Passing a stimulus ontology filepath to run_pipeline queries LIMS in order to get up-to-date stimulus ontology info, then writes it to that path. This test reads in an input json, which might (in practice: does) contain an ontology path, then argues that to run_pipeline. This:
overrides the existing file at that path, if the test runner is so permitted
fails, if not
Instead, we should make two changes:
(must do) This test should make sure that any paths it writes to are within its tmpdir
(should do) We should deprecate the existing stimulus_ontology_file parameter of run_sweep_extraction and replace it with an interface whose default behavior is more sensible.
wbwakeman
commented
4 years ago
Passing a stimulus ontology filepath to
run_pipelinequeries LIMS in order to get up-to-date stimulus ontology info, then writes it to that path. This test reads in an input json, which might (in practice: does) contain an ontology path, then argues that to run_pipeline. This:Instead, we should make two changes:
stimulus_ontology_fileparameter ofrun_sweep_extractionand replace it with an interface whose default behavior is more sensible.