R/run_setup.R
In meerapatelmd/setupMetathesaurus: Setup UMLS Metathesaurus
Defines functions
run_setup
Documented in
run_setup
#' @title
#' Instantiate Postgres
#' @inherit setup description
#' @inheritParams pkg_args
#' @rdname run_setup
#' @export
#' @importFrom pg13 lsSchema send lsTables dropTable
#' @importFrom tibble as_tibble_col
#' @importFrom dplyr mutate select distinct filter
#' @importFrom stringr str_remove_all
#' @importFrom progress progress_bar
#' @importFrom glue glue
run_setup <-
function(conn,
conn_fun = "pg13::local_connect()",
schema = "umls",
path_to_rrfs,
steps = c(
"reset_schema",
"ddl_tables",
"copy_rrfs",
"add_indexes",
"log",
"setup_crosswalk"),
postprocess = TRUE,
mrconso_only = "DEPRECATED",
omop_only = "DEPRECATED",
english_only = TRUE,
log_schema = "public",
log_table_name = "setup_umls_log",
log_version,
log_release_date,
verbose = TRUE,
render_sql = TRUE,
render_only = FALSE) {
schema <- schema
if (missing(log_version) | missing(log_release_date)) {
stop("`log_version` and `log_release_date` are required.")
}
if (missing(conn)) {
conn <- eval(rlang::parse_expr(conn_fun))
on.exit(expr = pg13::dc(conn = conn), add = TRUE,
after = TRUE)
}
path_to_rrfs <- normalizePath(
path = path_to_rrfs,
mustWork = TRUE
)
##### Setup Objects
errors <- vector()
tables <-
c(
"AMBIGLUI",
"AMBIGSUI",
"DELETEDCUI",
"DELETEDLUI",
"DELETEDSUI",
"MERGEDCUI",
"MERGEDLUI",
"MRAUI",
"MRCOLS",
"MRCONSO",
"MRCUI",
"MRCXT",
"MRDEF",
"MRDOC",
"MRFILES",
"MRHIER",
"MRHIST",
"MRMAP",
"MRRANK",
"MRREL",
"MRSAB",
"MRSAT",
"MRSMAP",
"MRSTY",
"MRXNS_ENG",
"MRXNW_ENG",
"MRXW_BAQ",
"MRXW_CHI",
"MRXW_CZE",
"MRXW_DAN",
"MRXW_DUT",
"MRXW_ENG",
"MRXW_EST",
"MRXW_FIN",
"MRXW_FRE",
"MRXW_GER",
"MRXW_GRE",
"MRXW_HEB",
"MRXW_HUN",
"MRXW_ITA",
"MRXW_JPN",
"MRXW_KOR",
"MRXW_LAV",
"MRXW_NOR",
"MRXW_POL",
"MRXW_POR",
"MRXW_RUS",
"MRXW_SCR",
"MRXW_SPA",
"MRXW_SWE",
"MRXW_TUR"
)
if (english_only) {
tables <-
tables[!(tables %in% c(
'MRXW_BAQ',
'MRXW_CHI',
'MRXW_CZE',
'MRXW_DAN',
'MRXW_DUT',
'MRXW_EST',
'MRXW_FIN',
'MRXW_FRE',
'MRXW_GER',
'MRXW_GRE',
'MRXW_HEB',
'MRXW_HUN',
'MRXW_ITA',
'MRXW_JPN',
'MRXW_KOR',
'MRXW_LAV',
'MRXW_NOR',
'MRXW_POL',
'MRXW_POR',
'MRXW_RUS',
'MRXW_SCR',
'MRXW_SPA',
'MRXW_SWE',
'MRXW_TUR'
))]
}
if ("reset_schema" %in% steps) {
if (
pg13::schema_exists(conn = conn,
schema = schema)) {
pg13::send(
conn = conn,
sql_statement =
glue::glue("DROP SCHEMA {schema} CASCADE;"),
verbose = verbose,
render_sql = render_sql
)
}
pg13::send(
conn = conn,
sql_statement =
glue::glue("CREATE SCHEMA {schema};"),
verbose = verbose,
render_sql = render_sql
)
}
if ("ddl_tables" %in% steps) {
ddl <-
list(
MRCOLS =
'DROP TABLE IF EXISTS {schema}.MRCOLS;
CREATE TABLE {schema}.MRCOLS (
COL varchar(40),
DES varchar(200),
REF varchar(40),
MIN integer,
AV numeric(5,2),
MAX integer,
FIL varchar(50),
DTY varchar(40),
FILLER_COL INTEGER
)',
MRCONSO =
'DROP TABLE IF EXISTS {schema}.MRCONSO;
CREATE TABLE {schema}.MRCONSO (
CUI char(8) NOT NULL,
LAT char(3) NOT NULL,
TS char(1) NOT NULL,
LUI varchar(10) NOT NULL,
STT varchar(3) NOT NULL,
SUI varchar(10) NOT NULL,
ISPREF char(1) NOT NULL,
AUI varchar(9) NOT NULL,
SAUI varchar(50),
SCUI varchar(100),
SDUI varchar(100),
SAB varchar(40) NOT NULL,
TTY varchar(40) NOT NULL,
CODE varchar(100) NOT NULL,
STR text NOT NULL,
SRL integer NOT NULL,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRCUI =
'DROP TABLE IF EXISTS {schema}.MRCUI;
CREATE TABLE {schema}.MRCUI (
CUI1 char(8) NOT NULL,
VER varchar(10) NOT NULL,
REL varchar(4) NOT NULL,
RELA varchar(100),
MAPREASON text,
CUI2 char(8),
MAPIN char(1),
FILLER_COL INTEGER
)',
MRCXT =
'DROP TABLE IF EXISTS {schema}.MRCXT;
CREATE TABLE {schema}.MRCXT (
CUI char(8),
SUI varchar(10),
AUI varchar(9),
SAB varchar(40),
CODE varchar(100),
CXN integer,
CXL char(3),
MRCXTRANK integer,
CXS text,
CUI2 char(8),
AUI2 varchar(9),
HCD varchar(100),
RELA varchar(100),
XC varchar(1),
CVF integer,
FILLER_COL INTEGER
)',
MRDEF =
'DROP TABLE IF EXISTS {schema}.MRDEF;
CREATE TABLE {schema}.MRDEF (
CUI char(8) NOT NULL,
AUI varchar(9) NOT NULL,
ATUI varchar(11) NOT NULL,
SATUI varchar(50),
SAB varchar(40) NOT NULL,
DEF text NOT NULL,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRDOC =
'DROP TABLE IF EXISTS {schema}.MRDOC;
CREATE TABLE {schema}.MRDOC (
DOCKEY varchar(50) NOT NULL,
VALUE varchar(200),
TYPE varchar(50) NOT NULL,
EXPL text,
FILLER_COL INTEGER
)',
MRFILES =
'DROP TABLE IF EXISTS {schema}.MRFILES;
CREATE TABLE {schema}.MRFILES (
FIL varchar(50),
DES varchar(200),
FMT text,
CLS integer,
RWS integer,
BTS bigint,
FILLER_COL INTEGER
)',
MRHIER =
'DROP TABLE IF EXISTS {schema}.MRHIER;
CREATE TABLE {schema}.MRHIER (
CUI char(8) NOT NULL,
AUI varchar(9) NOT NULL,
CXN integer NOT NULL,
PAUI varchar(10),
SAB varchar(40) NOT NULL,
RELA varchar(100),
PTR text,
HCD varchar(100),
CVF integer,
FILLER_COL INTEGER
)',
MRHIST =
'DROP TABLE IF EXISTS {schema}.MRHIST;
CREATE TABLE {schema}.MRHIST (
CUI char(8),
SOURCEUI varchar(100),
SAB varchar(40),
SVER varchar(40),
CHANGETYPE text,
CHANGEKEY text,
CHANGEVAL text,
REASON text,
CVF integer,
FILLER_COL INTEGER
)',
MRMAP =
'DROP TABLE IF EXISTS {schema}.MRMAP;
CREATE TABLE {schema}.MRMAP (
MAPSETCUI char(8) NOT NULL,
MAPSETSAB varchar(40) NOT NULL,
MAPSUBSETID varchar(10),
MAPRANK integer,
MAPID varchar(50) NOT NULL,
MAPSID varchar(50),
FROMID varchar(50) NOT NULL,
FROMSID varchar(50),
FROMEXPR text NOT NULL,
FROMTYPE varchar(50) NOT NULL,
FROMRULE text,
FROMRES text,
REL varchar(4) NOT NULL,
RELA varchar(100),
TOID varchar(50),
TOSID varchar(50),
TOEXPR text,
TOTYPE varchar(50),
TORULE text,
TORES text,
MAPRULE text,
MAPRES text,
MAPTYPE varchar(50),
MAPATN varchar(100),
MAPATV text,
CVF integer,
FILLER_COL INTEGER
)',
MRRANK =
'DROP TABLE IF EXISTS {schema}.MRRANK;
CREATE TABLE {schema}.MRRANK (
MRRANK_RANK integer NOT NULL,
SAB varchar(40) NOT NULL,
TTY varchar(40) NOT NULL,
SUPPRESS char(1) NOT NULL,
FILLER_COL INTEGER
)',
MRREL =
