Newer
Older
Start <- function(..., # dim = indices/selectors,
# dim_var = 'var',
# dim_reorder = Sort/CircularSort,
# dim_tolerance = number,
# dim_depends = 'file_dim',
# dim_across = 'file_dim',
return_vars = NULL,
file_opener = NcOpener,
file_var_reader = NcVarReader,
file_dim_reader = NcDimReader,
file_data_reader = NcDataReader,
file_closer = NcCloser,
transform = NULL,
transform_params = NULL,
transform_vars = NULL,
transform_extra_cells = 0,
apply_indices_after_transform = FALSE,
pattern_dims = NULL,
metadata_dims = NULL,
Nicolau Manubens
committed
merge_across_dims = FALSE,
split_multiselected_dims = FALSE,
#, config_file = NULL
#dictionary_dim_names = ,
#dictionary_var_names =
dim_params <- list(...)
# Take *_var parameters apart
var_params_ind <- grep('_var$', names(dim_params))
var_params <- dim_params[var_params_ind]
# Check all *_var are NULL or vectors of character strings, and
# that they all have a matching dimension param.
i <- 1
for (var_param in var_params) {
if (!is.character(var_param)) {
stop("All '*_var' parameters must be character strings.")
} else if (!any(grepl(paste0('^', strsplit(names(var_params)[i],
'_var$')[[1]][1], '$'),
names(dim_params)))) {
stop(paste0("All '*_var' parameters must be associated to a dimension parameter. Found parameter '",
names(var_params)[i], "' but no parameter '",
strsplit(names(var_params)[i], '_var$')[[1]][1], "'."))
}
i <- i + 1
}
# Make the keys of 'var_params' to be the name of
# the corresponding dimension.
if (length(var_params) < 1) {
var_params <- NULL
} else {
names(var_params) <- gsub('_var$', '', names(var_params))
}
# Take *_reorder parameters apart
dim_reorder_params_ind <- grep('_reorder$', names(dim_params))
dim_reorder_params <- dim_params[dim_reorder_params_ind]
# Check all *_reorder are NULL or functions, and that they all have
# a matching dimension param.
i <- 1
for (dim_reorder_param in dim_reorder_params) {
if (!is.function(dim_reorder_param)) {
stop("All '*_reorder' parameters must be functions.")
} else if (!any(grepl(paste0('^', strsplit(names(dim_reorder_params)[i],
'_reorder$')[[1]][1], '$'),
names(dim_params)))) {
stop(paste0("All '*_reorder' parameters must be associated to a dimension parameter. Found parameter '",
names(dim_reorder_params)[i], "' but no parameter '",
strsplit(names(dim_reorder_params)[i], '_reorder$')[[1]][1], "'."))
} else if (!any(grepl(paste0('^', strsplit(names(dim_reorder_params)[i],
'_reorder$')[[1]][1], '$'),
names(var_params)))) {
stop(paste0("All '*_reorder' parameters must be associated to a dimension parameter associated to a ",
"variable. Found parameter '", names(dim_reorder_params)[i], "' and dimension parameter '",
strsplit(names(dim_reorder_params)[i], '_reorder$')[[1]][1], "' but did not find variable ",
"parameter '", strsplit(names(dim_reorder_params)[i], '_reorder$')[[1]][1], "_var'."))
}
i <- i + 1
}
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
# Make the keys of 'dim_reorder_params' to be the name of
# the corresponding dimension.
if (length(dim_reorder_params) < 1) {
dim_reorder_params <- NULL
} else {
names(dim_reorder_params) <- gsub('_reorder$', '', names(dim_reorder_params))
}
# Take *_tolerance parameters apart
tolerance_params_ind <- grep('_tolerance$', names(dim_params))
tolerance_params <- dim_params[tolerance_params_ind]
# Take *_depends parameters apart
depends_params_ind <- grep('_depends$', names(dim_params))
depends_params <- dim_params[depends_params_ind]
# Check all *_depends are NULL or vectors of character strings, and
# that they all have a matching dimension param.
i <- 1
for (depends_param in depends_params) {
if (!is.character(depends_param) || (length(depends_param) > 1)) {
stop("All '*_depends' parameters must be single character strings.")
} else if (!any(grepl(paste0('^', strsplit(names(depends_params)[i],
'_depends$')[[1]][1], '$'),
names(dim_params)))) {
stop(paste0("All '*_depends' parameters must be associated to a dimension parameter. Found parameter '",
names(depends_params)[i], "' but no parameter '",
strsplit(names(depends_params)[i], '_depends$')[[1]][1], "'."))
}
i <- i + 1
}
# Make the keys of 'depends_params' to be the name of
# the corresponding dimension.
if (length(depends_params) < 1) {
depends_params <- NULL
} else {
names(depends_params) <- gsub('_depends$', '', names(depends_params))
}
# Change name to depending_file_dims
depending_file_dims <- depends_params
# Take *_across parameters apart
across_params_ind <- grep('_across$', names(dim_params))
across_params <- dim_params[across_params_ind]
# Check all *_across are NULL or vectors of character strings, and
# that they all have a matching dimension param.
i <- 1
for (across_param in across_params) {
if (!is.character(across_param) || (length(across_param) > 1)) {
stop("All '*_across' parameters must be single character strings.")
