utils.R

hyfabric_source <- list.files(pattern = "hyfabric_.*.tar.gz")
hyfabric_version <- substr(hyfabric_source, 10, 14)

if(!(require(hyfabric, quietly = TRUE) && packageVersion("hyfabric") == hyfabric_version)) {
  dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE)
  
  .libPaths(Sys.getenv("R_LIBS_USER"))
  
  install.packages(hyfabric_source, lib = Sys.getenv("R_LIBS_USER"),
                    repos = NULL, type = "source")
}

fix_headwaters <- function(nhd_rds, out_gpkg, new_atts = NULL, 
                           nhdpath = nhdplusTools::nhdplus_path(), 
                           par = 6) {
  
  if(!file.exists(out_gpkg)) {
  nhd <- readRDS(nhd_rds)
  
  # Need to replace headwater flowlines with the trimmed burn line event.
  # Some headwater flowlines are not fully within the catchment they go with.
  ble <- sf::read_sf(nhdpath, "BurnLineEvent")
  
  ble <- dplyr::left_join(dplyr::select(sf::st_drop_geometry(nhd), COMID), 
                          ble, by = "COMID")
  
  ble <- sf::st_zm(sf::st_as_sf(ble))
  nhd <- sf::st_zm(nhd)
  
  sf::st_geometry(nhd)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1)] <- 
    sf::st_geometry(ble)[!sf::st_is_empty(sf::st_geometry(ble)) & (nhd$StartFlag == 1)]
  
  if(!is.null(new_atts)) {
    new_atts <- data.table::fread(new_atts, 
                                  integer64 = "character", 
                                  showProgress = FALSE)
    
    if("weight" %in% names(new_atts)) new_atts <- rename(new_atts, 
                                                        ArbolateSu = weight)
    
    nhd <- select(nhd, COMID, FromNode, ToNode, 
                  StartFlag, StreamCalc, Divergence, DnMinorHyd) %>%
      left_join(new_atts, by = c("COMID" = "comid")) %>%
      nhdplusTools::align_nhdplus_names()
  }
  
  nhd <- sf::st_sf(nhd)
  
  m_to_km <- (1/1000)
  
  nhd$LENGTHKM <- as.numeric(sf::st_length(sf::st_transform(nhd, 5070))) * m_to_km
  
  custom_net <- select(sf::st_drop_geometry(nhd), 
                       COMID, FromNode, ToNode, Divergence)
  
  custom_net <- nhdplusTools::get_tocomid(custom_net, remove_coastal = FALSE)
  
  custom_net <- select(custom_net, comid, override_tocomid = tocomid)

  nhd <- left_join(nhd, custom_net, by = c("COMID" = "comid"))
  
  nhd <- mutate(nhd, override_tocomid = ifelse(toCOMID == 0, override_tocomid, toCOMID))
  
  # is a headwater and for sure flows to something.  
  check <- !nhd$COMID %in% nhd$override_tocomid & 
    !(nhd$override_tocomid == 0 | is.na(nhd$override_tocomid) | 
        !nhd$override_tocomid %in% nhd$COMID)
  check_direction <- dplyr::filter(nhd, check)
  
  if(!all(check_direction$override_tocomid[check_direction$override_tocomid != 0] %in% nhd$COMID))
    stop("this won't work")
  
  matcher <- match(check_direction$override_tocomid, nhd$COMID)
  
  matcher <- nhd[matcher, ]
  
  fn_list <- Map(list, 
                 split(check_direction, seq_len(nrow(check_direction))), 
                 split(matcher, seq_len(nrow(matcher))))
  
  cl <- parallel::makeCluster(16)
    
  # check and fix these.
  new_geom <- pbapply::pblapply(cl = cl, 
                                 X = fn_list, 
                                 FUN = function(x) {
                                   nhdplusTools::fix_flowdir(x[[1]]$COMID, 
                                               fn_list = list(flowline = x[[1]], 
                                                              network = x[[2]], 
                                                              check_end = "end"))
                                 })
  
  parallel::stopCluster(cl)
  
  # One is empty. Deal with it and remove from the replacement.
  error_index <- sapply(new_geom, inherits, what = "try-error")
  errors <- filter(nhd, COMID %in% check_direction$COMID[error_index])
  check[which(nhd$COMID %in% errors$COMID)] <- FALSE
  
  if(!all(sapply(sf::st_geometry(errors), sf::st_is_empty))) {
    stop("Errors other than empty geometry from fix flowdir")
  }
  
  new_geom <- new_geom[!error_index]
  new_geom <- do.call(c, new_geom)
  st_geometry(nhd)[check] <- new_geom
  
  nhd <- dplyr::filter(nhd, COMID %in% new_atts$comid)
  
  nhd <- select(nhd, -override_tocomid)
  
