/
class-flow.R
1542 lines (1365 loc) · 40.7 KB
/
class-flow.R
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#' Build workflow
#'
#' Build workflow
#'
#' @param graph if add graph coordinates or not,
#' used for flow visualization on Seven Bridges platforms.
#' @param x.width x scale width
#' @param y.width y scale width
#' @param x.start node x start point for a flow
#' @param y.start node y start point for a flow
#' @param canvas_zoom zoom factor
#' @param canvas_x canvas x
#' @param canvas_y canvas y
#' @param ... extra arguments passed to SBGWorkflow
#'
#' @rdname Flow
#' @return a SBGWorkflow object.
#' @export SBGWorkflow
#' @exportClass SBGWorkflow
#' @aliases SBGWorkflow
#' @examples
#' f1 <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
#' f1 <- convert_app(f1)
#' # input matrix
#' f1$input_matrix()
#' # by name
#' f1$input_matrix(c("id", "type", "required", "link_to"))
#' # return only required
#' f1$input_matrix(required = TRUE)
#' # return everything
#' f1$input_matrix(NULL)
#' # return a output matrix with more informtion
#' f1$output_matrix()
#' # return only a few fields
#' f1$output_matrix(c("id", "type"))
#' # return everything
#' f1$output_matrix(NULL)
#' # flow inputs
#' f1$input_type()
#' # flow outouts
#' f1$output_type()
#' # flow input id
#' f1$input_id()
#' # linked input id
#' f1$linked_input_id()
#' # flow output id
#' f1$output_id()
#' # linked output id
#' f1$linked_output_id()
#' # link_map
#' f1$link_map()
#' # all step input id
#' f1$step_input_id()
#' # all step input full id with type
#' f1$step_input_id(TRUE)
#' # all step output id
#' f1$step_output_id()
#' # all step output full id with type
#' f1$step_output_id(TRUE)
#' # get inputs objects
#' f1$get_input("#clip3pNbases")
#' f1$get_input(c("#clip3pNbases", "#chimScoreMin"))
#' f1$get_input(c("#clip3pNbases", "#chimScoreMin", "#STAR.outFilterMismatchNoverLmax"))
#' # get outputs objects
#' f1$get_output("#log_files")
#' f1$get_output(c("#log_files", "intermediate_genome"))
#' f1$get_output(c("#log_files", "intermediate_genome", "#STAR.unmapped_reads"))
#' f1$get_output("#log_files")
#' # set flow input
#' f1$set_flow_input("#SBG_FASTQ_Quality_Detector.fastq")
#' f1$set_flow_output(c("#log_files", "intermediate_genome"))
#' # get required node
#' f1$get_required()
#' # set required node
#' f1$steps[[1]]$run$set_required("genomeChrBinNbits")
#' f1$get_required()
#' f1$steps[[1]]$run$set_required("genomeChrBinNbits", FALSE)
#' f1$get_required()
#' # get Tool object from Flow by id and name
#' f1$list_tool()
#' # return two
#' f1$get_tool("STAR")
#' # return one
#' f1$get_tool("^STAR$")
#' # get included input ports
#' f1$get_input_port()
#' # set included input ports
#' f1$set_input_port(c("#STAR.alignSJDBoverhangMin", "chimScoreSeparation"))
#' f1$get_input_port()
#' f1$set_input_port(c("#STAR.alignSJDBoverhangMin", "chimScoreSeparation"), FALSE)
#' f1$get_input_port()
#' f1$get_input_node()
#' f1$get_output_node()
#' f1$get_input_exposed()
#' f1$step_input_id(TRUE)
#' f1$input_id()
#' f1$set_flow_input("#STAR.reads")
#' f1$input_id()
#' # batch
#' f1$set_batch("sjdbGTFfile", c("metadata.sample_id", "metadata.library_id"))
#' f1$set_batch("sjdbGTFfile", type = "ITEM")
#' # add source to id
#' f1$link_map()
#' f1$add_source_to_id(c("test1", "test2"), c("#STAR.genome", "#STAR.reads"))
#' f1$link_map()
SBGWorkflow <- setRefClass(
"SBGWorkflow",
contains = c("Workflow", "SBG"),
fields = list(
"sbg:canvas_zoom" = "numericORNULL",
"sbg:canvas_y" = "numericORNULL",
"sbg:canvas_x" = "numericORNULL",
"sbg:batchInput" = "characterORNULL",
"sbg:batchBy" = "listORNULL",
"y" = "numericORNULL",
"x" = "numericORNULL"
),
methods = list(
initialize = function(id = NULL,
label = NULL,
canvas_zoom = 1,
canvas_y = NULL,
canvas_x = NULL,
batchInput = NULL,
batchBy = NULL,
steps = list(), ...) {
stopifnot(!is.null(id))
stopifnot(!is.null(label))
args <- mget(
names(formals()),
sys.frame(sys.nframe())
)
nms <- c(
"canvas_x", "canvas_y",
"canvas_zoom", "update",
"batchInput", "batchBy"
)
for (nm in nms) {
.self$field(paste0("sbg:", nm), args[[nm]])
}
steps <<- steps
callSuper(id = id, label = label, ...)
