From 944b5df18109dc6b048f0cc8fc34f3e9df970347 Mon Sep 17 00:00:00 2001
From: Costa <47926492N@ICO.SCS.local>
Date: Mon, 20 Dec 2021 16:08:10 +0100
Subject: [PATCH] Updating documentation.
---
Docs/Readme.md | 395 ++++++++++++++++++++++++--------
Docs/sqlFunctions-doc.Rmd | 394 ++++++++++++++++++++++++--------
Docs/sqlFunctions-doc.html | 447 +++++++++++++++++++++++++++++--------
3 files changed, 940 insertions(+), 296 deletions(-)
diff --git a/Docs/Readme.md b/Docs/Readme.md
index 4fff343..e264a6e 100644
--- a/Docs/Readme.md
+++ b/Docs/Readme.md
@@ -8,6 +8,7 @@
sqlGenOVID
sqlWriteTemp
sqlSincBD
+sqlMultiSamples
@@ -19,7 +20,7 @@
Removes from Database the last (or the amount specified) entry.
### Usage
-sqlDropLast(conn, tablename, droplast=1)
+sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)
### Arguments
Argument|Description
@@ -27,6 +28,7 @@ Argument|Description
conn|connection handle returned by odbcConnect.
tablename|character: a database table name accessible from the connected DSN.
droplast|the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Removes from Database the last (or the amount specified) entry.
@@ -42,10 +44,17 @@ sqlDropLast(dta, "TableTest")
### Function
```r
-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<-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)}
}
```
@@ -94,13 +103,14 @@ sqlInitialize<-function(){
Creates a Back Up copy of the database.
### Usage
-sqlBackUp(dbfile=file,bu.dir="BU_OVARIO")
+sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)
### Arguments
Argument|Description
---|---
dbfile| Database File location.
-bu.dir| Directory under the DB file where the back up will be placed.
+conn|connection handle returned by odbcConnect.
+bu.dir|Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database.
### Details
Creates a Back Up copy of the database. It adds the date in front of the back up file.
@@ -116,7 +126,10 @@ sqlBackUp()
### Function
```r
-sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
+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)
bu_path<-gsub(db,bu.dir,dbfile)
if (!dir.exists(bu_path)){
@@ -136,7 +149,7 @@ sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
Shows if there are already samples from the specified NHCs.
### Usage
-sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)
+sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -144,6 +157,7 @@ Argument|Description
conn|connection handle returned by odbcConnect.
nhcs|Character vector with the NHCs to test.
verb|Verbose: if TRUE, all the columns from "SAMPLES" table are printed.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Takes the NHCs listed in the nhcs vector and checks if there are already samples from those patients.
@@ -160,18 +174,27 @@ sqlShowSamples()
### Function
```r
-sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
+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"){
+ 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"])
+ }
+ if (dbtype == "UM"){
+ db<-c("dbtables"="MUESTRAS", "dbcode"="UMID", "dbsamples"="CODIGO")
+ query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
+ }
+ if (nrow(sqlQuery(conn, query) %>% filter(NHC %in% nhcs)) == 0){
+ return("No hay muestras de ningún paciente.")
+ }
if (isFALSE(verb)){
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) %>%
- group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhcs),all=T)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs) %>%
+ group_by(NHC,UQ(rlang::sym(db["dbcode"]))) %>% summarise(Samples=length(UQ(rlang::sym(db["dbsamples"]))), Names=paste0(UQ(rlang::sym(db["dbsamples"])), collapse = ";")) %>%
+ merge(data.frame(NHC=nhcs),all=T) %>% mutate(NHC=factor(NHC,levels = nhcs)) %>% arrange(NHC)
}else{
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
}
}
```
@@ -181,10 +204,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
## sqlGenOVID
### Description
-Generates new consecutive OVID code for the patients that are not found in the DB.
+Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
### Usage
-sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)
+sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -193,9 +216,10 @@ conn|connection handle returned by odbcConnect.
nhcs|Character vector with the NHCs to test.
verb|Verbose: if TRUE (default), it prints the data.frame with the generated OVID codes.
sinc|If TRUE (default is FALSE for security), it adds the new entries to the "OVID" table in the DB.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
-Generates new consecutive OVID code for the patients that are not found in the DB.
+Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
### Value
If verb is TRUE, it returns a data.frame.