  # remove remnant attributes
  nhd <- select(nhd, -FromNode, -ToNode, -StartFlag -StreamCalc, -Divergence, -DnMinorHyd)
  
  warning("naive duplication!")
    nhd <- nhd[!duplicated(nhd$COMID), ]
  
  sf::write_sf(nhd, out_gpkg, "reference_flowlines")
  
  }
  return(out_gpkg)
}

## Is available in sbtools now, but will leave till on cran.
#' Retrieves files from SB in facet file_structure
#' @param sbitem (character) ScienceBase item ID
#' @param out_dir (directory) directory where files are downloaded
#' 
# Retrieve files from SB if files not listed under sbtools
retrieve_sb <- function(sbitem, out_dir){
  
  item <- item_get(sbitem)
  
  linked_files <- 
    lapply(item$facets, function(x) 
    {
      list(name = x$name, 
           files = lapply(x$files, function(y, out_path)
           {
             
             out_file <- file.path(out_path, y$name)
             download.file(y$downloadUri, out_file, mode = "wb")
             
             list(fname = y$name,
                  url = y$downloadUri)
             
           }, 
           out_path = file.path(data_dir, x$name)))
    })
}


#' Documents why streamgage is excluded from POIs
#' @param source (character) data source
#' @param reason (character) reason gage is excluded
#' @return writes output to file
#' 
gage_document <- function(data, source, drop_reason){
  if(!file.exists("cache/dropped_gages.csv")){
    write.csv(data %>% mutate(data_source = source, reason = drop_reason),
              "cache/dropped_gages.csv", quote = F, row.names = F)
  } else {
    write.table(data %>%
                  mutate(data_source = source, reason = drop_reason),
                file = "cache/dropped_gages.csv", append = T, sep = ",", 
                col.names = F, row.names = F, quote = F)
  }
}


#' Merges geopackages together to create CONUs geopackage of features
#' @param feat (character) Type of feature to merge (POIs, segments) character
#' @param in_gpkg  (character) geopackage to merge (GF, ND_, etc.)
#' @param out_gpkg (character) Name of output geopackage
#' @return output geopackage of CONUS for given features
#'
Merge_VPU <- function(feat, in_gpkg, out_gpkg){

  if(needs_layer(out_gpkg, feat)) {
    all_sf <- paste0(feat, "_CONUS")
    #VPUs <- c("03N", "03S", "03W")
    #VPUs <- c("10L", "10U")
    VPUs <-c(paste0("0", c(1:2)), "03N", "03S", "03W", paste0("0", c(4:9)),
             as.character(11:18), "10U", "10L")
    featCON <- do.call("rbind", lapply(VPUs, function(x) {
      tryCatch({
        layer <- ifelse(feat %in% c("POIs", "nhd_flowline", "unassigned_gages", "unassigned_TE",
                                    "reference_flowline", "reference_catchment"), 
                                    feat, paste0(feat, "_", x))
        read_sf(file.path("cache", paste0(in_gpkg, x, ".gpkg")), 
                layer)}, 
        error = function(e) stop(paste("didn't find", x,
                                       "\n Original error was", e)))
    }))
    write_sf(featCON, out_gpkg, feat)
  }
}

#' Capture all catchments (flowline, sink, etc.) in a given RPU
#' @param fcats (sf data.frame) NHDPlusv2.1 National geodatabase catchment layer
#' @param the_RPU (character) RPU to retrive full catchment set.
#' @param fl_rds character path to flowline rds file
#' @param nhd_gdb character path to NHD geodatabase
#' @return (sf data.frame) with FEATUREID, RPUID, FTYPE, TERMINAFL 
cat_rpu <- function(fcats, nhd_gdb){
  
  fl <- read_sf(nhd_gdb, "NHDFlowline_Network") %>%
    align_nhdplus_names()
  
  # read the CatchmentSP
  cats <- readRDS(fcats) %>%
    st_as_sf() %>%
    st_drop_geometry() %>%
    dplyr::select(FEATUREID, SOURCEFC)
  
