Nothing
R/DataSpaceStudies.R
In DataSpaceR: Interface to 'the CAVD DataSpace'
#' @title The DataSpaceStudies class
#'
#' @description
#' An R6 class for DataSpace Study data.
#'
#' @section Constructor:
#' \code{DataSpaceConnection$getStudies()}
#'
#' @seealso \code{\link{connectDS}} \code{\link{DataSpaceConnection}}
#'
#' @examples
#' \dontrun{
#' # Create a connection (Initiate a DataSpaceConnection object)
#' con <- connectDS()
#'
#' # Get group by `study_id` or pass a filtered `availableStudies` object.
#' studies <- con$getStudies(c("vtn505", "cvd408"))
#' studies <- con$getStudies(
#' con$availableStudies[grepl("BAMA", data_availability) & species == "Human"]
#' )
#'
#' # Load BAMA to the studies object.
#' studies$loadAssayDatasets("BAMA")
#' studies$datasets$BAMA
#'
#' # Inspect variable information of the BAMA dataset
#' studies$datasetDescriptions$BAMA
#'
#' # Inspect treatment arm information for all studies in study object
#' studies$treatmentArm
#'
#' }
#'
DataSpaceStudies <- R6Class(
classname = "DataSpaceStudies",
inherit = DataSpaceConnection,
public = list(
#' @description
#' Initialize \code{DataSpaceStudy} class.
#' See \code{\link{DataSpaceConnection}}.
#' @param studyIds A character. Name of the study to retrieve.
#' as URL, path and username.
initialize = function(studyIds) {
studyIds <- studyIds[studyIds != ""]
private$.studyIds <- checkStudies(studyIds, private$.shared$.config$labkeyUrlBase)
private$.publicationIds <- private$.shared$.availablePublications[
sapply(strsplit(related_studies, ", "), \(.) any(. %in% private$.studyIds)) &
publication_data_available == TRUE,
publication_id
]
private$.mabMixIds <- private$.shared$.mabStudies[
strsplit(studies_available, ", ") |> sapply(\(sa) any(sa %in% private$.studyIds)),
mab_mix_id
] |>
unique()
private$.mabIds <- private$.shared$.mabMix[mab_mix_id %in% private$.mabMixIds, mab_id] |>
unique()
private$.shared$.config$labkeyStudyUrlPaths <- getStudyUrlPaths(private$.studyIds)
self$refresh()
NULL
},
#' @description
#' Print \code{DataSpaceStudy} class.
print = function() {
cat("<DataSpaceStudies>")
cat("\n Studies:", paste(private$.studyIds, collapse = ", "))
cat("\n Available integrated datasets:")
if (nrow(private$.availableIntegratedDatasets) > 0) {
cat(paste("\n -", unique(private$.availableIntegratedDatasets$assay_label)), sep = "")
}
cat("\n Available non-integrated datasets:")
if (nrow(private$.availableNIDatasets) > 0) {
cat(paste("\n -", unique(private$.availableNIDatasets$assay_label)), sep = "")
}
cat("\n Available publication datasets:")
if (length(private$.publicationIds) > 0) {
cat(paste("\n -", unique(private$.shared$.availablePublications[publication_id %in% private$.publicationIds, label])), sep = "")
}
cat("\n Available Studies objects:")
cat(paste0("\n - ", DataSpaceStudies$active |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Studies methods:")
cat(paste0("\n - ", DataSpaceStudies$public_methods |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Connection objects:")
cat(paste0("\n - ", DataSpaceConnection$active |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Connection methods:")
cat(paste0("\n - ", DataSpaceConnection$public_methods |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n")
},
#' @description
#' Load datasets to the studies object from an availableDatasets object.
#' @param availableDatasets An `availableDatasets` object or vector of `study_id` values.
#' @param downloadDir Optional, a character path specifying a directory to download.
#' nonstandard datasets. The default is the working temp directory.
loadAvailableDatasets = function(availableDatasets = self$availableDatasets, downloadDir = tempdir()) {
if(is.character(availableDatasets)){
availableDatasets = self$availableDatasets[assay_identifier %in% availableDatasets]
if(nrow(availableDatasets) == 0)
stop("Charactor vector of assay identifiers passed did not return any available datasets from `availableDatasets`.")