'DROP TABLE IF EXISTS {schema}.MRREL;
CREATE TABLE {schema}.MRREL (
CUI1 char(8) NOT NULL,
AUI1 varchar(9),
STYPE1 varchar(50) NOT NULL,
REL varchar(4) NOT NULL,
CUI2 char(8) NOT NULL,
AUI2 varchar(9),
STYPE2 varchar(50) NOT NULL,
RELA varchar(100),
RUI varchar(10) NOT NULL,
SRUI varchar(50),
SAB varchar(40) NOT NULL,
SL varchar(40) NOT NULL,
RG varchar(10),
DIR varchar(1),
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRSAB =
'DROP TABLE IF EXISTS {schema}.MRSAB;
CREATE TABLE {schema}.MRSAB (
VCUI char(8),
RCUI char(8),
VSAB varchar(40) NOT NULL,
RSAB varchar(40) NOT NULL,
SON text NOT NULL,
SF varchar(40) NOT NULL,
SVER varchar(40),
VSTART char(8),
VEND char(8),
IMETA varchar(10) NOT NULL,
RMETA varchar(10),
SLC text,
SCC text,
SRL integer NOT NULL,
TFR integer,
CFR integer,
CXTY varchar(50),
TTYL varchar(400),
ATNL text,
LAT char(3),
CENC varchar(40) NOT NULL,
CURVER char(1) NOT NULL,
SABIN char(1) NOT NULL,
SSN text NOT NULL,
SCIT text NOT NULL,
FILLER_COL INTEGER
)',
MRSAT =
'DROP TABLE IF EXISTS {schema}.MRSAT;
CREATE TABLE {schema}.MRSAT (
CUI char(8) NOT NULL,
LUI varchar(10),
SUI varchar(10),
METAUI varchar(100),
STYPE varchar(50) NOT NULL,
CODE varchar(100),
ATUI varchar(11) NOT NULL,
SATUI varchar(50),
ATN varchar(100) NOT NULL,
SAB varchar(40) NOT NULL,
ATV text,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRSMAP =
'DROP TABLE IF EXISTS {schema}.MRSMAP;
CREATE TABLE {schema}.MRSMAP (
MAPSETCUI char(8) NOT NULL,
MAPSETSAB varchar(40) NOT NULL,
MAPID varchar(50) NOT NULL,
MAPSID varchar(50),
FROMEXPR text NOT NULL,
FROMTYPE varchar(50) NOT NULL,
REL varchar(4) NOT NULL,
RELA varchar(100),
TOEXPR text,
TOTYPE varchar(50),
CVF integer,
FILLER_COL INTEGER
)',
MRSTY =
'DROP TABLE IF EXISTS {schema}.MRSTY;
CREATE TABLE {schema}.MRSTY (
CUI char(8) NOT NULL,
TUI char(4) NOT NULL,
STN varchar(100) NOT NULL,
STY varchar(50) NOT NULL,
ATUI varchar(11) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRXNS_ENG =
'DROP TABLE IF EXISTS {schema}.MRXNS_ENG;
CREATE TABLE {schema}.MRXNS_ENG (
LAT char(3) NOT NULL,
NSTR text NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXNW_ENG =
'DROP TABLE IF EXISTS {schema}.MRXNW_ENG;
CREATE TABLE {schema}.MRXNW_ENG (
LAT char(3) NOT NULL,
NWD varchar(100) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRAUI =
'DROP TABLE IF EXISTS {schema}.MRAUI;
CREATE TABLE {schema}.MRAUI (
AUI1 varchar(9) NOT NULL,
CUI1 char(8) NOT NULL,
VER varchar(10) NOT NULL,
REL varchar(4),
RELA varchar(100),
MAPREASON text NOT NULL,
AUI2 varchar(9) NOT NULL,
CUI2 char(8) NOT NULL,
MAPIN char(1) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_BAQ =
'DROP TABLE IF EXISTS {schema}.MRXW_BAQ;
CREATE TABLE {schema}.MRXW_BAQ (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_CHI =
'DROP TABLE IF EXISTS {schema}.MRXW_CHI;
CREATE TABLE {schema}.MRXW_CHI (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_CZE =
'DROP TABLE IF EXISTS {schema}.MRXW_CZE;
CREATE TABLE {schema}.MRXW_CZE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_DAN =
'DROP TABLE IF EXISTS {schema}.MRXW_DAN;
CREATE TABLE {schema}.MRXW_DAN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_DUT =
'DROP TABLE IF EXISTS {schema}.MRXW_DUT;
CREATE TABLE {schema}.MRXW_DUT (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_ENG =
'DROP TABLE IF EXISTS {schema}.MRXW_ENG;
CREATE TABLE {schema}.MRXW_ENG (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_EST =
'DROP TABLE IF EXISTS {schema}.MRXW_EST;
CREATE TABLE {schema}.MRXW_EST (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_FIN =
'DROP TABLE IF EXISTS {schema}.MRXW_FIN;
CREATE TABLE {schema}.MRXW_FIN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_FRE =
'DROP TABLE IF EXISTS {schema}.MRXW_FRE;
CREATE TABLE {schema}.MRXW_FRE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_GER =
'DROP TABLE IF EXISTS {schema}.MRXW_GER;
CREATE TABLE {schema}.MRXW_GER (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_GRE =
'DROP TABLE IF EXISTS {schema}.MRXW_GRE;
CREATE TABLE {schema}.MRXW_GRE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_HEB =
'DROP TABLE IF EXISTS {schema}.MRXW_HEB;
CREATE TABLE {schema}.MRXW_HEB (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_HUN =
'DROP TABLE IF EXISTS {schema}.MRXW_HUN;
CREATE TABLE {schema}.MRXW_HUN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_ITA =
'DROP TABLE IF EXISTS {schema}.MRXW_ITA;
CREATE TABLE {schema}.MRXW_ITA (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_JPN =
'DROP TABLE IF EXISTS {schema}.MRXW_JPN;
CREATE TABLE {schema}.MRXW_JPN (
LAT char(3) NOT NULL,
WD varchar(500) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_KOR =
'DROP TABLE IF EXISTS {schema}.MRXW_KOR;
CREATE TABLE {schema}.MRXW_KOR (
LAT char(3) NOT NULL,
WD varchar(500) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_LAV =
'DROP TABLE IF EXISTS {schema}.MRXW_LAV;
CREATE TABLE {schema}.MRXW_LAV (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_NOR =
'DROP TABLE IF EXISTS {schema}.MRXW_NOR;
CREATE TABLE {schema}.MRXW_NOR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_POL =
'DROP TABLE IF EXISTS {schema}.MRXW_POL;
CREATE TABLE {schema}.MRXW_POL (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_POR =
'DROP TABLE IF EXISTS {schema}.MRXW_POR;
CREATE TABLE {schema}.MRXW_POR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_RUS =
'DROP TABLE IF EXISTS {schema}.MRXW_RUS;
CREATE TABLE {schema}.MRXW_RUS (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SCR =
'DROP TABLE IF EXISTS {schema}.MRXW_SCR;
CREATE TABLE {schema}.MRXW_SCR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SPA =
'DROP TABLE IF EXISTS {schema}.MRXW_SPA;
CREATE TABLE {schema}.MRXW_SPA (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SWE =
'DROP TABLE IF EXISTS {schema}.MRXW_SWE;
CREATE TABLE {schema}.MRXW_SWE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_TUR =
'DROP TABLE IF EXISTS {schema}.MRXW_TUR;