},
copy_obj = function() {
"this is a hack to make copy of reference cwl object"
tmp <- tempfile()
write(toJSON(pretty = TRUE), tmp)
res <- convert_app(tmp)
file.remove(tmp)
res
},
set_flow_output = function(oid = NULL, add = TRUE) {
"Expose tool output node as flow output, default is additative, if add = FALSE, this will overwrite and only made provided id outputs of flow."
# just add to output node
if (!length(oid)) return(NULL)
# get exist
if (add) {
old.id <- output_id()
oid <- unique(c(old.id, oid))
}
oi <- sapply(oid, .id_only)
ol <- get_output(oid, TRUE)
sol <- as(ol, "SBGWorkflowOutputParameterList")
lst <- lapply(sol, function(ol) {
.id <- ol$id
nm <- names(oi[oi == .id])
# should be full name
ol$source <- set_box(nm)
ol
})
sol <- do.call(
"SBGWorkflowOutputParameterList",
lst
)
for (i in 1:length(sol)) {
sol[[i]]$"sbg:includeInPorts" <- TRUE
}
outputs <<- sol
addGraph(.self)
},
set_flow_input = function(iid = NULL, add = TRUE) {
# validate if the input is File or File...
"Expose tool input node as flow input, default is additative, if add = FALSE, this will overwrite and only made provided id inputs of flow."
.id <- step_input_id(TRUE)
if (!all(iid %in% .id)) {
stop("input id doesn't exist")
}
if (add) {
oid <- input_id()
nid <- iid[which(is.na(match(sapply(iid, .id_only), oid)))]
.nnl <- get_input(id = nid)
if (length(.nnl) == 1) {
.nnl <- list(.nnl)
} else {
.nnl <- as.list(.nnl)
}
inl <- do.call("IPList", c(.nnl, as.list(inputs)))
} else {
nid <- iid
inl <- get_input(id = nid, TRUE)
}
# get connected from step list
sapply(nid, function(x) {
tool.id <- get_tool_id_from_full(x)
sins <- get_step(id = tool.id)$inputs
idx <- which(x == sapply(sins, function(i) i$id))
input.id <- get_input_id_from_full(x)
sins[[idx]]$source <- set_box(input.id)
})
for (i in 1:length(inl)) {
# all exposed
inl[[i]]$"sbg:includeInPorts" <- TRUE
}
inputs <<- inl
addGraph(.self)
},
linked_output_id = function() {
"output id that linked to an input"
res <- unlist(sapply(steps, function(s) {
if (length(s$inputs)) {
sapply(s$inputs, function(i) {
res <- i$source
if (length(res)) {
return(unname(i$source))
} else {
return(NULL)
}
})
} else {
return(NULL)
}
}))
res[is_full_name(res)]
},
linked_input_id = function() {
"input id that linked to an output"
res <- unlist(sapply(steps, function(s) {
if (length(s$inputs)) {
sapply(s$inputs, function(i) {
res <- i$source
if (length(res)) {
return(unname(i$id))
} else {
return(NULL)
}
})
} else {
return(NULL)
}
}))
res[is_full_name(res)]
},
link_map = function() {
"show a table of all linked nodes"
lst <- lapply(steps, function(s) {
ilst <- s$inputs
res <- do.call(rbind, lapply(ilst, function(ii) {
ii <- ii$toList()
if ("source" %in% names(ii)) {
data.frame(
id = unname(ii$id),
source = as.character(ii$source),
type = "input",
stringsAsFactors = TRUE
)
} else {
NULL
}
}))
if (length(res)) {
rownames(res) <- NULL
res
} else {
NULL
}
})
r1 <- do.call(rbind, lst)
lst <- lapply(outputs, function(o) {
data.frame(
id = unname(o$id),
source = as.character(o$source),
type = "output",
stringsAsFactors = TRUE
)
})
r2 <- do.call(rbind, lst)
rbind(r1, r2)
# output
},
get_id_by_source = function(sname) {
lm <- link_map()
paste0(as.character(lm[which(lm$source == sname), "id"]), collapse = " | ")
},
