Merge pull request #2 from Allen-Bayern/_2020

A little bit misakes.

load_UMLS.sh

@@ -1,7 +1,9 @@
 #!/usr/bin zsh
 
+# change the user and database according to your parctice.
+
 echo "Loading UMLS 2020 tables and data"
 psql -U postgres -d umls -f pgsql_all_tables.sql
 echo "Tables loaded"
-psql -U jmbanda -d umls2018aa -f pgsql_index.sql
+psql -U postgres -d umls -f pgsql_index.sql
 echo "Indexing Ready"

pgsql_all_tables.sql

@@ -7,12 +7,11 @@ This script has been tested in PostgreSQL 8.2.3 on Mac OS 10.4.10
 
 # The script can also work with PostgreSQL 11.2 and UMLS-2020AB by Zhao Zhengyang ([email protected])
 Thank you for Mr Banda and Mr Bedrick!
-Please point each 'COPY' statement to your local '/tmp/META' installation directory, or wherever you have stored the .RRF files output by MetamorphoSys. 
 This script has been tested in PostgreSQL 11.2 on Linux (Deepin 20.1, Debain 10 cored).
 
 */
 
-create schema if not exists _2020ab;
+create schema if not exists _2020ab; /* You can change the schema name as your wish. */
 set schema '_2020ab';
 
 DROP TABLE if exists MRCOLS;
@@ -28,6 +27,7 @@ CREATE TABLE MRCOLS (
 	dummy char(1)
 );
 
+---change the path of RRF file according the practice---
 COPY MRCOLS FROM '/media/yuebing/new_dev/umls/2020AB/META/MRCOLS.RRF' 
 WITH DELIMITER AS '|' NULL AS '';
 ALTER TABLE MRCOLS DROP COLUMN dummy;
@@ -339,6 +339,34 @@ CREATE TABLE MRXNW_ENG (
 COPY MRXNW_ENG FROM '/media/yuebing/new_dev/umls/2020AB/META/MRXNW_ENG.RRF' WITH DELIMITER AS '|' NULL AS '';
 ALTER TABLE MRXNW_ENG DROP COLUMN dummy;
 
+DROP TABLE if exists MRXW_ENG;
+CREATE TABLE MRXW_ENG (
+	LAT	char(3) NOT NULL,
+	WD	varchar(100) NOT NULL,
+	CUI	char(12) NOT NULL,
+	LUI	char(12) NOT NULL,
+	SUI	char(12) NOT NULL,
+	dummy char(1)
+);
+COPY MRXW_ENG FROM '/media/yuebing/new_dev/umls/2020AB/META/MRXW_ENG.RRF' WITH DELIMITER AS '|' NULL AS '';
+ALTER TABLE MRXW_ENG DROP COLUMN dummy;
+
+/*  Because I only use English items, I deleted the load of MRXW_XXX loaders except English one.
+	If you want to load another language, you can rewrite the SQL expression as follows:
+
+	DROP TABLE if exists MRXW_LAN; ---'LAN' means the language.---
+	CREATE TABLE MRXW_ENG (
+		LAT	char(3) NOT NULL,
+		WD	varchar(100) NOT NULL,
+		CUI	char(12) NOT NULL,
+		LUI	char(12) NOT NULL,
+		SUI	char(12) NOT NULL,
+		dummy char(1)
+	);
+	COPY MRXW_LAN FROM '/your/path/META/MRXW_ENG.RRF' WITH DELIMITER AS '|' NULL AS '';
+	ALTER TABLE MRXW_LAN DROP COLUMN dummy;
+ */
+
 DROP TABLE if exists MRAUI;
 CREATE TABLE MRAUI (
 	AUI1	varchar(9) NOT NULL,
@@ -352,7 +380,7 @@ CREATE TABLE MRAUI (
 	MAPIN	char(1) NOT NULL,
 	dummy char(1)
 );
-COPY MRAUI FROM '/media/yuebing/new_dev/umls/2020AB/META//MRAUI.RRF' WITH DELIMITER AS '|' NULL AS '';
+COPY MRAUI FROM '/media/yuebing/new_dev/umls/2020AB/META/MRAUI.RRF' WITH DELIMITER AS '|' NULL AS '';
 ALTER TABLE MRAUI DROP COLUMN dummy;
 
 
@@ -374,7 +402,7 @@ CREATE TABLE AMBIGLUI (
 	dummy char(1)
 );
 