CREATE TABLE {schema}.MRXW_TUR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
AMBIGSUI =
'DROP TABLE IF EXISTS {schema}.AMBIGSUI;
CREATE TABLE {schema}.AMBIGSUI (
SUI varchar(10) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
AMBIGLUI =
'DROP TABLE IF EXISTS {schema}.AMBIGLUI;
CREATE TABLE {schema}.AMBIGLUI (
LUI varchar(10) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
DELETEDCUI =
'DROP TABLE IF EXISTS {schema}.DELETEDCUI;
CREATE TABLE {schema}.DELETEDCUI (
PCUI char(8) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
DELETEDLUI =
'DROP TABLE IF EXISTS {schema}.DELETEDLUI;
CREATE TABLE {schema}.DELETEDLUI (
PLUI varchar(10) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
DELETEDSUI =
'DROP TABLE IF EXISTS {schema}.DELETEDSUI;
CREATE TABLE {schema}.DELETEDSUI (
PSUI varchar(10) NOT NULL,
LAT char(3) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
MERGEDCUI =
'DROP TABLE IF EXISTS {schema}.MERGEDCUI;
CREATE TABLE {schema}.MERGEDCUI (
PCUI char(8) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
MERGEDLUI =
'DROP TABLE IF EXISTS {schema}.MERGEDLUI;
CREATE TABLE {schema}.MERGEDLUI (
PLUI varchar(10),
LUI varchar(10),
FILLER_COL INTEGER
)')
ddl <- ddl[tables]
for (i in seq_along(ddl)) {
pg13::send(
conn = conn,
sql_statement = glue::glue(ddl[[i]]),
verbose = verbose,
render_sql = render_sql
)
}
}
if ("copy_rrfs" %in% steps) {
rrf_files <-
list.files(
path = path_to_rrfs,
recursive = TRUE,
pattern = "[.]RRF$",
full.names = TRUE
) %>%
tibble::as_tibble_col("filePaths") %>%
dplyr::mutate(baseNames = basename(filePaths)) %>%
dplyr::mutate(tableNames = stringr::str_remove_all(baseNames, "[.]RRF$")) %>%
dplyr::filter(tableNames %in% tables) %>%
dplyr::select(filePaths) %>%
dplyr::distinct() %>%
unlist()
pb <- progress::progress_bar$new(
format = " :what [:bar] :current/:total :percent :elapsedfull",
total = length(tables),
clear = FALSE,
width = 60
)
pb$tick(0)
Sys.sleep(0.2)
errors <- vector()
for (i in 1:length(tables)) {
table <- tables[i]
rrf_path <- path.expand(
grep(
pattern = table,
rrf_files,
value = TRUE
)
)
pb$tick(tokens = list(what = table))
Sys.sleep(1)
cat("\n")
sql <- glue::glue(
"COPY {schema}.{table} FROM '{rrf_path}' WITH DELIMITER E'|' CSV QUOTE E'\b';")
output <-
tryCatch(
pg13::send(
conn = conn,
sql_statement = sql,
verbose = verbose,
render_sql = render_sql
),
error = function(e) "Error"
)
if (identical(output, "Error")) {
errors <-
c(
errors,
table
)
}
}
if (length(errors) > 0) {
typewrite("Tables:")
tables %>%
purrr::map(~ typewrite(.))
typewrite_warning("Some tables did not copy:")
errors %>%
purrr::map(~ typewrite(italicize(.)))
} else {
typewrite("All tables copied:")
tables %>%
purrr::map(~ typewrite(.))
}
}
# Log
if ("log" %in% steps) {
sql_statement <-
glue::glue(
"
CREATE TABLE IF NOT EXISTS {log_schema}.{log_table_name} (
sm_datetime timestamp without time zone NOT NULL,
sm_version varchar(100) NOT NULL,
sm_release_date varchar(25) NOT NULL,
sm_schema varchar(25) NOT NULL,
ambiglui int,
ambigsui int,
deletedcui int,
deletedlui int,
deletedsui int,
mergedcui int,
mergedlui int,
mraui int,
mrcols int,
mrconso int,
mrcui int,
mrcxt int,
mrdef int,
mrdoc int,
mrfiles int,
mrhier int,
mrhist int,
mrmap int,
mrrank int,
mrrel int,
mrsab int,
mrsat int,
mrsmap int,
mrsty int,
mrxns_eng int,
mrxnw_eng int,
mrxw_eng int
);
")
pg13::send(conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql)
table_names <-
pg13::ls_tables(
conn = conn,
schema = schema,
verbose = verbose,
render_sql = render_sql
)
current_row_count <-
table_names %>%
purrr::map(function(x) {
pg13::query(
conn = conn,
sql_statement = pg13::render_row_count(
schema = schema,
tableName = x
)
)
}) %>%
purrr::set_names(tolower(table_names)) %>%
dplyr::bind_rows(.id = "Table") %>%
dplyr::rename(Rows = count) %>%
tidyr::pivot_wider(
names_from = "Table",
values_from = "Rows"
) %>%
dplyr::mutate(
sm_datetime = as.character(Sys.time()),
sm_version = log_version,
sm_release_date = log_release_date,
sm_schema = schema
) %>%
dplyr::select(
sm_datetime,
sm_version,
sm_release_date,
sm_schema,
dplyr::all_of(c(
'ambiglui',
'ambigsui',
'deletedcui',
'deletedlui',
'deletedsui',
'mergedcui',
'mergedlui',
'mraui',
'mrcols',
'mrconso',
'mrcui',
'mrcxt',
'mrdef',
'mrdoc',
'mrfiles',
'mrhier',
'mrhist',
'mrmap',
'mrrank',
'mrrel',
'mrsab',
'mrsat',
'mrsmap',
'mrsty',
'mrxns_eng',
'mrxnw_eng',
'mrxw_eng'
))
)
current_row_count <-
unname(unlist(current_row_count))
sql_statement <-
glue::glue(
"
INSERT INTO {log_schema}.{log_table_name}
VALUES ({glue::glue_collapse(glue::single_quote(current_row_count), sep = ', ')})
;
"
)
pg13::send(conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql)
cli::cat_line()
cli::cat_boxx("Log Results",
float = "center"
)
sql_statement <-
glue::glue(
"
SELECT *
FROM {log_schema}.{log_table_name}
WHERE sm_datetime IN (SELECT MAX(sm_datetime) FROM {log_schema}.{log_table_name});
"
)
updated_log <-
pg13::query(
conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql,
checks = ''
)
print(tibble::as_tibble(updated_log))
cli::cat_line()
}
if ("add_indexes" %in% steps) {
indexes <-
c(
"CREATE INDEX X_MRCOC_CUI1 ON {schema}.MRCOC(CUI1);",
"CREATE INDEX X_MRCOC_AUI1 ON {schema}.MRCOC(AUI1);",
"CREATE INDEX X_MRCOC_CUI2 ON {schema}.MRCOC(CUI2);",
"CREATE INDEX X_MRCOC_AUI2 ON {schema}.MRCOC(AUI2);",
"CREATE INDEX X_MRCOC_SAB ON {schema}.MRCOC(SAB);",
"CREATE INDEX X_MRCONSO_CUI ON {schema}.MRCONSO(CUI);",
"ALTER TABLE {schema}.MRCONSO ADD CONSTRAINT X_MRCONSO_PK PRIMARY KEY (AUI);",
"CREATE INDEX X_MRCONSO_SUI ON {schema}.MRCONSO(SUI);",
"CREATE INDEX X_MRCONSO_LUI ON {schema}.MRCONSO(LUI);",
"CREATE INDEX X_MRCONSO_CODE ON {schema}.MRCONSO(CODE);",
"CREATE INDEX X_MRCONSO_SAB_TTY ON {schema}.MRCONSO(SAB,TTY);",
"CREATE INDEX X_MRCONSO_SCUI ON {schema}.MRCONSO(SCUI);",
"CREATE INDEX X_MRCONSO_STR ON {schema}.MRCONSO(STR);",
"CREATE INDEX X_MRCXT_CUI ON {schema}.MRCXT(CUI);",
"CREATE INDEX X_MRCXT_AUI ON {schema}.MRCXT(AUI);",
