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Log2file #293

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merged 8 commits into from
Apr 19, 2016
Merged

Log2file #293

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ad8e7db
Add more debug logging
jankatins Apr 10, 2016
d5f43f2
Add log to file
jankatins Apr 10, 2016
5390b93
Refactor sending an error message
jankatins Apr 13, 2016
37db6e3
Fix default options for jupyter.logfile
jankatins Apr 14, 2016
d426422
Add more debugging output
jankatins Apr 15, 2016
75aea9d
PEP8 -aehm- flyingsheep fixes :-)
jankatins Apr 15, 2016
02aae2c
Refactor: promote some functions
jankatins Apr 18, 2016
b4e3eeb
Refactor: move inline functions in execute to Executer methods
jankatins Apr 18, 2016
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322 changes: 173 additions & 149 deletions R/execution.r
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@ NULL

setClassUnion('recordedplotOrNULL', members = c('recordedplot', 'NULL'))

setClassUnion('listOrNULL', members = c('list', 'NULL'))

displayenv <- environment(publish_mimebundle)

# create an empty named list
Expand Down Expand Up @@ -59,6 +61,7 @@ format_stack <- function(calls) {
paste0(tb, line_refs)
}


Executor <- setRefClass(
'Executor',
fields = list(
Expand All @@ -68,179 +71,191 @@ Executor <- setRefClass(
payload = 'list',
err = 'list',
interrupted = 'logical',
last_recorded_plot = 'recordedplotOrNULL'),
last_recorded_plot = 'recordedplotOrNULL',
current_request = 'listOrNULL',
nframe = 'integer'),
methods = list(

is.silent = function() {
current_request$content$silent
},

send_error_msg = function(msg) {
if (!is_silent()) return()
send_response('stream', current_request, 'iopub',
list(name = 'stderr', text = msg))

},

display_data = function(data, metadata = NULL) {
if (is.null(metadata)) {
metadata <- namedlist()
}
send_response('display_data', current_request, 'iopub', list(
source = 'R display func',
data = data,
metadata = metadata))

invisible(TRUE)
},

page = function(mimebundle) {
payload <<- c(payload, list(list(source = 'page', data = mimebundle)))
},

# .Last doesn’t seem to work, so replicating behavior
quit = function(save = 'default', status = 0, runLast = TRUE) {
save <- switch(save,
default = , yes = TRUE,
no = FALSE,
ask = ask('Save workspace image? [y/n/c]: '),
stop('unknown `save` value'))
if (is.null(save)) return() # cancel
if (runLast) {
if (!is.null(.GlobalEnv$.Last)) .GlobalEnv$.Last()
if (!is.null(.GlobalEnv$.Last.sys)) .GlobalEnv$.Last.sys()
}
if (save) NULL # TODO: actually save history
payload <<- c(payload, list(list(source = 'ask_exit')))
},

handle_error = function(e) {
log_debug('Error output: %s', toString(e))
calls <- head(sys.calls()[-seq_len(nframe + 1L)], -3)

msg <- paste0(toString(e), 'Traceback:\n')
stack_info <- format_stack(calls)

err <<- list(ename = 'ERROR', evalue = toString(e), traceback = as.list(c(msg, stack_info)))
if (!is.silent()) {
send_response('error', current_request, 'iopub', c(err, list(
execution_count = execution_count)))
}
},

send_plot = function(plotobj) {
formats <- namedlist()
metadata <- namedlist()
for (mime in getOption('jupyter.plot_mimetypes')) {
tryCatch({
formats[[mime]] <- mime2repr[[mime]](plotobj, attr(plotobj, '.irkernel_width'), attr(plotobj, '.irkernel_height'))
}, error = handle_error)
# Isolating SVGs (putting them in an iframe) avoids strange
# interactions with CSS on the page.
if (identical(mime, 'image/svg+xml')) {
metadata[[mime]] <- list(isolated = TRUE)
}
}
publish_mimebundle(formats, metadata)
},

handle_display_error = function(e){
# This is used with withCallingHandler and only has two additional
# calls at the end instead of the 3 for tryCatch... (-2 at the end)
# we also remove the tryCatch and mime2repr stuff at the head of the callstack (+7)
calls <- head(sys.calls()[-seq_len(nframe + 7L)], -2)
stack_info <- format_stack(calls)
msg <- sprintf('ERROR while rich displaying an object: %s\nTraceback:\n%s\n',
toString(e),
paste(stack_info, collapse = '\n'))
log_debug(msg)
send_error_msg(msg)
},

