functions to query PEP pg database closes #2

R/get_data.R

@@ -0,0 +1,104 @@
+library(DBI)
+library(dbplyr)
+library(dplyr)
+library(RPostgres)
+library(sf)
+library(arrow)
+library(geoarrow)
+
+get_deployments <- function() {
+  tryCatch(
+    {
+      con <- dbConnect(
+        RPostgres::Postgres(),
+        dbname = "pep",
+        host = Sys.getenv("PEP_PG_IP"),
+        user = keyringr::get_kc_account("pgpep_londonj"),
+        password = keyringr::decrypt_kc_pw("pgpep_londonj")
+      )
+    },
+    error = function(cond) {
+      print("Unable to connect to Database.")
+    }
+  )
+
+  tbl_speno <- dplyr::tbl(con, in_schema("capture", "for_telem"))
+
+  tbl_deploy <- dplyr::tbl(con, in_schema("telem", "tbl_tag_deployments")) |>
+    dplyr::filter(species %in% c("Pv")) |>
+    dplyr::mutate(species = case_when(
+      species == "Pv" ~ "Harbor seal",
+      .default = NA
+    )) |>
+    dplyr::left_join(tbl_speno, by = c("speno", "species")) |>
+    dplyr::collect()
+
+  dbDisconnect(con)
+
+  return(tbl_deploy)
+}
+
+
+get_locations <- function(tbl_deploy = NULL) {
+  tryCatch(
+    {
+      con <- dbConnect(
+        RPostgres::Postgres(),
+        dbname = "pep",
+        host = Sys.getenv("PEP_PG_IP"),
+        user = keyringr::get_kc_account("pgpep_londonj"),
+        password = keyringr::decrypt_kc_pw("pgpep_londonj")
+      )
+    },
+    error = function(cond) {
+      print("Unable to connect to Database.")
+    }
+  )
+
+  locs_obs <- sf::st_read(con, Id("telem", "geo_wc_locs_qa")) |>
+    dplyr::collect() |> 
+    dplyr::left_join(tbl_deploy) |>
+    dplyr::select(
+      speno, deployid, ptt, instr, tag_family, type, quality, locs_dt, latitude, longitude,
+      error_radius, error_semi_major_axis, error_semi_minor_axis,
+      error_ellipse_orientation, project, species, age, sex, qa_status, deploy_dt, end_dt,
+      deploy_lat, deploy_long, capture_lat, capture_long, geom
+    ) |>
+    dplyr::filter(species == "Harbor seal")
+
+  dbDisconnect(con)
+
+  return(locs_obs)
+}
+
+
+get_timelines <- function(tbl_deploy = NULL) {
+  tryCatch(
+    {
+      con <- dbConnect(
+        RPostgres::Postgres(),
+        dbname = "pep",
+        host = Sys.getenv("PEP_PG_IP"),
+        user = keyringr::get_kc_account("pgpep_londonj"),
+        password = keyringr::decrypt_kc_pw("pgpep_londonj")
+      )
+    },
+    error = function(cond) {
+      print("Unable to connect to Database.")
+    }
+  )
+
+  tbl_timelines <- dplyr::tbl(con, in_schema("telem", "tbl_wc_histos_timeline_qa")) |>
+    dplyr::collect() |> 
+    dplyr::left_join(tbl_deploy, by = c("deployid")) |>
+    dplyr::filter(species %in% c("Pv")) |>
+    dplyr::mutate(species = case_when(
+      species == "Pv" ~ "Harbor seal",
+      .default = NA
+    )) 
+
+  dbDisconnect(con)
+
+  return(tbl_timelines)
+}
+