Remove SQL helpers: now use etnservice dependency instead

R/get_acoustic_deployments.R

@@ -53,171 +53,3 @@ get_acoustic_deployments <- function(connection,
   out <- conduct_parent_to_helpers(api)
   return(out)
 }
-
-#' get_acoustic_deployments() sql helper
-#'
-#' @inheritParams get_acoustic_deployments()
-#' @noRd
-#'
-get_acoustic_deployments_sql <- function(deployment_id = NULL,
-                                         receiver_id = NULL,
-                                         acoustic_project_code = NULL,
-                                         station_name = NULL,
-                                         open_only = FALSE) {
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-
-  # Check connection
-  check_connection(connection)
-
-  # Check deployment_id
-  if (is.null(deployment_id)) {
-    deployment_id_query <- "True"
-  } else {
-    deployment_id <- check_value(
-      deployment_id,
-      list_deployment_ids(api = FALSE),
-      "receiver_id"
-    )
-    deployment_id_query <- glue::glue_sql(
-      "dep.id_pk IN ({deployment_id*})",
-      .con = connection
-    )
-  }
-
-  # Check receiver_id
-  if (is.null(receiver_id)) {
-    receiver_id_query <- "True"
-  } else {
-    receiver_id <- check_value(
-      receiver_id,
-      list_receiver_ids(api = FALSE),
-      "receiver_id"
-    )
-    receiver_id_query <- glue::glue_sql(
-      "receiver.receiver IN ({receiver_id*})",
-      .con = connection
-    )
-  }
-
-  # Check acoustic_project_code
-  if (is.null(acoustic_project_code)) {
-    acoustic_project_code_query <- "True"
-  } else {
-    acoustic_project_code <- check_value(
-      acoustic_project_code,
-      list_acoustic_project_codes(api = FALSE),
-      "acoustic_project_code",
-      lowercase = TRUE
-    )
-    acoustic_project_code_query <- glue::glue_sql(
-      "LOWER(network_project.projectcode) IN ({acoustic_project_code*})",
-      .con = connection
-    )
-  }
-
-  # Check station_name
-  if (is.null(station_name)) {
-    station_name_query <- "True"
-  } else {
-    station_name <- check_value(
-      station_name,
-      list_station_names(api = FALSE),
-      "station_name"
-    )
-    station_name_query <- glue::glue_sql(
-      "dep.station_name IN ({station_name*})",
-      .con = connection
-    )
-  }
-
-  # Build query
-  query <- glue::glue_sql("
-    SELECT
-      dep.id_pk AS deployment_id,
-      receiver.receiver AS receiver_id,
-      network_project.projectcode AS acoustic_project_code,
-      dep.station_name AS station_name,
-      location_name AS station_description,
-      location_manager AS station_manager,
-      dep.deploy_date_time AS deploy_date_time,
-      dep.deploy_lat AS deploy_latitude,
-      dep.deploy_long AS deploy_longitude,
-      dep.intended_lat AS intended_latitude,
-      dep.intended_long AS intended_longitude,
-      dep.mooring_type AS mooring_type,
-      dep.bottom_depth AS bottom_depth,
-      dep.riser_length AS riser_length,
-      dep.instrument_depth AS deploy_depth,
-      dep.battery_install_date AS battery_installation_date,
-      dep.drop_dead_date AS battery_estimated_end_date,
-      dep.activation_datetime AS activation_date_time,
-      dep.recover_date_time AS recover_date_time,
-      dep.recover_lat AS recover_latitude,
-      dep.recover_long AS recover_longitude,
-      dep.download_date_time AS download_date_time,
-      dep.data_downloaded AS download_file_name,
-      dep.valid_data_until_datetime AS valid_data_until_date_time,
-      dep.sync_date_time AS sync_date_time,
-      dep.time_drift AS time_drift,
-      dep.ar_battery_install_date AS ar_battery_installation_date,
-      dep.ar_confirm AS ar_confirm,
-      dep.transmit_profile AS transmit_profile,
-      dep.transmit_power_output AS transmit_power_output,
-      dep.log_temperature_stats_period AS log_temperature_stats_period,
-      dep.log_temperature_sample_period AS log_temperature_sample_period,
-      dep.log_tilt_sample_period AS log_tilt_sample_period,
-      dep.log_noise_stats_period AS log_noise_stats_period,
-      dep.log_noise_sample_period AS log_noise_sample_period,
-      dep.log_depth_stats_period AS log_depth_stats_period,
-      dep.log_depth_sample_period AS log_depth_sample_period,
-      dep.comments AS comments
-      -- dep.project: dep.project_fk instead
-      -- dep.check_complete_time
-      -- dep.voltage_at_deploy
-      -- dep.voltage_at_download
-      -- dep.location_description
-      -- dep.date_created
-      -- dep.date_modified
-      -- dep.distance_to_mouth
-      -- dep.source
-      -- dep.acousticreleasenumber: cpod
-      -- dep.hydrophonecablelength: cpod
-      -- dep.recordingname: cpod
-      -- dep.hydrophonesensitivity: cpod
-      -- dep.amplifiersensitivity: cpod
-      -- dep.sample_rate: cpod
-      -- dep.external_id
-    FROM
-      acoustic.deployments AS dep
-      LEFT JOIN acoustic.receivers AS receiver
-        ON dep.receiver_fk = receiver.id_pk
-      LEFT JOIN common.projects AS network_project
-        ON dep.project_fk = network_project.id
-    WHERE
-      dep.deployment_type = 'acoustic_telemetry'
-      AND {deployment_id_query}
-      AND {receiver_id_query}
-      AND {acoustic_project_code_query}
-      AND {station_name_query}
-    ", .con = connection)
-  deployments <- DBI::dbGetQuery(connection, query)
-
-  # Filter on open deployments
-  if (open_only) {
-    deployments <- filter(deployments, is.na(.data$recover_date_time))
-  }
-
-  # Sort data
-  deployments <-
-    deployments %>%
-    dplyr::arrange(
-      .data$acoustic_project_code,
-      factor(.data$station_name, levels = list_station_names(api = FALSE)),
-      .data$deploy_date_time
-    )
-  # Close connection
-  DBI::dbDisconnect(connection)
-  # Return acoustic deployments
-  dplyr::as_tibble(deployments)
-}

