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Completar compatibilidad con MU.

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Costa 2 years ago
parent
commit
a87460b6bb
2 changed files with 203 additions and 84 deletions
  1. +198
    -79
      sqlFunctions.R
  2. +5
    -5
      workflow.R

+ 198
- 79
sqlFunctions.R

@ -1,9 +1,16 @@
require(RODBC) require(RODBC)
sqlDropLast<-function(conn, tablename, droplast=1){
sqlDropLast<-function(conn, tablename, droplast=1,dbtype=NULL){
if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
table<-sqlFetch(conn, tablename) table<-sqlFetch(conn, tablename)
table<-table[1:(nrow(table)-droplast),] table<-table[1:(nrow(table)-droplast),]
sqlSave(conn, table, tablename = tablename, safer = F)
if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
if (dbtype == "UM"){
sqlDrop(conn, tablename)
sqlSave(conn, table, tablename = tablename, safer = F)}
} }
sqlInitialize<-function(){ sqlInitialize<-function(){
@ -15,7 +22,10 @@ sqlInitialize<-function(){
source("ruta_database.R", encoding = "UTF-8") source("ruta_database.R", encoding = "UTF-8")
} }
sqlBackUp<-function(dbfile=file,bu.dir){
sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){
if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){bu.dir<-"BU_UM"}
if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"BU_OVARIO"}
db=strsplit(dbfile, "/")[[1]]%>% tail(n=1) db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
bu_path<-gsub(db,bu.dir,dbfile) bu_path<-gsub(db,bu.dir,dbfile)
if (!dir.exists(bu_path)){ if (!dir.exists(bu_path)){
@ -26,7 +36,10 @@ sqlBackUp<-function(dbfile=file,bu.dir){
file.copy(dbfile, cp_bu) file.copy(dbfile, cp_bu)
} }
sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype){
sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype == "OV"){ if (dbtype == "OV"){
db<-c("dbtables"="SAMPLES", "dbcode"="OVID", "dbsamples"="samples") db<-c("dbtables"="SAMPLES", "dbcode"="OVID", "dbsamples"="samples")
query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"]) query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
@ -47,7 +60,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype){
} }
} }
sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){
sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype == "OV"){ if (dbtype == "OV"){
db<-c("dbcode"="OVID") db<-c("dbcode"="OVID")
} }
@ -66,7 +82,8 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){
} }
if(dbtype=="UM"){ if(dbtype=="UM"){
dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id) dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
dbid$Id<-rownames(dbid)
dbid$Id<-as.numeric(rownames(dbid))
dbid$NHC<-as.numeric(dbid$NHC)
} }
rownames(dbid)<-as.character(1:nrow(dbid)) rownames(dbid)<-as.character(1:nrow(dbid))
dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC)) dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
@ -81,100 +98,202 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){
} }
} }
sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T){
upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
if (samples.mod){
## Generar código para las nuevas muestras
samples<-sqlFetch(conn, "SAMPLES")
if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1
}else{
next.samp<-1
sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype=="OV"){
upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
if (samples.mod){
## Generar código para las nuevas muestras
samples<-sqlFetch(conn, "SAMPLES")
if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1
}else{
next.samp<-1
}
last.samp<-next.samp+(length(nhcs)-1)
new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
}
if (clinics.mod){
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(conn, "CLINICS")
ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
upd.clinics$NHC<-as.character(upd.clinics$NHC)
for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
} }
last.samp<-next.samp+(length(nhcs)-1)
new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
}
if (clinics.mod){
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(conn, "CLINICS")
ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
upd.clinics$NHC<-as.character(upd.clinics$NHC)
for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
## Exportar tablas a la plantilla de entrada para su rellenado
wb <- loadWorkbook(file)
writeData(wb, "NHC", upd.ovid)
if (samples.mod){writeData(wb,"samples",samples.exp)}
if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
saveWorkbook(wb,file,overwrite = TRUE)
}
if (dbtype=="UM"){
upd.umid<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
if (samples.mod){
## Generar código para las nuevas muestras
samples<-sqlFetch(conn, "MUESTRAS")
if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){
next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1
}else{
next.samp<-1
}
last.samp<-next.samp+(length(nhcs)-1)
new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
new.samp.df<-merge(sqlFetch(dta,"UMID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "CODIGO"=new.samp))
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
}
if (clinics.mod){
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(conn, "CLINICOS")
umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
upd.clinics<-merge(umid.new,upd.clinics %>% select(-Id), all.x=T, by="UMID")
upd.clinics$NHC<-as.character(upd.clinics$NHC)
for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
}
## Exportar tablas a la plantilla de entrada para su rellenado
wb <- loadWorkbook(file)
writeData(wb, "NHC", upd.umid)
if (samples.mod){writeData(wb,"samples",samples.exp)}
if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
saveWorkbook(wb,file,overwrite = TRUE)
} }
## Exportar tablas a la plantilla de entrada para su rellenado
wb <- loadWorkbook(file)
