`validate_file_names` returns "Invalid data.files entered"

[earnaud]

Hi,

when I am using EMLassemblyline::template_taxonomic_coverage(), an error occurs on validate_file_names:

Templating taxonomic coverage ...
Error in EDIutils::validate_file_names(path = fun.args$data.path, data.files = fun.args$taxa.table) : 
  Invalid data.files entered: /home/pndb-elie/dataPackagesOutput/emlAssemblyLine/test_emldp/decomp.csv

I use a path in the path argument and let data.files take its default value (aka path). By manual tests, I see that this error occurs at the condition:

sum(use_i) == length(data.files)

But sum_i has length equals to the vector of files in path directory. So it could not have length equals to data.files. I think the condition could be re-written:

length(which(sum(use_i))) == length(data.files)

[clnsmth]

Hi @earnaud. I'm unable to reproduce this error. Would you mind forwarding the function call?

A potential issue is that taxa.table doesn't accept the full file name (i.e. /this/is/my/path/decomp.csv), it should be only the file name (e.g. decomp.csv).

We could perhaps change this if there's a strong argument for it.

[earnaud]

Hi @clnsmth,

Here is a caption of my screen after having tested template_taxonomic_coverage() with my inputs from MetaShARK:

Browse[1]> rv$taxa.table
[1] "/home/pndb-elie/dataPackagesOutput/emlAssemblyLine/test_emldp/Nitrogen_fixation.csv"
Browse[1]> rv$taxa.table <- basename(rv$taxa.table)
Browse[1]> template_taxonomic_coverage(
+         paste(
+           savevar$emlal$selectDP$dp_path,
+           savevar$emlal$selectDP$dp_name,
+           "data_objects",
+           sep = "/"
+         ),
+         taxa.table = rv$taxa.table,
+         taxa.col = rv$taxa.col,
+         taxa.name.type = rv$taxa.name.type,
+         taxa.authority = rv$taxa.authority
+       )
Templating taxonomic coverage ...
Error in validate_arguments(fun.name = "template_taxonomic_coverage",  : 
  Input argument "taxa.name.type" must be "scientific", "common", or "both".
Browse[1]> template_taxonomic_coverage(
+         paste(
+           savevar$emlal$selectDP$dp_path,
+           savevar$emlal$selectDP$dp_name,
+           "data_objects",
+           sep = "/"
+         ),
+         paste(
+           savevar$emlal$selectDP$dp_path,
+           savevar$emlal$selectDP$dp_name,
+           "data_objects",
+           sep = "/"
+         ),
+         taxa.table = rv$taxa.table,
+         taxa.col = rv$taxa.col,
+         taxa.name.type = rv$taxa.name.type,
+         taxa.authority = rv$taxa.authority
+       )
Templating taxonomic coverage ...
Error in validate_arguments(fun.name = "template_taxonomic_coverage",  : 
  Input argument "taxa.name.type" must be "scientific", "common", or "both".

Here are my inputs:

$taxa.authority
[1] "Catalogue of Life (COL)"

$taxa.table
[1] "Nitrogen_fixation.csv"

$taxa.col
[1] "YEAR"

$complete
[1] TRUE

$taxa.name.type
[1] "scientific name" "common name"    

[clnsmth]

Try taxa.name.type = "both"

[earnaud]

Hi again ! I found what was messing up concerning this issue, and it was my bad: I confused "data.path" argument in {EMLassemblyline}'s function and "data.files" argument in {EDIutils}'s function.

[earnaud]

Well .. sorry: it actually does not work.

Warning: Error in EDIutils::validate_file_names: Invalid data.files entered: /home/pndb-elie/dataPackagesOutput/emlAssemblyLine/Test_emldp/Test/data_objects/decomp.csv
  [No stack trace available]

> file.exists("/home/pndb-elie/dataPackagesOutput/emlAssemblyLine/Test_emldp/Test/data_objects/decomp.csv")
[1] TRUE

[clnsmth]

Hmmm ... this error message suggests an outdated version of validate_file_names(). Does a fresh install of EDIutils fix this?

[clnsmth]

This function is deprecated in the new release on the main branch. The previous version of EDIutils is on the deprecated branch and will be permanently deleted on 2022-06-01.