R/get_acoustic_projects.R

@@ -30,58 +30,3 @@ get_acoustic_projects <- function(connection,
   out <- conduct_parent_to_helpers(api)
   return(out)
 }
-#' get_acoustic_projects() sql helper
-#'
-#' @inheritParams get_acoustic_projects()
-#' @noRd
-#'
-get_acoustic_projects_sql <- function(acoustic_project_code = NULL) {
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-  # Check connection
-  check_connection(connection)
-
-  # Check acoustic_project_code
-  if (is.null(acoustic_project_code)) {
-    acoustic_project_code_query <- "True"
-  } else {
-    acoustic_project_code <- check_value(
-      acoustic_project_code,
-      list_acoustic_project_codes(api = FALSE),
-      "acoustic_project_code",
-      lowercase = TRUE
-    )
-    acoustic_project_code_query <- glue::glue_sql(
-      "LOWER(project.project_code) IN ({acoustic_project_code*})",
-      .con = connection
-    )
-  }
-
-  project_sql <- glue::glue_sql(
-    readr::read_file(system.file("sql", "project.sql", package = "etn")),
-    .con = connection
-  )
-
-  # Build query
-  query <- glue::glue_sql("
-    SELECT
-      project.*
-    FROM
-      ({project_sql}) AS project
-    WHERE
-      project_type = 'acoustic'
-      AND {acoustic_project_code_query}
-    ", .con = connection)
-  projects <- DBI::dbGetQuery(connection, query)
-
-  # Sort data
-  projects <-
-    projects %>%
-    dplyr::arrange(.data$project_code)
-
-  # Close connection
-  DBI::dbDisconnect(connection)
-
-  # Return acoustic projects
-  dplyr::as_tibble(projects)
-}

R/get_animal_projects.R

@@ -30,15 +30,3 @@ get_animal_projects <- function(connection,
   out <- conduct_parent_to_helpers(api)
   return(out)
 }
-
-#' get_animal_projects() sql helper
-#'
-#' @inheritParams get_animal_projects()
-#' @noRd
-#'
-get_animal_projects_sql <- function(animal_project_code = NULL) {
-  do.call(getFromNamespace("get_animal_projects", ns = "etnservice"),
-          args = list(credentials = get_credentials(),
-                      animal_project_code = animal_project_code)
-  )
-}