writeData(wb, "NHC", upd.ovid)
if (samples.mod){writeData(wb,"samples",samples.exp)}
if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
saveWorkbook(wb,file,overwrite = TRUE)
} }
sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){
## Añadir código de muestra nueva a la base de datos
nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (sinc.samples & nrow(upd.samples) > 0){
upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
upd.samples$TIL_date<-as.Date(upd.samples$TIL_date)
### !! Atención, esto cambia la base de datos:
sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date"))
print("Tabla SAMPLES sincronizada.")
## Añadir código de muestra nueva a la base de datos
if (dbtype == "OV"){
print("DB OV detectada")
nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
if (sinc.samples & nrow(upd.samples) > 0){
upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
upd.samples$TIL_date<-as.Date(upd.samples$TIL_date)
### !! Atención, esto cambia la base de datos:
sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date"))
print("Tabla SAMPLES sincronizada.")
}
}
if (dbtype == "UM"){
print("DB UM detectada")
nsamples<-sqlFetch(conn, "MUESTRAS") %>% nrow
upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
if (sinc.samples & nrow(upd.samples) > 0){
upd.samples$FECHA_RECEPCION<-as.Date(upd.samples$FECHA_RECEPCION)
upd.samples$TIPO<-as.character(upd.samples$TIPO)
upd.samples$OBS<-as.character(upd.samples$OBS)
### !! Atención, esto cambia la base de datos:
sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
print("Tabla MUESTRAS sincronizada.")
}
} }
## Añadir datos clínicos modificados a la base de datos ## Añadir datos clínicos modificados a la base de datos
upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
rownames(clinics.mod)<-rnames
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
for (i in fechas){
clinics.mod[,i]<-as.Date(clinics.mod[,i])
if (dbtype == "OV"){
upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
rownames(clinics.mod)<-rnames
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
for (i in fechas){
clinics.mod[,i]<-as.Date(clinics.mod[,i])
}
sqlUpdate(conn, clinics.mod,"CLINICS")
print("Tabla CLINICS modificada.")
}
}
if (dbtype == "UM"){
upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
rownames(clinics.mod)<-rnames
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
for (i in fechas){
clinics.mod[,i]<-as.Date(clinics.mod[,i])
}
sqlUpdate(conn, clinics.mod,"CLINICOS")
print("Tabla CLINICOS modificada.")
} }
sqlUpdate(conn, clinics.mod,"CLINICS")
print("Tabla CLINICS modificada.")
} }
## Añadir datos clínicos nuevos a la base de datos ## Añadir datos clínicos nuevos a la base de datos
nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
varTypes<-rep("Date",length(fechas))
names(varTypes)<-fechas
for (i in fechas){
clinics.new[,i]<-as.Date(clinics.new[,i])
if (dbtype == "OV"){
nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
varTypes<-rep("Date",length(fechas))
names(varTypes)<-fechas
for (i in fechas){
clinics.new[,i]<-as.Date(clinics.new[,i])
}
sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
print("Tabla CLINICS sincronizada.")
}
}
if (dbtype == "UM"){
nsamples.clin<-sqlFetch(conn, "CLINICOS") %>% nrow
umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(conn, "CLINICOS") %>% pull(UMID))]
clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC)
if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.new)[grepl("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)]
varTypes<-rep("Date",length(fechas))
names(varTypes)<-fechas
for (i in fechas){
clinics.new[,i]<-as.Date(clinics.new[,i])
}
sqlSave(conn, clinics.new, tablename="CLINICOS", append = T, varTypes = varTypes)
print("Tabla CLINICOS sincronizada.")
} }
sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
print("Tabla CLINICS sincronizada.")
} }
} }
sqlMultiSamples<-function(kbl=F, NHC=F){
query<-sqlQuery(dta, "SELECT M.UMID,U.NHC,M.FECHA_RECEPCION,M.CODIGO,C.CODIGO,R.CODIGO
FROM ((MUESTRAS M
sqlMultiSamples<-function(kbl=F, NHC=F, full=F){
query<-sqlQuery(dta, "SELECT U.UMID,U.NHC,M.FECHA_RECEPCION,M.TIPO,M.CODIGO,C.CODIGO,R.CODIGO,R.ESTADO
FROM ((UMID U
LEFT OUTER JOIN MUESTRAS M ON U.UMID=M.UMID)
LEFT OUTER JOIN CNAG C ON M.CODIGO=C.CODIGO) LEFT OUTER JOIN CNAG C ON M.CODIGO=C.CODIGO)
LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO)
LEFT OUTER JOIN UMID U ON U.UMID=M.UMID") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2")
LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2")
if (full==F){query<- query %>% filter(!is.na(CODIGO))}
if (NHC==F){query<- query %>% select(-NHC)}
query<-query %>% mutate( query<-query %>% mutate(
CNAG=case_when(!is.na(CNAG)~"X",TRUE~""), CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
RNADNA=case_when(!is.na(RNADNA)~"X",TRUE~"")
)
RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
(!is.na(RNADNA) & (is.na(ESTADO)))~".",
TRUE~"")
) %>% select(-ESTADO)
if (kbl==T){ if (kbl==T){
query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped")) query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
}else{ }else{

+ 5
- 5
workflow.R

@ -1,13 +1,13 @@
source("sqlFunctions.R")
## Asegurarse de que la variable file sea la que nos corresponde:
file
source("sqlFunctions.R", encoding = "UTF-8")
# Cargar dependencias # Cargar dependencias
sqlInitialize() sqlInitialize()
## Asegurarse de que la variable file sea la que nos corresponde:
file
# Crear copia de seguridad # Crear copia de seguridad
sqlBackUp(bu.dir="BU_OVARIO")
sqlBackUp()
# Inicializar conexión # Inicializar conexión
dta<-odbcConnectAccess2007(access.file = file, dta<-odbcConnectAccess2007(access.file = file,

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