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fvsOL: fix RSQLite drift in temp-table writes #29

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fvsOL: fix RSQLite drift in temp-table writes #29

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bfe7edb
fvsOL: fix dbWriteTable() temp-table writes for RSQLite >= 3
RoopsyDaisy Jun 1, 2026
abe9a55
fvsOL: fix dbWriteTable() in the XLSX-export handler for RSQLite >= 3
claude Jun 2, 2026
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4 changes: 2 additions & 2 deletions fvsOL/R/externalCallable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ extnMakeRun <- function (prjDir=getwd(),title=NULL,standIDs=NULL,
dbExecute(dbcon,'drop table if exists temp.Stds')
qry = paste0("select ",paste(fields,collapse=",")," from ",stdInit,
' where lower(variant) like "%',tolower(variant),'%"')
dbWriteTable(dbcon,DBI::SQL("temp.Stds"),data.frame(SelStds = standIDs))
dbWriteTable(dbcon,"Stds",data.frame(SelStds = standIDs),temporary=TRUE,overwrite=TRUE)
qry = paste0(qry," and ",sidid," in (select SelStds from temp.Stds)")

fvsInit = try(dbGetQuery(dbcon,qry))
Expand Down Expand Up @@ -847,7 +847,7 @@ extnAddStands <- function(prjDir=getwd(),runUUID,stands,
unlist(lapply(fvsRun$stands,function(x) x$sid))))
if (nrow(getStds) == 0) return(nadd)

dbWriteTable(dbcon,name=DBI::SQL("temp.getStds"),value=getStds,overwrite=TRUE)
dbWriteTable(dbcon,name="getStds",value=getStds,temporary=TRUE,overwrite=TRUE)
variant = substring(fvsRun$FVSpgm,4)
dbExecute(dbcon,'drop table if exists temp.Stds')
qry = paste0("select ",paste(fields,collapse=",")," from ",stdInit,
Expand Down
4 changes: 2 additions & 2 deletions fvsOL/R/fvsRunUtilities.R
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Expand Up @@ -1339,7 +1339,7 @@ cat ("globals$fvsRun$refreshDB=",globals$fvsRun$refreshDB,"\n")
dbExecute(dbGlb$dbIcon,'drop table if exists temp.Stds')
if (length(input$inStds))
{
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.Stds"),data.frame(SelStds = input$inStds))
dbWriteTable(dbGlb$dbIcon,"Stds",data.frame(SelStds = input$inStds),temporary=TRUE,overwrite=TRUE)
} else return()
} else {
# use if inAddGrp
Expand All @@ -1356,7 +1356,7 @@ cat ("globals$fvsRun$refreshDB=",globals$fvsRun$refreshDB,"\n")
}
if (length(stds) == 0) return()
dbExecute(dbGlb$dbIcon,'drop table if exists temp.Stds')
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.Stds"),data.frame(SelStds = stds))
dbWriteTable(dbGlb$dbIcon,"Stds",data.frame(SelStds = stds),temporary=TRUE,overwrite=TRUE)
}
qry = paste0('select ',paste0(fields,collapse=","),' from ',stdInit,
' where ',sidid,' in (select SelStds from temp.Stds)')
Expand Down
20 changes: 9 additions & 11 deletions fvsOL/R/server.R
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Expand Up @@ -2480,7 +2480,7 @@ cat ("in reloadStandSelection\n")
if (class(grps) == "try-error" || is.null(grps) || nrow(grps) == 0)
{
dbExecute(dbGlb$dbIcon,"drop table if exists temp.Grps")
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.Grps"),data.frame(Stand_ID="",Grp=""))
dbWriteTable(dbGlb$dbIcon,"Grps",data.frame(Stand_ID="",Grp=""),temporary=TRUE,overwrite=TRUE)
updateSelectInput(session=session, inputId="inGrps",choices=list())
updateSelectInput(session=session, inputId="ExtGroups",choices=list())
updateSelectInput(session=session, inputId="inStds",list())
Expand Down Expand Up @@ -2514,7 +2514,7 @@ cat ("in reloadStandSelection\n")
"StandPlot_ID" else "Stand_ID","Grp")
dd = as.data.frame(dd)
dbExecute(dbGlb$dbIcon,"drop table if exists temp.Grps")
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.Grps"),dd)
dbWriteTable(dbGlb$dbIcon,"Grps",dd,temporary=TRUE,overwrite=TRUE)
selGrp = dbGetQuery(dbGlb$dbIcon,
'select distinct Grp from temp.Grps order by Grp')[,1]

