05-26 16:07:21] SQL: DROP TABLE IF EXISTS patelm9.V20210526160721; #> [2021-05-26 16:07:21] Sending... #> [2021-05-26 16:07:21] Sending...complete #> [2021-05-26 16:07:21] Dropping patelm9.V20210526160721...complete #> [V] [S] 4322976 Procedure [SNOMED 71388002] [Procedure] [Procedure] #> [V] [S] 4029205 Procedure by method [SNOMED 128927009] [Procedure] [Procedure] #> [V] [S] 4297090 Evaluation procedure [SNOMED 386053000] [Procedure] [Procedure] #> [V] [S] 4048365 Measurement [SNOMED 122869004] [Measurement] [Procedure] #> [V] [S] 4038498 Cell count [SNOMED 118218001] [Measurement] [Procedure] #> [V] [S] 4339397 Blood cell count [SNOMED 88308000] [Measurement] [Procedure] #> *[V] [S] 4298431 White blood cell count [SNOMED 767002] [Measurement] [Procedure] #> [V] [S] 4174071 White blood cell estimate [SNOMED 42396003] [Measurement] [Procedure] #> [V] [S] 4013251 Differential white blood cell count procedure [SNOMED 165511009] [Measurement] [Procedure] #> [V] [S] 4014488 White blood cell count, automated, cerebrospinal fluid [SNOMED 104112007] [Measurement] [Procedure] #> [V] [S] 4152974 Plasma cell count [SNOMED 270924002] [Measurement] [Procedure] #> [V] [S] 4016931 White blood cell count, automated, pleural fluid [SNOMED 104119003] [Measurement] [Procedure] #> [V] [S] 2212810 Mononuclear cell antigen, quantitative (eg, flow cytometry), not otherwise specified, each antigen [CPT4 86356] [Measurement] [CPT4] #> [V] [S] 4015169 Lymphocytes and monocytes, count, blood [SNOMED 104105003] [Measurement] [Procedure] #> [V] [S] 4016930 White blood cell count, automated, peritoneal fluid [SNOMED 104115009] [Measurement] [Procedure] #> [V] [S] 4097616 Reversed neutrophil/lymphocyte ratio measurement [SNOMED 250298004] [Measurement] [Procedure] #> [V] [S] 4041973 Granulocyte count [SNOMED 118138007] [Measurement] [Procedure] #> ... #> [V] [S] 4039856 T lymphocyte count [SNOMED 118136006] [Measurement] [Procedure] #> [V] [S] 44807689 Count of cells negative for CD33 antigen and positive for CD34 antigen [SNOMED 797791000000108] [Measurement] [Procedure] #> [V] [S] 4154342 Granulocyte percent differential count [SNOMED 271042003] [Measurement] [Procedure] #> [V] [S] 4014490 Neutrophil count, automated, urine [SNOMED 104123006] [Measurement] [Procedure] #> [V] [S] 37208690 Lymphocyte percent count in blood [SNOMED 1107971000000104] [Measurement] [Procedure] #> [V] [S] 37208689 Lymphocyte count in blood [SNOMED 1107961000000106] [Measurement] [Procedure] #> [V] [S] 4041971 B lymphocyte count [SNOMED 118135005] [Measurement] [Procedure] #> [V] [S] 2212811 Natural killer (NK) cells, total count [CPT4 86357] [Measurement] [CPT4] #> [V] [S] 40484040 Count of eosinophils in urine specimen [SNOMED 442562007] [Measurement] [Procedure] #> [V] [S] 4236306 Percentage plasma cell count [SNOMED 407663004] [Measurement] [Procedure] #> ... #> [V] [S] 44809933 Natural killer (dim) cell absolute count [SNOMED 876601000000102] [Measurement] [Procedure] #> [V] [S] 4268302 Total B lymphocyte count [SNOMED 401074004] [Measurement] [Procedure] #> [V] [S] 4014756 T cells, total count [SNOMED 104373001] [Measurement] [Procedure] #> [V] [S] 4100147 Neutrophil band count [SNOMED 25340006] [Measurement] [Procedure] #> [V] [S] 44809936 Natural killer (bright) cell percentage of lymphocytes [SNOMED 876681000000107] [Measurement] [Procedure] #> [V] [S] 4195185 Myelocyte percent differential count [SNOMED 313696009] [Measurement] [Procedure] #> [V] [S] 2212809 B cells, total count [CPT4 86355] [Measurement] [CPT4] #> [V] [S] 4193711 Promyelocyte percent differential count [SNOMED 313478005] [Measurement] [Procedure] #> [V] [S] 4193954 Total T lymphocyte count [SNOMED 391575009] [Measurement] [Procedure] #> [V] [S] 4153001 Neutrophil percent differential count [SNOMED 271035003] [Measurement] [Procedure] #> ... #> [V] [S] 4212900 T cell total % [SNOMED 391560001] [Measurement] [Procedure] #> [V] [S] 44807941 Band neutrophil percent differential count [SNOMED 827591000000105] [Measurement] [Procedure]