add_source_to_id = function(sources, ids) {
if (length(sources) != length(ids)) {
stop("sources and ids lengths must be the same")
}
for (i in 1:length(sources)) {
.s <- get_step(id = get_tool_id_from_full(ids[i]))
idx <- which(sapply(.s$inputs, function(x) {
x$id == ids[i]
}))
.s$inputs[[idx]]$source <- c(.s$inputs[[idx]]$source, set_box(sources[i]))
}
.self
},
list_tool = function() {
"list all tools included in this flow"
res <- lapply(steps, function(x) {
data.frame(
label = x$run$label,
sbgid = x$run$id,
id = x$id,
stringsAsFactors = TRUE
)
})
res <- do.call(rbind, res)
rownames(res) <- NULL
res
},
get_tool = function(name = NULL, id = NULL) {
"get a tool object by name or id, name support pattern match"
if (is.null(name) && is.null(id)) {
stop("please provide name or id")
}
dt <- list_tool()
if (!is.null(name)) {
idx <- which(grepl(name, dt$label))
}
if (!is.null(id)) {
idx <- which(id == dt$id)
}
if (length(idx) == 0) {
return(NULL)
} else if (length(idx) == 1) {
return(steps[[idx]]$run)
} else if (length(idx) > 1) {
return(lapply(steps[idx], function(x) x$run))
}
},
get_step = function(name = NULL, id = NULL) {
"get step object by name or id, name support pattern match"
if (is.null(name) && is.null(id)) {
stop("please provide name or id")
}
dt <- list_tool()
if (!is.null(name)) {
idx <- which(grepl(name, dt$label))
}
if (!is.null(id)) {
idx <- which(id == dt$id)
}
if (length(idx) == 0) {
return(NULL)
} else if (length(idx) == 1) {
return(steps[[idx]])
} else if (length(idx) > 1) {
return(steps[idx])
}
},
get_input = function(ids, force = FALSE) {
"get input by pure input id from all steps"
ids <- addIdNum(ids)
idx <- is_full_name(ids)
res <- NULL
if (sum(idx)) {
ids.full <- ids[idx]
tool.name <- get_tool_id_from_full(ids[idx])
input.name <- get_input_id_from_full(ids[idx])
for (i in 1:length(tool.name)) {
res <- c(res, get_tool(id = tool.name[i])$get_input(id = input.name[i]))
}
}
if (sum(!idx)) {
for (.id in ids[!idx]) {
for (i in seq_len(length(steps))) {
r <- steps[[i]]$run
idx <- which(.id == r$input_id())
if (length(idx)) {
res <- c(res, r$inputs[[idx]])
}
}
}
}
if (force) {
if (length(res)) {
return(do.call("InputParameterList", res))
} else {
return(NULL)
}
} else {
if (length(res) > 1) {
return(do.call("InputParameterList", res))
} else if (length(res) == 1) {
return(res[[1]])
} else {
return(NULL)
}
}
},
get_output = function(ids, force = FALSE) {
"get output by pure output id from all steps"
res <- NULL
ids <- addIdNum(ids)
idx <- is_full_name(ids)
if (sum(idx)) {
ids.full <- ids[idx]
tool.name <- get_tool_id_from_full(ids[idx])
output.name <- get_input_id_from_full(ids[idx])
for (i in 1:length(tool.name)) {
res <- c(res, get_tool(id = tool.name[i])$get_output(id = output.name[i]))
}
}
if (sum(!idx)) {
for (.id in ids[!idx]) {
for (i in seq_len(length(steps))) {
r <- steps[[i]]$run
idx <- which(.id == r$output_id())
if (length(idx)) {
res <- c(res, r$outputs[[idx]])
}
}
}
}
if (force) {
if (length(res)) {
return(do.call("OutputParameterList", res))
} else {
return(NULL)
}
} else {
if (length(res) > 1) {
return(do.call("OutputParameterList", res))
} else if (length(res) == 1) {
return(res[[1]])
} else {
return(NULL)
}
}
},
input_type = function() {
"Show a vector of flow input type, names of them are input id."
