Deprecate Molfiles

[tsufz]

In addition: Warning message:
In createMolfile(as.numeric(c[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]])) :
NAs introduced by coercion

Is this related to #175 ? Issue #175 should be documented better. Where to set the levels?

Molfile generation is a deprecated feature in my opinion and thus should be optional step. Could be implemented with a switch in mbworkflow. Default is no molfile generation.

[tsufz]

Okay, was my own stupidity as I forgot to set the babel dir.... aargh... However, molfiles should be deprecated or optional. The deletion of molfiles is an additional step I would like to avoid.

It would be also appreciated if:

1. An existing recdata folder can be overwritten by yes / no.
2. An existing recdata folder can be owerwritten by an override via a switch.

The background is that is is annoying (and time consuming) to copy the folder always to another place while processing records with fine granulated CE options or different experimental settings.

But maybe, the implementation of issue #178 would be another way out of the latter without touching the mbWorkflow too much.
However, I would pe

[schymane]

If we deprecate mol files, will we result in inconsistencies between what massbank.jp and massbank.eu need? MassBank.jp will still require mol file uploads, so if we no longer generate them, this will be worse than just generating them but not using them? One could set a switch, for instance.

[tsufz]

No need to deprecate molfile generation at this point, just a reminder to keep it in mind.

[schymane]

We should revisit this deprecation, it's a quite time-consuming part of the workflow now for extensive lists where no-one actually has a use for the molfiles anymore ... massbank.jp is no longer accepting records and with the move to MassBank-data we no longer need them ...
Is the simplest option just to do a switch on/off in the settings and set default to NOT generating molfiles?

[tsufz]

I feel okay for switching it off/on in the settings. We should focus on important issues.

[meowcat]

yes, we can do that...

[tsufz]

Decision to finally remove molfile generation during RMassBank TC on 19 August 2020

[sneumann]

Hi, while debugging #250 I am getting locally the following error:

mbWorkflow: Step 6. Generate molfiles
Error: processing vignette 'RMassBankXCMS.Rnw' failed with diagnostics:
 chunk 10 
Error in createMolfile(as.numeric(c[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]])) : 
  Pubchem and Cactus both seem to be down.
--- failed re-building 'RMassBankXCMS.Rnw'

so first thing after the next BioC build should be to drop molfile creation.
Yours, Steffen

[tsufz]

@meowcat Did we deprecate the molfile creation already? Would also affect the babel issue #301.