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changes to try to get maps to ftp--broken still though
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Liz.Dawson authored and Liz.Dawson committed Jul 12, 2022
1 parent e5b0d9c commit 29b1b3d
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Showing 3 changed files with 396 additions and 6 deletions.
12 changes: 6 additions & 6 deletions code/functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,7 @@ make_varplot_wrapper <- function(maxyr,
# path = dir_googledrive_upload,
# overwrite = FALSE)

dir_googledrive_upload0 <- googledrive::drive_ls(path = googledrive:as_id(dir_googledrive_upload)) %>%
dir_googledrive_upload0 <- googledrive::drive_ls(path = googledrive::as_id(dir_googledrive_upload)) %>%
dplyr::filter(name == "anom") %>%
dplyr::select("id") %>%
unlist() %>%
Expand Down Expand Up @@ -1206,12 +1206,12 @@ make_figure <- function(
}

### rename "current" plots for easy finding ------------------------------------
if (i == iterate[length(iterate)] & file_end %in% c("anom", "daily")) {
# if (i == iterate[length(iterate)] & file_end %in% c("anom", "daily")) {
temp <- list.files(path = dir_out, pattern = filename0, full.names = TRUE)
for (iiii in 1:length(temp)){
file.copy(from = temp[iiii], to = gsub(pattern = max_date, replacement = "current", x = temp[iiii]))
file.copy(from = temp[iiii], overwrite = TRUE, to = gsub(pattern = max_date, replacement = "current", x = temp[iiii]))
}
}
# }

### Upload to google drive ------------------------------------------------------

Expand All @@ -1229,10 +1229,10 @@ make_figure <- function(

if (!(is.null(dir_googledrive_upload))) {
temp <- list.files(path = dir_out, pattern = filename0, full.names = TRUE)
if (i == iterate[length(iterate)] & file_end %in% c("anom", "daily")) {
#if (i == iterate[length(iterate)] & file_end %in% c("anom", "daily")) {
temp <- c(temp,
list.files(path = dir_out, pattern = sub(pattern = max_date, replacement = "current", x = filename0), full.names = TRUE))
}
# }
for (iii in 1:length(temp)) {
drive_upload(
media = temp[iii],
Expand Down
252 changes: 252 additions & 0 deletions code/run_AI.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,252 @@
#' ---------------------------
#' title: Survey Daily and Anomaly Temperature Plot
#' OG author: Jason Conner
#' maintained: Emily Markowitz and Liz Dawson (May 2022)
#' purpose: run script
#' ---------------------------

# Knowns -----------------------------------------------------------------------

maxyr <- 2022
data_source <- "gd" # google drive
dates0 <- "latest" # "all" # latest # "all", #"2021-06-05",# Sys.Date(), # as.character(seq(as.Date("2022-07-30"), as.Date("2022-08-14"), by="days"))
shapef <- FALSE #set to TRUE to run make_grid_wrapper to run shapefiles for EBS and AI
var <- "bt"

googledrive_dl <- TRUE
dir_googledrive_log <- "https://docs.google.com/spreadsheets/d/16CJA6hKOcN1a3QNpSu3d2nTGmrmBeCdmmBCcQlLVqrE/edit#gid=315914502"
#dir_googledrive_upload_bs = "https://drive.google.com/drive/u/2/folders/1wvLejYW73nd0v_lOejmAdoCBbD2kUsbf" #NULL #"https://drive.google.com/drive/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
dir_googledrive_upload_ai = "https://drive.google.com/drive/u/2/folders/17rHN6GTkw5ywMXJ6VfyOkKXr7FY7o7B3" #NULL #"https://drive.google.com/drive/folders/1SeNOAh5-muQ2BDgOHWZWwYIoLl68DHWX"
#dir_googledrive_upload_test = "https://drive.google.com/drive/folders/1rsR0aFfFzrspTBFU48Bb26EJvdhIZSpl"