@@ -209,23 +233,41 @@ sqlGenOVID(sinc=T)
### Function
```r
-sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
- ovid<-sqlFetch(conn,"OVID")
+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"}
- new.nhc<-nhcs[!nhcs %in% ovid$NHC]
- next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
+ if (dbtype == "OV"){
+ db<-c("dbcode"="OVID")
+ }
+ if (dbtype == "UM"){
+ db<-c("dbcode"="UMID")
+ }
+
+ dbid<-sqlFetch(conn,db["dbcode"])
+
+ new.nhc<-nhcs[!nhcs %in% dbid$NHC]
+ next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
last.num<-next.num+(length(new.nhc)-1)
- upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
- rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
- upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
+ newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
+ if(dbtype=="OV"){
+ dbid<-rbind(dbid,newtab)
+ }
+ if(dbtype=="UM"){
+ dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
+ dbid$Id<-as.numeric(rownames(dbid))
+ dbid$NHC<-as.numeric(dbid$NHC)
+ }
+ rownames(dbid)<-as.character(1:nrow(dbid))
+ dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
if (sinc){
### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.ovid, tablename="OVID", append = T)
+ sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
print("La base ha sido actualizada.")
}
if (verb){
- return(upd.ovid)
+ return(dbid)
}
}
```
@@ -235,10 +277,10 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
## sqlWriteTemp
### Description
-Fills the Query Template file with the OVID and OV newly generated codes.
+Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.
### Usage
-sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T)
+sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL)
### Arguments
Argument|Description
@@ -248,9 +290,10 @@ nhcs|Character vector with the NHCs to test.
file|Template file that will be used to interact with the DB.
samples.mod|If TRUE (default), it fills the "samples" template sheet.
clinics.mod|If TRUE (default), it fills the "CLINICS" template sheet.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
-Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.
+Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.
### Value
Invisibly for success (and failures cause errors).
@@ -265,37 +308,74 @@ sqlWriteTemp()
### Function
```r
-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)
}
```
@@ -307,7 +387,7 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
Updates the DB with the information filled in the template file.
### Usage
-sqlSincBD(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F)
+sqlSincBD(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -316,6 +396,7 @@ conn|connection handle returned by odbcConnect.
filetemp|Template file that will be used to interact with the DB.
sinc.samples|If TRUE (default is FALSE for security), it updates the SAMPLES table in the DB with the information in the "samples" template sheet.
clinics.mod|If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the "CLINICS" template sheet.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Updates the DB with the information filled in the template file. All the "samples" entries are added as new rows (as all samples are new even if the patient was already in the DB). The new patients included in the "CLINICS" sheet are introduced in the DB as new rows and the ones that were already there are modified in its previous row location.
@@ -334,52 +415,168 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
### Function
```r
-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)
- ### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_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
- 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
- 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.")
}
}
-```
\ No newline at end of file
+```
+
+---
+
+## sqlMultiSamples
+
+### Description
+Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+### Usage
+sqlMultiSamples(kbl=F, NHC=F, full=F)
+
+### Arguments
+Argument|Description
+---|---
+kbl|formats the output table with the kableEstra style. Defaults to F.
+NHC|adds the NHC to the table in addition to the UMID. Defaults to F.
+full|prints also the patients that doesn't appear in the MUESTRAS table. Defaults to F.
+
+### Details
+Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+### Value
+A data.frame or a kableExtra table.
+
+### Examples
+```r
+dta<-odbcConnect("test")
+sqlMultiSamples()
+```
+
+### Function
+```r
+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 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(
+ CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
+ RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
+ (!is.na(RNADNA) & (is.na(ESTADO)))~".",
+ TRUE~"")
+ ) %>% select(-ESTADO)
+ if (kbl==T){
+ query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
+ }else{
+ return(query)
+ }
+}
+```
diff --git a/Docs/sqlFunctions-doc.Rmd b/Docs/sqlFunctions-doc.Rmd
index 0929061..5f00f51 100644
--- a/Docs/sqlFunctions-doc.Rmd
+++ b/Docs/sqlFunctions-doc.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(echo = TRUE)
Removes from Database the last (or the amount specified) entry.
### Usage
-sqlDropLast(conn, tablename, droplast=1)
+sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)
### Arguments
Argument|Description
@@ -26,6 +26,7 @@ Argument|Description
conn|connection handle returned by odbcConnect.
tablename|character: a database table name accessible from the connected DSN.
droplast|the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Removes from Database the last (or the amount specified) entry.
@@ -41,10 +42,17 @@ sqlDropLast(dta, "TableTest")
### Function
```r
-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<-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)}
}
```
@@ -93,13 +101,14 @@ sqlInitialize<-function(){
Creates a Back Up copy of the database.