} else if (!any(grepl(paste0('^', strsplit(names(across_params)[i],
'_across$')[[1]][1], '$'),
names(dim_params)))) {
stop(paste0("All '*_across' parameters must be associated to a dimension parameter. Found parameter '",
names(across_params)[i], "' but no parameter '",
strsplit(names(across_params)[i], '_across$')[[1]][1], "'."))
}
i <- i + 1
}
# Make the keys of 'across_params' to be the name of
# the corresponding dimension.
if (length(across_params) < 1) {
across_params <- NULL
} else {
names(across_params) <- gsub('_across$', '', names(across_params))
}
# Change name to inner_dims_across_files
inner_dims_across_files <- across_params
Nicolau Manubens
committed
# Check merge_across_dims
if (!is.logical(merge_across_dims)) {
stop("Parameter 'merge_across_dims' must be TRUE or FALSE.")
}
# Leave alone the dimension parameters in the variable dim_params
if (length(c(var_params_ind, dim_reorder_params_ind, tolerance_params_ind,
depends_params_ind, across_params_ind)) > 0) {
dim_params <- dim_params[-c(var_params_ind, dim_reorder_params_ind,
tolerance_params_ind, depends_params_ind,
across_params_ind)]
Nicolau Manubens
committed
# Reallocating pairs of across file and inner dimensions if they have
# to be merged. They are put one next to the other to ease merge later.
if (merge_across_dims) {
for (inner_dim_across in names(inner_dims_across_files)) {
inner_dim_pos <- which(names(dim_params) == inner_dim_across)
file_dim_pos <- which(names(dim_params) == inner_dims_across_files[[inner_dim_across]])
Nicolau Manubens
committed
new_pos <- inner_dim_pos
if (file_dim_pos < inner_dim_pos) {
new_pos <- new_pos - 1
}
Nicolau Manubens
committed
dim_params_to_move <- dim_params[c(inner_dim_pos, file_dim_pos)]
dim_params <- dim_params[-c(inner_dim_pos, file_dim_pos)]
new_dim_params <- list()
if (new_pos > 1) {
new_dim_params <- c(new_dim_params, dim_params[1:(new_pos - 1)])
}
new_dim_params <- c(new_dim_params, dim_params_to_move)
if (length(dim_params) >= new_pos) {
new_dim_params <- c(new_dim_params, dim_params[new_pos:length(dim_params)])
}
Nicolau Manubens
committed
}
}
}
dim_names <- names(dim_params)
if (is.null(dim_names)) {
stop("At least one pattern dim must be specified.")
}
# Look for chunked dims
chunks <- vector('list', length(dim_names))
names(chunks) <- dim_names
for (dim_name in dim_names) {
if (!is.null(attr(dim_params[[dim_name]], 'chunk'))) {
chunks[[dim_name]] <- attr(dim_params[[dim_name]], 'chunk')
attributes(dim_params[[dim_name]]) <- attributes(dim_params[[dim_name]])[-which(names(attributes(dim_params[[dim_name]])) == 'chunk')]
} else {
chunks[[dim_name]] <- c(chunk = 1, n_chunks = 1)
}
}
# This is a helper function to compute the chunk indices to take once the total
# number of indices for a dimension has been discovered.
chunk_indices <- function(n_indices, chunk, n_chunks, dim_name) {
if (n_chunks > n_indices) {
stop("Requested to divide dimension '", dim_name, "' of length ",
n_indices, " in ", n_chunks, " chunks, which is not possible.")
}
chunks_to_extend <- n_indices - chunk_sizes[1] * n_chunks
if (chunks_to_extend > 0) {
chunk_sizes[1:chunks_to_extend] <- chunk_sizes[1:chunks_to_extend] + 1
}
chunk_size <- chunk_sizes[chunk]
offset <- 0
if (chunk > 1) {
offset <- sum(chunk_sizes[1:(chunk - 1)])
}
indices <- 1:chunk_sizes[chunk] + offset
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
# Check pattern_dims
if (is.null(pattern_dims)) {
.warning(paste0("Parameter 'pattern_dims' not specified. Taking the first dimension, '",
dim_names[1], "' as 'pattern_dims'."))
pattern_dims <- dim_names[1]
} else if (is.character(pattern_dims) && (length(pattern_dims) > 0)) {
pattern_dims <- unique(pattern_dims)
} else {
stop("Parameter 'pattern_dims' must be a vector of character strings.")
}
if (any(names(var_params) %in% pattern_dims)) {
stop("'*_var' parameters specified for pattern dimensions. Remove or fix them.")
}
# Find the pattern dimension with the pattern specifications
found_pattern_dim <- NULL
for (pattern_dim in pattern_dims) {
# Check all specifications in pattern_dim are valid
dat <- datasets <- dim_params[[pattern_dim]]
if (is.null(dat) || !(is.character(dat) && all(nchar(dat) > 0)) && !is.list(dat)) {
stop(paste0("Parameter '", pattern_dim,
"' must be a list of lists with pattern specifications or a vector of character strings."))
}
if (!is.null(dim_reorder_params[[pattern_dim]])) {
.warning(paste0("A reorder for the selectors of '", pattern_dim,
"' has been specified, but it is a pattern dimension and the reorder will be ignored."))
}
if (is.null(found_pattern_dim)) {
found_pattern_dim <- pattern_dim
} else {
stop("Found more than one pattern dim with pattern specifications (list of lists). One and only one pattern dim must contain pattern specifications.")