  # read the Flowlines
  flowln_df <- fl %>%
    st_as_sf() %>%
    st_drop_geometry() %>%
    select(COMID, FTYPE, TerminalFl, RPUID)%>%
    rename(FEATUREID = COMID) %>%
    rename(TERMINALFL = TerminalFl)%>%
    filter(FEATUREID %in% cats$FEATUREID)
  
  # Read in sinks
  sink_df <- sf::st_read(nhd_gdb, layer = "Sink") %>%
    st_drop_geometry() %>%
    dplyr::select(SINKID, RPUID = InRPU) %>%
    dplyr::rename(FEATUREID = SINKID) %>%
    dplyr::mutate(FTYPE = "Sink", TERMINALFL = 0) %>%
    dplyr::filter(!FEATUREID %in% flowln_df$FEATUREID)
  
  #combine all the RPUIDs
  lkup_rpu <- rbind(flowln_df, sink_df)
  
  # FEATUREID 10957920, 20131674, 24534636 - this are the ids of the missing, checked on map,
  #     they look like they should not be used

  # add the records for the missing
  missrec_df <- data.frame(FEATUREID=c(10957920, 20131674, 245346360), 
                           RPUID = c("03a", "03d", "17b"),
                           TERMINALFL = c(0, 0, 0)) %>%
    mutate(FTYPE = "")
  
  lkup_rpu2 <- rbind(lkup_rpu, missrec_df)
  return(lkup_rpu2)
}

merge_conus <- function(rpu_vpu, rpu_vpu_out,
                        lookup_table_refactor, 
                        reconciled_layer, 
                        divide_layer, 
                        agg_fline_layer,
                        agg_cats_layer,
                        mapped_outlets_layer) {
  
  vpus <- unique(rpu_vpu$vpuid)
  
  #gf_gpkgs <- paste0("cache/refactor_", vpus, ".gpkg")
  gf_gpkgs <- paste0("cache/GF_", vpus, ".gpkg")
  
  hydrofab::assign_global_identifiers(
    gpkgs = gf_gpkgs, 
    outfiles = gsub("cache", "temp", gf_gpkgs), 
    flowpath_layer = agg_fline_layer, #reconciled_layer, 
    mapped_POI_layer = mapped_outlets_layer, 
    divide_layer = agg_cats_layer, #divide_layer, 
    lookup_table_layer = lookup_table_refactor, 
    flowpath_edge_list = catchment_network_table, 
    update_terminals = TRUE, 
    return_lookup = TRUE, 
    verbose = TRUE)
  
}



merge_refactor <- function(rpus, 
                           rpu_vpu_out, 
                           lookup_table_refactor, 
                           reconciled_layer,
                           divide_layer, 
                           split_divide_layer,
                           agg_fline_layer,
                           agg_cats_layer,
                           mapped_outlets_layer) {
  
  
  out <- rep(list(list()), length(rpus))
  names(out) <- rpus
  
  s <- 10000000
  
  for(rpu in rpus) {
    print(rpu)

    refactor_gpkg <- file.path("cache", paste0(rpu, "_refactor.gpkg"))
    aggregate_gpkg <- file.path("cache", paste0(rpu, "_aggregate.gpkg"))
    
    out[[rpu]] <- setNames(list(sf::read_sf(aggregate_gpkg, lookup_table_refactor), 
                                 sf::read_sf(refactor_gpkg, reconciled_layer), 
                                 sf::read_sf(refactor_gpkg, divide_layer), 
                                 sf::read_sf(refactor_gpkg, split_divide_layer),
                                 sf::read_sf(aggregate_gpkg, agg_fline_layer), 
                                 sf::read_sf(aggregate_gpkg, agg_cats_layer), 
                                 sf::read_sf(aggregate_gpkg, mapped_outlets_layer)),
                            c(lookup_table_refactor, 
                              reconciled_layer, 
                              divide_layer, 
                              split_divide_layer,
                              agg_fline_layer, 
                              agg_cats_layer, 
                              mapped_outlets_layer))#,

    ### RECONCILED ###
    
    out[[rpu]][[reconciled_layer]] <- select(out[[rpu]][[reconciled_layer]], 
                                             ID, toID, LENGTHKM, TotDASqKM, member_COMID, 
                                             LevelPathID = orig_levelpathID)
    
    out[[rpu]][[reconciled_layer]]$newID <- 
      seq(s, by = 1, length.out = nrow(out[[rpu]][[reconciled_layer]]))
    
    s <- max(out[[rpu]][[reconciled_layer]]$newID) + 1
    
    # get a toID that matches the new IDs
    out[[rpu]][[reconciled_layer]] <- left_join(out[[rpu]][[reconciled_layer]], 
                                                select(st_drop_geometry(out[[rpu]][[reconciled_layer]]), 
                             ID, newtoID = newID), 
                   by = c("toID" = "ID"))
    