# The surveys this script will be covering
dat_survreg <- data.frame(reg_shapefile = "EBS_SHELF",
region_long = "Eastern Bering Sea",
SRVY = "EBS",
region = "BS",
vessel_id = c(94, 162), # CHANGE
vessel_shape = c("V", "A"), # CHANGE
reg_dates = "May 25 - Aug 03 2022") # CHANGE
dat_survreg <- dplyr::bind_rows(dat_survreg,
data.frame(reg_shapefile = "NBS_SHELF",
region_long = "Northern Bering Sea",
SRVY = "NBS",
region = "BS",
vessel_id = c(94, 162), # CHANGE
vessel_shape = c("V", "A"), # CHANGE
reg_dates = "Aug 03 - Aug 28 2022")) # CHANGE
dat_survreg <- dplyr::bind_rows(dat_survreg,
data.frame(reg_shapefile = "AI",
region_long = "Aleutian Islands",
SRVY = "AI",
region = "AI",
vessel_id = c(148, 176), # CHANGE
vessel_shape = c("OEX", "AP"), # CHANGE
reg_dates = "Jun 07 - Aug 17 2022")) # CHANGE
# dat_survreg <- dplyr::bind_rows(dat_survreg,
# data.frame(reg_shapefile = "GOA",
# region_long = "Gulf of Alaska",
# SRVY = "GOA",
# region = "GOA",
# vessel_id = c(148, 176), # CHANGE
# vessel_shape = c("OEX", "SS"), # CHANGE
# reg_dates = "May 25 - Aug 04")) # CHANGE

# SIGN INTO GOOGLE DRIVE--------------------------------------------------------
## This sign in needs to be here for the Task Scheduler to run, please do not comment out.
googledrive::drive_deauth()
googledrive::drive_auth()
1

# SOURCE SUPPORT SCRIPTS -------------------------------------------------------
## Actually we cant use the here package, here - it actually causes issues with
## the tasks scheduler, which has no concept of a project root folder.
#dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
#dir_wd <- "G:/EBSother/GAPsurveyTemperatureMap/"
#dir_wd <- paste0(getwd(), "/")
dir_wd <-"C:/Users/liz.dawson/Work/R/GAPSurveyTemperatureMap/"
#dir_wd <- "C:/Users/caitlin.akselrud/Work/survey-live-temperature-map/"

# sink(file=paste0(dir_wd, "/output/", Sys.Date(), "_log.txt")) # save console output

source(file = paste0(dir_wd,"code/functions.R"))
# source(file = paste0(dir_wd, "code/data_dl.R")) # you don't unnecessarily run this each time
source(file = paste0(dir_wd, "code/data.R"))
if (googledrive_dl == TRUE) {
source(file = paste0(dir_wd, "code/ftp.R")) # removed in gitignore - ask for premission
}

# Map --------------------------------------------------------------------------
# ## AI --------------------------------------------------------------------------
SRVY <- "AI"
region_akgfmaps = "ai"
plot_subtitle = "NOAA Fisheries Aleutian Islands Bottom Trawl Survey"
dir_googledrive_upload <- (dir_googledrive_upload_ai)
plot_anom <- FALSE
show_planned_stations <- FALSE
survey_area <- akgfmaps::get_base_layers(select.region = region_akgfmaps, set.crs = "auto")
survey_area$survey.grid <- rgdal::readOGR(dsn = paste0(dir_wd, '/shapefiles/'),# Prepare map objects
layer = "aigrid_trawable_thru2018_Emily",
verbose=F) %>%
sp::spTransform(x = ., CRS(survey_area$crs$input)) %>%
st_as_sf(x = .) %>%
dplyr::rename(station = ID,
stratum = STRATUM) %>%
dplyr::filter(stratum %in% unique(goa_strata0$stratum) &
stratum != 0) %>% # land
sp::merge(
x = .,
y = goa_strata0 %>%
dplyr::filter(survey == "AI") %>%
dplyr::mutate(SRVY = "AI",
region = stringr::str_to_title(inpfc_area),
region = dplyr::case_when(
region %in% c("Western Aleutians", "Chirikof") ~ "Western Aleutians",
TRUE ~ region)) %>%
dplyr::select(SRVY, stratum, region) %>%
dplyr::distinct(),
all.x = TRUE) %>%
dplyr::arrange(region)
survey_area$survey.grid1 <- survey_area$survey.grid

if(shapef == TRUE)
{
make_grid_wrapper(maxyr = maxyr, # Blank grid plot
SRVY = SRVY,
haul = haul,
dat_survreg = dat_survreg,
dir_googledrive_upload = dir_googledrive_upload,
survey_area = survey_area,
data_source = data_source,
plot_subtitle = plot_subtitle,
dir_wd = dir_wd)
}

make_varplot_wrapper(maxyr = maxyr, # Daily plot
SRVY = SRVY,
haul = haul,
dat_survreg = dat_survreg,
var = var,
dir_googledrive_upload = dir_googledrive_upload,
dates0 = dates0,
survey_area = survey_area,
plot_subtitle = plot_subtitle,
show_planned_stations = show_planned_stations,
data_source = data_source,
plot_anom = plot_anom,
dir_wd = dir_wd)
# make_varplot_wrapper(maxyr = maxyr, # Anom and mean plot
# SRVY = SRVY,
# haul = haul,
# dat_survreg = dat_survreg,
# var = var,
# dir_googledrive_upload = dir_googledrive_upload,
# dates0 = "latest",
# survey_area = survey_area,
# plot_subtitle = plot_subtitle,
# show_planned_stations = show_planned_stations,
# data_source = data_source,
# plot_daily = FALSE,
# plot_anom = TRUE,
# plot_mean = TRUE,
# dir_wd = dir_wd)

