Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update test for nc #74

Merged
merged 2 commits into from
Mar 10, 2025
+64 −27
Merged

update test for nc #74

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
d5dc1c4
update test for nc
lilyclements Mar 9, 2025
af0a0ec
reformat for readability
lilyclements Mar 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
53 changes: 26 additions & 27 deletions R/nc_functions.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ nc_get_dim_min_max <- function(nc, dimension, time_as_date = TRUE) {
if (units$hasatt && units$value == "julian_day") {
time_vals <- as.character(as.Date(vals, origin = structure(-2440588, class = "Date")))
} else {
pcict_time <- ncdf4.helpers::nc.get.time.series(nc, time.dim.name = dimension)
posixct_time <- PCICt::as.POSIXct.PCICt(pcict_time)
pcict_time <- get_nc_time_series(nc, time.dim.name = dimension)
posixct_time <- convert_pcict_to_posixct(pcict_time)
time_vals <- as.character(as.Date(posixct_time))
}
})
Expand Down Expand Up @@ -103,8 +103,7 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
warning("Cannot subset data when some dimension axes cannot be identified.")
start <- NA
count <- NA
}
else {
} else {
start <- c()
count <- c()
for(dim in c("X", "Y", "Z", "T", "S")) {
Expand All @@ -120,28 +119,24 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
if(units$hasatt && units$value == "julian_day") {
# RDotNet interprets Date class as numeric so character needed to preserve date
time_vals <- as.Date(curr_dim_values, origin = structure(-2440588, class = "Date"))
}
else {
pcict_time <- ncdf4.helpers::nc.get.time.series(nc, time.dim.name = dim_var)
posixct_time <- PCICt::as.POSIXct.PCICt(pcict_time)
} else {
pcict_time <- get_nc_time_series(nc, time.dim.name = dim_var)
posixct_time <- convert_pcict_to_posixct(pcict_time)
time_vals <- as.Date(posixct_time)
}
ind <- which(time_vals >= boundary[[dim_var]][[1]] & time_vals <= boundary[[dim_var]][[2]])
})
}
else ind <- which(curr_dim_values >= boundary[[dim_var]][1] & curr_dim_values <= boundary[[dim_var]][2])
} else ind <- which(curr_dim_values >= boundary[[dim_var]][1] & curr_dim_values <= boundary[[dim_var]][2])
# TODO This is temporary solution for when there is only one value for a dimension and there are rounding difference
if(length(ind) == 0 && length(curr_dim_values) == 1 && round(curr_dim_values, 3) == round(boundary[[dim_var]][1], 3) && round(curr_dim_values, 3) == round(boundary[[dim_var]][2], 3)) ind <- 1
if(length(ind) == 0) {
stop("No values within the range specified for ", dim_var, ".")
}
else {
} else {
start <- c(start, min(ind))
count <- c(count, length(ind))
dim_values[[dim_var]] <- dim_values[[dim_var]][ind]
}
}
else {
} else {
start <- c(start, 1)
count <- c(count, length(curr_dim_values))
}
Expand All @@ -152,8 +147,7 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
count <- rep(-1, length(dim_axes))
}
}
}
else {
} else {
start <- rep(1, length(dim_axes))
count <- rep(-1, length(dim_axes))
}
Expand Down Expand Up @@ -192,8 +186,7 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
count_list[[i]] <- curr_count
dim_values_list[[i]] <- curr_dim_values
}
}
else {
} else {
start_list[[1]] <- start
count_list[[1]] <- count
dim_values_list[[1]] <- dim_values
Expand All @@ -214,8 +207,7 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
curr_dim_names <- get_nc_dim_names(nc, var)
if(!setequal(curr_dim_names, dim_names)) {
warning("The dimensions of", var, "do not match the other variables.", var, "will be dropped.")
}
else {
} else {
included_vars <- c(included_vars, var)
curr_var_data[[var]] <- as.vector(get_ncvar_values(nc, var, start = start_list[[i]], count = count_list[[i]]))
}
Expand All @@ -234,11 +226,10 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
units <- get_nc_attribute(nc, time_var, "units")
if(units$hasatt && units$value == "julian_day") {
time_df[["date"]] <- as.Date(raw_time, origin = structure(-2440588, class = "Date"))
}
else {
pcict_time <- ncdf4.helpers::nc.get.time.series(nc, time.dim.name = time_var)
} else {
pcict_time <- get_nc_time_series(nc, time.dim.name = time_var)
pcict_time <- pcict_time[time_ind]
posixct_time <- PCICt::as.POSIXct.PCICt(pcict_time)
posixct_time <- convert_pcict_to_posixct(pcict_time)
time_df[["date"]] <- as.Date(posixct_time)
time_df[["datetime"]] <- posixct_time
}
Expand All @@ -251,9 +242,7 @@ nc_as_data_frame <- function(nc, vars, keep_raw_time = TRUE, include_metadata =
}
var_data_list[[i]] <- curr_var_data
}
if(length(var_data_list) > 1) {
var_data <- dplyr::bind_rows(var_data_list)
}
if(length(var_data_list) > 1) var_data <- dplyr::bind_rows(var_data_list)
else if(length(var_data_list) == 1) var_data <- var_data_list[[1]]
else var_data_list <- data.frame()