    # find updates that we need to apply
    update <- rpu_vpu_out[!rpu_vpu_out$toCOMID %in% out[[rpu]][[lookup_table_refactor]]$NHDPlusV2_COMID &
                            rpu_vpu_out$COMID %in% out[[rpu]][[lookup_table_refactor]]$NHDPlusV2_COMID, ]
    
    # apply these updates for follow up if we got any
    if(nrow(update) > 0) {
      update <- left_join(update, out[[rpu]][[lookup_table_refactor]], 
                          by = c("COMID" = "NHDPlusV2_COMID")) %>%
        left_join(select(out[[rpu]][[lookup_table_refactor]],
                         NHDPlusV2_COMID, to_member_COMID = member_COMID), 
                  by = c("toCOMID" = "NHDPlusV2_COMID"))
      
      out[[rpu]][[reconciled_layer]] <- left_join(out[[rpu]][[reconciled_layer]], 
                                                  select(update, reconciled_ID, toCOMID),
                     by = c("ID" = "reconciled_ID"))
    }
    
    #### LOOKUP TABLE ####
    
    update_id <- sf::st_drop_geometry(select(out[[rpu]][[reconciled_layer]], 
                                             old_ID = ID, ID = newID))
    
    out[[rpu]][[lookup_table_refactor]] <- out[[rpu]][[lookup_table_refactor]] %>%
      left_join(update_id, by = c("reconciled_ID" = "old_ID")) %>%
      select(-reconciled_ID, reconciled_ID = ID) %>%
      left_join(update_id, by = c("aggregated_flowpath_ID" = "old_ID")) %>%
      select(-aggregated_flowpath_ID, aggregated_flowpath_ID = ID) %>%
      left_join(update_id, by = c("aggregated_divide_ID" = "old_ID")) %>%
      select(-aggregated_divide_ID, aggregated_divide_ID = ID) %>%
      left_join(sf::st_drop_geometry(select(out[[rpu]][[reconciled_layer]], 
                                            ID = newID, LevelPathID)),
                by = c("reconciled_ID" = "ID"))
    
    #### DIVIDE LAYER ####
    
    out[[rpu]][[divide_layer]] <- left_join(rename(out[[rpu]][[divide_layer]], 
                                                   old_ID = ID),
                                            update_id, by = c("old_ID"))
    
    out[[rpu]][[divide_layer]] <- select(out[[rpu]][[divide_layer]], 
                                         ID, areasqkm, member_COMID)
    
    out[[rpu]][[divide_layer]]$rpu <- rep(rpu, nrow(out[[rpu]][[divide_layer]]))
    
    #### aggregate layers ####
    
    for(l in c(agg_cats_layer, agg_fline_layer)) { #, mapped_outlets_layer
      
      out[[rpu]][[l]] <- left_join(rename(out[[rpu]][[l]], old_ID = ID),
                                   update_id, 
                                   by = c("old_ID"))
      
      if("toID" %in% names(out[[rpu]][[l]])) {
        out[[rpu]][[l]] <- left_join(rename(out[[rpu]][[l]], old_toID = toID),
                                     rename(update_id, toID = ID), 
                                     by = c("old_toID" = "old_ID"))
        
        sets <- select(st_drop_geometry(out[[rpu]][[l]]), ID, old_ID, old_set = set) %>%
          mutate(old_set = strsplit(old_set, ",")) %>%
          tidyr::unnest(cols = old_set) %>%
          mutate(old_set = as.integer(old_set)) %>%
          left_join(rename(update_id, set = ID), by  = c("old_set" = "old_ID")) %>%
          select(-old_set, -old_ID)
        
        sets <- split(sets$set, sets$ID)
        
        sets <- data.frame(ID = as.integer(names(sets))) %>%
          mutate(set = unname(sets))
        
        out[[rpu]][[l]] <- left_join(select(out[[rpu]][[l]], -set),
                                     sets, by = "ID")
        
        out[[rpu]][[l]] <- select(out[[rpu]][[l]], -old_ID, -old_toID)
        