"CREATE INDEX X_MRCXT_SAB ON {schema}.MRCXT(SAB);",
"CREATE INDEX X_MRDEF_CUI ON {schema}.MRDEF(CUI);",
"CREATE INDEX X_MRDEF_AUI ON {schema}.MRDEF(AUI);",
"ALTER TABLE {schema}.MRDEF ADD CONSTRAINT X_MRDEF_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRDEF_SAB ON {schema}.MRDEF(SAB);",
"CREATE INDEX X_MRHIER_CUI ON {schema}.MRHIER(CUI);",
"CREATE INDEX X_MRHIER_AUI ON {schema}.MRHIER(AUI);",
"CREATE INDEX X_MRHIER_SAB ON {schema}.MRHIER(SAB);",
"CREATE INDEX X_MRHIER_PTR ON {schema}.MRHIER(PTR);",
"CREATE INDEX X_MRHIER_PAUI ON {schema}.MRHIER(PAUI);",
"CREATE INDEX X_MRHIST_CUI ON {schema}.MRHIST(CUI);",
"CREATE INDEX X_MRHIST_SOURCEUI ON {schema}.MRHIST(SOURCEUI);",
"CREATE INDEX X_MRHIST_SAB ON {schema}.MRHIST(SAB);",
"ALTER TABLE {schema}.MRRANK ADD CONSTRAINT X_MRRANK_PK PRIMARY KEY (SAB,TTY);",
"CREATE INDEX X_MRREL_CUI1 ON {schema}.MRREL(CUI1);",
"CREATE INDEX X_MRREL_AUI1 ON {schema}.MRREL(AUI1);",
"CREATE INDEX X_MRREL_CUI2 ON {schema}.MRREL(CUI2);",
"CREATE INDEX X_MRREL_AUI2 ON {schema}.MRREL(AUI2);",
"ALTER TABLE {schema}.MRREL ADD CONSTRAINT X_MRREL_PK PRIMARY KEY (RUI);",
"CREATE INDEX X_MRREL_SAB ON {schema}.MRREL(SAB);",
"ALTER TABLE {schema}.MRSAB ADD CONSTRAINT X_MRSAB_PK PRIMARY KEY (VSAB);",
"CREATE INDEX X_MRSAB_RSAB ON {schema}.MRSAB(RSAB);",
"CREATE INDEX X_MRSAT_CUI ON {schema}.MRSAT(CUI);",
"CREATE INDEX X_MRSAT_METAUI ON {schema}.MRSAT(METAUI);",
"ALTER TABLE {schema}.MRSAT ADD CONSTRAINT X_MRSAT_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRSAT_SAB ON {schema}.MRSAT(SAB);",
"CREATE INDEX X_MRSAT_ATN ON {schema}.MRSAT(ATN);",
"CREATE INDEX X_MRSTY_CUI ON {schema}.MRSTY(CUI);",
"ALTER TABLE {schema}.MRSTY ADD CONSTRAINT X_MRSTY_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRSTY_STY ON {schema}.MRSTY(STY);",
"CREATE INDEX X_MRXNS_ENG_NSTR ON {schema}.MRXNS_ENG(NSTR);",
"CREATE INDEX X_MRXNW_ENG_NWD ON {schema}.MRXNW_ENG(NWD);",
"CREATE INDEX X_MRXW_BAQ_WD ON {schema}.MRXW_BAQ(WD);",
"CREATE INDEX X_MRXW_CZE_WD ON {schema}.MRXW_CZE(WD);",
"CREATE INDEX X_MRXW_DAN_WD ON {schema}.MRXW_DAN(WD);",
"CREATE INDEX X_MRXW_DUT_WD ON {schema}.MRXW_DUT(WD);",
"CREATE INDEX X_MRXW_ENG_WD ON {schema}.MRXW_ENG(WD);",
"CREATE INDEX X_MRXW_FIN_WD ON {schema}.MRXW_FIN(WD);",
"CREATE INDEX X_MRXW_FRE_WD ON {schema}.MRXW_FRE(WD);",
"CREATE INDEX X_MRXW_GER_WD ON {schema}.MRXW_GER(WD);",
"CREATE INDEX X_MRXW_HEB_WD ON {schema}.MRXW_HEB(WD);",
"CREATE INDEX X_MRXW_HUN_WD ON {schema}.MRXW_HUN(WD);",
"CREATE INDEX X_MRXW_ITA_WD ON {schema}.MRXW_ITA(WD);",
"CREATE INDEX X_MRXW_JPN_WD ON {schema}.MRXW_JPN(WD);",
"CREATE INDEX X_MRXW_NOR_WD ON {schema}.MRXW_NOR(WD);",
"CREATE INDEX X_MRXW_POR_WD ON {schema}.MRXW_POR(WD);",
"CREATE INDEX X_MRXW_RUS_WD ON {schema}.MRXW_RUS(WD);",
"CREATE INDEX X_MRXW_SPA_WD ON {schema}.MRXW_SPA(WD);",
"CREATE INDEX X_MRXW_SWE_WD ON {schema}.MRXW_SWE(WD);",
"CREATE INDEX X_AMBIGSUI_SUI ON {schema}.AMBIGSUI(SUI);",
"CREATE INDEX X_AMBIGLUI_LUI ON {schema}.AMBIGLUI(LUI);"
)
pb <- progress::progress_bar$new(
format = " [:bar] :current/:total :percent :elapsedfull",
total = length(indexes),
clear = FALSE,
width = 60
)
pb$tick(0)
Sys.sleep(0.2)
errors <- vector()
for (i in 1:length(indexes)) {
index <- glue::glue(indexes[i])
pb$tick()
Sys.sleep(1)
cat("\n")
output <-
tryCatch(
pg13::send(
conn = conn,
sql_statement = index,
verbose = verbose,
render_sql = render_sql
),
error = function(e) "Error"
)
if (identical(output, "Error")) {
errors <-
c(
errors,
index
)
}
}
if (length(errors) > 0) {
typewrite_warning("Some indexes failed:")
errors %>%
purrr::map(~ typewrite(italicize(.)))
}
}
if ("setup_crosswalk" %in% steps) {
setup_crosswalk_schema(
conn = conn,
crosswalk_schema = "umls_crosswalk"
)
}
if (postprocess) {
run_postprocessing(
conn = conn,
umls_version = log_version,
umls_release_dt = log_release_date,
verbose = verbose,
render_sql = render_sql,
render_only = render_only
)
}
}
#' @title
#' Run Postprocessing Only
#' @rdname run_postprocessing
#' @export
#' @importFrom rlang parse_expr
#' @importFrom pg13 dc send
run_postprocessing <-
function(conn,
conn_fun = "pg13::local_connect()",
umls_version,
umls_release_dt,
verbose = TRUE,
render_sql = TRUE,
render_only = FALSE) {
if (missing(umls_version)|missing(umls_release_dt)) {
stop("`umls_version` and `umls_release_dt` are required.")
}
if (missing(conn)) {
conn <- eval(rlang::parse_expr(conn_fun))
on.exit(expr = pg13::dc(conn = conn), add = TRUE,
after = TRUE)
}
postprocess_sqls <-
list.files(system.file(package = "metathesaurus",
"sql",
"Hierarchy"),
full.names = TRUE,
pattern = "[.]{1}sql$")
for (postprocess_sql in postprocess_sqls) {
sql_statement <-
paste(readLines(con = postprocess_sql),
collapse = "\n")
sql_statement <-
glue::glue(sql_statement)
pg13::send(
conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql,
checks = ''
)
}
}
meerapatelmd/setupMetathesaurus documentation built on May 25, 2022, 6:19 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions run_setup
Documented in run_setup
#' @title
#' Instantiate Postgres
#' @inherit setup description
#' @inheritParams pkg_args
#' @rdname run_setup
#' @export
#' @importFrom pg13 lsSchema send lsTables dropTable
#' @importFrom tibble as_tibble_col
#' @importFrom dplyr mutate select distinct filter
#' @importFrom stringr str_remove_all
#' @importFrom progress progress_bar
#' @importFrom glue glue
run_setup <-
function(conn,
conn_fun = "pg13::local_connect()",
schema = "umls",
path_to_rrfs,
steps = c(
"reset_schema",
"ddl_tables",
"copy_rrfs",
"add_indexes",
"log",
"setup_crosswalk"),
postprocess = TRUE,
mrconso_only = "DEPRECATED",
omop_only = "DEPRECATED",
english_only = TRUE,
log_schema = "public",
log_table_name = "setup_umls_log",
log_version,
log_release_date,
verbose = TRUE,
render_sql = TRUE,
render_only = FALSE) {
schema <- schema
if (missing(log_version) | missing(log_release_date)) {
stop("`log_version` and `log_release_date` are required.")