### Usage
-sqlBackUp(dbfile=file,bu.dir="BU_OVARIO")
+sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)
### Arguments
Argument|Description
---|---
dbfile| Database File location.
-bu.dir| Directory under the DB file where the back up will be placed.
+conn|connection handle returned by odbcConnect.
+bu.dir|Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database.
### Details
Creates a Back Up copy of the database. It adds the date in front of the back up file.
@@ -115,7 +124,10 @@ sqlBackUp()
### Function
```r
-sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
+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)
bu_path<-gsub(db,bu.dir,dbfile)
if (!dir.exists(bu_path)){
@@ -135,7 +147,7 @@ sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
Shows if there are already samples from the specified NHCs.
### Usage
-sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)
+sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -143,6 +155,7 @@ Argument|Description
conn|connection handle returned by odbcConnect.
nhcs|Character vector with the NHCs to test.
verb|Verbose: if TRUE, all the columns from "SAMPLES" table are printed.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Takes the NHCs listed in the nhcs vector and checks if there are already samples from those patients.
@@ -159,18 +172,27 @@ sqlShowSamples()
### Function
```r
-sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
+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"){
+ 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"])
+ }
+ if (dbtype == "UM"){
+ db<-c("dbtables"="MUESTRAS", "dbcode"="UMID", "dbsamples"="CODIGO")
+ query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
+ }
+ if (nrow(sqlQuery(conn, query) %>% filter(NHC %in% nhcs)) == 0){
+ return("No hay muestras de ningún paciente.")
+ }
if (isFALSE(verb)){
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) %>%
- group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhcs),all=T)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs) %>%
+ group_by(NHC,UQ(rlang::sym(db["dbcode"]))) %>% summarise(Samples=length(UQ(rlang::sym(db["dbsamples"]))), Names=paste0(UQ(rlang::sym(db["dbsamples"])), collapse = ";")) %>%
+ merge(data.frame(NHC=nhcs),all=T) %>% mutate(NHC=factor(NHC,levels = nhcs)) %>% arrange(NHC)
}else{
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
}
}
```
@@ -180,10 +202,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
## sqlGenOVID
### Description
-Generates new consecutive OVID code for the patients that are not found in the DB.
+Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
### Usage
-sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)
+sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -192,9 +214,10 @@ conn|connection handle returned by odbcConnect.
nhcs|Character vector with the NHCs to test.
verb|Verbose: if TRUE (default), it prints the data.frame with the generated OVID codes.
sinc|If TRUE (default is FALSE for security), it adds the new entries to the "OVID" table in the DB.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
-Generates new consecutive OVID code for the patients that are not found in the DB.
+Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
### Value
If verb is TRUE, it returns a data.frame.
@@ -208,23 +231,41 @@ sqlGenOVID(sinc=T)
### Function
```r
-sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
- ovid<-sqlFetch(conn,"OVID")
+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"}
- new.nhc<-nhcs[!nhcs %in% ovid$NHC]
- next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
+ if (dbtype == "OV"){
+ db<-c("dbcode"="OVID")
+ }
+ if (dbtype == "UM"){
+ db<-c("dbcode"="UMID")
+ }
+
+ dbid<-sqlFetch(conn,db["dbcode"])
+
+ new.nhc<-nhcs[!nhcs %in% dbid$NHC]
+ next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
last.num<-next.num+(length(new.nhc)-1)
- upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
- rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
- upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
+ newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
+ if(dbtype=="OV"){
+ dbid<-rbind(dbid,newtab)
+ }
+ if(dbtype=="UM"){
+ dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
+ dbid$Id<-as.numeric(rownames(dbid))
+ dbid$NHC<-as.numeric(dbid$NHC)
+ }
+ rownames(dbid)<-as.character(1:nrow(dbid))
+ dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
if (sinc){
### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.ovid, tablename="OVID", append = T)
+ sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
print("La base ha sido actualizada.")
}
if (verb){
- return(upd.ovid)
+ return(dbid)
}
}
```
@@ -234,10 +275,10 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
## sqlWriteTemp
### Description
-Fills the Query Template file with the OVID and OV newly generated codes.
+Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.
### Usage
-sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T)
+sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL)
### Arguments
Argument|Description
@@ -247,9 +288,10 @@ nhcs|Character vector with the NHCs to test.
file|Template file that will be used to interact with the DB.
samples.mod|If TRUE (default), it fills the "samples" template sheet.
clinics.mod|If TRUE (default), it fills the "CLINICS" template sheet.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
-Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.
+Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.
### Value
Invisibly for success (and failures cause errors).
@@ -264,37 +306,74 @@ sqlWriteTemp()
### Function
```r
-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)
}
```
@@ -306,7 +385,7 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
Updates the DB with the information filled in the template file.
### Usage
-sqlSincBD(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F)
+sqlSincBD(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL)
### Arguments
Argument|Description
@@ -315,6 +394,7 @@ conn|connection handle returned by odbcConnect.
filetemp|Template file that will be used to interact with the DB.
sinc.samples|If TRUE (default is FALSE for security), it updates the SAMPLES table in the DB with the information in the "samples" template sheet.
clinics.mod|If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the "CLINICS" template sheet.
+dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
### Details
Updates the DB with the information filled in the template file. All the "samples" entries are added as new rows (as all samples are new even if the patient was already in the DB). The new patients included in the "CLINICS" sheet are introduced in the DB as new rows and the ones that were already there are modified in its previous row location.
@@ -333,52 +413,168 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
### Function
```r
-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$IQ_date)
- ### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date"))
- print("Tabla SAMPLES sincronizada.")
+ ## Añadir código de muestra nueva a la base de datos
+ if (dbtype == "OV"){
+ print("DB OV detectada")
+ nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
+ upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
+ if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
+
+ if (sinc.samples & nrow(upd.samples) > 0){
+ upd.samples$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$OBS)
+ ### !! Atención, esto cambia la base de datos:
+ sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
+ print("Tabla MUESTRAS sincronizada.")
+ }
}
## Añadir datos clínicos modificados a la base de datos
- upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
- ovid.mod<-upd.clinics$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$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
+ rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
+ clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
+ rownames(clinics.mod)<-rnames
+
+ ### !! Atención, esto cambia la base de datos:
+ if (sinc.clinics){
+ fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
+ for (i in fechas){
+ clinics.mod[,i]<-as.Date(clinics.mod[,i])
+ }
+ sqlUpdate(conn, clinics.mod,"CLINICOS")
+ print("Tabla CLINICOS modificada.")
}
- sqlUpdate(conn, clinics.mod,"CLINICS")
- print("Tabla CLINICS modificada.")
}
## Añadir datos clínicos nuevos a la base de datos
- nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
- ovid.new<-upd.clinics$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.")
}
}
-```
\ No newline at end of file
+```
+
+---
+
+## sqlMultiSamples
+
+### Description
+Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+### Usage
+sqlMultiSamples(kbl=F, NHC=F, full=F)
+
+### Arguments
+Argument|Description
+---|---
+kbl|formats the output table with the kableEstra style. Defaults to F.
+NHC|adds the NHC to the table in addition to the UMID. Defaults to F.
+full|prints also the patients that doesn't appear in the MUESTRAS table. Defaults to F.
+
+### Details
+Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+### Value
+A data.frame or a kableExtra table.
+
+### Examples
+```r
+dta<-odbcConnect("test")
+sqlMultiSamples()
+```
+
+### Function
+```r
+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 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(
+ CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
+ RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
+ (!is.na(RNADNA) & (is.na(ESTADO)))~".",
+ TRUE~"")
+ ) %>% select(-ESTADO)
+ if (kbl==T){
+ query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
+ }else{
+ return(query)
+ }
+}
+```
diff --git a/Docs/sqlFunctions-doc.html b/Docs/sqlFunctions-doc.html
index e3eb3f8..e7d4a33 100644
--- a/Docs/sqlFunctions-doc.html
+++ b/Docs/sqlFunctions-doc.html
@@ -176,6 +176,7 @@ pre code {
sqlGenOVID
sqlWriteTemp
sqlSincBD
+sqlMultiSamples
@@ -188,7 +189,7 @@ pre code {
Usage
-
sqlDropLast(conn, tablename, droplast=1)
+
sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)
Arguments
@@ -216,6 +217,10 @@ pre code {
droplast |
the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line. |
+
+| dbtype |
+used to manually specify the database type. It defaults to NULL and the type is deduced. |
+
@@ -234,10 +239,17 @@ sqlDropLast(dta, "TableTest")
Function
-
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<-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)}
}
@@ -298,11 +310,15 @@ sqlDropLast(dta, "TableTest")
Usage
-
sqlBackUp(dbfile=file,bu.dir=“BU_OVARIO”)
+
sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)
Arguments
+
+
+
+
+| conn |
+connection handle returned by odbcConnect. |
+
+
| bu.dir |
-Directory under the DB file where the back up will be placed. |
+Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database. |
@@ -336,7 +356,10 @@ sqlBackUp()
Function
-
sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
+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)
bu_path<-gsub(db,bu.dir,dbfile)
if (!dir.exists(bu_path)){
@@ -357,11 +380,15 @@ sqlBackUp()
Usage
-
sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)
+
sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)
Arguments
+
+
+
+
+
+| dbtype |
+used to manually specify the database type. It defaults to NULL and the type is deduced. |
+
@@ -400,18 +431,27 @@ sqlShowSamples()
Function
-
sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
+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"){
+ 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"])
+ }
+ if (dbtype == "UM"){
+ db<-c("dbtables"="MUESTRAS", "dbcode"="UMID", "dbsamples"="CODIGO")
+ query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
+ }
+ if (nrow(sqlQuery(conn, query) %>% filter(NHC %in% nhcs)) == 0){
+ return("No hay muestras de ningún paciente.")