getInputType(toList())
},
output_type = function() {
"Show a vector of flow output type, names of them are output id."
getOutputType(toList())
},
input_id = function() {
"show input id"
res <- unname(sapply(inputs, function(i) i$id))
if (length(res)) {
return(res)
} else {
return(NULL)
}
},
output_id = function() {
"show output id"
res <- unname(sapply(outputs, function(o) o$id))
if (length(res)) {
return(res)
} else {
return(NULL)
}
},
input_matrix = function(new.order = c("id", "label", "type", "required", "prefix", "fileTypes"), required = NULL) {
"This return a matrix of input parameters, by default, following the order id, label, type, required, prefix, fileTypes. new.order accept names of column you want to print, but it has to be a field of inputs. When its set to NULL, it prints all fields. When required = TRUE, only print required field."
res <- suppressWarnings(as(inputs, "data.frame"))
if ("link_to" %in% new.order || is.null(new.order)) {
res$link_to <- sapply(res$id, .self$get_id_by_source)
}
if (!is.null(required)) {
stopifnot(is.logical(required))
res <- res[res$required == required, ]
if (!nrow(res)) {
return(NULL)
}
}
if (!is.null(new.order)) {
new.order <- intersect(new.order, names(res))
res[, new.order]
} else {
res
}
},
output_matrix = function(new.order = c("id", "label", "type", "fileTypes")) {
"This return a matrix of output parameters, by default, following the order id, label, type, fileTypes. new.order accept names of column you want to print, but it has to be a field of outputs. When its set to NULL, it prints all fields. When required = TRUE, only print required field."
res <- suppressWarnings(as(outputs, "data.frame"))
if ("link_to" %in% new.order || is.null(new.order)) {
lm <- link_map()
res$link_to <- sapply(res$id, function(i) {
paste0(as.character(lm[which(lm$id == i), "source"]), collapse = " | ")
})
}
if (!is.null(new.order)) {
new.order <- intersect(new.order, names(res))
res[, new.order]
} else {
res
}
},
step_input_id = function(full = FALSE) {
"Show step input id, default names of them is tool id. When full = TRUE, show full name then names of vector is type."
unlist(sapply(steps, function(x) {
x$run$input_id(full = full)
}))
},
step_output_id = function(full = FALSE) {
"Show step output id, default names of them is tool id. when full = TRUE, show full name then names of vector is type."
unlist(sapply(steps, function(x) {
x$run$output_id(full = full)
}))
},
get_required = function() {
"show flow required input id and types"
nms <- unlist(sapply(steps, function(x) {
x$run$get_required()
}))
# get exposed from workflow
it <- input_type()
enms <- names(it)
res <- intersect(names(nms), enms)
if (length(res)) {
it[enms %in% res]
} else {
return(NULL)
}
},
set_required = function(ids, required = TRUE) {
"Set a input node required (TRUE) or not required (FALSE) this require full input id (with tool id prefix) such as #STAR.alignIntronMax"
tool.name <- get_tool_id_from_full(ids)
input.name <- get_input_id_from_full(ids)
tools <- get_tool(tool.name)
for (i in 1:length(tool.name)) {
tools[[i]]$set_required(input.name, required)
}
},
get_input_port = function() {
"show included port of all inputs"
unlist(sapply(steps, function(x) {
x$run$get_input_port()
}))
},
set_input_port = function(ids, include = TRUE) {
"set included port for provided input id(s)"
ids <- add_sharp(ids)
idx <- is_full_name(ids)
if (sum(idx)) {
ids.full <- ids[idx]
tool.name <- get_tool_id_from_full(ids[idx])
input.name <- get_input_id_from_full(ids[idx])
for (i in 1:length(tool.name)) {
get_tool(id = tool.name[i])$set_input_port(id = input.name[i], include = include)
}
}
if (sum(!idx)) {
for (.id in ids[!idx]) {
get_input(id = .id)$field("sbg:includeInPorts", include)
}
}
},
get_input_node = function() {
"get input file nodes id"
it <- input_type()
add_sharp(names(it[it %in% c("File", "File...")]))
},
get_output_node = function() {
"get output file nodes id"
it <- output_type()
add_sharp(names(it[it %in% c("File", "File...")]))
},
get_input_exposed = function() {
"exposed input id other than file"
it <- input_type()
add_sharp(names(it[!it %in% c("File", "File...")]))
