New command: sort

[matentzn]

See mapping-commons/sssom#39

We need a command that uses the canonical column order to sort an entire mapping set data frame correctly.

[cmungall]

I think this lower priority now we can just do sssom dosql SELECT * FROM match ORDER BY ...

[hrshdhgd]

Implement ^^^ as a test. (test/test.sh)

[matentzn]

We need to be able to sort the columns by their canonical order, with a method like
https://github.com/mapping-commons/sssom-py/pull/158/files#diff-8e0eb781f6bf2cf74b9c6a904555d8bd7f214fef45ea8e55da8527f834e600e4L191

I am happy if the sort function could simply build on the the dosql command, in combination with a canonical column ordering.

[hrshdhgd]

It seems like Mapping(**mdict) already sorts the column names in the order it appears in sssom.yaml as slots thus keeping it a standard sequence. So a sort method is not needed(?).

So everytime we read a file using read_sssom_table() , the columns are sorted automatically. I confirmed this using a test case.

cc: @matentzn , @cmungall

[matentzn]

Sort needs to sort also the rows!

This here seems wrong:
https://github.com/monarch-initiative/mondo/blob/master/src/ontology/mappings/mondo_broadmatch_icd10cm.sssom.tsv

You can see it has a subject_label right at the end, while I would expect it to be after subject_id!

[hrshdhgd]

Aah .. I see why that's happening. Easy fix!

[hrshdhgd]

Now for rows, what would be the sort-by rule?

EDIT: Spoke to Chris and he said just a simple ascending ordered sort of the first column rows should suffice for now.

[hrshdhgd]

Columns have been sorted!

[hrshdhgd]

Columns & rows have been sorted