Nextflow: splitCsv does not handle quoted values containing commas correctly

[wflynny]

Bug report

It appears that .splitCsv does not handle quoted tokens containing commas correctly.

Expected behavior and actual behavior

Given a token wrapped in quotes "1,234", I would expect .splitCsv to parse this as a single value [.., '1,234', ...]. However, it breaks this token into two, leaving a singular quote with each half [..., "1, 234", ...].

Steps to reproduce the problem

Using the following test case above as test.csv

value_1,value_2,value_3
100,10.1%,300
"9,600",98.9%,"24,155"

and parsing as

Channel
    .fromPath("test.csv")
    .splitCsv(header: true, quote: '\"')
    .subscribe { println "$it" }

I've tried a variety of values of quote above to no avail (I'm new to Groovy so advice on how to best specify this option would be helpful).

Program output

Expected output

[value_1: 100, value_2: 10.1%, value_3: 300]
[value_1: '9,600', value_2: 98.9%, value_3: '24,155']

Actual output

[value_1: 100, value_2: 10.1%, value_3: 300]
[value_1: "9, value_2: 600", value_3: 98.9%]

Environment

• Nextflow version: 19.01.0.5050
• Java version: 1.8.0_73
• Operating system: CentOS 6.7

Additional context

I think the issue is related to how StringUtils.splitPreserveAllTokens is used in csvSplitter.groovy. The line is tokenized by , first then quotes are removed, but the tokenization by .splitPreserveAllTokens doesn't respect quotes:

import org.apache.commons.lang.StringUtils
line = '"9,600",86.3%,"23,000"'
println StringUtils.splitPreserveAllTokens(line, ",")

yields 5 tokens:

["9, 600", 86.3%, "23, 000"]

Perhaps regex is needed to extract the proper tokens (example), then quotes can be removed from them:

line = '"9,600",86.3%,"23,000"'
println line.split(",(?=(?:[^\"]*\"[^\"]*\")*[^\"]*\$)", -1)

yields the desired 3 tokens

["9,600", 86.3%, "23,000"]

[edgano]

I'm not sure why you want this behaviour...CSV stands for "Comma-separated values"
Maybe could be nice to be able to indicate the splitter character on the .splitCsv
But I'm not sure it makes sense to not split when a comma is found (if any other splitter char is defined)

[wflynny]

@edgano Well, for one, the tools I'm using generate CSV files with quoted values. Further, it seems to be a widely accepted interpretation of the CSV specification.

[edgano]

Yep, the quotes are not the "problem"...
The problem I see, is to avoid splitting a value with comma. But I assume it will be possible to take the element inside the quotes as a literal

[wflynny]

Quotation handling should take precedent over splitting on the separator, be it a comma or another sep value passed to .splitCsv, but also possibly over newline handling as well. Typical CSV parse implementations handle the latter differently, but nonetheless this is a more general problem with .splitCSV than just handling commas.

Anyway, comma handling might be solved just with the regex above, then stripping quotes if they exist from the tokens.

[pditommaso]

Yes, you are right. This is a bug.

[wflynny]

@pditommaso Thank you for the quick response and fix. I can confirm this is working for my pipelines using

NXF_VER=19.04.0-SNAPSHOT nextflow run ...