R/get_cpod_projects.R

@@ -30,58 +30,3 @@ get_cpod_projects <- function(connection,
   out <- conduct_parent_to_helpers(api)
   return(out)
 }
-
-#' get_cpod_projects() sql helper
-#'
-#' @inheritParams get_cpod_projects()
-#' @noRd
-#'
-get_cpod_projects_sql <- function(cpod_project_code = NULL) {
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-  # Check connection
-  check_connection(connection)
-
-  # Check cpod_project_code
-  if (is.null(cpod_project_code)) {
-    cpod_project_code_query <- "True"
-  } else {
-    cpod_project_code <- check_value(
-      cpod_project_code,
-      list_cpod_project_codes(connection),
-      "cpod_project_code",
-      lowercase = TRUE
-    )
-    cpod_project_code_query <- glue::glue_sql(
-      "LOWER(project.project_code) IN ({cpod_project_code*})",
-      .con = connection
-    )
-  }
-
-  project_sql <- glue::glue_sql(
-    readr::read_file(system.file("sql", "project.sql", package = "etn")),
-    .con = connection
-  )
-
-  # Build query
-  query <- glue::glue_sql("
-    SELECT
-      project.*
-    FROM
-      ({project_sql}) AS project
-    WHERE
-      project_type = 'cpod'
-      AND {cpod_project_code_query}
-    ", .con = connection)
-  projects <- DBI::dbGetQuery(connection, query)
-
-  # Close connection
-  DBI::dbDisconnect(connection)
-
-  # Sort data
-  projects <-
-    projects %>%
-    dplyr::arrange(.data$project_code)
-
-  dplyr::as_tibble(projects)
-}

R/list_acoustic_project_codes.R

@@ -17,30 +17,3 @@ list_acoustic_project_codes <- function(connection,
   out <- conduct_parent_to_helpers(api, json = TRUE)
   return(out)
 }
-
-#' list_acoustic_project_codes() sql helper
-#'
-#' @inheritParams list_acoustic_project_codes()
-#' @noRd
-#'
-list_acoustic_project_codes_sql <- function(){
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-  # Check connection
-  check_connection(connection)
-  project_sql <- glue::glue_sql(
-    readr::read_file(system.file("sql", "project.sql", package = "etn")),
-    .con = connection
-  )
-  query <- glue::glue_sql(
-    "SELECT DISTINCT project_code FROM ({project_sql}) AS project WHERE project_type = 'acoustic'",
-    .con = connection
-  )
-  data <- DBI::dbGetQuery(connection, query)
-
-  # Close connection
-  DBI::dbDisconnect(connection)
-
-  # Return acoustic_project_codes
-  sort(data$project_code)
-}

R/list_animal_ids.R

@@ -20,26 +20,3 @@ list_animal_ids <- function(connection,
   return(out)
 }
 
-#' list_animal_ids() sql helper
-#'
-#' @inheritParams list_animal_ids()
-#' @noRd
-#'
-list_animal_ids_sql <- function() {
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-  # Check connection
-  check_connection(connection)
-
-  query <- glue::glue_sql(
-    "SELECT DISTINCT id_pk FROM common.animal_release",
-    .con = connection
-  )
-  data <- DBI::dbGetQuery(connection, query)
-
-  # Close connection
-  DBI::dbDisconnect(connection)
-
-  # Return animal ids
-  sort(data$id_pk)
-}

R/list_cpod_project_codes.R

@@ -16,31 +16,3 @@ list_cpod_project_codes <- function(connection, api = TRUE){
   return(out)
 }
 
-#' list_cpod_project_codes() sql helper
-#'
-#' @inheritParams list_cpod_project_codes()
-#' @noRd
-#'
-list_cpod_project_codes_sql <- function() {
-
-  # Create connection
-  connection <- do.call(connect_to_etn, get_credentials())
-  # Check connection
-  check_connection(connection)
-
-  project_query <- glue::glue_sql(
-    readr::read_file(system.file("sql", "project.sql", package = "etn")),
-    .con = connection
-  )
-  query <- glue::glue_sql(
-    "SELECT DISTINCT project_code FROM ({project_query}) AS project WHERE project_type = 'cpod'",
-    .con = connection
-  )
-  data <- DBI::dbGetQuery(connection, query)
-
-  # Close connection
-  DBI::dbDisconnect(connection)
-
-  # Return cpod project codes
-  sort(data$project_code)
-}