}
if(any(availableDatasets$dataset_type == "Publication Data")){
warning("Publication data in `availalableDatasets` ignored. Use `getPublicationDatasets` to download those.")
}
availableDatasets <- availableDatasets[dataset_type %in% c("Integrated Assay", "Non-Integrated Assay")]
if(nrow(availableDatasets) == 0) stop("No integrated or non-integrated assays to get.")
if(any(availableDatasets$dataset_type == "Integrated Assay")){
assays <- availableDatasets[dataset_type == "Integrated Assay"]$assay_identifier |>
unique()
filter <- makeFilter(c("study_prot", "IN", paste(unique(availableDatasets$study_id), collapse = ";")))
assayData <- assays |>
lapply(\(assay)
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "study",
queryName = assay,
viewName = NULL,
colFilter = filter,
colNameOpt = "fieldname",
method = "GET",
) |> setDT()
)
names(assayData) <- assays
}
if(any(availableDatasets$dataset_type == "Non-Integrated Assay")){
niData <-
private$.availableDocuments[
assay_identifier %in% availableDatasets$assay_identifier & document_type == "Non-Integrated Assay",
.SD |>
downloadDocuments(downloadDir) |>
unzipDocuments() |>
loadDocuments() |>
_[,.(datasets, assay_identifier, unzipDir)]
]
nsd <- unique(niData$assay_identifier)
names(nsd) <- nsd
appendData <- lapply(
nsd,
\(nm) rbindlist(niData[assay_identifier == nm, datasets], fill = T)
)
assayData <- append(assayData, appendData)
availableDatasets[niData[,.(assay_identifier, unzipDir)], on = "assay_identifier", unzipDir := i.unzipDir]
} else {
availableDatasets[,unzipDir := NA]
}
private$.datasets <- assayData
if("BCR_Sequence" %in% assays){
message("Querying BCR sequence study data, this may take a few minutes...")
bcr_sequence <-
Map(
\(studyId)
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath="CAVD",
schemaName="CDS",
queryName="bcr_sequence_alignment_prot",
colFilter=makeFilter(c("prot", "IN", studyId)),
colNameOpt="rname"
) |> setDT(),
private$.studyIds
) |> rbindlist()
private$.datasets <- append(
private$.datasets,
list(
alignments = bcr_sequence[,.(cell_id,sequence_id,stop_codon,vj_in_frame,productive,rev_comp,complete_vdj,v_call,d_call,j_call,sequence_alignment,germline_alignment,sequence_alignment_aa,germline_alignment_aa,v_alignment_start,v_alignment_end,d_alignment_start,d_alignment_end,j_alignment_start,j_alignment_end,v_sequence_alignment,v_sequence_alignment_aa,v_germline_alignment,v_germline_alignment_aa,d_sequence_alignment,d_sequence_alignment_aa,d_germline_alignment,d_germline_alignment_aa,j_sequence_alignment,j_sequence_alignment_aa,j_germline_alignment,j_germline_alignment_aa,fwr1,fwr1_aa,cdr1,cdr1_aa,fwr2,fwr2_aa,cdr2,cdr2_aa,fwr3,fwr3_aa,fwr4,fwr4_aa,cdr3,cdr3_aa,junction,junction_length,junction_aa,junction_aa_length,v_score,d_score,j_score,v_cigar,d_cigar,j_cigar,v_support,d_support,j_support,v_identity,d_identity,j_identity,v_sequence_start,v_sequence_end,v_germline_start,v_germline_end,d_sequence_start,d_sequence_end,d_germline_start,d_germline_end,j_sequence_start,j_sequence_end,j_germline_start,j_germline_end,fwr1_start,fwr1_end,cdr1_start,cdr1_end,fwr2_start,fwr2_end,cdr2_start,cdr2_end,fwr3_start,fwr3_end,fwr4_start,fwr4_end,cdr3_start,cdr3_end,np1,np1_length,np2,np2_length,run_application,d_frame,c_call,c_alignment_start,c_alignment_end,c_sequence_alignment,c_sequence_alignment_aa,c_germline_alignment,c_germline_alignment_aa,c_score,c_cigar,c_support,c_identity,c_sequence_start,c_sequence_end,c_germline_start,c_germline_end)],