        out[[rpu]][[l]] <- out[[rpu]][[l]][c("ID", "toID", "set", 
                                             names(out[[rpu]][[l]])[!names(out[[rpu]][[l]]) %in% 
                                                                      c("ID", "toID", "set", 
                                                                        attr(out[[rpu]][[l]], "sf_column"))],
                                             attr(out[[rpu]][[l]], "sf_column"))]
        
        out[[rpu]][[l]]$set <- sapply(out[[rpu]][[l]]$set, paste, collapse = ",")
      } else {
        
        out[[rpu]][[l]] <- select(out[[rpu]][[l]], -old_ID)
        
        out[[rpu]][[l]] <- out[[rpu]][[l]][c("ID", 
                                             names(out[[rpu]][[l]])[!names(out[[rpu]][[l]]) %in% 
                                                                      c("ID", 
                                                                        attr(out[[rpu]][[l]], "sf_column"))],
                                             attr(out[[rpu]][[l]], "sf_column"))]
      }
    }
    
  }
  
  out <- setNames(lapply(names(out[[1]]), function(x, out) {
    dplyr::bind_rows(lapply(out, function(df, n) {
      if("COMID" %in% names(df[[n]]) && is.numeric(df[[n]]$COMID)) 
        df[[n]]$COMID <- as.character(df[[n]]$COMID)
      df[[n]]
    }, n = x))
  }, out = out), names(out[[1]]))

  if("toCOMID" %in% names(out[[reconciled_layer]])) {
    
    # blow up so we have unique COMIDs to join on.
    # need to keep the top most of any splits (the .1 variety)
    # this makes sure out toCOMID assignments go to the right new id.
    long_form <- st_drop_geometry(out[[reconciled_layer]]) %>%
      select(newID, member_COMID) %>%
      mutate(member_COMID = strsplit(member_COMID, ",")) %>%
      tidyr::unnest(cols = member_COMID) %>%
      filter(grepl("\\.1$", member_COMID) | !grepl("\\.", member_COMID)) %>%
      mutate(NHDPlusV2_COMID = as.integer(member_COMID)) %>%
      select(-member_COMID, update_newtoID = newID)
    
    # NOTE: if the missing tocomid is in the next VPU they will still be NA
    out[[reconciled_layer]] <- left_join(out[[reconciled_layer]], 
                                         long_form, by = c("toCOMID" = "NHDPlusV2_COMID"))
    out[[reconciled_layer]]$newtoID[!is.na(out[[reconciled_layer]]$toCOMID)] <- 
      out[[reconciled_layer]]$update_newtoID[!is.na(out[[reconciled_layer]]$toCOMID)]
    
    # now use updates from refactored ids with aggregate
    long_form <- st_drop_geometry(out[[agg_fline_layer]]) %>%
      select(ID, set) %>%
      mutate(set = strsplit(set, ",")) %>%
      tidyr::unnest(cols = set) %>%
      mutate(set = as.integer(set)) %>%
      select(update_newtoID = ID, refactor_ID = set)
    
    # join updated toID from refactor so we can update as needed
    out[[agg_fline_layer]] <- out[[agg_fline_layer]] %>%
      # this adds a "new_toID" containing the refactor id that the 
      # aggregate flowpaths we are updating need to go to.
      left_join(select(st_drop_geometry(out[[reconciled_layer]]), 
                       ID = newID, new_toID = update_newtoID),
                by = "ID") %>%
      # we need to handle sets of refactor ids and get the right aggregate toID
      left_join(long_form, by = c("new_toID" = "refactor_ID"))
    # need to update the field to reflect the information joined just above.
    out[[agg_fline_layer]]$new_toID[!is.na(out[[agg_fline_layer]]$update_newtoID)] <-
      out[[agg_fline_layer]]$update_newtoID[!is.na(out[[agg_fline_layer]]$update_newtoID)]
    
    # now do the actual toID updates
    out[[agg_fline_layer]]$toID[!is.na(out[[agg_fline_layer]]$new_toID)] <- 
      out[[agg_fline_layer]]$new_toID[!is.na(out[[agg_fline_layer]]$new_toID)]
    
    out[[agg_fline_layer]] <- select(out[[agg_fline_layer]], -new_toID, -update_newtoID)
  }
  
  out[[split_divide_layer]] <- rename(out[[split_divide_layer]], comid_part = FEATUREID)
  
  out[[reconciled_layer]] <- select(out[[reconciled_layer]], ID = newID, 
                                    toID = newtoID, LENGTHKM, TotDASqKM, 
                                    member_COMID, LevelPathID, refactor_ID = ID)
  
  out
}

# FIXME: THESE FUNCTIONS SHOULD COME FROM hyFab
#' Extract nexus locations for Reference POIs
#' @param gpkg a reference hydrofabric gpkg
#' @param type the type of desired POIs
#' @param verbose should messages be emitted?
#' @return data.frame with ID, type columns
#' @export
nexus_from_poi = function(mapped_POIs,
                          type = c('HUC12', 'Gages', 'TE', 'NID', 'WBIn', 'WBOut'),
                          verbose = TRUE){
  
