Draft: error handling in autoreporting tool

[Lipastomies]

This PR is a draft for how handling could be.

The basic idea is that users do not want to see stack traces, so they aren't printed when the script errors out. Instead, human-readable explanation is printed to stdout where it is possible (aka where the correct variables are available), and the stack trace is printed to a file (and/or stderr?). A return code of 1 will be sent in case of any error, and 0 in case of no errors.

I'd be happy to hear if this sounds sensible, and if there are other possible ways that might be more suitable.

also aims to fix #68

[Fedja]

you can explicitly check that and give the exact column not in the data.

[Fedja]

might be good to start using actual logger package (https://docs.python.org/3/library/logging.html) ... it would be easier to control what level of logging goes where. Also keeping in mind usage of this in pipelining... now we would miss the stacktrace when running via WDL or if we add that to WDL output, we error out as the file might not exist. logging package would allow different configuration options depending on running mode.

[Fedja]

make that annotation file required in argparse if it's expected.....

autoreporting/Scripts/main.py flagship/meta/finngen_R4_T2D_meta.gz --ld-api online --gnomad-genome-path "../autoreport_resources/gnomad.genomes.r2.1.sites.liftover.b38.finngen.r2pos.af.ac.an.tsv.gz" --gnomad-exome-path "../autoreport_resources/gnomad.exomes.r2.1.sites.liftover.b38.finngen.r2pos.af.ac.an.tsv.gz" --functional-path "../autoreport_resources/fin_enriched_genomes_select_columns.txt.gz" --column-labels "#CHR" "POS" "REF" "ALT" "ESTONIA_pval" "ESTONIA_beta" "FINNGEN_maf_controls" --sign-treshold 5.0e-8 --ld-r2 0.4 --alt-sign-treshold 1e-4  --ignore-region '6:23000000-38000000' --efo-codes EFO_0001360
input file: flagship/meta/finngen_R4_T2D_meta.gz
filter & group SNPs
Annotate SNPs
Traceback (most recent call last):
  File "autoreporting/Scripts/main.py", line 125, in <module>
    main(args)
  File "autoreporting/Scripts/main.py", line 53, in main
    functional_path=args.functional_path, prefix=args.prefix, columns=columns)
  File "/mnt/disks/r4/mitja/autoreporting/Scripts/annotate.py", line 81, in annotate
    raise FileNotFoundError("Tabix index for file {} not found. Make sure that the file is properly indexed.".format(finngen_path))
FileNotFoundError: Tabix index for file  not found. Make sure that the file is properly indexed.

[Lipastomies]

Here's a try at using the logging crate in the repository. @Fedja do you think something like this could work? The basic idea is that everything is reported in pretty much the same way as before, except that it's done through a logger. In the beginning of the script, the logging level is set, which means that e.g. when using the widdle, we can log everything, and when run normally, the logging can be less distracting.

There's quite a lot of merge conflicts but those are fairly straightforward to clear, mainly due to code changing in similar places.