handle_value = function(obj) {
log_debug("Value output...")
mimebundle <- prepare_mimebundle(obj, .self$handle_display_error)
if (length(intersect(class(obj), getOption('jupyter.pager_classes'))) > 0) {
log_debug('Showing pager: %s', paste(capture.output(str(mimebundle$data)), collapse = '\n'))
page(mimebundle)
} else {
log_debug('Sending display_data: %s', paste(capture.output(str(mimebundle$data)), collapse = '\n'))
send_response('display_data', current_request, 'iopub', mimebundle)
}
},

stream = function(output, streamname) {
log_debug('Stream output: %s', output)
send_response('stream', current_request, 'iopub', list(
name = streamname,
text = paste(output, collapse = '\n')))
},

handle_graphics = function(plotobj) {
log_debug("Graphics output...")
if (!plot_builds_upon(last_recorded_plot, plotobj)) {
log_debug('Sending plot...')
send_plot(last_recorded_plot)
}
# need to be set here to capture the size and have it available when the plot is sent
attr(plotobj, '.irkernel_width') <- getOption('repr.plot.width', repr_option_defaults$repr.plot.width)
attr(plotobj, '.irkernel_height') <- getOption('repr.plot.height', repr_option_defaults$repr.plot.height)
last_recorded_plot <<- plotobj
},

handle_message = function(o) {
log_debug('Message output: %s', o)
stream(paste(o$message, collapse = ''), 'stderr')
},

handle_warning = function(o) {
call <- if (is.null(o$call)) '' else paste('In', deparse(o$call)[[1]])
log_debug('Warning output: %s', sprintf('Warning message:\n%s: %s', call, o$message))
stream(sprintf('Warning message:\n%s: %s', call, o$message), 'stderr')
},

execute = function(request) {
send_response('status', request, 'iopub', list(
execution_state = 'busy'))
send_response('execute_input', request, 'iopub', list(
code = request$content$code,
execution_count = execution_count))

silent <- request$content$silent

display_data <- function(data, metadata = NULL) {
if (is.null(metadata)) {
metadata <- namedlist()
}
send_response('display_data', request, 'iopub', list(
source = 'R display func',
data = data,
metadata = metadata))

invisible(TRUE)
}

# Make the current request available to other functions
current_request <<- request
# reset ...
payload <<- list()
err <<- list()

# Push the display function into the IRdisplay namespace
# This looks awkward, but we do need to get a reference to the execution
# state into a global environment.
# TODO: move to initialize?
unlockBinding('base_display', displayenv)
assign('base_display', display_data, pos = displayenv)

payload <<- list()

page <- function(mimebundle) {
payload <<- c(payload, list(list(source = 'page', data = mimebundle)))
}

options(pager = function(files, header, title, delete.file) {
text <- title
for (path in files) {
text <- c(text, header, readLines(path))
}
if (delete.file) file.remove(files)
page(list('text/plain' = paste(text, collapse = '\n')))
})

# .Last doesn’t seem to work, so replicating behavior
quit <- function(save = 'default', status = 0, runLast = TRUE) {
save <- switch(save,
default = , yes = TRUE,
no = FALSE,
ask = ask('Save workspace image? [y/n/c]: '),
stop('unknown `save` value'))
if (is.null(save)) return() # cancel
if (runLast) {
if (!is.null(.GlobalEnv$.Last)) .GlobalEnv$.Last()
if (!is.null(.GlobalEnv$.Last.sys)) .GlobalEnv$.Last.sys()
}
if (save) NULL # TODO: actually save history
payload <<- c(payload, list(list(source = 'ask_exit')))
}
assign('base_display', .self$display_data, pos = displayenv)

# shade base::quit
assign('quit', quit, envir = .GlobalEnv)
assign('q', quit, envir = .GlobalEnv)

send_plot <- function(plotobj) {
formats <- namedlist()
metadata <- namedlist()
for (mime in getOption('jupyter.plot_mimetypes')) {
tryCatch({
formats[[mime]] <- mime2repr[[mime]](plotobj, attr(plotobj, '.irkernel_width'), attr(plotobj, '.irkernel_height'))
}, error = handle_error)
# Isolating SVGs (putting them in an iframe) avoids strange
# interactions with CSS on the page.
if (identical(mime, 'image/svg+xml')) {
metadata[[mime]] <- list(isolated = TRUE)
}
}
publish_mimebundle(formats, metadata)
}
assign('quit', .self$quit, envir = .GlobalEnv)
assign('q', .self$quit, envir = .GlobalEnv)

err <<- list()
nframe <- NULL # find out stack depth in notebook cell

# find out stack depth in notebook cell
# TODO: maybe replace with a single call on first execute and rest reuse the value?
tryCatch(evaluate(
'stop()',
stop_on_error = 1L,
output_handler = new_output_handler(error = function(e) nframe <<- sys.nframe())))