sequences = bcr_sequence[,.(cell_id,sequence_id,sequence_nt,sequence_aa,chain)],
runInformation = labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath="CAVD",
schemaName="CDS",
queryName="alignment_run",
colSelect="run_application,run_information",
colFilter=makeFilter(c("run_application", "IN", paste(unique(bcr_sequence$run_application), collapse = ";"))),
colNameOpt="rname"
) |> setDT()
)
)
}
setDatasetNames(private$.datasets)
varInfo <- availableDatasets[, .N, .(assay_identifier, dataset_type, unzipDir)][
,.(
varInfo = ifelse(
dataset_type == "Integrated Assay",
list(
getVarInfo(assay_identifier, names(private$.datasets[[assay_identifier]]), private$.shared$.config$labkeyUrlBase)
),
list(sprintf("Non-integrated data variable info found at %s", unzipDir))
)
), assay_identifier
]
private$.variableDefinitions <- varInfo$varInfo
names(private$.variableDefinitions) <- varInfo$assay_identifier
if("BCR_Sequence" %in% assays){
private$.variableDefinitions <- append(
private$.variableDefinitions, list(
sequence = getVarInfo("sequence", names(private$.datasets$sequence), private$.shared$.config$labkeyUrlBase, "CDS"),
alignment = getVarInfo("alignment", names(private$.datasets$alignment), private$.shared$.config$labkeyUrlBase, "CDS"),
runInformation = getVarInfo("alignment_run", names(private$.datasets$runInformation), private$.shared$.config$labkeyUrlBase, "CDS")
)
)
}
},
#' @description
#' Refresh the study object to update available datasets and treatment info.
refresh = function() {
private$.fetchAvailableDatasets()
NULL
}
),
active = list(
#' @field studies A character vector of `study_id` values found in the object.
studies = function() {
private$.studyIds
},
#' @field availableDatasets A table of datasets available in
#' the \code{DataSpaceStudies} object.
availableDatasets = function() {
datasets <- rbind(
private$.availableIntegratedDatasets,
private$.availableNIDatasets
)
attr(datasets, "dsr_type") <- "availableDatasets"
return(datasets)
},
#' @field datasets A list of data.table objects containing the
#' availableDatasets that were loaded.
datasets = function() {
if(all(private$.shared$.availableStudies[study_id %in% private$.studyIds, is.na(data_availability)]))
warning("No study data is associated with this object")
else if(length(private$.datasets) == 0)
warning("No datasets loaded. Please run the `loadAvailableDatasets` method")
else private$.datasets
},
#' @field variableDefinitions A list of data.table objects containing the
#' data dictionaries of the integrated data loaded.
variableDefinitions = function() {
private$.variableDefinitions
},
#' @field treatmentArm A data.table. The table of treatment arm
#' information for the connected study. Not available for all study
#' connection.
treatmentArm = function() {
private$.treatmentArm
},
#' @field studyInfo A list. Stores the information about the study.