+ }
if (isFALSE(verb)){
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) %>%
- group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhcs),all=T)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs) %>%
+ group_by(NHC,UQ(rlang::sym(db["dbcode"]))) %>% summarise(Samples=length(UQ(rlang::sym(db["dbsamples"]))), Names=paste0(UQ(rlang::sym(db["dbsamples"])), collapse = ";")) %>%
+ merge(data.frame(NHC=nhcs),all=T) %>% mutate(NHC=factor(NHC,levels = nhcs)) %>% arrange(NHC)
}else{
- sqlQuery(conn, "SELECT O.NHC,S.*
- FROM SAMPLES S
- INNER JOIN OVID O
- ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
+ sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
}
}
@@ -421,11 +461,11 @@ sqlShowSamples()
sqlGenOVID
Description
-
Generates new consecutive OVID code for the patients that are not found in the DB.
+
Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
Usage
-
sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)
+
sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)
Arguments
@@ -457,12 +497,16 @@ sqlShowSamples()
sinc |
If TRUE (default is FALSE for security), it adds the new entries to the “OVID” table in the DB. |
+
+| dbtype |
+used to manually specify the database type. It defaults to NULL and the type is deduced. |
+
Details
-
Generates new consecutive OVID code for the patients that are not found in the DB.
+
Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
Value
@@ -476,23 +520,41 @@ sqlGenOVID(sinc=T)
Function
-
sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
- ovid<-sqlFetch(conn,"OVID")
+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"){
+ db<-c("dbcode"="OVID")
+ }
+ if (dbtype == "UM"){
+ db<-c("dbcode"="UMID")
+ }
- new.nhc<-nhcs[!nhcs %in% ovid$NHC]
- next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
+ dbid<-sqlFetch(conn,db["dbcode"])
+
+ new.nhc<-nhcs[!nhcs %in% dbid$NHC]
+ next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
last.num<-next.num+(length(new.nhc)-1)
- upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
- rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
- upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
+ newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
+ if(dbtype=="OV"){
+ dbid<-rbind(dbid,newtab)
+ }
+ if(dbtype=="UM"){
+ dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
+ dbid$Id<-as.numeric(rownames(dbid))
+ dbid$NHC<-as.numeric(dbid$NHC)
+ }
+ rownames(dbid)<-as.character(1:nrow(dbid))
+ dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
if (sinc){
### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.ovid, tablename="OVID", append = T)
+ sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
print("La base ha sido actualizada.")
}
if (verb){
- return(upd.ovid)
+ return(dbid)
}
}
@@ -502,15 +564,19 @@ sqlGenOVID(sinc=T)
sqlWriteTemp
Description
-
Fills the Query Template file with the OVID and OV newly generated codes.
+
Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.
Usage
-
sqlWriteTemp(conn=dta, nhcs=nhc.test, file=“queryOV.xlsx”, samples.mod=T, clinics.mod=T)
+
sqlWriteTemp(conn=dta, nhcs=nhc.test, file=“queryOV.xlsx”, samples.mod=T, clinics.mod=T, dbtype=NULL)
Arguments
+
+
+
+
+
+| dbtype |
+used to manually specify the database type. It defaults to NULL and the type is deduced. |
+
Details
-
Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of “CLINICS” table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.
+
Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of “CLINICS” table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.
