May2023

bootstrap/initial/data/config.JSON

@@ -7,6 +7,6 @@
   "report_name": "SmartDots_Report_Event_398",
   "report_title": "SmartDots Report for event 398",
   "report_tokens": "tokens goes here",
-  "mode_definition": "standard",
+  "mode_definition": "multistage",
   "strata": ["strata"]
 }

bootstrap/smartdots_db.R

@@ -36,9 +36,9 @@ unlink(zipfile)
 ad <- ad[,names(ad) != "Comment"]
 
 # set experise of event organiser to 1
-if (all(is.na(ad$expertise[ad$TypeAnnotation == "eventOrganizer"]))) {
+if (all(is.na(ad$expertise[ad$TypeAnnotation == "Organizer" |ad$TypeAnnotation == "eventDelegate" |ad$TypeAnnotation == "eventOrganizer"|ad$TypeAnnotation == "Delegate"]))) {
   message("setting eventOrganiser expertise to 'expert' as none was provided.")
-  ad$expertise[ad$TypeAnnotation == "eventOrganizer"] <- 1
+  ad$expertise[ad$TypeAnnotation == "Organizer"|ad$TypeAnnotation == "eventDelegate" |ad$TypeAnnotation == "eventOrganizer"|ad$TypeAnnotation == "Delegate"] <- 1
 }
 