-COPY AMBIGLUI FROM '/tmp/META/AMBIGLUI.RRF' WITH DELIMITER AS '|' NULL AS '';
+COPY AMBIGLUI FROM '/media/yuebing/new_dev/umls/2020AB/META/AMBIGLUI.RRF' WITH DELIMITER AS '|' NULL AS '';
 ALTER TABLE AMBIGLUI DROP COLUMN dummy;
 
 

pgsql_index.sql

@@ -2,18 +2,18 @@
 	Created by: 
 	Yeb Havinga, MSc
 	[email protected]
+
 	Modified by:
 	Juan M. Banda 
 	[email protected]
+
+	Tested by:
 	Zhao Zhengyang
 	[email protected]
 */
 
-CREATE INDEX X_MRCOC_CUI1 ON MRCOC(CUI1);
-CREATE INDEX X_MRCOC_AUI1 ON MRCOC(AUI1);
-CREATE INDEX X_MRCOC_CUI2 ON MRCOC(CUI2);
-CREATE INDEX X_MRCOC_AUI2 ON MRCOC(AUI2);
-CREATE INDEX X_MRCOC_SAB ON MRCOC(SAB);
+--- I deleted the expression where tables does not exist in this version. ---
+
 CREATE INDEX X_MRCONSO_CUI ON MRCONSO(CUI);
 ALTER TABLE MRCONSO ADD CONSTRAINT X_MRCONSO_PK PRIMARY KEY (AUI);
 CREATE INDEX X_MRCONSO_SUI ON MRCONSO(SUI);
@@ -22,9 +22,6 @@ CREATE INDEX X_MRCONSO_CODE ON MRCONSO(CODE);
 CREATE INDEX X_MRCONSO_SAB_TTY ON MRCONSO(SAB,TTY);
 CREATE INDEX X_MRCONSO_SCUI ON MRCONSO(SCUI);
 CREATE INDEX X_MRCONSO_STR ON MRCONSO(STR);
-CREATE INDEX X_MRCXT_CUI ON MRCXT(CUI);
-CREATE INDEX X_MRCXT_AUI ON MRCXT(AUI);
-CREATE INDEX X_MRCXT_SAB ON MRCXT(SAB);
 CREATE INDEX X_MRDEF_CUI ON MRDEF(CUI);
 CREATE INDEX X_MRDEF_AUI ON MRDEF(AUI);
 ALTER TABLE MRDEF ADD CONSTRAINT X_MRDEF_PK PRIMARY KEY (ATUI);
@@ -56,23 +53,7 @@ ALTER TABLE MRSTY ADD CONSTRAINT X_MRSTY_PK PRIMARY KEY (ATUI);
 CREATE INDEX X_MRSTY_STY ON MRSTY(STY);
 CREATE INDEX X_MRXNS_ENG_NSTR ON MRXNS_ENG(NSTR);
 CREATE INDEX X_MRXNW_ENG_NWD ON MRXNW_ENG(NWD);
-CREATE INDEX X_MRXW_BAQ_WD ON MRXW_BAQ(WD);
-CREATE INDEX X_MRXW_CZE_WD ON MRXW_CZE(WD);
-CREATE INDEX X_MRXW_DAN_WD ON MRXW_DAN(WD);
-CREATE INDEX X_MRXW_DUT_WD ON MRXW_DUT(WD);
 CREATE INDEX X_MRXW_ENG_WD ON MRXW_ENG(WD);
-CREATE INDEX X_MRXW_FIN_WD ON MRXW_FIN(WD);
-CREATE INDEX X_MRXW_FRE_WD ON MRXW_FRE(WD);
-CREATE INDEX X_MRXW_GER_WD ON MRXW_GER(WD);
-CREATE INDEX X_MRXW_HEB_WD ON MRXW_HEB(WD);
-CREATE INDEX X_MRXW_HUN_WD ON MRXW_HUN(WD);
-CREATE INDEX X_MRXW_ITA_WD ON MRXW_ITA(WD);
-CREATE INDEX X_MRXW_JPN_WD ON MRXW_JPN(WD);
-CREATE INDEX X_MRXW_NOR_WD ON MRXW_NOR(WD);
-CREATE INDEX X_MRXW_POR_WD ON MRXW_POR(WD);
-CREATE INDEX X_MRXW_RUS_WD ON MRXW_RUS(WD);
-CREATE INDEX X_MRXW_SPA_WD ON MRXW_SPA(WD);
-CREATE INDEX X_MRXW_SWE_WD ON MRXW_SWE(WD);
 CREATE INDEX X_AMBIGSUI_SUI ON AMBIGSUI(SUI);
 CREATE INDEX X_AMBIGLUI_LUI ON AMBIGLUI(LUI);
 VACUUM ANALYZE;