},
set_batch = function(input = NULL,
criteria = NULL,
type = c("ITEM", "CRITERIA")) {
"Set a flow input node into a batch mode, this is now required before you execute a batch task on a batch-not-enabled flow."
lst <- batch(input = input, criteria = criteria, type = type)
lst$batch_by$type <- tolower(lst$batch_by$type)
# flow level
.self$field("sbg:batchInput", addIdNum(lst$batch_input))
.self$field("sbg:batchBy", lst$batch_by)
# step level
idx <- which(sapply(.self$inputs, function(x) x$id) == addIdNum(input))
.self$inputs[[idx]]$field("batchType", tail(criteria, 1))
.self
},
run = function(run_inputs = list(), engine = c("bunny", "rabix", "cwlrun")) {
"Run this tool with inputs locally. Engines supported: bunny, rabix, cwlrun. Inputs accept list or JSON."
engine <- match.arg(engine)
run_inputs <- lapply(run_inputs, asTaskInput)
switch(engine,
bunny = {
test_tool_bunny(.self, run_inputs)
},
cwlrun = {
test_tool_cwlrun(.self, run_inputs)
},
rabix = {
test_tool_rabix(.self, run_inputs)
}
)
}
)
)
#' @rdname Flow
#'
#' @export Flow
#' @aliases Flow
Flow <- function(...,
graph = TRUE,
x.width = 1000,
y.width = 400,
x.start = 100,
y.start = 200,
canvas_zoom = 1,
canvas_x = 40,
canvas_y = 130) {
obj <- SBGWorkflow(...)
if (graph) {
obj <- addGraph(obj,
x.width = x.width,
y.width = y.width,
x.start = x.start,
y.start = y.start,
canvas_zoom = canvas_zoom,
canvas_x = canvas_x,
canvas_y = canvas_y
)
}
obj
}
#' @rdname Flow
#' @export
#' @param e1 either Tool App or Workflow object
#' @param e2 either Tool App or Workflow object
#' @docType methods
#' @aliases "+",Tool,Tool-method
setMethod("+", c("Tool", "Tool"), function(e1, e2) {
# find the x1
o <- e1$output_id(TRUE)
i <- e2$input_id(TRUE)
idx <- match(names(o), names(i))
if (!all(is.na(idx))) {
if (sum(!is.na(idx)) == 1) {
# return a Workflow
.out.id <- o[which(!is.na(idx))]
.in.id <- i[idx[!is.na(idx)]]
.out1 <- o
.out2 <- e2$output_id(TRUE)
o1 <- do.call(
"WorkflowStepOutputList",
lapply(.out1, function(oid) WorkflowStepOutput(id = oid))
)
o2 <- do.call(
"WorkflowStepOutputList",
lapply(.out2, function(oid) WorkflowStepOutput(id = oid))
)
# insert int id
steplst <- SBGStepList(
SBGStep(
id = getId(e1),
run = e1,
outputs = o1
),
SBGStep(
id = getId(e2),
run = e2,
outputs = o2,
inputs = WorkflowStepInputList(
WorkflowStepInput(
id = .in.id,
source = c(.out.id)
)
)
)
)
# make rest inports
return(steplst)
} else {
stop("multiple matching found, no sure which one to connect")
}
} else {
stop("no input match ouput types")
}
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "+",WorkflowStepList,Tool-method
setMethod("+", c("WorkflowStepList", "Tool"), function(e1, e2) {
t.last <- e1[[length(e1)]]$run
t.new <- (t.last + e2)[2]
do.call(SBGStepList, c(as.list(e1), as.list(t.new)))
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "+",WorkflowStepList,WorkflowStepList-method
setMethod("+", c("WorkflowStepList", "WorkflowStepList"), function(e1, e2) {
do.call("WorkflowStepList", c(as.list(e1), as.list(e2)))
})
# Fix me
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "+",App,App-method
setMethod("+", c("App", "App"), function(e1, e2) {
convert_app(e1) + convert_app(e2)
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "+",WorkflowStepList,App-method
setMethod("+", c("WorkflowStepList", "App"), function(e1, e2) {
t.last <- e1[[length(e1)]]$run
t.new <- (t.last + convert_app(e2))[2]
do.call(SBGStepList, c(as.list(e1), as.list(t.new)))
})
# linear connection
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%"
setGeneric("%>>%", function(e1, e2) standardGeneric("%>>%"))
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%",Tool,Tool-method
