fixed liz_test folder URLs, plus made appropriate chantes to run.R so…

… it should run smoothly on Caitlin's user of the VM
afsc-gap-products · Jul 12, 2022 · 50f8fee · 50f8fee
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commit 50f8fee
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Showing 4 changed files with 98 additions and 58 deletions.
diff --git a/code/functions.R b/code/functions.R
@@ -328,11 +328,11 @@ make_varplot_wrapper <- function(maxyr,
   #                          path = dir_googledrive_upload,
   #                          overwrite = FALSE)
 
-    dir_googledrive_upload0 <- googledrive::drive_ls(path = googledrive::as_id(dir_googledrive_upload)) %>% 
-    dplyr::filter(name == "anom") %>% 
-    dplyr::select("id") %>% 
-    unlist() %>% 
-    googledrive::as_id()
+    # dir_googledrive_upload0 <- googledrive::drive_ls(path = googledrive::as_id(dir_googledrive_upload)) %>% 
+    # dplyr::filter(name == "anom") %>% 
+    # dplyr::select("id") %>% 
+    # unlist() %>% 
+    # googledrive::as_id()
 
   if (plot_mean) {
 

diff --git a/code/run.R b/code/run.R
@@ -15,7 +15,7 @@ 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/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
+#dir_googledrive_upload_bs = "https://drive.google.com/drive/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
 dir_googledrive_upload_ai = "https://drive.google.com/drive/folders/1SeNOAh5-muQ2BDgOHWZWwYIoLl68DHWX"
 #dir_googledrive_upload_test = "https://drive.google.com/drive/folders/1rsR0aFfFzrspTBFU48Bb26EJvdhIZSpl"
 
@@ -63,11 +63,10 @@ googledrive::drive_auth()
 ## 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 <- 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"))
@@ -152,9 +151,9 @@ make_varplot_wrapper(maxyr = maxyr,                               # Daily plot
 
 ## send all current files to the FTP -------------------------------------------
 # vars here defined in ftp.R
-dir_out <- paste0(getwd(),"/output/",maxyr,"_",SRVY,"/")
+dir_out <- paste0(dir_wd,"/output/",maxyr,"_",SRVY,"/")
 temp <- list.files(path = dir_out, pattern = "current_daily", full.names = FALSE)
-dest <- dev_bs
+dest <- dev_ai
 
 for (iiii in 1:length(temp)) {
   print(temp[iiii])
@@ -167,39 +166,105 @@ for (iiii in 1:length(temp)) {
     .opts=curlOptions(verbose=TRUE))
 }
 
-
 # NBS + EBS Maps --------------------------------------------------------------
 
+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/folders/1vWza36Dog0SpZLcTN22wD-iCEn6ooGCM"
+#dir_googledrive_upload_ai = "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/"
+
+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
+}
+
 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 %>%
+plot_anom <- FALSE
+survey_area$survey.grid <- survey_area$survey.grid %>% 
   sf::st_transform(x = ., survey_area$crs$input) %>%
   dplyr::rename(station = STATIONID) %>%
-  sp::merge(x = .,
+  sp::merge(x = ., 
             y = haul %>%
-              dplyr::rename(station = stationid) %>%
-              dplyr::select(station, stratum) %>%
-              dplyr::distinct(),
-            all.x = TRUE) %>%
+              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_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
@@ -215,37 +280,18 @@ make_varplot_wrapper(maxyr = maxyr,                               # Daily plot
                      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(getwd(),"/output/",maxyr,"_",SRVY,"/")
+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()
diff --git a/code/run_AI.R b/code/run_AI.R
@@ -16,7 +16,7 @@ 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_ai = "https://drive.google.com/drive/u/0/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 
@@ -67,8 +67,6 @@ googledrive::drive_auth()
 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"))
@@ -249,4 +247,3 @@ for (iiii in 1:length(temp)) {
 #     .opts=curlOptions(verbose=TRUE))
 # }
 # 
-# # sink()
diff --git a/code/run_BS.R b/code/run_BS.R
@@ -6,7 +6,6 @@
 #' ---------------------------
 
 # Knowns -----------------------------------------------------------------------
-#sink(file="C:/Users/liz.dawson/Desktop/job1.log",split=TRUE,type="output")
 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"))
@@ -15,7 +14,7 @@ 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_bs = "https://drive.google.com/drive/u/0/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"
 
@@ -67,8 +66,6 @@ googledrive::drive_auth()
 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"))
@@ -82,7 +79,7 @@ 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
+plot_anom <- FALSE
 survey_area$survey.grid <- survey_area$survey.grid %>% 
   sf::st_transform(x = ., survey_area$crs$input) %>%
   dplyr::rename(station = STATIONID) %>%