manual build steps work by changing "curated.tsv" for each CURATED bu…

…ild target and running "make.sh"

cumulus_library_opioid/vocab/analyze/curate.sql

@@ -35,33 +35,40 @@ order by trim(STR);
 delete from curated where (RXCUI like '%RXCUI%');
 
 -- ##############################################
-call log('RXNCONSO_curated', 'refresh'); 
+call log('RXNCONSO_curated', 'refresh');
 
 drop    table if exists     RXNCONSO_curated;
 create  table               RXNCONSO_curated
-(
-    RXCUI   varchar(8)      NOT NULL,
-    STR     varchar(3000)   NOT NULL,
-    TTY     varchar(20)     NOT NULL,
-    SAB     varchar(20)     NOT NULL,
-    CODE    varchar(50)     NOT NULL,
-    keyword_str varchar(50) NULL,
-    keyword_len int         NULL
-);
-
-insert  into RXNCONSO_curated
-        ( RXCUI,   STR,   TTY,   SAB,   CODE)
-select  distinct
-        C.RXCUI, C.STR, C.TTY, C.SAB, C.CODE
-from    rxnorm.RXNCONSO as C, curated
+select  C.*
+from    all_rxcui_str.RXNCONSO_curated C, curated
 where   C.RXCUI = curated.RXCUI
-order by RXCUI,STR;
-
-update  RXNCONSO_curated C, keywords K
-set
-    C.keyword_str = K.STR,
-    C.keyword_len = K.LEN
-where lower(C.STR) like concat('%',K.STR, '%');
+order by C.RXCUI, C.STR;
+
+--    drop    table if exists     RXNCONSO_curated;
+--    create  table               RXNCONSO_curated
+--    (
+--        RXCUI   varchar(8)      NOT NULL,
+--        STR     varchar(3000)   NOT NULL,
+--        TTY     varchar(20)     NOT NULL,
+--        SAB     varchar(20)     NOT NULL,
+--        CODE    varchar(50)     NOT NULL,
+--        keyword_str varchar(50) NULL,
+--        keyword_len int         NULL
+--    );
+--
+--    insert  into RXNCONSO_curated
+--            ( RXCUI,   STR,   TTY,   SAB,   CODE, keyword_str, keyword_len)
+--    select  distinct
+--            C.RXCUI, C.STR, C.TTY, C.SAB, C.CODE
+--    from    all_rxcui_str.RXNCONSO as C, curated
+--    where   C.RXCUI = curated.RXCUI
+--    order by RXCUI,STR;
+--
+--    update  RXNCONSO_curated C, keywords K
+--    set
+--        C.keyword_str = K.STR,
+--        C.keyword_len = K.LEN
+--    where lower(C.STR) like concat('%',K.STR, '%');
 
 --    call create_index('RXNCONSO_curated','STR(255)');
 --    call create_index('RXNCONSO_curated','RXCUI');

cumulus_library_opioid/vocab/common/keywords/keywords.curated.sql

@@ -1,5 +1,3 @@
--- Its unclear where all_rxcui_str.RXNCONSO_curated comes from
-
 -- #############################################################################
 call log('keywords_db.sql', 'begin');
 
@@ -17,6 +15,5 @@ from    RXNCONSO_curated
 where   keyword_len >= 4
 order by RXCUI,STR;
 
-
 -- #############################################################################
 call log('keywords_db.sql', 'done');

cumulus_library_opioid/vocab/common/umls/umls_cui_rxcui.sql → cumulus_library_opioid/vocab/common/umls/all_rxcui_str.sql

@@ -1,22 +1,56 @@
 -- ##############################################
-call log('all_rxcui_str.sql', 'begin');
+call log('all_rxcui_str.sql', 'refresh');
 
-drop   table if exists   MRCONSO_drug;
-create table             MRCONSO_drug
-select distinct * from umls.MRCONSO
-where SAB in ('ATC','CVX','DRUGBANK','GS','MMSL','MMX','MTHCMSFRFMTHSPL','NDDF','RXNORM','SNOMEDCT_US','USP','VANDF');
+-- ##############################################
+call log('RXNCONSO_curated', 'refresh');
 
-call create_index('MRCONSO_drug', 'CUI');
-call create_index('MRCONSO_drug', 'CODE,SAB');
+drop    table if exists     RXNCONSO_curated;
+create  table               RXNCONSO_curated
+(
+    RXCUI   varchar(8)      NOT NULL,
+    STR     varchar(3000)   NOT NULL,
+    TTY     varchar(20)     NOT NULL,
+    SAB     varchar(20)     NOT NULL,
+    CODE    varchar(50)     NOT NULL,
+    keyword_str varchar(50) NULL,
+    keyword_len int         NULL
+);
+
+insert  into RXNCONSO_curated
+        ( RXCUI,   STR,   TTY,   SAB,   CODE)
+select  distinct
+        C.RXCUI, C.STR, C.TTY, C.SAB, C.CODE
+from    rxnorm.RXNCONSO as C
+order by RXCUI,STR;
+
+update  RXNCONSO_curated C, keywords K
+set
+    C.keyword_str = K.STR,
+    C.keyword_len = K.LEN
+where lower(C.STR) like concat('%',K.STR, '%');
+
+-- ##############################################
+call log('rxcui_str', 'refresh');
 
 drop    table if exists rxcui_str;
 create  table           rxcui_str
 select distinct RXCUI, STR from rxnorm.RXNCONSO order by RXCUI,STR;
 
 call create_index('rxcui_str', 'RXCUI');
-call create_index('rxcui_str', 'STR');
+call create_index('rxcui_str', 'STR(255)');
+
+-- ##############################################
+call log('MRCONSO_drug', 'refresh');
+
+drop   table if exists   MRCONSO_drug;
+create table             MRCONSO_drug
+select distinct * from umls.MRCONSO
+where SAB in ('ATC','CVX','DRUGBANK','GS','MMSL','MMX','MTHCMSFRFMTHSPL','NDDF','RXNORM','SNOMEDCT_US','USP','VANDF');
+
+call create_index('MRCONSO_drug', 'CUI');
+call create_index('MRCONSO_drug', 'CODE,SAB');
 
---    TODO: deprecated?
+--    TODO: deprecated
 --    drop    table if exists rxcui_cui;
 --    create  table           rxcui_cui
 --    select  distinct R.RXCUI, U.CUI, U.SAB, U.CODE