}
}
}
if (is.null(found_pattern_dim)) {
.warning(paste0("Could not find any pattern dim with explicit data set descriptions (in the form of list of lists). Taking the first pattern dim, '", pattern_dims[1], "', as dimension with pattern specifications."))
found_pattern_dim <- pattern_dims[1]
}
Nicolau Manubens
committed
# Look for _var params that should be requested automatically.
for (dim_name in dim_names) {
if (!(dim_name %in% pattern_dims)) {
if (!is.null(attr(dim_params[[dim_name]], 'values'))) {
if (attr(dim_params[[dim_name]], 'values') && !(dim_name %in% var_params)) {
.warning(paste0("Found specified values for dimension '", dim_name, "' but no '",
dim_name, "_var' requested. ", '"', dim_name, "_var = '",
dim_name, "'", '"', " has been automatically added to ",
"the Start call."))
var_params <- c(var_params, setNames(list(dim_name), dim_name))
Nicolau Manubens
committed
}
}
}
}
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
# Check all *_tolerance are NULL or vectors of character strings, and
# that they all have a matching dimension param.
i <- 1
for (tolerance_param in tolerance_params) {
if (!any(grepl(paste0('^', strsplit(names(tolerance_params)[i],
'_tolerance$')[[1]][1], '$'),
names(dim_params)))) {
stop(paste0("All '*_tolerance' parameters must be associated to a dimension parameter. Found parameter '",
names(tolerance_params)[i], "' but no parameter '",
strsplit(names(tolerance_params)[i], '_tolerance$')[[1]][1], "'."))
} else if (!any(grepl(paste0('^', strsplit(names(tolerance_params)[i],
'_tolerance$')[[1]][1], '$'),
names(var_params)))) {
stop(paste0("All '*_tolerance' parameters must be associated to a dimension parameter associated to a ",
"variable. Found parameter '", names(tolerance_params)[i], "' and dimension parameter '",
strsplit(names(tolerance_params)[i], '_tolerance$')[[1]][1], "' but did not find variable ",
"parameter '", strsplit(names(tolerance_params)[i], '_tolerance$')[[1]][1], "_var'."))
}
i <- i + 1
}
# Make the keys of 'tolerance_params' to be the name of
# the corresponding dimension.
if (length(tolerance_params) < 1) {
tolerance_params <- NULL
} else {
names(tolerance_params) <- gsub('_tolerance$', '', names(tolerance_params))
}
# Check metadata_dims
if (!is.null(metadata_dims)) {
if (is.na(metadata_dims)) {
metadata_dims <- NULL
} else if (!is.character(metadata_dims) || (length(metadata_dims) < 1)) {
stop("Parameter 'metadata' dims must be a vector of at least one character string.")
}
} else {
metadata_dims <- pattern_dims
}
# Once the pattern dimension with dataset specifications is found,
# the variable 'dat' is mounted with the information of each
# dataset.
# Take only the datasets for the requested chunk
dats_to_take <- chunk_indices(length(dim_params[[found_pattern_dim]]),
chunks[[found_pattern_dim]]['chunk'],
chunks[[found_pattern_dim]]['n_chunks'],
found_pattern_dim)
dim_params[[found_pattern_dim]] <- dim_params[[found_pattern_dim]][dats_to_take]
dat <- datasets <- dim_params[[found_pattern_dim]]
dat_info_names <- c('name', 'path')#, 'nc_var_name', 'suffix', 'var_min', 'var_max', 'dimnames')
dat_to_fetch <- c()
dat_names <- c()
if (!is.list(dat)) {
dat <- as.list(dat)
} else {
if (!any(sapply(dat, is.list))) {
dat <- list(dat)
}
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
}
for (i in 1:length(dat)) {
if (is.character(dat[[i]]) && length(dat[[i]]) == 1 && nchar(dat[[i]]) > 0) {
if (grepl('^(\\./|\\.\\./|/.*/|~/)', dat[[i]])) {
dat[[i]] <- list(path = dat[[i]])
} else {
dat[[i]] <- list(name = dat[[i]])
}
} else if (!is.list(dat[[i]])) {
stop(paste0("Parameter '", pattern_dim,
"' is incorrect. It must be a list of lists or character strings."))
}
#if (!(all(names(dat[[i]]) %in% dat_info_names))) {
# stop("Error: parameter 'dat' is incorrect. There are unrecognized components in the information of some of the datasets. Check 'dat' in ?Load for details.")
#}
if (!('name' %in% names(dat[[i]]))) {
dat[[i]][['name']] <- paste0('dat', i)
if (!('path' %in% names(dat[[i]]))) {
stop(paste0("Parameter '", found_pattern_dim,
"' is incorrect. A 'path' should be provided for each dataset if no 'name' is provided."))
}
} else if (!('path' %in% names(dat[[i]]))) {
dat_to_fetch <- c(dat_to_fetch, i)
}
#if ('path' %in% names(dat[[i]])) {
# if (!('nc_var_name' %in% names(dat[[i]]))) {
# dat[[i]][['nc_var_name']] <- '$var_name$'
# }
# if (!('suffix' %in% names(dat[[i]]))) {
# dat[[i]][['suffix']] <- ''
# }
# if (!('var_min' %in% names(dat[[i]]))) {
# dat[[i]][['var_min']] <- ''
# }
# if (!('var_max' %in% names(dat[[i]]))) {
# dat[[i]][['var_max']] <- ''
# }
#}
dat_names <- c(dat_names, dat[[i]][['name']])
}
if ((length(dat_to_fetch) > 0) && (length(dat_to_fetch) < length(dat))) {
.warning("'path' has been provided for some datasets. Any information in the configuration file related to these will be ignored.")