}
if (missing(conn)) {
conn <- eval(rlang::parse_expr(conn_fun))
on.exit(expr = pg13::dc(conn = conn), add = TRUE,
after = TRUE)
}
path_to_rrfs <- normalizePath(
path = path_to_rrfs,
mustWork = TRUE
)
##### Setup Objects
errors <- vector()
tables <-
c(
"AMBIGLUI",
"AMBIGSUI",
"DELETEDCUI",
"DELETEDLUI",
"DELETEDSUI",
"MERGEDCUI",
"MERGEDLUI",
"MRAUI",
"MRCOLS",
"MRCONSO",
"MRCUI",
"MRCXT",
"MRDEF",
"MRDOC",
"MRFILES",
"MRHIER",
"MRHIST",
"MRMAP",
"MRRANK",
"MRREL",
"MRSAB",
"MRSAT",
"MRSMAP",
"MRSTY",
"MRXNS_ENG",
"MRXNW_ENG",
"MRXW_BAQ",
"MRXW_CHI",
"MRXW_CZE",
"MRXW_DAN",
"MRXW_DUT",
"MRXW_ENG",
"MRXW_EST",
"MRXW_FIN",
"MRXW_FRE",
"MRXW_GER",
"MRXW_GRE",
"MRXW_HEB",
"MRXW_HUN",
"MRXW_ITA",
"MRXW_JPN",
"MRXW_KOR",
"MRXW_LAV",
"MRXW_NOR",
"MRXW_POL",
"MRXW_POR",
"MRXW_RUS",
"MRXW_SCR",
"MRXW_SPA",
"MRXW_SWE",
"MRXW_TUR"
)
if (english_only) {
tables <-
tables[!(tables %in% c(
'MRXW_BAQ',
'MRXW_CHI',
'MRXW_CZE',
'MRXW_DAN',
'MRXW_DUT',
'MRXW_EST',
'MRXW_FIN',
'MRXW_FRE',
'MRXW_GER',
'MRXW_GRE',
'MRXW_HEB',
'MRXW_HUN',
'MRXW_ITA',
'MRXW_JPN',
'MRXW_KOR',
'MRXW_LAV',
'MRXW_NOR',
'MRXW_POL',
'MRXW_POR',
'MRXW_RUS',
'MRXW_SCR',
'MRXW_SPA',
'MRXW_SWE',
'MRXW_TUR'
))]
}
if ("reset_schema" %in% steps) {
if (
pg13::schema_exists(conn = conn,
schema = schema)) {
pg13::send(
conn = conn,
sql_statement =
glue::glue("DROP SCHEMA {schema} CASCADE;"),
verbose = verbose,
render_sql = render_sql
)
}
pg13::send(
conn = conn,
sql_statement =
glue::glue("CREATE SCHEMA {schema};"),
verbose = verbose,
render_sql = render_sql
)
}
if ("ddl_tables" %in% steps) {
ddl <-
list(
MRCOLS =
'DROP TABLE IF EXISTS {schema}.MRCOLS;
CREATE TABLE {schema}.MRCOLS (
COL varchar(40),
DES varchar(200),
REF varchar(40),
MIN integer,
AV numeric(5,2),
MAX integer,
FIL varchar(50),
DTY varchar(40),
FILLER_COL INTEGER
)',
MRCONSO =
'DROP TABLE IF EXISTS {schema}.MRCONSO;
CREATE TABLE {schema}.MRCONSO (
CUI char(8) NOT NULL,
LAT char(3) NOT NULL,
TS char(1) NOT NULL,
LUI varchar(10) NOT NULL,
STT varchar(3) NOT NULL,
SUI varchar(10) NOT NULL,
ISPREF char(1) NOT NULL,
AUI varchar(9) NOT NULL,
SAUI varchar(50),
SCUI varchar(100),
SDUI varchar(100),
SAB varchar(40) NOT NULL,
TTY varchar(40) NOT NULL,
CODE varchar(100) NOT NULL,
STR text NOT NULL,
SRL integer NOT NULL,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRCUI =
'DROP TABLE IF EXISTS {schema}.MRCUI;
CREATE TABLE {schema}.MRCUI (
CUI1 char(8) NOT NULL,
VER varchar(10) NOT NULL,
REL varchar(4) NOT NULL,
RELA varchar(100),
MAPREASON text,
CUI2 char(8),
MAPIN char(1),
FILLER_COL INTEGER
)',
MRCXT =
'DROP TABLE IF EXISTS {schema}.MRCXT;
CREATE TABLE {schema}.MRCXT (
CUI char(8),
SUI varchar(10),
AUI varchar(9),
SAB varchar(40),
CODE varchar(100),
CXN integer,
CXL char(3),
MRCXTRANK integer,
CXS text,
CUI2 char(8),
AUI2 varchar(9),
HCD varchar(100),
RELA varchar(100),
XC varchar(1),
CVF integer,
FILLER_COL INTEGER
)',
MRDEF =
'DROP TABLE IF EXISTS {schema}.MRDEF;
CREATE TABLE {schema}.MRDEF (
CUI char(8) NOT NULL,
AUI varchar(9) NOT NULL,
ATUI varchar(11) NOT NULL,
SATUI varchar(50),
SAB varchar(40) NOT NULL,
DEF text NOT NULL,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRDOC =
'DROP TABLE IF EXISTS {schema}.MRDOC;
CREATE TABLE {schema}.MRDOC (
DOCKEY varchar(50) NOT NULL,
VALUE varchar(200),
TYPE varchar(50) NOT NULL,
EXPL text,
FILLER_COL INTEGER
)',
MRFILES =
'DROP TABLE IF EXISTS {schema}.MRFILES;
CREATE TABLE {schema}.MRFILES (
FIL varchar(50),
DES varchar(200),
FMT text,
CLS integer,
RWS integer,
BTS bigint,
FILLER_COL INTEGER
)',
MRHIER =
'DROP TABLE IF EXISTS {schema}.MRHIER;
CREATE TABLE {schema}.MRHIER (
CUI char(8) NOT NULL,
AUI varchar(9) NOT NULL,
CXN integer NOT NULL,
PAUI varchar(10),
SAB varchar(40) NOT NULL,
RELA varchar(100),
PTR text,
HCD varchar(100),
CVF integer,
FILLER_COL INTEGER
)',
MRHIST =
'DROP TABLE IF EXISTS {schema}.MRHIST;
CREATE TABLE {schema}.MRHIST (
CUI char(8),
SOURCEUI varchar(100),
SAB varchar(40),
SVER varchar(40),
CHANGETYPE text,
CHANGEKEY text,
CHANGEVAL text,
REASON text,
CVF integer,
FILLER_COL INTEGER
)',
MRMAP =
'DROP TABLE IF EXISTS {schema}.MRMAP;
CREATE TABLE {schema}.MRMAP (
MAPSETCUI char(8) NOT NULL,
MAPSETSAB varchar(40) NOT NULL,
MAPSUBSETID varchar(10),
MAPRANK integer,
MAPID varchar(50) NOT NULL,
MAPSID varchar(50),
FROMID varchar(50) NOT NULL,
FROMSID varchar(50),
FROMEXPR text NOT NULL,
FROMTYPE varchar(50) NOT NULL,
FROMRULE text,
FROMRES text,
REL varchar(4) NOT NULL,
RELA varchar(100),
TOID varchar(50),
TOSID varchar(50),
TOEXPR text,
TOTYPE varchar(50),
TORULE text,
TORES text,
MAPRULE text,
MAPRES text,
MAPTYPE varchar(50),
MAPATN varchar(100),
MAPATV text,
CVF integer,
FILLER_COL INTEGER
)',
MRRANK =
'DROP TABLE IF EXISTS {schema}.MRRANK;
CREATE TABLE {schema}.MRRANK (
MRRANK_RANK integer NOT NULL,
SAB varchar(40) NOT NULL,
TTY varchar(40) NOT NULL,
SUPPRESS char(1) NOT NULL,
FILLER_COL INTEGER
)',
MRREL =
'DROP TABLE IF EXISTS {schema}.MRREL;
CREATE TABLE {schema}.MRREL (
CUI1 char(8) NOT NULL,
AUI1 varchar(9),
STYPE1 varchar(50) NOT NULL,
REL varchar(4) NOT NULL,
CUI2 char(8) NOT NULL,
AUI2 varchar(9),
STYPE2 varchar(50) NOT NULL,
RELA varchar(100),
RUI varchar(10) NOT NULL,
SRUI varchar(50),
SAB varchar(40) NOT NULL,
SL varchar(40) NOT NULL,
RG varchar(10),
DIR varchar(1),
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRSAB =
'DROP TABLE IF EXISTS {schema}.MRSAB;
CREATE TABLE {schema}.MRSAB (
VCUI char(8),
RCUI char(8),
VSAB varchar(40) NOT NULL,
