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Fix JSON parsing conflict #52

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Merged
atharvashahane28 merged 3 commits into from
Oct 14, 2025
Merged

Fix JSON parsing conflict #52

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a7e8d81
feat: use jsonlite for consistent data formatting in results of flow
atharvashahane28 Oct 14, 2025
10e0843
tests: fix loc test
atharvashahane28 Oct 14, 2025
8d6a1db
tests: fix terra::rast input type conflict
atharvashahane28 Oct 14, 2025
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52 changes: 38 additions & 14 deletions R/flow.R
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Original file line number Diff line number Diff line change
Expand Up @@ -161,20 +161,32 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
result <- vector("list", length = n + 1)
for (i in seq_along(pred_weeks)) {
result[[i]] <- list(
week = pred_weeks[i],
url = if (save_local) png_local_paths[i] else png_urls[i],
legend = if (save_local) json_local_paths[i] else symbology_urls[i],
type = flow_type
# week = pred_weeks[i],
# url = if (save_local) png_local_paths[i] else png_urls[i],
# legend = if (save_local) json_local_paths[i] else symbology_urls[i],
# type = flow_type
week = jsonlite::unbox(as.integer(pred_weeks[i])),
url = jsonlite::unbox(as.character(if (save_local) png_local_paths[i] else png_urls[i])),
legend = jsonlite::unbox(as.character(if (save_local) json_local_paths[i] else symbology_urls[i])),
type = jsonlite::unbox(as.character(flow_type))
)
log_progress(paste0("Cached result for week ", pred_weeks[i], ": url=", result[[i]]$url, ", legend=", result[[i]]$legend))
}
log_progress(if (save_local) "Returned cached result from local_temp_path" else "Returned cached result from S3")
return(
list(
start = list(week = week, taxa = taxa, loc = loc),
status = "cached",
# start = list(week = week, taxa = taxa, loc = loc),
# status = "cached",
# result = result,
# geotiff = if (save_local) tiff_local_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
start = list(
week = jsonlite::unbox(as.integer(week)),
taxa = jsonlite::unbox(as.character(taxa)),
location = lapply(strsplit(loc, ";")[[1]], function(pair) as.numeric(strsplit(pair, ",")[[1]]))
),
status = jsonlite::unbox("cached"),
result = result,
geotiff = if (save_local) tiff_local_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
geotiff = jsonlite::unbox(as.character(if (save_local) tiff_local_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")))
)
)
}
Expand Down Expand Up @@ -336,20 +348,32 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
result <- vector("list", length = n + 1)
for (i in seq_along(pred_weeks)) {
result[[i]] <- list(
week = pred_weeks[i],
url = if (save_local) png_paths[i] else png_urls[i],
legend = if (save_local) symbology_paths[i] else symbology_urls[i],
type = flow_type
# week = pred_weeks[i],
# url = if (save_local) png_paths[i] else png_urls[i],
# legend = if (save_local) symbology_paths[i] else symbology_urls[i],
# type = flow_type
week = jsonlite::unbox(as.integer(pred_weeks[i])),
url = jsonlite::unbox(as.character(if (save_local) png_paths[i] else png_urls[i])),
legend = jsonlite::unbox(as.character(if (save_local) symbology_paths[i] else symbology_urls[i])),
type = jsonlite::unbox(as.character(flow_type))
)
}

log_progress("Flow function complete. Returning result.")
return(
list(
start = list(week = week, taxa = taxa, loc = loc),
status = "success",
# start = list(week = week, taxa = taxa, loc = loc),
# status = "success",
# result = result,
# geotiff = if (save_local) tiff_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
start = list(
week = jsonlite::unbox(as.integer(week)),
taxa = jsonlite::unbox(as.character(taxa)),
location = lapply(strsplit(loc, ";")[[1]], function(pair) as.numeric(strsplit(pair, ",")[[1]]))
),
status = jsonlite::unbox("success"),
result = result,
geotiff = if (save_local) tiff_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
geotiff = jsonlite::unbox(as.character(if (save_local) tiff_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")))
)
)
}
7 changes: 4 additions & 3 deletions tests/testthat/test-flow.R
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,8 @@ test_that("output taxa matches input", {
test_that("output loc matches input", {
params <- standard_flow_input()
res <- flow(loc = params$loc, week = params$week, taxa = params$taxa, n = params$n, direction = params$direction, save_local = params$save_local)
expect_true(res$start$loc == params$loc)
input_loc <- as.numeric(strsplit(params$loc, ",")[[1]])
expect_true(all(res$start$location[[1]] == input_loc))
})

test_that("output week matches input", {
Expand Down Expand Up @@ -122,12 +123,12 @@ test_that("total is not constrained by individual taxa NAs", {
# Make a total projection
params$taxa <- "total"
expect_no_error(total_result <- do.call(flow, params))
total <- terra::rast(total_result$geotiff)
total <- terra::rast(as.character(total_result$geotiff))

# Same start but for american black duck
params$taxa <- "ambduc"
expect_no_error(ambduc_result <- do.call(flow, params))
ambduc <- terra::rast(ambduc_result$geotiff)
ambduc <- terra::rast(as.character(ambduc_result$geotiff))

# There should be more NA's in the American black duck result than in the total
ambduc_nas <- terra::values(ambduc) |> is.na() |> sum()
Expand Down