}
if (length(dat_to_fetch) > 0) {
stop("Specified only the name for some data sets, but not the path ",
"pattern. This option has not been yet implemented.")
}
# Reorder inner_dims_across_files (to make the keys be the file dimensions,
# and the values to be the inner dimensions that go across it).
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
if (!is.null(inner_dims_across_files)) {
# Reorder: example, convert list(ftime = 'chunk', ensemble = 'member', xx = 'chunk')
# to list(chunk = c('ftime', 'xx'), member = 'ensemble')
new_idaf <- list()
for (i in names(inner_dims_across_files)) {
if (!(inner_dims_across_files[[i]] %in% names(new_idaf))) {
new_idaf[[inner_dims_across_files[[i]]]] <- i
} else {
new_idaf[[inner_dims_across_files[[i]]]] <- c(new_idaf[[inner_dims_across_files[[i]]]], i)
}
}
inner_dims_across_files <- new_idaf
}
# Check return_vars
if (is.null(return_vars)) {
return_vars <- list()
# if (length(var_params) > 0) {
# return_vars <- as.list(paste0(names(var_params), '_var'))
# } else {
# return_vars <- list()
# }
}
if (!is.list(return_vars)) {
stop("Parameter 'return_vars' must be a list or NULL.")
}
if (length(return_vars) > 0 && is.null(names(return_vars))) {
# names(return_vars) <- rep('', length(return_vars))
stop("Parameter 'return_vars' must be a named list.")
}
i <- 1
while (i <= length(return_vars)) {
# if (names(return_vars)[i] == '') {
# if (!(is.character(return_vars[[i]]) && (length(return_vars[[i]]) == 1))) {
# stop("The ", i, "th specification in 'return_vars' is malformed.")
# }
# if (!grepl('_var$', return_vars[[i]])) {
# stop("The ", i, "th specification in 'return_vars' is malformed.")
# }
# dim_name <- strsplit(return_vars[[i]], '_var$')[[1]][1]
# if (!(dim_name %in% names(var_params))) {
# stop("'", dim_name, "_var' requested in 'return_vars' but ",
# "no '", dim_name, "_var' specified in the .Load call.")
# }
# names(return_vars)[i] <- var_params[[dim_name]]
# return_vars[[i]] <- found_pattern_dim
# } else
if (length(return_vars[[i]]) > 0) {
if (!is.character(return_vars[[i]])) {
stop("The ", i, "th specification in 'return_vars' is malformed. It ",
"must be a vector of character strings of valid file dimension ",
"names.")
}
}
i <- i + 1
}
# Check synonims
if (!is.null(synonims)) {
error <- FALSE
if (!is.list(synonims)) {
error <- TRUE
}
for (synonim_entry in names(synonims)) {
if (!(synonim_entry %in% names(dim_params)) &&
!(synonim_entry %in% names(return_vars))) {
error <- TRUE
}
if (!is.character(synonims[[synonim_entry]]) ||
length(synonims[[synonim_entry]]) < 1) {
error <- TRUE
}
}
if (error) {
stop("Parameter 'synonims' must be a named list, where the names are ",
"a name of a requested dimension or variable and the values are ",
"vectors of character strings with at least one alternative name ",
" for each dimension or variable in 'synonims'.")
}
}
if (length(unique(names(synonims))) < length(names(synonims))) {
stop("There must not be repeated entries in 'synonims'.")
}
if (length(unique(unlist(synonims))) < length(unlist(synonims))) {
stop("There must not be repeated values in 'synonims'.")
}
# Make that all dims and vars have an entry in synonims, even if only dim_name = dim_name
dim_entries_to_add <- which(!(names(dim_params) %in% names(synonims)))
if (length(dim_entries_to_add) > 0) {
synonims[names(dim_params)[dim_entries_to_add]] <- as.list(names(dim_params)[dim_entries_to_add])
}
var_entries_to_add <- which(!(names(var_params) %in% names(synonims)))
if (length(var_entries_to_add) > 0) {
synonims[names(var_params)[var_entries_to_add]] <- as.list(names(var_params)[var_entries_to_add])
}
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
# Check selector_checker
if (is.null(selector_checker) || !is.function(selector_checker)) {
stop("Parameter 'selector_checker' must be a function.")
}
# Check file_opener
if (is.null(file_opener) || !is.function(file_opener)) {
stop("Parameter 'file_opener' must be a function.")
}
# Check file_var_reader
if (!is.null(file_var_reader) && !is.function(file_var_reader)) {
stop("Parameter 'file_var_reader' must be a function.")
}
# Check file_dim_reader
if (!is.null(file_dim_reader) && !is.function(file_dim_reader)) {
stop("Parameter 'file_dim_reader' must be a function.")
}
# Check file_data_reader
if (is.null(file_data_reader) || !is.function(file_data_reader)) {
stop("Parameter 'file_data_reader' must be a function.")
