Metadata issue in docker

[elnurgar]

Hi Adriano,

I have an issue with metadata. It worked well with positive mode data but doesn't work with negative. I thought that it is because of metadata file, so I used the same template as POS, just replaced in data name POS by NEG (the rest is the same), and still has this error.

I checked twice, between filename and ATTRIBUTE_species is well a tabulation.

It would be greatful maybe to do a small check before beginning the treatment to be sure if all data is ok or not.

Thank you very much,
Merry Christmas and Happy New Year!
Kind regards,
Elnur

[Adafede]

Hi @elnurgar,

The issue does not seem to relate to the polarity but really to the metadata file itself probably not corresponding to what is in your file(s)?
Could you send the files for a deeper check maybe?
Else I can't help much.

Regarding the "sanity check" at first, what would you have in mind?

Best wishes too,
Adriano

[elnurgar]

@Adafede thank you for your quick reply. I sent you by email.

Kind regards,
Elnur

[Adafede]

Hi @elnurgar,

I looked at the files and see no obvious reason why this should fail.
Could you eventually try once again? It should fail almost instantaneously normally.
Maybe then with a new clean install?

Else, could you send me the docker command you were using?

On a side note, I implemented some basic checks following your suggestion, see:

• https://taxonomicallyinformedannotation.github.io/tima/#validate-your-data
• https://taxonomicallyinformedannotation.github.io/tima/vignettes/tima.html#tldr
• https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/0-validating.html
• https://taxonomicallyinformedannotation.github.io/tima/man/validate_inputs.html

Hope this helps

[elnurgar]

Hi @Adafede ,

Thank you for your help. I will try to run on clean version. Here is the command that I run on docker:

docker run --user tima-user -v ".:/home/tima-user/.tima/data" -p 3840:3838 adafede/tima-r Rscript -e "tima::run_app()"