Value
@@ -558,37 +628,74 @@ sqlWriteTemp()
Function
-
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$NHC)
+ for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
+ }
+
+ ## Exportar tablas a la plantilla de entrada para su rellenado
+ wb <- loadWorkbook(file)
+ writeData(wb, "NHC", upd.umid)
+ if (samples.mod){writeData(wb,"samples",samples.exp)}
+ if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
+ saveWorkbook(wb,file,overwrite = TRUE)
}
-
- ## Exportar tablas a la plantilla de entrada para su rellenado
- wb <- loadWorkbook(file)
- writeData(wb, "NHC", upd.ovid)
- if (samples.mod){writeData(wb,"samples",samples.exp)}
- if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
- saveWorkbook(wb,file,overwrite = TRUE)
}
@@ -601,7 +708,7 @@ sqlWriteTemp()
Usage
-
sqlSincBD(conn=dta, filetemp=“QueryOV.xlsx”, sinc.samples=F, sinc.clinics=F)
+
sqlSincBD(conn=dta, filetemp=“queryOV.xlsx”, sinc.samples=F, sinc.clinics=F, dbtype=NULL)
Arguments
@@ -633,6 +740,10 @@ sqlWriteTemp()
clinics.mod |
If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the “CLINICS” template sheet. |
+
+| dbtype |
+used to manually specify the database type. It defaults to NULL and the type is deduced. |
+
@@ -654,53 +765,193 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
Function
-
sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){
- ## Añadir código de muestra nueva a la base de datos
- nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
- upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
- if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
+sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){
+ if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
+ if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
- if (sinc.samples & nrow(upd.samples) > 0){
- upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
- ### !! Atención, esto cambia la base de datos:
- sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date"))
- print("Tabla SAMPLES sincronizada.")
+ ## Añadir código de muestra nueva a la base de datos
+ if (dbtype == "OV"){
+ print("DB OV detectada")
+ nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
+ upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
+ if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
+
+ if (sinc.samples & nrow(upd.samples) > 0){
+ upd.samples$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$OBS)
+ ### !! Atención, esto cambia la base de datos:
+ sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
+ print("Tabla MUESTRAS sincronizada.")
+ }
}
## Añadir datos clínicos modificados a la base de datos
- upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
- ovid.mod<-upd.clinics$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$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
+ rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
+ clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
+ rownames(clinics.mod)<-rnames
+
+ ### !! Atención, esto cambia la base de datos:
+ if (sinc.clinics){
+ fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
+ for (i in fechas){
+ clinics.mod[,i]<-as.Date(clinics.mod[,i])
+ }
+ sqlUpdate(conn, clinics.mod,"CLINICOS")
+ print("Tabla CLINICOS modificada.")
}
- sqlUpdate(conn, clinics.mod,"CLINICS")
- print("Tabla CLINICS modificada.")
}
## Añadir datos clínicos nuevos a la base de datos
- nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
- ovid.new<-upd.clinics$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$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
+ clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
+ if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
+
+ ### !! Atención, esto cambia la base de datos:
+ if (sinc.clinics){
+ fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
+ varTypes<-rep("Date",length(fechas))
+ names(varTypes)<-fechas
+ for (i in fechas){
+ clinics.new[,i]<-as.Date(clinics.new[,i])
+ }
+ sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
+ print("Tabla CLINICS sincronizada.")
}
- sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
- print("Tabla CLINICS sincronizada.")
}
+ if (dbtype == "UM"){
+ nsamples.clin<-sqlFetch(conn, "CLINICOS") %>% nrow
+ umid.new<-upd.clinics$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.")
+ }
+ }
+}
+
+
+
+
+
sqlMultiSamples
+
+
Description
+
Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+
+
Usage
+
sqlMultiSamples(kbl=F, NHC=F, full=F)
+
+
+
Arguments
+
+
+
+
+
+
+
+
+
+
+| kbl |
+formats the output table with the kableEstra style. Defaults to F. |
+
+
+| NHC |
+adds the NHC to the table in addition to the UMID. Defaults to F. |
+
+
+| full |
+prints also the patients that doesn’t appear in the MUESTRAS table. Defaults to F. |
+
+
+
+
+
+
Details
+
Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
+
+
+
Value
+
A data.frame or a kableExtra table.
+
+
+
Examples
+
dta<-odbcConnect("test")
+sqlMultiSamples()
+
+
+
Function
+
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 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(
+ CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
+ RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
+ (!is.na(RNADNA) & (is.na(ESTADO)))~".",
+ TRUE~"")
+ ) %>% select(-ESTADO)
+ if (kbl==T){
+ query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
+ }else{
+ return(query)
+ }
}