}
# Check file_closer
if (is.null(file_closer) || !is.function(file_closer)) {
stop("Parameter 'file_closer' must be a function.")
}
# Check transform
if (!is.null(transform)) {
if (!is.function(transform)) {
stop("Parameter 'transform' must be a function.")
}
}
# Check transform_params
if (!is.null(transform_params)) {
if (!is.list(transform_params)) {
stop("Parameter 'transform_params' must be a list.")
}
if (is.null(names(transform_params))) {
stop("Parameter 'transform_params' must be a named list.")
}
}
# Check transform_vars
if (!is.null(transform_vars)) {
if (!is.character(transform_vars)) {
stop("Parameter 'transform_vars' must be a vector of character strings.")
}
}
if (any(!(transform_vars %in% names(return_vars)))) {
stop("All the variables specified in 'transform_vars' must also be specified in 'return_vars'.")
}
# Check apply_indices_after_transform
if (!is.logical(apply_indices_after_transform)) {
stop("Parameter 'apply_indices_after_transform' must be either TRUE or FALSE.")
# Check transform_extra_cells
if (!is.numeric(transform_extra_cells)) {
stop("Parameter 'transform_extra_cells' must be numeric.")
}
transform_extra_cells <- round(transform_extra_cells)
Nicolau Manubens
committed
# Check split_multiselected_dims
if (!is.logical(split_multiselected_dims)) {
stop("Parameter 'split_multiselected_dims' must be TRUE or FALSE.")
}
# Check retrieve
if (!is.logical(retrieve)) {
stop("Parameter 'retrieve' must be TRUE or FALSE.")
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
# Check num_procs
if (!is.null(num_procs)) {
if (!is.numeric(num_procs)) {
stop("Parameter 'num_procs' must be numeric.")
} else {
num_procs <- round(num_procs)
}
}
# Check silent
if (!is.logical(silent)) {
stop("Parameter 'silent' must be logical.")
}
dim_params[[found_pattern_dim]] <- dat_names
if (!silent) {
.message(paste0("Exploring files... This will take a variable amount ",
"of time depending on the issued request and the ",
"performance of the file server..."))
}
if (!is.character(debug)) {
dims_to_check <- c('time')
} else {
dims_to_check <- debug
debug <- TRUE
}
############################## READING FILE DIMS ############################
# Check that no unrecognized variables are present in the path patterns
# and also that no file dimensions are requested to THREDDs catalogs.
# And in the mean time, build all the work pieces and look for the
# first available file of each dataset.
array_of_files_to_load <- NULL
array_of_not_found_files <- NULL
indices_of_first_files_with_data <- vector('list', length(dat))
selectors_of_first_files_with_data <- vector('list', length(dat))
found_file_dims <- vector('list', length(dat))
expected_inner_dims <- vector('list', length(dat))
dataset_has_files <- rep(FALSE, length(dat))
#print("A")
for (i in 1:length(dat)) {
#print("B")
dat_selectors <- dim_params
dat_selectors[[found_pattern_dim]] <- dat_selectors[[found_pattern_dim]][i]
dim_vars <- paste0('$', dim_names, '$')
file_dims <- which(sapply(dim_vars, grepl, dat[[i]][['path']], fixed = TRUE))
if (length(file_dims) > 0) {
file_dims <- dim_names[file_dims]
}
file_dims <- unique(c(pattern_dims, file_dims))
found_file_dims[[i]] <- file_dims
expected_inner_dims[[i]] <- dim_names[which(!(dim_names %in% file_dims))]
# (Check the depending_file_dims).
if (any(c(names(depending_file_dims), unlist(depending_file_dims)) %in%
expected_inner_dims[[i]])) {
stop(paste0("The dimension dependancies specified in ",
"'depending_file_dims' can only be between file ",
"dimensions, but some inner dimensions found in ",
"dependancies for '", dat[[i]][['name']], "', which ",
"has the following file dimensions: ",
paste(paste0("'", file_dims, "'"), collapse = ', '), "."))
} else {
a <- names(depending_file_dims) %in% file_dims
b <- unlist(depending_file_dims) %in% file_dims
ab <- a & b
if (any(!ab)) {
.warning(paste0("Detected some dependancies in 'depending_file_dims' with ",
"non-existing dimension names. These will be disregarded."))
depending_file_dims <- depending_file_dims[-which(!ab)]
}
if (any(names(depending_file_dims) == unlist(depending_file_dims))) {
depending_file_dims <- depending_file_dims[-which(names(depending_file_dims) == unlist(depending_file_dims))]
}
}
# (Check the inner_dims_across_files).
if (any(!(names(inner_dims_across_files) %in% file_dims)) ||
any(!(unlist(inner_dims_across_files) %in% expected_inner_dims[[i]]))) {
stop(paste0("All relationships specified in ",
"dimension and a file dimension. Found wrong ",
"specification for '", dat[[i]][['name']], "', which ",
"has the following file dimensions: ",
paste(paste0("'", file_dims, "'"), collapse = ', '),
", and the following inner dimensions: ",
paste(paste0("'", expected_inner_dims[[i]], "'"),
collapse = ', '), "."))