 # Change the Strata variable in the ad database if needed

data_checker.R

@@ -1,97 +1,102 @@
-## perform some sanity checks on the data
-
-library(icesTAF)
-library(jsonlite)
-library(tidyr)
-
-# # load configuration
-config <- read_json("bootstrap/data/config.json", simplifyVector = TRUE)
-
-# get data from bootstrap folder  -------------------------------
-ad <- read.taf("bootstrap/data/smartdots_db/ad.csv")
-
-# tag some feilds as missing?
-
-# some messages to the user ------
-frmt_vector <- function(x) {
-  namesx <- names(x)
-  namesx[namesx == ""] <- "<missing>"
-  paste(paste0(namesx, ": ", x), collapse = ", ")
-}
-
-check_ad <- function(ad, what = "ad") {
-  checks <-
-    list(
-      c("Summary of ", what),
-      c("number of annotations: ", nrow(ad)),
-      c("samples with missing area: ", sum(ad$ices_area == "")),
-      c("samples with missing stock: ", sum(is.na(ad$stock) | ad$stock == "")),
-      c("samples with missing prep_method: ", sum(is.na(ad$prep_method) | ad$prep_method == "")),
-      c("prep_method names: ", frmt_vector(table(ad$prep_method))),
-      c("Advanced reader annotations: ", sum(ad$expertise)),
-      c("Samples with missing strata: ", sum(is.na(ad$strata)))
-    )
-
-  check_text <- paste(sapply(checks, paste, collapse = ""), collapse = "\n * ")
-
-  # other checks
-  multiple_annotations <-
-    ad %>%
-    dplyr::group_by(EventID, event_name, ices_area, FishID, reader) %>%
-    dplyr::count() %>%
-    dplyr::filter(n > 1) %>%
-    dplyr::rename(annotations = n)
-
-  if (nrow(multiple_annotations) > 0) {
-    txt <- paste(capture.output(print(multiple_annotations)), collapse = "\n")
-    image_urls <-
-      sprintf(
-        "https://smartdots.ices.dk/manage/viewDetailsImage?tblEventID=%i&SmartImageID=%i",
-        multiple_annotations$EventID,
-        multiple_annotations$FishID)
-
-    check_text <-
-      paste0(check_text,
-             "\n\n*****************\n",
-               "**** Warning ****\n",
-               "*****************\n\n",
-             "Some readers have multiple annotations:\n\n",
-             txt,
-             "\n\nSee annotated images here:\n\t",
-             paste(image_urls, collapse = "\n\t")
-      )
-
-  }
-
-
-  if (sum(ad$expertise) == 0) {
-    check_text <-
-      paste0(check_text,
-             "\n\n*****************\n",
-               "**** Warning ****\n",
-               "*****************\n\n",
-             "** There are no advanced readers!                           **\n",
-             "** the report scripts require there to be advanced readers. **"
-      )
-
-  }
-
-
-  msg(check_text, "\n")
-}
-
-
-
-if (config$onlyApproved == FALSE) {
-  # check all data
-  msg("Checking ALL data for Event: ", config$event_id)
-
-  check_ad(ad, "ALL (approved and unapproved) annotations (sets of dots)")
-}
-
-msg("Checking approved data for Event: ", config$event_id)
-
-check_ad(ad, "approved annotations (sets of dots)")
-
-
-# done
+## perform some sanity checks on the data
+
+
+library(icesTAF)
+library(jsonlite)
+library(tidyr)
+
+# # load configuration
+#config <- read_json("bootstrap/data/config.json", simplifyVector = TRUE)
+config <- read_json("bootstrap/initial/data/config.json", simplifyVector = TRUE)
+
+# get data from bootstrap folder  -------------------------------
+#ad <- read.taf("bootstrap/smartdots_db/ad.csv")
+ad <- read.taf("bootstrap/data/smartdots_db/ad.csv")
+#ad <- read.taf("bootstrap/ad.csv")
+
+# tag some feilds as missing?
+
+# some messages to the user ------
+frmt_vector <- function(x) {
+  namesx <- names(x)
+  namesx[namesx == ""] <- "<missing>"
+  paste(paste0(namesx, ": ", x), collapse = ", ")
+}
+
+check_ad <- function(ad, what = "ad") {
+  checks <-
+    list(
+      c("Summary of ", what),
+      c("number of annotations: ", nrow(ad)),
+      c("samples with missing area: ", sum(ad$ices_area == "")),
+      c("samples with missing stock: ", sum(is.na(ad$stock) | ad$stock == "")),
+      c("samples with missing prep_method: ", sum(is.na(ad$prep_method) | ad$prep_method == "")),
+      c("prep_method names: ", frmt_vector(table(ad$prep_method))),
+      c("Advanced reader annotations: ", sum(ad$expertise)),
+      c("Samples with missing strata: ", sum(is.na(ad$strata)))
+    )
+
+  check_text <- paste(sapply(checks, paste, collapse = ""), collapse = "\n * ")
+
+  # other checks
+  multiple_annotations <-
+    ad %>%
+    dplyr::group_by(EventID, event_name, ices_area, FishID, reader) %>%
+    dplyr::count() %>%
+    dplyr::filter(n > 1) %>%
+    dplyr::rename(annotations = n)
+
+  if (nrow(multiple_annotations) > 0) {
+    txt <- paste(capture.output(print(multiple_annotations)), collapse = "\n")
+    image_urls <-
+      sprintf(
+        "https://smartdots.ices.dk/manage/viewDetailsImage?tblEventID=%i&SmartImageID=%i",
+        multiple_annotations$EventID,
+        multiple_annotations$FishID)
+
+    check_text <-
+      paste0(check_text,
+             "\n\n*****************\n",
+               "**** Warning ****\n",
+               "*****************\n\n",
+             "Some readers have multiple annotations:\n\n",
+             txt,
+             "\n\nSee annotated images here:\n\t",
+             paste(image_urls, collapse = "\n\t")
+      )
+
+  }
+
+
+  if (sum(ad$expertise) == 0) {
+    check_text <-
+      paste0(check_text,
+             "\n\n*****************\n",
+               "**** Warning ****\n",
+               "*****************\n\n",
+             "** There are no advanced readers!                           **\n",
+             "** the report scripts require there to be advanced readers. **"
+      )
+
+  }
+
+
+  msg(check_text, "\n")
+}
+
+
+
+if (config$onlyApproved == FALSE) {
+  # check all data
+  msg("Checking ALL data for Event: ", config$event_id)
+
+  check_ad(ad, "ALL (approved and unapproved) annotations (sets of dots)")
+}
+
+msg("Checking approved data for Event: ", config$event_id)
+
+check_ad(ad, "approved annotations (sets of dots)")
+
+
+# done
+