R/labkey.transform.R

In Rlabkey: Data Exchange Between R and 'LabKey' Server

##
#  Copyright (c) 2018 LabKey Corporation
# 
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
##

labkey.transform.readRunPropertiesFile <- function(runInfoPath)
{
    # read in the run properties from the TSV
    lines = readLines(runInfoPath);

    # make a pass through the vector to normalize
    rows <- c()
    rowCount = 1
    i = 1
    while (i <= length(lines))
    {
        # split the line into the various parts (tab separated)
        parts <- strsplit(lines[i], split="\t")[[1]];

        if (length(parts) == 0)
        {
            # multiline value parsing (only)
            prev <- rowCount-1
            if (i > 1 && length(rows[prev]) < 3)
            {
                res <- concatenateMultiLine(lines, i-1, i)
                rows[prev] <- res$value

                # increment the line index
                i = i + res$skipped
            }
        }
        else
        {
            rows[rowCount] <- lines[i]
            i = i + 1
        }
        rowCount = length(rows) + 1
    }

    # set up a data frame to store the run properties
    properties = data.frame(NA, NA, NA, NA);
    colnames(properties) = c("name", "val1", "val2", "val3");

    # each line has a run property with the name, val1, val2, etc.
    for (i in 1:length(rows))
    {
        # split the line into the various parts (tab separated)
        parts = strsplit(rows[i], split="\t")[[1]];

        # if the line does not have 4 parts, add NA's as needed
        if (length(parts) < 4)
        {
            for (j in 1:4)
            {
                if (is.na(parts[j]))
                {
                    parts[j] = NA;
                }
            }
        }
        # add the parts for the given run property to the properties data frame
        properties[i,] = parts;
    }

  return (properties)
}

# Helper function to concatenate values with newlines in the middle
concatenateMultiLine <- function(lines, idx, start)
{
    # create a data structure to return results
    ret <- list(0, lines[idx])
    names(ret) <- c("skipped", "value")

    count = 0
    for (i in start:length(lines))
    {
        parts <- strsplit(lines[i], split="\t")[[1]];

        if (length(parts) == 0)
        {
            #
            lines[idx] <- paste(lines[idx], "\n")
        }
        else
        {
            ret$skipped <- count+1
            ret$value <- paste(lines[idx], lines[i])
            break
        }
        count = count + 1
    }
    return (ret)
}

labkey.transform.getRunPropertyValue <- function(runProps, propName)
{
    value = NA;
    if (any(runProps$name == propName))
    {
        value = runProps$val1[runProps$name == propName];

        # return NA for an empty string
        if (nchar(value) == 0)
        {
            value = NA;
        }
    }
    return (value)
}