}
# (Check the return_vars).
j <- 1
while (j <= length(return_vars)) {
if (any(!(return_vars[[j]] %in% file_dims))) {
if (any(return_vars[[j]] %in% expected_inner_dims[[i]])) {
stop("Found variables in 'return_vars' requested ",
"for some inner dimensions (for dataset '",
dat[[i]][['name']], "'), but variables can only be ",
"requested for file dimensions.")
} else {
stop("Found variables in 'return_vars' requested ",
"for non-existing dimensions.")
}
}
j <- j + 1
}
if (!is.null(metadata_dims)) {
if (any(!(metadata_dims %in% file_dims))) {
stop("All dimensions in 'metadata_dims' must be file dimensions.")
}
# (Check the *_var parameters).
if (any(!(unlist(var_params) %in% names(return_vars)))) {
Nicolau Manubens
committed
vars_to_add <- which(!(unlist(var_params) %in% names(return_vars)))
new_return_vars <- vector('list', length(vars_to_add))
names(new_return_vars) <- unlist(var_params)
return_vars <- c(return_vars, new_return_vars)
.warning(paste0("All '*_var' params must associate a dimension to one of the ",
"requested variables in 'return_vars'. The following variables",
" have been added to 'return_vars': ",
paste(paste0("'", unlist(var_params), "'"), collapse = ', ')))
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
}
replace_values <- vector('list', length = length(file_dims))
names(replace_values) <- file_dims
# Take the first selector for all possible file dimensions
for (file_dim in file_dims) {
if (file_dim %in% names(var_params)) {
.warning(paste0("The '", file_dim, "_var' param will be ignored since '",
file_dim, "' is a file dimension (for the dataset with pattern ",
dat[[i]][['path']], ")."))
}
if (!is.list(dat_selectors[[file_dim]]) ||
(is.list(dat_selectors[[file_dim]]) &&
length(dat_selectors[[file_dim]]) == 2 &&
is.null(names(dat_selectors[[file_dim]])))) {
dat_selectors[[file_dim]] <- list(dat_selectors[[file_dim]])
}
first_class <- class(dat_selectors[[file_dim]][[1]])
first_length <- length(dat_selectors[[file_dim]][[1]])
for (j in 1:length(dat_selectors[[file_dim]])) {
sv <- selector_vector <- dat_selectors[[file_dim]][[j]]
if (!identical(first_class, class(sv)) ||
!identical(first_length, length(sv))) {
stop("All provided selectors for depending dimensions must ",
"be vectors of the same length and of the same class.")
}
if (is.character(sv) && !((length(sv) == 1) && (sv[1] %in% c('all', 'first', 'last')))) {
dat_selectors[[file_dim]][[j]] <- selector_checker(selectors = sv,
return_indices = FALSE)
# Take chunk if needed
dat_selectors[[file_dim]][[j]] <- dat_selectors[[file_dim]][[j]][chunk_indices(length(dat_selectors[[file_dim]][[j]]),
chunks[[file_dim]]['chunk'],
chunks[[file_dim]]['n_chunks'],
file_dim)]
} else if (!(is.numeric(sv) ||
(is.character(sv) && (length(sv) == 1) && (sv %in% c('all', 'first', 'last'))) ||
(is.list(sv) && (length(sv) == 2) && (all(sapply(sv, is.character)) ||
all(sapply(sv, is.numeric)))))) {
stop("All explicitly provided selectors for file dimensions must be character strings.")
}
}
sv <- dat_selectors[[file_dim]][[1]]
if (is.character(sv) && !((length(sv) == 1) && (sv[1] %in% c('all', 'first', 'last')))) {
replace_values[[file_dim]] <- dat_selectors[[file_dim]][[1]][1]
}
}
#print("C")
# Now we know which dimensions whose selectors are provided non-explicitly.
undefined_file_dims <- file_dims[which(sapply(replace_values, is.null))]
defined_file_dims <- file_dims[which(!(file_dims %in% undefined_file_dims))]
# Quickly check if the depending dimensions are provided properly.
for (file_dim in file_dims) {
if (file_dim %in% names(depending_file_dims)) {
## TODO: Detect multi-dependancies and forbid.
if (all(c(file_dim, depending_file_dims[[file_dim]]) %in% defined_file_dims)) {
if (length(dat_selectors[[file_dim]]) != length(dat_selectors[[depending_file_dims[[file_dim]]]][[1]])) {
stop(paste0("If providing selectors for the depending ",
"dimension '", file_dim, "', a ",
"vector of selectors must be provided for ",
depending_file_dims[[file_dim]], "'."))
} else if (!all(names(dat_selectors[[file_dim]]) == dat_selectors[[depending_file_dims[[file_dim]]]][[1]])) {
stop(paste0("If providing selectors for the depending ",
"dimension '", file_dim, "', the name of the ",
"provided vectors of selectors must match ",
"exactly the selectors of the dimension it ",
"depends on, '", depending_file_dims[[file_dim]], "'."))
}
}
}
}
# Find the possible values for the selectors that are provided as
# indices. If the requested file is on server, impossible operation.
if (length(grep("^http", dat[[i]][['path']])) > 0) {
if (length(undefined_file_dims) > 0) {
stop(paste0("All selectors for the file dimensions must be ",
"character strings if requesting data to a remote ",
"server. Found invalid selectors for the file dimensions ",
paste(paste0("'", undefined_file_dims, "'"), collapse = ', '), "."))
