Create a Scout major release

[northwestwitch]

Things to include in this release:

• [ ] Change how loqusDB params are provided in config file. The current situation is the following: Scout accepts the following loqus connection params:

• A dictionary

• A list of dictionaries, whenever more than one Loqus instance should be used

• What I think it should become in the future: a dictionary with loqus instance IDs as keys and instance settings dictionaries as values.

• [ ] Modify CLI and Flask app to accept ONE config file only. Simplify and describe the associated procedure of loading this config file.

• [ ] Indexes fix when doing the major (entails downtime)

• [ ] A refactor pass on the variant(s) views and controllers, grouping more shared functionality from all different variant types minimising repetition, reinforce separation of request handling (into views) and actual logic (into controllers) and db access (into adapter).

• [ ] Refactor in the CLI: scout load report instead of scout load report1, scout load report2 etc

• [ ] remove deprecated code (CG) API scout_load method

• [ ] refactor all the load/update commands to accept a download folder (that is created by e.g. download everything)

??? Please add more!

[dnil]

We could do the gene-panels-to-include-regions as well, but that will require more coordination with MIP.

[dnil]

Also perhaps index fixes would go well with this. While not major on their own, the downtime required when updating would be more acceptable with a major. The rank -> rank score is probably not slow, but e.g. adding SVs to the gene-variant search would be.

[dnil]

DarkMode? 😸

[northwestwitch]

DarkMode?

I think DarkMode can be fixed relatively easily as a mnor!

[dnil]

Refactoring of the variant and variants view/controllers is another of those that I glance at sometimes but where it would be great to have extensive verification afterwards.

[moonso]

New release = NEW DETECTIVE!!!

[dnil]

It must already be clear? 😉

[dnil]

Ask @hassanfa or @Mropat, but https://store.steampowered.com/app/632470/Disco_Elysium/ sure made an impression.

[mikaell]

I would like to remove multiple config names for the same internal name. Only allow the name bam_file (or whatever is used the most) and remove the rest.

In case.py it is handled like below.

  bam_path_options = ["alignment_path", "bam_path", "bam_file"]
    for option in bam_path_options:
        if sample.get(option) and not sample.get(option).strip() == "":
            if "bam_file" in ind_info:
                LOG.warning(
                    "Multiple alignment paths given for individual %s in load config. Using %s",
                    ind_info["individual_id"],
                    ind_info["bam_file"],
                )
            else:
                ind_info["bam_file"] = sample[option]```