RSAB varchar(40) NOT NULL,
SON text NOT NULL,
SF varchar(40) NOT NULL,
SVER varchar(40),
VSTART char(8),
VEND char(8),
IMETA varchar(10) NOT NULL,
RMETA varchar(10),
SLC text,
SCC text,
SRL integer NOT NULL,
TFR integer,
CFR integer,
CXTY varchar(50),
TTYL varchar(400),
ATNL text,
LAT char(3),
CENC varchar(40) NOT NULL,
CURVER char(1) NOT NULL,
SABIN char(1) NOT NULL,
SSN text NOT NULL,
SCIT text NOT NULL,
FILLER_COL INTEGER
)',
MRSAT =
'DROP TABLE IF EXISTS {schema}.MRSAT;
CREATE TABLE {schema}.MRSAT (
CUI char(8) NOT NULL,
LUI varchar(10),
SUI varchar(10),
METAUI varchar(100),
STYPE varchar(50) NOT NULL,
CODE varchar(100),
ATUI varchar(11) NOT NULL,
SATUI varchar(50),
ATN varchar(100) NOT NULL,
SAB varchar(40) NOT NULL,
ATV text,
SUPPRESS char(1) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRSMAP =
'DROP TABLE IF EXISTS {schema}.MRSMAP;
CREATE TABLE {schema}.MRSMAP (
MAPSETCUI char(8) NOT NULL,
MAPSETSAB varchar(40) NOT NULL,
MAPID varchar(50) NOT NULL,
MAPSID varchar(50),
FROMEXPR text NOT NULL,
FROMTYPE varchar(50) NOT NULL,
REL varchar(4) NOT NULL,
RELA varchar(100),
TOEXPR text,
TOTYPE varchar(50),
CVF integer,
FILLER_COL INTEGER
)',
MRSTY =
'DROP TABLE IF EXISTS {schema}.MRSTY;
CREATE TABLE {schema}.MRSTY (
CUI char(8) NOT NULL,
TUI char(4) NOT NULL,
STN varchar(100) NOT NULL,
STY varchar(50) NOT NULL,
ATUI varchar(11) NOT NULL,
CVF integer,
FILLER_COL INTEGER
)',
MRXNS_ENG =
'DROP TABLE IF EXISTS {schema}.MRXNS_ENG;
CREATE TABLE {schema}.MRXNS_ENG (
LAT char(3) NOT NULL,
NSTR text NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXNW_ENG =
'DROP TABLE IF EXISTS {schema}.MRXNW_ENG;
CREATE TABLE {schema}.MRXNW_ENG (
LAT char(3) NOT NULL,
NWD varchar(100) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRAUI =
'DROP TABLE IF EXISTS {schema}.MRAUI;
CREATE TABLE {schema}.MRAUI (
AUI1 varchar(9) NOT NULL,
CUI1 char(8) NOT NULL,
VER varchar(10) NOT NULL,
REL varchar(4),
RELA varchar(100),
MAPREASON text NOT NULL,
AUI2 varchar(9) NOT NULL,
CUI2 char(8) NOT NULL,
MAPIN char(1) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_BAQ =
'DROP TABLE IF EXISTS {schema}.MRXW_BAQ;
CREATE TABLE {schema}.MRXW_BAQ (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_CHI =
'DROP TABLE IF EXISTS {schema}.MRXW_CHI;
CREATE TABLE {schema}.MRXW_CHI (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_CZE =
'DROP TABLE IF EXISTS {schema}.MRXW_CZE;
CREATE TABLE {schema}.MRXW_CZE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_DAN =
'DROP TABLE IF EXISTS {schema}.MRXW_DAN;
CREATE TABLE {schema}.MRXW_DAN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_DUT =
'DROP TABLE IF EXISTS {schema}.MRXW_DUT;
CREATE TABLE {schema}.MRXW_DUT (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_ENG =
'DROP TABLE IF EXISTS {schema}.MRXW_ENG;
CREATE TABLE {schema}.MRXW_ENG (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_EST =
'DROP TABLE IF EXISTS {schema}.MRXW_EST;
CREATE TABLE {schema}.MRXW_EST (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_FIN =
'DROP TABLE IF EXISTS {schema}.MRXW_FIN;
CREATE TABLE {schema}.MRXW_FIN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_FRE =
'DROP TABLE IF EXISTS {schema}.MRXW_FRE;
CREATE TABLE {schema}.MRXW_FRE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_GER =
'DROP TABLE IF EXISTS {schema}.MRXW_GER;
CREATE TABLE {schema}.MRXW_GER (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_GRE =
'DROP TABLE IF EXISTS {schema}.MRXW_GRE;
CREATE TABLE {schema}.MRXW_GRE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_HEB =
'DROP TABLE IF EXISTS {schema}.MRXW_HEB;
CREATE TABLE {schema}.MRXW_HEB (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_HUN =
'DROP TABLE IF EXISTS {schema}.MRXW_HUN;
CREATE TABLE {schema}.MRXW_HUN (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_ITA =
'DROP TABLE IF EXISTS {schema}.MRXW_ITA;
CREATE TABLE {schema}.MRXW_ITA (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_JPN =
'DROP TABLE IF EXISTS {schema}.MRXW_JPN;
CREATE TABLE {schema}.MRXW_JPN (
LAT char(3) NOT NULL,
WD varchar(500) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_KOR =
'DROP TABLE IF EXISTS {schema}.MRXW_KOR;
CREATE TABLE {schema}.MRXW_KOR (
LAT char(3) NOT NULL,
WD varchar(500) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_LAV =
'DROP TABLE IF EXISTS {schema}.MRXW_LAV;
CREATE TABLE {schema}.MRXW_LAV (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_NOR =
'DROP TABLE IF EXISTS {schema}.MRXW_NOR;
CREATE TABLE {schema}.MRXW_NOR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_POL =
'DROP TABLE IF EXISTS {schema}.MRXW_POL;
CREATE TABLE {schema}.MRXW_POL (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_POR =
'DROP TABLE IF EXISTS {schema}.MRXW_POR;
CREATE TABLE {schema}.MRXW_POR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_RUS =
'DROP TABLE IF EXISTS {schema}.MRXW_RUS;
CREATE TABLE {schema}.MRXW_RUS (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SCR =
'DROP TABLE IF EXISTS {schema}.MRXW_SCR;
CREATE TABLE {schema}.MRXW_SCR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SPA =
'DROP TABLE IF EXISTS {schema}.MRXW_SPA;
CREATE TABLE {schema}.MRXW_SPA (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_SWE =
'DROP TABLE IF EXISTS {schema}.MRXW_SWE;
CREATE TABLE {schema}.MRXW_SWE (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
MRXW_TUR =
'DROP TABLE IF EXISTS {schema}.MRXW_TUR;
CREATE TABLE {schema}.MRXW_TUR (
LAT char(3) NOT NULL,
WD varchar(200) NOT NULL,