}
dataset_has_files[i] <- TRUE
} else {
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
# Iterate over the known dimensions to find the first existing file.
# The path to the first existing file will be used to find the
# values for the non explicitly defined selectors.
first_file <- NULL
first_file_selectors <- NULL
if (length(undefined_file_dims) > 0) {
replace_values[undefined_file_dims] <- '*'
}
## TODO: What if length of defined_file_dims is 0? code might crash (in practice it worked for an example case)
files_to_check <- sapply(dat_selectors[defined_file_dims], function(x) length(x[[1]]))
sub_array_of_files_to_check <- array(1:prod(files_to_check), dim = files_to_check)
j <- 1
#print("D")
while (j <= prod(files_to_check) && is.null(first_file)) {
selector_indices <- which(sub_array_of_files_to_check == j, arr.ind = TRUE)[1, ]
selectors <- sapply(1:length(defined_file_dims),
function (x) {
vector_to_pick <- 1
if (defined_file_dims[x] %in% names(depending_file_dims)) {
vector_to_pick <- selector_indices[which(defined_file_dims == depending_file_dims[[defined_file_dims[x]]])]
}
dat_selectors[defined_file_dims][[x]][[vector_to_pick]][selector_indices[x]]
})
replace_values[defined_file_dims] <- selectors
file_path <- .ReplaceVariablesInString(dat[[i]][['path']], replace_values)
file_path <- Sys.glob(file_path)
if (length(file_path) > 0) {
first_file <- file_path[1]
first_file_selectors <- selectors
}
j <- j + 1
}
#print("E")
# Start looking for values for the non-explicitly defined selectors.
if (is.null(first_file)) {
.warning(paste0("No found files for the datset '", dat[[i]][['name']],
"'. Provide existing selectors for the file dimensions ",
" or check and correct its path pattern: ", dat[[i]][['path']]))
} else {
dataset_has_files[i] <- TRUE
## TODO: Improve message here if no variable found:
if (length(undefined_file_dims) > 0) {
# Looking for the first values, parsed from first_file.
first_values <- vector('list', length = length(undefined_file_dims))
names(first_values) <- undefined_file_dims
found_values <- 0
stop <- FALSE
try_dim <- 1
last_success <- 1
while ((found_values < length(undefined_file_dims)) && !stop) {
u_file_dim <- undefined_file_dims[try_dim]
if (is.null(first_values[[u_file_dim]])) {
path_with_globs_and_tag <- .ReplaceVariablesInString(dat[[i]][['path']],
replace_values[-which(file_dims == u_file_dim)],
allow_undefined_key_vars = TRUE)
found_value <- .FindTagValue(path_with_globs_and_tag,
first_file, u_file_dim)
if (!is.null(found_value)) {
found_values <- found_values + 1
last_success <- try_dim
first_values[[u_file_dim]] <- found_value
replace_values[[u_file_dim]] <- found_value
}
}
try_dim <- (try_dim %% length(undefined_file_dims)) + 1
if (try_dim == last_success) {
stop <- TRUE
}
}
if (found_values < length(undefined_file_dims)) {
stop(paste0("Path pattern of dataset '", dat[[i]][['name']],
"' is too complex. Could not automatically ",
"detect values for all non-explicitly defined ",
"indices. Check its pattern: ", dat[[i]][['path']]))
}
## TODO: Replace ReplaceGlobExpressions by looped call to FindTagValue? As done above
## Maybe it can solve more cases actually. I got warnings in ReplGlobExp with a typical
## cmor case, requesting all members and chunks for fixed var and sdate. Not fixing
## sdate raised 'too complex' error.
# Replace shell globs in path pattern and keep the file_dims as tags
dat[[i]][['path']] <- .ReplaceGlobExpressions(dat[[i]][['path']], first_file, replace_values,
file_dims, dat[[i]][['name']], FALSE)
# Now time to look for the available values for the non
# explicitly defined selectors for the file dimensions.
#print("H")
# Check first the ones that do not depend on others.
ufd <- c(undefined_file_dims[which(!(undefined_file_dims %in% names(depending_file_dims)))],
undefined_file_dims[which(undefined_file_dims %in% names(depending_file_dims))])
for (u_file_dim in ufd) {
replace_values[undefined_file_dims] <- first_values
replace_values[[u_file_dim]] <- '*'
depended_dim <- NULL
depended_dim_values <- NA
selectors <- dat_selectors[[u_file_dim]][[1]]
if (u_file_dim %in% names(depending_file_dims)) {
depended_dim <- depending_file_dims[[u_file_dim]]
depended_dim_values <- dat_selectors[[depended_dim]][[1]]
dat_selectors[[u_file_dim]] <- vector('list', length = length(depended_dim_values))
names(dat_selectors[[u_file_dim]]) <- depended_dim_values
} else {
dat_selectors[[u_file_dim]] <- list()
}
if (u_file_dim %in% unlist(depending_file_dims)) {
depending_dims <- names(depending_file_dims)[which(sapply(depending_file_dims, function(x) u_file_dim %in% x))]
replace_values[depending_dims] <- rep('*', length(depending_dims))
}
for (j in 1:length(depended_dim_values)) {
parsed_values <- c()
if (!is.null(depended_dim)) {
replace_values[[depended_dim]] <- depended_dim_values[j]
}
path_with_globs <- .ReplaceVariablesInString(dat[[i]][['path']], replace_values)
found_files <- Sys.glob(path_with_globs)
## TODO: Enhance this error message, or change by warning.
## Raises if a wrong sdate is specified, for example.
if (length(found_files) == 0) {
.warning(paste0("Could not find files for any '", u_file_dim,
"' for '", depended_dim, "' = '",
depended_dim_values[j], "'."))
