retrieving just one result /attribute

[nsheff]

In my hands, when I use retrieve with a database backend, giving it a result_identifier has no effect.

It always gives me back the entire sample, not just the particular attribute I am requesting.

[donaldcampbelljr]

I am unable to replicate this issue on my machine using the pipestat_table branch. I tried sample and project level reporting and retrieving for a database backend.

output:

Results when using result_identifier = "project_integer"

100

Results when not using result_identifier

{'project_string': 'misc string to report', 'project_integer': 100, 'project_name': 'random_project_id_2', 'id': 2}

Commands:

    results8 = psm2.retrieve(project_name="random_project_id_2", result_identifier="project_integer",
                             pipeline_type='project')
    print(results8)

    results9 = psm2.retrieve(project_name="random_project_id_2",
                             pipeline_type='project')
    print(results9)

[nsheff]

I'm using that branch, for a sample pipeline,and psm.retrieve("mysample", "result_id") returns the entire thing; the same as psm.retrieve("mysample").

So I'm doing: psm.retrieve("mysample")["result_id"] and that works,but I should be able to do psm.retrieve("mysample", "result_id").

I guess I will either create a MWE or just fix it

[nsheff]

I'm using database backend

[nsheff]

fascinating... psm.retrieve("mysample", result_identifier="result_id") works.... so it only works if I name that second arg. but it should be working without it being named....

[nsheff]

Here's a MWE:

bbc = BedBaseConf("bedbase.org/config/bedbase2.yaml")

bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984")  # gives the entire sample

bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", "bedfile")  # doesn't work, gives the entire sample

bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", result_identifier="bedfile")  # works

[nsheff]

Ok I figured it. it was very confusing, but the retrieve function on the main PipestatManager class has a different signature from the one on the backend. I didn't realize that, and I was expecting it to work like that.

We will need to change that signature. I suggest:

• we PipestatManager.retrieve expect record_identifer instead of sample_name and project_name, so it can match the backend signature.
• we eliminate the _get_record_identifier concept
• we could handle doing both types using a separate function, if necessary (like, retrieve_project to access project-level attributes, instead of overloading retrieve)

[donaldcampbelljr]

The input arguments order doesn't match across the pipestat.py retrieve function and the dbbackend version. I assume that's what's causing issues?

[donaldcampbelljr]

I'll check the other functions signatures on Monday to ensure consistency.

[nsheff]

The input arguments order doesn't match across the pipestat.py retrieve function and the dbbackend version. I assume that's what's causing issues?

sort of -- it's not so much the order, it's that the signature is not the same (the arguments differ).

this will require some rethinking about how to manage project vs sample records, though.

[donaldcampbelljr]

I did another pass on the signatures along with some other polishing. This should now be working as expected.