CUI char(8) NOT NULL,
LUI varchar(10) NOT NULL,
SUI varchar(10) NOT NULL,
FILLER_COL INTEGER
)',
AMBIGSUI =
'DROP TABLE IF EXISTS {schema}.AMBIGSUI;
CREATE TABLE {schema}.AMBIGSUI (
SUI varchar(10) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
AMBIGLUI =
'DROP TABLE IF EXISTS {schema}.AMBIGLUI;
CREATE TABLE {schema}.AMBIGLUI (
LUI varchar(10) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
DELETEDCUI =
'DROP TABLE IF EXISTS {schema}.DELETEDCUI;
CREATE TABLE {schema}.DELETEDCUI (
PCUI char(8) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
DELETEDLUI =
'DROP TABLE IF EXISTS {schema}.DELETEDLUI;
CREATE TABLE {schema}.DELETEDLUI (
PLUI varchar(10) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
DELETEDSUI =
'DROP TABLE IF EXISTS {schema}.DELETEDSUI;
CREATE TABLE {schema}.DELETEDSUI (
PSUI varchar(10) NOT NULL,
LAT char(3) NOT NULL,
PSTR text NOT NULL,
FILLER_COL INTEGER
)',
MERGEDCUI =
'DROP TABLE IF EXISTS {schema}.MERGEDCUI;
CREATE TABLE {schema}.MERGEDCUI (
PCUI char(8) NOT NULL,
CUI char(8) NOT NULL,
FILLER_COL INTEGER
)',
MERGEDLUI =
'DROP TABLE IF EXISTS {schema}.MERGEDLUI;
CREATE TABLE {schema}.MERGEDLUI (
PLUI varchar(10),
LUI varchar(10),
FILLER_COL INTEGER
)')
ddl <- ddl[tables]
for (i in seq_along(ddl)) {
pg13::send(
conn = conn,
sql_statement = glue::glue(ddl[[i]]),
verbose = verbose,
render_sql = render_sql
)
}
}
if ("copy_rrfs" %in% steps) {
rrf_files <-
list.files(
path = path_to_rrfs,
recursive = TRUE,
pattern = "[.]RRF$",
full.names = TRUE
) %>%
tibble::as_tibble_col("filePaths") %>%
dplyr::mutate(baseNames = basename(filePaths)) %>%
dplyr::mutate(tableNames = stringr::str_remove_all(baseNames, "[.]RRF$")) %>%
dplyr::filter(tableNames %in% tables) %>%
dplyr::select(filePaths) %>%
dplyr::distinct() %>%
unlist()
pb <- progress::progress_bar$new(
format = " :what [:bar] :current/:total :percent :elapsedfull",
total = length(tables),
clear = FALSE,
width = 60
)
pb$tick(0)
Sys.sleep(0.2)
errors <- vector()
for (i in 1:length(tables)) {
table <- tables[i]
rrf_path <- path.expand(
grep(
pattern = table,
rrf_files,
value = TRUE
)
)
pb$tick(tokens = list(what = table))
Sys.sleep(1)
cat("\n")
sql <- glue::glue(
"COPY {schema}.{table} FROM '{rrf_path}' WITH DELIMITER E'|' CSV QUOTE E'\b';")
output <-
tryCatch(
pg13::send(
conn = conn,
sql_statement = sql,
verbose = verbose,
render_sql = render_sql
),
error = function(e) "Error"
)
if (identical(output, "Error")) {
errors <-
c(
errors,
table
)
}
}
if (length(errors) > 0) {
typewrite("Tables:")
tables %>%
purrr::map(~ typewrite(.))
typewrite_warning("Some tables did not copy:")
errors %>%
purrr::map(~ typewrite(italicize(.)))
} else {
typewrite("All tables copied:")
tables %>%
purrr::map(~ typewrite(.))
}
}
# Log
if ("log" %in% steps) {
sql_statement <-
glue::glue(
"
CREATE TABLE IF NOT EXISTS {log_schema}.{log_table_name} (
sm_datetime timestamp without time zone NOT NULL,
sm_version varchar(100) NOT NULL,
sm_release_date varchar(25) NOT NULL,
sm_schema varchar(25) NOT NULL,
ambiglui int,
ambigsui int,
deletedcui int,
deletedlui int,
deletedsui int,
mergedcui int,
mergedlui int,
mraui int,
mrcols int,
mrconso int,
mrcui int,
mrcxt int,
mrdef int,
mrdoc int,
mrfiles int,
mrhier int,
mrhist int,
mrmap int,
mrrank int,
mrrel int,
mrsab int,
mrsat int,
mrsmap int,
mrsty int,
mrxns_eng int,
mrxnw_eng int,
mrxw_eng int
);
")
pg13::send(conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql)
table_names <-
pg13::ls_tables(
conn = conn,
schema = schema,
verbose = verbose,
render_sql = render_sql
)
current_row_count <-
table_names %>%
purrr::map(function(x) {
pg13::query(
conn = conn,
sql_statement = pg13::render_row_count(
schema = schema,
tableName = x
)
)
}) %>%
purrr::set_names(tolower(table_names)) %>%
dplyr::bind_rows(.id = "Table") %>%
dplyr::rename(Rows = count) %>%
tidyr::pivot_wider(
names_from = "Table",
values_from = "Rows"
) %>%
dplyr::mutate(
sm_datetime = as.character(Sys.time()),
sm_version = log_version,
sm_release_date = log_release_date,
sm_schema = schema
) %>%
dplyr::select(
sm_datetime,
sm_version,
sm_release_date,
sm_schema,
dplyr::all_of(c(
'ambiglui',
'ambigsui',
'deletedcui',
'deletedlui',
'deletedsui',
'mergedcui',
'mergedlui',
'mraui',
'mrcols',
'mrconso',
'mrcui',
'mrcxt',
'mrdef',
'mrdoc',
'mrfiles',
'mrhier',
'mrhist',
'mrmap',
'mrrank',
'mrrel',
'mrsab',
'mrsat',
'mrsmap',
'mrsty',
'mrxns_eng',
'mrxnw_eng',
'mrxw_eng'
))
)
current_row_count <-
unname(unlist(current_row_count))
sql_statement <-
glue::glue(
"
INSERT INTO {log_schema}.{log_table_name}
VALUES ({glue::glue_collapse(glue::single_quote(current_row_count), sep = ', ')})
;
"
)
pg13::send(conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql)
cli::cat_line()
cli::cat_boxx("Log Results",
float = "center"
)
sql_statement <-
glue::glue(
"
SELECT *
FROM {log_schema}.{log_table_name}
WHERE sm_datetime IN (SELECT MAX(sm_datetime) FROM {log_schema}.{log_table_name});
"
)
updated_log <-
pg13::query(
conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql,
checks = ''
)
print(tibble::as_tibble(updated_log))
cli::cat_line()
}
if ("add_indexes" %in% steps) {
indexes <-
c(
"CREATE INDEX X_MRCOC_CUI1 ON {schema}.MRCOC(CUI1);",
"CREATE INDEX X_MRCOC_AUI1 ON {schema}.MRCOC(AUI1);",
"CREATE INDEX X_MRCOC_CUI2 ON {schema}.MRCOC(CUI2);",
"CREATE INDEX X_MRCOC_AUI2 ON {schema}.MRCOC(AUI2);",
"CREATE INDEX X_MRCOC_SAB ON {schema}.MRCOC(SAB);",
"CREATE INDEX X_MRCONSO_CUI ON {schema}.MRCONSO(CUI);",