dat_selectors[[u_file_dim]][[j]] <- NA
} else {
for (found_file in found_files) {
path_with_globs_and_tag <- .ReplaceVariablesInString(dat[[i]][['path']],
replace_values[-which(file_dims == u_file_dim)],
allow_undefined_key_vars = TRUE)
parsed_values <- c(parsed_values,
.FindTagValue(path_with_globs_and_tag, found_file,
u_file_dim))
}
dat_selectors[[u_file_dim]][[j]] <- selector_checker(selectors = selectors,
var = unique(parsed_values),
return_indices = FALSE)
# Take chunk if needed
dat_selectors[[u_file_dim]][[j]] <- dat_selectors[[u_file_dim]][[j]][chunk_indices(length(dat_selectors[[u_file_dim]][[j]]),
chunks[[u_file_dim]]['chunk'],
chunks[[u_file_dim]]['n_chunks'],
u_file_dim)]
}
}
}
#print("I")
} else {
dat[[i]][['path']] <- .ReplaceGlobExpressions(dat[[i]][['path']], first_file, replace_values,
defined_file_dims, dat[[i]][['name']], FALSE)
}
}
}
# Now fetch for the first available file
if (dataset_has_files[i]) {
known_dims <- file_dims
} else {
known_dims <- defined_file_dims
}
replace_values <- vector('list', length = length(known_dims))
names(replace_values) <- known_dims
files_to_load <- sapply(dat_selectors[known_dims], function(x) length(x[[1]]))
files_to_load[found_pattern_dim] <- 1
sub_array_of_files_to_load <- array(1:prod(files_to_load),
dim = files_to_load)
names(dim(sub_array_of_files_to_load)) <- known_dims
sub_array_of_not_found_files <- array(!dataset_has_files[i],
dim = files_to_load)
names(dim(sub_array_of_not_found_files)) <- known_dims
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
j <- 1
while (j <= prod(files_to_load)) {
selector_indices <- which(sub_array_of_files_to_load == j, arr.ind = TRUE)[1, ]
names(selector_indices) <- known_dims
selectors <- sapply(1:length(known_dims),
function (x) {
vector_to_pick <- 1
if (known_dims[x] %in% names(depending_file_dims)) {
vector_to_pick <- selector_indices[which(known_dims == depending_file_dims[[known_dims[x]]])]
}
dat_selectors[known_dims][[x]][[vector_to_pick]][selector_indices[x]]
})
names(selectors) <- known_dims
replace_values[known_dims] <- selectors
if (!dataset_has_files[i]) {
if (any(is.na(selectors))) {
replace_values <- replace_values[-which(names(replace_values) %in% names(selectors[which(is.na(selectors))]))]
}
file_path <- .ReplaceVariablesInString(dat[[i]][['path']], replace_values, TRUE)
sub_array_of_files_to_load[j] <- file_path
} else {
if (any(is.na(selectors))) {
replace_values <- replace_values[-which(names(replace_values) %in% names(selectors[which(is.na(selectors))]))]
file_path <- .ReplaceVariablesInString(dat[[i]][['path']], replace_values, TRUE)
sub_array_of_files_to_load[j] <- file_path
sub_array_of_not_found_files[j] <- TRUE
} else {
file_path <- .ReplaceVariablesInString(dat[[i]][['path']], replace_values)
sub_array_of_files_to_load[j] <- file_path
if (is.null(indices_of_first_files_with_data[[i]])) {
if (!(length(grep("^http", file_path)) > 0)) {
if (!file.exists(file_path)) {
file_path <- NULL
}
}
if (!is.null(file_path)) {
test_file <- NULL
## TODO: suppress error messages
test_file <- file_opener(file_path)
if (!is.null(test_file)) {
selector_indices[which(known_dims == found_pattern_dim)] <- i
indices_of_first_files_with_data[[i]] <- selector_indices
selectors_of_first_files_with_data[[i]] <- selectors
file_closer(test_file)
}
}
}
}
}
j <- j + 1
}
# Extend array as needed progressively
if (is.null(array_of_files_to_load)) {
array_of_files_to_load <- sub_array_of_files_to_load
array_of_not_found_files <- sub_array_of_not_found_files
} else {
array_of_files_to_load <- .MergeArrays(array_of_files_to_load, sub_array_of_files_to_load,
along = found_pattern_dim)
## TODO: file_dims, and variables like that.. are still ok now? I don't think so
array_of_not_found_files <- .MergeArrays(array_of_not_found_files, sub_array_of_not_found_files,
along = found_pattern_dim)
}
dat[[i]][['selectors']] <- dat_selectors
}
if (all(sapply(indices_of_first_files_with_data, is.null))) {
stop("No data files found for any of the specified datasets.")
}
########################### READING INNER DIMS. #############################
#print("J")
## TODO: To be run in parallel (local multi-core)
# Now time to work out the inner file dimensions.
# First pick the requested variables.
dims_to_iterate <- NULL
for (return_var in names(return_vars)) {