studyInfo = function() {
private$.shared$.availableStudies[study_id %in% private$.studyIds]
}
),
private = list(
.studyIds = character(),
.publicationIds = character(),
.mabMixIds = character(),
.mabIds = character(),
.availableIntegratedDatasets = data.table(),
.availableDocuments = data.table(),
.availableNIDatasets = data.table(),
.datasets = list(),
.variableDefinitions = list(),
.dataDir = character(),
.treatmentArm = data.table(),
.fetchAvailableDatasets = function(){
private$.fetchAvailableIntegratedDatasets()
private$.fetchAvailableDocuments()
private$.fetchTreatmentArm()
private$.fetchAvailableNIDatasets()
},
.fetchAvailableIntegratedDatasets = function() {
private$.availableIntegratedDatasets <-
Map(\(path, study_id) {
labkey.executeSql(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = path,
schemaName = "study",
sql = datasetCountQuery(),
colNameOpt = "fieldname"
) |>
suppressWarnings() |>
setDT() |>
_[,`:=`(study_id = study_id, dataset_type = "Integrated Assay")] |>
_[,.(study_id, dataset_type, assay_identifier, assay_label)]
},
private$.shared$.config$labkeyStudyUrlPaths,
names(private$.shared$.config$labkeyStudyUrlPaths)) |>
rbindlist() |>
_[order(study_id, assay_identifier)]
},
.fetchAvailableNIDatasets = function(){
private$.availableNIDatasets <-
private$.availableDocuments[
document_type == "Non-Integrated Assay",
.(study_id, dataset_type = document_type, assay_identifier, assay_label = document_label)
]
},
.fetchAvailableDocuments = function() {
colSelect <- c("document_id", "label", "filename", "document_type", "assay_identifier")
private$.availableDocuments <- merge(
labkey.selectRows(
private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "document",
colNameOpt = "fieldname",
colSelect = colSelect
) |>
setDT(),
labkey.selectRows(
private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "studydocument",
colNameOpt = "fieldname",
colSelect = c("document_id", "prot")
) |>
setDT(),
by = "document_id"
) |>
setcolorder(c("prot", colSelect)) |>
setnames(c("prot", "filename", "label"), c("study_id", "remote_path", "document_label")) |>
_[study_id %in% private$.studyIds] |>
_[, url := URLencode(
paste0(
private$.shared$.config$labkeyUrlBase,
"/cds/CAVD/getStudyDocument.view?",
"study=", study_id,
"&documentId=", document_id,
"&filename=", remote_path
)
)]
},
.fetchTreatmentArm = function() {
colSelect <- c(
"arm_id", "arm_part", "arm_group", "arm_name",
"randomization", "coded_label", "last_day", "description"
)
private$.treatmentArm <-
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "treatmentarm",
colSelect = colSelect,
colNameOpt = "fieldname",
method = "GET"
) |>
suppressWarnings() |>
setDT() |>
setkey(arm_id) |>
_[,study_id := gsub("^([a-z]{3}[0-9]+)-.+", "\\1", arm_id, )] |>
setcolorder(c("study_id", colSelect)) |>
_[study_id %in% private$.studyIds]
}
)
)
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#' @title The DataSpaceStudies class
#'
#' @description
#' An R6 class for DataSpace Study data.
#'
#' @section Constructor:
#' \code{DataSpaceConnection$getStudies()}
#'
#' @seealso \code{\link{connectDS}} \code{\link{DataSpaceConnection}}
#'
#' @examples
#' \dontrun{
#' # Create a connection (Initiate a DataSpaceConnection object)
#' con <- connectDS()
#'
#' # Get group by `study_id` or pass a filtered `availableStudies` object.
#' studies <- con$getStudies(c("vtn505", "cvd408"))
#' studies <- con$getStudies(
#' con$availableStudies[grepl("BAMA", data_availability) & species == "Human"]
#' )
#'
#' # Load BAMA to the studies object.
#' studies$loadAssayDatasets("BAMA")
#' studies$datasets$BAMA
#'
#' # Inspect variable information of the BAMA dataset
#' studies$datasetDescriptions$BAMA
#'
#' # Inspect treatment arm information for all studies in study object
#' studies$treatmentArm
#'
#' }
#'
DataSpaceStudies <- R6Class(
classname = "DataSpaceStudies",
inherit = DataSpaceConnection,
public = list(
#' @description
#' Initialize \code{DataSpaceStudy} class.
#' See \code{\link{DataSpaceConnection}}.
#' @param studyIds A character. Name of the study to retrieve.
#' as URL, path and username.
initialize = function(studyIds) {
studyIds <- studyIds[studyIds != ""]
private$.studyIds <- checkStudies(studyIds, private$.shared$.config$labkeyUrlBase)
private$.publicationIds <- private$.shared$.availablePublications[
sapply(strsplit(related_studies, ", "), \(.) any(. %in% private$.studyIds)) &
publication_data_available == TRUE,
publication_id
]
private$.mabMixIds <- private$.shared$.mabStudies[
strsplit(studies_available, ", ") |> sapply(\(sa) any(sa %in% private$.studyIds)),
mab_mix_id
] |>
unique()
private$.mabIds <- private$.shared$.mabMix[mab_mix_id %in% private$.mabMixIds, mab_id] |>
unique()
private$.shared$.config$labkeyStudyUrlPaths <- getStudyUrlPaths(private$.studyIds)
self$refresh()
NULL
},
#' @description
#' Print \code{DataSpaceStudy} class.