  # Will either be inferred - or - reference... use "unique" ID (comid facepalm).
  
  valid_types = c('HUC12', 'Gages', 'TE', 'NID', 'WBIn', 'WBOut', "Conf", "Term", "Elev", "Travel", "Con")
  
  if(!all(type %in% valid_types)){
    bad_ids = type[!which(type %in% valid_types)]
    stop(bad_ids, " are not valid POI types. Only ", paste(valid_types, collapse = ", "), " are valid")
  }
  
  if(is.null(type)){
    type = valid_types
  }
  
  nexus_locations  = mapped_POIs %>%
    st_drop_geometry()  %>%
    select(ID, identifier, paste0("Type_", type)) %>%
    mutate_at(vars(matches("Type_")), as.character) %>%
    mutate(poi_id = as.character(identifier),
           identifier = NULL) %>%
    group_by(ID, poi_id) %>%
    ungroup() %>%
    pivot_longer(-c(poi_id, ID)) %>%
    filter(!is.na(value)) %>%
    mutate(type = gsub("Type_", "", name),
           name = NULL)
  
  
  nexus_locations
}

#' Generate Lookup table for Aggregated Nextwork
#' @param gpkg to the aggregated network. The look up table will be added here as a layer called "lookup_table"
#' @param flowpath_name the name of the flowpath layer in gpkg
#' @param refactored_fabric the gpkg for the corresponding VPU reference fabric
#' @return data.frame
#' @export
#' @importFrom sf read_sf st_drop_geometry write_sf
#' @importFrom dplyr mutate select full_join left_join
#' @importFrom tidyr unnest

generate_lookup_table = function(nl,
                                 mapped_POIs) {
  
  # THIS IS THE CODE ABOVE!!!!
  nexus_locations = nexus_from_poi(mapped_POIs, verbose = FALSE)
  
  lu = nl$lookup_table %>%
    select(reconciled_ID, NHDPlusV2_COMID)

  names(nl$flowpaths) <- tolower(names(nl$flowpaths))
  
  nl$flowpaths <- rename(nl$flowpaths, member_COMID = set)
  
  lu2 = nl$flowpaths %>%
    st_drop_geometry() %>%
    select(
      aggregated_ID = id,
      toID        = toid,
      member_COMID  = member_comid,
      divide_ID   = id,
      POI_ID = poi_id,
      mainstem_id = levelpathid
    ) %>%
    mutate(member_COMID = strsplit(member_COMID, ","),
           POI_ID = as.integer(POI_ID)) %>%
    unnest(col = 'member_COMID') %>%
    mutate(NHDPlusV2_COMID_part = sapply( strsplit(member_COMID, "[.]"), 
                                          FUN = function(x){ x[2] }),
           NHDPlusV2_COMID_part = ifelse(is.na(NHDPlusV2_COMID_part), 1L, 
                                         as.integer(NHDPlusV2_COMID_part)),
           NHDPlusV2_COMID = sapply( strsplit(member_COMID, "[.]"),
                                     FUN = function(x){ as.numeric(x[1]) })
    ) %>%
    full_join(lu,
              by = "NHDPlusV2_COMID")
  
  
    group_by(aggregated_ID) %>%
    arrange(hydroseq) %>%
    mutate(POI_ID  = c(POI_ID[1],  rep(NA, n()-1))) %>%
    ungroup() %>%
    select(-hydroseq, - member_COMID) %>%
    left_join(select(nexus_locations, POI_ID = poi_id, value, type),
              by = "POI_ID") %>%
    select(NHDPlusV2_COMID, NHDPlusV2_COMID_part,
           reconciled_ID,
           aggregated_ID, toID, mainstem = mainstem_id,
           POI_ID, POI_TYPE = type, POI_VALUE = value)
  
  
  write_sf(lu2, gpkg, "lookup_table")
  
  return(gpkg)
  
}