Expand Down Expand Up @@ -380,3 +369,13 @@ close_nc_file <- function(nc) {
process_nc_file <- function(nc, vars, keep_raw_time, include_metadata, boundary, lon_points, lat_points, id_points, show_requested_points, great_circle_dist) {
nc_as_data_frame(nc, vars, keep_raw_time, include_metadata, boundary, lon_points, lat_points, id_points, show_requested_points, great_circle_dist)
}

# Wrapper for getting time series
get_nc_time_series <- function(nc, time.dim.name) {
ncdf4.helpers::nc.get.time.series(nc, time.dim.name)
}

# Wrapper for converting PCICt time to POSIXct
convert_pcict_to_posixct <- function(pcict_time) {
PCICt::as.POSIXct.PCICt(pcict_time)
}
38 changes: 38 additions & 0 deletions tests/testthat/test-n_functions.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -157,4 +157,42 @@ test_that("multiple_nc_as_data_frame handles empty directory", {
result <- multiple_nc_as_data_frame("mock_path", vars = c("var1"))

expect_equal(nrow(result), 0) # Should return an empty data frame
})

test_that("nc_get_dim_min_max correctly converts time when time_as_date is TRUE", {
local_mocked_bindings(
# Mock NetCDF axes to mark "time" as a time dimension
get_nc_dim_axes = function(nc) list(time = "T"),

# Mock NetCDF attribute function to return time units as "julian_day"
get_nc_attribute = function(nc, dimension, attr) {
if (dimension == "time" && attr == "units") {
return(list(hasatt = TRUE, value = "julian_day"))
} else {
return(list(hasatt = FALSE))
}
},

# Mock NetCDF time series retrieval
get_nc_time_series = function(nc, time.dim.name) {
c(0, 1, 2, 3, 4, 5) # Simulating 6 days from origin
},

# Mock PCICt time conversion
convert_pcict_to_posixct = function(pcict_time) {
as.POSIXct("2000-01-01") + (pcict_time * 86400) # Convert days to POSIXct time
}
)

# Fake NetCDF structure
mock_nc <- list(
dim = list(time = list(vals = c(0, 1, 2, 3, 4, 5))) # Simulated time values
)

result <- nc_get_dim_min_max(mock_nc, "time", time_as_date = TRUE)

# Expected output: min and max dates converted from Julian
expected_dates <- as.character(as.Date(c(0, 5), origin = structure(-2440588, class = "Date")))

expect_equal(result, expected_dates) # Ensures conversion works correctly
})