[Feature Request] Export to Json

[HLWeil]

Is your feature request related to a problem? Please describe. For interoperation with the ISA-Tools, the ArcCommander should be able to export the ARC ISAXLSX Files to ISAJson.

Describe the solution you'd like arc export maybe? arc investigation export

Additional context

I think two major questions arise:

• Is there one command for each type of export (e.g. isa-json, ms database exports...) or might this be handled by a flag?
• What are the output objects? The whole investigation might be exported to a single investigation.json, including all info from the investigation, study and assay xlsx files. Alternatively single assays or processes or even persons might be exported. In this case, there could be an import and export subcommand for each object included in the ArcCommander command tree. E.g. arc study person import and arc study person export This might allow for easy re-use of repetitive information.

@omaus @Brilator What do you think?

[HLWeil]

As a standard output a process sequence can be exported by using the -ps (--processsequence) flag (ddbff92397e72eedf33b8d9f4b89493a7bb7a110)

This might be used as a toplevel output including all assay and run informations but also as a backtrace format for single final data files.

[HLWeil]

Alternatively to using the -p (--path) argument, an output file could be conveniently created by using the > operator. Problem with this is, that both the exported json and the general log info are written to stdout. Question is if this should be separated, so tools can access the json separately. A workaround at the moment is to use the -v (--verbosity) argument: e.g.

arc -v 0 export

@JonasLukasczyk

[HLWeil]

Close this for now as functionality was added in #66. Will reopen if improvements are required.