Expand Down Expand Up @@ -2545,7 +2545,7 @@ cat ("inGrps inAnyAll inStdFindBut\n")
updateSelectInput(session=session, inputId="inStds", choices=list())
} else {
dbExecute(dbGlb$dbIcon,"drop table if exists temp.SGrps")
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.SGrps"),data.frame(SelGrps = input$inGrps))
dbWriteTable(dbGlb$dbIcon,"SGrps",data.frame(SelGrps = input$inGrps),temporary=TRUE,overwrite=TRUE)
sid = if (input$inTabs %in% c("FVS_PlotInit","FVS_PlotInit_Plot"))
"StandPlot_ID" else "Stand_ID"
stds = try(dbGetQuery(dbGlb$dbIcon,paste0('select ',sid,' from temp.Grps ',
Expand Down Expand Up @@ -2584,7 +2584,7 @@ cat ("input$inStdFind=",input$inStdFind,"\n")
}
else{
dbExecute(dbGlb$dbIcon,"drop table if exists temp.SEGrps")
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.SEGrps"),data.frame(SelGrps = input$ExtGroups))
dbWriteTable(dbGlb$dbIcon,"SEGrps",data.frame(SelGrps = input$ExtGroups),temporary=TRUE,overwrite=TRUE)
sid = if (input$inTabs %in% c("FVS_PlotInit","FVS_PlotInit_Plot"))"StandPlot_ID" else "Stand_ID"
stds = try(dbGetQuery(dbGlb$dbIcon,paste0('select distinct ',sid,' from temp.Grps ',
'where Grp in (select SelGrps from temp.SEGrps)')))
Expand Down Expand Up @@ -4823,10 +4823,9 @@ cat ("in buildKeywords, oReopn=",oReopn," kwPname=",kwPname,"\n")
"where KeywordFile = '",globals$fvsRun$uuid,"';"))
if (nrow(cases) == 0) return()
cat ("download run as xlsx, ncases=",nrow(cases),"\n")
tmp = paste0("tmp",gsub("-","",runuuid),Sys.getpid(),"genoutput")
dbExecute(dbGlb$dbOcon,paste0("attach database ':memory:' as ",tmp))
casesToGet = paste0(tmp,".casesToGet")
dbWriteTable(dbGlb$dbOcon,name=DBI::SQL(casesToGet),value=cases,overwirte=TRUE)
casesToGet = "temp.casesToGet"

@wagnerds wagnerds Jun 4, 2026

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Thank you for your contribution and making these important updates. I am working on determining the reasoning for originally naming the temporary database with the run id and pid at this location and whether the change to a much simpler identifier will have any unanticipated effects.

dbExecute(dbGlb$dbOcon,"drop table if exists temp.casesToGet")
dbWriteTable(dbGlb$dbOcon,"casesToGet",cases,temporary=TRUE,overwrite=TRUE)
out = list()
cmpYes = if ("CmpMetaData" %in% tabs)
{
Expand All @@ -4845,7 +4844,6 @@ cat ("download run as xlsx, ncases=",nrow(cases),"\n")
out[[tab]] = dat
cat ("qry=",qry," class(dat)=",class(dat),"\n")
}
dbExecute(dbGlb$dbOcon,paste0("detach database ",tmp,";"))
if (length(out)) write.xlsx(file=tf,out)
}, contentType=NULL)
## dlPrjBackup
Expand Down Expand Up @@ -5644,7 +5642,7 @@ cat ("mapDsRunList input$mapDsRunList=",input$mapDsRunList,"\n")
# if there are reps (same stand more than once), just use the first rep, ignore the others
cases = cases[!duplicated(cases$StandID),]
dbExecute(dbGlb$dbOcon,"drop table if exists temp.mapsCases")
dbWriteTable(dbGlb$dbOcon,DBI::SQL("temp.mapsCases"),cases[,1,drop=FALSE])
dbWriteTable(dbGlb$dbOcon,"mapsCases",cases[,1,drop=FALSE],temporary=TRUE,overwrite=TRUE)
tabs = setdiff(myListTables(dbGlb$dbOcon),
c("CmpSummary","FVS_Cases","CmpSummary_East"))
tables = list()
Expand Down Expand Up @@ -5794,7 +5792,7 @@ cat ("left to get: length(uidsToGet)=",length(uidsToGet),
})
if (is.null(inInit)) inInit = getTableName(dbGlb$dbIcon,"FVS_StandInit")
cat ("mapDsRunList trying to use the table=",inInit,"\n")
dbWriteTable(dbGlb$dbIcon,DBI::SQL("temp.uidsToGet"),data.frame(stds=uidsToGet),overwrite=TRUE)
dbWriteTable(dbGlb$dbIcon,"uidsToGet",data.frame(stds=uidsToGet),temporary=TRUE,overwrite=TRUE)
sid = if (inInit %in% c("FVS_PlotInit","FVS_PlotInit_Plot"))
"StandPlot_ID" else "Stand_ID"
qry = paste0("select distinct ",sid," as Stand_ID,Latitude,Longitude from ",inInit,
Expand Down
2 changes: 1 addition & 1 deletion fvsOL/R/writeKeyFile.R
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Expand Up @@ -433,7 +433,7 @@ writeKeyFile <- function (globals,dbIcon,keyFileName=NULL,verbose=TRUE)
if (length(stds)==0) return(paste0("No stands to process. Run =",
globals$fvsRun$title," uuid=",globals$fvsRun$uuid))
dbExecute(dbIcon,'drop table if exists temp.RunStds')
dbWriteTable(dbIcon,DBI::SQL("temp.RunStds"),data.frame(RunStds = stds))
dbWriteTable(dbIcon,"RunStds",data.frame(RunStds = stds),temporary=TRUE,overwrite=TRUE)

# get the preferred ids depending on the table that was used to build the run
intable=toupper(globals$fvsRun$refreshDB)
Expand Down