"ALTER TABLE {schema}.MRCONSO ADD CONSTRAINT X_MRCONSO_PK PRIMARY KEY (AUI);",
"CREATE INDEX X_MRCONSO_SUI ON {schema}.MRCONSO(SUI);",
"CREATE INDEX X_MRCONSO_LUI ON {schema}.MRCONSO(LUI);",
"CREATE INDEX X_MRCONSO_CODE ON {schema}.MRCONSO(CODE);",
"CREATE INDEX X_MRCONSO_SAB_TTY ON {schema}.MRCONSO(SAB,TTY);",
"CREATE INDEX X_MRCONSO_SCUI ON {schema}.MRCONSO(SCUI);",
"CREATE INDEX X_MRCONSO_STR ON {schema}.MRCONSO(STR);",
"CREATE INDEX X_MRCXT_CUI ON {schema}.MRCXT(CUI);",
"CREATE INDEX X_MRCXT_AUI ON {schema}.MRCXT(AUI);",
"CREATE INDEX X_MRCXT_SAB ON {schema}.MRCXT(SAB);",
"CREATE INDEX X_MRDEF_CUI ON {schema}.MRDEF(CUI);",
"CREATE INDEX X_MRDEF_AUI ON {schema}.MRDEF(AUI);",
"ALTER TABLE {schema}.MRDEF ADD CONSTRAINT X_MRDEF_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRDEF_SAB ON {schema}.MRDEF(SAB);",
"CREATE INDEX X_MRHIER_CUI ON {schema}.MRHIER(CUI);",
"CREATE INDEX X_MRHIER_AUI ON {schema}.MRHIER(AUI);",
"CREATE INDEX X_MRHIER_SAB ON {schema}.MRHIER(SAB);",
"CREATE INDEX X_MRHIER_PTR ON {schema}.MRHIER(PTR);",
"CREATE INDEX X_MRHIER_PAUI ON {schema}.MRHIER(PAUI);",
"CREATE INDEX X_MRHIST_CUI ON {schema}.MRHIST(CUI);",
"CREATE INDEX X_MRHIST_SOURCEUI ON {schema}.MRHIST(SOURCEUI);",
"CREATE INDEX X_MRHIST_SAB ON {schema}.MRHIST(SAB);",
"ALTER TABLE {schema}.MRRANK ADD CONSTRAINT X_MRRANK_PK PRIMARY KEY (SAB,TTY);",
"CREATE INDEX X_MRREL_CUI1 ON {schema}.MRREL(CUI1);",
"CREATE INDEX X_MRREL_AUI1 ON {schema}.MRREL(AUI1);",
"CREATE INDEX X_MRREL_CUI2 ON {schema}.MRREL(CUI2);",
"CREATE INDEX X_MRREL_AUI2 ON {schema}.MRREL(AUI2);",
"ALTER TABLE {schema}.MRREL ADD CONSTRAINT X_MRREL_PK PRIMARY KEY (RUI);",
"CREATE INDEX X_MRREL_SAB ON {schema}.MRREL(SAB);",
"ALTER TABLE {schema}.MRSAB ADD CONSTRAINT X_MRSAB_PK PRIMARY KEY (VSAB);",
"CREATE INDEX X_MRSAB_RSAB ON {schema}.MRSAB(RSAB);",
"CREATE INDEX X_MRSAT_CUI ON {schema}.MRSAT(CUI);",
"CREATE INDEX X_MRSAT_METAUI ON {schema}.MRSAT(METAUI);",
"ALTER TABLE {schema}.MRSAT ADD CONSTRAINT X_MRSAT_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRSAT_SAB ON {schema}.MRSAT(SAB);",
"CREATE INDEX X_MRSAT_ATN ON {schema}.MRSAT(ATN);",
"CREATE INDEX X_MRSTY_CUI ON {schema}.MRSTY(CUI);",
"ALTER TABLE {schema}.MRSTY ADD CONSTRAINT X_MRSTY_PK PRIMARY KEY (ATUI);",
"CREATE INDEX X_MRSTY_STY ON {schema}.MRSTY(STY);",
"CREATE INDEX X_MRXNS_ENG_NSTR ON {schema}.MRXNS_ENG(NSTR);",
"CREATE INDEX X_MRXNW_ENG_NWD ON {schema}.MRXNW_ENG(NWD);",
"CREATE INDEX X_MRXW_BAQ_WD ON {schema}.MRXW_BAQ(WD);",
"CREATE INDEX X_MRXW_CZE_WD ON {schema}.MRXW_CZE(WD);",
"CREATE INDEX X_MRXW_DAN_WD ON {schema}.MRXW_DAN(WD);",
"CREATE INDEX X_MRXW_DUT_WD ON {schema}.MRXW_DUT(WD);",
"CREATE INDEX X_MRXW_ENG_WD ON {schema}.MRXW_ENG(WD);",
"CREATE INDEX X_MRXW_FIN_WD ON {schema}.MRXW_FIN(WD);",
"CREATE INDEX X_MRXW_FRE_WD ON {schema}.MRXW_FRE(WD);",
"CREATE INDEX X_MRXW_GER_WD ON {schema}.MRXW_GER(WD);",
"CREATE INDEX X_MRXW_HEB_WD ON {schema}.MRXW_HEB(WD);",
"CREATE INDEX X_MRXW_HUN_WD ON {schema}.MRXW_HUN(WD);",
"CREATE INDEX X_MRXW_ITA_WD ON {schema}.MRXW_ITA(WD);",
"CREATE INDEX X_MRXW_JPN_WD ON {schema}.MRXW_JPN(WD);",
"CREATE INDEX X_MRXW_NOR_WD ON {schema}.MRXW_NOR(WD);",
"CREATE INDEX X_MRXW_POR_WD ON {schema}.MRXW_POR(WD);",
"CREATE INDEX X_MRXW_RUS_WD ON {schema}.MRXW_RUS(WD);",
"CREATE INDEX X_MRXW_SPA_WD ON {schema}.MRXW_SPA(WD);",
"CREATE INDEX X_MRXW_SWE_WD ON {schema}.MRXW_SWE(WD);",
"CREATE INDEX X_AMBIGSUI_SUI ON {schema}.AMBIGSUI(SUI);",
"CREATE INDEX X_AMBIGLUI_LUI ON {schema}.AMBIGLUI(LUI);"
)
pb <- progress::progress_bar$new(
format = " [:bar] :current/:total :percent :elapsedfull",
total = length(indexes),
clear = FALSE,
width = 60
)
pb$tick(0)
Sys.sleep(0.2)
errors <- vector()
for (i in 1:length(indexes)) {
index <- glue::glue(indexes[i])
pb$tick()
Sys.sleep(1)
cat("\n")
output <-
tryCatch(
pg13::send(
conn = conn,
sql_statement = index,
verbose = verbose,
render_sql = render_sql
),
error = function(e) "Error"
)
if (identical(output, "Error")) {
errors <-
c(
errors,
index
)
}
}
if (length(errors) > 0) {
typewrite_warning("Some indexes failed:")
errors %>%
purrr::map(~ typewrite(italicize(.)))
}
}
if ("setup_crosswalk" %in% steps) {
setup_crosswalk_schema(
conn = conn,
crosswalk_schema = "umls_crosswalk"
)
}
if (postprocess) {
run_postprocessing(
conn = conn,
umls_version = log_version,
umls_release_dt = log_release_date,
verbose = verbose,
render_sql = render_sql,
render_only = render_only
)
}
}
#' @title
#' Run Postprocessing Only
#' @rdname run_postprocessing
#' @export
#' @importFrom rlang parse_expr
#' @importFrom pg13 dc send
run_postprocessing <-
function(conn,
conn_fun = "pg13::local_connect()",
umls_version,
umls_release_dt,
verbose = TRUE,
render_sql = TRUE,
render_only = FALSE) {
if (missing(umls_version)|missing(umls_release_dt)) {
stop("`umls_version` and `umls_release_dt` are required.")
}
if (missing(conn)) {
conn <- eval(rlang::parse_expr(conn_fun))
on.exit(expr = pg13::dc(conn = conn), add = TRUE,
after = TRUE)
}
postprocess_sqls <-
list.files(system.file(package = "metathesaurus",
"sql",
"Hierarchy"),
full.names = TRUE,
pattern = "[.]{1}sql$")
for (postprocess_sql in postprocess_sqls) {
sql_statement <-
paste(readLines(con = postprocess_sql),
collapse = "\n")
sql_statement <-
glue::glue(sql_statement)
pg13::send(
conn = conn,
sql_statement = sql_statement,
verbose = verbose,
render_sql = render_sql,
checks = ''
)
}
}
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