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Merge pull request #1102 from mcneilco/1096-read-optional-experiment-…
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…status-from-sel-file-header-block

1096 read optional experiment status from sel file header block
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@philippcheung
philippcheung authored May 12, 2023
2 parents 1af1bd4 + cbbb73e commit b871998
Showing 1 changed file with 76 additions and 12 deletions.
88 changes: 76 additions & 12 deletions modules/GenericDataParser/src/server/generic_data_parser.R
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Original file line number Diff line number Diff line change
Expand Up @@ -108,9 +108,9 @@ validateMetaData <- function(metaData, configList, username, formatSettings = li
} else {
expectedDataFormat <- data.frame(
headers = c("Format",paste0(racas::applicationSettings$client.protocol.label," Name"),"Assay Tree Rule",paste0(racas::applicationSettings$client.experiment.label, " Name"),paste0(racas::applicationSettings$client.experiment.label," Details"),"Scientist","Notebook","In Life Notebook",
"Short Description", paste0(racas::applicationSettings$client.experiment.label," Keywords"), "Page","Assay Date"),
class = c("Text", "Text", "Text", "Text", "Text","Text","Text", "Text", "Text", "Text", "Text", "Date"),
isNullable = c(FALSE, FALSE, TRUE,FALSE, TRUE,FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE)
"Short Description", paste0(racas::applicationSettings$client.experiment.label," Keywords"), "Page","Assay Date","Experiment Status"),
class = c("Text", "Text", "Text", "Text", "Text","Text","Text", "Text", "Text", "Text", "Text", "Date", "Text"),
isNullable = c(FALSE, FALSE, TRUE,FALSE, TRUE,FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)
)
projectRequired <- !is.null(configList$client.include.project) && configList$client.include.project
shouldSaveProject <- !is.null(configList$client.save.project) && configList$client.save.project
Expand Down Expand Up @@ -203,6 +203,14 @@ validateMetaData <- function(metaData, configList, username, formatSettings = li
validatedMetaData$Scientist <- validateScientist(validatedMetaData$Scientist, configList, testMode)
}


if ("Experiment Status" %in% names(validatedMetaData)) {
if (!is.null(validatedMetaData$"Experiment Status")) {
validatedMetaData$"Experiment Status" = validateExperimentStatus(validatedMetaData$"Experiment Status", configList, testMode)
}
}


projectRequired <- !is.null(configList$client.include.project) && configList$client.include.project
shouldSaveProject <- !is.null(configList$client.save.project) && configList$client.save.project
projectRowSupplied <- !is.null(metaData$Project)
Expand All @@ -213,7 +221,6 @@ validateMetaData <- function(metaData, configList, username, formatSettings = li
if (shouldSaveProject & projectRowSupplied & !projectRowSuppliedButEmpty) {
validatedMetaData$Project <- validateProject(validatedMetaData$Project, configList, username, validatedMetaData[,paste0(racas::applicationSettings$client.protocol.label," Name")], errorEnv)
}

if(!is.null(validatedMetaData[paste0(racas::applicationSettings$client.experiment.label," Name")]) && grepl("CREATETHISEXPERIMENT$", validatedMetaData[paste0(racas::applicationSettings$client.experiment.label," Name")])) {
validatedMetaData[paste0(racas::applicationSettings$client.experiment.label," Name")] <- trim(gsub("CREATETHISEXPERIMENT$", "", validatedMetaData[paste0(racas::applicationSettings$client.experiment.label," Name")]))
duplicateExperimentNamesAllowed <- TRUE
Expand Down Expand Up @@ -2111,7 +2118,7 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric
# creates an experiment using the metaData
#
# Args:
# metaData: A data.frame including "Experiment Name", "Scientist", "Notebook", "Page", and "Assay Date"
# metaData: A data.frame including "Experiment Name", "Experiment Status", "Scientist", "Notebook", "Page", and "Assay Date"
# protocol: A list that is a protocol
# lsTransaction: A list that is a lsTransaction tag
# pathToGenericDataFormatExcelFile: Currently unused; the file path to the uploaded Excel file
Expand Down Expand Up @@ -2163,10 +2170,13 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric
codeType = "assay",
codeKind = "scientist",
lsTransaction= lsTransaction)
experimentStatus <- racas::applicationSettings$server.sel.experimentStatus
experimentStatus <- metaData$"Experiment Status"
if (is.null(experimentStatus) || experimentStatus == "") {
experimentStatus <- "approved"
experimentStatus <- racas::applicationSettings$server.sel.experimentStatus
}
if (is.null(experimentStatus) || experimentStatus == "") {
experimentStatus <- "approved"
}
experimentValues[[length(experimentValues)+1]] <- createStateValue(
recordedBy = recordedBy,
lsType = "codeValue",
Expand Down Expand Up @@ -2372,6 +2382,60 @@ validateProject <- function(projectName, configList, username, protocolName = NU
return("")
}
}