## send all current files to the FTP -------------------------------------------
# vars here defined in ftp.R
dir_out <- paste0(dir_wd,"/output/",maxyr,"_",SRVY,"/")
temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
dest <- dev_ai

for (iiii in 1:length(temp)) {
print(temp[iiii])

RCurl::ftpUpload(
what = paste0(dir_out, "/", temp[iiii]),
asText = FALSE,
to = paste0(glue::glue("{protocol}://STOR@{server}/{dest}/", temp[iiii])),
userpwd = paste0(user,":", pass),
.opts=curlOptions(verbose=TRUE))
}


# NBS + EBS Maps --------------------------------------------------------------
#
# SRVY <- "BS"
# region_akgfmaps = "bs.all"
# plot_subtitle <- "NOAA Fisheries Bering Sea Bottom Trawl Survey"
# dir_googledrive_upload <- (dir_googledrive_upload_bs)
# survey_area <- akgfmaps::get_base_layers(select.region = region_akgfmaps, set.crs = "auto")
# show_planned_stations <- TRUE
# plot_anom <- TRUE
# survey_area$survey.grid <- survey_area$survey.grid %>%
# sf::st_transform(x = ., survey_area$crs$input) %>%
# dplyr::rename(station = STATIONID) %>%
# sp::merge(x = .,
# y = haul %>%
# dplyr::rename(station = stationid) %>%
# dplyr::select(station, stratum) %>%
# dplyr::distinct(),
# all.x = TRUE) %>%
# dplyr::mutate(region = "Bering Sea")
# survey_area$place.labels$y[survey_area$place.labels$lab == "200 m"] <- -60032.7
#
# if(shapef == TRUE)
# {
# make_grid_wrapper(maxyr = maxyr, # Blank grid plot
# SRVY = SRVY,
# haul = haul,
# dat_survreg = dat_survreg,
# dir_googledrive_upload = dir_googledrive_upload,
# survey_area = survey_area,
# data_source = data_source,
# plot_subtitle = plot_subtitle,
# dir_wd = dir_wd)
# }
#
# make_varplot_wrapper(maxyr = maxyr, # Daily plot
# SRVY = SRVY,
# haul = haul,
# dat_survreg = dat_survreg,
# var = var,
# dir_googledrive_upload = dir_googledrive_upload,
# dates0 = dates0,
# survey_area = survey_area,
# plot_subtitle = plot_subtitle,
# show_planned_stations = show_planned_stations,
# data_source = data_source,
# plot_anom = plot_anom,
# dir_wd = dir_wd)
# # make_varplot_wrapper(maxyr = maxyr, # Anom and mean plot
# # SRVY = SRVY,
# # haul = haul,
# # dat_survreg = dat_survreg,
# # var = var,
# # dir_googledrive_upload = dir_googledrive_upload,
# # dates0 = "latest",
# # survey_area = survey_area,
# # plot_subtitle = plot_subtitle,
# # show_planned_stations = show_planned_stations,
# # data_source = data_source,
# # plot_daily = FALSE,
# # plot_anom = FALSE, # anom plot here doesnt make sense to print until the end
# # plot_mean = TRUE,
# # dir_wd = dir_wd)
#
## send all current files to the FTP -------------------------------------------
# vars here defined in ftp.R
# dir_out <- paste0(dir_wd, "/output/", maxyr, "_",SRVY,"/")
# temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
# dest <- dev_bs
#
# for (iiii in 1:length(temp)) {
# print(temp[iiii])
#
# RCurl::ftpUpload(
# what = paste0(dir_out, "/", temp[iiii]),
# asText = FALSE,
# to = paste0(glue::glue("{protocol}://STOR@{server}/{dest}/", temp[iiii])),
# userpwd = paste0(user,":", pass),
# .opts=curlOptions(verbose=TRUE))
# }
#
# # sink()
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