setMethod("%>>%", c("Tool", "Tool"), function(e1, e2) {
# assumption here is linear connection
o <- e1$output_id(TRUE)
i <- e2$input_id(TRUE)
idx <- match(names(o), names(i))
if (!all(is.na(idx))) {
if (sum(!is.na(idx)) == 1) {
# return a Workflow
.out.id <- get_input_id_from_full(o[which(!is.na(idx))])
.in.id <- get_input_id_from_full(i[idx[!is.na(idx)]])
} else {
stop("multiple matching found, no sure which one to connect")
}
} else {
stop("no input match ouput types")
}
link(e1, e2, .out.id, .in.id)
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%",Workflow,Tool-method
setMethod("%>>%", c("Workflow", "Tool"), function(e1, e2) {
# fix
slist <- e1$steps + e2
new.flow <- Flow(id = e1$id, label = e1$label, steps = slist)
e1$steps <- slist
e1$outputs <- new.flow$outputs
e1
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%",Workflow,Workflow-method
setMethod("%>>%", c("Workflow", "Workflow"), function(e1, e2) {
e1$steps <- e1$steps + e2$steps
e1
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%",App,App-method
setMethod("%>>%", c("App", "App"), function(e1, e2) {
# convert_app(e1) %>>% convert_app(e2)
stop("not implemented yet")
})
#' @rdname Flow
#' @export
#' @docType methods
#' @aliases "%>>%",Workflow,App-method
setMethod("%>>%", c("Workflow", "App"), function(e1, e2) {
slist <- e1$steps + convert_app(e2)
new.flow <- Flow(id = e1$id, label = e1$label, steps = slist)
# udpate step list
e1$steps <- slist
# update workflow
e1$outputs <- new.flow$outputs
e1
})
# assign coordinates
# add output port
# coersion
setAs(
"CommandOutputParameter", "WorkflowOutputParameter",
function(from) {
WorkflowOutputParameter(
type = from$type,
label = from$label,
description = from$description,
streamable = from$streamable,
default = from$default,
id = from$id
)
}
)
setAs(
"CommandOutputParameter", "SBGWorkflowOutputParameter",
function(from) {
SBGWorkflowOutputParameter(
type = from$type,
label = from$label,
description = from$description,
streamable = from$streamable,
default = from$default,
id = from$id
)
}
)
setAs(
"OutputParameterList", "WorkflowOutputParameterList",
function(from) {
lst <- lapply(from, function(x) as(x, "WorkflowOutputParameter"))
do.call("WorkflowOutputParameterList", lst)
}
)
setAs(
"OutputParameterList", "SBGWorkflowOutputParameterList",
function(from) {
lst <- lapply(from, function(x) as(x, "SBGWorkflowOutputParameter"))
do.call("SBGWorkflowOutputParameterList", lst)
}
)
getOutputById <- function(sl, id) {
lst <- lapply(sl, function(s) {
ol <- s$run$outputs
lapply(ol, function(o) {
if (o$id %in% id) {
return(o)
} else {
return(NULL)
}
})
})
lst <- do.call(c, lst)
lst <- lst[!sapply(lst, is.null)]
do.call("OutputParameterList", lst)
}
# asign step list coordinates
setGeneric("addGraph", function(obj, ...) standardGeneric("addGraph"))
setMethod("addGraph", "SBGStepList", function(obj,
x.width = 1000,
y.width = 400,
x.start = 100,
y.start = 200) {
N <- length(obj)
if (N) {
x.step <- x.width / (N + 1)
# x from 100
# y from 200
for (i in 1:N) {
obj[[i]]$field("sbg:x", x.start + x.step * (i - 1))
obj[[i]]$field("sbg:y", y.start)
}
}
obj
})
setMethod(
"addGraph", "SBGWorkflow",
function(obj,
x.width = 1000,
y.width = 400,
x.start = 100,
y.start = 200,
canvas_zoom = 1,
canvas_x = 40,
canvas_y = 130) {
obj$steps <- addGraph(obj$steps)
slst <- obj$steps
x.step <- x.width / (length(slst) + 1)
# outputs
os <- obj$outputs
N <- length(os)
if (N) {
y.step <- y.width / (N + 1)
for (i in 1:N) {
x <- obj$outputs[[i]]$field("sbg:x")
y <- obj$outputs[[i]]$field("sbg:y")
if (is.null(x) || is.null(y)) {
obj$outputs[[i]]$field("sbg:x", x.width - x.step)
obj$outputs[[i]]$field("sbg:y", y.start + y.step * (i - 1))
}
}
}
# inputs