print = function() {
cat("<DataSpaceStudies>")
cat("\n Studies:", paste(private$.studyIds, collapse = ", "))
cat("\n Available integrated datasets:")
if (nrow(private$.availableIntegratedDatasets) > 0) {
cat(paste("\n -", unique(private$.availableIntegratedDatasets$assay_label)), sep = "")
}
cat("\n Available non-integrated datasets:")
if (nrow(private$.availableNIDatasets) > 0) {
cat(paste("\n -", unique(private$.availableNIDatasets$assay_label)), sep = "")
}
cat("\n Available publication datasets:")
if (length(private$.publicationIds) > 0) {
cat(paste("\n -", unique(private$.shared$.availablePublications[publication_id %in% private$.publicationIds, label])), sep = "")
}
cat("\n Available Studies objects:")
cat(paste0("\n - ", DataSpaceStudies$active |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Studies methods:")
cat(paste0("\n - ", DataSpaceStudies$public_methods |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Connection objects:")
cat(paste0("\n - ", DataSpaceConnection$active |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n Available Connection methods:")
cat(paste0("\n - ", DataSpaceConnection$public_methods |> names() |> cleanReservedDataSpaceR6()), sep = "")
cat("\n")
},
#' @description
#' Load datasets to the studies object from an availableDatasets object.
#' @param availableDatasets An `availableDatasets` object or vector of `study_id` values.
#' @param downloadDir Optional, a character path specifying a directory to download.
#' nonstandard datasets. The default is the working temp directory.
loadAvailableDatasets = function(availableDatasets = self$availableDatasets, downloadDir = tempdir()) {
if(is.character(availableDatasets)){
availableDatasets = self$availableDatasets[assay_identifier %in% availableDatasets]
if(nrow(availableDatasets) == 0)
stop("Charactor vector of assay identifiers passed did not return any available datasets from `availableDatasets`.")
}
if(any(availableDatasets$dataset_type == "Publication Data")){
warning("Publication data in `availalableDatasets` ignored. Use `getPublicationDatasets` to download those.")
}
availableDatasets <- availableDatasets[dataset_type %in% c("Integrated Assay", "Non-Integrated Assay")]
if(nrow(availableDatasets) == 0) stop("No integrated or non-integrated assays to get.")
if(any(availableDatasets$dataset_type == "Integrated Assay")){
assays <- availableDatasets[dataset_type == "Integrated Assay"]$assay_identifier |>
unique()
filter <- makeFilter(c("study_prot", "IN", paste(unique(availableDatasets$study_id), collapse = ";")))
assayData <- assays |>
lapply(\(assay)
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "study",
queryName = assay,
viewName = NULL,
colFilter = filter,
colNameOpt = "fieldname",
method = "GET",
) |> setDT()
)
names(assayData) <- assays
}
if(any(availableDatasets$dataset_type == "Non-Integrated Assay")){
niData <-
private$.availableDocuments[
assay_identifier %in% availableDatasets$assay_identifier & document_type == "Non-Integrated Assay",
.SD |>
downloadDocuments(downloadDir) |>
unzipDocuments() |>
loadDocuments() |>
_[,.(datasets, assay_identifier, unzipDir)]
]
nsd <- unique(niData$assay_identifier)
names(nsd) <- nsd
appendData <- lapply(
nsd,
\(nm) rbindlist(niData[assay_identifier == nm, datasets], fill = T)
)
assayData <- append(assayData, appendData)
availableDatasets[niData[,.(assay_identifier, unzipDir)], on = "assay_identifier", unzipDir := i.unzipDir]
} else {
availableDatasets[,unzipDir := NA]
}
private$.datasets <- assayData
if("BCR_Sequence" %in% assays){
message("Querying BCR sequence study data, this may take a few minutes...")