handle_error <- function(e) {
calls <- head(sys.calls()[-seq_len(nframe + 1L)], -3)

msg <- paste0(toString(e), 'Traceback:\n')
stack_info <- format_stack(calls)

err <<- list(ename = 'ERROR', evalue = toString(e), traceback = as.list(c(msg, stack_info)))
if (!silent) {
send_response('error', request, 'iopub', c(err, list(
execution_count = execution_count)))
}
}

if (silent) {
stream <- function(s, n) {}
handle_value <- identity
handle_graphics <- identity
handle_message <- identity
handle_warning <- identity
oh <- if (is.silent()) {
new_output_handler(
text = identity,
graphics = identity,
message = identity,
warning = identity,
error = identity,
value = identity)
} else {
handle_display_error <- function(e){
# This is used with withCallingHandler and only has two additional
# calls at the end instead of the 3 for tryCatch... (-2 at the end)
# we also remove the tryCatch and mime2repr stuff at the head of the callstack (+7)
calls <- head(sys.calls()[-seq_len(nframe + 7L)], -2)
stack_info <- format_stack(calls)
msg <- sprintf('ERROR while rich displaying an object: %s\nTraceback:\n%s\n',
toString(e),
paste(stack_info, collapse='\n'))
log_debug(msg)
if (!silent) {
send_response('stream', request, 'iopub', list(
name = 'stderr',
text = msg))
}
}
handle_value <- function(obj) {
mimebundle <- prepare_mimebundle(obj, handle_display_error)
if (length(intersect(class(obj), getOption('jupyter.pager_classes'))) > 0) {
log_debug('Showing pager: %s', paste(capture.output(str(mimebundle$data)), collapse = '\n'))
page(mimebundle)
} else {
log_debug('Sending display_data: %s', paste(capture.output(str(mimebundle$data)), collapse = '\n'))
send_response('display_data', request, 'iopub', mimebundle)
}
}

stream <- function(output, streamname) {
send_response('stream', request, 'iopub', list(
name = streamname,
text = paste(output, collapse = '\n')))
}

handle_graphics <- function(plotobj) {
if (!plot_builds_upon(last_recorded_plot, plotobj)) {
send_plot(last_recorded_plot)
}
# need to be set here to capture the size and have it available when the plot is sent
attr(plotobj, '.irkernel_width') <- getOption('repr.plot.width', repr_option_defaults$repr.plot.width)
attr(plotobj, '.irkernel_height') <- getOption('repr.plot.height', repr_option_defaults$repr.plot.height)
last_recorded_plot <<- plotobj
}

handle_message <- function(o) {
stream(paste(o$message, collapse = ''), 'stderr')
}

handle_warning <- function(o) {
call <- if (is.null(o$call)) '' else paste('In', deparse(o$call)[[1]])
stream(sprintf('Warning message:\n%s: %s', call, o$message), 'stderr')
}
new_output_handler(
text = function(o) stream(o, 'stdout'),
graphics = .self$handle_graphics,
message = .self$handle_message,
warning = .self$handle_warning,
error = .self$handle_error,
value = .self$handle_value)
}

oh <- new_output_handler(
text = function(o) stream(o, 'stdout'),
graphics = handle_graphics,
message = handle_message,
warning = handle_warning,
error = handle_error,
value = handle_value)

interrupted <<- FALSE
last_recorded_plot <<- NULL

log_debug('Executing code: %s', request$content$code)
tryCatch(
evaluate(
request$content$code,
Expand All @@ -250,7 +265,7 @@ execute = function(request) {
interrupt = function(cond) interrupted <<- TRUE,
error = handle_error) # evaluate does not catch errors in parsing

if ((!silent) & (!is.null(last_recorded_plot))) {
if ((!is.silent()) & (!is.null(last_recorded_plot))) {
send_plot(last_recorded_plot)
}

Expand Down Expand Up @@ -279,14 +294,23 @@ execute = function(request) {
abort_queued_messages()
}

if (!silent) {
if (!is.silent()) {
execution_count <<- execution_count + 1L
}
},

initialize = function(...) {
execution_count <<- 1L
err <<- list()
options(pager = function(files, header, title, delete.file) {
text <- title
for (path in files) {
text <- c(text, header, readLines(path))
}
if (delete.file) file.remove(files)
page(list('text/plain' = paste(text, collapse = '\n')))
})

callSuper(...)
})
)
1 change: 1 addition & 0 deletions R/kernel.r
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -372,6 +372,7 @@ main <- function(connection_file = '') {
# pass it as a separate command line argument.
connection_file <- commandArgs(TRUE)[[1]]
}
log_debug('Starting the R kernel...')
kernel <- Kernel$new(connection_file = connection_file)
kernel$run()
}