Merge pull request #52 from BiodiversiteQuebec/feature/inject-teledetection-data

Feature/inject teledetection data #50

Author: vcameron1

R/coleo_inject.R

@@ -49,7 +49,7 @@ coleo_inject <- function(df, media_path = NULL, schema = 'public') {
   #==========================================================================
   # 1. Extract tables to be injected
   #==========================================================================
-  campaign_type <- unique(df$campaigns_type)
+  campaign_type <- coleo_return_campaign_type(df)
   tables <- coleo_return_required_tables(campaign_type)
 
   #==========================================================================
@@ -70,13 +70,21 @@ coleo_inject <- function(df, media_path = NULL, schema = 'public') {
       tables <- tables[!tables %in% "observations_landmarks_lookup"]
     }
     df_id <- coleo_inject_vegetation_transect_campaigns(df)
-  } else {
+  ## Inject campaigns
+  } else if ("campaigns_type" %in% colnames(df)) {
     df_id <- coleo_inject_table(df, "campaigns", schema = schema)
-  }
-
-  if(!any(sapply(df_id$campaign_error, is.null))) {
+    if(!any(sapply(df_id$campaign_error, is.null))) {
     cat("Only data for successfully injected campaigns are injected in the next tables. These following lines failed to inject: ", paste0(which(!sapply(df_id$campaign_error, is.null)), collapse = ", "), "\n")
   }
+  ## Inject remote sensing events
+  } else if ("remote_sensing_events_date_start" %in% colnames(df)) {
+    df_id <- coleo_inject_table(df, "remote_sensing_events", schema = schema)
+    if(!any(sapply(df_id$remote_sensing_event_error, is.null))) {
+    cat("Only data for successfully injected remote sensing indicators are injected in the next tables. These following lines failed to inject: ", paste0(which(!sapply(df_id$remote_sensing_indicators_error, is.null)), collapse = ", "), "\n")
+    }
+  }
+
+  
 
   #==========================================================================
   # 3. Inject other tables

R/coleo_prep_input_data.R

@@ -33,6 +33,19 @@ coleo_prep_input_data <- function(df, db_table, schema = "public") {
       suppressMessages()
   }
 
+  # Add remote_sensing_indicator_id to required table
+  if (db_table == "remote_sensing_events") {
+    df <- df |>
+      dplyr::nest_by(remote_sensing_indicators_name) |>
+      dplyr::mutate(coleo_id = list(coleo_request_by_code(human_code = remote_sensing_indicators_name, table = "remote_sensing_indicators", schema = schema)),
+            remote_sensing_indicator_id = coleo_extract_id(coleo_id)) |>
+      dplyr::select(-remote_sensing_indicators_name, -coleo_id) |>
+      dplyr::relocate(remote_sensing_indicator_id) |>
+      tidyr::unnest(cols = c(data)) |>
+      dplyr::ungroup() |>
+      suppressMessages()
+  }
+
   # Campaigns table specific manipulations
   if (db_table == "campaigns") {
     ## Add site_id to campaigns table

R/coleo_request.R

@@ -75,6 +75,7 @@ coleo_request_by_code <- function(human_code, table, schema = "public", perform
   names(requested_code) <- switch(table,
                                   cells = "cell_code",
                                   sites = "site_code",
+                                  remote_sensing_indicators = "name",
                                   stop("idk what to do with that"))
 
   written_req <- coleo_begin_req(schema) |>

tests/testthat/test-coleo_inject.R

@@ -95,6 +95,21 @@ test_that("coleo_inject injects all data", {
                             "obs_species_variable"))
 })
 
+# Expect one dataframe with two row being returned
+test_that("coleo_inject injects remote sensing data", {
+
+	# Mock data
+	rs_data <- structure(list(remote_sensing_indicators_name = "NDSI", cells_cell_code = "105_101", 
+    remote_sensing_events_date_start = paste0(sample(1000:3000,1),"-02-24"), remote_sensing_events_date_end = NA_character_, 
+    remote_sensing_obs_metric = "max", remote_sensing_obs_value = 90), row.names = 1L, class = "data.frame")
+
+	# Perform injection
+	out_inject <- coleo_inject(rs_data, schema = "coleo_test")
+
+	# Expect a dataframe with 1 rows
+	expect_true(is.null(out_inject$remote_sensing_event_error[[1]]))
+})
+
 
 #############################################
 # Test coleo_inject_general