validateExperimentStatus <- function(experimentStatusToValidate, configList, testMode = FALSE) {
# validates that the supplied experiment status is in the code values

# Args:
# experimentStatusToValidate: A string belonging to the experiment(type) status(kind) codetable
# configList: Also known as racas::applicationSettings
# testMode: If true, the function bypasses Roo services and gives a database-independent answer
#
# Returns:
# The experiment status code value, and the empty string if they are not
require('utils')
require('RCurl')
require('rjson')

response <- NULL

if (!testMode) {
response <- tryCatch({
url <- paste0(racas::applicationSettings$server.nodeapi.path, "/api/codetables/experiment/status")
getURL(URLencode(url))
}, error = function(e) {
addError( paste("There was an error in validating the experiment status", experimentStatusToValidate))
return("")
})
} else { # In test mode, provide the three possible answers
if (experimentStatusToValidate == "unknownStatus") {
response <- ""
} else if (experimentStatusToValidate == "") {
response <- "Cannot GET /api/codetables/experiment/status"
} else {
response <- toJSON(list(experimentStatus = experimentStatusToValidate))
}
}

experimentStatus <- tryCatch({
response <- jsonlite::fromJSON(response)
matchingStatus <- response[tolower(response$code) == tolower(experimentStatusToValidate), ]
print("matching status")
print(matchingStatus)
if (nrow(response) == 0 || nrow(matchingStatus) == 0) {
addError( paste0("The experiment status you supplied, '", experimentStatusToValidate, "', is not a valid experiment status. Please select a valid experiment status"))
return("")
} else {
return(matchingStatus[1,]$code)
}
}, error = function(e) {
addError( paste("There was an error in validating the experiment status name:", experimentStatusToValidate))
return("")
})

return(experimentStatus)
}

validateScientist <- function(scientistName, configList, testMode = FALSE) {
# validates that the supplied scientist's name is on file with Roo services
#
Expand Down Expand Up @@ -3446,7 +3510,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL,
validatedMetaData <- validatedMetaDataList$validatedMetaData
duplicateExperimentNamesAllowed <- validatedMetaDataList$duplicateExperimentNamesAllowed
useExisting <- validatedMetaDataList$useExisting

inputFormat <- as.character(validatedMetaData$Format)

rawOnlyFormat <- inputFormat %in% names(customFormatSettings)
Expand Down Expand Up @@ -3710,6 +3774,9 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL,
summaryInfo$info$"Format" <- as.character(validatedMetaData$Format)
summaryInfo$info[configList$client.protocol.label] <- as.character(validatedMetaData[,paste0(racas::applicationSettings$client.protocol.label," Name")])
summaryInfo$info[configList$client.experiment.label] <- as.character(validatedMetaData[,paste0(racas::applicationSettings$client.experiment.label," Name")])
if (!is.null(validatedMetaData$"Experiment Status")) {
summaryInfo$info$"Experiment Status" <- as.character(validatedMetaData$"Experiment Status")
}
summaryInfo$info$"Scientist" <- validatedMetaData$Scientist
summaryInfo$info$"Notebook" <- validatedMetaData$Notebook
if(!is.null(validatedMetaData$Page)) {
Expand Down Expand Up @@ -3862,7 +3929,7 @@ parseGenericData <- function(request) {
# This is used for development: outputs the JSON rather than sending it to the
# server and does not wrap everything in tryCatch so debug will keep printing
developmentMode <- messenger()$devMode

# Collect the information from the request
request <- as.list(request)
pathToGenericDataFormatExcelFile <- request$fileToParse
Expand Down Expand Up @@ -4663,6 +4730,3 @@ createColumnOrderStates <- function(exptDataColumns=selColumnOrderInfo, errorEnv
}
return(experimentStates)
}



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