bcr_sequence <-
Map(
\(studyId)
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath="CAVD",
schemaName="CDS",
queryName="bcr_sequence_alignment_prot",
colFilter=makeFilter(c("prot", "IN", studyId)),
colNameOpt="rname"
) |> setDT(),
private$.studyIds
) |> rbindlist()
private$.datasets <- append(
private$.datasets,
list(
alignments = bcr_sequence[,.(cell_id,sequence_id,stop_codon,vj_in_frame,productive,rev_comp,complete_vdj,v_call,d_call,j_call,sequence_alignment,germline_alignment,sequence_alignment_aa,germline_alignment_aa,v_alignment_start,v_alignment_end,d_alignment_start,d_alignment_end,j_alignment_start,j_alignment_end,v_sequence_alignment,v_sequence_alignment_aa,v_germline_alignment,v_germline_alignment_aa,d_sequence_alignment,d_sequence_alignment_aa,d_germline_alignment,d_germline_alignment_aa,j_sequence_alignment,j_sequence_alignment_aa,j_germline_alignment,j_germline_alignment_aa,fwr1,fwr1_aa,cdr1,cdr1_aa,fwr2,fwr2_aa,cdr2,cdr2_aa,fwr3,fwr3_aa,fwr4,fwr4_aa,cdr3,cdr3_aa,junction,junction_length,junction_aa,junction_aa_length,v_score,d_score,j_score,v_cigar,d_cigar,j_cigar,v_support,d_support,j_support,v_identity,d_identity,j_identity,v_sequence_start,v_sequence_end,v_germline_start,v_germline_end,d_sequence_start,d_sequence_end,d_germline_start,d_germline_end,j_sequence_start,j_sequence_end,j_germline_start,j_germline_end,fwr1_start,fwr1_end,cdr1_start,cdr1_end,fwr2_start,fwr2_end,cdr2_start,cdr2_end,fwr3_start,fwr3_end,fwr4_start,fwr4_end,cdr3_start,cdr3_end,np1,np1_length,np2,np2_length,run_application,d_frame,c_call,c_alignment_start,c_alignment_end,c_sequence_alignment,c_sequence_alignment_aa,c_germline_alignment,c_germline_alignment_aa,c_score,c_cigar,c_support,c_identity,c_sequence_start,c_sequence_end,c_germline_start,c_germline_end)],
sequences = bcr_sequence[,.(cell_id,sequence_id,sequence_nt,sequence_aa,chain)],
runInformation = labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath="CAVD",
schemaName="CDS",
queryName="alignment_run",
colSelect="run_application,run_information",
colFilter=makeFilter(c("run_application", "IN", paste(unique(bcr_sequence$run_application), collapse = ";"))),
colNameOpt="rname"
) |> setDT()
)
)
}
setDatasetNames(private$.datasets)
varInfo <- availableDatasets[, .N, .(assay_identifier, dataset_type, unzipDir)][
,.(
varInfo = ifelse(
dataset_type == "Integrated Assay",
list(
getVarInfo(assay_identifier, names(private$.datasets[[assay_identifier]]), private$.shared$.config$labkeyUrlBase)
),
list(sprintf("Non-integrated data variable info found at %s", unzipDir))
)
), assay_identifier
]
private$.variableDefinitions <- varInfo$varInfo
names(private$.variableDefinitions) <- varInfo$assay_identifier
if("BCR_Sequence" %in% assays){
private$.variableDefinitions <- append(
private$.variableDefinitions, list(
sequence = getVarInfo("sequence", names(private$.datasets$sequence), private$.shared$.config$labkeyUrlBase, "CDS"),
alignment = getVarInfo("alignment", names(private$.datasets$alignment), private$.shared$.config$labkeyUrlBase, "CDS"),
runInformation = getVarInfo("alignment_run", names(private$.datasets$runInformation), private$.shared$.config$labkeyUrlBase, "CDS")
)
)
}
},
#' @description
#' Refresh the study object to update available datasets and treatment info.
refresh = function() {
private$.fetchAvailableDatasets()
NULL
}
),
active = list(
#' @field studies A character vector of `study_id` values found in the object.
studies = function() {
private$.studyIds
},
#' @field availableDatasets A table of datasets available in
#' the \code{DataSpaceStudies} object.
