source('interfaces.R')
source('createPatches.R')
source('stitchArchive.R')

dataPath = 'data'
inspectRead = 10
inspectReason = 'test selection of max IsolNr (only). mo and RIS can be NA'

reads = read_rds(file.path(dataPath, 'reads.rds'))
reads = reads %>% add_row(read = inspectRead, desription = inspectReason)
write_rds(reads, file.path(dataPath, 'reads.rds'))

tFiles = read_rds(file.path(dataPath, 'tFilesInfo.rds'))
tFileOvw = read_rds(file.path(dataPath, 'tFileOvw.rds'))

updateFileOvw = F
if (updateFileOvw) {
  # on 2022-10-20 tFiles was up-to-date, due to the daily update.
  tFiles = read_rds(file.path(dataPath, 'tFilesInfo.rds'))
  # However, tFileOvw somehow wasn't
  
  # get the last date that is present in the data sofar
  maxDate = tFileOvw %>% pull(fileDate) %>% max(na.rm = T)
  # catch up with today
  nDaysToUpdate = difftime(today(), maxDate) %>% as.numeric()
  daysToUpdate = (maxDate + 1:nDaysToUpdate)
  
  tInfoDays = tFiles %>% filter(fileDate %in% daysToUpdate)
  tFileOvwToday = deriveFileOverview(tInfoDays)
  a = assert_that(nrow(tFileOvwToday) > 0, 
                  msg = 'derivederiveFileOverview() failed')
  
  tFileOvw = tFileOvw %>% ungroup() %>% 
    add_row(tFileOvwToday) %>% 
    filter(!is.na(fileDate))
  
  # write_rds(tFiles, file.path(dataPath, 'tFilesInfo.rds')) Was up-to-date on 2022-10-20
  write_rds(tFileOvw, file.path(dataPath, 'tFileOvw.rds'))
}

# define the patch periods
tPeriods = tribble(
  ~startDate,        ~endDate,
  ymd('2022-01-01'), ymd('2022-02-01') - 1,
  ymd('2022-02-01'), ymd('2022-03-01') - 1
  # ymd('2022-03-01'), ymd('2022-04-01') - 1,
  # ymd('2022-04-01'), ymd('2022-05-01') - 1,
  # ymd('2022-05-01'), ymd('2022-06-01') - 1,
  # ymd('2022-06-01'), ymd('2022-07-01') - 1,
  # ymd('2022-07-01'), ymd('2022-08-01') - 1,
  # ymd('2022-08-01'), ymd('2022-09-01') - 1,
  # ymd('2022-09-01'), ymd('2022-10-01') - 1,
  # ymd('2022-10-01'), ymd('2022-10-20') - 1
  # ymd('2022-09-01'), ymd('2022-10-20')
)

createPatches(tPeriods, dataPath, tFiles, tFileOvw)
# stitch together patches created by createPatches.R
# readAllPatches() assumes that all bk_*.rds files are in the 'data' path and 
# that they all need to be read for stitching
tPatches = readAllPatches()# %>% filter(from >= '2022-01-01', to <= (ymd('2022-05-01') - 1))
minFrom = min(tPatches$from, na.rm = T)
maxTo   = max(tPatches$to, na.rm = T)
cat(paste0('Stitching patches: ', minFrom, ' - ', maxTo, '\n'))
tStitched = stitchPatches(tPatches, dataPath = 'data', reqColumns = abAbbrevs)
tStitched %>% write_rds(file = paste0('data/read_', inspectRead, '_', minFrom, '_', 
                                      maxTo, '_x', today(), '.rds'),
                        compress = 'gz')