#' Refresh our cache of the motus database of metadata for tags,
#' receivers, projects, and species.
#'
#' This refresh is wrapped in a transaction. Before the transaction
#' is committed, we commit the git repo version of the DB, and
#' grab that commit hash.
#'
#' For each table X, if the appropriate query fails, we leave X as-is.
#'
#' @return a named logical vector indicating whether the query to update
#' each table succeeded.
#'
#' @export
#'
#' @author John Brzustowski \email{jbrzusto@@REMOVE_THIS_PART_fastmail.fm}
#'
refreshMotusMetaDBCache = function() {
funName = "refreshMotusMetaDBCache"
## shorthand for path to cache
db = MOTUS_METADB_CACHE
## tables updated successfully? assume not
rv = c(tags = FALSE,
tagDeps = FALSE,
recvDeps = FALSE,
antDeps = FALSE,
species = FALSE,
projs = FALSE,
paramOverrides = FALSE
)
## try to lock the db (by trying to lock its name)
lockSymbol(db)
## make sure we unlock the meta DB when this function exits, even on error
## NB: the runMotusProcessServer script also drops any locks held by a given
## processServer after the latter exits.
on.exit(lockSymbol(db, lock=FALSE))
## make sure we have a local copy of the motus-metadata-repo, for tracking changes
## to metadata
if (! file.exists(file.path(MOTUS_PATH$METADATA_HISTORY, ".git"))) {
safeSys(paste("git clone", MOTUS_METADATA_HISTORY_REPO, MOTUS_PATH$METADATA_HISTORY), quote=FALSE)
}
## create the database if it doesn't exist
if (! file.exists(db)) {
## create the database directly from the schema
safeSys("sqlite3", db, noQuote="<", system.file("motusMetadataSchema.sql", package="motusServer"))
}
## connect
meta = safeSQL(db)
## begin the update-metadata transaction
meta("BEGIN EXCLUSIVE TRANSACTION")
## grab projects
p = motusListProjects()
if (nrow(p) < 20) { ## arbitrary sanity check
stop("upstream listprojects API failing sanity check")
}
## fill in *something* for missing project labels (first 3 words with underscores)
fix = is.na(p$label)
p$label[fix] = unlist(lapply(strsplit(gsub(" - ", " ", p$name[fix]), " ", fixed=TRUE), function(n) paste(head(n, 3), collapse="_")))
rv["projs"] = TRUE
## replace copy of projects
meta("delete from projs")
dbWriteTable(meta$con, "projs", p, append=TRUE, row.names=FALSE)
## grab tags
tryCatch({
t = motusSearchTags()
if (nrow(t) < 1000) { ## arbitrary sanity check
stop("upstream searchtags API failing sanity check")
}
updateMetadataForTags(t, meta, p=p)
rv[c("tags", "projs", "tagDeps")] = TRUE
}, error = function(e) {
motusLog("%s: tagdeps: %s", funName, as.character(e))
})
## grab species
tryCatch({
t = motusListSpecies()
if (nrow(t) < 1000) { ## arbitrary sanity check
stop("upstream listspecies API failing sanity check")
}
meta("delete from species")
dbWriteTable(meta$con, "species", t[,c("id", "english", "french", "scientific", "group", "sort")], append=TRUE, row.names=FALSE)
rv["species"] = TRUE
}, error = function(e) {
motusLog("%s: species: %s", funName, as.character(e))
})
## grab receivers
tryCatch({
recv = data_frame()
ant = data_frame()
## Note: because the motus query isn't returning fields for which there's no data,
## we have to explicitly construct NAs
for(pid in p$id) {
if (pid == 0)
next
r = motusListSensorDeps(projectID=pid)
if (isTRUE(nrow(r) > 0)) {
if ("antennas" %in% names(r)) {
for (i in seq_len(nrow(r))) {
if (isTRUE(nrow(r$antennas[[i]]) > 0)) {
ant = bind_rows(ant, cbind(deployID=r$deployID[[i]], r$antennas[[i]]))
}
}
}
r$projectID = pid
r$antennas = NULL
recv = bind_rows(recv, r)
}
}
recv = recv %>% as.data.frame
## workaround until upstream changes format of serial numbers for Lotek receivers
recv$serno = sub("(SRX600|SRX800|SRX-DL)", "Lotek", perl=TRUE, recv$serno)
recv$receiverType = ifelse(grepl("^SG-", recv$serno, perl=TRUE), "SENSORGNOME", ifelse(grepl("^CTT-", recv$serno, perl=TRUE), "SENSORSTATION", ifelse(grepl("^SEI_", recv$serno, perl=TRUE), "SIGMA8", "LOTEK")))
if (nrow(recv) < 100 || nrow(ant) < 100) { ## arbitrary sanity check
stop("upstream listsensordeps API failing sanity check")
}
meta("delete from recvDeps")
dbWriteTable(meta$con, "recvDeps", recv, append=TRUE, row.names=FALSE)
rv["recvDeps"] = TRUE
## End any unterminated receiver deployments on receivers which have a later deployment.
## The earlier deployment is ended 1 second before the (earliest) later one begins.
meta("update recvDeps set tsEnd = (select min(t2.tsStart) - 1 from recvDeps as t2 where t2.tsStart > recvDeps.tsStart and recvDeps.serno=t2.serno) where tsEnd is null and tsStart is not null");
## update slim copy of receiver deps in mysql database
MotusDB("delete from recvDeps")
slimRecvDeps = dbGetQuery(meta$con, "select projectID, deviceID, tsStart, tsEnd from recvDeps order by projectID, deviceID, tsStart")
dbWriteTable(MotusDB$con, "recvDeps", slimRecvDeps,
append=TRUE, row.names=FALSE)
write.csv(slimRecvDeps,
file.path(MOTUS_PATH$METADATA_HISTORY, "receiver_deployments.csv"), row.names=FALSE)
meta("delete from antDeps")
dbWriteTable(meta$con, "antDeps", ant %>% as.data.frame, append=TRUE, row.names=FALSE)
rv["antDeps"] = TRUE
## create GPS fix table
## 2017-12-21 FIXME: probably obsolete; used in tagview(), but does anything on the
## server side use those coordinates?
meta("delete from recvGPS")
meta("insert or ignore into recvGPS select deviceID, tsStart, latitude as lat, longitude as lon, elevation as elev from recvDeps")
}, error = function(e) {
motusLog("%s: recvDeps: %s", funName, as.character(e))
})
## DEPRECATED: copy paramOverrides table from paramOverrides database until there's a motus
## API call to fetch these
tryCatch({
sql = ensureParamOverridesTable()
t = sql("select * from paramOverrides")
sql(.CLOSE=TRUE)
meta("delete from paramOverrides")
dbWriteTable(meta$con, "paramOverrides", t, append=TRUE, row.names=FALSE)
rv["paramOverrides"] = TRUE
write.csv(t[order(t$projectID, t$serno, t$tsStart),],
file.path(MOTUS_PATH$METADATA_HISTORY, "parameter_overrides.csv"), row.names=FALSE)
}, error = function(e) {
motusLog("%s: paramOverrides: %s", funName, as.character(e))
})
## commit any changes to the git repo that tracks history
commitMetadataHistory(meta)
## and now the moment we've all been waiting for
meta("COMMIT")
dbDisconnect(meta$con)
plotTagTimeline()
return (rv)
}
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