availableDatasets = function() {
datasets <- rbind(
private$.availableIntegratedDatasets,
private$.availableNIDatasets
)
attr(datasets, "dsr_type") <- "availableDatasets"
return(datasets)
},
#' @field datasets A list of data.table objects containing the
#' availableDatasets that were loaded.
datasets = function() {
if(all(private$.shared$.availableStudies[study_id %in% private$.studyIds, is.na(data_availability)]))
warning("No study data is associated with this object")
else if(length(private$.datasets) == 0)
warning("No datasets loaded. Please run the `loadAvailableDatasets` method")
else private$.datasets
},
#' @field variableDefinitions A list of data.table objects containing the
#' data dictionaries of the integrated data loaded.
variableDefinitions = function() {
private$.variableDefinitions
},
#' @field treatmentArm A data.table. The table of treatment arm
#' information for the connected study. Not available for all study
#' connection.
treatmentArm = function() {
private$.treatmentArm
},
#' @field studyInfo A list. Stores the information about the study.
studyInfo = function() {
private$.shared$.availableStudies[study_id %in% private$.studyIds]
}
),
private = list(
.studyIds = character(),
.publicationIds = character(),
.mabMixIds = character(),
.mabIds = character(),
.availableIntegratedDatasets = data.table(),
.availableDocuments = data.table(),
.availableNIDatasets = data.table(),
.datasets = list(),
.variableDefinitions = list(),
.dataDir = character(),
.treatmentArm = data.table(),
.fetchAvailableDatasets = function(){
private$.fetchAvailableIntegratedDatasets()
private$.fetchAvailableDocuments()
private$.fetchTreatmentArm()
private$.fetchAvailableNIDatasets()
},
.fetchAvailableIntegratedDatasets = function() {
private$.availableIntegratedDatasets <-
Map(\(path, study_id) {
labkey.executeSql(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = path,
schemaName = "study",
sql = datasetCountQuery(),
colNameOpt = "fieldname"
) |>
suppressWarnings() |>
setDT() |>
_[,`:=`(study_id = study_id, dataset_type = "Integrated Assay")] |>
_[,.(study_id, dataset_type, assay_identifier, assay_label)]
},
private$.shared$.config$labkeyStudyUrlPaths,
names(private$.shared$.config$labkeyStudyUrlPaths)) |>
rbindlist() |>
_[order(study_id, assay_identifier)]
},
.fetchAvailableNIDatasets = function(){
private$.availableNIDatasets <-
private$.availableDocuments[
document_type == "Non-Integrated Assay",
.(study_id, dataset_type = document_type, assay_identifier, assay_label = document_label)
]
},
.fetchAvailableDocuments = function() {
colSelect <- c("document_id", "label", "filename", "document_type", "assay_identifier")
private$.availableDocuments <- merge(
labkey.selectRows(
private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "document",
colNameOpt = "fieldname",
colSelect = colSelect
) |>
setDT(),
labkey.selectRows(
private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "studydocument",
colNameOpt = "fieldname",
colSelect = c("document_id", "prot")
) |>
setDT(),
by = "document_id"
) |>
setcolorder(c("prot", colSelect)) |>
setnames(c("prot", "filename", "label"), c("study_id", "remote_path", "document_label")) |>
_[study_id %in% private$.studyIds] |>
_[, url := URLencode(
paste0(
private$.shared$.config$labkeyUrlBase,
"/cds/CAVD/getStudyDocument.view?",
"study=", study_id,
"&documentId=", document_id,
"&filename=", remote_path
)
)]
},
.fetchTreatmentArm = function() {
colSelect <- c(
"arm_id", "arm_part", "arm_group", "arm_name",
"randomization", "coded_label", "last_day", "description"
)
private$.treatmentArm <-
labkey.selectRows(
baseUrl = private$.shared$.config$labkeyUrlBase,
folderPath = "CAVD",
schemaName = "CDS",
queryName = "treatmentarm",
colSelect = colSelect,
colNameOpt = "fieldname",
method = "GET"
) |>
suppressWarnings() |>
setDT() |>
setkey(arm_id) |>
_[,study_id := gsub("^([a-z]{3}[0-9]+)-.+", "\\1", arm_id, )] |>
setcolorder(c("study_id", colSelect)) |>
_[study_id %in% private$.studyIds]
}
)
)
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